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Sample records for human ancient mtdna

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

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    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.

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

    Science.gov (United States)

    Endicott, Phillip; Sanchez, Juan J; Pichler, Irene; Brotherton, Paul; Brooks, Jerome; Egarter-Vigl, Eduard; Cooper, Alan; Pramstaller, Peter

    2009-06-19

    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. 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. 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.

  3. Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations

    OpenAIRE

    Wallace, Douglas C.; Stugard, Carol; Murdock, Deborah; Schurr, Theodore; Brown, Michael D

    1997-01-01

    Nuclear-localized mtDNA pseudogenes might explain a recent report describing a heteroplasmic mtDNA molecule containing five linked missense mutations dispersed over the contiguous mtDNA CO1 and CO2 genes in Alzheimer’s disease (AD) patients. To test this hypothesis, we have used the PCR primers utilized in the original report to amplify CO1 and CO2 sequences from two independent ρ° (mtDNA-less) cell lines. CO1 and CO2 sequences amplified from both of the ρ° cells, ...

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

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    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

  5. Ancient mtDNA sequences from the First Australians revisited

    National Research Council Canada - National Science Library

    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

    2016-01-01

    ... [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...

  6. Multiplexed SNP Typing of Ancient DNA Clarifies the Origin of Andaman mtDNA Haplogroups amongst South Asian Tribal Populations

    Science.gov (United States)

    Endicott, Phillip; Metspalu, Mait; Stringer, Chris; Macaulay, Vincent; Cooper, Alan; Sanchez, Juan J.

    2006-01-01

    The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups ∼30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity. PMID:17218991

  7. [Heteroplasmy in human mtDNA control region].

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    Cao, Yang; Wan, Li-Hua; Gu, Lin-Gang; Huang, Ying-Xue; Xiu, Cong-Xian; Hu, Shu-Hui; Mi, Can

    2006-06-01

    To observe the length heteroplasmy and point heteroplasmy in human mtDNA control region. The peripheral blood, buccal cell, and single hair shaft from 50 individuals and 16 family members, related in their maternallineage were analyzed by direct sequencing, and clones from 20 individuals whose mtDNA sequences have a T-C transition at 16189 nt were sequenced. No point heteroplasmy were observed in peripheral blood, buccal cell, single hair shaft from the same individual, neither in maternally related individuals. Length heteroplasmy was observed in those individuals with a homopolymeric tract and the different clones from the same individual has different proportions of length variants, but the hair shafts from the same individual were very similar to the measurements made from blood DNA. No length heteroplasmy was observed between different tissues from the same individual. mtDNA sequences have a characteristic of high consistency and genetic stability, mtDNA sequencing is a suitable tool for forensic applications such as individual identification.

  8. The genetics of the pre-Roman Iberian Peninsula: a mtDNA study of ancient Iberians.

    Science.gov (United States)

    Sampietro, M L; Caramelli, D; Lao, O; Calafell, F; Comas, D; Lari, M; Agustí, B; Bertranpetit, J; Lalueza-Fox, C

    2005-09-01

    The Iberians developed a surprisingly sophisticated culture in the Mediterranean coast of the Iberian Peninsula from the 6th century BC until their conquest by the Romans in the 2nd century BC. They spoke and wrote a non-Indo-European language that still cannot be understood; their origins and relationships with other non-Indo-European peoples, like the Etruscans, are unclear, since their funerary practices were based on the cremation of bodies, and therefore anthropology has been unable to approach the study of this people. We have retrieved mitochondrial DNA (mtDNA) from a few of the scarce skeletal remains that have been preserved, some of them belonging to ritualistically executed individuals. The most stringent authentication criteria proposed for ancient DNA, such as independent replication, amino-acid analysis, quantitation of template molecules, multiple extractions and cloning of PCR products, have been followed to obtain reliable sequences from the mtDNA hypervariable region 1 (HVR1), as well as some haplogroup diagnostic SNPs. Phylogeographic analyses show that the haplogroup composition of the ancient Iberians was very similar to that found in modern Iberian Peninsula populations, suggesting a long-term genetic continuity since pre-Roman times. Nonetheless, there is less genetic diversity in the ancient Iberians than is found among modern populations, a fact that could reflect the small population size at the origin of the population sampled, and the heterogenic tribal structure of the Iberian society. Moreover, the Iberians were not especially closely related to the Etruscans, which points to considerable genetic heterogeneity in Pre-Roman Western Europe.

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

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    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.

  10. No evidence of Neandertal mtDNA contribution to early modern humans.

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    David Serre

    2004-03-01

    Full Text Available The retrieval of mitochondrial DNA (mtDNA sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not found among current humans. However, these results do not definitively resolve the question of a possible Neandertal contribution to the gene pool of modern humans since such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils. Here we address these issues by the analysis of 24 Neandertal and 40 early modern human remains. The biomolecular preservation of four Neandertals and of five early modern humans was good enough to suggest the preservation of DNA. All four Neandertals yielded mtDNA sequences similar to those previously determined from Neandertal individuals, whereas none of the five early modern humans contained such mtDNA sequences. In combination with current mtDNA data, this excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution.

  11. Palaeoparasitology - Human Parasites in Ancient Material.

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    Araújo, Adauto; Reinhard, Karl; Ferreira, Luiz Fernando

    2015-01-01

    Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Does aerobic exercises induce mtDNA mutation in human blood ...

    African Journals Online (AJOL)

    The aim of this study was to determine the effect of eight weeks aerobic training on mitochondrial DNA (mtDNA) mutation in human blood leucocytes. Twenty untrained healthy students (training group: n =10, age = 20.7±1.5 yrs, weight = 67.7±10 kg, BF% = 17.5±7.35 & control group: n =10, age = 21±1.3 yrs, weight ...

  13. Heteroplasmy of the human mtDNA control region remains constant during life.

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    Lagerström-Fermér, M; Olsson, C; Forsgren, L; Syvänen, A C

    2001-05-01

    In a longitudinal, retrospective study, we monitored the level of heteroplasmy at nucleotide position (nt) 309 and nt 16189 of the control region of human mtDNA. As a unique source of DNA, we analyzed multiple cervical-cell samples collected, during 1 or 2 decades, from four women with heteroplasmy at either nt 309 or nt 16189. According to accurate, quantitative analysis by solid-phase minisequencing, the level of heteroplasmy remained stable in the cervical-cell samples from all four women during the time studied. We also analyzed autopsy samples from several different tissues, all containing nt 309 in heteroplasmic form, of one of the women, who was deceased. On the basis of our results, heteroplasmy in the control region of mtDNA seems to be inherited and is not the result of somatic age-related accumulation.

  14. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.

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    Lippold, Sebastian; Xu, Hongyang; Ko, Albert; Li, Mingkun; Renaud, Gabriel; Butthof, Anne; Schröder, Roland; Stoneking, Mark

    2014-01-01

    Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.

  15. Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes.

    Science.gov (United States)

    Pierson, Melanie J; Martinez-Arias, Rosa; Holland, Barbara R; Gemmell, Neil J; Hurles, Matthew E; Penny, David

    2006-10-01

    The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near Oceania, where evidence of human settlement dates from as early as 40,000 years ago. Archeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began approximately 5,500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm that the female settlers of Remote Oceania descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.

  16. Human uses of ultrasound: ancient and modern.

    Science.gov (United States)

    Wade, G

    2000-03-01

    For untold millennia certain animals have used ultrasound to probe places where light is unavailable, echo-locating bats being among the most adept. With ultrasonics, bats can quickly and safely 'see' at night in pursuing insects or flying in dark caves. Unable to hear ultrasound, humans have nevertheless made use of it. They did this anciently by taming wolves, with their keen ultrasonic hearing, for aiding in the hunt. Currently, they are doing this by developing technology to detect, generate and process ultrasound for searching in air or other gases, in water or other liquids, and in solids. The story of these technological developments is a large and fascinating mirror of human history involving the advent of such discoveries and inventions as magnetostriction, piezoelectricity, sonar, ultrasonic microscopy, etc.--the list is long. By now we are skilled in probing for underwater objects, the internal structure in materials, organs inside the human body, etc.--again the list is long. A number of different ultrasonic systems can be categorized into one of three key generic approaches: pulse-echo exploration, intensity mapping, and phase-amplitude measurement. In addition, each of these categories can be combined with the others to produce hybrid systems for which an unambiguous categorization is difficult or impossible. Challenging problems remain but solutions are being found. New principles and techniques are being discovered that will improve the use of ultrasound. Employing tomo-holographic techniques to reduce ambiguity in probing three-dimensional objects, near-field techniques to boost resolution and using limited-diffraction beams to provide image construction with ultra high frame rates are cases in point.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    We have used a systematic protocol for extracting, quantitating, sexing and validating ancient human mitochondrial and nuclear DNA of one male and one female Beothuk, a Native American population from Newfoundland, which became extinct approximately 180 years ago. They carried mtDNA haplotypes......, which fall within haplogroups X and C, consistent with Northeastern Native populations today. In addition we have sexed the male using a novel-sexing assay and confirmed the authenticity of his Y chromosome with the presence of the Native American specific Y-QM3 single nucleotide polymorphism (SNP......, Nonosabasut) were of admixed (European-Native American) descent. We also analyzed patterns of DNA damage in the clones of authentic mtDNA sequences; there is no tendency for DNA damage to occur preferentially at previously defined mutational hotspots, suggesting that such mutational hotspots...

  18. Extensive human DNA contamination in extracts from ancient dog bones and teeth.

    Science.gov (United States)

    Malmström, Helena; Storå, Jan; Dalén, Love; Holmlund, Gunilla; Götherström, Anders

    2005-10-01

    Ancient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148-bp human-specific and a 152-bp dog-specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time polymerase chain reaction (PCR), and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating aDNA cannot separate contamination from ancient human DNA the way they are presently used.

  19. 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...

  20. Length heteroplasmy in the first hypervariable segment of the human mtDNA control region.

    Science.gov (United States)

    Bendall, K E; Sykes, B C

    1995-08-01

    The first hypervariable segment of the human mtDNA control region contains a homopolymeric tract of cytosines between nt 16184 and 16193, interrupted at position 16189 by a thymine, according to the Cambridge reference sequence. A variant commonly found in population screening is a T-to-C transition at nt 16189, resulting in an uninterrupted homopolymeric tract. Direct sequencing of individuals with this variant produces a characteristic blurred sequence in nucleotides beyond the tract. Sequencing clones from these individuals revealed that this is caused by high levels of length heteroplasmy in the homopolymeric tract and low levels of length heteroplasmy in the four adenines following the tract. We have developed a rapid method involving densitometry of sequencing gels to quantify the relative proportions of different length variants present in an individual. We have used this to study the proportions of length variants in individuals from three twin pairs and two maternal lineages. While unrelated individuals usually have different proportions of length variants, all maternally related individuals studied have the same proportions, even if they are only distantly related. It is not obvious how identical heteroplasmic profiles are maintained in maternally related individuals, but some possible mechanisms are suggested.

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

    Science.gov (United States)

    Warinner, Christina; Matias Rodrigues, João F.; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y.; Tito, Raul Y.; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C.; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars; Samaniego Castruita, José Alfredo; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian; Olsen, Jesper V.; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M.; Collins, Matthew J.; Gilbert, M. Thomas P.; Rühli, Frank; Cappellini, Enrico

    2014-01-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral 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) the first evidence of ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction 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 calculus permits the simultaneous investigation of pathogen activity, host immunity, and diet, thereby extending the direct investigation of common diseases into the human evolutionary past. PMID:24562188

  2. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus.

    Science.gov (United States)

    Ozga, Andrew T; Nieves-Colón, Maria A; Honap, Tanvi P; Sankaranarayanan, Krithivasan; Hofman, Courtney A; Milner, George R; Lewis, Cecil M; Stone, Anne C; Warinner, Christina

    2016-06-01

    Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

    Science.gov (United States)

    Ozga, Andrew T.; Nieves‐Colón, Maria A.; Honap, Tanvi P.; Sankaranarayanan, Krithivasan; Hofman, Courtney A.; Milner, George R.; Lewis, Cecil M.; Stone, Anne C.

    2016-01-01

    ABSTRACT Objectives Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700‐year‐old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in‐solution capture techniques, followed by Illumina high‐throughput sequencing. Results Full mitogenomes (7–34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220–228, 2016. © 2016 The Authors American Journal of Physical Anthropology

  4. [Genetic ecological monitoring in human populations: heterozygosity, mtDNA haplotype variation, and genetic load].

    Science.gov (United States)

    Balanovskiĭ, O P; Koshel', S M; Zaporozhchenko, V V; Pshenichnov, A S; Frolova, S A; Kuznetsova, M A; Baranova, E E; Teuchezh, I E; Kuznetsova, A A; Romashkina, M V; Utevskaia, O M; Churnosov, M I; Villems, R; Balanovskaia, E V

    2011-11-01

    Yu. P. Altukhov suggested that heterozygosity is an indicator of the state of the gene pool. The idea and a linked concept of genetic ecological monitoring were applied to a new dataset on mtDNA variation in East European ethnic groups. Haplotype diversity (an analog of the average heterozygosity) was shown to gradually decrease northwards. Since a similar trend is known for population density, interlinked changes were assumed for a set of parameters, which were ordered to form a causative chain: latitude increases, land productivity decreases, population density decreases, effective population size decreases, isolation of subpopulations increases, genetic drift increases, and mtDNA haplotype diversity decreases. An increase in genetic drift increases the random inbreeding rate and, consequently, the genetic load. This was confirmed by a significant correlation observed between the incidence of autosomal recessive hereditary diseases and mtDNA haplotype diversity. Based on the findings, mtDNA was assumed to provide an informative genetic system for genetic ecological monitoring; e.g., analyzing the ecology-driven changes in the gene pool.

  5. Molecular Gender Determination of Ancient Human from Malay Peninsular

    OpenAIRE

    Z. A.S. Hisham; S. Sahidan; M. A.W. Rohaya; M. Y.S. Afeefah; Z. A.I. Zarina; J. A.N.N. Hidayah; R. M.A. Nadiah; Z. A. Zaidah

    2009-01-01

    Problem statement: DNA samples from fourteen modern human bloods (seven males and seven females) and two ancient skeletal samples excavated from Kalumpang Island and Dungun, Peninsular Malaysia were subjected for molecular genders determination using specific primers of human AMELX and AMELY. Approach: A standard multiple PCR mixture with forward primer and either a human X-specific reverse primer for AMELX or a human Y-specific reverse primer for AMELY amplifications were used to assess the ...

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

    Directory of Open Access Journals (Sweden)

    Bouakaze Caroline

    2010-01-01

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

  7. The study of human Y chromosome variation through ancient DNA.

    Science.gov (United States)

    Kivisild, Toomas

    2017-05-01

    High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

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

    Science.gov (United States)

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

    2013-01-01

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

  9. Somatic mtDNA mutation spectra in the aging human putamen.

    Directory of Open Access Journals (Sweden)

    Siôn L Williams

    Full Text Available The accumulation of heteroplasmic mitochondrial DNA (mtDNA deletions and single nucleotide variants (SNVs is a well-accepted facet of the biology of aging, yet comprehensive mutation spectra have not been described. To address this, we have used next generation sequencing of mtDNA-enriched libraries (Mito-Seq to investigate mtDNA mutation spectra of putamen from young and aged donors. Frequencies of the "common" deletion and other "major arc" deletions were significantly increased in the aged cohort with the fold increase in the frequency of the common deletion exceeding that of major arc deletions. SNVs also increased with age with the highest rate of accumulation in the non-coding control region which contains elements necessary for translation and replication. Examination of predicted amino acid changes revealed a skew towards pathogenic SNVs in the coding region driven by mutation bias. Levels of the pathogenic m.3243A>G tRNA mutation were also found to increase with age. Novel multimeric tandem duplications that resemble murine control region multimers and yeast ρ(- mtDNAs, were identified in both young and aged specimens. Clonal ∼50 bp deletions in the control region were found at high frequencies in aged specimens. Our results reveal the complex manner in which the mitochondrial genome alters with age and provides a foundation for studies of other tissues and disease states.

  10. Human tuberculosis predates domestication in ancient Syria.

    Science.gov (United States)

    Baker, Oussama; Lee, Oona Y-C; Wu, Houdini H T; Besra, Gurdyal S; Minnikin, David E; Llewellyn, Gareth; Williams, Christopher M; Maixner, Frank; O'Sullivan, Niall; Zink, Albert; Chamel, Bérénice; Khawam, Rima; Coqueugniot, Eric; Helmer, Daniel; Le Mort, Françoise; Perrin, Pascale; Gourichon, Lionel; Dutailly, Bruno; Pálfi, György; Coqueugniot, Hélène; Dutour, Olivier

    2015-06-01

    The question of pre-neolithic tuberculosis is still open in paleopathological perspective. One of the major interests is to explore what type of infection could have existed around the early stage of animal domestication. Paleopathological lesions evoking skeletal TB were observed on five human skeletons coming from two PPNB sites in Syria, which belongs to the geographical cradle of agriculture. These sites represent respectively pre-domestication phase (Dja'de el Mughara, Northern Syria, 8800-8300 BCE cal.) and early domestication phase (Tell Aswad, Southern Syria, 8200-7600 BCE cal.). MicroCT scan analyses were performed on two specimens (one per site) and revealed microscopic changes in favor of TB infection. Detection of lipid biomarkers is positive for two specimens (one per site). Initial molecular analysis further indicates the presence of TB in one individual from Dja'de. Interestingly, no morphological evidence of TB was observed on animal remains of wild and newly domesticated species, discovered in these sites. These observations strongly suggest the presence of human tuberculosis before domestication and at its early stages. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Li, Yingrui; Lindgreen, Stinus

    2010-01-01

    We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an...... for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit....

  12. Phylotyping and functional analysis of two ancient human microbiomes.

    Directory of Open Access Journals (Sweden)

    Raúl Y Tito

    Full Text Available BACKGROUND: The Human Microbiome Project (HMP is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. METHODOLOGY/PRINCIPAL FINDINGS: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.

  13. 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...... to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5...... times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA...

  14. Ancient human footprints in Ciur-Izbuc Cave, Romania.

    Science.gov (United States)

    Webb, David; Robu, Marius; Moldovan, Oana; Constantin, Silviu; Tomus, Bogdan; Neag, Ionel

    2014-09-01

    In 1965, Ciur-Izbuc Cave in the Carpathian Mountains of Romania was discovered to contain about 400 ancient human footprints. At that time, researchers interpreted the footprints to be those of a man, woman and child who entered the cave by an opening which is now blocked but which was usable in antiquity. The age of the prints (≈10-15 ka BP) was based partly on their association with cave bear (Ursus spelaeus) footprints and bones, and the belief that cave bears became extinct near the end of the last ice age. Since their discovery, the human and bear evidence and the cave itself have attracted spelunkers and other tourists, with the result that the ancient footprints are in danger of destruction by modern humans. In an effort to conserve the footprints and information about them and to reanalyze them with modern techiques, Ciur-Izbuc Cave was restudied in summer of 2012. Modern results are based on fewer than 25% of the originally described human footprints, the rest having been destroyed. It is impossible to confirm some of the original conclusions. The footprints do not cluster about three different sizes, and the number of individuals is estimated to be six or seven. Two cases of bears apparently overprinting humans help establish antiquity, and C-14 dates suggest a much greater age than originally thought. Unfortunately, insufficient footprints remain to measure movement variables such as stride length. However, detailed three-dimensional mapping of the footprints does allow a more precise description of human movements within the cave. © 2014 Wiley Periodicals, Inc.

  15. Almost all human genes resulted from ancient duplication

    Science.gov (United States)

    Britten, Roy J.

    2006-01-01

    Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins. PMID:17146051

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... useful for the improved ancient DNA extraction in anthropology and archeology. Key words: Ancient DNA, fossil bone, RT-PCR. INTRODUCTION. Ancient DNA research, defined as the retrieval and analysis of DNA sequences from various degraded biological source materials, has promoted many.

  17. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

    Science.gov (United States)

    Eriksson, Anders; Manica, Andrea

    2012-01-01

    Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure. PMID:22893688

  18. Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool.

    Science.gov (United States)

    Helgason, Agnar; Lalueza-Fox, Carles; Ghosh, Shyamali; Sigurethardóttir, Sigrún; Sampietro, Maria Lourdes; Gigli, Elena; Baker, Adam; Bertranpetit, Jaume; Arnadóttir, Lilja; Thornorsteinsdottir, Unnur; Stefánsson, Kári

    2009-01-01

    A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.

  19. Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region.

    Science.gov (United States)

    Hernández, Candela L; Reales, Guillermo; Dugoujon, Jean-Michel; Novelletto, Andrea; Rodríguez, Juan Nicolás; Cuesta, Pedro; Calderón, Rosario

    2014-01-24

    The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region. The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population. The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements

  20. Satellite Perspectives on Highland - Lowland Human Interaction in Ancient Syria

    Science.gov (United States)

    Lönnqvist, M.; Törmä, M.; Lönnqvist, K.; Nuñez, M.

    2012-08-01

    Nowadays we can travel by GoogleEarth 3D to Syria (http://www.worldcountries.info/GoogleEarth/GoogleEarth-Syria.php) and zoom in on the desert landscape of the mountainous region of Jebel Bishri between the Euphrates river and the Syrian Desert. This is the area, where the Finnish archaeological survey and mapping project SYGIS worked in 2000-2010 studying the relationship of humans with their environment from ancient times to the present. What kind of landscape views and visions did the ancients have and how did they utilize them? The present paper focuses on seeking answers for these questions by combining satellite data sources, such as imagery and radar data, with location information of archaeological remains collected on the ground. Landsat as well as QuickBird imagery have been fused with SRTM mission and ASTER DEM data in creating 3D landscape models and fly-over simulations. The oasis of El Kowm on the western piedmont of the mountain seems to have served as a base camp for early huntergatherers and pastoral nomads dwelling seasonally in the region of Jebel Bishri. According to the archaeological finds, the interaction between the lowland and the mountain people already started during the Palaeolithic era but was continued by pastoral nomads of the region from the Neolithic period onwards. The Upper Palaeolithic period meant a clear change in cognitive thinking and obviously in understanding the properties of landscape, visibility and perceiving sceneries in 3D. Mobility of hunter-gatherers and pastoral nomads is based on subsistence economy, but mobility also enhances visions and prospects of phenomena appearing in the horizon.

  1. Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion.

    Science.gov (United States)

    Duggan, Ana T; Evans, Bethwyn; Friedlaender, Françoise R; Friedlaender, Jonathan S; Koki, George; Merriwether, D Andrew; Kayser, Manfred; Stoneking, Mark

    2014-05-01

    Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  2. Phytolith assemblages along a gradient of ancient human disturbance in western Amazonia

    Directory of Open Access Journals (Sweden)

    Crystal eMcmichael

    2015-12-01

    Full Text Available The ecological status of prehistoric Amazonian forests remains widely debated. The concept of ancient Amazonia as a pristine wilderness is largely discredited, but the alternative hypothesis of extensive anthropogenic landscape remains untested in many regions. We assessed the degree of ancient human impacts across western Amazonia based on archaeological and paleoecological data using methodologies that would allow inter-regional comparisons. We also aimed to establish baselines for estimating the legacies of ancient disturbances on modern vegetation. We analyzed charcoal and phytolith assemblages from soil samples from an archaeological site, sites in close proximity to archaeological sites, sites from riverine and interfluvial forests, and a biological research station believed to contain some of the least disturbed forests within Amazonia. We then quantitatively compared phytolith assemblages within and between the surveyed regions. Palm enrichment was evident at the archaeological site, and the biological station survey contained little to no evidence of ancient human activity. The other sites exhibited a gradient of ancient disturbance across the landscape. The phytolith assemblages showed statistically significant between-region variations that indicated our metrics were sufficiently sensitive to detecting ancient disturbance. Our data highlight the spatial heterogeneity of ancient human disturbances in Amazonian forests. The quantification of these disturbances provides empirical data and a more concrete link between the composition of the modern forest and ancient disturbance regimes. Accounting for ancient disturbances will allow a deeper understanding of the landscape heterogeneity observed in the modern forests.

  3. Identification of a new human mtDNA polymorphism (A14290G in the NADH dehydrogenase subunit 6 gene

    Directory of Open Access Journals (Sweden)

    M. Houshmand

    2006-06-01

    Full Text Available Leber's hereditary optic neuropathy (LHON is a maternally inherited form of retinal ganglion cell degeneration leading to optic atrophy in young adults. Several mutations in different genes can cause LHON (heterogeneity. The ND6 gene is one of the mitochondrial genes that encodes subunit 6 of complex I of the respiratory chain. This gene is a hot spot gene. Fourteen Persian LHON patients were analyzed with single-strand conformational polymorphism and DNA sequencing techniques. None of these patients had four primary mutations, G3460A, G11788A, T14484C, and G14459A, related to this disease. We identified twelve nucleotide substitutions, G13702C, T13879C, T14110C, C14167T, G14199T, A14233G, G14272C, A14290G, G14365C, G14368C, T14766C, and T14798C. Eleven of twelve nucleotide substitutions had already been reported as polymorphism. One of the nucleotide substitutions (A14290G has not been reported. The A14290G nucleotide substitution does not change its amino acid (glutamic acid. We looked for base conservation using DNA star software (MEGALIGN program as a criterion for pathogenic or nonpathogenic nucleotide substitution in A14290G. The results of ND6 gene alignment in humans and in other species (mouse, cow, elegans worm, and Neurospora crassa mold revealed that the 14290th base was not conserved. Fifty normal controls were also investigated for this polymorphism in the Iranian population and two had A14290G polymorphism (4%. This study provides evidence that the mtDNA A14290G allele is a new nonpathogenic polymorphism. We suggest follow-up studies regarding this polymorphism in different populations.

  4. Human aging and somatic point mutations in mtDNA: a comparative study of generational differences (grandparents and grandchildren

    Directory of Open Access Journals (Sweden)

    Anderson Nonato do Rosário Marinho

    2011-01-01

    Full Text Available The accumulation of somatic mutations in mtDNA is correlated with aging. In this work, we sought to identify somatic mutations in the HVS-1 region (D-loop of mtDNA that might be associated with aging. For this, we compared 31 grandmothers (mean age: 63 ± 2.3 years and their 62 grandchildren (mean age: 15 ± 4.1 years, the offspring of their daughters. Direct DNA sequencing showed that mutations absent in the grandchildren were detected in a presumably homoplasmic state in three grandmothers and in a heteroplasmic state in an additional 13 grandmothers; no mutations were detected in the remaining 15 grandmothers. However, cloning followed by DNA sequencing in 12 grandmothers confirmed homoplasia in only one of the three mutations previously considered to be homoplasmic and did not confirm heteroplasmy in three out of nine grandmothers found to be heteroplasmic by direct sequencing. Thus, of 12 grandmothers in whom mtDNA was analyzed by cloning, eight were heteroplasmic for mutations not detected in their grandchildren. In this study, the use of genetically related subjects allowed us to demonstrate the occurrence of age-related (> 60 years old mutations (homoplasia and heteroplasmy. It is possible that both of these situations (homoplasia and heteroplasmy were a long-term consequence of mitochondrial oxidative phosphorylation that can lead to the accumulation of mtDNA mutations throughout life.

  5. Human aging and somatic point mutations in mtDNA: A comparative study of generational differences (grandparents and grandchildren).

    Science.gov (United States)

    do Rosário Marinho, Anderson Nonato; de Moraes, Milene Raiol; Santos, Sidney; Ribeiro-Dos-Santos, Andrea

    2011-01-01

    The accumulation of somatic mutations in mtDNA is correlated with aging. In this work, we sought to identify somatic mutations in the HVS-1 region (D-loop) of mtDNA that might be associated with aging. For this, we compared 31 grandmothers (mean age: 63 ± 2.3 years) and their 62 grandchildren (mean age: 15 ± 4.1 years), the offspring of their daughters. Direct DNA sequencing showed that mutations absent in the grandchildren were detected in a presumably homoplasmic state in three grandmothers and in a heteroplasmic state in an additional 13 grandmothers; no mutations were detected in the remaining 15 grandmothers. However, cloning followed by DNA sequencing in 12 grandmothers confirmed homoplasia in only one of the three mutations previously considered to be homoplasmic and did not confirm heteroplasmy in three out of nine grandmothers found to be heteroplasmic by direct sequencing. Thus, of 12 grandmothers in whom mtDNA was analyzed by cloning, eight were heteroplasmic for mutations not detected in their grandchildren. In this study, the use of genetically related subjects allowed us to demonstrate the occurrence of age-related (> 60 years old) mutations (homoplasia and heteroplasmy). It is possible that both of these situations (homoplasia and heteroplasmy) were a long-term consequence of mitochondrial oxidative phosphorylation that can lead to the accumulation of mtDNA mutations throughout life.

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

    African Journals Online (AJOL)

    ... was shown to consists of intact DNA that is virtually free of RNA, resulting in a more accurate representation of gene expression using RTPCR and PCR amplification methods. In this study, the results demonstrate that RT-PCR method can be useful for the improved ancient DNA extraction in anthropology and archeology.

  7. Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set.

    Science.gov (United States)

    Allard, Marc W; Polanskey, Deborah; Miller, Kevin; Wilson, Mark R; Monson, Keith L; Budowle, Bruce

    2005-03-10

    The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n=217) were observed in the African American data set (n=1148). These SNPs ranged from having 1-39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each) observed included 16093, 16129, 16189, 16311, 16362, 16519, 146, 150, 152, 189, and 195. These rapidly changing sites are consistent with other published analyses. Only 34 SNPs are needed to identify all clusters containing 10 or more individuals in the African American data set. The results show that the African American SWGDAM mtDNA data set contains variation consistent with that described in continental African populations. Thirteen of the 18 haplogroups previously observed in African populations were observed and include: L1a, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e1, L3e2, L3e3, L3e4 and L3f. Haplogroup L2a is the most commonly observed cluster (18.8%) in the African American data set. The next most common haplogroups in the African American data set include the clusters L1c (11.0%), L1b (9.1%), L3e2 (9.0%) and L3b (8.1%). Approximately 8% of the haplogroups observed within African Americans were common in European Caucasians or East Asians; these were H (n=32), J (n=4), K (n=5), T (n=2), U5 (n=6), U6 (n=9 also known from North Africa), A (n=12), B (n=7), C (n=4), and M (n=16), respectively. The European Caucasian and East Asian

  8. Probabilistic Methods for the Inference of Selection and Demography from Ancient Human Genomes

    OpenAIRE

    Racimo, Fernando

    2016-01-01

    Recently developed technologies for the recovery and sequencing of ancient DNA have generated an explosion of paleogenomic data in the last five years. In particular, human paleogenomics has become a thriving field for understanding evolutionary patterns of different hominin groups over time. However, there is still a dearth of statistical tools that can allow biologists to discern meaningful patterns from ancient genomes. Here, I present three methods designed for inferring past demographic ...

  9. Thimerosal-Derived Ethylmercury Is a Mitochondrial Toxin in Human Astrocytes: Possible Role of Fenton Chemistry in the Oxidation and Breakage of mtDNA

    Directory of Open Access Journals (Sweden)

    Martyn A. Sharpe

    2012-01-01

    Full Text Available Thimerosal generates ethylmercury in aqueous solution and is widely used as preservative. We have investigated the toxicology of Thimerosal in normal human astrocytes, paying particular attention to mitochondrial function and the generation of specific oxidants. We find that ethylmercury not only inhibits mitochondrial respiration leading to a drop in the steady state membrane potential, but also concurrent with these phenomena increases the formation of superoxide, hydrogen peroxide, and Fenton/Haber-Weiss generated hydroxyl radical. These oxidants increase the levels of cellular aldehyde/ketones. Additionally, we find a five-fold increase in the levels of oxidant damaged mitochondrial DNA bases and increases in the levels of mtDNA nicks and blunt-ended breaks. Highly damaged mitochondria are characterized by having very low membrane potentials, increased superoxide/hydrogen peroxide production, and extensively damaged mtDNA and proteins. These mitochondria appear to have undergone a permeability transition, an observation supported by the five-fold increase in Caspase-3 activity observed after Thimerosal treatment.

  10. Insights into Ancient Human Populations and their Environment through Stable Isotope Analysis

    Science.gov (United States)

    Macko, S. A.

    2011-12-01

    Fundamental to the understanding of human history is the ability to make interpretations based on artifacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information concerning incidence of disease, population interactions, genetic defects and diet. Stable isotopes have long been used to interpret diet and trophic interactions in modern ecosystems. We suggest that the isotope compositions of a commonly overlooked material, human hair, is an ideal tool to be used in gleaning information, especially on human diets, about ancient civilizations. Hair can be well-preserved and is amenable to routine measurements of 13C, 15N and 34S isotope analyses and distinguishing sources of nutrition. We have isotopically characterized hair from both modern and ancient individuals. There is a wide diversity in isotope values owing, at least partially, to the levels of seafood, corn-fed animals and other grains in diet. Using these isotope tracers, new information regarding historical figures (George Washington, 1799 AD) to perhaps the most ancient of mummies, the Chinchorro of Chile (more than 7000 BP) as well as the Moche of Peru (1500 BP) and the best preserved mummy, the Neolithic Ice Man of the Oetztaler Alps (5200 BP), have been deciphered. It appears that the often-overlooked hair in archaeological sites represents a significant approach for understanding ancient human communities and their environments, as well as new perspectives on our use of our own modern nutritional sources.

  11. New paleoradiological investigations of ancient human remains from North West Lombardy archaeological excavations

    Energy Technology Data Exchange (ETDEWEB)

    Licata, Marta; Borgo, Melania; Armocida, Giuseppe; Nicosia, Luca; Ferioli, Elena [University of Insubria (Varese), Department of Biotechnology and Life Sciences, Varese (Italy)

    2016-03-15

    Since its birth in 1895, radiology has been used to study ancient mummies. The purpose of this article is to present paleoradiological investigations conducted on several medieval human remains in Varese province. Anthropological (generic identification) and paleopathological analyses were carried out with the support of diagnostic imaging (X-ray and CT scans). Human remains were discovered during excavations of medieval archaeological sites in northwest Lombardy. Classical physical anthropological methods were used for the macroscopic identification of the human remains. X-ray and CT scans were performed on the same scanner (16-layer Hitachi Eclos 16 X-ray equipment). Radiological analysis permitted investigating (1) the sex, (2) age of death, (3) type of trauma, (4) therapeutic interventions and (5) osteomas in ancient human remains. In particular, X-ray and CT examinations showed dimorphic facial traits on the mummified skull, and the same radiological approaches allowed determining the age at death from a mummified lower limb. CT analyses allow investigating different types of traumatic lesions in skulls and postcranial skeleton portions and reconstructing the gait and functional outcomes of a fractured femur. Moreover, one case of possible Gardner's syndrome (GS) was postulated from observing multiple osteomas in an ancient skull. Among the medical tests available to the clinician, radiology is the most appropriate first-line procedure for a diagnostic approach to ancient human remains because it can be performed without causing any significant damage to the specimen. (orig.)

  12. Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia.

    Directory of Open Access Journals (Sweden)

    Paola Pollegioni

    Full Text Available Common walnut (Juglans regia L is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J. regia evolved over many centuries under the influence of human management and exploitation. We evaluated the hypothesis that the current distribution of natural genetic resources of common walnut in Asia is, at least in part, the product of ancient anthropogenic dispersal, human cultural interactions, and afforestation. Genetic analysis combined with ethno-linguistic and historical data indicated that ancient trade routes such as the Persian Royal Road and Silk Road enabled long-distance dispersal of J. regia from Iran and Trans-Caucasus to Central Asia, and from Western to Eastern China. Ancient commerce also disrupted the local spatial genetic structure of autochthonous walnut populations between Tashkent and Samarkand (Central-Eastern Uzbekistan, where the northern and central routes of the Northern Silk Road converged. A significant association between ancient language phyla and the genetic structure of walnut populations is reported even after adjustment for geographic distances that could have affected both walnut gene flow and human commerce over the centuries. Beyond the economic importance of common walnut, our study delineates an alternative approach for understanding how the genetic resources of long-lived perennial tree species may be affected by the interaction of geography and human history.

  13. An ancient founder mutation in PROKR2 impairs human reproduction.

    Science.gov (United States)

    Avbelj Stefanija, Magdalena; Jeanpierre, Marc; Sykiotis, Gerasimos P; Young, Jacques; Quinton, Richard; Abreu, Ana Paula; Plummer, Lacey; Au, Margaret G; Balasubramanian, Ravikumar; Dwyer, Andrew A; Florez, Jose C; Cheetham, Timothy; Pearce, Simon H; Purushothaman, Radhika; Schinzel, Albert; Pugeat, Michel; Jacobson-Dickman, Elka E; Ten, Svetlana; Latronico, Ana Claudia; Gusella, James F; Dode, Catherine; Crowley, William F; Pitteloud, Nelly

    2012-10-01

    Congenital gonadotropin-releasing hormone (GnRH) deficiency manifests as absent or incomplete sexual maturation and infertility. Although the disease exhibits marked locus and allelic heterogeneity, with the causal mutations being both rare and private, one causal mutation in the prokineticin receptor, PROKR2 L173R, appears unusually prevalent among GnRH-deficient patients of diverse geographic and ethnic origins. To track the genetic ancestry of PROKR2 L173R, haplotype mapping was performed in 22 unrelated patients with GnRH deficiency carrying L173R and their 30 first-degree relatives. The mutation's age was estimated using a haplotype-decay model. Thirteen subjects were informative and in all of them the mutation was present on the same ~123 kb haplotype whose population frequency is ≤10%. Thus, PROKR2 L173R represents a founder mutation whose age is estimated at approximately 9000 years. Inheritance of PROKR2 L173R-associated GnRH deficiency was complex with highly variable penetrance among carriers, influenced by additional mutations in the other PROKR2 allele (recessive inheritance) or another gene (digenicity). The paradoxical identification of an ancient founder mutation that impairs reproduction has intriguing implications for the inheritance mechanisms of PROKR2 L173R-associated GnRH deficiency and for the relevant processes of evolutionary selection, including potential selective advantages of mutation carriers in genes affecting reproduction.

  14. Keeping mtDNA in shape between generations.

    Directory of Open Access Journals (Sweden)

    James B Stewart

    2014-10-01

    Full Text Available Since the unexpected discovery that mitochondria contain their own distinct DNA molecules, studies of the mitochondrial DNA (mtDNA have yielded many surprises. In animals, transmission of the mtDNA genome is explicitly non-Mendelian, with a very high number of genome copies being inherited from the mother after a drastic bottleneck. Recent work has begun to uncover the molecular details of this unusual mode of transmission. Many surprising variations in animal mitochondrial biology are known; however, a series of recent studies have identified a core of evolutionarily conserved mechanisms relating to mtDNA inheritance, e.g., mtDNA bottlenecks during germ cell development, selection against specific mtDNA mutation types during maternal transmission, and targeted destruction of sperm mitochondria. In this review, we outline recent literature on the transmission of mtDNA in animals and highlight the implications for human health and ageing.

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2013-04-01

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

  18. Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics

    Science.gov (United States)

    Ottoni, Claudio; Girdland Flink, Linus; 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; Çakırlar, Canan; Çevik, Özlem; Hoelzel, A. Rus; Mashkour, Marjan; Mohaseb Karimlu, Azadeh Fatemeh; Sheikhi Seno, Shiva; 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; Strand Vidarsdottir, Una; Burger, Joachim; Cucchi, Thomas; Dobney, Keith; Larson, Greger

    2013-01-01

    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. PMID:23180578

  19. Ancient gene flow from early modern humans into Eastern Neanderthals.

    Science.gov (United States)

    Kuhlwilm, Martin; Gronau, Ilan; Hubisz, Melissa J; de Filippo, Cesare; Prado-Martinez, Javier; Kircher, Martin; Fu, Qiaomei; Burbano, Hernán A; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Željko; Gušic, Ivan; Marques-Bonet, Tomas; Andrés, Aida M; Viola, Bence; Pääbo, Svante; Meyer, Matthias; Siepel, Adam; Castellano, Sergi

    2016-02-25

    It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

  20. Ancient gene flow from early modern humans into Eastern Neanderthals

    Science.gov (United States)

    Kuhlwilm, Martin; Gronau, Ilan; Hubisz, Melissa J.; de Filippo, Cesare; Prado-Martinez, Javier; Kircher, Martin; Fu, Qiaomei; Burbano, Hernán A.; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Željko; Gušic, Ivan; Marques-Bonet, Tomas; Andrés, Aida M.; Viola, Bence; Pääbo, Svante; Meyer, Matthias; Siepel, Adam; Castellano, Sergi

    2016-01-01

    It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here, we analyze the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and of modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously reported. PMID:26886800

  1. Direct evidence of milk consumption from ancient human dental calculus

    DEFF Research Database (Denmark)

    Warinner, C.; Hendy, J.; Speller, C.

    2014-01-01

    Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines...... of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption...

  2. Ancient DNA in human bone remains from Pompeii archaeological site.

    Science.gov (United States)

    Cipollaro, M; Di Bernardo, G; Galano, G; Galderisi, U; Guarino, F; Angelini, F; Cascino, A

    1998-06-29

    aDNA extraction and amplification procedures have been optimized for Pompeian human bone remains whose diagenesis has been determined by histological analysis. Single copy genes amplification (X and Y amelogenin loci and Y specific alphoid repeat sequences) have been performed and compared with anthropometric data on sexing.

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

    Directory of Open Access Journals (Sweden)

    Fernando Racimo

    2016-04-01

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

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

    Science.gov (United States)

    Racimo, Fernando; Renaud, Gabriel; Slatkin, Montgomery

    2016-04-01

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

  5. 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.

  6. The impact of lead pollution on human health (environment in Ancient Rome

    Directory of Open Access Journals (Sweden)

    Sič Magdolna

    2012-01-01

    Full Text Available Having in mind that the lead coming from mines and foundries, from the water conducted thought the aqueducts and finally from food and wine, endangered to a great extent the health of Roman population, in this paper the author tackles the possible impact of lead from these sources onto human health (environment in Ancient Rome, as well as the debated question whether the lead pollution was one of the factors that caused the fall of the Roman Empire.

  7. Introduction to "Digital Humanities in Ancient Jewish, Christian and Arabic Traditions"

    Directory of Open Access Journals (Sweden)

    Claire Clivaz

    2016-04-01

    Full Text Available This special JRMDC number brings together articles based on eight papers presented at the Digital Humanities (DH consultation of the annual meeting of the Society of Biblical Literature (SBL. These eight articles focus on Digital Humanities (DH in Ancient Jewish, Christian and Arabic traditions. The first part of this introduction focuses on general considerations concerning the encounter between digital culture and biblical and religious studies, and introduces the first article by Caroline Schroeder. The second part of this introduction maps a number of key issues across the Digital Humanities which appear in the seven specific case studies presented in the other articles in this issue.

  8. Nuclear pseudogenes of mtDNA (NUMTS) suggest repeated distant inter-species hybridization among direct human ancestors

    OpenAIRE

    Gunbin, Konstantin; Popadin, Konstantin; Peshkin, Leonid; Annis, Sofia; Fleischmann, Zoe; Markuzon, Natasha; Kratysberg, Yevgenya; Ackermann, Rebecca; Khrapko, Konstantin

    2017-01-01

    Introduction: Increasingly, the emergence and evolution of our species is being tied to genetic exchange between divergent lineages within ~1Ma (e.g., Neanderthals, Denisovans). However, little is known about genetic exchange during earlier (pre-1Ma) human evolution and between more divergent lineages. Results: We present evidence of hybridization within human lineage, show that it likely happened between highly divergent (~4.5My) lineages, more than once. We use analysis of nuclear pseudogen...

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

    Directory of Open Access Journals (Sweden)

    Treena Swanston

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

  10. Persistent heteroplasmy of a mutation in the human mtDNA control region: hypermutation as an apparent consequence of simple-repeat expansion/contraction.

    Science.gov (United States)

    Howell, N; Smejkal, C B

    2000-05-01

    In the genealogical and phylogenetic analyses that are reported here, we obtained evidence for an unusual pattern of mutation/reversion in the human mitochondrial genome. The cumulative results indicate that, when there is a T-->C polymorphism at nt 16189 and a C-->T substitution at nt 16192, there is an extremely high rate of reversion (hypermutation) at the latter site. The apparent reversion rate is sufficiently high that there is persistent heteroplasmy at nt 16192 in maternal lineages and at the phylogenetic level, a situation that is similar to that observed for the rapid expansion/contraction of simple repeats within the control region. This is the first specific instance in which the mutation frequency at one site in the D-loop is markedly influenced by the local sequence "context." The 16189 T-->C polymorphism lengthens a (C:G)n simple repeat, which then undergoes expansion and contraction, probably through replication slippage. This proclivity toward expansion/contraction is more pronounced when there is a C residue, rather than a T, at nt 16192. The high T-->C reversion frequency at nt 16192 apparently is the result of polymerase misincorporation or slippage during replication, the same mechanism that also causes the expansion/contraction of this simple-repeat sequence. In addition to the first analysis of this mitochondrial hypermutation process, these results also yield mechanistic insights into the expansion/contraction of simple-repeat sequences in mtDNA.

  11. Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool.

    Directory of Open Access Journals (Sweden)

    Agnar Helgason

    2009-01-01

    Full Text Available A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.

  12. Circulating mitochondrial DNA as biomarker linking environmental chemical exposure to early preclinical lesions elevation of mtDNA in human serum after exposure to carcinogenic halo-alkane-based pesticides.

    Science.gov (United States)

    Budnik, Lygia T; Kloth, Stefan; Baur, Xaver; Preisser, Alexandra M; Schwarzenbach, Heidi

    2013-01-01

    There is a need for a panel of suitable biomarkers for detection of environmental chemical exposure leading to the initiation or progression of degenerative diseases or potentially, to cancer. As the peripheral blood may contain increased levels of circulating cell-free DNA in diseased individuals, we aimed to evaluate this DNA as effect biomarker recognizing vulnerability after exposure to environmental chemicals. We recruited 164 individuals presumably exposed to halo-alkane-based pesticides. Exposure evaluation was based on human biomonitoring analysis; as biomarker of exposure parent halo-methanes, -ethanes and their metabolites, as well as the hemoglobin-adducts methyl valine and hydroxyl ethyl valine in blood were used, complemented by expert evaluation of exposure and clinical intoxication symptoms as well as a questionnaire. Assessment showed exposures to halo alkanes in the concentration range being higher than non-cancer reference doses (RfD) but (mostly) lower than the occupational exposure limits. We quantified circulating DNA in serum from 86 individuals with confirmed exposure to off-gassing halo-alkane pesticides (in storage facilities or in home environment) and 30 non-exposed controls, and found that exposure was significantly associated with elevated serum levels of circulating mitochondrial DNA (in size of 79 bp, mtDNA-79, p = 0.0001). The decreased integrity of mtDNA (mtDNA-230/mtDNA-79) in exposed individuals implicates apoptotic processes (p = 0.015). The relative amounts of mtDNA-79 in serum were positively associated with the lag-time after intoxication to these chemicals (r = 0.99, pvulnerable risk groups after exposure to toxic/carcinogenic chemicals.

  13. Circulating mitochondrial DNA as biomarker linking environmental chemical exposure to early preclinical lesions elevation of mtDNA in human serum after exposure to carcinogenic halo-alkane-based pesticides.

    Directory of Open Access Journals (Sweden)

    Lygia T Budnik

    Full Text Available There is a need for a panel of suitable biomarkers for detection of environmental chemical exposure leading to the initiation or progression of degenerative diseases or potentially, to cancer. As the peripheral blood may contain increased levels of circulating cell-free DNA in diseased individuals, we aimed to evaluate this DNA as effect biomarker recognizing vulnerability after exposure to environmental chemicals. We recruited 164 individuals presumably exposed to halo-alkane-based pesticides. Exposure evaluation was based on human biomonitoring analysis; as biomarker of exposure parent halo-methanes, -ethanes and their metabolites, as well as the hemoglobin-adducts methyl valine and hydroxyl ethyl valine in blood were used, complemented by expert evaluation of exposure and clinical intoxication symptoms as well as a questionnaire. Assessment showed exposures to halo alkanes in the concentration range being higher than non-cancer reference doses (RfD but (mostly lower than the occupational exposure limits. We quantified circulating DNA in serum from 86 individuals with confirmed exposure to off-gassing halo-alkane pesticides (in storage facilities or in home environment and 30 non-exposed controls, and found that exposure was significantly associated with elevated serum levels of circulating mitochondrial DNA (in size of 79 bp, mtDNA-79, p = 0.0001. The decreased integrity of mtDNA (mtDNA-230/mtDNA-79 in exposed individuals implicates apoptotic processes (p = 0.015. The relative amounts of mtDNA-79 in serum were positively associated with the lag-time after intoxication to these chemicals (r = 0.99, p<0.0001. Several months of post-exposure the specificity of this biomarker increased from 30% to 97% in patients with intoxication symptoms. Our findings indicate that mitochondrial DNA has a potential to serve as a biomarker recognizing vulnerable risk groups after exposure to toxic/carcinogenic chemicals.

  14. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth.

    Science.gov (United States)

    Korlević, Petra; Gerber, Tobias; Gansauge, Marie-Theres; Hajdinjak, Mateja; Nagel, Sarah; Aximu-Petri, Ayinuer; Meyer, Matthias

    2015-08-01

    Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem.

  15. Ancient human genomes suggest three ancestral populations for present-day Europeans

    Science.gov (United States)

    Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

    2014-01-01

    We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages. PMID:25230663

  16. MtDNA variation and human-mediated introgression of indigenous sus populations on several Indonesian Islands

    OpenAIRE

    ISHIGURO, Naotaka; INOSHIMA, Yasuo; Sasaki, Motoki; Matsui, Akira; Hongo, Hitomi; TAKAHASHI, Ryouhei; WAHONO ESTHI, Prasetyaningtyas; ITA, Djuwita; SRIHADI, AGUNGPRIYONO; SUPRATIKNO; KUSDIANTORO; ELHAYAT, Labiro; TEGUH, Budipitojo; WORO DANUR, Wendo; DEWI KANIA, Musana

    2012-01-01

    o examine the genetic origin of the domestic pig, the distribution of wild boar, and human-mediated translocation of the domestic pig, we collected 223 samples from domestic pigs and wild boars from eight Indonesian islands, sequenced the control region of mitochondrial DNA (mtDNA) from each sample, and compared these sequences with previously determined sequences from East and Southeast Asian domestic pigs and wild boars. Three Sus species (S. scrofa, S.verrucosus, and S. celebensis) were id...

  17. Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands.

    Science.gov (United States)

    Delfin, Frederick; Myles, Sean; Choi, Ying; Hughes, David; Illek, Robert; van Oven, Mannis; Pakendorf, Brigitte; Kayser, Manfred; Stoneking, Mark

    2012-02-01

    Although genetic studies have contributed greatly to our understanding of the colonization of Near and Remote Oceania, important gaps still exist. One such gap is the Solomon Islands, which extend between Bougainville and Vanuatu, thereby bridging Near and Remote Oceania, and include both Austronesian-speaking and Papuan-speaking groups. Here, we describe patterns of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in over 700 individuals from 18 populations in the Solomons, including 11 Austronesian-speaking groups, 3 Papuan-speaking groups, and 4 Polynesian Outliers (descended via back migration from Polynesia). We find evidence for ancient (pre-Lapita) colonization of the Solomons in old NRY paragroups as well as from M2-M353, which probably arose in the Solomons ∼9,200 years ago and is the most frequent NRY haplogroup there. There are no consistent genetic differences between Austronesian-speaking and Papuan-speaking groups, suggesting extensive genetic contact between them. Santa Cruz, which is located in Remote Oceania, shows unusually low frequencies of mtDNA and NRY haplogroups of recent Asian ancestry. This is in apparent contradiction with expectations based on archaeological and linguistic evidence for an early (∼3,200 years ago), direct colonization of Santa Cruz by Lapita people from the Bismarck Archipelago, via a migration that "leapfrogged" over the rest of the Solomons. Polynesian Outliers show dramatic island-specific founder events involving various NRY haplogroups. We also find that NRY, but not mtDNA, genetic distance is correlated with the geographic distance between Solomons groups and that historically attested spheres of cultural interaction are associated with the recent genetic structure of Solomons groups, as revealed by mtDNA HV1 sequence and Y-STR haplotype diversity. Our results fill an important lacuna in human genetic studies of Oceania and aid in understanding the colonization and genetic history of

  18. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, 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...

  19. Documenting the diet in ancient human populations through stable isotope analysis of hair.

    Science.gov (United States)

    Macko, S A; Engel, M H; Andrusevich, V; Lubec, G; O'Connell, T C; Hedges, R E

    1999-01-29

    Fundamental to the understanding of human history is the ability to make interpretations based on artefacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information, for example, concerning incidence of disease, genetic defects and diet. Stable isotopic compositions, especially those made on isolates of collagen from bones, have been used to help suggest principal dietary components. A significant problem in the use of collagen is its long-term stability, and the possibility of isotopic alteration during early diagenesis, or through contaminating condensation reactions. In this study, we suggest that a commonly overlooked material, human hair, may represent an ideal material to be used in addressing human diets of ancient civilizations. Through the analysis of the amino-acid composition of modern hair, as well as samples that were subjected to radiation (thus simulating ageing of the hair) and hair from humans that is up to 5200 years old, we have observed little in the way of chemical change. The principal amino acids observed in all of these samples are essentially identical in relative abundances and content. Dominating the compositions are serine, glutamic acid, threonine, glycine and leucine, respectively accounting for approximately 15%, 17%, 10%, 8% and 8% of the total hydrolysable amino acids. Even minor components (for example, alanine, valine, isoleucine) show similar constancy between the samples of different ages. This constancy clearly indicates minimal alteration of the amino-acid composition of the hair. Further, it would indicate that hair is well preserved and is amenable to isotopic analysis as a tool for distinguishing sources of nutrition. Based on this observation, we have isotopically characterized modern individuals for whom the diet has been documented. Both stable nitrogen and carbon isotope compositions were assessed, and together provide an

  20. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

    Science.gov (United States)

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

    2013-04-01

    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 polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (pNeandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European populations.

  1. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

    Directory of Open Access Journals (Sweden)

    Omer Gokcumen

    2013-04-01

    Full Text Available 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 polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵. Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003 and positive Tajima's D (p = 0.00285 statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European

  2. Human cadaveric dissection: a historical account from ancient Greece to the modern era

    Science.gov (United States)

    2015-01-01

    The review article attempts to focus on the practice of human cadaveric dissection during its inception in ancient Greece in 3rd century BC, revival in medieval Italy at the beginning of 14th century and subsequent evolution in Europe and the United States of America over the centuries. The article highlights on the gradual change in attitude of religious authorities towards human dissection, the shift in the practice of human dissection being performed by barber surgeons to the anatomist himself dissecting the human body and the enactment of prominent legislations which proved to be crucial milestones during the course of the history of human cadaveric dissection. It particularly emphasizes on the different means of procuring human bodies which changed over the centuries in accordance with the increasing demand due to the rise in popularity of human dissection as a tool for teaching anatomy. Finally, it documents the rise of body donation programs as the source of human cadavers for anatomical dissection from the second half of the 20th century. Presently innovative measures are being introduced within the body donation programs by medical schools across the world to sensitize medical students such that they maintain a respectful, compassionate and empathetic attitude towards the human cadaver while dissecting the same. Human dissection is indispensable for a sound knowledge in anatomy which can ensure safe as well as efficient clinical practice and the human dissection lab could possibly be the ideal place to cultivate humanistic qualities among future physicians in the 21st century. PMID:26417475

  3. Study of dental occlusion in ancient human remains: a methodological approach.

    Science.gov (United States)

    Fiorin, Elena; Cadafalch, Joan; Ceperuelo, Dolors; Adserias Adserias, Maria José; Chimenos-Küstner, Eduard; Malgosa, Assumpció

    2014-09-01

    The anthropological dental and maxillary study in human skeletal remains usually refers to alterations or conditions of the oral cavity. These alterations could have repercussions on life style, dietary habits and diseases. In this particular context, dental occlusion is not often analyzed due to the fragmented condition of the remains, and especially due to the lack of methodology adapted to study ancient remains. The aim of this study is to propose an anthropological method based on clinical dental practice. In the method presented in this work, odontological parameters such as overjet, overbite, and Angle's Classification of Malocclusion, are evaluated.

  4. Analysis of ancient human DNA and primer contamination: one step backward one step forward.

    Science.gov (United States)

    Deguilloux, Marie-France; Ricaud, Séverine; Leahy, Rachael; Pemonge, Marie-Hélène

    2011-07-15

    The analysis of DNA from archaeological human remains is plagued by a unique set of methodological problems concerning contamination with modern exogenous DNA. Through an original approach, we propose complementary methods to identify all potential sources of contamination and complete guidelines for the validation of ancient human sequences. The study presented was conducted on non-European human samples (Polynesian and Amerindian) which were collected with all precautions during excavation. This permitted us to distinguish without ambiguity authentic and contaminant sequences. The samples' origins and histories were perfectly known, allowing us to trace all potential contamination sources and to determine the efficiency of precautions followed during all steps of the study. The data obtained confirm that precautions taken during sampling effectively prevent contamination. However, we demonstrate that human contamination can also be introduced during genetic analyses even if all precautions are strictly followed. Indeed, numerous human contaminations were detected in template-PCR products and negative controls, resulting in a striking diversity of contaminant mitochondrial DNA sequences. We argue that this contamination partly derives from the primers. To our knowledge, no previous experiment has been performed to investigate primers as a possible source of human contamination despite the fact that this specific type of contamination poses a real problem in terms of validating ancient human DNA studies. Finally, we confirm that the detection of contaminants in negative controls is clearly related to the number of PCR cycles used. This study enhances our understanding of contamination processes and confirms that, in reality, an absolutely contamination-free situation cannot be obtained. As a consequence, we propose improvements to the guidelines usually followed in the field in order to take the highly probable contamination of PCR reagents, including primers, into

  5. Ancient clam gardens, traditional management portfolios, and the resilience of coupled human-ocean systems

    Directory of Open Access Journals (Sweden)

    Julia Jackley

    2016-12-01

    Full Text Available Indigenous communities have actively managed their environments for millennia using a diversity of resource use and conservation strategies. Clam gardens, ancient rock-walled intertidal beach terraces, represent one example of an early mariculture technology that may have been used to improve food security and confer resilience to coupled human-ocean systems. We surveyed a coastal landscape for evidence of past resource use and management to gain insight into ancient resource stewardship practices on the central coast of British Columbia, Canada. We found that clam gardens are embedded within a diverse portfolio of resource use and management strategies and were likely one component of a larger, complex resource management system. We compared clam diversity, density, recruitment, and biomass in three clam gardens and three unmodified nonwalled beaches. Evidence suggests that butter clams (Saxidomus gigantea had 1.96 times the biomass and 2.44 times the density in clam gardens relative to unmodified beaches. This was due to a reduction in beach slope and thus an increase in the optimal tidal range where clams grow and survive best. The most pronounced differences in butter clam density between nonwalled beaches and clam gardens were found at high tidal elevations at the top of the beach. Finally, clam recruits (0.5-2 mm in length tended to be greater in clam gardens compared to nonwalled beaches and may be attributed to the addition of shell hash by ancient people, which remains on the landscape today. As part of a broader social-ecological system, clam garden sites were among several modifications made by humans that collectively may have conferred resilience to past communities by providing reliable and diverse access to food resources.

  6. 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.

  7. 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

  8. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.

    Directory of Open Access Journals (Sweden)

    Matthew F Barber

    2016-05-01

    Full Text Available Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by bacteria. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with opportunistic bacterial pathogens causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions.

  9. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.

    Science.gov (United States)

    Barber, Matthew F; Kronenberg, Zev; Yandell, Mark; Elde, Nels C

    2016-05-01

    Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by bacteria. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with opportunistic bacterial pathogens causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions.

  10. De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology.

    Science.gov (United States)

    Zhadanov, Sergey I; Atamanov, Vasiliy V; Zhadanov, Nikolay I; Schurr, Theodore G

    2006-01-01

    Recent studies suggest that certain mutations with phylogeographic importance as haplogroup markers may also influence the phenotypic expression of particular mitochondrial disorders. One such disorder, Leber's hereditary optic neuropathy (LHON), demonstrates a clear expression bias in mtDNAs belonging to haplogroup J, a West Eurasian maternal lineage defined by polymorphic markers that have been called 'secondary' disease mutations. In this report, we present evidence for a de novo heteroplasmic COX2 mutation associated with a LHON clinical phenotype. This particular mutation-at nucleotide position 7,598-occurs in West Eurasian haplogroup H, the most common maternal lineage among individuals of European descent, whereas previous studies have detected this mutation only in East Eurasian haplogroup E. A review of the available mtDNA sequence data indicates that the COX2 7598 mutation occurs as a homoplasic event at the tips of these phylogenetic branches, suggesting that it could be a variant that is rapidly eliminated by selection. This finding points to the potential background influence of polymorphisms on the expression of mild deleterious mutations such as LHON mtDNA defects and further highlights the difficulties in distinguishing deleterious mtDNA changes from neutral polymorphisms and their significance in the development of mitochondriopathies.

  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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Human retinal transmitochondrial cybrids with J or H mtDNA haplogroups respond differently to ultraviolet radiation: implications for retinal diseases.

    Directory of Open Access Journals (Sweden)

    Deepika Malik

    Full Text Available It has been recognized that cells do not respond equally to ultraviolet (UV radiation but it is not clear whether this is due to genetic, biochemical or structural differences of the cells. We have a novel cybrid (cytoplasmic hybrids model that allows us to analyze the contribution of mitochondrial DNA (mtDNA to cellular response after exposure to sub-lethal dose of UV. mtDNA can be classified into haplogroups as defined by accumulations of specific single nucleotide polymorphisms (SNPs. Recent studies have shown that J haplogroup is high risk for age-related macular degeneration while the H haplogroup is protective. This study investigates gene expression responses in J cybrids versus H cybrids after exposure to sub-lethal doses of UV-radiation.Cybrids were created by fusing platelets isolated from subjects with either H (n = 3 or J (n = 3 haplogroups with mitochondria-free (Rho0 ARPE-19 cells. The H and J cybrids were cultured for 24 hours, treated with 10 mJ of UV-radiation and cultured for an additional 120 hours. Untreated and treated cybrids were analyzed for growth rates and gene expression profiles. The UV-treated and untreated J cybrids had higher growth rates compared to H cybrids. Before treatment, J cybrids showed lower expression levels for CFH, CD55, IL-33, TGF-A, EFEMP-1, RARA, BCL2L13 and BBC3. At 120 hours after UV-treatment, the J cybrids had decreased CFH, RARA and BBC3 levels but increased CD55, IL-33 and EFEMP-1 compared to UV-treated H cybrids.In cells with identical nuclei, the cellular response to sub-lethal UV-radiation is mediated in part by the mtDNA haplogroup. This supports the hypothesis that differences in growth rates and expression levels of complement, inflammation and apoptosis genes may result from population-specific, hereditary SNP variations in mtDNA. Therefore, when analyzing UV-induced damage in tissues, the mtDNA haplogroup background may be important to consider.

  13. Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains.

    Science.gov (United States)

    Pilli, Elena; Modi, Alessandra; Serpico, Ciro; Achilli, Alessandro; Lancioni, Hovirag; Lippi, Barbara; Bertoldi, Francesca; Gelichi, Sauro; Lari, Martina; Caramelli, David

    2013-01-01

    Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14(th) century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as "virgin samples" (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called "lab samples"(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from "lab samples" are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the "virgin samples" set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between "lab" and "virgin" samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.

  14. New Genetic and Linguistic Analyses Show Ancient Human Influence on Baobab Evolution and Distribution in Australia

    Science.gov (United States)

    Rangan, Haripriya; Bell, Karen L.; Baum, David A.; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A.; Murphy, Daniel J.

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

  15. Aesthetics of the Human Image in Life and Iconography of the Ancient Philosophers in Art

    Directory of Open Access Journals (Sweden)

    Dorofeev, Daniil

    2015-04-01

    Full Text Available The acoustic and visual understanding of man is a hotly debated issue in contemporary culture. I found it important therefore to look at certain historical, cultural, aesthetical, philosophical and anthropological peculiarities of human image in Antiquity as reflected in the arts. The following aspects deserve special attention: the visualization of sense and values; the interaction of “ethos” (character and “soma” (body; the influence of the plastic images on the narrative ones; a normative typology of man; the significance of visual and acoustic perception. In this context, I studied ancient physiognomic; Aristotelian understanding of the acoustic and plastic arts; genesis, evolution and significance of the sculptural portrait image of man and the image of philosopher in Antiquity. I also pay attention to some methodological aspects of the study. As a result, there emerges an integral image of philosopher, which allows looking at the Greek culture from a fresh angle.

  16. 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.

  17. Major population expansion of East Asians began before neolithic time: evidence of mtDNA genomes.

    Science.gov (United States)

    Zheng, Hong-Xiang; Yan, Shi; Qin, Zhen-Dong; Wang, Yi; Tan, Jing-Ze; Li, Hui; Jin, Li

    2011-01-01

    It is a major question in archaeology and anthropology whether human populations started to grow primarily after the advent of agriculture, i.e., the Neolithic time, especially in East Asia, which was one of the centers of ancient agricultural civilization. To answer this question requires an accurate estimation of the time of lineage expansion as well as that of population expansion in a population sample without ascertainment bias. In this study, we analyzed all available mtDNA genomes of East Asians ascertained by random sampling, a total of 367 complete mtDNA sequences generated by the 1000 Genome Project, including 249 Chinese (CHB, CHD, and CHS) and 118 Japanese (JPT). We found that major mtDNA lineages underwent expansions, all of which, except for two JPT-specific lineages, including D4, D4b2b, D4a, D4j, D5a2a, A, N9a, F1a1'4, F2, B4, B4a, G2a1 and M7b1'2'4, occurred before 10 kya, i.e., before the Neolithic time (symbolized by Dadiwan Culture at 7.9 kya) in East Asia. Consistent to this observation, the further analysis showed that the population expansion in East Asia started at 13 kya and lasted until 4 kya. The results suggest that the population growth in East Asia constituted a need for the introduction of agriculture and might be one of the driving forces that led to the further development of agriculture.

  18. Simulation of dental microwear: Characteristic traces by opal phytoliths give clues to ancient human dietary behavior.

    Science.gov (United States)

    Gügel, I L; Grupe, G; Kunzelmann, K H

    2001-02-01

    In order to further evaluate the process of microwear formation on human dental enamel, microwear was experimentally produced by a chewing simulation with an Academic Center for Dentistry Amsterdam (ACTA) device. For this simulation, several cereal species were processed according to historical milling techniques, the experimental results of which were compared with those obtained from cereals processed after modern techniques, and also with natural microwear on early medieval human molars. Comparison of simulated microwear pits with natural microwear pits showed that the simulation led to traces which matched those found on the historical teeth in terms of both size and shape. Experimentally produced microwear pits were especially characteristic for the cereal species used in the simulations, and both pit morphology and enamel loss were a function of cereal phytolith content. Despite the high variability of phytolith size and shape, certain types are characteristic for certain cereals, which in turn are capable of producing cereal-specific microwear. This experimental approach is likely to further define ancient human dietary behavior, including food processing. Copyright 2001 Wiley-Liss, Inc.

  19. "Modeling ancient Egyptian embalming": radiological assessment of experimentally mummified human tissue by CT and MRI.

    Science.gov (United States)

    Panzer, Stephanie; Borumandi, Farzad; Wanek, Johann; Papageorgopoulou, Christina; Shved, Natallia; Colacicco, Giovanni; Rühli, Frank J

    2013-11-01

    To assess changes in different tissues during the process of artificial mummification by natron using computed tomography (CT) and magnetic resonance imaging (MRI), and to translate the results to image interpretation in paleoradiological studies of ancient mummies. A human lower limb (LL) was amputated from a female donor 24 h post-mortem and mummified by artificial natron (54 % NaCl, 16 % Na2SO4, 18 % Na2CO3 12 % NaHCO3) in ancient Egyptian style. The LL was kept in a fume hood at 16-25 °C and 30-75 % relative humidity. CT and MRI were performed at specific intervals with quantitative evaluation of Hounsfield units (HU) and signal intensities (SI). Evaluated tissues showed different HU and SI changes during the experimental mummification. All tissues revealed an overall but varying increase of HU in CT examinations. All tissues except for the compact bone revealed an overall but varying decrease of SI in the IR and T2-weighted sequences of the MRI. Typical findings included a distinct increase of HU in the cutis at the end of the study and a temporary increase of SI in the IR and T2-weighted sequences in all muscle groups. Radiological findings showed a regular, controlled and effective dehydration by the applied natron without detectable putrefaction. Evaluated tissues revealed different radiological changes during the experiment, which altogether led to preservation of the tissues without radiologically identifiable destruction. The cutis revealed radiological signs of direct interaction with the natron in the form of covering and possibly permeation.

  20. Modeling ancient Egyptian mummification on fresh human tissue: macroscopic and histological aspects.

    Science.gov (United States)

    Papageorgopoulou, Christina; Shved, Natallia; Wanek, Johann; Rühli, Frank J

    2015-06-01

    Many studies have been concerned with the ancient Egyptian mummification method; nevertheless, little effort has been made to explore it experimentally. The goal of this study is to apply evidence-based diagnostic criteria and state-of-the art methodology in order to improve knowledge on soft tissues preservation and postmortem alterations. Two human lower limbs (LL) from a female donor were (1) "naturally" mummified by dry heat and (2) artificially in natron. At specific time intervals a macroscopic and radiological examination of the LL was performed and skin and muscle samples were taken for histological and biomolecular analysis. Temperature, humidity, pH, and weight of the LL were systematically measured. The mummification by dry heat was stopped after 7 days due to unexpected lack of mummification progress. The mummification in natron was completed successfully after 208 days. The humidity, the external temperature, and the pH were proven with Pearson correlation and principal component analysis as important factors for the mummification process. The steady removal of water from the tissues through the natron has prevented the putrefaction. This is also evident in the absence of bacteria or fungi through the microbiological analysis. The histological analysis revealed very good preservation of the skin and the muscle tissues. In the muscular sample certain degree of structural disintegration can be seen, particularly affecting the epimysium whilst in the skin samples the epidermis, especially the stratum corneum, is mostly affected. The samples show better preservation compared with ancient Egyptian sections and other mummified tissues from historic or forensic context. © 2015 Wiley Periodicals, Inc.

  1. 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...

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

    Science.gov (United States)

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

    2011-11-01

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

  3. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M Vargas

    2014-01-01

    the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern...

  4. Phytolith assemblages along a gradient of ancient human disturbance in western Amazonia

    NARCIS (Netherlands)

    McMichael, C.N.H.; Piperno, D.R.; Neves, E.G.; Bush, M.B.; Almeida, F.O.; Mongelo, G.; Eyjolfsdottir, M.B.

    2015-01-01

    The ecological status of prehistoric Amazonian forests remains widely debated. The concept of ancient Amazonia as a pristine wilderness is largely discredited, but the alternative hypothesis of extensive anthropogenic landscapes remains untested in many regions. We assessed the degree of ancient

  5. Paleogenomics: Investigation of an ancient family of repetitive sequences present in great numbers in human genome

    Energy Technology Data Exchange (ETDEWEB)

    Zietkiewicz, E.; Labuda, D. [Universite de Montreal, Que (Canada); Jurka, J. [Linus Pauling Institute, Palo Alto, CA (United States)

    1994-09-01

    Paleogenomics is the research activity aiming to reconstruct ancient genetic events and/or structures from the {open_quotes}fossil{close_quotes} genomic record. With about 120,000 copies, mammalian interspersed repeats, MIRs, represent the second most abundant family of short interspersed repeats in human DNA, only outnumbered by Alu elements. MIR consensus sequence of 100 nucleotides was reconstructed from 455 mutated copies preserved in contemporary genome (GenBank release 69). As no division into subfamilies was observed, we assume that this consensus represents an ancestral MIR sequence. To find out how far MIRs can be traced down the phylogenetic tree, we examined their distribution in a variety of mammalian and non-mammalian DNAs. Oligonucleotide primers based on the MIR consensus were used, one at a time, for PCR amplification of the genomic fragments flanked by MIR repeats (inter-MIR-PCR). Significant amplification in DNA samples from a variety of placental orders as well as marsupials and monotremes indicates that MIRs originated in early mammals. Sequence analysis is consistent with their proliferation during the Mesozoic era. Electrophoretic profiles of inter-MIR-PCR products are distinct among different species. Intra-species comparison of multiple human samples reveals polymorphic bands segregating as Mendelian traits which can be used as genetic markers in both mapping and fingerprinting.

  6. 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

    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 Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We...... argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past....

  7. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.

    Science.gov (United States)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M Vargas; Parker, Brian J; Rasmussen, Morten; Lindgreen, Stinus; Lilje, Berit; Tobin, Desmond J; Kelly, Theresa K; Vang, Søren; Andersson, Robin; Jones, Peter A; Hoover, Cindi A; Tikhonov, Alexei; Prokhortchouk, Egor; Rubin, Edward M; Sandelin, Albin; Gilbert, M Thomas P; Krogh, Anders; Willerslev, Eske; Orlando, Ludovic

    2014-03-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics.

  8. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

    Directory of Open Access Journals (Sweden)

    Mayra Eduardoff

    2017-09-01

    Full Text Available The analysis of mitochondrial DNA (mtDNA has proven useful in forensic genetics and ancient DNA (aDNA studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR is commonly sequenced using established Sanger-type Sequencing (STS protocols involving fragment sizes down to approximately 150 base pairs (bp. Recent developments include Massively Parallel Sequencing (MPS of (multiplex PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less, and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples, and tested challenging forensic samples (n = 2 as well as compromised solid tissue samples (n = 15 up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS

  9. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

    Science.gov (United States)

    Eduardoff, Mayra; Xavier, Catarina; Strobl, Christina; Casas-Vargas, Andrea; Parson, Walther

    2017-01-01

    The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for

  10. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

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

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the ...

  11. Distribution and chemical speciation of arsenic in ancient human hair using synchrotron radiation.

    Science.gov (United States)

    Kakoulli, Ioanna; Prikhodko, Sergey V; Fischer, Christian; Cilluffo, Marianne; Uribe, Mauricio; Bechtel, Hans A; Fakra, Sirine C; Marcus, Matthew A

    2014-01-07

    Pre-Columbian populations that inhabited the Tarapacá mid river valley in the Atacama Desert in Chile during the Middle Horizon and Late Intermediate Period (AD 500-1450) show patterns of chronic poisoning due to exposure to geogenic arsenic. Exposure of these people to arsenic was assessed using synchrotron-based elemental X-ray fluorescence mapping, X-ray absorption spectroscopy, X-ray diffraction and Fourier transform infrared spectromicroscopy measurements on ancient human hair. These combined techniques of high sensitivity and specificity enabled the discrimination between endogenous and exogenous processes that has been an analytical challenge for archeological studies and criminal investigations in which hair is used as a proxy of premortem metabolism. The high concentration of arsenic mainly in the form of inorganic As(III) and As(V) detected in the hair suggests chronic arsenicism through ingestion of As-polluted water rather than external contamination by the deposition of heavy metals due to metallophilic soil microbes or diffusion of arsenic from the soil. A decrease in arsenic concentration from the proximal to the distal end of the hair shaft analyzed may indicate a change in the diet due to mobility, though chemical or microbiologically induced processes during burial cannot be entirely ruled out.

  12. Investigation of yeast genes possibly involved in mtDNA stability ...

    African Journals Online (AJOL)

    Phelim Isichei

    function and structure on mtDNA stability in yeast, our results did not support those findings in C. elegans. The human homolog of this ... Mutations in nuclear genes encoding proteins involved in. mtDNA maintenance can result in ... The characteristics of Caenorhabditis elegans make it a perfect complement to the yeast ...

  13. The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

    Directory of Open Access Journals (Sweden)

    Chang Seok Oh

    2015-01-01

    Full Text Available Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods.

  14. Pattern Recognition of mtDNA with Associative Models

    Directory of Open Access Journals (Sweden)

    Acevedo María Elena

    2016-01-01

    Full Text Available In this paper we applied an associative memory for the pattern recognition of mtDNA that can be useful to identify bodies and human remains. In particular, we used both morphological hetroassociative memories: max and min. We process the problem of pattern recognition as a classification task. Our proposal showed a correct recall, we obtained the 100% of recalling of all the learned patterns. We simulated a corrupted sample of mtDNA by adding noise of two types: additive and subtractive. The memory showed a correct recall when we applied less or equal than 55% of both types of noise.

  15. Lead (Pb) Isotope Baselines for Studies of Ancient Human Migration and Trade in the Maya Region.

    Science.gov (United States)

    Sharpe, Ashley E; Kamenov, George D; Gilli, Adrian; Hodell, David A; Emery, Kitty F; Brenner, Mark; Krigbaum, John

    2016-01-01

    We examined the potential use of lead (Pb) isotopes to source archaeological materials from the Maya region of Mesoamerica. The main objectives were to determine if: 1) geologic terrains throughout the Maya area exhibit distinct lead isotope ratios (206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb), and 2) a combination of lead and strontium ratios can enhance sourcing procedures in the Mesoamerica region. We analyzed 60 rock samples for lead isotope ratios and a representative subset of samples for lead, uranium, and thorium concentrations across the Maya region, including the Northern Lowlands of the Mexican Yucatan Peninsula, the Southern Lowlands of Guatemala and Belize, the Volcanic Highlands, the Belizean Maya Mountains, and the Metamorphic Province/Motagua Valley. Although there is some overlap within certain sub-regions, particularly the geologically diverse Metamorphic Province, lead isotopes can be used to distinguish between the Northern Lowlands, the Southern Lowlands, and the Volcanic Highlands. The distinct lead isotope ratios in the sub-regions are related to the geology of the Maya area, exhibiting a general trend in the lowlands of geologically younger rocks in the north to older rocks in the south, and Cenozoic volcanic rocks in the southern highlands. Combined with other sourcing techniques such as strontium (87Sr/86Sr) and oxygen (δ18O), a regional baseline for lead isotope ratios can contribute to the development of lead isoscapes in the Maya area, and may help to distinguish among geographic sub-regions at a finer scale than has been previously possible. These isotope baselines will provide archaeologists with an additional tool to track the origin and movement of ancient humans and artifacts across this important region.

  16. Lead (Pb) Isotope Baselines for Studies of Ancient Human Migration and Trade in the Maya Region

    Science.gov (United States)

    Kamenov, George D.; Gilli, Adrian; Hodell, David A.; Emery, Kitty F.; Brenner, Mark; Krigbaum, John

    2016-01-01

    We examined the potential use of lead (Pb) isotopes to source archaeological materials from the Maya region of Mesoamerica. The main objectives were to determine if: 1) geologic terrains throughout the Maya area exhibit distinct lead isotope ratios (206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb), and 2) a combination of lead and strontium ratios can enhance sourcing procedures in the Mesoamerica region. We analyzed 60 rock samples for lead isotope ratios and a representative subset of samples for lead, uranium, and thorium concentrations across the Maya region, including the Northern Lowlands of the Mexican Yucatan Peninsula, the Southern Lowlands of Guatemala and Belize, the Volcanic Highlands, the Belizean Maya Mountains, and the Metamorphic Province/Motagua Valley. Although there is some overlap within certain sub-regions, particularly the geologically diverse Metamorphic Province, lead isotopes can be used to distinguish between the Northern Lowlands, the Southern Lowlands, and the Volcanic Highlands. The distinct lead isotope ratios in the sub-regions are related to the geology of the Maya area, exhibiting a general trend in the lowlands of geologically younger rocks in the north to older rocks in the south, and Cenozoic volcanic rocks in the southern highlands. Combined with other sourcing techniques such as strontium (87Sr/86Sr) and oxygen (δ18O), a regional baseline for lead isotope ratios can contribute to the development of lead isoscapes in the Maya area, and may help to distinguish among geographic sub-regions at a finer scale than has been previously possible. These isotope baselines will provide archaeologists with an additional tool to track the origin and movement of ancient humans and artifacts across this important region. PMID:27806065

  17. Ancient cellular structures and modern humans: change of survival strategies before prolonged low solar activity period

    Science.gov (United States)

    Ragulskaya, Mariya; Rudenchik, Evgeniy; Gromozova, Elena; Voychuk, Sergei; Kachur, Tatiana

    The study of biotropic effects of modern space weather carries the information about the rhythms and features of adaptation of early biological systems to the outer space influence. The influence of cosmic rays, ultraviolet waves and geomagnetic field on early life has its signs in modern biosphere processes. These phenomena could be experimentally studied on present-day biological objects. Particularly inorganic polyphosphates, so-called "fossil molecules", attracts special attention as the most ancient molecules which arose in inanimate nature and have been accompanying biological objects at all stages of evolution. Polyphosphates-containing graves of yeast's cells of Saccharomyces cerevisiae strain Y-517, , from the Ukrainian Collection of Microorganisms was studied by daily measurements during 2000-2013 years. The IZMIRAN daily data base of physiological parameters dynamics during 2000-2013 years were analyzed simultaneously (25 people). The analysis showed significant simultaneous changes of the statistical parameters of the studied biological systems in 2004 -2006. The similarity of simultaneous changes of adaptation strategies of human organism and the cell structures of Saccharomyces cerevisiae during the 23-24 cycles of solar activity are discussed. This phenomenon could be due to a replacement of bio-effective parameters of space weather during the change from 23rd to 24th solar activity cycle and nonstandard geophysical peculiarities of the 24th solar activity cycle. It could be suggested that the observed similarity arose as the optimization of evolution selection of the living systems in expectation of probable prolonged period of low solar activity (4-6 cycles of solar activity).

  18. Lead (Pb Isotope Baselines for Studies of Ancient Human Migration and Trade in the Maya Region.

    Directory of Open Access Journals (Sweden)

    Ashley E Sharpe

    Full Text Available We examined the potential use of lead (Pb isotopes to source archaeological materials from the Maya region of Mesoamerica. The main objectives were to determine if: 1 geologic terrains throughout the Maya area exhibit distinct lead isotope ratios (206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb, and 2 a combination of lead and strontium ratios can enhance sourcing procedures in the Mesoamerica region. We analyzed 60 rock samples for lead isotope ratios and a representative subset of samples for lead, uranium, and thorium concentrations across the Maya region, including the Northern Lowlands of the Mexican Yucatan Peninsula, the Southern Lowlands of Guatemala and Belize, the Volcanic Highlands, the Belizean Maya Mountains, and the Metamorphic Province/Motagua Valley. Although there is some overlap within certain sub-regions, particularly the geologically diverse Metamorphic Province, lead isotopes can be used to distinguish between the Northern Lowlands, the Southern Lowlands, and the Volcanic Highlands. The distinct lead isotope ratios in the sub-regions are related to the geology of the Maya area, exhibiting a general trend in the lowlands of geologically younger rocks in the north to older rocks in the south, and Cenozoic volcanic rocks in the southern highlands. Combined with other sourcing techniques such as strontium (87Sr/86Sr and oxygen (δ18O, a regional baseline for lead isotope ratios can contribute to the development of lead isoscapes in the Maya area, and may help to distinguish among geographic sub-regions at a finer scale than has been previously possible. These isotope baselines will provide archaeologists with an additional tool to track the origin and movement of ancient humans and artifacts across this important region.

  19. Mitochondrial DNA Suggests a Western Eurasian Origin for Ancient (Proto-) Bulgarians.

    Science.gov (United States)

    Nesheva, D V; Karachanak-Yankova, S; Lari, M; Yordanov, Y; Galabov, A; Caramelli, D; Toncheva, D

    2015-01-01

    Ancient (proto-) Bulgarians have long been thought of as a Turkic population. However, evidence found in the past three decades shows that this is not the case. Until now, this evidence has not included ancient mitochondrial DNA (mtDNA) analysis. To fill this void, we collected human remains from the 8th to the 10th century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in northeastern Bulgaria, and Tuhovishte (Satovcha region) in southwestern Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and western Eurasian populations. Our results suggest a western Eurasian matrilineal origin for proto-Bulgarians, as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data that will further clarify proto-Bulgarian origins, thereby adding new clues to the current understanding of European genetic evolution.

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

    Science.gov (United States)

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

    2015-02-01

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

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

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    Won-Joon Lee

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

  2. Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm.

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    Candela L Hernández

    Full Text Available Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of "migratory routes" in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians--from Huelva and Granada provinces--and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.

  3. Burying dogs in ancient Cis-Baikal, Siberia: temporal trends and relationships with human diet and subsistence practices.

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    Robert J Losey

    Full Text Available The first objective of this study is to examine temporal patterns in ancient dog burials in the Lake Baikal region of Eastern Siberia. The second objective is to determine if the practice of dog burial here can be correlated with patterns in human subsistence practices, in particular a reliance on terrestrial mammals. Direct radiocarbon dating of a suite of the region's dog remains indicates that these animals were given burial only during periods in which human burials were common. Dog burials of any kind were most common during the Early Neolithic (∼7-8000 B.P., and rare during all other time periods. Further, only foraging groups seem to have buried canids in this region, as pastoralist habitation sites and cemeteries generally lack dog interments, with the exception of sacrificed animals. Stable carbon and nitrogen isotope data indicate that dogs were only buried where and when human diets were relatively rich in aquatic foods, which here most likely included river and lake fish and Baikal seal (Phoca sibirica. Generally, human and dog diets appear to have been similar across the study subregions, and this is important for interpreting their radiocarbon dates, and comparing them to those obtained on the region's human remains, both of which likely carry a freshwater old carbon bias. Slight offsets were observed in the isotope values of dogs and humans in our samples, particularly where both have diets rich in aquatic fauna. This may result from dietary differences between people and their dogs, perhaps due to consuming fish of different sizes, or even different tissues from the same aquatic fauna. This paper also provides a first glimpse of the DNA of ancient canids in Northeast Asia.

  4. Burying dogs in ancient Cis-Baikal, Siberia: temporal trends and relationships with human diet and subsistence practices.

    Science.gov (United States)

    Losey, Robert J; Garvie-Lok, Sandra; Leonard, Jennifer A; Katzenberg, M Anne; Germonpré, Mietje; Nomokonova, Tatiana; Sablin, Mikhail V; Goriunova, Olga I; Berdnikova, Natalia E; Savel'ev, Nikolai A

    2013-01-01

    The first objective of this study is to examine temporal patterns in ancient dog burials in the Lake Baikal region of Eastern Siberia. The second objective is to determine if the practice of dog burial here can be correlated with patterns in human subsistence practices, in particular a reliance on terrestrial mammals. Direct radiocarbon dating of a suite of the region's dog remains indicates that these animals were given burial only during periods in which human burials were common. Dog burials of any kind were most common during the Early Neolithic (∼7-8000 B.P.), and rare during all other time periods. Further, only foraging groups seem to have buried canids in this region, as pastoralist habitation sites and cemeteries generally lack dog interments, with the exception of sacrificed animals. Stable carbon and nitrogen isotope data indicate that dogs were only buried where and when human diets were relatively rich in aquatic foods, which here most likely included river and lake fish and Baikal seal (Phoca sibirica). Generally, human and dog diets appear to have been similar across the study subregions, and this is important for interpreting their radiocarbon dates, and comparing them to those obtained on the region's human remains, both of which likely carry a freshwater old carbon bias. Slight offsets were observed in the isotope values of dogs and humans in our samples, particularly where both have diets rich in aquatic fauna. This may result from dietary differences between people and their dogs, perhaps due to consuming fish of different sizes, or even different tissues from the same aquatic fauna. This paper also provides a first glimpse of the DNA of ancient canids in Northeast Asia.

  5. Ancient mitogenomics

    DEFF Research Database (Denmark)

    Ho, Simon Y. W.; Gilbert, Tom

    2010-01-01

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

  6. 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…

  7. 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

  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. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

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    Marc García-Garcerà

    Full Text Available BACKGROUND: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus that was treated with a depurinating agent (bleach, an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain, and a Neandertal sample from the El Sidrón site (Asturias, Spain. The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively, that we positively know are contaminants. CONCLUSIONS: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

  11. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

    Science.gov (United States)

    García-Garcerà, Marc; Gigli, Elena; Sanchez-Quinto, Federico; Ramirez, Oscar; Calafell, Francesc; Civit, Sergi; Lalueza-Fox, Carles

    2011-01-01

    Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

  12. Replication Errors Made During Oogenesis Lead to Detectable De Novo mtDNA Mutations in Zebrafish Oocytes with a Low mtDNA Copy Number.

    Science.gov (United States)

    Otten, Auke B C; Stassen, Alphons P M; Adriaens, Michiel; Gerards, Mike; Dohmen, Richard G J; Timmer, Adriana J; Vanherle, Sabina J V; Kamps, Rick; Boesten, Iris B W; Vanoevelen, Jo M; Muller, Marc; Smeets, Hubert J M

    2016-12-01

    Of all pathogenic mitochondrial DNA (mtDNA) mutations in humans, ∼25% is de novo, although the occurrence in oocytes has never been directly assessed. We used next-generation sequencing to detect point mutations directly in the mtDNA of 3-15 individual mature oocytes and three somatic tissues from eight zebrafish females. Various statistical and biological filters allowed reliable detection of de novo variants with heteroplasmy ≥1.5%. In total, we detected 38 de novo base substitutions, but no insertions or deletions. These 38 de novo mutations were present in 19 of 103 mature oocytes, indicating that ∼20% of the mature oocytes carry at least one de novo mutation with heteroplasmy ≥1.5%. This frequency of de novo mutations is close to that deducted from the reported error rate of polymerase gamma, the mitochondrial replication enzyme, implying that mtDNA replication errors made during oogenesis are a likely explanation. Substantial variation in the mutation prevalence among mature oocytes can be explained by the highly variable mtDNA copy number, since we previously reported that ∼20% of the primordial germ cells have a mtDNA copy number of ≤73 and would lead to detectable mutation loads. In conclusion, replication errors made during oogenesis are an important source of de novo mtDNA base substitutions and their location and heteroplasmy level determine their significance. Copyright © 2016 by the Genetics Society of America.

  13. Variable copy number of mitochondrial DNA (mtDNA) predicts worse prognosis in advanced gastric cancer patients.

    Science.gov (United States)

    Zhang, Guanjun; Qu, Yiping; Dang, Siwen; Yang, Qi; Shi, Bingyin; Hou, Peng

    2013-10-21

    Change of mitochondrial DNA (mtDNA) copy number is widely reported in various human cancers, including gastric cancer, and is considered to be an important hallmark of cancers. However, there is remarkably little consensus on the value of variable mtDNA content in the prognostic evaluation of this cancer. Using real-time quantitative PCR approach, we examined mtDNA copy number in a cohort of gastric cancers and normal gastric tissues, and explored the association of variable mtDNA content with clinical outcomes of gastric cancer patients. Our data showed that the majority of gastric cancer patients had low mtDNA content as compared to control subjects although the relative mean mtDNA content was higher in the former than the latter. Moreover, we found that variable mtDNA content was strongly associated with lymph node metastasis and cancer-related death of the patients with late-stage tumors. Notably, variable mtDNA content did not affect overall survival of gastric cancer patients, however, we found that increased mtDNA content was associated with poor survival in the patients with late-stage tumors. In this study, we demonstrated that variable mtDNA content markedly increased the risk of lymph node metastasis and high mortality of the patients with late-stage tumors. Additionally, we found a strong link between increased mtDNA content and worse survival of the patients with late-stage tumors. Taken together, variable mtDNA content may be a valuable poor prognostic factor for advanced gastric cancer patients. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1344721463103353.

  14. 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

    To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in ph...

  15. Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans.

    Directory of Open Access Journals (Sweden)

    Jac M M J G Aarts

    Full Text Available Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions.

  16. Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans

    Science.gov (United States)

    Alink, Gerrit M.; Scherjon, Fulco; MacDonald, Katharine; Smith, Alison C.; Nijveen, Harm; Roebroeks, Wil

    2016-01-01

    Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions. PMID:27655273

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

    DEFF Research Database (Denmark)

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

    Human worm infections have, to a large extent, been eradicated in countries with high sanitary standards by preventing the fecal-oral transmission of infective eggs. It is possible to study parasite infections among past populations by retrieving and analyzing parasite eggs using...... paleoparasitological techniques such as morphological examination and molecular identification. Hard-shelled parasite eggs can be recovered from the environment even after extended periods of time and they have shown to be excellent reservoirs of ancient DNA (aDNA). aDNA analysis has enabled identifying which species...... 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...

  18. Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML.

    Science.gov (United States)

    Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique; Bridon, Gaëlle; Wang, Xiaoming; Xu, ChangJiang; MacLean, Neil; Siriwardena, Thirushi P; Gronda, Marcela; Yehudai, Dana; Sriskanthadevan, Shrivani; Avizonis, Daina; Shamas-Din, Aisha; Minden, Mark D; Bader, Gary D; Laposa, Rebecca; Schimmer, Aaron D

    2017-05-11

    Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human acute myeloid leukemia (AML) samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared with normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared with normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we used a nucleoside analog 2'3'-dideoxycytidine (ddC), which is phosphorylated to the activated antimetabolite, 2'3'-dideoxycytidine triphosphate by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase γ. ddC was preferentially activated in AML cells compared with normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitor cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. © 2017 by The American Society of Hematology.

  19. Inferences of Recent and Ancient Human Population History Using Genetic and Non-Genetic Data

    Science.gov (United States)

    Kitchen, Andrew

    2008-01-01

    I have adopted complementary approaches to inferring human demographic history utilizing human and non-human genetic data as well as cultural data. These complementary approaches form an interdisciplinary perspective that allows one to make inferences of human history at varying timescales, from the events that occurred tens of thousands of years…

  20. Mosaicism for mitochondrial DNA polymorphic variants in placenta has implications for the feasibility of prenatal diagnosis in mtDNA diseases.

    Science.gov (United States)

    Marchington, David R; Scott-Brown, Martin; Barlow, David H; Poulton, Joanna

    2006-07-01

    Women who have had a child with mitochondrial DNA (mtDNA) disease need to know the risk of recurrence, but this risk is difficult to estimate because mutant and wild-type (normal) mtDNA coexist in the same person (heteroplasmy). The possibility that a single sample may not reflect the whole organism both impedes prenatal diagnosis of most mtDNA diseases, and suggests radical alternative strategies such as nuclear transfer. We used naturally occurring mtDNA variants to investigate mtDNA segregation in placenta. Using large samples of control placenta, we demonstrated that the level of polymorphic heteroplasmic mtDNA variants is very similar in mother, cord blood and placenta. However, where placental samples were very small (sample (CVS) may be unrepresentative of the whole placenta. Duplicates may be necessary where CVS are small. However, the close correlation of mutant load in maternal, fetal blood and placental mtDNA suggests that the average load in placenta does reflect the load of mutant mtDNA in the baby. Provided that segregation of neutral and pathogenic mtDNA mutants is similar in utero, our results are generally encouraging for developing prenatal diagnosis for mtDNA diseases. Identifying mtDNA segregation in human placenta suggests studies of relevance to placental evolution and to developmental biology.

  1. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

    Science.gov (United States)

    Warinner, Christina; Speller, Camilla; Collins, Matthew J.

    2015-01-01

    The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. PMID:25487328

  2. African origin for Madagascan dogs revealed by mtDNA analysis.

    Science.gov (United States)

    Ardalan, Arman; Oskarsson, Mattias C R; van Asch, Barbara; Rabakonandriania, Elisabeth; Savolainen, Peter

    2015-05-01

    Madagascar was one of the last major land masses to be inhabited by humans. It was initially colonized by Austronesian speaking Indonesians 1500-2000 years ago, but subsequent migration from Africa has resulted in approximately equal genetic contributions from Indonesia and Africa, and the material culture has mainly African influences. The dog, along with the pig and the chicken, was part of the Austronesian Neolithic culture, and was furthermore the only domestic animal to accompany humans to every continent in ancient times. To illuminate Madagascan cultural origins and track the initial worldwide dispersal of dogs, we here investigated the ancestry of Madagascan dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared it with that from potential ancestral populations in Island Southeast Asia (n=219) and sub-Saharan Africa (n=493). We found that 90% of the Madagascan dogs carried a haplotype that was also present in sub-Saharan Africa and that the remaining lineages could all be attributed to a likely origin in Africa. By contrast, only 26% of Madagascan dogs shared haplotypes with Indonesian dogs, and one haplotype typical for Austronesian dogs, carried by more than 40% of Indonesian and Polynesian dogs, was absent among the Madagascan dogs. Thus, in contrast to the human population, Madagascan dogs seem to trace their origin entirely from Africa. These results suggest that dogs were not brought to Madagascar by the initial Austronesian speaking colonizers on their transoceanic voyage, but were introduced at a later stage, together with human migration and cultural influence from Africa.

  3. Female and male perspectives on the neolithic transition in Europe: clues from ancient and modern genetic data.

    Directory of Open Access Journals (Sweden)

    Rita Rasteiro

    Full Text Available The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA and Y chromosome (NRY data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality.

  4. Low copy number of mitochondrial DNA (mtDNA) predicts worse prognosis in early-stage laryngeal cancer patients.

    Science.gov (United States)

    Dang, Siwen; Qu, Yiping; Wei, Jing; Shao, Yuan; Yang, Qi; Ji, Meiju; Shi, Bingyin; Hou, Peng

    2014-02-05

    Alterations in mitochondrial DNA (mtDNA) copy number have been widely reported in various human cancers, and been considered to be an important hallmark of cancers. However, little is known about the value of copy number variations of mtDNA in the prognostic evaluation of laryngeal cancer. Using real-time quantitative PCR method, we investigated mtDNA copy number in a cohort of laryngeal cancers (n =204) and normal laryngeal tissues (n =40), and explored the association of variable mtDNA copy number with clinical outcomes of laryngeal cancer patients. Our data showed that the relative mean mtDNA content was higher in the laryngeal cancer patients (11.91 ± 4.35 copies) than the control subjects (4.72 ± 0.70 copies). Moreover, we found that mtDNA content was negatively associated with cigarette smoking (pack-years), tumor invasion, and TNM stage. Notably, variable mtDNA content did not affect overall survival of laryngeal cancer patients. However, when the patients were categorized into early-stage and late-stage tumor groups according to TNM stage, we found that low mtDNA content was strongly associated with poor survival in the former, but not in the latter. The present study demonstrated that low mtDNA content was strongly correlated with some of clinicopathological characteristics, such as cigarette smoking, tumor invasion and TNM stage. In addition, we found a strong link between low mtDNA content and worse survival of the patients with early-stage tumors. Taken together, low copy number of mtDNA may be a useful poor prognostic factor for early-stage laryngeal cancer patients. The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1841771572115955.

  5. Leber Hereditary Optic Neuropathy: Exemplar of an mtDNA Disease.

    Science.gov (United States)

    Wallace, Douglas C; Lott, Marie T

    2017-01-01

    The report in 1988 that Leber Hereditary Optic Neuropathy (LHON) was the product of mitochondrial DNA (mtDNA) mutations provided the first demonstration of the clinical relevance of inherited mtDNA variation. From LHON studies, the medical importance was demonstrated for the mtDNA showing its coding for the most important energy genes, its maternal inheritance, its high mutation rate, its presence in hundreds to thousands of copies per cell, its quantitatively segregation of biallelic genotypes during both mitosis and meiosis, its preferential effect on the most energetic tissues including the eye and brain, its wide range of functional polymorphisms that predispose to common diseases, and its accumulation of mutations within somatic tissues providing the aging clock. These features of mtDNA genetics, in combination with the genetics of the 1-2000 nuclear DNA (nDNA) coded mitochondrial genes, is not only explaining the genetics of LHON but also providing a model for understanding the complexity of many common diseases. With the maturation of LHON biology and genetics, novel animal models for complex disease have been developed and new therapeutic targets and strategies envisioned, both pharmacological and genetic. Multiple somatic gene therapy approaches are being developed for LHON which are applicable to other mtDNA diseases. Moreover, the unique cytoplasmic genetics of the mtDNA has permitted the first successful human germline gene therapy via spindle nDNA transfer from mtDNA mutant oocytes to enucleated normal mtDNA oocytes. Such LHON lessons are actively being applied to common ophthalmological diseases like glaucoma and neurological diseases like Parkinsonism.

  6. Differences in Strength and Timing of the mtDNA Bottleneck between Zebrafish Germline and Non-germline Cells

    Directory of Open Access Journals (Sweden)

    Auke B.C. Otten

    2016-07-01

    Full Text Available We studied the mtDNA bottleneck in zebrafish to elucidate size, timing, and variation in germline and non-germline cells. Mature zebrafish oocytes contain, on average, 19.0 × 106 mtDNA molecules with high variation between oocytes. During embryogenesis, the mtDNA copy number decreases to ∼170 mtDNA molecules per primordial germ cell (PGC, a number similar to that in mammals, and to ∼50 per non-PGC. These occur at the same developmental stage, implying considerable variation in mtDNA copy number in (non-PGCs of the same female, dictated by variation in the mature oocyte. The presence of oocytes with low mtDNA numbers, if similar in humans, could explain how (de novo mutations can reach high mutation loads within a single generation. High mtDNA copy numbers in mature oocytes are established by mtDNA replication during oocyte development. Bottleneck differences between germline and non-germline cells, due to early differentiation of PGCs, may account for different distribution patterns of familial mutations.

  7. Histological analysis and ancient DNA amplification of human bone remains found in caius iulius polybius house in pompeii.

    Science.gov (United States)

    Cipollaro, M; Di Bernado, G; Forte, A; Galano, G; De Masi, L; Galderisi, U; Guarino, F M; Angelini, F; Cascino, A

    1999-09-01

    Thirteen skeletons found in the Caius Iulius Polybius house, which has been the object of intensive study since its discovery in Pompeii 250 years ago, have provided an opportunity to study either bone diagenesis by histological investigation or ancient DNA by polymerase chain reaction analysis. DNA analysis was done by amplifying both X- and Y-chromosomes amelogenin loci and Y-specific alphoid repeat locus. The von Willebrand factor (vWF) microsatellite locus on chromosome 12 was also analyzed for personal identification in two individuals showing alleles with 10/11 and 12/12 TCTA repeats, respectively. Technical problems were the scarcity of DNA content from osteocytes, DNA molecule fragmentation, microbial contamination which change bone structure, contaminating human DNA which results from mishandling, and frequent presence of Taq DNA polymerase inhibiting molecules like polyphenols and heavy metals. The results suggest that the remains contain endogenous human DNA that can be amplified and analyzed. The amplifiability of DNA corresponds to the bone preservation and dynamics of the burial conditions subsequent to the 79 A.D. eruption.

  8. New Ancient Egyptian Human Mummies from the Valley of the Kings, Luxor: Anthropological, Radiological, and Egyptological Investigations

    Directory of Open Access Journals (Sweden)

    Frank Rühli

    2015-01-01

    Full Text Available The Valley of the Kings (arab. Wadi al Muluk; KV situated on the West Bank near Luxor (Egypt was the site for royal and elite burials during the New Kingdom (ca. 1500–1100 BC, with many tombs being reused in subsequent periods. In 2009, the scientific project “The University of Basel Kings’ Valley Project” was launched. The main purpose of this transdisciplinary project is the clearance and documentation of nonroyal tombs in the surrounding of the tomb of Pharaoh Thutmosis III (ca. 1479–1424 BC; KV 34. This paper reports on newly discovered ancient Egyptian human mummified remains originating from the field seasons 2010–2012. Besides macroscopic assessments, the remains were conventionally X-rayed by a portable X-ray unit in situ inside KV 31. These image data serve as basis for individual sex and age determination and for the study of probable pathologies and embalming techniques. A total of five human individuals have been examined so far and set into an Egyptological context. This project highlights the importance of ongoing excavation and science efforts even in well-studied areas of Egypt such as the Kings’ Valley.

  9. New Ancient Egyptian Human Mummies from the Valley of the Kings, Luxor: Anthropological, Radiological, and Egyptological Investigations.

    Science.gov (United States)

    Rühli, Frank; Ikram, Salima; Bickel, Susanne

    2015-01-01

    The Valley of the Kings (arab. Wadi al Muluk; KV) situated on the West Bank near Luxor (Egypt) was the site for royal and elite burials during the New Kingdom (ca. 1500-1100 BC), with many tombs being reused in subsequent periods. In 2009, the scientific project "The University of Basel Kings' Valley Project" was launched. The main purpose of this transdisciplinary project is the clearance and documentation of nonroyal tombs in the surrounding of the tomb of Pharaoh Thutmosis III (ca. 1479-1424 BC; KV 34). This paper reports on newly discovered ancient Egyptian human mummified remains originating from the field seasons 2010-2012. Besides macroscopic assessments, the remains were conventionally X-rayed by a portable X-ray unit in situ inside KV 31. These image data serve as basis for individual sex and age determination and for the study of probable pathologies and embalming techniques. A total of five human individuals have been examined so far and set into an Egyptological context. This project highlights the importance of ongoing excavation and science efforts even in well-studied areas of Egypt such as the Kings' Valley.

  10. Ancient Asexuals

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 1. Ancient Asexuals. T Ramakrishna Rao. General Article Volume 15 Issue 1 January 2010 pp 45-50. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/015/01/0045-0050. Keywords. Asexuals ...

  11. Docosahexaenoic Acid (DHA: An Ancient Nutrient for the Modern Human Brain

    Directory of Open Access Journals (Sweden)

    Joanne Bradbury

    2011-05-01

    Full Text Available Modern humans have evolved with a staple source of preformed docosahexaenoic acid (DHA in the diet. An important turning point in human evolution was the discovery of high-quality, easily digested nutrients from coastal seafood and inland freshwater sources. Multi-generational exploitation of seafood by shore-based dwellers coincided with the rapid expansion of grey matter in the cerebral cortex, which characterizes the modern human brain. The DHA molecule has unique structural properties that appear to provide optimal conditions for a wide range of cell membrane functions. This has particular implications for grey matter, which is membrane-rich tissue. An important metabolic role for DHA has recently been identified as the precursor for resolvins and protectins. The rudimentary source of DHA is marine algae; therefore it is found concentrated in fish and marine oils. Unlike the photosynthetic cells in algae and higher plants, mammalian cells lack the specific enzymes required for the de novo synthesis of alpha-linolenic acid (ALA, the precursor for all omega-3 fatty acid syntheses. Endogenous synthesis of DHA from ALA in humans is much lower and more limited than previously assumed. The excessive consumption of omega-6 fatty acids in the modern Western diet further displaces DHA from membrane phospholipids. An emerging body of research is exploring a unique role for DHA in neurodevelopment and the prevention of neuropsychiatric and neurodegenerative disorders. DHA is increasingly being added back into the food supply as fish oil or algal oil supplementation.

  12. 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...

  13. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    DEFF Research Database (Denmark)

    Malaspinas, Anna-Sapfo; Lao, Oscar; Schroeder, Hannes

    2014-01-01

    Understanding the peopling of the Americas remains an important and challenging question. Here, we present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as ‘Botocudos’. We...

  14. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    NARCIS (Netherlands)

    A.-S. Malaspinas (Anna-Sapfo); O. Lao Grueso (Oscar); H. Schroeder (Hannes); M.A. Rasmussen (Morten); M. Raghavan (Maanasa); I. Moltke (Ida); P.F. Campos (Paula F.); F.S. Sagredo (Francisca Santana); S. Rasmussen (Simon); V.F. Gonçalves (Vanessa F.); A. Albrechtsen (Anders); M.E. Allentoft (Morten E.); P.L.F. Johnson (Philip L.F.); M. Li (Mingkun); S. Reis (Silvia); D.V. Bernardo (Danilo V.); M. Degiorgio (Michael); C. Duggan; M. Bastos (Murilo); Y. Wang (Yong); J. Stenderup (Jesper); J.V. Moreno-Mayar (J. Victor); S. Brunak (S.); T. Sicheritz-Ponten (Thomas); E. Hodges (Emily); G.J. Hannon (Gregory J.); L. Orlando (Ludovic); T.D. Price (T. Douglas); J.D. Jensen (Jeffrey D.); R. Nielsen (Rasmus); J. Heinemeier (Jan); J. Olsen (Jesper); C. Rodrigues-Carvalho (Claudia); M.M. Lahr (Marta Mirazon); W.A. Neves (Walter A.); M.H. Kayser (Manfred); T. Higham (Thomas); M. Stoneking (Mark); S.D.J. Pena (Sergio D.J.); E. Willerslev (Eske)

    2014-01-01

    textabstractSummary Understanding the peopling of the Americas remains an important and challenging question. Here, we present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as

  15. Comparison of two Neolithic mtDNA haplotypes from a Czech excavation site with the results of mitochondrial DNA studies on European Neolithic and Mesolithic individuals

    Czech Academy of Sciences Publication Activity Database

    Votrubová, J.; Emmerová, B.; Brzobohatá, Hana; Šumberová, Radka; Vaněk, D.

    2017-01-01

    Roč. 6, December (2017), "e125"-"e128" ISSN 1875-1768 R&D Projects: GA ČR GB14-36938G Institutional support: RVO:67985912 Keywords : ancient DNA * mtDNA * sequencing * haplotype * haplogroup Subject RIV: AC - Archeology, Anthropology, Ethnology http://www.fsigeneticssup.com/article/S1875-1768(17)30162-2/pdf

  16. Uniqueness of human running coordination: The integration of modern and ancient evolutionary innovations

    Directory of Open Access Journals (Sweden)

    John eKiely

    2016-04-01

    Full Text Available Running is a pervasive activity across human cultures and a cornerstone of contemporary health, fitness and sporting activities. Yet for the overwhelming predominance of human existence running was an essential prerequisite for survival. A means to hunt, and a means to escape when hunted. In a very real sense humans have evolved to run. Yet curiously, perhaps due to running’s cultural ubiquity and the natural ease with which we learn to run, we rarely consider the uniqueness of human bipedal running within the animal kingdom. Our unique upright, single stance, bouncing running gait imposes a unique set of coordinative difficulties. Challenges demanding we precariously balance our fragile brains in the very position where they are most vulnerable to falling injury while simultaneously retaining stability, steering direction of travel, and powering the upcoming stride: all within the abbreviated time-frames afforded by short, violent ground contacts separated by long flight times. These running coordination challenges are solved through the tightly-integrated blending of primitive evolutionary legacies, conserved from reptilian and vertebrate lineages, and comparatively modern, more exclusively human, innovations. The integrated unification of these top-down and bottom-up control processes bestows humans with an agile control system, enabling us to readily modulate speeds, change direction, negotiate varied terrains and to instantaneously adapt to changing surface conditions. The seamless integration of these evolutionary processes is facilitated by pervasive, neural and biological, activity-dependent adaptive plasticity. Over time, and with progressive exposure, this adaptive plasticity shapes neural and biological structures to best cope with regularly imposed movement challenges. This pervasive plasticity enables the gradual construction of a robust system of distributed coordinated control, comprised of processes that are so deeply

  17. Oxytocin Pathway Genes: Evolutionary Ancient System Impacting on Human Affiliation, Sociality, and Psychopathology.

    Science.gov (United States)

    Feldman, Ruth; Monakhov, Mikhail; Pratt, Maayan; Ebstein, Richard P

    2016-02-01

    Oxytocin (OT), a nonapeptide signaling molecule originating from an ancestral peptide, appears in different variants across all vertebrate and several invertebrate species. Throughout animal evolution, neuropeptidergic signaling has been adapted by organisms for regulating response to rapidly changing environments. The family of OT-like molecules affects both peripheral tissues implicated in reproduction, homeostasis, and energy balance, as well as neuromodulation of social behavior, stress regulation, and associative learning in species ranging from nematodes to humans. After describing the OT-signaling pathway, we review research on the three genes most extensively studied in humans: the OT receptor (OXTR), the structural gene for OT (OXT/neurophysin-I), and CD38. Consistent with the notion that sociality should be studied from the perspective of social life at the species level, we address human social functions in relation to OT-pathway genes, including parenting, empathy, and using social relationships to manage stress. We then describe associations between OT-pathway genes with psychopathologies involving social dysfunctions such as autism, depression, or schizophrenia. Human research particularly underscored the involvement of two OXTR single nucleotide polymorphisms (rs53576, rs2254298) with fewer studies focusing on other OXTR (rs7632287, rs1042778, rs2268494, rs2268490), OXT (rs2740210, rs4813627, rs4813625), and CD38 (rs3796863, rs6449197) single nucleotide polymorphisms. Overall, studies provide evidence for the involvement of OT-pathway genes in human social functions but also suggest that factors such as gender, culture, and early environment often confound attempts to replicate first findings. We conclude by discussing epigenetics, conceptual implications within an evolutionary perspective, and future directions, especially the need to refine phenotypes, carefully characterize early environments, and integrate observations of social behavior across

  18. The human skin: a meeting ground for the ideas about macrocosm and microcosm in ancient and Medieval and Greek literature.

    Science.gov (United States)

    Diamandopoulos, A A; Goudas, P; Diamandopoulos, A H

    2001-12-01

    We have been interested in the cleansing capacity of skin during the recent years. In a paper of ours (1) we presented a few references to Hippocrates' and Galen's ideas on the subject, while the main body of the article was based on the 17th-20th centuries' relative practices. In a second paper (2), we were mainly testing the ancient and Medieval Greek ideas on skin catharsis against some clinical work of ours. In this paper we now present the ideas of the pagan and Byzantine Greek authors (5th cent. BC - 10th cent. AD) on the relationship of the human body to the natural and man-made world. Special emphasis is given to the relationship between purification through the skin and world purification. Based on the similarity of the Empedokles' concept of the four elements and Hippocrates' thesis concerning the four humours, the Earth itself was personified and became a living organism that felt cold, perspired and became dry. Man started to seek a natural explanation for his diseases and alterations of his body functions. Hence, perspiration, fever, urination, headache, stroke, were explained in cosmological terms. Extracts from many medical and non-medical writers, like Empedocles, Hippocrates, Aristotle, Galen, the Fathers of the Church, Meletius latrosophista, Theophilus Protospatharius, Michael Psellus and other sources are presented, in order to show the close relationship between an abundance of diseases and an array of natural phenomena.

  19. Determination of the elemental status of ancient human bones from Bockenheim/Rheinland-Pfalz by PIGE and PIXE

    Energy Technology Data Exchange (ETDEWEB)

    Jankuhn, St. E-mail: jankuhn@rz.uni-leipzig.de; Vogt, J.; Butz, T

    2000-03-01

    Continuing the investigations on ancient human bones of the Merowingian period (6-8th century AD) [St. Jankuhn, T. Butz, R.-H. Flagmeyer, T. Reinert, J. Vogt, J. Hammerl, R. Protsch von Zieten, M. Wolf, H. Baumann, K. Bethge, I. Symietz, in: J.L. Duggan, I.L. Morgan (Eds.), CP392, Appl. of Accelerators in Res. and Ind., AIP, Woodbury, NY, 1997, p. 575], we have prepared a series of 57 samples of bone from the so-called Ward's triangle. This region is an inner part of the femoral neck and one of the areas of high fracture risk in the case of osteoporosis. The bones were excavated from a former cemetery near Bockenheim/Rheinland-Pfalz, Germany. Firstly, the sample preparation method will be described. Secondly, the experimental setup will be outlined for the ion beam methods proton backscattering (PBS), proton induced {gamma}-ray emission (PIGE), and proton induced X-ray emission (PIXE) which are implemented simultaneously at the 2 MV Van de Graaff accelerator of the Universitaet Leipzig. Thirdly, the concentrations of the main and trace elements will be presented in the form of a correlation matrix for the elements detected by PIGE and PIXE. From this, a correlation coefficient matrix is derived whose values will be discussed in detail.

  20. In search of the genetic footprints of Sumerians: a survey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq

    Directory of Open Access Journals (Sweden)

    Olivieri Anna

    2011-10-01

    Full Text Available Abstract Background For millennia, the southern part of the Mesopotamia has been a wetland region generated by the Tigris and Euphrates rivers before flowing into the Gulf. This area has been occupied by human communities since ancient times and the present-day inhabitants, the Marsh Arabs, are considered the population with the strongest link to ancient Sumerians. Popular tradition, however, considers the Marsh Arabs as a foreign group, of unknown origin, which arrived in the marshlands when the rearing of water buffalo was introduced to the region. Results To shed some light on the paternal and maternal origin of this population, Y chromosome and mitochondrial DNA (mtDNA variation was surveyed in 143 Marsh Arabs and in a large sample of Iraqi controls. Analyses of the haplogroups and sub-haplogroups observed in the Marsh Arabs revealed a prevalent autochthonous Middle Eastern component for both male and female gene pools, with weak South-West Asian and African contributions, more evident in mtDNA. A higher male than female homogeneity is characteristic of the Marsh Arab gene pool, likely due to a strong male genetic drift determined by socio-cultural factors (patrilocality, polygamy, unequal male and female migration rates. Conclusions Evidence of genetic stratification ascribable to the Sumerian development was provided by the Y-chromosome data where the J1-Page08 branch reveals a local expansion, almost contemporary with the Sumerian City State period that characterized Southern Mesopotamia. On the other hand, a more ancient background shared with Northern Mesopotamia is revealed by the less represented Y-chromosome lineage J1-M267*. Overall our results indicate that the introduction of water buffalo breeding and rice farming, most likely from the Indian sub-continent, only marginally affected the gene pool of autochthonous people of the region. Furthermore, a prevalent Middle Eastern ancestry of the modern population of the marshes of

  1. Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil

    DEFF Research Database (Denmark)

    Gonçalves, Vanessa Faria; Stenderup, Jesper; Rodrigues-Carvalho, Cláudia

    2013-01-01

    genetic and morphological data on Paleoa-mericans. Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil. The identification of these two Polynesian...... haplogroups was confirmed in independent replications in Brazil and Denmark, ensuring reliability of the data. Parallel analysis of 12 other Botocudo individuals yielded only the well-known Amerindian mtDNA hap-logroup C1. Potential scenarios to try to help understand these results are presented and discussed...

  2. The Application of Scanning Electron Microscopy with Energy-Dispersive X-Ray Spectroscopy (SEM-EDX) in Ancient Dental Calculus for the Reconstruction of Human Habits

    Czech Academy of Sciences Publication Activity Database

    Fialová, D.; Skoupý, Radim; Drozdová, E.; Paták, Aleš; Piňos, Jakub; Šín, L.; Beňuš, R.; Klíma, B.

    2017-01-01

    Roč. 23, č. 6 (2017), s. 1207-1213 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : ancient dental calculus * SEM-EDX * human habits * the Great Moravian Empire * Napoleonic Wars Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.891, year: 2016

  3. Interaction of pyroclastic density currents with human settlements: Evidence from ancient Pompeii

    Science.gov (United States)

    Gurioli, Lucia; Pareschi, M. Teresa; Zanella, Elena; Lanza, Roberto; Deluca, Enrico; Bisson, Marina

    2005-06-01

    Integrating field observations and rock-magnetic measurements, we report how a turbulent pyroclastic density current interacted with and moved through an urban area. The data are from the most energetic, turbulent pyroclastic density current of the A.D. 79 eruption of Vesuvius, Italy, which partially destroyed the Roman city of Pompeii. Our results show that the urban fabric was able to divide the lower portion of the current into several streams that followed the city walls and the intracity roads. Vortices, revealed by upstream particle orientations and decreases in deposit temperature, formed downflow of obstacles or inside cavities. Although these perturbations affected only the lower part of the current and were localized, they could represent, in certain cases, cooler zones within which chances of human survival are increased. Our integrated field data for pyroclastic density current temperature and flow direction, collected for the first time across an urban environment, enable verification of coupled thermodynamic numerical models and their hazard simulation abilities.

  4. Geochemistry Meets Anthropology: the use of Sr Isotopes as Tracers for Ancient Human Migration.

    Science.gov (United States)

    Solis, G.; Schaaf, P.; Hernandez, T.; Horn, P.; Manzanilla, L.

    2005-12-01

    Sr isotopes have increasingly become an important tool in archeology and anthropology in determining provenance of humans. By comparing isotopic signatures of human teeth and bone with the soil environment, Sr isotope ratios have been used as tracers identifying living areas. Sr isotope ratios in tooth enamel reflect the source of diet during youth, whereas ratios in dentine and bones come from the food growing in local geologies around the time of death. However, since analytical procedures vary from lab to lab we present here our new technique and how it affects results. We studied 11 teeth and 12 bone samples from the archeological site of Teotihuacan, central Mexico, as well as soil and water from the locality. Mechanical sample preparation of all teeth involved isolation of the enamel layer with the aid of an orthodontical micro-tool. For some enamel samples up to three fractions (two leachates and residue) were obtained for measurement. Thoroughly cleaned bone material underwent no leaching. As an example, 87Sr/86Sr results from a sample with ratios of 0.70477 for bone (which is identical to highland soil), 0.70530 for first leachate, 0.70590 for second leachate, and 0.70668 (mean accuracy +/- 0.00004) for enamel, clearly show enamel contamination by mobile Sr probably from soil. We thus find that repeated cleaning and particularly repeated leaching procedures, including isotopic measurement of the leachates, are critical to differentiate primary from secondary Sr isotope ratios as product of interaction of soil, sediments and water from the substrate where burials took place.

  5. 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.

  6. Japanese Wolves are Genetically Divided into Two Groups Based on an 8-Nucleotide Insertion/Deletion within the mtDNA Control Region.

    Science.gov (United States)

    Ishiguro, Naotaka; Inoshima, Yasuo; Yanai, Tokuma; Sasaki, Motoki; Matsui, Akira; Kikuchi, Hiroki; Maruyama, Masashi; Hongo, Hitomi; Vostretsov, Yuri E; Gasilin, Viatcheslav; Kosintsev, Pavel A; Quanjia, Chen; Chunxue, Wang

    2016-02-01

    The mitochondrial DNA (mtDNA) control region (198- to 598-bp) of four ancient Canis specimens (two Canis mandibles, a cranium, and a first phalanx) was examined, and each specimen was genetically identified as Japanese wolf. Two unique nucleotide substitutions, the 78-C insertion and the 482-G deletion, both of which are specific for Japanese wolf, were observed in each sample. Based on the mtDNA sequences analyzed, these four specimens and 10 additional Japanese wolf samples could be classified into two groups- Group A (10 samples) and Group B (4 samples)-which contain or lack an 8-bp insertion/deletion (indel), respectively. Interestingly, three dogs (Akita-b, Kishu 25, and S-husky 102) that each contained Japanese wolf-specific features were also classified into Group A or B based on the 8-bp indel. To determine the origin or ancestor of the Japanese wolf, mtDNA control regions of ancient continental Canis specimens were examined; 84 specimens were from Russia, and 29 were from China. However, none of these 113 specimens contained Japanese wolf-specific sequences. Moreover, none of 426 Japanese modern hunting dogs examined contained these Japanese wolf-specific mtDNA sequences. The mtDNA control region sequences of Groups A and B appeared to be unique to grey wolf and dog populations.

  7. 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...

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

    Directory of Open Access Journals (Sweden)

    Andrea Splendiani

    Full Text Available 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.

  9. Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA

    Directory of Open Access Journals (Sweden)

    Rosvold Jørgen

    2012-09-01

    Full Text Available Abstract Background Red deer (Cervus elaphus have been an important human resource for millennia, experiencing intensive human influence through habitat alterations, hunting and translocation of animals. In this study we investigate a time series of ancient and contemporary DNA from Norwegian red deer spanning about 7,000 years. Our main aim was to investigate how increasing agricultural land use, hunting pressure and possibly human mediated translocation of animals have affected the genetic diversity on a long-term scale. Results We obtained mtDNA (D-loop sequences from 73 ancient specimens. These show higher genetic diversity in ancient compared to extant samples, with the highest diversity preceding the onset of agricultural intensification in the Early Iron Age. Using standard diversity indices, Bayesian skyline plot and approximate Bayesian computation, we detected a population reduction which was more prolonged than, but not as severe as, historic documents indicate. There are signs of substantial changes in haplotype frequencies primarily due to loss of haplotypes through genetic drift. There is no indication of human mediated translocations into the Norwegian population. All the Norwegian sequences show a western European origin, from which the Norwegian lineage diverged approximately 15,000 years ago. Conclusions Our results provide direct insight into the effects of increasing habitat fragmentation and human hunting pressure on genetic diversity and structure of red deer populations. They also shed light on the northward post-glacial colonisation process of red deer in Europe and suggest increased precision in inferring past demographic events when including both ancient and contemporary DNA.

  10. Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania.

    Science.gov (United States)

    Nagle, Nano; Ballantyne, Kaye N; van Oven, Mannis; Tyler-Smith, Chris; Xue, Yali; Wilcox, Stephen; Wilcox, Leah; Turkalov, Rust; van Oorschot, Roland A H; van Holst Pellekaan, Sheila; Schurr, Theodore G; McAllister, Peter; Williams, Lesley; Kayser, Manfred; Mitchell, R John

    2017-03-01

    Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.

  11. 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.

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

    Science.gov (United States)

    Vanek, Daniel; Saskova, Lenka; Koch, Hubert

    2009-06-01

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

  13. 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

  14. Tracheostomy in ancient Egypt.

    Science.gov (United States)

    Blomstedt, Patric

    2014-08-01

    It has often been reported that the ancient Egyptians performed tracheostomies. An analysis of this claim demonstrates it to be founded on only two depictions from the Protodynastic period (thirty-first century bc). These depictions are difficult to reconcile with tracheostomy from an anatomical point of view and can more easily be explained as human sacrifices. Considering that Egyptian surgery included only minor procedures even at its zenith during later dynastic periods, it is difficult to imagine that they would have developed such an advanced procedure at such an early date.

  15. Phylogeography of mtDNA haplogroup R7 in the Indian peninsula

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    Shukla Parul

    2008-08-01

    Full Text Available Abstract Background Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic speaking populations originated in India or derive from a relatively recent migration from further East. Results Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of ~12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1, is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between

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

    Energy Technology Data Exchange (ETDEWEB)

    Capasso, L.; Di Tota, G. [National Aechaeological Museum, Chieta, (Italy); Bondioli, L. [Prehistory and Ethnology Museum, Rome (Italy)

    1997-12-31

    Full text: The authors describe the results of an assay based on the comparison between chemical composition of dental calculus and bone respectively obtained from teeth and bones of ancient skeletons. The chemical analysis has been performed by synchrotron light. The concentrations of the following oligoelements having paleonutritional correlations were analysed: Fe, Cu, Zn, Pb, Sr and Ca. The authors demonstrate that- in a given individual the concentration of such elements in the bone sample were in the range of those obtained for the same elements in the sample of dental calculus. Such correspondence suggests that the chemical analysis of dental calculus may give paleonutritional indications analogous to those deriving from the analysis of bone samples. The authors underline also that the use of dental calculus has a distinct advantage over the use of bone samples, since it may allow a diachronic investigation. In fact, dental calculus typically presents a concentric pattern of growth, and the chemical composition of each layer may vary in accordance with temporal dietary variations. This is not the case for bone. This fact is the theoretical basis for the possible future development of techniques directed to the reconstruction of variations in the dietary habits of ancient individuals, possibly in relation to environmental seasonal changes.

  17. Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

    Directory of Open Access Journals (Sweden)

    Cook James M

    2009-03-01

    Full Text Available Abstract Background Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306 of our global sample of individuals was infected with the plutWB1 isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWB1 is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWB1 infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may

  18. 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

  19. High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice.

    Science.gov (United States)

    Amanzougaghene, Nadia; Mumcuoglu, Kosta Y; Fenollar, Florence; Alfi, Shir; Yesilyurt, Gonca; Raoult, Didier; Mediannikov, Oleg

    2016-01-01

    The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A.

  20. Neonatal medicine in ancient art.

    Science.gov (United States)

    Yurdakök, Murat

    2010-01-01

    There are a limited number of artistic objects from ancient times with particular importance in neonatal medicine. The best examples are figurines from ancient Egypt of Isis nursing Horus, showing the importance of breastfeeding. The earliest images of the human fetus were made by the Olmecs in Mexico around 1200- 400 BCE. One of the earliest representations of congenital anomalies is a figurine of diencephalic twins thought to be the goddess of Anatolia, dated to around 6500 BCE. In addition to these figurines, three sets of twins in the ancient world have medical importance, and Renaissance artists often used them as a subject for their paintings: "direct suckling animals" (Romulus and Remus), "heteropaternal superfecundation" (mother: Leda, fathers: Zeus, the king of the Olympian gods, and Leda's husband, Tyndareus), and "twin-to-twin transfusion" in monozygotic twins (Jacob and Esau).

  1. 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

  2. News from the west: ancient DNA from a French megalithic burial chamber.

    Science.gov (United States)

    Deguilloux, Marie-France; Soler, Ludovic; Pemonge, Marie-Hélène; Scarre, Chris; Joussaume, Roger; Laporte, Luc

    2011-01-01

    Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices. Copyright © 2010 Wiley-Liss, Inc.

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

    Directory of Open Access Journals (Sweden)

    Alice A Storey

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

  4. 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 (∼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. PMID:20689597

  5. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13% than among extant Danes and Scandinavians (approximately 2.5% as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  6. Ancient voyaging and Polynesian origins.

    Science.gov (United States)

    Soares, Pedro; Rito, Teresa; Trejaut, Jean; Mormina, Maru; Hill, Catherine; Tinkler-Hundal, Emma; Braid, Michelle; Clarke, Douglas J; Loo, Jun-Hun; Thomson, Noel; Denham, Tim; Donohue, Mark; Macaulay, Vincent; Lin, Marie; Oppenheimer, Stephen; Richards, Martin B

    2011-02-11

    The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ~4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3-4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a "voyaging corridor" between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  7. 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…

  8. Plants and Humans in the Near East and the Caucasus: Ancient and Traditional Uses of Plants as Food and Medicine, a Diachronic Ethnobotanical Review

    Directory of Open Access Journals (Sweden)

    Naomi F. Miller

    2014-02-01

    Full Text Available Review of Plants and Humans in the Near East and the Caucasus: Ancient and Traditional Uses of Plants as Food and Medicine, a Diachronic Ethnobotanical Review (2 vols. Vol. 1: The Landscapes. The Plants: Ferns and Gymnosperms. Vol. 2: The Plants: Angiosperms. Diego Rivera Núñez, Gonzalo Matilla Séiquer, Concepción Obón, Francisco Alcaraz Ariza. 2011. Ediciones de la Unverisdad de Murcia. Pp. 1056. EUR 23.76 (paperback. ISBN 978-84-15463-07-08 (2 vols., 978-84-15463-05-4 (vol. 1, 978-84-15463-06-1 (vol. 2.

  9. Trading mtDNA uncovers its role in metastasis

    Science.gov (United States)

    Ishikawa, Kaori

    2009-01-01

    It has been controversial for many years of whether mtDNA mutations are involved in phenotypes related to cancer due to the difficulty in excluding possible involvement of nuclear DNA mutations in these phenotypes. We addressed this issue by complete trading of mtDNAs between tumor cells expressing different metastatic phenotypes. Resultant trans-mitochondrial cybrids share the same nuclear background, but possess mtDNA from tumor cells expressing different metastatic phenotypes, and thus can be used to uncover the role of mtDNA in these phenotypes. The results showed that mtDNA controls development of metastasis in tumor cells, while tumor development is controlled by nuclear genome. PMID:19372745

  10. MtDNA mutagenesis impairs elimination of mitochondria during erythroid maturation leading to enhanced erythrocyte destruction

    NARCIS (Netherlands)

    Ahlqvist, K.J.; Leoncini, S.; Pecorelli, A.; Wortmann, S.B.; Ahola, S.; Forsstrom, S.; Guerranti, R.; Felice, C. De; Smeitink, J.; Ciccoli, L.; Hamalainen, R.H.; Suomalainen, A.

    2015-01-01

    Haematopoietic progenitor cells show special sensitivity to mitochondrial DNA (mtDNA) mutagenesis, which suggests that increased mtDNA mutagenesis could underlie anemias. Here we show that elevated mtDNA mutagenesis in mice with a proof-reading deficient mtDNA polymerase (PolG) leads to incomplete

  11. Colour Perception in Ancient World

    Science.gov (United States)

    Nesterov, D. I.; Fedorova, M. Yu

    2017-11-01

    How did the human thought form the surrounding color information into the persistent semantic images of a mythological, pseudoscientific and religious nature? The concepts associated with colour perception are suggested. The existence of colour environment does not depend on the human consciousness. The colour culture formation is directly related to the level of the human consciousness development and the possibility to influence the worldview and culture. The colour perception of a person goes through the stages similar to the development of colour vision in a child. Like any development, the colour consciousness has undergone stages of growth and decline, evolution and stagnation. The way of life and difficult conditions for existence made their own adjustments to the development of the human perception of the surrounding world. Wars have been both a powerful engine of progress in all spheres of life and a great destructive force demolishing the already created and preserved heritage. The surrounding world has always been interesting for humans, evoked images and fantasies in the consciousness of ancient people. Unusual and inexplicable natural phenomena spawned numerous legends and myths which was reflected in the ancient art and architecture and, accordingly, in a certain manifestation of colour in the human society. The colour perception of the ancient man, his pragmatic, utilitarian attitude to colour is considered as well as the influence of dependence on external conditions of existence and their reflection in the colour culture of antiquity. “Natural Science” conducts research in the field of the colour nature and their authorial interpretation of the Hellenic period. Several authorial concepts of the ancient world have been considered.

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

    Directory of Open Access Journals (Sweden)

    Alice Beau

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

  13. Multiple maternal origins of native modern and ancient horse populations in China.

    Science.gov (United States)

    Lei, C Z; Su, R; Bower, M A; Edwards, C J; Wang, X B; Weining, S; Liu, L; Xie, W M; Li, F; Liu, R Y; Zhang, Y S; Zhang, C M; Chen, H

    2009-12-01

    To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.

  14. Ancient medicine--a review.

    Science.gov (United States)

    Zuskin, Eugenija; Lipozencić, Jasna; Pucarin-Cvetković, Jasna; Mustajbegović, Jadranka; Schachter, Neil; Mucić-Pucić, Branka; Neralić-Meniga, Inja

    2008-01-01

    Different aspects of medicine and/or healing in several societies are presented. In the ancient times as well as today medicine has been closely related to magic, science and religion. Various ancient societies and cultures had developed different views of medicine. It was believed that a human being has two bodies: a visible body that belongs to the earth and an invisible body of heaven. In the earliest prehistoric days, a different kind of medicine was practiced in countries such as Egypt, Greece, Rome, Mesopotamia, India, Tibet, China, and others. In those countries, "medicine people" practiced medicine from the magic to modern physical practices. Medicine was magical and mythological, and diseases were attributed mostly to the supernatural forces. The foundation of modern medicine can be traced back to ancient Greeks. Tibetan culture, for instance, even today, combines spiritual and practical medicine. Chinese medicine developed as a concept of yin and yang, acupuncture and acupressure, and it has even been used in the modern medicine. During medieval Europe, major universities and medical schools were established. In the ancient time, before hospitals had developed, patients were treated mostly in temples.

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

    DEFF Research Database (Denmark)

    Campos, Paula; Willerslev, Eske; Sher, Andrei

    2010-01-01

    The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived...... in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental...... change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations....

  16. An investigation into the ancient abortion laws: comparing ancient Persia with ancient Greece and Rome.

    Science.gov (United States)

    Yarmohammadi, Hassan; Zargaran, Arman; Vatanpour, Azadeh; Abedini, Ehsan; Adhami, Siamak

    2013-01-01

    Since the dawn of medicine, medical rights and ethics have always been one of mankind's concerns. In any civilisation, attention paid to medical laws and ethics depends on the progress of human values and the advancement of medical science. The history of various civilisations teaches that each had its own views on medical ethics, but most had something in common. Ancient civilisations such as Greece, Rome, or Assyria did not consider the foetus to be alive and therefore to have human rights. In contrast, ancient Persians valued the foetus as a living person equal to others. Accordingly, they brought laws against abortion, even in cases of sexual abuse. Furthermore, abortion was considered to be a murder and punishments were meted out to the mother, father, and the person performing it.

  17. Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus

    Directory of Open Access Journals (Sweden)

    Dunn Catherine A

    2005-04-01

    Full Text Available Abstract Background Sperm adhesion molecule 1 (SPAM1 is the major mammalian testicular hyaluronidase and is expressed at high levels in sperm cells. SPAM1 protein is important for penetration of the cumulus cell layer surrounding the ovum, and is also involved in zona pellucida binding and sperm intracellular signalling. A previous study had identified SPAM1 as one of the many human genes that initiate within a transposable element. Results Examination of the human, mouse and rat SPAM1 loci revealed that transcripts initiate within the pol gene of an endogenous retrovirus (ERV element. This is highly unusual, as all previously identified ERV-initiated cellular gene transcripts initiate within the viral long terminal repeat promoter. The SPAM1 locus therefore represents an example of the evolution of a promoter from protein-coding sequence. We have identified novel alternative promoter and splicing variants of human and murine SPAM1. We show that all transcript variants are expressed primarily in the testis and are predicted to encode identical proteins. Conclusion The testis-specific promoters of the human and mouse SPAM1 genes are derived from sequence that was originally part of an ERV pol gene. This represents the first known example of an ERV-derived promoter acting in a gender-specific manner.

  18. Medicine in Ancient Assur

    DEFF Research Database (Denmark)

    Arbøll, Troels Pank

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

  19. Ancient Astronomy in Armenia

    Science.gov (United States)

    Parsamian, Elma S.

    2007-08-01

    The most important discovery, which enriched our knowledge of ancient astronomy in Armenia, was the complex of platforms for astronomical observations on the Small Hill of Metzamor, which may be called an ancient “observatory”. Investigations on that Hill show that the ancient inhabitants of the Armenian Highlands have left us not only pictures of celestial bodies, but a very ancient complex of platforms for observing the sky. Among the ancient monuments in Armenia there is a megalithic monument, probably, being connected with astronomy. 250km South-East of Yerevan there is a structure Zorats Kar (Karahunge) dating back to II millennium B.C. Vertical megaliths many of which are more than two meters high form stone rings resembling ancient stone monuments - henges in Great Britain and Brittany. Medieval observations of comets and novas by data in ancient Armenian manuscripts are found. In the collection of ancient Armenian manuscripts (Matenadaran) in Yerevan there are many manuscripts with information about observations of astronomical events as: solar and lunar eclipses, comets and novas, bolides and meteorites etc. in medieval Armenia.

  20. Mitochondrial DNA analysis of ancient Peruvian highlanders.

    Science.gov (United States)

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

    2006-09-01

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

  1. Human-Environment Interactions during the Last 8000 Years in the Environs of the Ancient City of Ephesus, Western Turkey

    Science.gov (United States)

    Stock, F.; Knipping, M.; Pint, A.; Brückner, H.

    2014-12-01

    About 6 millennia ago the maximum Holocene transgression reached c. 20 km inland. Thereafter, the coastline has continuously shifted westwards due to the progradation of the Küçük Menderes delta and its tributaries. Consequently, settlement and harbour sites were established following the retreating coastline. Our interdisciplinary geoarchaeological research focuses on (i) the detection of spatial and temporal shifts in the coastline during the past millennia and the human response to these changes; (ii) the human impact on the landscape, especially in the environs of the Roman Harbour and the harbour canal; (iii) the reconstruction of the vegetation history of the Ephesia. More than 200 drill cores were retrieved from geo-bioarchives. For a better understanding of the depositional environments, we carried out geochemical, sedimentological, microfaunal, palynological and parasitological analyses in Ephesus' harbours and in the environs of two Neolithic settlement sites. Diagnostic ceramic finds, AMS-14C age estimates and a tephra layer were used for the chronological framework.The results reveal human impact in sediments: early agricultural use in the Neolithic period; several meters of sediment with a high concentration of fig and grape seeds in the Koressos harbour during the 6th-3rd centuries BC; an accelerated sedimentation rate up to the factor of ten in Hellenistic and Roman times. Heavy metal pollution, sugar melon and fruit tree pollen, as well as eggs of intestinal parasites occur in the Roman harbour and its canal during the prosperity period of the city. Pollen analysis revealed the dominance of deciduous oak, in a landscape with human impact, already since the 6th millennium BC. From Hellenistic times onwards, fruit trees appear next to crop and pasture farming. After the decline of the city in the 7th century AD, pine trees became dominant, presumably on abandoned land. In the Belevi swamp to the northeast of Ephesus, the ash from the Minoan

  2. 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

    2015-01-01

    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. PMID:25487340

  3. Evolutionary diversity of bile salts in reptiles and mammals, including analysis of ancient human and extinct giant ground sloth coprolites

    Directory of Open Access Journals (Sweden)

    Hofmann Alan F

    2010-05-01

    Full Text Available Abstract Background Bile salts are the major end-metabolites of cholesterol and are also important in lipid and protein digestion and in influencing the intestinal microflora. We greatly extend prior surveys of bile salt diversity in both reptiles and mammals, including analysis of 8,000 year old human coprolites and coprolites from the extinct Shasta ground sloth (Nothrotherium shastense. Results While there is significant variation of bile salts across species, bile salt profiles are generally stable within families and often within orders of reptiles and mammals, and do not directly correlate with differences in diet. The variation of bile salts generally accords with current molecular phylogenies of reptiles and mammals, including more recent groupings of squamate reptiles. For mammals, the most unusual finding was that the Paenungulates (elephants, manatees, and the rock hyrax have a very different bile salt profile from the Rufous sengi and South American aardvark, two other mammals classified with Paenungulates in the cohort Afrotheria in molecular phylogenies. Analyses of the approximately 8,000 year old human coprolites yielded a bile salt profile very similar to that found in modern human feces. Analysis of the Shasta ground sloth coprolites (approximately 12,000 years old showed the predominant presence of glycine-conjugated bile acids, similar to analyses of bile and feces of living sloths, in addition to a complex mixture of plant sterols and stanols expected from an herbivorous diet. Conclusions The bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution, with some bile salt modifications only found within single groups such as marsupials. Analysis of the evolution of bile salt structures in different species provides a potentially rich model system for the evolution of a complex biochemical pathway in vertebrates. Our results also demonstrate the stability of bile salts in coprolites

  4. Evolutionary diversity of bile salts in reptiles and mammals, including analysis of ancient human and extinct giant ground sloth coprolites

    Science.gov (United States)

    2010-01-01

    Background Bile salts are the major end-metabolites of cholesterol and are also important in lipid and protein digestion and in influencing the intestinal microflora. We greatly extend prior surveys of bile salt diversity in both reptiles and mammals, including analysis of 8,000 year old human coprolites and coprolites from the extinct Shasta ground sloth (Nothrotherium shastense). Results While there is significant variation of bile salts across species, bile salt profiles are generally stable within families and often within orders of reptiles and mammals, and do not directly correlate with differences in diet. The variation of bile salts generally accords with current molecular phylogenies of reptiles and mammals, including more recent groupings of squamate reptiles. For mammals, the most unusual finding was that the Paenungulates (elephants, manatees, and the rock hyrax) have a very different bile salt profile from the Rufous sengi and South American aardvark, two other mammals classified with Paenungulates in the cohort Afrotheria in molecular phylogenies. Analyses of the approximately 8,000 year old human coprolites yielded a bile salt profile very similar to that found in modern human feces. Analysis of the Shasta ground sloth coprolites (approximately 12,000 years old) showed the predominant presence of glycine-conjugated bile acids, similar to analyses of bile and feces of living sloths, in addition to a complex mixture of plant sterols and stanols expected from an herbivorous diet. Conclusions The bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution, with some bile salt modifications only found within single groups such as marsupials. Analysis of the evolution of bile salt structures in different species provides a potentially rich model system for the evolution of a complex biochemical pathway in vertebrates. Our results also demonstrate the stability of bile salts in coprolites preserved in arid climates

  5. Resolving the bulk δ 15N values of ancient human and animal bone collagen via compound-specific nitrogen isotope analysis of constituent amino acids

    Science.gov (United States)

    Styring, Amy K.; Sealy, Judith C.; Evershed, Richard P.

    2010-01-01

    Stable nitrogen isotope analysis is a fundamental tool in assessing dietary preferences and trophic positions within contemporary and ancient ecosystems. In order to assess more fully the dietary contributions to human tissue isotope values, a greater understanding of the complex biochemical and physiological factors which underpin bulk collagen δ 15N values is necessary. Determinations of δ 15N values of the individual amino acids which constitute bone collagen are necessary to unravel these relationships, since different amino acids display different δ 15N values according to their biosynthetic origins. A range of collagen isolates from archaeological faunal and human bone ( n = 12 and 11, respectively), representing a spectrum of terrestrial and marine protein origins and diets, were selected from coastal and near-coastal sites at the south-western tip of Africa. The collagens were hydrolysed and δ 15N values of their constituent amino acids determined as N-acetylmethyl esters (NACME) via gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). The analytical approach employed accounts for 56% of bone collagen nitrogen. Reconstruction of bulk bone collagen δ 15N values reveals a 2‰ offset from bulk collagen δ 15N values which is attributable to the δ 15N value of the amino acids which cannot currently be determined by GC-C-IRMS, notably arginine which comprises 53% of the nitrogen unaccounted for (23% of the total nitrogen). The δ 15N values of individual amino acids provide insights into both the contributions of various amino acids to the bulk δ 15N value of collagen and the factors influencing trophic position and the nitrogen source at the base of the food web. The similarity in the δ 15N values of alanine, glutamate, proline and hydroxyproline reflects the common origin of their amino groups from glutamate. The depletion in the δ 15N value of threonine with increasing trophic level indicates a fundamental difference between

  6. Ancient mitochondrial DNA from Malaysian hair samples: some indications of Southeast Asian population movements.

    Science.gov (United States)

    Ricaut, François-X; Bellatti, M; Lahr, Marta Mirazon

    2006-01-01

    The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia ( approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene.

  7. SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort.

    Science.gov (United States)

    Rueda, Manuel; Torkamani, Ali

    2017-08-18

    Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians. We have developed SG-ADVISER mtDNA, a web server to facilitate the analysis and interpretation of mtDNA genomic data coming from next generation sequencing (NGS) experiments. The server was built in the context of our SG-ADVISER framework and on top of the MtoolBox platform (Calabrese et al., Bioinformatics 30(21):3115-3117, 2014), and includes most of its functionalities (i.e., assembly of mitochondrial genomes, heteroplasmic fractions, haplogroup assignment, functional and prioritization analysis of mitochondrial variants) as well as a back-end and a front-end interface. The server has been tested with unpublished data from 200 individuals of a healthy aging cohort (Erikson et al., Cell 165(4):1002-1011, 2016) and their data is made publicly available here along with a preliminary analysis of the variants. We observed that individuals over ~90 years old carried low levels of heteroplasmic variants in their genomes. SG-ADVISER mtDNA is a fast and functional tool that allows for variant calling and annotation of human mtDNA data coming from NGS experiments. The server was built with simplicity in mind, and builds on our own experience in interpreting mtDNA variants in the context of sudden death and rare diseases. Our objective is to provide an interface for non-bioinformaticians aiming to acquire (or contrast) mtDNA annotations via MToolBox. SG-ADVISER web server is freely available to all users at https://genomics.scripps.edu/mtdna .

  8. MtDNA T4216C variation in multiple sclerosis

    DEFF Research Database (Denmark)

    Andalib, Sasan; Emamhadi, Mohammadreza; Yousefzadeh-Chabok, Shahrokh

    2016-01-01

    MtDNA T4216C variation has frequently been investigated in Multiple Sclerosis (MS) patients; nonetheless, controversy has existed about the evidence of association of this variation with susceptibility to MS. The present systematic review and meta-analysis converge the results of the preceding...

  9. The Mind of the Ancient Physical Philosophers

    OpenAIRE

    Joan Torello

    2015-01-01

    Although this conception of the soul belonged to an ancient tradition expressed already in Homer and Orphism, the thesis of Anaximenes that conceived air as a physical substrate of the human soul, which was continued by Heraclitus, Democritus and Diogenes of Apollonia, was considered the first theory of antiquity on the human psyche in science and philosophy. It is presented here.

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

    Science.gov (United States)

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

    2015-07-08

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

  11. 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

    2007-03-20

    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.

  12. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies

    Directory of Open Access Journals (Sweden)

    Specht Günther

    2010-03-01

    Full Text Available Abstract Background Mitochondrial DNA (mtDNA is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. Description eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle, security aspects (by using database technology and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs. It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. Conclusions The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

  13. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies.

    Science.gov (United States)

    Weissensteiner, Hansi; Schönherr, Sebastian; Specht, Günther; Kronenberg, Florian; Brandstätter, Anita

    2010-03-09

    Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle), security aspects (by using database technology) and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs). It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

  14. Reconstructing an Ancient Wonder.

    Science.gov (United States)

    Imhof, Christopher J.

    2001-01-01

    Describes a Montessori class project involving the building of a model of the ancient Briton monument, Stonehenge. Illustrates how the flexibility of the Montessori elementary curriculum encourages children to make their own toys and learn from the process. (JPB)

  15. Physicians of ancient India.

    Science.gov (United States)

    Saini, Anu

    2016-01-01

    A survey of Indian medical historiography will reveal no dearth of work on the systems of medicine and medical literature of ancient India. However, the people who were responsible for the healing have not received much attention. This article traces the evolution of the physician as a professional in ancient India. This article reviews the secondary literature on healing and medical practice in India, specifically pertaining to the individual medical practitioner, drawing from varied sources. The healers of ancient India hailed from different castes and classes. They were well-respected and enjoyed state patronage. They were held to the highest ethical standards of the day and were bound by a strict code of conduct. They underwent rigorous training in both medicine and surgery. Most physicians were multi-skilled generalists, and expected to be skilled in elocution and debate. They were reasonably well-off financially. The paper also briefly traces the evolution of medicinal ideas in ancient India.

  16. Physicians of ancient India

    Directory of Open Access Journals (Sweden)

    Anu Saini

    2016-01-01

    Full Text Available A survey of Indian medical historiography will reveal no dearth of work on the systems of medicine and medical literature of ancient India. However, the people who were responsible for the healing have not received much attention. This article traces the evolution of the physician as a professional in ancient India. This article reviews the secondary literature on healing and medical practice in India, specifically pertaining to the individual medical practitioner, drawing from varied sources. The healers of ancient India hailed from different castes and classes. They were well-respected and enjoyed state patronage. They were held to the highest ethical standards of the day and were bound by a strict code of conduct. They underwent rigorous training in both medicine and surgery. Most physicians were multi-skilled generalists, and expected to be skilled in elocution and debate. They were reasonably well-off financially. The paper also briefly traces the evolution of medicinal ideas in ancient India.

  17. Ancient Egyptian Astronomical Calander

    Science.gov (United States)

    Marshall, Patrice; Lodhi, M. A. K.

    2001-03-01

    In this paper, we discuss how certain astronomical concepts are related to the ancient Egyptian culture and their daily life. One of them is different ways of creating their calendar systems. The ancient Egyptian calendar seems to have quite a bit of its origin in astronomy and its development over the course of history. There is an important role played by events, as determined in the heavens, in developing their calendar system. Along with astronomical observations by the ancient people of Egypt, there were several outside cultures that helped develop their calendar system and Egyptian idea of how life was created on this planet, most notably the inclusion of the star Sirius in the constellation of Canis Major. We give a brief discussion of these influences. For the ancient Egyptians, the cycle of life and death is a concept that ties in with a calendar system used to determine daily events.

  18. [Tuberculosis in ancient Egypt].

    Science.gov (United States)

    Ziskind, B; Halioua, B

    2007-12-01

    Did Tuberculosis plague Ancient Egypt five millennia ago? Some medical papyri appear to evoke tuberculosis. Egyptian physicians did not individualize it, but they seem to have noticed some of its clinical expressions, such as cough, cervical adenitis, and cold abscesses. In Egyptian iconography, some cases of hump-backs were probably due to Pott's disease of the spine Descriptive paleopathology, born with the 20th century, has identified pulmonary and especially spinal lesions compatible with tuberculosis. Progress of molecular biology has made a decisive contribution with the diagnosis of tuberculosis on ancient samples. Tuberculosis has been identified using PCR in nearly a third of the Egyptian mummies recently examined. Spoligotyping has made it possible to re-evaluate the phylogenic tree of the Mycobacterium tuberculosis complex in Ancient Egypt. Tuberculosis certainly plagued the Nile Valley and appears to have been an important cause of mortality in Ancient Egypt.

  19. COII/tRNA[sup Lys] intergenic 9-bp deletion and other mtDNA markers clearly reveal that the Tharus (Southern Nepal) have oriental affinities

    Energy Technology Data Exchange (ETDEWEB)

    Passarino, G.; Semino, O.; Santachiara-Benerecetti, A.S.; Modiano, G. (Universita di Tor Vergata (Romania))

    1993-09-01

    The authors searched for the East Asian mtDNA 9-bp deletion in the intergenic COII/tRNA[sup Lys] region in a sample of 107 Tharus (50 from central Terai and 57 from eastern Terai), a population whose anthropological origin has yet to be completely clarified. The deletion, detected by electrophoresis of the PCR-amplified nt 7392-8628 mtDNA fragment after digestion with HaeIII, was found in about 8% of both Tharu groups but was found in none of the 76 Hindus who were examined as a non-Oriental neighboring control population. A complete triplication of the 9-bp unit, the second case so far reported, was also observed in one eastern Tharu. All the mtDNAs with the deletion, and that with the triplication, were further characterized (by PCR amplification of the relevant mTDNA fragments and their digestion with the appropriate enzymes) to locate them in the Ballinger et al. phylogeny of East Asian mtDNA haplotypes. The deletion was found to be associated with four different haplotypes, two of which are reported for the first time. One of the deletions and especially the triplication could be best explained by the assumption of novel length-change events. Ballinger's classification of East Asian mtDNA haplotypes is mainly based on the phenotypes for the DdeI site at nt 10394 and the AluI site at nt 10397. Analysis of the entire Tharu sample revealed that more than 70% of the Tharus have both sites, the association of which has been suggested as an ancient East Asian peculiarity. These results conclusively indicate that the Tharus have a predominantly maternal Oriental ancestry. Moreover, they show at least one and perhaps two further distinct length mutations, and this suggests that the examined region is a hot spot of rearrangements. 21 refs., 5 figs., 6 tabs.

  20. Using Ancient Samples in Projection Analysis

    Directory of Open Access Journals (Sweden)

    Melinda A. Yang

    2016-01-01

    Full Text Available Projection analysis is a tool that extracts information from the joint allele frequency spectrum to better understand the relationship between two populations. In projection analysis, a test genome is compared to a set of genomes from a reference population. The projection’s shape depends on the historical relationship of the test genome’s population to the reference population. Here, we explore in greater depth the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model, or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model. We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present-day population or not. Second, we compute projections for several published ancient genomes. We compare two Neanderthals and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these five ancient genomes to assess how well the observed projections are recovered.

  1. Mitochondrial Disease: mtDNA and Protein Segregation Mysteries in iPSCs

    OpenAIRE

    Pickrell, Alicia M.; Youle, Richard J.

    2013-01-01

    Mitochondrial diseases cause a range of clinical manifestations even in patients carrying the same mtDNA mutations. New work reveals that a common disease-associated mtDNA mutation is selectively segregated from wild-type mtDNA during the reprogramming of induced pluripotent stem cells and that high levels of this mutation in differentiated neurons upregulate Parkin-mediated mitophagy.

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

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    Dan Bar Yaacov

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

  3. Plasmodium vivax populations revisited: mitochondrial genomes of temperate strains in Asia suggest ancient population expansion

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    Miao Miao

    2012-02-01

    Full Text Available Abstract Background Plasmodium vivax is the most widely distributed human malaria parasite outside of Africa, and its range extends well into the temperate zones. Previous studies provided evidence for vivax population differentiation, but temperate vivax parasites were not well represented in these analyses. Here we address this deficit by using complete mitochondrial (mt genome sequences to elucidate the broad genetic diversity and population structure of P. vivax from temperate regions in East and Southeast Asia. Results From the complete mtDNA sequences of 99 clinical samples collected in China, Myanmar and Korea, a total of 30 different haplotypes were identified from 26 polymorphic sites. Significant differentiation between different East and Southeast Asian parasite populations was observed except for the comparison between populations from Korea and southern China. Haplotype patterns and structure diversity analysis showed coexistence of two different groups in East Asia, which were genetically related to the Southeast Asian population and Myanmar population, respectively. The demographic history of P. vivax, examined using neutrality tests and mismatch distribution analyses, revealed population expansion events across the entire P. vivax range and the Myanmar population. Bayesian skyline analysis further supported the occurrence of ancient P. vivax population expansion. Conclusions This study provided further resolution of the population structure and evolution of P. vivax, especially in temperate/warm-temperate endemic areas of Asia. The results revealed divergence of the P. vivax populations in temperate regions of China and Korea from other populations. Multiple analyses confirmed ancient population expansion of this parasite. The extensive genetic diversity of the P. vivax populations is consistent with phenotypic plasticity of the parasites, which has implications for malaria control.

  4. Evidence of rheumatoid arthritis in ancient India.

    Science.gov (United States)

    Sturrock, R D; Sharma, J N; Buchanan, W W

    1977-01-01

    The scarcity of references in ancient medical literature to any disease resembling rheumatoid arthritis (RA) has led many Western rheumatologists to believe that rheumatoid arthritis is a disease of relatively recent origin. In a recent paper on this problem, Short traces the first adequate description of what was probably rheumatoid arthritis to Thomas Sydenham (1624-1689) and emphasizes that European and Greek medical literature before Sydenham's time may have confused gout and other forms of polyarthritis as manifestations of the same disease (1). Studies in human paleopathology have as yet produced no convincing evidence for the existenct of RA in ancient human remains, but Short suggested that a study of the ancient medical literature of the Eastern civilizations may provide some new information on the true antiquity of rheumatoid arthritis.

  5. Ancient Human Footprints in Mexico?

    National Research Council Canada - National Science Library

    Holden, Constance

    2005-01-01

    .... Geochronologist Silvia Gonzalez of Liverpool John Moores University in the UK stumbled upon the prints in an abandoned quarry along what had once been a lake in the Valsequillo basin in central Mexico...

  6. Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta).

    Science.gov (United States)

    Song, Hojun; Moulton, Matthew J; Whiting, Michael F

    2014-01-01

    Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.

  7. Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta.

    Directory of Open Access Journals (Sweden)

    Hojun Song

    Full Text Available Nuclear mitochondrial pseudogenes (numts are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.

  8. Dentistry in ancient mesopotamia.

    Science.gov (United States)

    Neiburger, E J

    2000-01-01

    Sumer, an empire in ancient Mesopotamia (southern Iraq), is well known as the cradle of our modern civilization and the home of biblical Abraham. An analysis of skeletal remains from cemeteries at the ancient cities of Ur and Kish (circa 2000 B.C.), show a genetically homogeneous, diseased, and short-lived population. These ancient Mesopotamians suffered severe dental attrition (95 percent), periodontal disease (42 percent), and caries (2 percent). Many oral congenital and neoplastic lesions were noted. During this period, the "local dentists" knew only a few modern dental techniques. Skeletal (dental) evidence indicates that the population suffered from chronic malnutrition. Malnutrition was probably caused by famine, which is substantiated in historic cuneiform and biblical writings, geologic strata samples, and analysis of skeletal and forensic dental pathology. These people had modern dentition but relatively poor dental health. The population's lack of malocclusions, caries, and TMJ problems appear to be due to flat plane occlusion.

  9. Dwarfs in ancient Egypt.

    Science.gov (United States)

    Kozma, Chahira

    2006-02-15

    Ancient Egypt was one of the most advanced and productive civilizations in antiquity, spanning 3000 years before the "Christian" era. Ancient Egyptians built colossal temples and magnificent tombs to honor their gods and religious leaders. Their hieroglyphic language, system of organization, and recording of events give contemporary researchers insights into their daily activities. Based on the record left by their art, the ancient Egyptians documented the presence of dwarfs in almost every facet of life. Due to the hot dry climate and natural and artificial mummification, Egypt is a major source of information on achondroplasia in the old world. The remains of dwarfs are abundant and include complete and partial skeletons. Dwarfs were employed as personal attendants, animal tenders, jewelers, and entertainers. Several high-ranking dwarfs especially from the Old Kingdom (2700-2190 BCE) achieved important status and had lavish burial places close to the pyramids. Their costly tombs in the royal cemeteries and the inscriptions on their statutes indicate their high-ranking position in Egyptian society and their close relation to the king. Some of them were Seneb, Pereniankh, Khnumhotpe, and Djeder. There were at least two dwarf gods, Ptah and Bes. The god Ptah was associated with regeneration and rejuvenation. The god Bes was a protector of sexuality, childbirth, women, and children. He was a favored deity particularly during the Greco-Roman period. His temple was recently excavated in the Baharia oasis in the middle of Egypt. The burial sites and artistic sources provide glimpses of the positions of dwarfs in daily life in ancient Egypt. Dwarfs were accepted in ancient Egypt; their recorded daily activities suggest assimilation into daily life, and their disorder was not shown as a physical handicap. Wisdom writings and moral teachings in ancient Egypt commanded respect for dwarfs and other individuals with disabilities. Copyright (c) 2005 Wiley-Liss, Inc.

  10. mtDNA structure: the women who formed the Brazilian Northeast.

    Science.gov (United States)

    Schaan, Ana Paula; Costa, Lorenna; Santos, Diego; Modesto, Antonio; Amador, Marcos; Lopes, Camile; Rabenhorst, Sílvia Helena; Montenegro, Raquel; Souza, Bruno D A; Lopes, Thayson; Yoshioka, France Keiko; Pinto, Giovanny; Silbiger, Vivian; Ribeiro-Dos-Santos, Ândrea

    2017-08-09

    The distribution of mitochondrial DNA (mtDNA) lineages in Brazil is heterogeneous due to different regional colonization dynamics. Northeastern Brazil, although being an important region in terms of human imigration and ethnic admixture, has little information regarding its population mtDNA composition. Here, we determine which mitochondrial lineages contributed to the formation of the Northeastern Brazilian population. Our sample consisted of 767 individuals distributed as follows i) 550 individuals from eight Northeastern states (Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe, and Bahia) which were sequenced for mtDNA hypervariable segments I, II, and III; ii) 217 individuals from Alagoas and Pernambuco (previously published data). Data analysis was performed through sequence alignment and Haplogrep 2.0 haplogroup assignment tools. Furthermore, maternal ancestry distribution was contextualized and, when possible, related to historical events to better understand the biological interactions and population dynamics that occurred in this region since the beginning of colonization. Unexpectedly, Amerindian mitochondrial ancestry was the highest in the Northeastern region overall, followed by African, European and non-Amerindian Asian, unlike previous results for this region. Alagoas and Pernambuco states, however, showed a larger African mtDNA frequency. The Northeastern region showed an intraregional heterogeneous distribution regarding ancestral groups, in which states/mesoregions located to the north had a prevalent Amerindian ancestral frequency and those to the south had predominance of African ancestry. Moreover, results showed great diversity of European haplogroups and the presence of non-Amerindian Asian haplogroups. Our findings are in disagreement with previous investigations that suggest African mitochondrial ancestry is the most prevalent in the Brazilian Northeast. The predominance of Amerindian lineages exemplifies the

  11. MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania.

    Science.gov (United States)

    Ballantyne, Kaye N; van Oven, Mannis; Ralf, Arwin; Stoneking, Mark; Mitchell, R John; van Oorschot, Roland A H; Kayser, Manfred

    2012-07-01

    Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for

  12. Sequence polymorphisms of mtDNA HV1, HV2, and HV3 regions in the Malay population of Peninsular Malaysia.

    Science.gov (United States)

    Nur Haslindawaty, Abd Rashid; Panneerchelvam, Sundararajulu; Edinur, Hisham Atan; Norazmi, Mohd Nor; Zafarina, Zainuddin

    2010-09-01

    The uniparentally inherited mitochondrial DNA (mtDNA) is in the limelight for the past two decades, in studies relating to demographic history of mankind and in forensic kinship testing. In this study, human mtDNA hypervariable segments 1, 2, and 3 (HV1, HV2, and HV3) were analyzed in 248 unrelated Malay individuals in Peninsular Malaysia. Combined analyses of HV1, HV2, and HV3 revealed a total of 180 mtDNA haplotypes with 149 unique haplotypes and 31 haplotypes occurring in more than one individual. The genetic diversity was estimated to be 99.47%, and the probability of any two individuals sharing the same mtDNA haplotype was 0.93%. The most frequent mtDNA haplotype (73, 146, 150, 195, 263, 315.1C, 16140, 16182C, 16183C, 16189, 16217, 16274, and 16335) was shared by 11 (4.44%) individuals. The nucleotide diversity and mean of pair-wise differences were found to be 0.036063 ± 0.020101 and 12.544022 ± 6.230486, respectively.

  13. Ancient Chinese constellations

    Science.gov (United States)

    Xu, Junjun

    2011-06-01

    China, a country with a long history and a specific culture, has also a long and specific astronomy. Ancient Chinese astronomers observed the stars, named and distributed them into constellations in a very specific way, which is quite different from the current one. Around the Zodiac, stars are divided into four big regions corresponding with the four orientations, and each is related to a totem, either the Azure Dragon, the Vermilion Bird, the White Tiger or the Murky Warrior. We present a general pattern of the ancient Chinese constellations, including the four totems, their stars and their names.

  14. Ancient Climatic Architectural Design Approach

    Directory of Open Access Journals (Sweden)

    Nasibeh Faghih

    2013-01-01

    Full Text Available Ancient climatic architecture had found out a series of appropriate responses for the best compatibility with the critical climate condition for instance, designing ‘earth sheltered houses’ and ‘courtyard houses’. They could provide human climatic comfort without excessive usage of fossil fuel resources. Owing to the normal thermal conditions in the ground depth, earth sheltered houses can be slightly affected by thermal fluctuations due to being within the earth. In depth further than 6.1 meters, temperature alternation is minute during the year, equaling to average annual temperature of outside. More to the point, courtyard buildings as another traditional design approach, have prepared controlled climatic space based on creating the maximum shade in the summer and maximum solar heat absorption in the winter. The courtyard houses served the multiple functions of lighting to the rooms, acting as a heat absorber in the summer and a radiator in the winter, as well as providing an open space inside for community activities. It must be noted that they divided into summer and winter zones located in south and north of the central courtyard where residents were replaced into them according to changing the seasons. Therefore, Ancient climatic buildings provided better human thermal comfort in comparison with the use contemporary buildings of recent years, except with the air conditioning

  15. 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

  16. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis).

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J; Robertson, Bruce C

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  17. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis.

    Directory of Open Access Journals (Sweden)

    Nicolas Dussex

    Full Text Available The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis. Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410, historical (n = 15 and fossil samples (n = 4 showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  18. Evolutionary Analyses of Entire Genomes Do Not Support the Association of mtDNA Mutations with Ras/MAPK Pathway Syndromes

    Science.gov (United States)

    Cerezo, María; Balboa, Emilia; Heredia, Claudia; Castro-Feijóo, Lidia; Rica, Itxaso; Barreiro, Jesús; Eirís, Jesús; Cabanas, Paloma; Martínez-Soto, Isabel; Fernández-Toral, Joaquín; Castro-Gago, Manuel; Pombo, Manuel; Carracedo, Ángel; Barros, Francisco

    2011-01-01

    Background There are several known autosomal genes responsible for Ras/MAPK pathway syndromes, including Noonan syndrome (NS) and related disorders (such as LEOPARD, neurofibromatosis type 1), although mutations of these genes do not explain all cases. Due to the important role played by the mitochondrion in the energetic metabolism of cardiac muscle, it was recently proposed that variation in the mitochondrial DNA (mtDNA) genome could be a risk factor in the Noonan phenotype and in hypertrophic cardiomyopathy (HCM), which is a common clinical feature in Ras/MAPK pathway syndromes. In order to test these hypotheses, we sequenced entire mtDNA genomes in the largest series of patients suffering from Ras/MAPK pathway syndromes analyzed to date (n = 45), most of them classified as NS patients (n = 42). Methods/Principal Findings The results indicate that the observed mtDNA lineages were mostly of European ancestry, reproducing in a nutshell the expected haplogroup (hg) patterns of a typical Iberian dataset (including hgs H, T, J, and U). Three new branches of the mtDNA phylogeny (H1j1, U5b1e, and L2a5) are described for the first time, but none of these are likely to be related to NS or Ras/MAPK pathway syndromes when observed under an evolutionary perspective. Patterns of variation in tRNA and protein genes, as well as redundant, private and heteroplasmic variants, in the mtDNA genomes of patients were as expected when compared with the patterns inferred from a worldwide mtDNA phylogeny based on more than 8700 entire genomes. Moreover, most of the mtDNA variants found in patients had already been reported in healthy individuals and constitute common polymorphisms in human population groups. Conclusions/Significance As a whole, the observed mtDNA genome variation in the NS patients was difficult to reconcile with previous findings that indicated a pathogenic role of mtDNA variants in NS. PMID:21526175

  19. Evolutionary analyses of entire genomes do not support the association of mtDNA mutations with Ras/MAPK pathway syndromes.

    Directory of Open Access Journals (Sweden)

    Alberto Gómez-Carballa

    Full Text Available BACKGROUND: There are several known autosomal genes responsible for Ras/MAPK pathway syndromes, including Noonan syndrome (NS and related disorders (such as LEOPARD, neurofibromatosis type 1, although mutations of these genes do not explain all cases. Due to the important role played by the mitochondrion in the energetic metabolism of cardiac muscle, it was recently proposed that variation in the mitochondrial DNA (mtDNA genome could be a risk factor in the Noonan phenotype and in hypertrophic cardiomyopathy (HCM, which is a common clinical feature in Ras/MAPK pathway syndromes. In order to test these hypotheses, we sequenced entire mtDNA genomes in the largest series of patients suffering from Ras/MAPK pathway syndromes analyzed to date (n = 45, most of them classified as NS patients (n = 42. METHODS/PRINCIPAL FINDINGS: The results indicate that the observed mtDNA lineages were mostly of European ancestry, reproducing in a nutshell the expected haplogroup (hg patterns of a typical Iberian dataset (including hgs H, T, J, and U. Three new branches of the mtDNA phylogeny (H1j1, U5b1e, and L2a5 are described for the first time, but none of these are likely to be related to NS or Ras/MAPK pathway syndromes when observed under an evolutionary perspective. Patterns of variation in tRNA and protein genes, as well as redundant, private and heteroplasmic variants, in the mtDNA genomes of patients were as expected when compared with the patterns inferred from a worldwide mtDNA phylogeny based on more than 8700 entire genomes. Moreover, most of the mtDNA variants found in patients had already been reported in healthy individuals and constitute common polymorphisms in human population groups. CONCLUSIONS/SIGNIFICANCE: As a whole, the observed mtDNA genome variation in the NS patients was difficult to reconcile with previous findings that indicated a pathogenic role of mtDNA variants in NS.

  20. Ancient Chinese Precedents in China

    National Research Council Canada - National Science Library

    Geddis, Robert

    1999-01-01

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

  1. Ancient Greek psychotherapy for contemporary nurses.

    Science.gov (United States)

    Kourkouta, Lambrini

    2002-08-01

    Ancient Greek physicians as well as philosophers were fully cognizant of a human being's psychological function and used their particular art to influence individual or social behavior in accordance with their pursuit. This art or technique favorably compares with several of the methods currently called supportive psychotherapy. This psychotherapy was the first form of care for people with mental health problems. Nurses who base their practice on ancient Greek psychotherapy see the patient as a whole, a person who creates meaning in life. Applying the philosophical principles of ancient Greeks helps nurses understand the behavior of people with mental health problems and recognize and facilitate adaptive satisfaction of these psychological needs. In addition, psychiatric nurses are able to help distressed individuals understand their fears and anxieties, so they are freed from the causes of their symptoms that led them to seek therapy in the first place. Consequently, this understanding can make psychiatric nurses' work a living experience and add meaning to their work.

  2. Ancient ports of Kalinga

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    The ancient Kingdom of Kalinga mentioned in the Hathigumpha inscription of Kharavela (1st century B.C.) extended from the mouths of the Ganges to the estuary of Godavari river on the East Coast. Ptolemy (100 A.D.) mentions that Paluru (District...

  3. 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…

  4. Mathematics in Ancient India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 10. Mathematics in Ancient India - Diophantine Equations: The Kuttaka. Amartya Kumar Dutta. Series Article Volume 7 Issue 10 October 2002 pp 6-22. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Mathematics in Ancient India

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 4. Mathematics in Ancient India - An Overview. Amartya Kumar Dutta. Series Article Volume 7 Issue 4 April 2002 pp 4-19. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/007/04/0004-0019. Keywords.

  6. ANCIENT INDIAN BACTERIOLOGY

    Science.gov (United States)

    Sircar, N. N.

    1991-01-01

    An attempt has been made in this paper to disseminate the formation of basic knowledge of bacteriology in ancient India. In the aetiology of many diseases microbial relation plays a role which was realized by the modern medicine only a century ago. PMID:22556529

  7. 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.

  8. Ancient Egypt: Personal Perspectives.

    Science.gov (United States)

    Wolinski, Arelene

    This teacher resource book provides information on ancient Egypt via short essays, photographs, maps, charts, and drawings. Egyptian social and religious life, including writing, art, architecture, and even the practice of mummification, is conveniently summarized for the teacher or other practitioner in a series of one to three page articles with…

  9. 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…

  10. Mathematics in Ancient India

    Indian Academy of Sciences (India)

    SERIES I ARTICLE. Mathematics in Ancient India. 3. Brahmagupta's Lemma: The Samasabhavana. Amartya Kumar Dutta is an Associate Professor of. Mathematics at the. Indian Statistical. Institute, Kolkata. His research interest is in commutative algebra. Part 1, An overview, Reso- nance, VoL7, No.4, pp.4-19,. 2002. Part 2.

  11. The effects of a wheat germ rich diet on oxidative mtDNA damage, mtDNA copy number and antioxidant enzyme activities in aging Drosophila.

    Science.gov (United States)

    Mutlu, Ayse Gul

    2013-03-01

    The free radical theory of aging posits that the accumulation of macromolecular damage induced by toxic reactive oxygen species plays a central role in the aging process. Therefore consumption of dietary antioxidants appears to be of great importance. Wheat germ have strong antioxidant properties. Aim of this study is investigate the effects of a wheat germ rich diet on oxidative mtDNA damage, mtDNA copy number and antioxidant enzyme activities in Drosophila. Current results suggested that dietary wheat germ enhances the activities of antioxidant enzymes in Drosophila. There was no statistically difference in mtDNA damage and mtDNA copy number results of "Wheat Germ" and "Refined White Flour" feed groups. mtDNA damage slightly increased with aging in both groups but these changes were no statistically different.

  12. Sacred psychiatry in ancient Greece.

    Science.gov (United States)

    Tzeferakos, Georgios; Douzenis, Athanasios

    2014-04-12

    From the ancient times, there are three basic approaches for the interpretation of the different psychic phenomena: the organic, the psychological, and the sacred approach. The sacred approach forms the primordial foundation for any psychopathological development, innate to the prelogical human mind. Until the second millennium B.C., the Great Mother ruled the Universe and shamans cured the different mental disorders. But, around 1500 B.C., the predominance of the Hellenic civilization over the Pelasgic brought great changes in the theological and psychopathological fields. The Hellenes eliminated the cult of the Great Mother and worshiped Dias, a male deity, the father of gods and humans. With the Father's help and divinatory powers, the warrior-hero made diagnoses and found the right therapies for mental illness; in this way, sacerdotal psychiatry was born.

  13. mtDNA from the early Bronze Age to the Roman period suggests a genetic link between the Indian subcontinent and Mesopotamian cradle of civilization.

    Science.gov (United States)

    Witas, Henryk W; Tomczyk, Jacek; Jędrychowska-Dańska, Krystyna; Chaubey, Gyaneshwer; Płoszaj, Tomasz

    2013-01-01

    Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth) of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa) and Tell Masaikh (ancient Kar-Assurnasirpal) Syrian archaeological sites, both in the middle Euphrates valley. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria. However, they are present in people inhabiting today's Tibet, Himalayas, India and Pakistan. We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya). They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region. None of the successfully identified nuclear alleles turned out to be ΔF508 CFTR, LCT-13910T or Δ32 CCR5.

  14. mtDNA from the early Bronze Age to the Roman period suggests a genetic link between the Indian subcontinent and Mesopotamian cradle of civilization.

    Directory of Open Access Journals (Sweden)

    Henryk W Witas

    Full Text Available Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa and Tell Masaikh (ancient Kar-Assurnasirpal Syrian archaeological sites, both in the middle Euphrates valley. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria. However, they are present in people inhabiting today's Tibet, Himalayas, India and Pakistan. We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya. They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region. None of the successfully identified nuclear alleles turned out to be ΔF508 CFTR, LCT-13910T or Δ32 CCR5.

  15. mtDNA and Y-chromosome diversity in Aymaras and Quechuas from Bolivia: different stories and special genetic traits of the Andean Altiplano populations.

    Science.gov (United States)

    Gayà-Vidal, Magdalena; Moral, Pedro; Saenz-Ruales, Nancy; Gerbault, Pascale; Tonasso, Laure; Villena, Mercedes; Vasquez, René; Bravi, Claudio M; Dugoujon, Jean-Michel

    2011-06-01

    Two Bolivian samples belonging to the two main Andean linguistic groups (Aymaras and Quechuas) were studied for mtDNA and Y-chromosome uniparental markers to evaluate sex-specific differences and give new insights into the demographic processes of the Andean region. mtDNA-coding polymorphisms, HVI-HVII control regions, 17 Y-STRs, and three SNPs were typed in two well-defined populations with adequate size samples. The two Bolivian samples showed more genetic differences for the mtDNA than for the Y-chromosome. For the mtDNA, 81% of Aymaras and 61% of Quechuas presented haplogroup B2. Native American Y-chromosomes were found in 97% of Aymaras (89% hg Q1a3a and 11% hg Q1a3*) and 78% of Quechuas (100% hg Q1a3a). Our data revealed high diversity values in the two populations, in agreement with other Andean studies. The comparisons with the available literature for both sets of markers indicated that the central Andean area is relatively homogeneous. For mtDNA, the Aymaras seemed to have been more isolated throughout time, maintaining their genetic characteristics, while the Quechuas have been more permeable to the incorporation of female foreigners and Peruvian influences. On the other hand, male mobility would have been widespread across the Andean region according to the homogeneity found in the area. Particular genetic characteristics presented by both samples support a past common origin of the Altiplano populations in the ancient Aymara territory, with independent, although related histories, with Peruvian (Quechuas) populations. Copyright © 2011 Wiley-Liss, Inc.

  16. Royal Jelly: An ancient remedy with remarkable antibacterial properties

    National Research Council Canada - National Science Library

    Fratini, Filippo; Cilia, Giovanni; Mancini, Simone; Felicioli, Antonio

    2016-01-01

    Royal Jelly (RJ), a honeybee hypopharyngeal gland secretion of young nurse and an exclusive nourishment for bee queen, has been used since ancient times for care and human health and it is still very important...

  17. The mtDNA ancestry of admixed Colombian populations.

    Science.gov (United States)

    Salas, A; Acosta, A; Alvarez-Iglesias, V; Cerezo, M; Phillips, C; Lareu, M V; Carracedo, A

    2008-01-01

    A total of 185 individuals from Colombia were sequenced for the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) genome, and a subset of these individuals were additionally genotyped for the second hypervariable segment (HVS-II). These individuals were collected according to their "self-reported ethnicity" in Colombia, comprising "Mestizos," "Mulatos," and "Afro-Colombians." We used databases containing more than 4,300 Native American lineages, 6,800 Africans, and 15,600 Europeans for population comparisons and phylogeographic inferences. We observe that Mulatos and Afro-Colombians have a dominant African mtDNA component, whereas Mestizos carry predominantly Native American haplotypes. All the populations analyzed have high diversity indices and there are no signatures of dramatic genetic drift episodes. Central and South America are the main candidate source populations of the Colombian Native American lineages, whereas west-central, southwest, and southeast Africa are the main original mtDNA sources for the African Colombian mtDNAs. We found that our results differ from those obtained in other studies for the same "population groups" in terms of haplogroup frequencies. This observation leads us to conclude that (i) self-reported ancestry is not a reliable proxy to indicate an individual's "ethnicity" in Colombia, (ii) our results do not support the use of outmoded race descriptions (Mestizos, Mulatos, etc.) mainly because these labels do not correspond to any genetically homogeneous population group, and (iii) studies relying on these terms to describe the population group of the individual, which then treat them as genetically homogeneous, carry a high risk of type I error (false positives) in medical studies in this country and of misinterpretation of the frequency of observed variation in forensic casework. (c) 2008 Wiley-Liss, Inc.

  18. Single-cell analysis of intercellular heteroplasmy of mtDNA in Leber hereditary optic neuropathy

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Y.; Sharpe, H.; Brown, N.

    1994-07-01

    The authors have investigated the distribution of mutant mtDNA molecules in single cells from a patient with Leber hereditary optic neuropathy (LHON). LHON is a maternally inherited disease that is characterized by a sudden-onset bilateral loss of central vision, which typically occurs in early adulthood. More than 50% of all LHON patients carry an mtDNA mutation at nucleotide position 11778. This nucleotide change converts a highly conserved arginine residue to histidine at codon 340 in the NADH-ubiquinone oxidoreductase subunit 4 (ND4) gene of mtDNA. In the present study, the authors used PCR amplification of mtDNA from lymphocytes to investigate mtDNA heteroplasmy at the single-cell level in a LHON patient. They found that most cells were either homoplasmic normal or homoplasmic mutant at nucleotide position 11778. Some (16%) cells contained both mutant and normal mtDNA.

  19. Possible role of mtDNA depletion and respiratory chain defects in aristolochic acid I-induced acute nephrotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Zhenzhou, E-mail: jiangcpu@yahoo.com.cn; Bao, Qingli, E-mail: bao_ql@126.com; Sun, Lixin, E-mail: slxcpu@126.com; Huang, Xin, E-mail: huangxinhx66@sohu.com; Wang, Tao, E-mail: wangtao1331@126.com; Zhang, Shuang, E-mail: cat921@sina.com; Li, Han, E-mail: hapo1101@163.com; Zhang, Luyong, E-mail: lyzhang@cpu.edu.cn

    2013-01-15

    This report describes an investigation of the pathological mechanism of acute renal failure caused by toxic tubular necrosis after treatment with aristolochic acid I (AAI) in Sprague–Dawley (SD) rats. The rats were gavaged with AAI at 0, 5, 20, or 80 mg/kg/day for 7 days. The pathologic examination of the kidneys showed severe acute tubular degenerative changes primarily affecting the proximal tubules. Supporting these results, we detected significantly increased concentrations of blood urea nitrogen (BUN) and creatinine (Cr) in the rats treated with AAI, indicating damage to the kidneys. Ultrastructural examination showed that proximal tubular mitochondria were extremely enlarged and dysmorphic with loss and disorientation of their cristae. Mitochondrial function analysis revealed that the two indicators for mitochondrial energy metabolism, the respiratory control ratio (RCR) and ATP content, were reduced in a dose-dependent manner after AAI treatment. The RCR in the presence of substrates for complex I was reduced more significantly than in the presence of substrates for complex II. In additional experiments, the activity of respiratory complex I, which is partly encoded by mitochondrial DNA (mtDNA), was more significantly impaired than that of respiratory complex II, which is completely encoded by nuclear DNA (nDNA). A real-time PCR assay revealed a marked reduction of mtDNA in the kidneys treated with AAI. Taken together, these results suggested that mtDNA depletion and respiratory chain defects play critical roles in the pathogenesis of kidney injury induced by AAI, and that the same processes might contribute to aristolochic acid-induced nephrotoxicity in humans. -- Highlights: ► AAI-induced acute renal failure in rats and the proximal tubule was the target. ► Tubular mitochondria were morphologically aberrant in ultrastructural examination. ► AAI impair mitochondrial bioenergetic function and mtDNA replication.

  20. 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.

  1. Modern Olympic Games: An Echo of the Ancient Athlete?

    Directory of Open Access Journals (Sweden)

    Tomaž Pavlin

    2015-07-01

    Full Text Available By the end of the 4th century AD, the ancient athletic competitions at the sanctuary of Olympia had been outlawed and relegated to history. Over the centuries, the shrine was demolished and buried by earthquakes. However, the Renaissance and humanism saw a gradual return of the notion of ancient gymnastics into European intellectual discourse, as well as increasing knowledge of the ancient Greek competitions at Olympia, which had been culturally separated from the Roman ludi and gladiators and now formed a historical example for modern sports. In Ljubljana, for example, the Sokol gymnasts stated in 1863 that gymnastics was an “art” rooted in ancient Greek history, and stressed the competitions of Olympia. In keeping with the development of gymnastics and sport and the increasing knowledge of ancient contests, Frenchman Pierre de Coubertin called in 1894 for the introduction of international sport competitions based on the Greek example.

  2. [Ancientness and maturity: two complementary qualities of forest ecosystems].

    Science.gov (United States)

    Cateau, Eugénie; Larrieu, Laurent; Vallauri, Daniel; Savoie, Jean-Marie; Touroult, Julien; Brustel, Hervé

    2015-01-01

    Ancientness and maturity are two major qualities of forest ecosystems. They are components of naturalness and are affected by human impact. These qualities and the associated terms are often mixed up and incorrectly used. We have carried out a synthesis in order to propose an adapted French terminology based on international literature. The topics of ancientness and maturity for biodiversity and soil characteristics are explained. This review leads us to submit different potential thresholds for ancientness and maturity. An analysis on ancientness and maturity on forest data for France leads to the conclusion that about 29% of all forests can be considered "ancient woodland", and less than 3% of the even-age forest is older than the harvesting age. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  3. Otology in ancient India.

    Science.gov (United States)

    Pothula, V B; Jones, T M; Lesser, T H

    2001-03-01

    Sushrutra Samhita is essentially a multi-volume textbook reporting the surgical practices of ancient India. It covers all aspects of surgery. However, specific references are made to otorhinological conditions, their description and subsequent treatments often being described in some detail. In this paper we outline the structure of the document and attempt to explain its underlying philosophies. We highlight the specific references to otological diseases and their treatment and draw the obvious comparisons with modern otological practice.

  4. Ancient Maritime Fish-Traps of Brittany (France): A Reappraisal of the Relationship Between Human and Coastal Environment During the Holocene

    Science.gov (United States)

    Langouët, Loïc; Daire, Marie-Yvane

    2009-12-01

    The present-day maritime landscape of Western France forms the geographical framework for a recent research project dedicated to the archaeological study of ancient fish-traps, combining regional-scale and site-scale investigations. Based on the compilation and exploitation of a large unpublished dataset including more than 550 sites, a preliminary synthetic study allows us to present some examples of synchronic and thematic approaches, and propose a morphological classification of the weirs. These encouraging first results open up new perspectives on fish-trap chronology closely linked to wider studies on Holocene sea-level changes.

  5. Decreased Circulating mtDNA Levels in Professional Male Volleyball Players.

    Science.gov (United States)

    Nasi, Milena; Cristani, Alessandro; Pinti, Marcello; Lamberti, Igor; Gibellini, Lara; De Biasi, Sara; Guazzaloca, Alessandro; Trenti, Tommaso; Cossarizza, Andrea

    2016-01-01

    Exercise exerts various effects on the immune system, and evidence is emerging on its anti-inflammatory effects; the mechanisms on the basis of these modifications are poorly understood. Mitochondrial DNA (mtDNA) released from damaged cells acts as a molecule containing the so-called damage-associated molecular patterns and can trigger sterile inflammation. Indeed, high plasma levels of mtDNA are associated to several inflammatory conditions and physiological aging and longevity. The authors evaluated plasma mtDNA in professional male volleyball players during seasonal training and the possible correlation between mtDNA levels and clinical parameters, body composition, and physical performance. Plasma mtDNA was quantified by real-time PCR every 2 mo in 12 professional volleyball players (PVPs) during 2 consecutive seasons. As comparison, 20 healthy nonathlete male volunteers (NAs) were analyzed. The authors found lower levels of mtDNA in plasma of PVPs than in NAs. However, PVPs showed a decrease of circulating mtDNA only in the first season, while no appreciable variations were observed during the second season. No correlation was observed among mtDNA, hematochemical, and anthropometric parameters. Regular physical activity appeared associated with lower levels of circulating mtDNA, further confirming the protective, anti-inflammatory effect of exercise.

  6. Detecting hybridization using ancient DNA

    Science.gov (United States)

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

    2016-01-01

    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 genome-wide sequence data, and discuss how these innovations have revised our understanding of human evolutionary history. PMID:26826668

  7. Origins of an Unmarked Georgia Cemetery Using Ancient DNA Analysis.

    Science.gov (United States)

    Ozga, Andrew T; Tito, Raúl Y; Kemp, Brian M; Matternes, Hugh; Obregon-Tito, Alexandra; Neal, Leslie; Lewis, Cecil M

    2015-04-01

    Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the cemetery. Through examination of hypervariable region I (HVR1) in the mitochondrial genome (mtDNA), we determined haplotypes for all 20 of these individuals. Eighteen of these individuals belong to the L or U haplogroups, suggesting that Avondale Burial Place was most likely used primarily as a resting place for African Americans. After the surrounding Bibb County community expressed interest in investigating potential ancestral relationships to those within the cemetery, eight potential descendants provided saliva to obtain mtDNA HVR1 information. Three individuals from Avondale Burial Place matched three individuals with oral history ties to the cemetery. Using the online tool EMPOP, we calculated the likelihood of these exact matches occurring by chance alone (< 1%). The present findings exhibit the importance of genetic analysis of cemetery origins when archaeological and osteological data are inconclusive for estimating ancestry of anonymous historical individuals.

  8. CT‐Based Assessment of Relative Soft‐Tissue Alteration in Different Types of Ancient Mummies

    National Research Council Canada - National Science Library

    Sydler, Christina; Öhrström, Lena; Rosendahl, Wilfried; Woitek, Ulrich; Rühli, Frank

    2015-01-01

    .... A total of 17 human mummies have been investigated by computed tomography (CT). Samples included artificially embalmed ancient Egyptian mummies, naturally mummified South American corpses, ice mummies...

  9. Tuberculosis in ancient times

    Directory of Open Access Journals (Sweden)

    Louise Cilliers

    2008-09-01

    Full Text Available In spite of an array of effective antibiotics, tuberculosis is still very common in developing countries where overcrowding, malnutrition and poor hygienic conditions prevail. Over the past 30 years associated HIV infection has worsened the situation by increasing the infection rate and mortality of tuberculosis. Of those diseases caused by a single organism only HIV causes more deaths internationally than tuberculosis. The tubercle bacillus probably first infected man in Neolithic times, and then via infected cattle, but the causative Mycobacteriacea have been in existence for 300 million years. Droplet infection is the most common way of acquiring tuberculosis, although ingestion (e.g. of infected cows’ milk may occur. Tuberculosis probably originated in Africa. The earliest path gnomonic evidence of human tuberculosis in man was found in osteo-archaeological findings of bone tuberculosis (Pott’s disease of the spine in the skeleton of anEgyptian priest from the 21st Dynasty (approximately 1 000 BC. Suggestive but not conclusiveevidence of tuberculotic lesions had been found in even earlier skeletons from Egypt and Europe. Medical hieroglyphics from ancient Egypt are silent on the disease, which could be tuberculosis,as do early Indian and Chinese writings. The Old Testament refers to the disease schachapeth, translated as phthisis in the Greek Septuagint. Although the Bible is not specific about this condition, tuberculosis is still called schachapeth in modern Hebrew. In pre-Hippocratic Greece Homer did not mention phthisis, a word meaning non-specific wasting of the body. However. Alexander of Tralles (6th century BC seemed to narrow the concept down to a specific disease, and in the Hippocratic Corpus (5th-4th centuries BC phthisis can be recognised as tuberculosis. It was predominantly a respiratory disease commonly seen and considered to be caused by an imbalance of bodily humours. It was commonest in autumn, winter and spring

  10. Heterozygous Polg mutation causes motor dysfunction due to mtDNA deletions

    Science.gov (United States)

    Fuke, Satoshi; Kametani, Mizue; Yamada, Kazuyuki; Kasahara, Takaoki; Kubota-Sakashita, Mie; Kujoth, Gregory C; Prolla, Tomas A; Hitoshi, Seiji; Kato, Tadafumi

    2014-01-01

    Objective Mutations in nuclear-encoded mitochondrial DNA (mtDNA) polymerase (POLG) are known to cause autosomal dominant chronic progressive external ophthalmoplegia (adCPEO) with accumulation of multiple mtDNA deletions in muscles. However, no animal model with a heterozygous Polg mutation representing mtDNA impairment and symptoms of CPEO has been established. To understand the pathogenic mechanism of CPEO, it is important to determine the age dependency and tissue specificity of mtDNA impairment resulting from a heterozygous mutation in the Polg gene in an animal model. Methods We assessed behavioral phenotypes, tissue-specific accumulation of mtDNA deletions, and its age dependency in heterozygous PolgD257A knock-in mice carrying a proofreading-deficient mutation in the Polg. Results Heterozygous PolgD257A knock-in mice exhibited motor dysfunction in a rotarod test. Polg+/D257A mice had significant accumulation of multiple mtDNA deletions, but did not show significant accumulation of point mutations or mtDNA depletion in the brain. While mtDNA deletions increased in an age-dependent manner regardless of the tissue even in Polg+/+ mice, the age-dependent accumulation of mtDNA deletions was enhanced in muscles and in the brain of Polg+/D257A mice. Interpretation Heterozygous PolgD257A knock-in mice showed tissue-specific, age-dependent accumulation of multiple mtDNA deletions in muscles and the brain which was likely to result in neuromuscular symptoms. Polg+/D257A mice may be used as an animal model of adCPEO associated with impaired mtDNA maintenance. PMID:25540805

  11. Clinically proven mtDNA mutations are not common in those with chronic fatigue syndrome.

    Science.gov (United States)

    Schoeman, Elizna M; Van Der Westhuizen, Francois H; Erasmus, Elardus; van Dyk, Etresia; Knowles, Charlotte V Y; Al-Ali, Shereen; Ng, Wan-Fai; Taylor, Robert W; Newton, Julia L; Elson, Joanna L

    2017-03-16

    Chronic Fatigue Syndrome (CFS) is a prevalent debilitating condition that affects approximately 250,000 people in the UK. There is growing interest in the role of mitochondrial function and mitochondrial DNA (mtDNA) variation in CFS. It is now known that fatigue is common and often severe in patients with mitochondrial disease irrespective of their age, gender or mtDNA genotype. More recently, it has been suggested that some CFS patients harbour clinically proven mtDNA mutations. MtDNA sequencing of 93 CFS patients from the United Kingdom (UK) and South Africa (RSA) was performed using an Ion Torrent Personal Genome Machine. The sequence data was examined for any evidence of clinically proven mutations, currently; more than 200 clinically proven mtDNA mutations point mutations have been identified. We report the complete mtDNA sequence of 93 CFS patients from the UK and RSA, without finding evidence of clinically proven mtDNA mutations. This finding demonstrates that clinically proven mtDNA mutations are not a common element in the aetiology of disease in CFS patients. That is patients having a clinically proven mtDNA mutation and subsequently being misdiagnosed with CFS are likely to be rare. The work supports the assertion that CFS should not be considered to fall within the spectrum of mtDNA disease. However, the current study cannot exclude a role for nuclear genes with a mitochondrial function, nor a role of mtDNA population variants in susceptibility to disease. This study highlights the need for more to be done to understand the pathophysiology of CFS.

  12. Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

    Science.gov (United States)

    Lindo, John; Achilli, Alessandro; Perego, Ugo A.; Archer, David; Valdiosera, Cristina; Petzelt, Barbara; Mitchell, Joycelynn; Worl, Rosita; Dixon, E. James; Fifield, Terence E.; Rasmussen, Morten; Willerslev, Eske; Cybulski, Jerome S.; Kemp, Brian M.; DeGiorgio, Michael; Malhi, Ripan S.

    2017-01-01

    Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome sequence of an ancient individual known as “Shuká Káa” (“Man Ahead of Us”) recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA haplogroups, we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas. PMID:28377518

  13. The ancient drug opium

    OpenAIRE

    M. Julyan; M. Dircksen

    2011-01-01

    The use of papaver somniferum (from the Latin fero ferre = ‘tobear/bring’ and somnium = ‘sleep’) as a narcotic, goes backto the 13th century BC. The works of ancient authors such asDioscorides, Celsus, Galen, Theophrastus and Pliny the Elderprovide us with detailed information about the morphology of theplant, its processing and the administration of the drug.1 Theseauthors make it clear that opium was mainly employed as anodyneand narcotic but they also documented its use as a drug inthe tre...

  14. Urology in ancient India.

    Science.gov (United States)

    Das, Sakti

    2007-01-01

    The practice of medical and surgical measures in the management of urological ailments prevailed in ancient India from the Vedic era around 3000 BC. Subsequently in the Samhita period, the two stalwarts - Charaka in medicine and Susruta in surgery elevated the art of medicine in India to unprecedented heights. Their elaboration of the etiopathological hypothesis and the medical and surgical treatments of various urological disorders of unparalleled ingenuity still remain valid to some extent in our contemporary understanding. The new generation of accomplished Indian urologists should humbly venerate the legacy of the illustrious pioneers in urology of our motherland.

  15. Urology in ancient India

    Directory of Open Access Journals (Sweden)

    Sakti Das

    2007-01-01

    Full Text Available The practice of medical and surgical measures in the management of urological ailments prevailed in ancient India from the Vedic era around 3000 BC. Subsequently in the Samhita period, the two stalwarts - Charaka in medicine and Susruta in surgery elevated the art of medicine in India to unprecedented heights. Their elaboration of the etiopathological hypothesis and the medical and surgical treatments of various urological disorders of unparalleled ingenuity still remain valid to some extent in our contemporary understanding. The new generation of accomplished Indian urologists should humbly venerate the legacy of the illustrious pioneers in urology of our motherland.

  16. Orthopedic surgery in ancient Egypt

    National Research Council Canada - National Science Library

    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...

  17. Distinct radiation responses after in vitro mtDNA depletion are potentially related to oxidative stress

    NARCIS (Netherlands)

    van Gisbergen, Marike W.; Voets, An M.; Biemans, Rianne; Hoffmann, Roland F.; Drittij-Reijnders, Marie-Jose; Haenen, Guido R. M. M.; Heijink, Irene H.; Rouschop, Kasper M. A.; Dubois, Ludwig J.; Lambin, Philippe

    2017-01-01

    Several clinically used drugs are mitotoxic causing mitochondrial DNA (mtDNA) variations, and thereby influence cancer treatment response. We hypothesized that radiation responsiveness will be enhanced in cellular models with decreased mtDNA content, attributed to altered reactive oxygen species

  18. Regionalized pathology correlates with augmentation of mtDNA copy numbers in a patient with myoclonic epilepsy with ragged-red fibers (MERRF-syndrome.

    Directory of Open Access Journals (Sweden)

    Anja Brinckmann

    Full Text Available Human patients with myoclonic epilepsy with ragged-red fibers (MERRF suffer from regionalized pathology caused by a mutation in the mitochondrial DNA (m.8344A→G. In MERRF-syndrome brain and skeletal muscles are predominantly affected, despite mtDNA being present in any tissue. In the past such tissue-specificity could not be explained by varying mtDNA mutation loads. In search for a region-specific pathology in human individuals we determined the mtDNA/nDNA ratios along with the mutation loads in 43 different post mortem tissue samples of a 16-year-old female MERRF patient and in four previously healthy victims of motor vehicle accidents. In brain and muscle we further determined the quantity of mitochondrial proteins (COX subunits II and IV, transcription factors (NRF1 and TFAM, and VDAC1 (Porin as a marker for the mitochondrial mass. In the patient the mutation loads varied merely between 89-100%. However, mtDNA copy numbers were increased 3-7 fold in predominantly affected brain areas (e.g. hippocampus, cortex and putamen and in skeletal muscle. Similar increases were absent in unaffected tissues (e.g. heart, lung, kidney, liver, and gastrointestinal organs. Such mtDNA copy number increase was not paralleled by an augmentation of mitochondrial mass in some investigated tissues, predominantly in the most affected tissue regions of the brain. We thus conclude that "futile" stimulation of mtDNA replication per se or a secondary failure to increase the mitochondrial mass may contribute to the regionalized pathology seen in MERRF-syndrome.

  19. No consistent evidence for association between mtDNA variants and Alzheimer disease

    Science.gov (United States)

    Hudson, G.; Sims, R.; Harold, D.; Chapman, J.; Hollingworth, P.; Gerrish, A.; Russo, G.; Hamshere, M.; Moskvina, V.; Jones, N.; Thomas, C.; Stretton, A.; Holmans, P.A.; O'Donovan, M.C.; Owen, M.J.; Williams, J.; Harold, Denise; Abraham, Richard; Hollingworth, Paul; Sims, Rebecca; Gerrish, Amy; Chapman, Jade; Russo, Giancarlo; Hamshere, Marian; Pahwa, Jaspreet Singh; Moskvina, Valentina; Dowzell, Kimberley; Williams, Amy; Jones, Nicola; Thomas, Charlene; Stretton, Alexandra; Morgan, Angharad; Lovestone, Simon; Powell, John; Proitsi, Petroula; Lupton, Michelle K; Brayne, Carol; Rubinsztein, David C.; Gill, Michael; Lawlor, Brian; Lynch, Aoibhinn; Morgan, Kevin; Brown, Kristelle; Passmore, Peter; Craig, David; McGuinness, Bernadette; Todd, Stephen; Johnston, Janet; Holmes, Clive; Mann, David; Smith, A. David; Love, Seth; Kehoe, Patrick G.; Hardy, John; Mead, Simon; Fox, Nick; Rossor, Martin; Collinge, John; Maier, Wolfgang; Jessen, Frank; Heun, Reiner; Kölsch, Heike; Schürmann, Britta; van den Bussche, Hendrik; Heuser, Isabella; Kornhuber, Johannes; Wiltfang, Jens; Dichgans, Martin; Frölich, Lutz; Hampel, Harald; Hüll, Michael; Rujescu, Dan; Goate, Alison; Kauwe, John S.K.; Cruchaga, Carlos; Nowotny, Petra; Morris, John C.; Mayo, Kevin; Livingston, Gill; Bass, Nicholas J.; Gurling, Hugh; McQuillin, Andrew; Gwilliam, Rhian; Deloukas, Panagiotis; Holmans, Peter; O'Donovan, Michael; Owen, Michael J.; Williams, Julie

    2012-01-01

    Objective: Although several studies have described an association between Alzheimer disease (AD) and genetic variation of mitochondrial DNA (mtDNA), each has implicated different mtDNA variants, so the role of mtDNA in the etiology of AD remains uncertain. Methods: We tested 138 mtDNA variants for association with AD in a powerful sample of 4,133 AD case patients and 1,602 matched controls from 3 Caucasian populations. Of the total population, 3,250 case patients and 1,221 elderly controls met the quality control criteria and were included in the analysis. Results: In the largest study to date, we failed to replicate the published findings. Meta-analysis of the available data showed no evidence of an association with AD. Conclusion: The current evidence linking common mtDNA variations with AD is not compelling. PMID:22442439

  20. Three Thousand Years of Continuity in the Maternal Lineages of Ancient Sheep (Ovis aries) in Estonia.

    Science.gov (United States)

    Rannamäe, Eve; Lõugas, Lembi; Speller, Camilla F; Valk, Heiki; Maldre, Liina; Wilczyński, Jarosław; Mikhailov, Aleksandr; Saarma, Urmas

    2016-01-01

    Although sheep (Ovis aries) have been one of the most exploited domestic animals in Estonia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the mitochondrial hypervariable region in 115 ancient sheep from 71 sites in Estonia (c. 1200 BC-AD 1900s), 19 ancient samples from Latvia, Russia, Poland and Greece (6800 BC-AD 1700), as well as 44 samples of modern Kihnu native sheep breed. Our analyses revealed: (1) 49 mitochondrial haplotypes, associated with sheep haplogroups A and B; (2) high haplotype diversity in Estonian ancient sheep; (3) continuity in mtDNA haplotypes through time; (4) possible population expansion during the first centuries of the Middle Ages (associated with the establishment of the new power regime related to 13th century crusades); (5) significant difference in genetic diversity between ancient populations and modern native sheep, in agreement with the beginning of large-scale breeding in the 19th century and population decline in local sheep. Overall, our results suggest that in spite of the observed fluctuations in ancient sheep populations, and changes in the natural and historical conditions, the utilisation of local sheep has been constant in the territory of Estonia, displaying matrilineal continuity from the Middle Bronze Age through the Modern Period, and into modern native sheep.

  1. 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...

  2. Science of exercise: ancient Indian origin.

    Science.gov (United States)

    Mondal, Samiran

    2013-08-01

    Many western literature on ancient exercise science were available. Unfortunately ancient Indian contribution in this area was ignored. The aim of this approach was to search ancient Indian literature on science of exercise. The researcher reviewed thoroughly complete Caraka Samhita (nearly ten thousand prose and verse) and the outcome was first time reported in this paper. More than one hundred and twenty slokes (aphorism) on exercise (vyayama) were discovered from Caraka Samhita. Oldest definition of exercise was found from Caraka Samhita, which was percolated from the world's oldest record of medicine practice. Caraka Samhita has been divided into eight section and it was observed that in each section vyayama (exercise) was specially referred whenever needed. The good effect, bad effect, contraindication and feature of correct exercise were mentioned in Caraka Samhita. The season and time of vyayama has also been mentioned. Caraka Samhita,also the world's oldest living evidence of exercise therapy literature prescribed twenty types of kaphaja (phlegm) diseases and many other diseases (obesity and diabetes etc.) can be cured or minimize the consequences through vyayama. According to Caraka Samhita, human is the combination of the body, mind and soul. This Samhita clearly suggested vyayama (exercise) for the body and yoga for mind and soul. From the ancient time India was familiar with the science of exercise and its beneficial effect. It was forgotten due to local ignorance and western influence. The contribution of Caraka Samhita and other ancient Indian literature on the science of exercise should be incorporated in all the appropriate places as early as possible.

  3. The orthopedic diseases of ancient Egypt.

    Science.gov (United States)

    Fritsch, Klaus O; Hamoud, Heshem; Allam, Adel H; Grossmann, Alexander; Nur El-Din, Abdel-Halim; Abdel-Maksoud, Gomaa; Soliman, Muhammad Al-Tohamy; Badr, Ibrahim; Sutherland, James D; Sutherland, M Linda; Akl, Mahmoud; Finch, Caleb E; Thomas, Gregory S; Wann, L Samuel; Thompson, Randall C

    2015-06-01

    CT scanning of ancient human remains has the potential to provide insights into health and diseases. While Egyptian mummies have undergone CT scans in prior studies, a systematic survey of the orthopedic conditions afflicting a group of these ancient individuals has never been carried out. We performed whole body CT scanning on 52 ancient Egyptian mummies using technique comparable to that of medical imaging. All of the large joints and the spine were systematically examined and osteoarthritic (OA) changes were scored 0-4 using Kellgren and Lawrence classification. The cruciate ligaments and menisci could be identified frequently. There were much more frequent OA changes in the spine (25 mummies) than in the large joints (15 cases of acromioclavicular and/or glenohumeral joint OA changes, five involvement of the ankle, one in the elbow, four in the knee, and one in the hip). There were six cases of scoliosis. Individual mummies had the following conditions: juvenile aseptic necrosis of the hip (Perthes disease), stage 4 osteochondritis dissecans of the knee, vertebral compression fracture, lateral patella-femoral joint hyper-compression syndrome, severe rotator cuff arthropathy, rotator cuff impingement, hip pincer impingement, and combined fracture of the greater trochantor and vertebral bodies indicating obvious traumatic injury. This report includes the most ancient discovery of several of these syndromes. Ancient Egyptians often suffered painful orthopedic conditions. The high frequency of scoliosis merits further study. The pattern of degenerative changes in the spine and joints may offer insights into activity levels of these people. © 2015 Wiley Periodicals, Inc.

  4. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation

    Directory of Open Access Journals (Sweden)

    Hellberg Michael E

    2006-03-01

    Full Text Available Abstract Background The mitochondrial DNA (mtDNA of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin, by contrast, appears to evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene from a coral species (Balanophyllia elegans known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison to another coral (Tubastrea coccinea. Results The mtDNA surveyed (630 bp of cytochrome oxidase subunit I was invariant among individuals sampled from 18 populations spanning 3000 km of the range of B. elegans, despite high levels of variation and population subdivision for allozymes over these same populations. The synonymous substitution rate between B. elegans and T. coccinea (0.05%/site/106 years is similar to that in most plants, but 50–100 times lower than rates typical for most animals. In addition, while substitutions to mtDNA in most animals exhibit a strong bias toward transitions, mtDNA from these corals does not. Conclusion Slow rates of mitochondrial nucleotide substitution result in low levels of intraspecific mtDNA variation in corals, even when nuclear loci vary. Slow mtDNA evolution appears to be the basal condition among eukaryotes. mtDNA substitution rates switch from slow to fast abruptly and unidirectionally. This switch may stem from the loss of just one or a few mitochondrion-specific DNA repair or replication genes.

  5. The Genetics of the Pre-Roman Iberian Peninsula: A mtDNA Study of Ancient Iberians

    National Research Council Canada - National Science Library

    Sampietro, M. L; Caramelli, D; Lao, O; Calafell, F; Comas, D; Lari, M; Agusti, B; Bertranpetit, J; Lalueza-Fox, C

    2005-01-01

    Summary The Iberians developed a surprisingly sophisticated culture in the Mediterranean coast of the Iberian Peninsula from the 6th century BC until their conquest by the Romans in the 2nd century BC...

  6. Kodamaea transpacifica f.a., sp. nov., a yeast species isolated from ephemeral flowers and insects in the Galapagos Islands and Malaysia: further evidence for ancient human transpacific contacts.

    Science.gov (United States)

    Freitas, Larissa F D; Carvajal Barriga, Enrique Javier; Barahona, Patricia Portero; Lachance, Marc-André; Rosa, Carlos A

    2013-11-01

    Twenty-four yeast strains were isolated from ephemeral flowers of Ipomoea spp. and Datura sp. and their associated insects in the Galápagos Archipelago, Ecuador, and from Ipomoea spp. and associated insects in the Cameron Highlands, Malaysia. Sequences of the D1/D2 domains of the large subunit rRNA gene indicated that these strains belong to a novel yeast species of the Kodamaea clade, although the formation of ascospores was not observed. The closest relative is Candida restingae. The human-mediated dispersion of this species by transpacific contacts in ancient times is suggested. The name Kodamaea transpacifica f.a., sp. nov. is proposed to accommodate these isolates. The type strain is CLQCA-24i-070(T) ( = CBS 12823(T) = NCYC 3852(T)); MycoBank number MB 803609.

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

    Directory of Open Access Journals (Sweden)

    Jan Cemper-Kiesslich

    2014-09-01

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

  8. 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 ...

  9. Ancient DNA: genomic amplification of Roman and medieval bovine bones

    Directory of Open Access Journals (Sweden)

    A. Valentini

    2010-04-01

    Full Text Available Cattle remains (bones and teeth of both roman and medieval age were collected in the archaeological site of Ferento (Viterbo, Italy with the aim of extracting and characterising nucleic acids. Procedures to minimize contamination with modern DNA and to help ancient DNA (aDNA preservation of the archaeological remains were adopted. Different techniques to extract aDNA (like Phenol/chloroform extraction from bovine bones were tested to identify the method that applies to the peculiar characteristics of the study site. Currently, aDNA investigation is mainly based on mtDNA, due to the ease of amplification of the small and high-copied genome and to its usefulness in evolutionary studies. Preliminary amplification of both mitochondrial and nuclear aDNA fragments from samples of Roman and medieval animals were performed and partial specific sequences of mitochondrial D-loop as well as of nuclear genes were obtained. The innovative amplification of nuclear aDNA could enable the analysis of genes involved in specific animal traits, giving insights of ancient economic and cultural uses, as well as providing information on the origin of modern livestock population.

  10. Characterization of Ancient Tripitaka

    Science.gov (United States)

    Gong, Y. X.; Geng, L.; Gong, D. C.

    2015-08-01

    Tripitaka is the world's most comprehensive version of Buddhist sutra. There are limited numbers of Tripitaka currently preserved, most of them present various patterns of degradation. As little is known about the materials and crafts used in Tripitaka, it appeared necessary to identify them, and to further define adapted conservation treatment. In this work, a study concerning the paper source and dyestuff of the Tripitaka from approximate 16th century was carried out using fiber analysis and thin-layer chromatography (TLC). The results proved that the papers were mainly made from hemp or bark of mulberry tree, and indigo was used for colorizing the paper. At the end, we provide with suggestions for protecting and restoring the ancient Tripitaka.

  11. Ancient Greek new music

    Directory of Open Access Journals (Sweden)

    Martin Žužek

    2000-12-01

    Full Text Available In this article I use a contextual approach to questions about the revolutionary »new music« in ancient Greece. This view is different from the nowadays most common formalistk view. Rather than analyze textual sources stylistically, I will try to present the available lata in the context of the structure and events of the Athenian society at a tirne when a wave of »new« poetics appeared. In the following discussion it is argued that the »new music« and the phenomena of the destruction of mousiké connected with it are not an esthetical novum, but more a consequence of the change of the discursive practice, where a musical poetry became less important and needless.

  12. Epilepsy in ancient India.

    Science.gov (United States)

    Manyam, B V

    1992-01-01

    The ancient Indian medical system, Ayurveda, meaning science of life, is the oldest system of medicine in the world. Epilepsy is defined as Apasmara: apa, meaning negation or loss of; smara, meaning recollection or consciousness. Aura was recognized and was called Apasmara Poorva Roopa. A large number of symptoms indicative of aura were listed. Worthy of mention are subjective sensation of sounds, sensation of darkness, feeling of delusion, and dream-like state. An actual attack of Apasmara includes falling down; shaking of the hands, legs, and body; rolling up of the eyes; grinding of the teeth; and foaming at the mouth. Four major types of epilepsy based on the disturbance of doshas (humors) that govern the physiological and physiochemical activities of the body are mentioned. Apasmara is considered a dangerous disease that is chronic and difficult to treat. Several causes are mentioned. Treatment included correcting the etiological factors and dietary regimen and avoiding dangerous places that may result in injuries.

  13. Characterization of Ancient Tripitaka

    Directory of Open Access Journals (Sweden)

    Y. X. Gong

    2015-08-01

    Full Text Available Tripitaka is the world’s most comprehensive version of Buddhist sutra. There are limited numbers of Tripitaka currently preserved, most of them present various patterns of degradation. As little is known about the materials and crafts used in Tripitaka, it appeared necessary to identify them, and to further define adapted conservation treatment. In this work, a study concerning the paper source and dyestuff of the Tripitaka from approximate 16th century was carried out using fiber analysis and thin-layer chromatography (TLC. The results proved that the papers were mainly made from hemp or bark of mulberry tree, and indigo was used for colorizing the paper. At the end, we provide with suggestions for protecting and restoring the ancient Tripitaka.

  14. 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.

  15. A decision support system for the reading of ancient documents

    DEFF Research Database (Denmark)

    Roued-Cunliffe, Henriette

    2011-01-01

    The research presented in this thesis is based in the Humanities discipline of Ancient History and begins by attempting to understand the interpretation process involved in reading ancient documents and how this process can be aided by computer systems such as Decision Support Systems (DSS......). The thesis balances between the use of IT tools to aid Humanities research and the understanding that Humanities research must involve human beings. It does not attempt to develop a system that can automate the reading of ancient documents. Instead it seeks to demonstrate and develop tools that can support...... this process in the five areas: remembering complex reasoning, searching huge datasets, international collaboration, publishing editions, and image enhancement. This research contains a large practical element involving the development of a DSS prototype. The prototype is used to illustrate how a DSS...

  16. Anticancer activity of botanical compounds in ancient fermented beverages (review).

    Science.gov (United States)

    McGovern, P E; Christofidou-Solomidou, M; Wang, W; Dukes, F; Davidson, T; El-Deiry, W S

    2010-07-01

    Humans around the globe probably discovered natural remedies against disease and cancer by trial and error over the millennia. Biomolecular archaeological analyses of ancient organics, especially plants dissolved or decocted as fermented beverages, have begun to reveal the preliterate histories of traditional pharmacopeias, which often date back thousands of years earlier than ancient textual, ethnohistorical, and ethnological evidence. In this new approach to drug discovery, two case studies from ancient Egypt and China illustrate how ancient medicines can be reconstructed from chemical and archaeological data and their active compounds delimited for testing their anticancer and other medicinal effects. Specifically, isoscopoletin from Artemisia argyi, artemisinin from Artemisia annua, and the latter's more easily assimilated semi-synthetic derivative, artesunate, showed the greatest activity in vitro against lung and colon cancers. In vivo tests of these compounds previously unscreened against lung and pancreatic cancers are planned for the future.

  17. DNA Extraction Procedures Meaningfully Influence qPCR-Based mtDNA Copy Number Determination

    OpenAIRE

    Guo, Wen; Jiang, Lan; Bhasin, Shalender; Khan, Shaharyar M.; Swerdlow, Russell H.

    2009-01-01

    Quantitative real time PCR (qPCR) is commonly used to determine cell mitochondrial DNA (mtDNA) copy number. This technique involves obtaining the ratio of an unknown variable (number of copies of an mtDNA gene) to a known parameter (number of copies of a nuclear DNA gene) within a genomic DNA sample. We considered the possibility that mtDNA: nuclear DNA (nDNA) ratio determinations could vary depending on the method of genomic DNA extraction used, and that these differences could substantively...

  18. [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

  19. Ancient history of flatfish research

    Science.gov (United States)

    Berghahn, Rüdiger; Bennema, Floris Pieter

    2013-01-01

    Owing to both their special appearance and behavior flatfish have attracted the special attention of people since ages. The first records of humans having been in touch with flatfish date back to the Stone Age about 15,000 years B.C. Detailed descriptions were already given in the classical antiquity and were taken up 1400 years later in the Renaissance by the first ichthyologists, encyclopédists, and also by practical men. This was more than 200 years before a number of common flatfish species were given their scientific names by Linnaeus in 1758. Besides morphology, remarkable and sometimes amusing naturalistic observations and figures are bequeathed. Ancient history of flatfish research is still a wide and open array. Examples are presented how the yield of information and interpretation from these times increases with interdisciplinary cooperation including archeologists, zoologists, ichthyologists, historians, art historians, fisheries and fishery biologist. The timeline of this contribution ends with the start of modern fishery research at the end of the 19th century in the course of the rapidly increasing exploitation of fish stocks.

  20. Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers

    Directory of Open Access Journals (Sweden)

    Helen D. Donoghue

    2017-10-01

    Full Text Available Diagnosis of leprosy and tuberculosis in archaeological material is most informative when based upon entire genomes. Ancient DNA (aDNA is often degraded but amplification of specific fragments also provides reliable diagnoses. Cell wall lipid biomarkers can distinguish ancient leprosy from tuberculosis and DNA extraction residues can be utilized. The diagnostic power of combined aDNA and lipid biomarkers is illustrated by key cases of ancient leprosy and/or tuberculosis. Human tuberculosis was demonstrated in a woman and child from Atlit-Yam (~9 ka in the Eastern Mediterranean and in the 600 BCE Egyptian “Granville” mummy. Both aDNA and lipids confirmed Pleistocene tuberculosis in a ~17 ka bison from Natural Trap Cave, Wyoming. Leprosy is exemplified by cases from Winchester (10th–12th centuries CE and Great Chesterford (5th–6th centuries CE. A mixed infection from Kiskundorozsma, Hungary (7th century CE allowed lipid biomarkers to assess the relative load of leprosy and tuberculosis. Essential protocols for aDNA amplification and analysis of mycolic, mycolipenic, mycocerosic acid, and phthiocerol lipid biomarkers are summarized. Diagnoses of ancient mycobacterial disease can be extended beyond the reach of whole genomics by combinations of aDNA amplification and lipid biomarkers, with sole use of the latter having the potential to recognize even older cases.

  1. Cosmologies of the ancient Mediterranean world

    Directory of Open Access Journals (Sweden)

    John T. Fitzgerald

    2013-07-01

    Full Text Available Cosmology is concerned with the order of the universe and seeks to provide an account, not only of that order, but also of the mind or reason behind it. In antiquity, the cosmos was usually understood religiously, such that the cosmologies of the ancient Mediterranean world were either religious in nature or constituted a reaction to a religiously conceived understanding of the structures of the universe. The oldest form in which ancient cosmologies occur is myth, which, owing to its elasticity as a form, enabled them to be appropriated, adapted and used by different groups. In addition, different cosmologies co-existed within the same ancient culture, each having an authoritative status. This article provides an introductory overview of these cosmological myths and argues that a comparative approach is the most fruitful way to study them. Emphasis is given to certain prominent cosmological topics, including theogony (the genesis of the divine or the relationship of the divine to the cosmos, cosmogony (the genesis of the cosmos, and anthropogony (the origin of humans within the cosmos. Although these myths vary greatly in terms of content and how they envision the origin of the cosmos, many of them depict death as part of the structure of the universe.

  2. Tamil merchant in ancient Mesopotamia

    National Research Council Canada - National Science Library

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

    2014-01-01

    .... 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...

  3. Astronomical Significance of Ancient Monuments

    Science.gov (United States)

    Simonia, I.

    2011-06-01

    Astronomical significance of Gokhnari megalithic monument (eastern Georgia) is considered. Possible connection of Amirani ancient legend with Gokhnari monument is discussed. Concepts of starry practicality and solar stations are proposed.

  4. Ancient and Current Chaos Theories

    Directory of Open Access Journals (Sweden)

    Güngör Gündüz

    2006-07-01

    Full Text Available Chaos theories developed in the last three decades have made very important contributions to our understanding of dynamical systems and natural phenomena. The meaning of chaos in the current theories and in the past is somewhat different from each other. In this work, the properties of dynamical systems and the evolution of chaotic systems were discussed in terms of the views of ancient philosophers. The meaning of chaos in Anaximenes’ philosophy and its role in the Ancient natural philosophy has been discussed in relation to other natural philosophers such as of Anaximander, Parmenides, Heraclitus, Empedocles, Leucippus (i.e. atomists and Aristotle. In addition, the fundamental concepts of statistical mechanics and the current chaos theories were discussed in relation to the views in Ancient natural philosophy. The roots of the scientific concepts such as randomness, autocatalysis, nonlinear growth, information, pattern, etc. in the Ancient natural philosophy were investigated.

  5. 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.

  6. Mitochondrial DNA (mtDNA) haplogroups in 1526 unrelated individuals from 11 Departments of Colombia.

    Science.gov (United States)

    Yunis, Juan J; Yunis, Emilio J

    2013-09-01

    The frequencies of four mitochondrial Native American DNA haplogroups were determined in 1526 unrelated individuals from 11 Departments of Colombia and compared to the frequencies previously obtained for Amerindian and Afro-Colombian populations. Amerindian mtDNA haplogroups ranged from 74% to 97%. The lowest frequencies were found in Departments on the Caribbean coast and in the Pacific region, where the frequency of Afro-Colombians is higher, while the highest mtDNA Amerindian haplogroup frequencies were found in Departments that historically have a strong Amerindian heritage. Interestingly, all four mtDNA haplogroups were found in all Departments, in contrast to the complete absence of haplogroup D and high frequencies of haplogroup A in Amerindian populations in the Caribbean region of Colombia. Our results indicate that all four Native American mtDNA haplogroups were widely distributed in Colombia at the time of the Spanish conquest.

  7. Mitochondrial DNA (mtDNA haplogroups in 1526 unrelated individuals from 11 Departments of Colombia

    Directory of Open Access Journals (Sweden)

    Juan J. Yunis

    2013-01-01

    Full Text Available The frequencies of four mitochondrial Native American DNA haplogroups were determined in 1526 unrelated individuals from 11 Departments of Colombia and compared to the frequencies previously obtained for Amerindian and Afro-Colombian populations. Amerindian mtDNA haplogroups ranged from 74% to 97%. The lowest frequencies were found in Departments on the Caribbean coast and in the Pacific region, where the frequency of Afro-Colombians is higher, while the highest mtDNA Amerindian haplogroup frequencies were found in Departments that historically have a strong Amerindian heritage. Interestingly, all four mtDNA haplogroups were found in all Departments, in contrast to the complete absence of haplogroup D and high frequencies of haplogroup A in Amerindian populations in the Caribbean region of Colombia. Our results indicate that all four Native American mtDNA haplogroups were widely distributed in Colombia at the time of the Spanish conquest.

  8. 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...

  9. Southeast Asian diversity: first insights into the complex mtDNA structure of Laos.

    Science.gov (United States)

    Bodner, Martin; Zimmermann, Bettina; Röck, Alexander; Kloss-Brandstätter, Anita; Horst, David; Horst, Basil; Sengchanh, Sourideth; Sanguansermsri, Torpong; Horst, Jürgen; Krämer, Tanja; Schneider, Peter M; Parson, Walther

    2011-02-18

    Vast migrations and subsequent assimilation processes have shaped the genetic composition of Southeast Asia, an area of close contact between several major ethnic groups. To better characterize the genetic variation of this region, we analyzed the entire mtDNA control region of 214 unrelated donors from Laos according to highest forensic quality standards. To detail the phylogeny, we inspected selected SNPs from the mtDNA coding region. For a posteriori data quality control, quasi-median network constructions and autosomal STR typing were performed. In order to describe the mtDNA setup of Laos more thoroughly, the data were subjected to population genetic comparisons with 16 East Asian groups. The Laos sample exhibited ample mtDNA diversity, reflecting the huge number of ethnic groups listed. We found several new, so far undescribed mtDNA lineages in this dataset and surrounding populations. The Laos population was characteristic in terms of haplotype composition and genetic structure, however, genetic comparisons with other Southeast Asian populations revealed limited, but significant genetic differentiation. Notable differences in the maternal relationship to the major indigenous Southeast Asian ethnolinguistic groups were detected. In this study, we portray the great mtDNA variety of Laos for the first time. Our findings will contribute to clarify the migration history of the region. They encourage setting up regional and subpopulation databases, especially for forensic applications. The Laotian sequences will be incorporated into the collaborative EMPOP mtDNA database http://www.empop.org upon publication and will be available as the first mtDNA reference data for this country.

  10. Southeast Asian diversity: first insights into the complex mtDNA structure of Laos

    Directory of Open Access Journals (Sweden)

    Horst Jürgen

    2011-02-01

    Full Text Available Abstract Background Vast migrations and subsequent assimilation processes have shaped the genetic composition of Southeast Asia, an area of close contact between several major ethnic groups. To better characterize the genetic variation of this region, we analyzed the entire mtDNA control region of 214 unrelated donors from Laos according to highest forensic quality standards. To detail the phylogeny, we inspected selected SNPs from the mtDNA coding region. For a posteriori data quality control, quasi-median network constructions and autosomal STR typing were performed. In order to describe the mtDNA setup of Laos more thoroughly, the data were subjected to population genetic comparisons with 16 East Asian groups. Results The Laos sample exhibited ample mtDNA diversity, reflecting the huge number of ethnic groups listed. We found several new, so far undescribed mtDNA lineages in this dataset and surrounding populations. The Laos population was characteristic in terms of haplotype composition and genetic structure, however, genetic comparisons with other Southeast Asian populations revealed limited, but significant genetic differentiation. Notable differences in the maternal relationship to the major indigenous Southeast Asian ethnolinguistic groups were detected. Conclusions In this study, we portray the great mtDNA variety of Laos for the first time. Our findings will contribute to clarify the migration history of the region. They encourage setting up regional and subpopulation databases, especially for forensic applications. The Laotian sequences will be incorporated into the collaborative EMPOP mtDNA database http://www.empop.org upon publication and will be available as the first mtDNA reference data for this country.

  11. Library construction for ancient genomics: single strand or double strand?

    Science.gov (United States)

    Bennett, E Andrew; Massilani, Diyendo; Lizzo, Giulia; Daligault, Julien; Geigl, Eva-Maria; Grange, Thierry

    2014-06-01

    A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform. Here we present in-depth comparisons of the different available library construction methods for DNA purified from 16 ancient and modern faunal and human remains, covering a range of different taphonomic and climatic conditions. We further present a DNA purification method for ancient samples that permits the concentration of a large volume of dissolved extract with minimal manipulation and methodological improvements to the single-stranded method to render it more economical and versatile, in particular to expand its use to both the Illumina and the Ion Torrent sequencing platforms. We show that the single-stranded library construction method improves the relative recovery of endogenous to exogenous DNA for most, but not all, of our ancient extracts.

  12. Sights of Freedom: Between Ancient and Modern Times

    Directory of Open Access Journals (Sweden)

    Ana Guerra Ribeiro de Oliveira

    2015-12-01

    Full Text Available The idea of liberty was lived and analysed during the whole cultural and ethical development of Ancient history, especially, according to Lima Vaz, in the confrontation between human action and Destine. The concern with the idea of liberty was discussed by important ancient authors such as Socrates, Plato, Aristotle and Cicero. Looking back to the past, Benjamin Constant realized another aspect of the Ancient liberty that may not have been understood by the Ancients themselves as liberty, which is the ability to participate collective, but directly, in political life and in the decisions of the polis. Constant believed, also, that the idea of individual liberty was only developed in Modern history; however, the pillars of legal and individual liberty were developed in ancient Rome. To achieve the several aspects of the idea of liberty is necessary to examine the philosophical effort to explain it along historical moments. Therefore, the aim of this work is to investigate how the idea of liberty was understood in ancient times and compare with the design developed by the philosophers of modern times, such as Rousseau, Benjamin Constant and Kant.

  13. Random mtDNA mutations modulate proliferation capacity in mouse embryonic fibroblasts

    Energy Technology Data Exchange (ETDEWEB)

    Kukat, Alexandra [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany); Edgar, Daniel [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Bratic, Ivana [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany); Maiti, Priyanka [Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany); Trifunovic, Aleksandra, E-mail: aleksandra.trifunovic@ki.se [Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, S-17171 Stockholm (Sweden); Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Cologne University Clinic, D-50674 Cologne (Germany)

    2011-06-10

    Highlights: {yields} Increased mtDNA mutations in MEFs lead to high level of spontaneous immortalization. {yields} This process is independent of endogenous ROS production. {yields} Aerobic glycolysis significantly contributes to spontaneous immortalization of MEFs. -- Abstract: An increase in mtDNA mutation load leads to a loss of critical cells in different tissues thereby contributing to the physiological process of organismal ageing. Additionally, the accumulation of senescent cells that display changes in metabolic function might act in an active way to further disrupt the normal tissue function. We believe that this could be the important link missing in our understanding of the molecular mechanisms of premature ageing in the mtDNA mutator mice. We tested proliferation capacity of mtDNA mutator cells in vitro. When cultured in physiological levels of oxygen (3%) their proliferation capacity is somewhat lower than wild-type cells. Surprisingly, in conditions of increased oxidative stress (20% O{sub 2}) mtDNA mutator mouse embryonic fibroblasts exhibit continuous proliferation due to spontaneous immortalization, whereas the same conditions promote senescence in wild-type cells. We believe that an increase in aerobic glycolysis observed in mtDNA mutator mice is a major mechanism behind this process. We propose that glycolysis promotes proliferation and allows a fast turnover of metabolites, but also leads to energy crisis due to lower ATP production rate. This could lead to compromised replication and/or repair and therefore, in rare cases, might lead to mutations in tumor suppressor genes and spontaneous immortalization.

  14. The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns.

    Science.gov (United States)

    Irwin, Jodi A; Ikramov, Abror; Saunier, Jessica; Bodner, Martin; Amory, Sylvain; Röck, Alexander; O'Callaghan, Jennifer; Nuritdinov, Abdurakhmon; Atakhodjaev, Sattar; Mukhamedov, Rustam; Parson, Walther; Parsons, Thomas J

    2010-05-01

    In order to better characterize and understand the mtDNA population genetics of Central Asia, the mtDNA control regions of over 1,500 individuals from Uzbekistan have been sequenced. Although all samples were obtained from individuals residing in Uzbekistan, individuals with direct ancestry from neighboring Central Asian countries are included. Individuals of Uzbek ancestry represent five distinct geographic regions of Uzbekistan: Fergana, Karakalpakstan, Khorezm, Qashkadarya, and Tashkent. Individuals with direct ancestry in nearby countries originate from Kazakhstan, Kyrgyzstan, Russia, Afghanistan, Turkmenistan, and Tajikistan. Our data reinforce the evidence of distinct clinal patterns that have been described among Central Asian populations with classical, mtDNA, and Y-chromosomal markers. Our data also reveal hallmarks of recent demographic events. Despite their current close geographic proximity, the populations with ancestry in neighboring countries show little sign of admixture and retain the primary mtDNA patterns of their source populations. The genetic distances and haplogroup distributions among the ethnic populations are more indicative of a broad east-west cline among their source populations than of their relatively small geographic distances from one another in Uzbekistan. Given the significant mtDNA heterogeneity detected, our results emphasize the need for heightened caution in the forensic interpretation of mtDNA data in regions as historically rich and genetically diverse as Central Asia.

  15. [Comparison of mtDNA extraction from different parts of sarcosaphagous insects].

    Science.gov (United States)

    Guo, Ya-Dong; Cai, Ji-Feng; Su, Ri-Na; Chang, Yun-Feng; Lan, Ling-Mei; Li, Xiang; Wen, Ji-Fang

    2010-10-01

    To explore mitochondrial DNA (mtDNA) extraction effects of different parts from sarcosaphagous insects using improved cetyltriethylammnonium bromide (CTAB) method. Thirteen Lucilia sericata (Meigen) and 13 Nicrophorus fossor (Erichson) were collected from the corpses of rabbits placed on the outdoor lawn in Huhehot district. Four parts (head, chest muscle, legs and wings) of insect were collected, and the mtDNA of all samples were extracted using CTAB method. The purity and concentration were tested using protein and nucleic acid spectrophotometry. The integrity of the extracted mtDNA and PCR products were checked by agarose gel electrophoresis. The PCR products were sequenced and the obtained sequences were imputed into GenBank for comparison. mtDNA were successfully extracted from 10 head samples, 6 legs samples, 4 wing samples and 13 chest muscle samples of the Lucilia sericata (Meigen). Also, mtDNA were successfully extracted from 5 head samples, 8 legs samples, 3 wing samples and 13 chest muscle samples of the Nicrophorus fossor (Erichson). mtDNA can be obtained from chest muscle and other parts of sarcosaphagous insects using the improved CTAB method.

  16. 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.

  17. High-quality mtDNA control region sequences from 680 individuals sampled across the Netherlands to establish a national forensic mtDNA reference database

    NARCIS (Netherlands)

    L.C. Chaitanya (Lakshmi); M. van Oven (Mannis); S. Brauer (Silke); B. Zimmermann (Bettina); G. Huber (Gabriela); C. Xavier (Catarina); W. Parson (Walther); P. de Knijff (Peter); M.H. Kayser (Manfred)

    2016-01-01

    textabstractThe use of mitochondrial DNA (mtDNA) for maternal lineage identification often marks the last resort when investigating forensic and missing-person cases involving highly degraded biological materials. As with all comparative DNA testing, a match between evidence and reference sample

  18. Autosomal recessive Wolfram syndrome associated with an 8.5 kb mtDNA single deletion

    Energy Technology Data Exchange (ETDEWEB)

    Barrientos, A.; Casademont, J.; Cardellach, F. [Universitat de Barcelona (Spain)] [and others

    1996-05-01

    Wolfram syndrome (MIM 222300) is characterized by optic atrophy, diabetes mellitus, diabetes insipidus, neurosensory hearing loss, urinary tract abnormalities, and neurological dysfunction. The association of clinical manifestations in tissues and organs unrelated functionally or embryologically suggested the possibility of a mitochondrial implication in the disease, which has been demonstrated in two sporadic cases. Nonetheless, familial studies suggested an autosomal recessive mode of transmission, and recent data demonstrated linkage with markers on the short arm of human chromosome 4. The patient reported here, as well as her parents and unaffected sister, carried a heteroplasmic 8.5-kb deletion in mtDNA. The deletion accounted for 23% of mitochondrial genomes in lymphocytes from the patient and {approximately}5% in the tissues studied from members of her family. The presence of the deletion in the patient in a proportion higher than in her unaffected parents suggests a putative defect in a nuclear gene that acts at the mitochondrial level. 39 refs., 6 figs., 3 tabs.

  19. Early Eurasian migration traces in the Tarim Basin revealed by mtDNA polymorphisms.

    Science.gov (United States)

    Cui, Yinqiu; Li, Chunxiang; Gao, Shizhu; Xie, Chengzhi; Zhou, Hui

    2010-08-01

    The mitochondrial DNA (mtDNA) polymorphisms of 58 samples from the Daheyan village located in the central Taklamakan Desert of the Tarim Basin were determined in this study. Among the 58 samples, 29 haplotypes belonging to 18 different haplogroups were analyzed. Almost all the mtDNAs belong to a subset of either the defined Western or Eastern Eurasian pool. Extensive Eastern Eurasian lineages exist in the Daheyan population in which Northern-prevalent haplogroups present higher frequencies. In the limited existing Western Eurasian lineages, two sub-haplogroups, U3 and X2, that are rare in Central Asia were found in this study, which may be indicative of the remnants of an early immigrant population from the Near East and Caucasus regions preserved only in the Tarim Basin. The presence of U3 in modern and archeological samples in the Tarim Basin suggests that the immigration took place earlier than 2,000 years ago and points to human continuity in this area, with at least one Western lineage originating from the Near East and Caucasus regions. Copyright 2010 Wiley-Liss, Inc.

  20. High pressure-induced mtDNA alterations in retinal ganglion cells and subsequent apoptosis

    Directory of Open Access Journals (Sweden)

    Sheng-Hai Zhang

    2016-11-01

    Full Text Available Purpose: Our previous study indicated that mitochondrial DNA (mtDNA damage and mutations are crucial to the progressive loss of retinal ganglion cells (RGCs in a glaucomatous rat model. In this study, we examined whether high pressure could directly cause mtDNA alterations and whether the latter could lead to mitochondrial dysfunction and RGC death.Methods: Primary cultured rat RGCs were exposed to 30 mm Hg of hydrostatic pressure (HP for 12, 24, 48, 72, 96, and 120 hours. mtDNA alterations and mtDNA repair/replication enzymes OGG1, MYH and POLG expressions were also analyzed. The RGCs were then infected with a lentiviral small hairpin RNA (shRNA expression vector targeting POLG (POLG-shRNA, and mtDNA alterations as well as mitochondrial function, including complex I/III activities and ATP production were subsequently studied at appropriate times. Finally, RGC apoptosis and the mitochondrial-apoptosis pathway-related protein cleaved caspase-3 were detected using a Terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL assay and western blotting, respectively. Results: mtDNA damage was observed as early as 48 hours after the exposure of RGCs to HP. At 120 h after HP, mtDNA damage and mutations significantly increased, reaching >40% and 4.8±0.3-fold, respectively, compared with the control values. Twelve hours after HP, the expressions of OGG1, MYH and POLG mRNA in the RGCs were obviously increased 5.02±0.6-fold (p<0.01, 4.3±0.2-fold (p<0.05, and 0.8±0.09-fold p<0.05. Western blot analysis showed that the protein levels of the three enzymes decreased at 72 and 120 hours after HP (p<0.05. After interference with POLG-shRNA, the mtDNA damage and mutations were significantly increased (p<0.01, while complex I/III activities gradually decreased (p<0.05. Corresponding decreases in membrane potential and ATP production appeared at 5 and 6 days after POLG-shRNA transfection respectively (p<0.05. Increases in the apoptosis of RGCs and

  1. Medicine and psychiatry in Western culture: Ancient Greek myths and modern prejudices.

    Science.gov (United States)

    Fornaro, Michele; Clementi, Nicoletta; Fornaro, Pantaleo

    2009-10-07

    The origins of Western culture extensively relate to Ancient Greek culture. While many ancient cultures have contributed to our current knowledge about medicine and the origins of psychiatry, the Ancient Greeks were among the best observers of feelings and moods patients expressed towards medicine and toward what today is referred to as 'psychopathology'. Myths and religious references were used to explain what was otherwise impossible to understand or be easily communicated. Most ancient myths focus on ambiguous feelings patients may have had towards drugs, especially psychotropic ones. Interestingly, such prejudices are common even today. Recalling ancient findings and descriptions made using myths could represent a valuable knowledge base for modern physicians, especially for psychiatrists and their patients, with the aim of better understanding each other and therefore achieving a better clinical outcome. This paper explores many human aspects and feelings towards doctors and their cures, referring to ancient myths and focusing on the perception of mental illness.

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

    Science.gov (United States)

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

    2015-12-01

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

  3. The rise and decline of character: humoral psychology in ancient and early modern medical theory

    NARCIS (Netherlands)

    Bos, J.

    2009-01-01

    Humoralism, the view that the human body is composed of a limited number of elementary fluids, is one of the most characteristic aspects of ancient medicine. The psychological dimension of humoral theory in the ancient world has thus far received a relatively small amount of scholarly attention.

  4. Burns treatment in ancient times.

    Science.gov (United States)

    Pećanac, Marija; Janjić, Zlata; Komarcević, Aleksandar; Pajić, Milos; Dobanovacki, Dusanka; Misković, Sanja Skeledzija

    2013-01-01

    Discovery of fire at the dawn of prehistoric time brought not only the benefits to human beings offering the light and heat, but also misfortune due to burns; and that was the beginning of burns treatment. Egyptian doctors made medicines from plants, animal products and minerals, which they combined with magic and religious procedures. The earliest records described burns dressings with milk from mothers of male babies. Goddess Isis was called upon to help. Some remedies and procedures proved so successful that their application continued for centuries. The Edwin Smith papyrus (1500 BC) mentioned the treatment of burns with honey and grease. Ebers Papyrus (1500 BC) contains descriptions of application of mud, excrement, oil and plant extracts. They also used honey, Aloe and tannic acid to heal burns. Ancient Egyptians did not know about microorganisms but they knew that honey, moldy bread and copper salts could prevent infections from dirt in burns healing. Thyme, opium and belladona were used for pain relief. In the 4th century BC, Hippocrates recorded that Greek and Roman doctors used rendered pig fat, resin and bitumen to treat burns. Mixture of honey and bran, or lotion of wine and myrrh were used by Celsus. Honey was also known in Ayurveda (Indian medicine) time. Ayurvedic records Characa and Sushruta included honey in their dressing aids to purify sores and promote the healing. Burn treatment in Chinese medicine was traditional. It was a compilation of philosophy, knowledge and herbal medicine. The successful treatment of burns started in recent time and it has been made possible by better knowledge of the pathophysiology of thermal injuries and their consequences, medical technology advances and improved surgical techniques.

  5. Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations.

    Directory of Open Access Journals (Sweden)

    Ernest Diez Benavente

    2017-09-01

    Full Text Available The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf or pig-tailed macaques (Macaca nemestrina (Mn. We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.

  6. Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

    KAUST Repository

    Diez Benavente, Ernest

    2017-09-18

    The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.

  7. A statistical framework for the interpretation of mtDNA mixtures: forensic and medical applications.

    Directory of Open Access Journals (Sweden)

    Thore Egeland

    Full Text Available BACKGROUND: Mitochondrial DNA (mtDNA variation is commonly analyzed in a wide range of different biomedical applications. Cases where more than one individual contribute to a stain genotyped from some biological material give rise to a mixture. Most forensic mixture cases are analyzed using autosomal markers. In rape cases, Y-chromosome markers typically add useful information. However, there are important cases where autosomal and Y-chromosome markers fail to provide useful profiles. In some instances, usually involving small amounts or degraded DNA, mtDNA may be the only useful genetic evidence available. Mitochondrial DNA mixtures also arise in studies dealing with the role of mtDNA variation in tumorigenesis. Such mixtures may be generated by the tumor, but they could also originate in vitro due to inadvertent contamination or a sample mix-up. METHODS/PRINCIPAL FINDINGS: We present the statistical methods needed for mixture interpretation and emphasize the modifications required for the more well-known methods based on conventional markers to generalize to mtDNA mixtures. Two scenarios are considered. Firstly, only categorical mtDNA data is assumed available, that is, the variants contributing to the mixture. Secondly, quantitative data (peak heights or areas on the allelic variants are also accessible. In cases where quantitative information is available in addition to allele designation, it is possible to extract more precise information by using regression models. More precisely, using quantitative information may lead to a unique solution in cases where the qualitative approach points to several possibilities. Importantly, these methods also apply to clinical cases where contamination is a potential alternative explanation for the data. CONCLUSIONS/SIGNIFICANCE: We argue that clinical and forensic scientists should give greater consideration to mtDNA for mixture interpretation. The results and examples show that the analysis of mtDNA

  8. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; 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......The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... (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...

  9. Reconstructing ancient genomes and epigenomes

    DEFF Research Database (Denmark)

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

    2015-01-01

    Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA...... 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....

  10. MtDNA COI-COII marker and drone congregation area: an efficient method to establish and monitor honeybee (Apis mellifera L.) conservation centres.

    Science.gov (United States)

    Bertrand, Bénédicte; Alburaki, Mohamed; Legout, Hélène; Moulin, Sibyle; Mougel, Florence; Garnery, Lionel

    2015-05-01

    Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of nonlocal subspecies of bees which has had an adverse impact on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. To restore the original diversity of this local honeybee subspecies, different conservation centres were set up in Europe. In this study, we established a black honeybee conservation centre Conservatoire de l'Abeille Noire d'Ile de France (CANIF) in the region of Ile-de-France, France. CANIF's honeybee colonies were intensively studied over a 3-year period. This study included a drone congregation area (DCA) located in the conservation centre. MtDNA COI-COII marker was used to evaluate the genetic diversity of CANIF's honeybee populations and the drones found and collected from the DCA. The same marker (mtDNA) was used to estimate the interactions and the haplotype frequency between CANIF's honeybee populations and 10 surrounding honeybee apiaries located outside of the CANIF. Our results indicate that the colonies of the conservation centre and the drones of the DCA show similar stable profiles compared to the surrounding populations with lower level of introgression. The mtDNA marker used on both DCA and colonies of the conservation centre seems to be an efficient approach to monitor and maintain the genetic diversity of the protected honeybee populations. © 2014 John Wiley & Sons Ltd.

  11. Skeletal dysplasia in ancient Egypt.

    Science.gov (United States)

    Kozma, Chahira

    2008-12-01

    The ancient Egyptian civilization lasted for over 3000 years and ended in 30 BCE. Many aspects of ancient Egyptian culture, including the existence of skeletal dysplasias, and in particular achondroplasia, are well known through the monuments and records that survived until modern times. The hot and dry climate in Egypt allowed for the preservation of bodies and skeletal anomalies. The oldest dwarf skeleton, the Badarian skeleton (4500 BCE), possibly represents an epiphyseal disorder. Among the remains of dwarfs with achondroplasia from ancient Egypt (2686-2190 BCE), exists a skeleton of a pregnant female, believed to have died during delivery with a baby's remains in situ. British museums have partial skeletons of dwarfs with achondroplasia, humeri probably affected with mucopolysaccharidoses, and a skeleton of a child with osteogenesis imperfecta. Skeletal dysplasia is also found among royal remains. The mummy of the pharaoh Siptah (1342-1197 BCE) shows a deformity of the left leg and foot. A mummified fetus, believed to be the daughter of king Tutankhamun, has scoliosis, spina bifida, and Sprengel deformity. In 2006 I reviewed the previously existing knowledge of dwarfism in ancient Egypt. The purpose of this second historical review is to add to that knowledge with an expanded contribution. The artistic documentation of people with skeletal dysplasia from ancient Egypt is plentiful including hundreds of amulets, statues, and drawing on tomb and temple walls. Examination of artistic reliefs provides a glance of the role of people with skeletal dysplasia and the societal attitudes toward them. Both artistic evidence and moral teachings in ancient Egypt reveal wide integration of individuals with disabilities into the society. Copyright (c) 2008 Wiley-Liss, Inc.

  12. Isotopic reconstruction of ancient human migrations: A comprehensive Sr isotope reference database for France and the first case study at Tumulus de Sables, south-western France

    Science.gov (United States)

    Willmes, M.; Boel, C.; Grün, R.; Armstrong, R.; Chancerel, A.; Maureille, B.; Courtaud, P.

    2012-04-01

    Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further

  13. Do mtDNA Deletions Play a Role in the Development of Nasal Polyposis?

    Directory of Open Access Journals (Sweden)

    Arzu Tatar

    2014-04-01

    Full Text Available Objective:Nasal polyposis (NP is an inflammatory disease of the nasal mucosa and paranasal sinuses. Mitochondria are the cellular organelles which produce cellular energy by Oxidative Phosphorylation (OXPHOS, and they have own inheritance material, mtDNA. mtDNA is affected by reactive oxygen samples (ROS which are produced by both OXPHOS and the inflammatory process. The aim of this study was to investigate the 4977 bp and 7400 bp deletions of mtDNA in nasal polyposis tissue, and to indicate the possible association of mtDNA deletions with NP. Methods:Thirty-three patients, aged 15 to 65 years, with nasal polyposis were selected to be assessed for mitochondrial DNA deletions. The patients with possible mtDNA mutations due to mitochondrial disease, being treated with radiotherapy, of advanced age, with a familiar history, aspirin hypersensitivity, or a history of asthma, were excluded. Polyp excision surgery was applied to the treatment of the NP, and after histopathological diagnosis 1x1 cm of polyp tissue samples were used to isolate mtDNA. The 4977 bp and 7400 bp deletion regions, and two control regions of mtDNA were assessed by using four pairs of primers. DNA extractions from the NP tissues and peripheral blood samples of the patients were made, and then Polymerase Chain Reactions (PCR were made. PCR products were separated in 2% agarose gel.Results:No patient had either the 4977 bp deletion or the 7400 bp deletion in their NP tissue, and neither were these deletions evident in their peripheral blood. Two control sequences, one of them from a non-deleted region, and the other from a possible deletion region, were detected in the NP tissues and peripheral blood of all the patients.Conclusions:We had anticipated that some mtDNA deletion might have occurred in NP tissue due to the increased ROS levels caused by chronic inflammation, but we did not detect any deletion. Probably, the duration of inflammation in NP is insufficient to form mtDNA

  14. The Ethical Power of Music: Ancient Greek and Chinese Thoughts

    Science.gov (United States)

    Wang, Yuhwen

    2004-01-01

    Both the ancient Chinese and Greeks from around the fifth century B.C. to around third century A.D. recognized the immense impact that music has on the development of one's personality, and both regarded it as crucial in the cultivation of proper disposition in youth. Music's power over one's ethos--that is, human disposition--was emphasized by…

  15. Ancient Embalming Techneques Amongst The Ogoni Tribe In ...

    African Journals Online (AJOL)

    Embalming is the art and science of temporary preserving human remains to forestall decomposition. It was first practiced by the ancient Egyptians dating back to 4000BC. This research was carried out to study the traditional method of embalmment by the Ogonis, a tribe in the Southern part of Nigeria. A total of 140 elders ...

  16. mtDNA Mutagenesis Disrupts Pluripotent Stem Cell Function by Altering Redox Signaling

    Directory of Open Access Journals (Sweden)

    Riikka H. Hämäläinen

    2015-06-01

    Full Text Available mtDNA mutagenesis in somatic stem cells leads to their dysfunction and to progeria in mouse. The mechanism was proposed to involve modification of reactive oxygen species (ROS/redox signaling. We studied the effect of mtDNA mutagenesis on reprogramming and stemness of pluripotent stem cells (PSCs and show that PSCs select against specific mtDNA mutations, mimicking germline and promoting mtDNA integrity despite their glycolytic metabolism. Furthermore, mtDNA mutagenesis is associated with an increase in mitochondrial H2O2, reduced PSC reprogramming efficiency, and self-renewal. Mitochondria-targeted ubiquinone, MitoQ, and N-acetyl-L-cysteine efficiently rescued these defects, indicating that both reprogramming efficiency and stemness are modified by mitochondrial ROS. The redox sensitivity, however, rendered PSCs and especially neural stem cells sensitive to MitoQ toxicity. Our results imply that stem cell compartment warrants special attention when the safety of new antioxidants is assessed and point to an essential role for mitochondrial redox signaling in maintaining normal stem cell function.

  17. Novel mtDNA mutations and oxidative phosphorylation dysfunction in Russian LHON families.

    Science.gov (United States)

    Brown, M D; Zhadanov, S; Allen, J C; Hosseini, S; Newman, N J; Atamonov, V V; Mikhailovskaya, I E; Sukernik, R I; Wallace, D C

    2001-07-01

    Leber's hereditary optic neuropathy (LHON) is characterized by maternally transmitted, bilateral, central vision loss in young adults. It is caused by mutations in the mitochondrial DNA (mtDNA) encoded genes that contribute polypeptides to NADH dehydrogenase or complex I. Four mtDNA variants, the nucleotide pair (np) 3460A, 11778A, 14484C, and 14459A mutations, are known as "primary" LHON mutations and are found in most, but not all, of the LHON families reported to date. Here, we report the extensive genetic and biochemical analysis of five Russian families from the Novosibirsk region of Siberia manifesting maternally transmitted optic atrophy consistent with LHON. Three of the five families harbor known LHON primary mutations. Complete sequence analysis of proband mtDNA in the other two families has revealed novel complex I mutations at nps 3635A and 4640C, respectively. These mutations are homoplasmic and have not been reported in the literature. Biochemical analysis of complex I in patient lymphoblasts and transmitochondrial cybrids demonstrated a respiration defect with complex-I-linked substrates, although the specific activity of complex I was not reduced. Overall, our data suggests that the spectrum of mtDNA mutations associated with LHON in Russia is similar to that in Europe and North America and that the np 3635A and 4640C mutations may be additional mtDNA complex I mutations contributing to LHON expression.

  18. The Ancient Maya Landscape: Facing the Challenges and Embracing the Promise of Integrating Archaeology, Remote Sensing, Soil Science and Hydrologic Modeling for Coupled Natural and Human Systems.

    Science.gov (United States)

    Murtha, T., Jr.; Duffy, C.; Cook, B. D.; Schroder, W.; Webster, D.; French, K. D.; Alcover, O.; Golden, C.; Balzotti, C.; Shaffer, D.

    2016-12-01

    Relying on a niche inheritance perspective, this paper discusses the long-term spatial and temporal dynamics of land-use management, agricultural decision making and patterns of resource availability in the tropical lowlands of Central America. We introduce and describe ongoing research that addresses a series of long standing questions about coupled natural and human history dynamics in the Central Maya lowlands, emphasizing the role of landscape and region to address these questions. First, we summarize the results of a CNH pilot study focused on the evolution of the regional landscape of Tikal, Guatemala. Particular attention is centered on how we integrated landscape survey, traditional archaeology and soil studies to understand the spatial and temporal dynamics of agricultural land use and intensification over a two thousand period. Additionally, we discuss how these results were integrated into remote sensing, hydrological and erosion models to better understand how past changes in available water and productive land compare to what we know about settlement patterns in the Tikal Region over that same time period. We not only describe how the Maya transformed this landscape, but also how the region influenced changing patterns of settlement and land use. We finish this section with a discussion of some of the unique challenges integrating archaeological information to study CNH dynamics during this pilot study. Second, we introduce a new project designed to `scale up' the pilot study for a macro-regional analysis of the lowland Maya landscape. The new project leverages a uniquely sampled LIDAR data set designed to refine measurements of above ground carbon storage. Our new project quantitatively examines these data for evidence for past human activity. Preliminary results offer a promising path for tightly integrating archaeology, natural science, remote sensing and modeling for studying CNH dynamics in the deep and recent past.

  19. Complete mitochondrial genomes of the human follicle mites Demodex brevis and D. folliculorum: novel gene arrangement, truncated tRNA genes, and ancient divergence between species.

    Science.gov (United States)

    Palopoli, Michael F; Minot, Samuel; Pei, Dorothy; Satterly, Alicia; Endrizzi, Julie

    2014-12-16

    Follicle mites of the genus Demodex are found on a wide diversity of mammals, including humans; surprisingly little is known, however, about the evolution of this association. Additional sequence information promises to facilitate studies of Demodex variation within and between host species. Here we report the complete mitochondrial genome sequences of two species of Demodex known to live on humans--Demodex brevis and D. folliculorum--which are the first such genomes available for any member of the genus. We analyzed these sequences to gain insight into the evolution of mitochondrial genomes within the Acariformes. We also used relaxed molecular clock analyses, based on alignments of mitochondrial proteins, to estimate the time of divergence between these two species. Both Demodex genomes shared a novel gene order that differs substantially from the ancestral chelicerate pattern, with transfer RNA (tRNA) genes apparently having moved much more often than other genes. Mitochondrial tRNA genes of both species were unusually short, with most of them unable to encode tRNAs that could fold into the canonical cloverleaf structure; indeed, several examples lacked both D- and T-arms. Finally, the high level of sequence divergence observed between these species suggests that these two lineages last shared a common ancestor no more recently than about 87 mya. Among Acariformes, rearrangements involving tRNA genes tend to occur much more often than those involving other genes. The truncated tRNA genes observed in both Demodex species would seem to require the evolution of extensive tRNA editing capabilities and/or coevolved interacting factors. The molecular machinery necessary for these unusual tRNAs to function might provide an avenue for developing treatments of skin disorders caused by Demodex. The deep divergence time estimated between these two species sets a lower bound on the time that Demodex have been coevolving with their mammalian hosts, and supports the

  20. Effects of modern and ancient human activities on mercury in the environment in Xi'an area, Shannxi Province, P.R. China

    Energy Technology Data Exchange (ETDEWEB)

    Jin Yongqing; Wang Xiaojuan [Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3 (Canada); Lu Julia [Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China); Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3 (Canada)], E-mail: julialu@ryerson.ca; Zhang Chengxiao [Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China)], E-mail: cxzhang@snnu.edu.cn; Duan Qingbo [Shaanxi Archaeology Institute, Xi' an 710054 (China)

    2008-05-15

    Samples of water, soil, sediment, and pomegranate were collected from Xi'an and the Qinshihuang Mausoleum in Shaanxi Province, China to assess the effects of human activities on mercury in the environment. The total mercury concentrations ranged from 3.9 to 992.7 ng L{sup -1} for the water samples, 40.6 to 2204.0 ng g{sup -1} for the soil samples, 14.2 to 376.7 ng g{sup -1} for the sediment samples, and 0.22 to 1.74 ng g{sup -1} for the pomegranates samples. The higher values in the water samples collected from the rivers closer to and downstream of the city resulted from wastewater discharges. The effects of the mercury buried in the Qinshihuang Mausoleum thousands of years ago on the environment were neither significant nor widespread. Immediate actions should be taken to stop the direct and continuous discharges of industrial and residential wastewaters to prevent mercury and other pollutants from accumulating and spreading in the area. - Urban activities are sources of mercury to the environment and the pomegranates grown over the burial mound of the Qinshihuang Mausoleum are not mercury-contaminated.

  1. 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 woo...

  2. Ancient India: The Asiatic Ethiopians.

    Science.gov (United States)

    Scott, Carolyn McPherson

    This curriculum unit was developed by a participant in the 1993 Fulbright-Hays Program "India: Continuity and Change." The unit attempts to place India in the "picture frame" of the ancient world as a part of a whole, not as a separate entity. Reading materials enable students to draw broader general conclusions based on the…

  3. Drinking habits in ancient India.

    Science.gov (United States)

    Somasundaram, Ottilingam; Raghavan, D Vijaya; Murthy, A G Tejus

    2016-01-01

    Consumption of one or other form of intoxicating substances has been present throughout the history of the world. This article traces such use in the Indian subcontinent, both in North and South India. References to the use of intoxicants are to be found in the Vedas, the Great Epics, and the ancient Tamil literature.

  4. The eye and its diseases in Ancient Egypt

    DEFF Research Database (Denmark)

    Andersen, S. Ry

    1997-01-01

    Ophthalmology, History of ophthalmology, eyes in the Ancient Egypt, eye disease in Ancient Egypt, porotic hyperostosis, mummification......Ophthalmology, History of ophthalmology, eyes in the Ancient Egypt, eye disease in Ancient Egypt, porotic hyperostosis, mummification...

  5. Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities.

    Science.gov (United States)

    Gomez, Céline; Dussert, Stéphane; Hamon, Perla; Hamon, Serge; Kochko, Alexandre de; Poncet, Valérie

    2009-07-16

    Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone. Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals. Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.

  6. DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated?

    Directory of Open Access Journals (Sweden)

    Alessandra eMaresca

    2015-03-01

    Full Text Available Autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN and Hereditary sensory neuropathy with dementia and hearing loss (HSN1E are two rare, overlapping neurodegenerative syndromes that have been recently linked to allelic dominant pathogenic mutations in the DNMT1 gene, coding for DNA (cytosine-5-methyltransferase 1. DNMT1 is the enzyme responsible for maintaining the nuclear genome methylation patterns during the DNA replication and repair, thus regulating gene expression. The mutations responsible for ADCA-DN and HSN1E affect the replication foci targeting sequence domain, which regulates DNMT1 binding to chromatin. DNMT1 dysfunction is anticipated to lead to a global alteration of the DNA methylation pattern with predictable downstream consequences on gene expression. Interestingly, ADCA-DN and HSN1E phenotypes share some clinical features typical of mitochondrial diseases, such as optic atrophy, peripheral neuropathy and deafness, and some biochemical evidence of mitochondrial dysfunction. The recent discovery of a mitochondrial isoform of DNMT1 and its proposed role in methylating mitochondrial DNA (mtDNA suggests that DNMT1 mutations may directly affect mtDNA and mitochondrial physiology. On the basis of this latter finding the link between DNMT1 abnormal activity and mitochondrial dysfunction in ADCA-DN and HSN1E appears intuitive, however mtDNA methylation remains highly debated. In the last years several groups demonstrated the presence of 5-methylcytosine in mtDNA by different approaches, but, on the other end, the opposite evidence that mtDNA is not methylated has also been published. Since over 1500 mitochondrial proteins are encoded by the nuclear genome, the altered methylation of these genes may well have a critical role in leading to the mitochondrial impairment observed in ADCA-DN and HSN1E. Thus, many open questions still remain unanswered, such as why mtDNA should be methylated, and how this process is

  7. Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.

    Science.gov (United States)

    Thai, Quan Ke; Chung, Dung Anh; Tran, Hoang-Dung

    2017-06-26

    Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.

  8. Agriculture - reconciling ancient tensions

    Directory of Open Access Journals (Sweden)

    David Atkinson

    2002-09-01

    Full Text Available Decision-making in agriculture has tended to be driven by factors other than environmental concerns. This may be changing, and perhaps the emphases of the two creation accounts in Genesis (responsible management or 'dominion', and active care may become more important. The paper examines a number of current developments in agriculture (synthetic fertilizers and pesticides, genetic manipulation, and organic versus industrial methodologies and discusses the issues they raise for agricultural productivity and the human communities dependent on farming. The questions raised are complex; we are faced with establishing a new paradigm for agricultural practice.

  9. Trichinella nativa haplotypes in Russia show diversity in cytochrome oxidase mtDNA gene.

    Science.gov (United States)

    Odoevskaya, Irina M; Spiridonov, Sergei E

    2016-11-15

    Partial nucleotide sequences of the two mitochondrial genes (cytB and COI) were obtained for 13 Trichinella isolates from different regions of the Russian Federation. All the cytB mtDNA sequences were identical with the sequences of T. nativa from Canada, showing no nucleotide differences between isolates. Analysis of partial COI mtDNA sequence confirmed the species identification and revealed differences between the studied isolates. Two T. nativa haplotypes, represented in the studied material by four samples, demonstrate limited geographical distribution. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis.

    OpenAIRE

    Melton, T; PETERSON, R.; Redd, A. J.; Saha, N; Sofro, A S; Martinson, J.; Stoneking, M.

    1995-01-01

    Polynesian genetic affinities to populations of Asia were studied using mtDNA markers. A total of 1,037 individuals from 12 populations were screened for a 9-bp deletion in the intergenic region between the COII and tRNA(Lys) genes that approaches fixation in Polynesians. Sequence-specific oligonucleotide probes that identify specific mtDNA control region nucleotide substitutions were used to describe variation in individuals with the 9-bp deletion. The 9-bp deletion was not observed in north...

  11. POLG1 p.R722H mutation associated with multiple mtDNA deletions and a neurological phenotype

    Directory of Open Access Journals (Sweden)

    Finnilä Saara

    2010-05-01

    Full Text Available Abstract Background The c.2447G>A (p.R722H mutation in the gene POLG1 of the catalytic subunit of human mitochondrial polymerase gamma has been previously found in a few occasions but its pathogenicity has remained uncertain. We set out to ascertain its contribution to neuromuscular disease. Methods Probands from two families with probable mitochondrial disease were examined clinically, muscle and buccal epithelial DNA were analyzed for mtDNA deletions, and the POLG1, POLG2, ANT1 and Twinkle genes were sequenced. Results An adult proband presented with progressive external ophthalmoplegia, sensorineural hearing impairment, diabetes mellitus, dysphagia, a limb myopathy and dementia. Brain MRI showed central and cortical atrophy, and 18F-deoxyglucose PET revealed reduced glucose uptake. Histochemical analysis of muscle disclosed ragged red fibers and cytochrome c oxidase-negative fibers. Electron microscopy showed subsarcolemmal aggregates of morphologically normal mitochondria. Multiple mtDNA deletions were found in the muscle, and sequencing of the POLG1 gene revealed a homozygous c.2447G>A (p.R722H mutation. His two siblings were also homozygous with respect to the p.R722H mutation and presented with dementia and sensorineural hearing impairment. In another family the p.R722H mutation was found as compound heterozygosity with the common p.W748S mutation in two siblings with mental retardation, ptosis, epilepsy and psychiatric symptoms. The estimated carrier frequency of the p.R722H mutation was 1:135 in the Finnish population. No mutations in POLG2, ANT1 and Twinkle genes were found. Analysis of the POLG1 sequence by homology modeling supported the notion that the p.R722H mutation is pathogenic. Conclusions The recessive c.2447G>A (p.R722H mutation in the linker region of the POLG1 gene is pathogenic for multiple mtDNA deletions in muscle and is associated with a late-onset neurological phenotype as a homozygous state. The onset of the disease

  12. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.

    Science.gov (United States)

    Renaud, Gabriel; Slon, Viviane; Duggan, Ana T; Kelso, Janet

    2015-10-12

    Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates. https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.

  13. Dreams in ancient Greek Medicine.

    Science.gov (United States)

    Laios, K; Moschos, M M; Koukaki, E; Vasilopoulos, E; Karamanou, M; Kontaxaki, M-I; Androutsos, G

    2016-01-01

    Dreams preoccupied the Greek and Roman world in antiquity, therefore they had a prominent role in social, philosophical, religious, historical and political life of those times. They were considered as omens and prophetic signs of future events in private and public life, and that was particularly accentuated when elements of actions which took place in the plot of dreams were associated directly or indirectly with real events. This is why it was important to use them in divination, and helped the growth of superstition and folklore believes. Medicine as a science and an anthropocentric art, could not ignore the importance of dreams, having in mind their popularity in antiquity. In ancient Greek medicine dreams can be divided into two basic categories. In the first one -which is related to religious medicine-dreams experienced by religionists are classified, when resorted to great religious sanctuaries such as those of Asclepius (Asclepieia) and Amphiaraos (Amfiaraeia). These dreams were the essential element for healing in this form of religious medicine, because after pilgrims underwent purifications they went to sleep in a special dwelling of the sanctuaries called "enkoimeterion" (Greek: the place to sleep) so that the healing god would come to their dreams either to cure them or to suggest treatment. In ancient Greek literature there are many reports of these experiences, but if there may be phenomena of self-suggestion, or they could be characterized as propaganda messages from the priesthood of each sanctuary for advertising purposes. The other category concerns the references about dreams found in ancient Greek medical literature, where one can find the attempts of ancient Greek physicians to interpret these dreams in a rational way as sings either of a corporal disease or of psychological distress. This second category will be the object of our study. Despite the different ways followed by each ancient Greek physician in order to explain dreams, their

  14. An ancestral human genetic variant linked to an ancient disease: A novel association of FMO2 polymorphisms with tuberculosis (TB in Ethiopian populations provides new insight into the differential ethno-geographic distribution of FMO2*1.

    Directory of Open Access Journals (Sweden)

    Ephrem Mekonnen

    Full Text Available The human FMO2 (flavin-containing monooxygenase 2 gene has been shown to be involved in innate immunity against microbial infections, including tuberculosis (TB, via the modulation of oxidative stress levels. It has also been found to possess a curious loss-of-function mutation (FMO2*1/FMO2*2 that demonstrates a distinctive differentiation in expression, function and ethno-geographic distribution. However, despite evidences of ethnic-specific genetic associations in the inflammatory profile of TB, no studies were done to investigate whether these patterns of variations correlate with evidences for the involvement of FMO2 in antimicrobial immune responses and ethnic differences in the distribution of FMO2 polymorphisms except for some pharmacogenetic data that suggest a potentially deleterious role for the functional variant (FMO2*1. This genetic epidemiological study was designed to investigate whether there is an association between FMO2 polymorphisms and TB, an ancient malady that remains a modern global health concern, in a sub-Saharan Africa setting where there is not only a relatively high co-prevalence of the disease and the ancestral FMO2*1 variant but also where both Mycobcaterium and Homo sapiens are considered to have originated and co-evolved. Blood samples and TB related clinical data were collected from ascertained TB cases and unrelated household controls (n = 292 from 3 different ethnic groups in Ethiopia. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of FMO2.We identified for the first time an association between FMO2 and TB both at the SNP and haplotype level. Two novel SNPs achieved a study-wide significance [chr1:171181877(A, p = 3.15E-07, OR = 4.644 and chr1:171165749(T, p = 3.32E-06, OR = 6.825] while multiple SNPs (22 showed nominal signals. The pattern of association suggested a protective effect of FMO2 against both active and latent TB

  15. Ancient aliens on mars

    CERN Document Server

    Bara, Mike

    2013-01-01

    Best-selling author and Secret Space Program researcher Bara brings us this lavishly illustrated volume on alien structures on Mars. Was there once a vast, technologically advanced civilization on Mars, and did it leave evidence of its existence behind for humans to find eons later? Did these advanced extraterrestrial visitors vanish in a solar system wide cataclysm of their own making, only to make their way to Earth and start anew? Was Mars once as lush and green as the Earth, and teeming with life? Did Mars once orbit a missing member of the solar system, a "Super Earth” that vanished in a disaster that devastated life on Earth and Venus and left us only the asteroid belt as evidence of its once grand existence? Did the survivors of this catastrophe leave monuments and temples behind, arranged in a mathematical precision designed to teach us the Secret of a new physics that could lift us back to the stars? Does the planet have an automated defense shield that swallows up robotic probes if they wander int...

  16. Ancient DNA extraction from plants.

    Science.gov (United States)

    Kistler, Logan

    2012-01-01

    A variety of protocols for DNA extraction from archaeological and paleobotanical plant specimens have been proposed. This is not surprising given the range of taxa and tissue types that may be preserved and the variety of conditions in which that preservation may take place. Commercially available DNA extraction kits can be used to recover ancient plant DNA, but modifications to standard approaches are often necessary to improve yield. In this chapter, I describe two protocols for extracting DNA from small amounts of ancient plant tissue. The CTAB protocol, which I recommend for use with single seeds, utilizes an incubation period in extraction buffer and subsequent chloroform extraction followed by DNA purification and suspension. The PTB protocol, which I recommend for use with gourd rind and similar tissues, utilizes an overnight incubation of pulverized tissue in extraction buffer, removal of the tissue by centrifugation, and DNA extraction from the buffer using commercial plant DNA extraction kits.

  17. Molecular analysis of ancient caries

    Science.gov (United States)

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

    2014-01-01

    An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains. PMID:25056622

  18. Medicine and psychiatry in Western culture: among Ancient Greek myths and modern prejudices.

    Science.gov (United States)

    Fornaro, Michele; Clementi, Nicoletta; Fornaro, Pantaleo

    2009-01-01

    While many ancient cultures contributed to our current knowledge about medicine and psychiatry origins, Ancient Greeks were among the best observers of feelings and moods patients could express toward medicine and toward what today referred as "psychopathology". Myths and religious references were used to explain what elsewhere impossible to understand or easily communicated. Most of ancient myths focus on ambiguous feelings patients could have towards drugs, especially psychotropic ones. Interestingly, such prejudices are common yet today. Recalling ancient findings and descriptions made using myths, should represent a valuable knowledge for modern physicians, especially for psychiatrists, and their patients, with the aim of better understanding each other and therefore achieving a better clinical outcome. The paper explores many human aspects and feelings toward doctors and their cures, referring to ancient myths, focusing on the perception of mental illness.

  19. The value of ancient architecture for educational program of masters of architectural space design

    Directory of Open Access Journals (Sweden)

    Prishchepa Aleksandr

    2017-01-01

    Full Text Available The existence of archaeological sites of ancient Greek colony-towns and medieval fortresses gives a real insight into the interaction of all spheres of human activity in ancient times. Ancient Greek Emporium is a vivid example of the architecture, art, archaeology and urban planning synthesis. Archaeological excavations provide an opportunity to study the artefacts of the ancient world belonging to several fields, such as sculpture, decorative arts, fashion design and household. Studying history of archaeology right on the place of excavation of an ancient city masters can imagine the scale of buildings, streets layout and location of business, administrative and residential buildings. It allows students to form professional way of thinking in a short period in order to gather the material and work on the master thesis.

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

    Digital Repository Service at National Institute of Oceanography (India)

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

    in Ancient Indian literature about the behaviour of shoreline which significantly affected the coastal human settlement. It is now generally agreed that glaceo-eustatic sea-level stood higher than the present in and around 6000 years BP 6–8 . During...) and developed full scale. Archaeological evidences such as Ancient shorelines of Gujarat, India, during the Indus civilization (Late Mid- Holocene): A study based on archaeological evidences Page 1 of 8Ancient shorelines of Gujarat, India, during the Indus...

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

    OpenAIRE

    FANG, Lei

    2014-01-01

    The origin of human civilization is based on agriculture and settlement, and the ancient villages preserved up to now can be rated as "museum and historical library of rural lifestyle and rural culture", which are of important historical and cultural value. Through the field survey of farming culture resources of ancient villages in Hongjiang City of Hunan Province, this article classifies and evaluates the farming culture and ancient village resources, and sets forth the following recommenda...

  2. Psychiatric Thoughts in Ancient India*

    OpenAIRE

    Ravi Abhyankar

    2015-01-01

    A review of the literature regarding psychiatric thoughts in ancient India is attempted. Besides interesting reading, many of the concepts are still relevant and can be used in day-to-day practice especially towards healthy and happy living. Certain concepts are surprisingly contemporary and valid today. They can be used in psychotherapy and counselling and for promoting mental health. However, the description and classification of mental illness is not in tune with modern psychiatry.

  3. Psychiatric thoughts in ancient India.

    Science.gov (United States)

    Abhyankar, Ravi

    2015-01-01

    A review of the literature regarding psychiatric thoughts in ancient India is attempted. Besides interesting reading, many of the concepts are still relevant and can be used in day-to-day practice especially towards healthy and happy living. Certain concepts are surprisingly contemporary and valid today. They can be used in psychotherapy and counselling and for promoting mental health. However, the description and classification of mental illness is not in tune with modern psychiatry.

  4. Psychiatric Thoughts in Ancient India*

    Science.gov (United States)

    Abhyankar, Ravi

    2015-01-01

    A review of the literature regarding psychiatric thoughts in ancient India is attempted. Besides interesting reading, many of the concepts are still relevant and can be used in day-to-day practice especially towards healthy and happy living. Certain concepts are surprisingly contemporary and valid today. They can be used in psychotherapy and counselling and for promoting mental health. However, the description and classification of mental illness is not in tune with modern psychiatry. PMID:25838724

  5. Myotonic dystrophy in Ancient Egypt.

    Science.gov (United States)

    Cattaino, G; Vicario, L

    1999-01-01

    Amenhotep IV, better known as Akhenaton, the heretical pharaoh, was a king of the New Kingdom of Ancient Egypt. Statues and reliefs of him show an unhealthy man whose body has abnormal features. By studying the pictures of Akhenaton (the mummy has not yet been found), we conclude that he may have been affected by myotonic dystrophy (MD). Moreover, the available data on his family suggest that MD may have caused the end of the royal bloodline of the Eighteenth Dynasty.

  6. Characterization of mtDNA haplogroups in 14 Mexican indigenous populations.

    Science.gov (United States)

    Peñaloza-Espinosa, Rosenda I; Arenas-Aranda, Diego; Cerda-Flores, Ricardo M; Buentello-Malo, Leonor; González-Valencia, Gerardo; Torres, Javier; Alvarez, Berenice; Mendoza, Irma; Flores, Mario; Sandoval, Lucila; Loeza, Francisco; Ramos, Irma; Muñoz, Leopoldo; Salamanca, Fabio

    2007-06-01

    In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca-Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua-Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua-Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua-Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.

  7. To study the relationship between cadmium, zinc and mtDNA copy ...

    African Journals Online (AJOL)

    Objective: To examine the variation of cadmium (Cd), zinc (Zn) and mitochondrial DNA (mtDNA) copy number in prostate cancer (PCa) patients and their age match controls and correlations with clinicopathological parameters. Subjects and methods: This study was conducted between January 2012 and January 2015.

  8. mtDNA sequence diversity of Hazara ethnic group from Pakistan.

    Science.gov (United States)

    Rakha, Allah; Fatima; Peng, Min-Sheng; Adan, Atif; Bi, Rui; Yasmin, Memona; Yao, Yong-Gang

    2017-09-01

    The present study was undertaken to investigate mitochondrial DNA (mtDNA) control region sequences of Hazaras from Pakistan, so as to generate mtDNA reference database for forensic casework in Pakistan and to analyze phylogenetic relationship of this particular ethnic group with geographically proximal populations. Complete mtDNA control region (nt 16024-576) sequences were generated through Sanger Sequencing for 319 Hazara individuals from Quetta, Baluchistan. The population sample set showed a total of 189 distinct haplotypes, belonging mainly to West Eurasian (51.72%), East & Southeast Asian (29.78%) and South Asian (18.50%) haplogroups. Compared with other populations from Pakistan, the Hazara population had a relatively high haplotype diversity (0.9945) and a lower random match probability (0.0085). The dataset has been incorporated into EMPOP database under accession number EMP00680. The data herein comprises the largest, and likely most thoroughly examined, control region mtDNA dataset from Hazaras of Pakistan. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Investigation of yeast genes possibly involved in mtDNA stability ...

    African Journals Online (AJOL)

    Screening of Caenorhabditis elegans genes possibly involved in the mitochondrial genome maintenance was performed using our previous validated method of RNAi combined with ethidium bromide. This was to knock down C. elegans genes homologous to yeast genes known to be involved in mtDNA stability but of ...

  10. Mitogenomic analyses from ancient DNA.

    Science.gov (United States)

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

    2013-11-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well. 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 yielded major progress with regard to both the phylogenetic positions of extinct species, as well as resolving population genetics questions in both extinct and extant species. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Orthopedic surgery in ancient Egypt.

    Science.gov (United States)

    Blomstedt, Patric

    2014-12-01

    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. I reviewed the original sources and also the modern literature regarding surgery in ancient Egypt, concentrating especially on orthopedic surgery. As is well known, both literary sources and the archaeological/osteological material bear witness to treatment of various fractures. The Egyptian painting, often claimed to depict the reduction of a dislocated shoulder according to Kocher's method, is, however, open to interpretation. Therapeutic amputations are never depicted or mentioned in the literary sources, while the specimens suggested to demonstrate such amputations are not convincing. The ancient Egyptians certainly treated fractures of various kinds, and with varying degrees of success. Concerning the reductions of dislocated joints and therapeutic amputations, there is no clear evidence for the existence of such procedures. It would, however, be surprising if dislocations were not treated, even though they have not left traces in the surviving sources. Concerning amputations, the general level of Egyptian surgery makes it unlikely that limb amputations were done, even if they may possibly have been performed under extraordinary circumstances.

  12. Dental surgery in ancient Egypt.

    Science.gov (United States)

    Blomstedt, Patric

    2013-01-01

    Many different surgical procedures have over the years been attributed to the ancient Egyptians. This is also true regarding the field of dental surgery. The existence of dentists in ancient Egypt is documented and several recipes exist concerning dental conditions. However, no indications of dental surgery are found in the medical papyri or in the visual arts. Regarding the osteological material/mummies, the possible indications of dental surgery are few and weak. There is not a single example of a clear tooth extraction, nor of a filling or of an artificial tooth. The suggested examples of evacuation of apical abscesses can be more readily explained as outflow sinuses. Regarding the suggested bridges, these are constituted of one find likely dating to the Old Kingdom, and one possibly, but perhaps more likely, dating to the Ptolemaic era. Both seem to be too weak to have served any possible practical purpose in a living patient, and the most likely explanation would be to consider them as a restoration performed during the mummification process. Thus, while a form of dentistry did certainly exist in ancient Egypt, there is today no evidence of dental surgery.

  13. Insertion of a self-splicing intron into the mtDNA of atriploblastic animal

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Y.; Halanych, K.; Boore, J.L.

    2006-04-14

    Nephtys longosetosa is a carnivorous polychaete worm that lives in the intertidal and subtidal zones with worldwide distribution (pleijel&rouse2001). Its mitochondrial genome has the characteristics typical of most metazoans: 37 genes; circular molecule; almost no intergenic sequence; and no significant gene rearrangements when compared to other annelid mtDNAs (booremoritz19981995). Ubiquitous features as small intergenic regions and lack of introns suggested that metazoan mtDNAs are under strong selective pressures to reduce their genome size allowing for faster replication requirements (booremoritz19981995Lynch2005). Yet, in 1996 two type I introns were found in the mtDNA of the basal metazoan Metridium senile (FigureX). Breaking a long-standing rule (absence of introns in metazoan mtDNA), this finding was later supported by the further presence of group I introns in other cnidarians. Interestingly, only the class Anthozoa within cnidarians seems to harbor such introns. Although several hundreds of triploblastic metazoan mtDNAs have been sequenced, this study is the first evidence of mitochondrial introns in triploblastic metazoans. The cox1 gene of N. longosetosa has an intron of almost 2 kbs in length. This finding represents as well the first instance of a group II intron (anthozoans harbor group I introns) in all metazoan lineages. Opposite trends are observed within plants, fungi and protist mtDNAs, where introns (both group I and II) and other non-coding sequences are widespread. Plant, fungal and protist mtDNA structure and organization differ enormously from that of metazoan mtDNA. Both, plant and fungal mtDNA are dynamic molecules that undergo high rates of recombination, contain long intergenic spacer regions and harbor both group I and group II introns. However, as metazoans they have a conserved gene content. Protists, on the other hand have a striking variation of gene content and introns that account for the genome size variation. In contrast to

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

    Science.gov (United States)

    von Rintelen, Thomas; Glaubrecht, Matthias

    2006-03-22

    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 to the substrate. Our data show that Corbicula on Sulawesi is polyphyletic, with the endemic riverine taxa in terminal position, and the lacustrine species flock being paraphyletic. Surprisingly, Posostrea is not confirmed as a genus distinct from Corbicula and genetic distances suggest a rather recent origin from the only other corbiculid species endemic to Lake Poso, the non-cementing Corbicula possoensis. While the cementing anomioides, despite its unique behavioural and morphological characteristics, clusters together with non-sessile Corbicula species, the latter exhibit strong genetic distances in the absence of morphological disparity and fall into several genetically rather distinct clades. These findings suggest that developmental plasticity of animals in ancient lakes rather than the antiquity of lineages might account for the unique morphology of some species.

  16. [The ancient Alexandria school of medicine].

    Science.gov (United States)

    Sallam, H N

    2002-01-01

    A famous medical school was established in old Alexandria during the third century BC. Although mainly Greek in essence, and following the Hippocratic teachings, it was heavily tainted by the medical practices of ancient Egypt. Anatomy was particularly advanced due to the possibility of dissecting the human body. The most important Alexandrian physicians were Herophilus and Erasistratus. Many graduates of this medical school traveled and practiced throughout the Mediterranean basin. Galen, the famous Roman physician studied in Alexandria before practicing in Rome. His teachings and writings survived well into the sixteenth century and formed the basis of more modern medical practices during the renaissance. These writings were conserved partly by Christian monks and partly by Arab and Jewish scholars of the middle ages. The medical school of Alexandria was still active until late in the 3rd century AD. However, it slipped slowly into oblivion after the fire of 389 AD, which also devastated its famous library.

  17. Ancient Maya astronomical tables from Xultun, Guatemala.

    Science.gov (United States)

    Saturno, William A; Stuart, David; Aveni, Anthony F; Rossi, Franco

    2012-05-11

    Maya astronomical tables are recognized in bark-paper books from the Late Postclassic period (1300 to 1521 C.E.), but Classic period (200 to 900 C.E.) precursors have not been found. In 2011, a small painted room was excavated at the extensive ancient Maya ruins of Xultun, Guatemala, dating to the early 9th century C.E. The walls and ceiling of the room are painted with several human figures. Two walls also display a large number of delicate black, red, and incised hieroglyphs. Many of these hieroglyphs are calendrical in nature and relate astronomical computations, including at least two tables concerning the movement of the Moon, and perhaps Mars and Venus. These apparently represent early astronomical tables and may shed light on the later books.

  18. Ecological divergence combined with ancient allopatry in lizard populations from a small volcanic island.

    Science.gov (United States)

    Suárez, N M; Pestano, J; Brown, R P

    2014-10-01

    Population divergence and speciation are often explained by geographical isolation, but may also be possible under high gene flow due to strong ecology-related differences in selection pressures. This study combines coalescent analyses of genetic data (11 microsatellite loci and 1 Kbp of mtDNA) and ecological modelling to examine the relative contributions of isolation and ecology to incipient speciation in the scincid lizard Chalcides sexlineatus within the volcanic island of Gran Canaria. Bayesian multispecies coalescent dating of within-island genetic divergence of northern and southern populations showed correspondence with the timing of volcanic activity in the north of the island 1.5-3.0 Ma ago. Coalescent estimates of demographic changes reveal historical size increases in northern populations, consistent with expansions from a volcanic refuge. Nevertheless, ecological divergence is also supported. First, the two morphs showed non-equivalence of ecological niches and species distribution modelling associated the northern morph with mesic habitat types and the southern morph with xeric habitat types. It seems likely that the colour morphs are associated with different antipredator strategies in the different habitats. Second, coalescent estimation of gene copy migration (based on microsatellites and mtDNA) suggest high rates from northern to southern morphs demonstrating the strength of ecology-mediated selection pressures that maintain the divergent southern morph. Together, these findings underline the complexity of the speciation process by providing evidence for the combined effects of ecological divergence and ancient divergence in allopatry. © 2014 John Wiley & Sons Ltd.

  19. Clinical features of MS associated with Leber hereditary optic neuropathy mtDNA mutations.

    Science.gov (United States)

    Pfeffer, Gerald; Burke, Ailbhe; Yu-Wai-Man, Patrick; Compston, D Alastair S; Chinnery, Patrick F

    2013-12-10

    To determine whether the association between multiple sclerosis (MS) and Leber hereditary optic neuropathy (LHON) (known as "Harding disease") is a chance finding, or the 2 disorders are mechanistically linked. We performed a United Kingdom-wide prospective cohort study of prevalent cases of MS with LHON mitochondrial DNA (mtDNA) mutations. The new cases were compared with published cases, enabling a comprehensive clinical description. We also performed a meta-analysis of studies screening patients with MS for LHON mtDNA mutations to find evidence of a genetic association. Twelve new patients were identified from 11 pedigrees, and 44 cases were identified in the literature. The combined cohort had the following characteristics: multiple episodes of visual loss, predominance for women, and lengthy time interval before the fellow eye is affected (average 1.66 years), which is very atypical of LHON; conversely, most patients presented without eye pain and had a poor visual prognosis, which is unusual for optic neuritis associated with MS. The number of UK cases of LHON-MS fell well within the range predicted by the chance occurrence of MS and the mtDNA mutations known to cause LHON. There was no association between LHON mtDNA mutations and MS in a meta-analysis of the published data. Although the co-occurrence of MS and LHON mtDNA mutations is likely to be due to chance, the resulting disorder has a distinct phenotype, implicating a mechanistic interaction. Patients with LHON-MS have a more aggressive course, and prognostication and treatment should be guarded.

  20. RNASEH1 Mutations Impair mtDNA Replication and Cause Adult-Onset Mitochondrial Encephalomyopathy

    Science.gov (United States)

    Reyes, Aurelio; Melchionda, Laura; Nasca, Alessia; Carrara, Franco; Lamantea, Eleonora; Zanolini, Alice; Lamperti, Costanza; Fang, Mingyan; Zhang, Jianguo; Ronchi, Dario; Bonato, Sara; Fagiolari, Gigliola; Moggio, Maurizio; Ghezzi, Daniele; Zeviani, Massimo

    2015-01-01

    Chronic progressive external ophthalmoplegia (CPEO) is common in mitochondrial disorders and is frequently associated with multiple mtDNA deletions. The onset is typically in adulthood, and affected subjects can also present with general muscle weakness. The underlying genetic defects comprise autosomal-dominant or recessive mutations in several nuclear genes, most of which play a role in mtDNA replication. Next-generation sequencing led to the identification of compound-heterozygous RNASEH1 mutations in two singleton subjects and a homozygous mutation in four siblings. RNASEH1, encoding ribonuclease H1 (RNase H1), is an endonuclease that is present in both the nucleus and mitochondria and digests the RNA component of RNA-DNA hybrids. Unlike mitochondria, the nucleus harbors a second ribonuclease (RNase H2). All affected individuals first presented with CPEO and exercise intolerance in their twenties, and these were followed by muscle weakness, dysphagia, and spino-cerebellar signs with impaired gait coordination, dysmetria, and dysarthria. Ragged-red and cytochrome c oxidase (COX)-negative fibers, together with impaired activity of various mitochondrial respiratory chain complexes, were observed in muscle biopsies of affected subjects. Western blot analysis showed the virtual absence of RNase H1 in total lysate from mutant fibroblasts. By an in vitro assay, we demonstrated that altered RNase H1 has a reduced capability to remove the RNA from RNA-DNA hybrids, confirming their pathogenic role. Given that an increasing amount of evidence indicates the presence of RNA primers during mtDNA replication, this result might also explain the accumulation of mtDNA deletions and underscores the importance of RNase H1 for mtDNA maintenance. PMID:26094573

  1. CINNAMON, CASSIA AND ANCIENT TRADE

    Directory of Open Access Journals (Sweden)

    Stephen George Haw

    2017-03-01

    Full Text Available Abstract: There is a widespread assumption that ancient “cinnamon” and “cassia” were the same as the spices now known by those names; that is, products obtained from trees of the genus Cinnamomum. This article argues that this is not the case, but that the “cinnamon” and “cassia” of ancient writers very probably came from plants native to northeast Africa, as several early writers actually state. Possible African sources of ancient “cinnamon” and “cassia” are suggested. The most probable principal source is identified as Cassia abbreviata. It is also argued that alleged identifications of cinnamon or cassia at archaeological sites in the Mediterranean region are questionable. It is shown that cinnamon and cassia did not figure in Southeast Asian and Chinese trade at an early period, and that Austronesian settlement of Madagascar occurred after the Classical period, probably during the second half of the first millennium CE, too late for Southeast Asians to have played any major role in trade with the Roman Empire. There is no good reason to believe that true cinnamon and cassia were traded to the western Indian Ocean and the Mediterranean region at any very early date. This article truly takes an interdisciplinary approach to its subject: the author is a botanist as well as a historian, and is able to use original Chinese sources. The question of whether ancient “cinnamon” and “cassia” were the same as modern cinnamon and cassia (products of trees of the genus Cinnamomum is a thorny one, which has been repeatedly debated in the past, usually with no very conclusive result. The most recent thorough discussion of the issue, by Lionel Casson, concluded that the ancient and modern products were the same. This article refutes that view: it is clear that Casson lacked the botanical knowledge necessary to reach a sound conclusion. The article deals with its subject thoroughly, examining archaeological as well as textual

  2. Ancient and contemporary history of artificial eyes.

    Science.gov (United States)

    Danz, W

    1990-01-01

    Throughout history, the human eye has been mentioned by authors as the most precious of gifts. It unveils the entire outer world to our consciousness, gives life expression and dignity to the face. The loss of an eye must therefore have always been regarded as the greatest misfortune. The ancient cultures of Babylon, Jericho, and Egypt used "art-eyes" in mummies, sarcophagus lids, and statues; they were made from precious stones, silver, gold, and copper as a symbol of light and life in their religious beliefs. Most of the recorded sources concerning the ancient practice of medicine were among the scrolls contained in the library of Alexandria. In the period between the Roman Colonial wars, the rise of Christianity and the fall of Alexandria to Arabs in 642 A.D., almost all of these sources, including those concerning the practice of Ophthalmology were lost. The largest collection of antiquity "art-eyes" and artificial eyes, mentioned in this paper, are found in the collection of the firm of Mueller and Sohne, Wiesbaden, Germany. They include the progress made in human artificial eyes to modern times. Historically, man has tried to alleviate the psychological suffering incurred by the loss of an eye, by hiding or covering the defacement with a patch. Of greater significance are the efforts made by the ophthalmologist and the ocularist (past and present) to restore functionally and cosmetically the natural facial appearance by means of an ocular prosthesis that corresponds to the remaining natural eye. Associated problems frequently concern both the reconstructive surgeon, who must be informed of the ocular prosthetic possibilities that are within the capacity of the ocularist, and the ocularist, who must create the prosthesis.

  3. Ascaris phylogeny based on multiple whole mtDNA genomes

    DEFF Research Database (Denmark)

    Nejsum, Peter; Hawash, Mohamed B. F.; Betson, Martha

    2017-01-01

    Ascaris lumbricoides and A. suum are two parasitic nematodes infecting humans and pigs, respectively. There has been considerable debate as to whether Ascaris in the two hosts should be considered a single or two separate species. Previous studies identified at least three major clusters (A, B...... and C) of human and pig Ascaris based on partial cox1 sequences. In the present study, we selected major haplotypes from these different clusters to characterize their whole mitochondrial genomes for phylogenetic analysis. We also undertook coalescent simulations to investigate the evolutionary history...... of the different Ascaris haplotypes. The topology of the phylogenetic tree based on complete mitochondrial genomic sequences was found to be similar to partial cox1 sequencing, but the support at internal nodes was higher in the former. Coalescent simulations suggested the presence of at least two divergence...

  4. Random point mutations with major effects on protein-coding genes are the driving force behind premature aging in mtDNA mutator mice.

    NARCIS (Netherlands)

    Edgar, D.; Shabalina, I.; Camara, Y.; Wredenberg, A.; Calvaruso, M.A.; Nijtmans, L.G.J.; Nedergaard, J.; Cannon, B.; Larsson, N.G.; Trifunovic, A.

    2009-01-01

    The mtDNA mutator mice have high levels of point mutations and linear deletions of mtDNA causing a progressive respiratory chain dysfunction and a premature aging phenotype. We have now performed molecular analyses to determine the mechanism whereby these mtDNA mutations impair respiratory chain

  5. [The history of medicine in the ancient time].

    Science.gov (United States)

    Tesarová, Drahomíra

    2012-01-01

    This article deals with the history of medicine in the ancient Greece; from the cult of the God Asklepios, to the founder of the scientific rational medicine, Hippokrates. The humoral theory of Hippokrates is explained (the human body consists from four liquids) and his ideal of a physician's approach to a patient is emphasized. In the Hellenistic period the medical development continued in the Alexandria Medical School (Herofilos and Erasistratos). At first, not much attention was given to medicine and scientific health prevention in ancient Rome. Only 293 AD have physicians from Greece first been invited to Rome--e.g. Asklepiades. During the reign of C. lulius Caesar, foreigners, who engaged in medical practice, were granted Roman citizenship and thanks to a number of benefits the medical condition in Roman Empire blossomed. Medical clinics (iatreia), infirmaries (valetudinaria) and, under the influence of Christianity, hospitals were established. In the 2nd century AD ancient medicine reached its climax with physician Galenos, who created the entire system of medical science and became the most significant, but also last medical figure of ancient Rome.

  6. The Ancient Greece's roots of Olimpism

    Directory of Open Access Journals (Sweden)

    Bubka Sergej Nazarovich

    2011-10-01

    Full Text Available The paper focused on the phenomena of sport in Ancient Greece along with history, traditions, religion, education, culture and art. Economic and political conditions are analysed which promote or hamper development of Olympic Games in Ancient Greece. Exceptional stability of Ancient Olympic games during more than eleven centuries are noted as well as their influence on the life of Greek polices of those days. Hellenistic period needs of individual consideration.

  7. Centripetal modules and ancient introns.

    Science.gov (United States)

    Roy, S W; Nosaka, M; de Souza, S J; Gilbert, W

    1999-09-30

    We have created an algorithm which instantiates the centripetal definition of modules, compact regions of protein structure, as introduced by Go and Nosaka (M. Go and M. Nosaka, 1987. Protein architecture and the origin of introns. Cold Spring Harbor Symp. Quant. Bio. 52, 915-924). That definition seeks the minima of a function that sums the squares of C-alpha carbon distances over a window around each amino acid residue in a three-dimensional protein structure and identifies such minima with module boundaries. We analyze a set of 44 ancient conserved proteins, with known three-dimensional structures, which have intronless homologues in bacteria and intron-containing homologues in the eukaryotes, with a corresponding set of 988 intron positions. We show that the phase zero intron positions are significantly correlated with the module boundaries (p = 0.0002), while the intron positions that lie within codons, in phase one and phase two, are not correlated with these 'centripetal' module boundaries. Furthermore, we analyze the phylogenetic distribution of intron positions and identify a subset of putatively 'ancient' intron positions: phase zero positions in one phylogenetic kingdom which have an associated intron either in an identical position or within three codons in another phylogenetic kingdom (a notion of intron sliding). This subset of 120 'ancient' introns lies closer to the module boundaries than does the full set of phase zero introns with high significance, a p-value of 0.008. We conclude that the behavior of this set of introns supports the prediction of a mixed theory: that some introns are very old and were used for exon shuffling in the progenote, while many introns have been lost and added since.

  8. [Female anthropology, physiology and disease in ancient Christian writers].

    Science.gov (United States)

    Prinzivalli, Emanuela

    2011-01-01

    Ancient Christian sources are rich in reference to the anthropology and physiology of the female. Christianity in the first centuries had multiple positions as concerns the doctrinal thoughts as well as the social practices. Christian anthropological doctrine has been developed along two exegetical lines, hinging on Genesis 1-3: the first views the human being as a whole psycophysical entity and thereby highlights the protological inferiority of the woman; the second, spiritual and Platonic, emphasizes the inner self and thus, in theory, is more equalitarian. Ancient philosophical theories regarding human generation, in particular those ofAristotle and the Stoics, are used, along with medical notions, by Christian theologians to elaborate the dogma of incarnation. However, in certain cases, as with the post partum virginity of Maria, medical theories are totally put aside. The stories recounting the miracles offer the possibility of understanding medical practices offemale conditions and the emotive reactions of the women.

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

    Directory of Open Access Journals (Sweden)

    Christina I Barrón-Ortiz

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

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

    Science.gov (United States)

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

    2017-01-01

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

  11. Mitochondrial mosaics in the liver of 3 infants with mtDNA defects

    Directory of Open Access Journals (Sweden)

    Scalais Emmanuel

    2009-06-01

    Full Text Available Abstract Background In muscle cytochrome oxidase (COX negative fibers (mitochondrial mosaics have often been visualized. Methods COX activity staining of liver for light and electron microscopy, muscle stains, blue native gel electrophoresis and activity assays of respiratory chain proteins, their immunolocalisation, mitochondrial and nuclear DNA analysis. Results Three unrelated infants showed a mitochondrial mosaic in the liver after staining for COX activity, i.e. hepatocytes with strongly reactive mitochondria were found adjacent to cells with many negative, or barely reactive, mitochondria. Deficiency was most severe in the patient diagnosed with Pearson syndrome. Ragged-red fibers were absent in muscle biopsies of all patients. Enzyme biochemistry was not diagnostic in muscle, fibroblasts and lymphocytes. Blue native gel electrophoresis of liver tissue, but not of muscle, demonstrated a decreased activity of complex IV; in both muscle and liver subcomplexes of complex V were seen. Immunocytochemistry of complex IV confirmed the mosaic pattern in two livers, but not in fibroblasts. MRI of the brain revealed severe white matter cavitation in the Pearson case, but only slight cortical atrophy in the Alpers-Huttenlocher patient, and a normal image in the 3rd. MtDNA in leucocytes showed a common deletion in 50% of the mtDNA molecules of the Pearson patient. In the patient diagnosed with Alpers-Huttenlocher syndrome, mtDNA was depleted for 60% in muscle. In the 3rd patient muscular and hepatic mtDNA was depleted for more than 70%. Mutations in the nuclear encoded gene of POLG were subsequently found in both the 2nd and 3rd patients. Conclusion Histoenzymatic COX staining of a liver biopsy is fast and yields crucial data about the pathogenesis; it indicates whether mtDNA should be assayed. Each time a mitochondrial disorder is suspected and muscle data are non-diagnostic, a liver biopsy should be recommended. Mosaics are probably more frequent

  12. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae.

    Directory of Open Access Journals (Sweden)

    Xiujuan Wang

    Full Text Available Two major transitions in animal evolution--the origins of multicellularity and bilaterality--correlate with major changes in mitochondrial DNA (mtDNA organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13-15 protein genes, 2 rRNA genes, and 2-27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida. Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements

  13. Ancient Indian Leaps into Mathematics

    CERN Document Server

    Yadav, B S

    2011-01-01

    This book presents contributions of mathematicians covering topics from ancient India, placing them in the broader context of the history of mathematics. Although the translations of some Sanskrit mathematical texts are available in the literature, Indian contributions are rarely presented in major Western historical works. Yet some of the well-known and universally-accepted discoveries from India, including the concept of zero and the decimal representation of numbers, have made lasting contributions to the foundation of modern mathematics. Through a systematic approach, this book examines th

  14. Ancient Chinese Astronomy - An Overview

    Science.gov (United States)

    Shi, Yunli

    Documentary and archaeological evidence testifies the early origin and continuous development of ancient Chinese astronomy to meet both the ideological and practical needs of a society largely based on agriculture. There was a long period when the beginning of the year, month, and season was determined by direct observation of celestial phenomena, including their alignments with respect to the local skyline. As the need for more exact study arose, new instruments for more exact observation were invented and the system of calendrical astronomy became entirely mathematized.

  15. [Urinary schistosomiasis in ancient Egypt].

    Science.gov (United States)

    Ziskind, Bernard

    2009-12-01

    First described by Theodor Bilharz in 1851, Schistosoma haematobium, the worm responsible for urinary schistosomiasis, was a major health problem along the Nile Valley until the present days. Haematuria, the main symptom of this parasitic disease, was known and treated in Egyptian medical papyri since 1550 B.C. A relationship between haematuria and the god Seth was envisaged. Sir Marc Armand Ruffer, pioneer of paleopathology, found (1910) calcified Schistosoma eggs in Egyptian mummies of the xxth dynasty, establishing that bilharzia plagued ancient Egypt people. The ELISA method demonstrated the Schistosoma circulating anodic antigen in 45% of mummies studied.

  16. Aiding the Interpretation of Ancient Documents

    DEFF Research Database (Denmark)

    Roued-Cunliffe, Henriette

    How can Decision Support System (DSS) software aid the interpretation process involved in the reading of ancient documents? This paper discusses the development of a DSS prototype for the reading of ancient texts. In this context the term ‘ancient documents’ is used to describe mainly Greek...... tool it is important first to comprehend the interpretation process involved in reading ancient documents. This is not a linear process but rather a recursive process where the scholar moves between different levels of reading, such as ‘understanding the meaning of a character’ or ‘understanding...

  17. The History and Practice of Ancient Astronomy

    CERN Document Server

    Evans, James

    1998-01-01

    The History and Practice of Ancient Astronomy combines new scholarship with hands-on science to bring readers into direct contact with the work of ancient astronomers. While tracing ideas from ancient Babylon to sixteenth-century Europe, the book places its greatest emphasis on the Greek period, when astronomers developed the geometric and philosophical ideas that have determined the subsequent character of Western astronomy. The author approaches this history through the concrete details of ancient astronomical practice. Carefully organized and generously illustrated, the book can teach reade

  18. Ancient water supports today's energy needs

    Science.gov (United States)

    D'Odorico, Paolo; Natyzak, Jennifer L.; Castner, Elizabeth A.; Davis, Kyle F.; Emery, Kyle A.; Gephart, Jessica A.; Leach, Allison M.; Pace, Michael L.; Galloway, James N.

    2017-05-01

    The water footprint for fossil fuels typically accounts for water utilized in mining and fuel processing, whereas the water footprint of biofuels assesses the agricultural water used by crops through their lifetime. Fossil fuels have an additional water footprint that is not easily accounted for: ancient water that was used by plants millions of years ago, before they were transformed into fossil fuel. How much water is mankind using from the past to sustain current energy needs? We evaluate the link between ancient water virtually embodied in fossil fuels to current global energy demands by determining the water demand required to replace fossil fuels with biomass produced with water from the present. Using equal energy units of wood, bioethanol, and biodiesel to replace coal, natural gas, and crude oil, respectively, the resulting water demand is 7.39 × 1013 m3 y-1, approximately the same as the total annual evaporation from all land masses and transpiration from all terrestrial vegetation. Thus, there are strong hydrologic constraints to a reliance on biofuel energy produced with water from the present because the conversion from fossil fuels to biofuels would have a disproportionate and unsustainable impact on the modern water. By using fossil fuels to meet today's energy needs, we are virtually using water from a geological past. The water cycle is insufficient to sustain the production of the fuel presently consumed by human societies. Thus, non-fuel-based renewable energy sources are needed to decrease mankind's reliance on fossil fuel energy without placing an overwhelming pressure on global freshwater resources.

  19. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel.

    Science.gov (United States)

    Mohandesan, Elmira; Speller, Camilla F; Peters, Joris; Uerpmann, Hans-Peter; Uerpmann, Margarethe; De Cupere, Bea; Hofreiter, Michael; Burger, Pamela A

    2017-03-01

    The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  20. Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France.

    Science.gov (United States)

    Schnitzler, Annik; Granado, José; Putelat, Olivier; Arbogast, Rose-Marie; Drucker, Dorothée; Eberhard, Anna; Schmutz, Anja; Klaefiger, Yuri; Lang, Gérard; Salzburger, Walter; Schibler, Joerg; Schlumbaum, Angela; Bocherens, Hervé

    2018-01-01

    In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.

  1. The psychology of animal companionship: Some ancient and modern views

    Directory of Open Access Journals (Sweden)

    Hennie Viviers

    2014-10-01

    Full Text Available The intuitive sensing of a mental bond between ourselves and animals, especially those that live very close to us, our companion animals, has been there since early history. Some ancient Israelite views testify to an irresistible anthropomorphising of their domestic animals (Jn 3:5–9 as well as an acknowledgement of the socio-psychological support provided by them (2 Sm 12:1c–4d. Is there indeed a mental overlap between humans and animals to explain this intuitive experiencing of a bond between ourselves and them since ancient times? Modern neuroscience, through neuro-imaging, has shown that dogs (at least are able to reciprocate our thoughts and feelings, be it in a limited way. They seem to have some limited form of a ‘theory of mind’ previously ascribed to humans only. This explains why they have been humans’ ‘best friend’ for the past 12 000 years since they were domesticated from wolves. The intuitions of the ancients and the findings of modern science confirm that we and non-human animals all form intrinsically part of the fascinating web of life. This fact should sensitise us as moral agents to preserve this life.

  2. Environmental health and hygiene in ancient India: an appraisal.

    Science.gov (United States)

    Pushpangadan, P; Sharma, J; Kaur, J

    1987-07-01

    The ancient Indians were the custodians of a highly evolved civilization with great awareness on the decisive importance as well as the vulnerability of man's natural environment. The ancient Indians sages and Rishis had considered human environment from the point of view of physical, chemical, biological and social process that influences directly or indirectly the health and well - being of the human kind. Their approach towards life was very comprehensive, highly integrated with the environment and, therefore, was ecologically sound and sustainable. It was aimed at promoting a peaceful coexistence with all the living organisms as well as a fuller harmony with the physical environment. The ancient masters tactfully implemented much of their value oriented teachings through certain rituals, taboos and totems and made the people to observe it as spiritual duty; the violation of which was feared an antispiritual. This approach had its astonishing impact and the people accepted these value oriented practices as a way of life and which in course of time became traditions for ages ensuring peaceful coexistence of human kind with other living organisms as well as with the physical environment. But with the advent of modern civilization most of these value oriented traditions are being either lost or discarded. The disappearance or disregard for such time tested environmental conservation or preservation oriented traditions had begun to show its detrimental effect on the life supporting system.

  3. Ancient Genomics and the Peopling of the Southwest Pacific

    Science.gov (United States)

    Skoglund, Pontus; Posth, Cosimo; Sirak, Kendra; Spriggs, Matthew; Valentin, Frederique; Bedford, Stuart; Clark, Geoffrey; Reepmeyer, Christian; Petchey, Fiona; Fernandes, Daniel; Fu, Qiaomei; Harney, Eadaoin; Lipson, Mark; Mallick, Swapan; Novak, Mario; Rohland, Nadin; Stewardson, Kristin; Abdullah, Syafiq; Cox, Murray P.; Friedlaender, Françoise R.; Friedlaender, Jonathan S.; Kivisild, Toomas; Koki, George; Kusuma, Pradiptajati; Merriwether, D. Andrew; Ricaut, Francois-X.; Wee, Joseph T. S.; Patterson, Nick; Krause, Johannes; Pinhasi, Ron; Reich, David

    2017-01-01

    The appearance of people associated with the Lapita culture in the South Pacific ~3,000 years ago1 marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long established Papuans of the New Guinea region is unclear. We report genome-wide ancient DNA data from four individuals from Vanuatu (~3100-2700 years before present) and Tonga (~2700-2300 years before present), and co-analyze them with 778 present-day East Asians and Oceanians. Today, indigenous peoples of the South Pacific harbor a mixture of ancestry from Papuans and a population of East Asian origin that does not exist in unmixed form today, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five percent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, prior to the further expansion into Remote Oceania2–5. However, our finding that the ancient individuals had little to no Papuan ancestry implies later human population movements that spread Papuan ancestry through the South Pacific after the islands’ first peopling. PMID:27698418

  4. The psychology of animal companionship: Some ancient and modern views

    Directory of Open Access Journals (Sweden)

    Hennie Viviers

    2014-02-01

    Full Text Available The intuitive sensing of a mental bond between ourselves and animals, especially those that live very close to us, our companion animals, has been there since early history. Some ancient Israelite views testify to an irresistible anthropomorphising of their domestic animals (Jn 3:5–9 as well as an acknowledgement of the socio-psychological support provided by them (2 Sm 12:1c–4d. Is there indeed a mental overlap between humans and animals to explain this intuitive experiencing of a bond between ourselves and them since ancient times? Modern neuroscience, through neuro-imaging, has shown that dogs (at least are able to reciprocate our thoughts and feelings, be it in a limited way. They seem to have some limited form of a ‘theory of mind’ previously ascribed to humans only. This explains why they have been humans’ ‘best friend’ for the past 12 000 years since they were domesticated from wolves. The intuitions of the ancients and the findings of modern science confirm that we and non-human animals all form intrinsically part of the fascinating web of life. This fact should sensitise us as moral agents to preserve this life.

  5. Foreign Guests in Ancient Greece

    Directory of Open Access Journals (Sweden)

    Zora Žbontar

    2013-12-01

    Full Text Available Xenía was a special relationship between a foreign guest and his host in Ancient Greece. The ritual of hosting a foreigner included an exchange of objects, feasting, and the establishment of friendship between people from different social backgrounds. This relationship implied trust, loyalty, friendship, and mutual aid between the people involved. Goods and services were also exchanged without any form of payment. There were no formal laws governing xenía – it was based entirely on a moral appeal. Mutual appreciation between the host and the guest was established during the ritual, but the host did retain a certain level of superiority over the guest. Xenía was one of the most important institutions in Ancient Greece. It had a lot of features and obligations similar to kinship and marriage. In literary sources the word xénos varies in meaning from “enemy stranger”, “friendly stranger”, “foreigner”, “guest”, “host” to “ritual friend”, and it is often hard to tell which usage is appropriate in a given passage. The paper describes the emphasis on hospitality towards foreigners. It presents an example of a depiction indicating xenía is presented, as well as several objects which were traded during the ritual. The paper also addresses the importance of hospitality in Greek drama in general, especially with examples of violations of the hospitality code.

  6. Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

    OpenAIRE

    Ávila-Arcos María C; Sandoval-Velasco Marcela; Schroeder Hannes; Carpenter Meredith L.; Malaspinas Anna-Sapfo; Wales Nathan; Peñaloza Fernando; Bustamante Carlos D.; Gilbert M. Thomas P.

    2015-01-01

    Application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double stranded and single stranded build protocols. Although both methods effectively enriched aDNA we observed consistent differences between the methods providing the opportunity to further explore parameters influencing WGC experiments. ...

  7. [Studies of mtDNA of Ustilago maydis. I. Cloning and gene mapping].

    Science.gov (United States)

    Feng, G H; Cheng, W; Lu, S Y

    1991-01-01

    This paper covers the following studies of mtDNA of Ustilago maydis. (1) By inserting the Bam HI and Pst I fragments of the mtDNA into the corresponding sites of pBR322, we cloned a unique sequence of 49.6 kb, accounting for 89.3% of the mitochondrial genome (60.7 kb). (2) With heterogenous genes from plants or fungi as probes, we identified seven genes, and mapped them onto the restriction map of the mt DNA. The genes were arranged in such an order: -UmCOB-UmOXII-S-rR NA-UmOXIII-L-rRNA-UmATPase6-UmOXI-. (3) We tried to express the three cloned genes, UmOXII, UmOXIII, and Um-ATPase 6, in E. coli maxcel expression system, but no specific protein was observed.

  8. Two distinct mtDNA lineages among captive African penguins in Japan.

    Science.gov (United States)

    Murata, Michiko; Murakami, Masaru

    2014-04-01

    The African penguin (Spheniscus demersus) is one of the world's most endangered seabirds. In Japan, although the number of African penguins in captivity continues to increase, genetic data have not been collected for either wild or captive populations. To reveal genetic diversity and characterization in captive African penguins, we analyzed the nucleotide sequences of mitochondrial DNA (mtDNA) from a sample of 236 African penguins. Analysis of 433 bp of the control region and 1,140 bp of cytochrome b sequences revealed the existence of two mtDNA clades. Control region haplotypes were much more divergent (d=3.39%) between the two clades than within each clade. The divergence of these clades may reflect differences at the subspecies or geographical population level in African penguins. These findings suggest that at least two distinct maternal lineages exist in the wild populations of the African penguin.

  9. Whole Genome mtDNA Sequencing on the Ion Torrent PGM

    OpenAIRE

    Powers, M.; Watkins, W; Potucek, Y.; Warner, Derek

    2012-01-01

    The mitochondrial genome is a 16.5 kb circular chromosome encoding 37 genes. Mutations in the mitochondrial genome have been linked to many diseases such as Autism, Kearns-Sayre syndrome (KSS), Leber's hereditary optic neuropathy (LHON), Leigh Syndrome, and myoclonic epilepsy with red ragged fibers (MERRF). In addition to clinical interest, there is strong interest in sequencing mtDNA for archeological and genealogical studies.

  10. Taenia solium cysticercosis in Bali, Indonesia: serology and mtDNA analysis.

    Science.gov (United States)

    Sudewi, A A R; Wandra, T; Artha, A; Nkouawa, A; Ito, A

    2008-01-01

    An active Taenia solium cysticercosis case in Bali, Indonesia, was followed-up by serology and computed tomography. Serology using semi-purified glycoprotein and recombinant antigens showed a drastic drop in titers after calcification of the cysts. Three paraffin-embedded cysts, prepared for histopathological examination, from three other patients were used for mtDNA analysis. The sequences of cox1 gene from T. solium cysticerci from Bali differed from those in Papua and other Asian countries.

  11. Peopling of Sahul: mtDNA Variation in Aboriginal Australian and Papua New Guinean Populations

    OpenAIRE

    Redd, Alan J.; Stoneking, Mark

    1999-01-01

    We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian po...

  12. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion

    DEFF Research Database (Denmark)

    Saillard, J; Forster, P; Lynnerup, N

    2000-01-01

    and is estimated to have originated lack...... the groups D2 and D3 found in Siberia and Alaska and are exclusively A2 but at the same time lack the A2 root type. The data are in agreement with the view that the present Greenland Eskimos essentially descend from Alaskan Neo-Eskimos. European mtDNA types are absent in our Eskimo sample....

  13. Tracing European Founder Lineages in the Near Eastern mtDNA Pool

    Science.gov (United States)

    Richards, Martin; Macaulay, Vincent; Hickey, Eileen; Vega, Emilce; Sykes, Bryan; Guida, Valentina; Rengo, Chiara; Sellitto, Daniele; Cruciani, Fulvio; Kivisild, Toomas; Villems, Richard; Thomas, Mark; Rychkov, Serge; Rychkov, Oksana; Rychkov, Yuri; Gölge, Mukaddes; Dimitrov, Dimitar; Hill, Emmeline; Bradley, Dan; Romano, Valentino; Calì, Francesco; Vona, Giuseppe; Demaine, Andrew; Papiha, Surinder; Triantaphyllidis, Costas; Stefanescu, Gheorghe; Hatina, Jiři; Belledi, Michele; Di Rienzo, Anna; Oppenheim, Ariella; Nørby, Søren; Al-Zaheri, Nadia; Santachiara-Benerecetti, Silvana; Scozzari, Rosaria; Torroni, Antonio; Bandelt, Hans-Jürgen

    2000-01-01

    Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2,804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans. PMID:11032788

  14. Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker

    Directory of Open Access Journals (Sweden)

    Tike Sartika

    2000-06-01

    Full Text Available Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5'-CATCTTGGCATCTTCAGTGCC-3' and DNA Light stranded Ll6750 (5'-AGGACTACGGCTTGAAAAGC-3' was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT, Hpall (C↓CGG, Mbol (↓GATC, Rsal (GT↓AC, NlaIII (CATG↓ and HaeIII (GG↓CC were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.

  15. The Mitochondrial DNA-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination.

    Science.gov (United States)

    Blomme, Jonas; Van Aken, Olivier; Van Leene, Jelle; Jégu, Teddy; De Rycke, Riet; De Bruyne, Michiel; Vercruysse, Jasmien; Nolf, Jonah; Van Daele, Twiggy; De Milde, Liesbeth; Vermeersch, Mattias; des Francs-Small, Catherine Colas; De Jaeger, Geert; Benhamed, Moussa; Millar, A Harvey; Inzé, Dirk; Gonzalez, Nathalie

    2017-05-01

    In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared with their animal counterparts, and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana Gain- and loss-of-function mutants provided evidence for a role of SWIB5 in influencing mtDNA architecture and homologous recombination at specific intermediate-sized repeats both under normal and genotoxic conditions. SWIB5 interacts with other mitochondrial SWIB proteins. Gene expression and mutant phenotypic analysis of SWIB5 and SWIB family members suggests a link between organellar genome maintenance and cell proliferation. Taken together, our work presents a protein family that influences mtDNA architecture and homologous recombination in plants and suggests a link between organelle functioning and plant development. © 2017 American Society of Plant Biologists. All rights reserved.

  16. The origin of Chinese domestic horses revealed with novel mtDNA variants.

    Science.gov (United States)

    Yang, Yunzhou; Zhu, Qiyun; Liu, Shuqin; Zhao, Chunjiang; Wu, Changxin

    2017-01-01

    The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe. © 2016 Japanese Society of Animal Science.

  17. [Comparison of mtDNA extracting methods for common sarcosaphagous insects].

    Science.gov (United States)

    Chen, Yao-Qing; Guo, Ya-Dong; Li, Mao-Zhi; Xiong, Feng; Li, Jian-Bo; Cai, Ji-Feng

    2011-08-01

    To compare effects of three different methods for mtDNA extraction from common sarcosaphagous insects including cetyl trimethyl ammonium bromide (CTAB) method, sodium dodecyl sulfate-potassium acetate (SDS-KAc) method and sodium dodecyl sulfate-proteinase K (SDS-PK) method. Seventy-two insects from four species [Chrysomya megacephala (Fabricius, 1784), Eusilpha bicolor (Fairmaire, 1896), Paraeutrichopus pecoudi (Mateu, 1954), Vespa velutina (Lepeletier, 1836)] were collected from the corpses of the rabbits in Changsha district. The total DNA of above samples was extracted by CTAB, SDS-Kac and SDS-PK methods. The purity and concentration of DNA were examined by protein-nucleic acid spectrophotometry, and mtDNA were amplified by specific primers and PCR products were detected by agarose gel electrophoresis. Then PCR products were sequenced and subsequently up-loaded to GenBank. mtDNA was successfully extracted with three methods from most of the samples. The SDS-PK method was better in DNA purity compared to other methods and the CTAB method was superior in extracting DNA from old samples, while SDS-KAc method showed no significant difference for extraction effects of different samples. The most appropriate method should be chosen depending on different situations. SDS-PK method is expected to obtain high-quality DNA, while CTAB method is preferred in extracting obsolete samples. SDS-KAc method is low cost and can be used in various kinds of preliminary experiments.

  18. Reproductive aging is associated with changes in oocyte mitochondrial dynamics, function, and mtDNA quantity.

    Science.gov (United States)

    Babayev, Elnur; Wang, Tianren; Szigeti-Buck, Klara; Lowther, Katie; Taylor, Hugh S; Horvath, Tamas; Seli, Emre

    2016-11-01

    Mitochondria affect numerous aspects of mammalian reproduction. We investigated whether the decrease in oocyte quality associated with aging is related to altered mitochondria. Oocytes from old (12 months) and young (9 weeks) C57BL/6J mice were compared in relation to: mitochondria morphology and dynamics (mitochondria density, coverage, size and shape) throughout folliculogenesis; levels of mitochondrial DNA (mtDNA); mitochondrial stress reflected in the expression of mitochondrial unfolded protein response (mt-UPR) genes; and levels of reactive oxygen species (ROS) under baseline conditions and following H 2 O 2 treatment. In old mice, mitochondria of primary follicle-enclosed oocytes were smaller, with lower mitochondria coverage (total mitochondria μm 2 /μm 2 cytosol area) (pchanges were not significant. Mature oocytes (Metaphase II-MII) from old mice had significantly less mtDNA (paged MII oocytes were also higher following pretreatment with H 2 O 2 (pAging is associated with altered mitochondrial morphological parameters and decreased mtDNA levels in oocytes, as well as an increase in ROS under stressful conditions and elevated expression of mitochondrial stress response gene Hspd1. Delineation of the mechanisms underlying mitochondrial changes associated with ageing may help in the development of diagnostic and therapeutic tools in reproductive medicine. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Pedigree models for complex human traits involving the mitochrondrial genome

    Energy Technology Data Exchange (ETDEWEB)

    Schork, N.J.; Guo, S.W. (Univ. of Michigan, Ann Arbor, MI (United States))

    1993-12-01

    Recent biochemical and molecular-genetic discoveries concerning variations in human mtDNA have suggested a role for mtDNA mutations in a number of human traits and disorders. Although the importance of these discoveries cannot be emphasized enough, the complex natures of mitochondrial biogenesis, mutant mtDNA phenotype expression, and the maternal inheritance pattern exhibited by mtDNA transmission make it difficult to develop models that can be used routinely in pedigree analyses to quantify and test hypotheses about the role of mtDNA in the expression of a trait. In the present paper, the authors describe complexities inherent in mitochondrial biogenesis and genetic transmission and show how these complexities can be incorporated into appropriate mathematical models. The authors offer a variety of likelihood-based models which account for the complexities discussed. The derivation of the models is meant to stimulate the construction of statistical tests for putative mtDNA contribution to a trait. Results of simulation studies which make use of the proposed models are described. The results of the simulation studies suggest that, although pedigree models of mtDNA effects can be reliable, success in mapping chromosomal determinants of a trait does not preclude the possibility that mtDNA determinants exist for the trait as well. Shortcomings inherent in the proposed models are described in an effort to expose areas in need of additional research. 58 refs., 5 figs., 2 tabs.

  20. Attitudes Toward Deviant Sex in Ancient Mesopotamia

    Science.gov (United States)

    Bullough, Vern L.

    1971-01-01

    The article concludes that the whole question of sexual life in ancient Mesopotamia is difficult to reconstruct and fraught with many uncertainties. Nevertheless, it seems certain that the ancient Mesopotamians had fewer prohibitions against sex than our own civilization, and regarded as acceptable many practices which later societies condemned.…

  1. On Ancient Babylonian Algebra and Geometry

    Indian Academy of Sciences (India)

    Introduction. In an earlier article [1] we had discussed some aspects of ancient Babylonian mathematics as deciphered froIn various clay tablets excavated from modern Iraq, viz. the Pythagoras theorem and also the sexagesimal num- ber system prevalent during the ancient Mesopotamian civilization. In this article, we study ...

  2. Physicians and surgeons in ancient India.

    Science.gov (United States)

    Ramachandran, C K

    1981-10-01

    This paper briefly recapitulates the evolution of ancient medical classics its origin, the Physicians and Surgeons and their contributions in its mythological and historical background. The significance of this science in the ancient days is also evidenced by the existence, of the two seats of learning-Takshasila and Kasi-in all its prolific profundity.

  3. Phylogenetic estimation of timescales using ancient DNA

    DEFF Research Database (Denmark)

    Molak, Martyna; Lorenzen, Eline; Shapiro, Beth

    2013-01-01

    analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise...

  4. Women--Sex Objects in Ancient Egypt.

    Science.gov (United States)

    Mutimer, Brian T. P.

    Although it has been said that the women in Ancient Egypt enjoyed a reasonable state of social and professional equality with men, this paper presents an alternate theory--that women were second-class citizens whose physical prowess was secondary to their role as sex objects. It appears that men and women in Ancient Egypt often participated in the…

  5. Physiology and proteomics research on the leaves of ancient Platycladus orientalis (L.) during winter.

    Science.gov (United States)

    Zhang, Sheng; Zhang, Lingling; Chai, Yongyu; Wang, Fei; Li, Yiming; Su, Li; Zhao, Zhong

    2015-08-03

    Ancient trees have an important value in humanities and history, and also have an important scientific value in the investigation of the decline and senescence mechanisms. Thus, we conducted an environmental stress study using ancient trees. To evaluate age-dependent changes in physiology and the leaf proteome, we assessed the low-temperature stress responses of 20 ± 5-, 500 ± 100- and 1200 ± 200-year-old Platycladus orientalis (L.) samples obtained outdoors during winter. Several physiological parameters were evaluated. Leaf proteomes were obtained using two-dimensional electrophoresis gels, and 77 protein spots were identified successfully using MALDI TOF/TOF MS/MS. The majority of the identified protein species were classified into functional categories including defense/stress-related, energy and carbohydrate metabolism, photosynthesis, and hormone-related functions. A general reduction in the abundance of protein species was observed as the age of the studied trees increased; reduction in photosynthesis and defense/stress-related categories were particularly apparent in the leaves of ancient trees. However, the number of protein species with functions in energy and carbohydrate metabolism increased with age. An increase in the abundance of lipid metabolism and hormone-related protein species was a primary characteristic of the leaves of ancient trees under low-temperature stress during winter. These results improve our understanding of the biochemical mechanisms of stress responses in ancient trees. Low temperature is the most common meteorological challenge in the study area. For evergreen plants, low-temperature stress has a great impact on the leaves of ancient P. orientalis. Thus, we conducted an environmental stress study using ancient trees. Recently, various studies were carried out in ancient trees. However, no information is available on the molecular mechanisms of defense to low-temperature stress in ancient trees. Therefore, this original study

  6. Mechanisms in ancient Chinese books with illustrations

    CERN Document Server

    Hsiao, Kuo-Hung

    2014-01-01

    This book presents a unique approach for studying mechanisms and machines with drawings that were depicted unclearly in ancient Chinese books. The historical, cultural and technical backgrounds of the mechanisms are explained, and various mechanisms described and illustrated in ancient books are introduced. By utilizing the idea for the conceptual design of modern mechanisms, all feasible designs of ancient mechanisms with uncertain members and joints that meet the technical standards of the subjects’ time periods are synthesized systematically. Ancient Chinese crossbows (the original crossbow and repeating crossbows), textile mechanisms (silk-reeling mechanism, spinning mechanisms, and looms), and many other artisan's tool mechanisms are used as illustrated examples.  Such an approach provides a logical method for the reconstruction designs of ancient mechanisms with uncertain structures. It also provides an innovative direction for researchers to further identify the original structures of mechanisms...

  7. MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation

    Directory of Open Access Journals (Sweden)

    Santa-Rita Pedro

    2005-06-01

    Full Text Available Abstract Background The picture of dog mtDNA diversity, as obtained from geographically wide samplings but from a small number of individuals per region or breed, has revealed weak geographic correlation and high degree of haplotype sharing between very distant breeds. We aimed at a more detailed picture through extensive sampling (n = 143 of four Portuguese autochthonous breeds – Castro Laboreiro Dog, Serra da Estrela Mountain Dog, Portuguese Sheepdog and Azores Cattle Dog-and comparatively reanalysing published worldwide data. Results Fifteen haplotypes belonging to four major haplogroups were found in these breeds, of which five are newly reported. The Castro Laboreiro Dog presented a 95% frequency of a new A haplotype, while all other breeds contained a diverse pool of existing lineages. The Serra da Estrela Mountain Dog, the most heterogeneous of the four Portuguese breeds, shared haplotypes with the other mainland breeds, while Azores Cattle Dog shared no haplotypes with the other Portuguese breeds. A review of mtDNA haplotypes in dogs across the world revealed that: (a breeds tend to display haplotypes belonging to different haplogroups; (b haplogroup A is present in all breeds, and even uncommon haplogroups are highly dispersed among breeds and continental areas; (c haplotype sharing between breeds of the same region is lower than between breeds of different regions and (d genetic distances between breeds do not correlate with geography. Conclusion MtDNA haplotype sharing occurred between Serra da Estrela Mountain dogs (with putative origin in the centre of Portugal and two breeds in the north and south of the country-with the Castro Laboreiro Dog (which behaves, at the mtDNA level, as a sub-sample of the Serra da Estrela Mountain Dog and the southern Portuguese Sheepdog. In contrast, the Azores Cattle Dog did not share any haplotypes with the other Portuguese breeds, but with dogs sampled in Northern Europe. This suggested that the

  8. mtDNA copy number in oocytes of different sizes from individual pre- and post-pubertal pigs

    DEFF Research Database (Denmark)

    Pedersen, Hanne Skovsgaard; Løvendahl, Peter; Larsen, Knud Erik

    2014-01-01

    individual donor was either high (≥100 000) or low (differences between pre- and post-pubertal oocytes. No differences were detected in mtDNA copy number using either of the two primers (Table 1). No linear correlation was detected between oocyte size and mtDNA copy number in pre...... Reproduction 131, 233–245). However, the correlation between size and mtDNA copy number in single oocytes has not been determined. This study describes the relation between oocytes of defined diameters from individual pre- and postpubertal pigs and mtDNA copy number. Cumulus-oocyte complexes were aspirated.......99–1.00) and amplification efficiencies (COX1, 91–104%; ND1, 84–92%). As inter-assay control, standard curves were compared using interaction with dates, showing no differences. mtDNA copy number between groups was compared by ANOVA after log-transformation of data. Relationship between oocyte size and mtDNA copy number...

  9. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues

    Directory of Open Access Journals (Sweden)

    Ding Guohui

    2010-03-01

    Full Text Available Abstract Background Expansion of multi-C2H2 domain zinc finger (ZNF genes, including the Krüppel-associated box (KRAB subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages. Advances in their cataloging and characterization suggest that the functions of the KRAB-ZNF gene family contributed to mammalian speciation. Results Here, we characterized the human 8q24.3 ZNF cluster on the genomic, the phylogenetic, the structural and the transcriptome level. Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517 of the seven locus members contain exons encoding KRAB domains, one (ZNF16 does not. They form a paralog group in which the encoded KRAB and ZNF protein domains generally share more similarities with each other than with other members of the human ZNF superfamily. The closest relatives with respect to their DNA-binding domain were ZNF7 and ZNF251. The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains. These findings underscore structural/functional constraints during evolution. Gene losses in the murine lineage (ZNF16, ZNF34, ZNF252, ZNF517 and potential protein truncations in primates (ZNF252 illustrate ongoing speciation processes. Tissue expression profiling by quantitative real-time PCR showed similar but distinct patterns for all tested ZNF genes with the most prominent expression in fetal brain. Based on accompanying expression signatures in twenty-six other human tissues ZNF34 and ZNF250 revealed the closest expression profiles. Together, the 8q24.3 ZNF genes can be assigned to a cerebellum, a testis or a prostate/thyroid subgroup. These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation. Promoter regions of the seven 8q24.3 ZNF genes display common characteristics like missing TATA-box, CpG island-association and transcription factor binding site (TFBS modules. Common TFBS

  10. [Polymorphism of mitochondrial genome noncoding regions in the three Kazakh populations inhabited different areas of Kazakhstan and in the samples of DNA from ancient people of Kazakhstan Altai].

    Science.gov (United States)

    Aĭtkhozhina, N A; Dzisiuk, N V; Liudvikova, E K

    2004-01-01

    Polymorphism of major noncoding region of mitochondrial DNA (mtDNA D-loop, 528 bp in length) from the three modem kazakh populations and from DNA samples of ancient people inhabited modern Kazakhstani Altai were studied. PCR and RFLP analysis of 13 sites of restriction--BamHI, EcoRV, Sau3AI (1 restriction site), KpnI (2 sites), HaeIII (3 sites), RsaI (5 restriction sites), were carried out. The distribution of each site frequencies was determined. Nucleotide diversity (h) and genetic distance between different kazakh population and other populations of world were estimated. The same RFLP analysis of the mitochondrial DNA control region was carried out for the paleogenomic samples. It was shown that two samples of ancient mitochondrial DNA were monomorphous throughout all analyzed restriction sites.

  11. Oldest epiphyseal osteochondroma in a subadult from Ancient Egypt.

    Science.gov (United States)

    Isidro, Albert; Catalán, Josep Maria; Prat, Carme; Torner, Ferran

    2017-08-01

    Benign bone tumours are pathologies frequently encountered in archaeological human remains, with the most common being osteoma and osteochondroma. We present the case of a juvenile individual recovered from the Necropolis of Sharuna, Middle Egypt and dated to the end of Old Kingdom and First Intermediate Period of Ancient Egypt (circa 2150 BC), showing an osteochondroma arising from the proximal epiphysis of the right tibia which, in all likelihood, affected the patellar tendon in life. Osteochondromas are usually discovered during childhood and adolescence. These lesions are commonly located at the metaphysis and diaphysis of long bones and directed away from the joint, with the epiphysis being a rare location. To our knowledge, there have been no similar cases published to date from ancient times and we conclude that this is the oldest case of epiphyseal osteochondroma reported.

  12. DNA from Pre-Clovis Human Coprolites in Oregon, North America

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Jenkins, Dennis L; Götherstrom, Anders

    2008-01-01

    Caves, south-central Oregon, by 12,300 (14)C yr. B.P., through recovery of human mtDNA from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are >1000 (14)C years earlier than currently...

  13. Antické inšpirácie pre hermeneutiku smrti (Ancient Inspirations for Hermeneutics of Death)

    OpenAIRE

    Anton Vydra

    2006-01-01

    The author in this paper investigates ancient understanding of death. There are three interesting problems in ancient thinking. First one, that Greek word sema means a sign but a tombstone, too. It is related to problem of a human memory (a Greek anamnesis). Second one that death is primarily darkening for ancient people. Thanatos – god of death – appears only as a fragment of goddess Night, his mother. Third one, that a fire (or light) is import for life of human being. But a fire has symbol...

  14. [Ancient Greek in modern language of medicine].

    Science.gov (United States)

    Marković, Vera

    2007-01-01

    In order to standardize language of medicine, it is essential to have a good command of ancient Greek and Latin. We cannot deny a huge impact of ancient Greek medicine on medical terminology. Compounds of Greek origin related to terms for organs, illnesses, inflammations, surgical procedures etc. have been listed as examples. They contain Greek prefixes and suffixes transcribed into Latin and they have been analysed. It may be concluded that the modern language of medicine basically represents the ancient Greek language transcribed into Latin.

  15. Geologically ancient DNA: fact or artefact?

    DEFF Research Database (Denmark)

    Hebsgaard, Martin Bay; Phillips, Matthew J.; Willerslev, Eske

    2005-01-01

    Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup...... and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication...... criteria for work with geologically ancient DNA....

  16. Ancient Greek in modern language of medicine

    Directory of Open Access Journals (Sweden)

    Marković Vera

    2007-01-01

    Full Text Available In order to standardize language of medicine, it is essential to have a good command of ancient Greek and Latin. We cannot deny a huge impact of ancient Greek medicine on medical terminology. Compounds of Greek origin related to terms for organs, illnesses, inflammations, surgical procedures etc. have been listed as examples. They contain Greek prefixes and suffixes transcribed into Latin and they have been analyzed. It may be concluded that the modern language of medicine basically represents the ancient Greek language transcribed into Latin.

  17. Truth Obviousness in Ancient Greek Philosophy

    OpenAIRE

    Halyna I. Budz

    2013-01-01

    The article examines the features of the axiomatic approach to the truth understanding in ancient Greek philosophy. Truth in the works by ancient philosophers has axiomatic essence, basing on divine origin of truth. As the truth has a divine origin, it is in reality. The reality, created by Gods is the solemn reality. Therefore, understanding of reality by man is the display of divine reality, which is true and clever. In of the context of ancient Greek philosophy, to know truth is to know so...

  18. Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

    Directory of Open Access Journals (Sweden)

    Lunt David H

    2008-07-01

    Full Text Available Abstract Background The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic reproduction including (i large "allelic" sequence divergence (ii lack of phylogenetic clustering of "alleles" within morphological species and (iii decay and loss of genes specific to meiosis and sexual reproduction. These genetic signatures can be hard to assess since it is difficult to demonstrate the allelic nature of very divergent sequences, divergence levels may be complicated by processes such as inter-specific hybridization, and genes may have secondary roles unrelated to sexual reproduction. Apomictic species of Meloidogyne root knot nematodes have been suggested previously to be ancient asexuals. Their relatives reproduce by meiotic parthenogenesis or facultative sexuality, which in combination with the abundance of nematode genomic sequence data, makes them a powerful system in which to study the consequences of reproductive mode on genomic divergence. Results Here, sequences from nuclear protein-coding genes are used to demonstrate that the first two predictions of ancient asexuality are found within the apomictic root knot nematodes. Alleles are more divergent in the apomictic taxa than in those species exhibiting recombination and do not group phylogenetically according to recognized species. In contrast some nuclear alleles, and mtDNA, are almost identical across species. Sequencing of Major Sperm Protein, a gamete-specific gene, from both meiotic and ameiotic species reveals no increase in evolutionary rate nor change in substitution pattern in the apomictic taxa, indicating that the locus

  19. Age-associated mitochondrial DNA mutations lead to small but significant changes in cell proliferation and apoptosis in human colonic crypts.

    NARCIS (Netherlands)

    Nooteboom, M.; Johnson, R.; Taylor, R.W.; Wright, N.A.; Lightowlers, R.N.; Kirkwood, T.B.; Mathers, J.C.; Turnbull, D.M.; Greaves, L.C.

    2010-01-01

    Mitochondrial DNA (mtDNA) mutations are a cause of human disease and are proposed to have a role in human aging. Clonally expanded mtDNA point mutations have been detected in replicating tissues and have been shown to cause respiratory chain (RC) defects. The effect of these mutations on other

  20. Materials design principles of ancient fish armour

    Science.gov (United States)

    Bruet, Benjamin J. F.; Song, Juha; Boyce, Mary C.; Ortiz, Christine

    2008-09-01

    Knowledge of the structure-property-function relationships of dermal scales of armoured fish could enable pathways to improved bioinspired human body armour, and may provide clues to the evolutionary origins of mineralized tissues. Here, we present a multiscale experimental and computational approach that reveals the materials design principles present within individual ganoid scales from the `living fossil' Polypterus senegalus. This fish belongs to the ancient family Polypteridae, which first appeared 96 million years ago during the Cretaceous period and still retains many of their characteristics. The mechanistic origins of penetration resistance (approximating a biting attack) were investigated and found to include the juxtaposition of multiple distinct reinforcing composite layers that each undergo their own unique deformation mechanisms, a unique spatial functional form of mechanical properties with regions of differing levels of gradation within and between material layers, and layers with an undetectable gradation, load-dependent effective material properties, circumferential surface cracking, orthogonal microcracking in laminated sublayers and geometrically corrugated junctions between layers.

  1. Clustering of Caucasian Leber hereditary optic neuropathy patients containing the 11778 or 14484 mutations on an mtDNA lineage

    Energy Technology Data Exchange (ETDEWEB)

    Brown, M.D.; Sun, F.; Wallace, D.C. [Emory Univ. School of Medicine, Atlanta, GA (United States)

    1997-02-01

    Leber hereditary optic neuropathy (LHON) is a type of blindness caused by mtDNA mutations. Three LHON mtDNA mutations at nucleotide positions 3460, 11778, and 14484 are specific for LHON and account for 90% of worldwide cases and are thus designated as {open_quotes}primary{close_quotes} LHON mutations. Fifteen other {open_quotes}secondary{close_quotes} LHON mtDNA mutations have been identified, but their pathogenicity is unclear. mtDNA haplotype and phylogenetic analysis of the primary LHON mutations in North American Caucasian patients and controls has shown that, unlike the 3460 and 11778 mutations, which are distributed throughout the European-derived (Caucasian) mtDNA phylogeny, patients containing the 14484 mutation tended to be associated with European mtDNA haplotype J. To investigate this apparent clustering, we performed {chi}{sup 2}-based statistical analyses to compare the distribution of LHON patients on the Caucasian phylogenetic tree. Our results indicate that, unlike the 3460 and 11778 mutations, the 14484 mutation was not distributed on the phylogeny in proportion to the frequencies of the major Caucasian mtDNA haplogroups found in North America. The 14484 mutation was next shown to occur on the haplogroup J background more frequently that expected, consistent with the observation that {approximately}75% of worldwide 14484-positive LHON patients occur in association with haplogroup J. The 11778 mutation also exhibited a moderate clustering on haplogroup J. These observations were supported by statistical analysis using all available mutation frequencies reported in the literature. This paper thus illustrates the potential importance of genetic background in certain mtDNA-based diseases, speculates on a pathogenic role for a subset of LHON secondary mutations and their interaction with primary mutations, and provides support for a polygenic model for LHON expression in some cases. 18 refs., 3 tabs.

  2. Therapeutic Targeting of the Mitochondria Initiates Excessive Superoxide Production and Mitochondrial Depolarization Causing Decreased mtDNA Integrity.

    Science.gov (United States)

    Pokrzywinski, Kaytee L; Biel, Thomas G; Kryndushkin, Dmitry; Rao, V Ashutosh

    2016-01-01

    Mitochondrial dysregulation is closely associated with excessive reactive oxygen species (ROS) production. Altered redox homeostasis has been implicated in the onset of several diseases including cancer. Mitochondrial DNA (mtDNA) and proteins are particularly sensitive to ROS as they are in close proximity to the respiratory chain (RC). Mitoquinone (MitoQ), a mitochondria-targeted redox agent, selectively damages breast cancer cells possibly through damage induced via enhanced ROS production. However, the effects of MitoQ and other triphenylphosphonium (TPP+) conjugated agents on cancer mitochondrial homeostasis remain unknown. The primary objective of this study was to determine the impact of mitochondria-targeted agent [(MTAs) conjugated to TPP+: mitoTEMPOL, mitoquinone and mitochromanol-acetate] on mitochondrial physiology and mtDNA integrity in breast (MDA-MB-231) and lung (H23) cancer cells. The integrity of the mtDNA was assessed by quantifying the degree of mtDNA fragmentation and copy number, as well as by measuring mitochondrial proteins essential to mtDNA stability and maintenance (TFAM, SSBP1, TWINKLE, POLG and POLRMT). Mitochondrial status was evaluated by measuring superoxide production, mitochondrial membrane depolarization, oxygen consumption, extracellular acidification and mRNA or protein levels of the RC complexes along with TCA cycle activity. In this study, we demonstrated that all investigated MTAs impair mitochondrial health and decrease mtDNA integrity in MDA-MB-231 and H23 cells. However, differences in the degree of mitochondrial damage and mtDNA degradation suggest unique properties among each MTA that may be cell line, dose and time dependent. Collectively, our study indicates the potential for TPP+ conjugated molecules to impair breast and lung cancer cells by targeting mitochondrial homeostasis.

  3. Homopolymeric tract heteroplasmy in mtDNA from tissues and single oocytes: Support for a genetic bottleneck

    Energy Technology Data Exchange (ETDEWEB)

    Marchington, D.R.; Hartshorne, G.M.; Barlow, D.; Poulton, J. [Univ. of Oxford (United Kingdom)

    1997-02-01

    While mtDNA polymorphisms at single base positions are common, the overwhelming majority of the mitochondrial genomes within a single individual are usually identical. When there is a point-mutation difference between a mother and her offspring, there may be a complete switching of mtDNA type within a single generation. It is generally assumed that there is a genetic bottleneck whereby a single or small number of founder mtDNA(s) populate the organism, but it is not known at which stages the restriction/amplification of mtDNA subtype(s) occur, and this uncertainty impedes antenatal diagnosis for mtDNA disorders. Length polymorphisms in homopolymeric tracts have been demonstrated in the large noncoding region of mtDNA. We have developed a new method, T-PCR (trimmed PCR), to quantitate heteroplasmy for two of these tracts (D310 and D16189). D310 variation is sufficient to indicate clonal origins of tissues and single oocytes. Tissues from normal individuals often possessed more than one length variant (heteroplasmy). However, there was no difference in the pattern of the length variants between somatic tissues in any control individual when bulk samples were taken. Oocytes from normal women undergoing in vitro fertilization were frequently heteroplasmic for length variants, and in two cases the modal length of the D310 tract differed in individual oocytes from the same woman. These data suggest that a restriction/amplification event, which we attribute to clonal expansion of founder mtDNA(s), has occurred by the time oocytes are mature, although further segregation may occur at a later stage. In contrast to controls, the length distribution of the D310 tract varied between tissues in a patient with heteroplasmic mtDNA rearrangements, suggesting that these mutants influence segregation. These findings have important implications for the genetic counselling of patients with pathogenic mtDNA mutations. 21 refs., 5 figs., 1 tab.

  4. [Medicine in ancient Mesopotamia--part 1].

    Science.gov (United States)

    Martins E Silva, J

    2009-01-01

    The present work summarizes the more elucidating aspects on the foundations and the practice of the medicine in Antique Mesopotamia, since the invention of the writing, more than 5000 thousand years ago, and the beginning of our era. The first part of the article includes a brief perspective about the political and social evolution that characterized those archaic civilizations, as well as the inventions and knowledge further used by the following Humanity's generations. Most of what is known on the subject, as well as the history and political-social events that occurred in the region during that remote epoch, resulted of the laborious decoding of about half a million small clay plates or fragments with text engravings in cuneiform characters that were discovered since the middle of the XIX century in the ruins of the main cities of the Babylonian and Assyrian empires. The second part embraces exclusively the main characteristics of the medicine in Ancient Mesopotamia, in its main facets: concept of disease, healers and practice. The disease was considered a divine punishment or resultant from a malign influence. In that base, the medicine began by being preventive, by the use of appropriate amulets, or by offerings or sacrifices intending to pacify those malign forces. The treatment of the generality of the diseases privileged the expulsion of those spirits and malign influences from the patient body, purifying it, which was done by the specific intervention of an ãshipu (clergyman-exorcist); not having results, the treatment was continued by the asû (practical healer) that appealed to a group of physical manipulations, limited surgical acts and the administration or application of prescriptions, resultants of the mixture of organic and inorganic substances. In case of failing, the patients (as well as individuals or rein leaders) could fall back upon a priest diviner (bârû) who, by examination of the organs of an animal especially sacrificed for the effect

  5. Low-dose rapamycin extends lifespan in a mouse model of mtDNA depletion syndrome.

    Science.gov (United States)

    Siegmund, Stephanie E; Yang, Hua; Sharma, Rohit; Javors, Martin; Skinner, Owen; Mootha, Vamsi; Hirano, Michio; Schon, Eric A

    2017-12-01

    Mitochondrial disorders affecting oxidative phosphorylation (OxPhos) are caused by mutations in both the nuclear and mitochondrial genomes. One promising candidate for treatment is the drug rapamycin, which has been shown to extend lifespan in multiple animal models, and which was previously shown to ameliorate mitochondrial disease in a knock-out mouse model lacking a nuclear-encoded gene specifying an OxPhos structural subunit (Ndufs4). In that model, relatively high-dose intraperitoneal rapamycin extended lifespan and improved markers of neurological disease, via an unknown mechanism. Here, we administered low-dose oral rapamycin to a knock-in (KI) mouse model of authentic mtDNA disease, specifically, progressive mtDNA depletion syndrome, resulting from a mutation in the mitochondrial nucleotide salvage enzyme thymidine kinase 2 (TK2). Importantly, low-dose oral rapamycin was sufficient to extend Tk2KI/KI mouse lifespan significantly, and did so in the absence of detectable improvements in mitochondrial dysfunction. We found no evidence that rapamycin increased survival by acting through canonical pathways, including mitochondrial autophagy. However, transcriptomics and metabolomics analyses uncovered systemic metabolic changes pointing to a potential 'rapamycin metabolic signature.' These changes also implied that rapamycin may have enabled the Tk2KI/KI mice to utilize alternative energy reserves, and possibly triggered indirect signaling events that modified mortality through developmental reprogramming. From a therapeutic standpoint, our results support the possibility that low-dose rapamycin, while not targeting the underlying mtDNA defect, could represent a crucial therapy for the treatment of mtDNA-driven, and some nuclear DNA-driven, mitochondrial diseases. © The Author 2017. Published by Oxford University Press.

  6. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods.

    Science.gov (United States)

    Schuenemann, Verena J; Peltzer, Alexander; Welte, Beatrix; van Pelt, W Paul; Molak, Martyna; Wang, Chuan-Chao; Furtwängler, Anja; Urban, Christian; Reiter, Ella; Nieselt, Kay; Teßmann, Barbara; Francken, Michael; Harvati, Katerina; Haak, Wolfgang; Schiffels, Stephan; Krause, Johannes

    2017-05-30

    Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt's past at a genome-wide level.

  7. Dental indicators of ancient dietary patterns: dental analysis in archaeology.

    Science.gov (United States)

    Forshaw, R

    2014-05-01

    What can the study of ancient teeth tell us about the dietary habits of our ancestors? Diet plays a prominent role in the organisation and evolution of human cultures and an increasingly diverse array of analytical techniques are available to help reconstruct diet in ancient populations. Dental palaeopathology is particularly important as it can provide direct evidence of the type of diet an individual consumed during life. Heavy occlusal tooth wear is the most frequent condition recognisable and an examination of both macro and microscopic patterns of wear can establish the differences between the hard fibrous diet typical of a hunter-gatherer, and a diet primarily consisting of softer plant foods consumed by an agriculturist. The distributions of trace elements and stable isotopes in food webs make it possible to use them as natural tracers of foodstuffs. Through a consideration of photosynthetic pathways, the ratios of the different stable isotopes of carbon and nitrogen can determine which specific groups of plants and animals were dominant in the food chains of various populations - a fact that has been used to trace the spread of agriculture in ancient civilisations.

  8. CPEO and KSS differ in the percentage and location of the mtDNA deletion.

    Science.gov (United States)

    López-Gallardo, Ester; López-Pérez, Manuel J; Montoya, Julio; Ruiz-Pesini, Eduardo

    2009-09-01

    Disorders caused by single mtDNA deletions are quite rare in the general population. To understand the molecular mechanism by which they come about and try to correlate the type of deletion with the phenotype of the patients, a very large cohort of affected individuals needs to be studied. We have performed a meta-analysis of 313 deletions found in CPEO, KSS and PS patients. Our results indicate that the percentage and location of the deletion show differences between these syndromes. Thus, the moment when the deletion is produced probably not only determines the affected tissues and the phenotype, but also the percentage and location of the deletion.

  9. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage.

    Science.gov (United States)

    Sardina, M T; Ballester, M; Marmi, J; Finocchiaro, R; van Kaam, J B C H M; Portolano, B; Folch, J M

    2006-08-01

    The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.

  10. Recognizing characters of ancient manuscripts

    Science.gov (United States)

    Diem, Markus; Sablatnig, Robert

    2010-02-01

    Considering printed Latin text, the main issues of Optical Character Recognition (OCR) systems are solved. However, for degraded handwritten document images, basic preprocessing steps such as binarization, gain poor results with state-of-the-art methods. In this paper ancient Slavonic manuscripts from the 11th century are investigated. In order to minimize the consequences of false character segmentation, a binarization-free approach based on local descriptors is proposed. Additionally local information allows the recognition of partially visible or washed out characters. The proposed algorithm consists of two steps: character classification and character localization. Initially Scale Invariant Feature Transform (SIFT) features are extracted which are subsequently classified using Support Vector Machines (SVM). Afterwards, the interest points are clustered according to their spatial information. Thereby, characters are localized and finally recognized based on a weighted voting scheme of pre-classified local descriptors. Preliminary results show that the proposed system can handle highly degraded manuscript images with background clutter (e.g. stains, tears) and faded out characters.

  11. Ancient and modern environmental DNA.

    Science.gov (United States)

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

    2015-01-19

    DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  12. Tamil Merchant in Ancient Mesopotamia: e109331

    National Research Council Canada - National Science Library

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

    2014-01-01

    .... 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...

  13. AN INTERESTING CASE OF ANCIENT SCHWANNOMA

    Directory of Open Access Journals (Sweden)

    Binu

    2015-01-01

    Full Text Available INTRODUCTION : Schwannoma is a common benign tumour of nerve sheath. Degenerating type of schwannoma is called ancient schwannoma. Ancient schwannomas of scalp are rare and are often misdiagnosed as sebaceous cyst or dermoid cyst. CASE REPORT : We present a thirty two year old male presented with scalp swel ling of eight years duration. X - ray showed no intracranial extension. He underwent excision of the tumour and histopathology was reported as ancient schwannoma. DISCUSSION : Histopathologically , ancient schwannomas charecterised by cellular Antoni type A ar eas and less cellular Antoni type - B areas. 9 th , 7 th , 11 th , 5 th and 4 th cranial nerves are often affected and may be associated with multiple neuro fibramatosis (Von - Recklinghausen’s disease. Impact : Case is presented for its rarity and possible pre - operative misdiagnosis

  14. VRIKSHAYURVEDA (Arboreal Medicine in Ancient India).

    Science.gov (United States)

    Ramachanran, C K

    1984-10-01

    This paper discusses the special branch of the Ancient Indian science on plant life as depicted by Vrikshayurveda, and the obvious relevance of the insights these provide to enrich our knowledge and practice in this field.

  15. NIMI TANTRA (Opthalmology of Ancient India).

    Science.gov (United States)

    Ramachandran, C K

    1984-04-01

    The art of opthalmology was well developed in ancient India and was known as Nimi Tantra. In this paper the author presents the main features of Nimi Tantra an authoritative treatises written by Nimi, a prominent opthalmologist of his time.

  16. Psychiatric nosology and taxonomy in ancient India.

    Science.gov (United States)

    Haldipur, C V

    1989-08-01

    This article considers the nosology and taxonomy of psychiatric disorders in Sushruta Samhita, an ancient Indian treatise on medicine. Some implications of this treatise for modern psychiatry are discussed.

  17. How Ancient Europeans Saw the World?

    Directory of Open Access Journals (Sweden)

    Aleksandar Bandović

    2016-02-01

    Full Text Available Review of the book: Peter Wells. How Ancient Europeans Saw the World: Vision, Patterns, and the Shaping of the Mind in Prehistoric Times. 2012. Princeton University Press. 285 pp.

  18. Dental health and disease in ancient Egypt.

    Science.gov (United States)

    Forshaw, R J

    2009-04-25

    In ancient Egypt the exceptionally dry climate together with the unique burial customs has resulted in the survival of large numbers of well-preserved skeletal and mummified remains. Examinations of these remains together with an analysis of the surviving documentary, archaeological and ethnographic evidence has enabled a detailed picture of the dental health of these ancient people to be revealed, perhaps more so than for any other civilisation in antiquity. In this, the first of two articles, the dental pathological conditions that afflicted the ancient Egyptians is considered. The commonest finding is that of tooth wear, which was often so excessive that it resulted in pulpal exposure. Multiple abscesses were frequently seen, but caries was not a significant problem. Overall the findings indicate that the various pathological conditions and non-pathological abnormalities of teeth evident in dentitions in the twenty-first century were also manifest in ancient Egypt, although the incidences of these conditions varies considerably between the civilisations.

  19. Vascular medicine and surgery in ancient Egypt.

    Science.gov (United States)

    Barr, Justin

    2014-07-01

    Lauded alike by ancient civilizations and modern society, pharaonic Egyptian medicine remains an object of fascination today. This article discusses its surprisingly sophisticated understanding of a cardiovascular system. The term "cardiovascular system," however, carries assumptions and meanings to a modern audience, especially readers of this journal, which simply do not apply when considering ancient conceptions of the heart and vessels. For lack of better language, this article will use "cardiovascular" and similar terms while recognizing the anachronistic inaccuracy. After briefly summarizing ancient Egyptian medicine generally, it will review the anatomy, pathology, and treatment of the vasculature. The practice of mummification in ancient Egypt provides a unique opportunity for paleopathology, and the conclusion will explore evidence of arterial disease from a modern scientific perspective. Copyright © 2014 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

  20. Earthquake Archaeology: a case study from Ancient Cnidus

    Science.gov (United States)

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

    2003-04-01

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

  1. Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures.

    Directory of Open Access Journals (Sweden)

    Raul J Cano

    Full Text Available Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.

  2. Nutritional characteristics of ancient Tuscan varieties of Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Lisetta Ghiselli

    2016-08-01

    Full Text Available Bread wheat (Triticum aestivum L. is an important cereal in human consumption. In recent years, there has been a growing interest in ancient wheat varieties. The latter represent an important source of germplasm, characterised by a broader genetic base and, therefore, a potential source of biodiversity. The objective of the study was to ascertain the optimal balance between the presence of secondary metabolites having beneficial effects on health and technological features that ensure successful baking quality. The experimental trial was performed in 2011-2012 on three organic farms located in three different areas within the province of Siena (Tuscany. In each location, an overall evaluation of the commercial, rheological and functional properties of five ancient Tuscan bread wheat varieties (Andriolo, Frassineto, Gentil rosso, Inallettabile 96, Verna as compared with a commercial modern variety (Palesio was carried out. The ancient varieties were compared both singularly (pure and in combination (mixtures of two varieties in equal proportion, respectively. Biometric and productive parameters were detected for each plot (32 plots in each farm. Macro- and trace elements, polyphenols, flavonoids and antioxidant activity (antiradical power, ARP were similarly determined on representative whole grain samples. Rheological analysis was carried out on flour samples. The multivariate statistical analysis using principal components analysis was performed on all variables analysed. The results showed a significant environment effect on the different parameters measured and did not reveal significant improvements in the variables measured when varieties were cultivated in mixtures. However, the study did reveal various interesting trends that are warranting of further investigation. The most interesting effect from a nutritional and functional point of view is the relationship between ARP, rheological properties, protein content and gluten content. These

  3. Science and Library in the Ancient Age

    Directory of Open Access Journals (Sweden)

    Hasan Sacit Keseroğlu

    2016-09-01

    Full Text Available Science assumes its contemporary identity as a result of the stages of magic, religion and reason. The religious stage starts with the invention of writing and this stage leaves its place to reason with Thales in Ancient Greece. Knowledge eludes from religious beliefs. Ways to reach accurate, reliable and realistic knowledge are sought, along with the answer for what knowledge is. Therefore, beginning of the science is taken into consideration together with science and philosophy. The purpose of this study is to approach knowledge and science of the ancient age in Mesopotamia, Egypt and Ancient Greece in general terms and to determine the relationship between the knowledge produced in those places and libraries established. The hypothesis has been determined as “Egypt and Mesopotamia at the starting point of the history of science and science, and libraries in Ancient Greece have developed parallelly to each other.” The scope of the study has been limited to Mesopotamia, Egypt and Ancient Greece; and Ancient Greece has been explained, with descriptive method, in the frame of the topics of Ionia, Athens, Hellenistic Period and Rome. Many archives and libraries have been established in the ancient age. The difference between an archive and a library has been mentioned first, and then, various libraries have been introduced such as Nineveh in Mesopotamia, Alexandria in Ancient Greece and many others in Egypt. It has been clearly distinguished that there had been a very tight relationship between knowledge production and library, especially with the Library of Alexandria.

  4. Lead in ancient Rome's city waters

    OpenAIRE

    Delile, Hugo; Blichert-Toft, Janne; Goiran, Jean-Philippe; Keay, Simon; Albarède, Francis

    2014-01-01

    International audience; It is now universally accepted that utilization of lead for domestic purposes and water distribution presents a major health hazard. The ancient Roman world was unaware of these risks. How far the gigantic network of lead pipes used in ancient Rome compromised public health in the city is unknown. Lead isotopes in sediments from the harbor of Imperial Rome register the presence of a strong anthropogenic component during the beginning of the Common Era and the Early Mid...

  5. Maternal history of oceania from complete mtDNA genomes: Contrasting ancient diversity with recent homogenization due to the Austronesian expansion

    NARCIS (Netherlands)

    C. Duggan; B. Evans (Bethwyn); F.R. Friedlaender (Françoise); J.S. Friedlaender (Jonathan); G. Koki (George); D.A. Merriwether (D. Andrew); M.H. Kayser (Manfred); M. Stoneking (Mark)

    2014-01-01

    textabstractArchaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago,

  6. 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.

  7. 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).

  8. Transnasal excerebration surgery in ancient Egypt.

    Science.gov (United States)

    Fanous, Andrew A; Couldwell, William T

    2012-04-01

    Ancient Egyptians were pioneers in many fields, including medicine and surgery. Our modern knowledge of anatomy, pathology, and surgical techniques stems from discoveries and observations made by Egyptian physicians and embalmers. In the realm of neurosurgery, ancient Egyptians were the first to elucidate cerebral and cranial anatomy, the first to describe evidence for the role of the spinal cord in the transmission of information from the brain to the extremities, and the first to invent surgical techniques such as trepanning and stitching. In addition, the transnasal approach to skull base and intracranial structures was first devised by Egyptian embalmers to excerebrate the cranial vault during mummification. In this historical vignette, the authors examine paleoradiological and other evidence from ancient Egyptian skulls and mummies of all periods, from the Old Kingdom to Greco-Roman Egypt, to shed light on the development of transnasal surgery in this ancient civilization. The authors confirm earlier observations concerning the laterality of this technique, suggesting that ancient Egyptian excerebration techniques penetrated the skull base mostly on the left side. They also suggest that the original technique used to access the skull base in ancient Egypt was a transethmoidal one, which later evolved to follow a transsphenoidal route similar to the one used today to gain access to pituitary lesions.

  9. Ancient Irrigation Canals Mapped from Corona Imageries and Their Implications in Juyan Oasis along the Silk Road

    Directory of Open Access Journals (Sweden)

    Ningke Hu

    2017-07-01

    Full Text Available Historical records and archaeological discoveries have shown that prosperous agricultural activities developed in the ancient Juyan Oasis of northwestern China, an important oasis that once flourished on the ancient Silk Road. However, how the irrigation canals were distributed in historical time was unknown. Here, we identified and mapped the spatial distribution of ancient abandoned irrigation canals that were built using CORONA photographs and field inspections. This work found that ancient irrigation canals are large-scale and distributed throughout the desertified environment, with three hierarchical organization of first-, second-, and third-order irrigation canals (the total length of the first- and second-order-irrigation canals is dramatically more than 392 km. This study further indicates that ancient irrigation methods and modern irrigation systems in arid regions of China share the same basic irrigation design. New visual and fine-scale evidence and spatial distribution of irrigation canals are provided to illustrate the development of the ancient irrigated agriculture that occurred in the Juyan Oasis. This work is useful for readers who are interested in the construction and organization approaches of irrigation canals used in ancient irrigated agriculture in arid regions. It also has implications for how ancient people balance the relationships between human needs and the eco-environment using reasonable water management methods, especially for decision-making in the efficient usage of limited water resources in the arid inland river basin.

  10. [Light and blindness in ancient Egypt].

    Science.gov (United States)

    Maria Rosso, Ana

    2010-01-01

    In Ancient Egypt, light and fire, which were closely related to the Sun God Ra, were the sources of life and well-being, while the dark meant danger and death. Similar to death, darkness drops on human beings in deep sleep and they enter a space inhabited by shadows. Dreams were believed to reveal an unknown world, to give the sleeper a glimpse into the future. Vision attracts distant objects and their light, on the other hand, can hurt the eyes like a burning flame. Eyes were the most important organ in Egyptian thought, as they allowed perception of the real world. Their importance has been immortalised in the myth of the Eye of Horus that explains the role of either eye. One represents the moonlight, which disperses the darkness of the night, and the other represents the sunshine, which creates life, and both could also represents the power of human intellect. Blindness, in turn, congenital or disease-related, was considered a divine punishment. A man, thus handicapped, would sink in a state of uncertainty and darkness. To protect the eyes from blindness, people used drops and ointments, which were believed to chase away all kinds of insects and demons that threatened with a variety of eye infections. Egyptian eye doctors or physicians, carried a special kit that contained green chrysocolla and a black kohl makeup, highly appreciated as prophylaxis because they personified Osiris' humours or body fluids. These products were offered to Gods to restore the brightness of divine glance and incite sun and moon to spread their beneficial light.

  11. mtDNA analysis of human remains from an early Danish Christian cemetery

    DEFF Research Database (Denmark)

    Rudbeck, Lars; Gilbert, M Thomas P; Willerslev, Eske

    2005-01-01

    One of Denmark's earliest Christian cemeteries is Kongemarken, dating to around AD 1000-1250. A feature of early Scandinavian Christian cemeteries is sex segregation, with females buried on the northern sides and males on the southern sides. However, such separation was never complete; in the few...... early Christian cemeteries excavated in Scandinavia, there were always a few males placed on the north side, and some females on the south side. At Kongemarken, several males with juxtaposed females were found on the north side of the cemetery. Thus, to evaluate possible kinship relationships, and more...

  12. The GHEP-EMPOP collaboration on mtDNA population data--A new resource for forensic casework.

    Science.gov (United States)

    Prieto, L; Zimmermann, B; Goios, A; Rodriguez-Monge, A; Paneto, G G; Alves, C; Alonso, A; Fridman, C; Cardoso, S; Lima, G; Anjos, M J; Whittle, M R; Montesino, M; Cicarelli, R M B; Rocha, A M; Albarrán, C; de Pancorbo, M M; Pinheiro, M F; Carvalho, M; Sumita, D R; Parson, W

    2011-03-01

    Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP-EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  13. The GHEP–EMPOP collaboration on mtDNA population data—A new resource for forensic casework

    Science.gov (United States)

    Prieto, L.; Zimmermann, B.; Goios, A.; Rodriguez-Monge, A.; Paneto, G.G.; Alves, C.; Alonso, A.; Fridman, C.; Cardoso, S.; Lima, G.; Anjos, M.J.; Whittle, M.R.; Montesino, M.; Cicarelli, R.M.B.; Rocha, A.M.; Albarrán, C.; de Pancorbo, M.M.; Pinheiro, M.F.; Carvalho, M.; Sumita, D.R.; Parson, W.

    2011-01-01

    Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP–EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). PMID:21075696

  14. Dysphagia is prevalent in patients with CPEO and single, large-scale deletions in mtDNA.

    Science.gov (United States)

    Hedermann, Gitte; Løkken, Nicoline; Dahlqvist, Julia R; Vissing, John

    2017-01-01

    The aim of this study was to assess the frequency of subjective and objective dysphagia in patients with chronic progressive external ophthalmoplegia (CPEO) due to single, large-scale deletions (LSDs) of mitochondrial DNA (mtDNA). Sixteen patients with CPEO and single LSDs of mtDNA were included in the study and compared to a control group of 12 patients with the m.3243A>G mtDNA mutation. Patients had to drink 80ml of water at 4°C as fast as they could (cold-water test) and fill out a standardized questionnaire about dysphagia. Eight patients (50%) with CPEO and single LSDs of mtDNA had a prolonged cold-water test, including one with a PEG-tube, who was unable to perform the test, and nine patients reported subjective swallowing problems (56.3%). All mitochondrial myopathy patients in the control group had a normal duration of the cold-water test. The study shows that dysphagia is a common problem in patients with CPEO and LSDs of mtDNA. Dysphagia seems to be progressive with age as abnormal swallowing occurred preferentially in persons ≥45years. The study shows that increased awareness of this symptom should be given to address appropriate treatment interventions and avoid complications such as social isolation, malnutrition and aspiration pneumonia. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  15. Identification of West Eurasian mitochondrial haplogroups by mtDNA SNP screening: results of the 2006-2007 EDNAP collaborative exercise

    DEFF Research Database (Denmark)

    Parson, Walther; Fendt, Liane; Ballard, David

    2008-01-01

    no previous experience with the technology and/or mtDNA analysis. The results of this collaborative exercise stimulate the expansion of screening methods in forensic laboratories to increase efficiency and performance of mtDNA typing, and thus demonstrates that mtDNA SNP typing is a powerful tool for forensic......The European DNA Profiling (EDNAP) Group performed a collaborative exercise on a mitochondrial (mt) DNA screening assay that targeted 16 nucleotide positions in the coding region and allowed for the discrimination of major west Eurasian mtDNA haplogroups. The purpose of the exercise was to evaluate...

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

    Science.gov (United States)

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

    2015-09-01

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

  17. Intracellular evolution of mitochondrial DNA (mtDNA) and the tragedy of the cytoplasmic commons.

    Science.gov (United States)

    Haig, David

    2016-06-01

    Mitochondria exist in large numbers per cell. Therefore, the strength of natural selection on individual mtDNAs for their contribution to cellular fitness is weak whereas the strength of selection in favor of mtDNAs that increase their own replication without regard for cellular functions is strong. This problem has been solved for most mitochondrial genes by their transfer to the nucleus but a few critical genes remain encoded by mtDNA. Organisms manage the evolution of mtDNA to prevent mutational decay of essential services mitochondria provide to their hosts. Bottlenecks of mitochondrial numbers in female germlines increase the homogeneity of mtDNAs within cells and allow intraorganismal selection to eliminate cells with low quality mitochondria. Mechanisms of intracellular "quality control" allow direct selection on the competence of individual mtDNAs. These processes maintain the integrity of mtDNAs within the germline but are inadequate to indefinitely maintain mitochondrial function in somatic cells. © 2016 WILEY Periodicals, Inc.

  18. MtDNA barcode identification of fish larvae in the southern Great Barrier Reef – Australia

    Directory of Open Access Journals (Sweden)

    Graham G. Pegg

    2006-10-01

    Full Text Available Planktonic larvae were captured above a shallow coral reef study site on the Great Barrier Reef (GBR around spring-summer new moon periods (October-February using light trap or net capture devices. Larvae were identified to the genus or species level by comparison with a phylogenetic tree of tropical marine fish species using mtDNA HVR1 sequence data. Further analysis showed that within-species HVR1 sequence variation was typically 1-3%, whereas between-species variation for the same genus ranged up to 50%, supporting the suitability of HVR1 for species identification. Given the current worldwide interest in DNA barcoding and species identification using an alternative mtDNA gene marker (cox1, we also explored the efficacy of different primer sets for amplification of cox1 in reef fish, and its suitability for species identification. Of those tested, the Fish-F1 and -R1 primer set recently reported by Ward et al. (2005 gave the best results.

  19. DNA barcode through cytochrome b gene information of mtDNA in native chicken strains.

    Science.gov (United States)

    Yacoub, Haitham Ahmed; Fathi, Moataz M; Mahmoud, Wael M

    2013-10-01

    This study was carried out to figure out the potentiality of a cytochrome b gene as a barcoding tool in discriminating native chicken strains and other Gallus gallus species. We performed PCR amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The results revealed that all Saudi chicken strains were identical to each other but when compared with other species of Gallus the differences were exciting. The phylogenetic tree revealed that there were seven clusters represented for native strains and were clustered together especially in black strain and dark brown ones. The results have confirmed that using cytochrome b gene to discriminate between Saudi chicken strains and other species of G. gallus fowl was a very sufficient tool. Moreover, we can consider short fragment of cytochrome b gene of mtDNA as a universal DNA barcode region. It was a much more accurate and efficient tool to discriminate interspecies than intraspecies. We think it needs more studies to confirm this concept, and we have to apply that tool for many species of vertebrate and invertebrate as well.

  20. Cryptic diversity in the mtDNA of the ornamental fish Carnegiella strigata.

    Science.gov (United States)

    Schneider, C H; Gross, M C; Terencio, M L; Porto, J I R

    2012-09-01

    Mitochondrial DNA ( mtDNA) sequences of the marbled hatchetfish Carnegiella strigata, an ornamental fish exported from the Negro River, was examined to determine its genetic diversity and population structure in blackwater rivers (Negro and Uatumã Rivers) in the central Amazon. Analyses of a 646 bp fragment of the ATPase 6/8 mtDNA gene revealed two monophyletic lineages of C. strigata with considerable genetic distance between them (10-12%), suggesting that these lineages should not be considered a single stock. Furthermore, there were strong differences in the geographical distribution of the lineages. These results indicate a past association between drainages of the Negro and Uatumã Rivers. They also suggest that, in the Negro River, its main tributary, the Branco River, may act as a geographical barrier and potentially an ecological barrier between populations of the middle and lower portions of the river. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  1. Differences in mtDNA haplogroup distribution among 3 Jewish populations alter susceptibility to T2DM complications

    Directory of Open Access Journals (Sweden)

    Dadon Sarah

    2008-04-01

    Full Text Available Abstract Background Recent genome-wide association studies searching for candidate susceptibility loci for common complex diseases such as type 2 diabetes mellitus (T2DM and its common complications have uncovered novel disease-associated genes. Nevertheless these large-scale population screens often overlook the tremendous variation in the mitochondrial genome (mtDNA and its involvement in complex disorders. Results We have analyzed the mitochondrial DNA (mtDNA genetic variability in Ashkenazi (Ash, Sephardic (Seph and North African (NAF Jewish populations (total n = 1179. Our analysis showed significant differences (p Conclusion Our findings support the possibility that recent bottleneck events leading to over-representation of minor mtDNA alleles in specific genetic isolates, could result in population-specific susceptibility loci to complex disorders.

  2. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

    DEFF Research Database (Denmark)

    Takahashi, Hiroshi; Møller, Peter Rask; Shedko, Sergei V.

    2016-01-01

    in Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type....... kaibarae, and P. bussei). The brackish-water, freshwater, and Omono types previously discovered in Japan were reidentified as P. pungitius, P. sinensis, and P. kaibarae, respectively. A marked incongruence was noted between the phylogenies of AFLP and mtDNA markers, suggesting the occasional occurrence...... of hybridization and mtDNA introgression among distinct species. Our results highlight that the marginal seas of Northeast Asia played a key role as barriers to or facilitators of gene flow in the evolution of species diversity of Pungitius concentrated in this region...

  3. New interpretation of the ancient constellations

    Science.gov (United States)

    Dementev, M. S.

    New method of study of the ancient constellations and mythes is discussed. It is based on the comparison of two maps - the sky and the Earth. The Stellar map is built in an equatorial system of coordinates, the geografic map - in the Mercator's projection and of the same scale. The former map is put on the laster one. The constellation of Pleiades (seven daughter of Atlant) is placed on the meridian of Atlant (Western coast of Africa). If the Stellar map is constructed for a epoch J-3000 (3000 years up to B.C.) then we could found the following. The constellations Andromeda (the daughter of the Ethiopian tsar), Cetus, Perseus and Cassiopeia (mother of Andromeda) are projected on the centre, south and west of Ancient Ethiopia and Mediterranean Sea, respectively. That is all the constellations fall to the places, where events described in mythes occured. A constellation Cepheus (Arabian name is "Burning") covers the Caucasus. Possibly, before a epoch J-1000 this group of stars was connected with Prometheus. It is known Prometheus was chained to the Caucasian rock because of stealing of a fire. Ancient Chineses divided the sky in other way. They called "The Heavenly Town" the area of sky consisting of stars in Herculis, Aquilae and Ophiuchi. Parts of the mentioned constellation were called as a provinces in Ancient China. If the Heavenly Town locate near the Ancient China then the Greek constellations (Andromeda, Perseus and Cetus) will appear over Africa. Three important conclusions follow from this: (i) the geography of the Earth is reflected on the sky; (ii) the ancient astronomers were investigating a connection between the sky and Earth; (iii) the ancient peoples exchanged by the information about a construction of the world.

  4. Ancient Greek with Thrasymachus: A Web Site for Learning Ancient Greek.

    Science.gov (United States)

    Barker, Alison

    2001-01-01

    Discusses a project that was begun as an attempt by two teachers of Ancient Greek to provide supplementary materials to accompany "Thrasymachus," a first-year textbook for learning ancient Greek. Provides a brief history and description of the project, the format of each chapter, a chronology for completion of materials for each chapter in the…

  5. Extensive Variation and Sub-Structuring in Lineage A mtDNA in Indian Sheep: Genetic Evidence for Domestication of Sheep in India

    Science.gov (United States)

    Singh, Sachin; Kumar Jr, Satish; Kolte, Atul P.; Kumar, Satish

    2013-01-01

    Previous studies on mitochondrial DNA analysis of sheep from different regions of the world have revealed the presence of two major- A and B, and three minor- C, D and E maternal lineages. Lineage A is more frequent in Asia and lineage B is more abundant in regions other than Asia. We have analyzed mitochondrial DNA sequences of 330 sheep from 12 different breeds of India. Neighbor-joining analysis revealed lineage A, B and C in Indian sheep. Surprisingly, multidimensional scaling plot based on FST values of control region of mtDNA sequences showed significant breed differentiation in contrast to poor geographical structuring reported earlier in this species. The breed differentiation in Indian sheep was essentially due to variable contribution of two major lineages to different breeds, and sub- structuring of lineage A, possibly the latter resulting from genetic drift. Nucleotide diversity of this lineage was higher in Indian sheep (0.014 ± 0.007) as compared to that of sheep from other regions of the world (0.009 ± 0.005 to 0.01 ± 0.005). Reduced median network analysis of control region and cytochrome b gene sequences of Indian sheep when analyzed along with available published sequences of sheep from other regions of the world showed that several haplotypes of lineage A were exclusive to Indian sheep. Given the high nucleotide diversity in Indian sheep and the poor sharing of lineage A haplotypes between Indian and non-Indian sheep, we propose that lineage A sheep has also been domesticated in the east of Near East, possibly in Indian sub-continent. Finally, our data provide support that lineage B and additional lineage A haplotypes of sheep might have been introduced to Indian sub-continent from Near East, probably by ancient sea trade route. PMID:24244282

  6. Human evolution

    DEFF Research Database (Denmark)

    Llamas, Bastien; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre

    2017-01-01

    The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins......, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become...

  7. MtDNA haplogroup analysis of black Brazilian and sub-Saharan populations: implications for the Atlantic slave trade.

    Science.gov (United States)

    Silva, Wilson Araújo; Bortolini, Maria Cátira; Schneider, Maria Paula Cruz; Marrero, Andrea; Elion, Jacques; Krishnamoorthy, Rajagopal; Zago, Marco Antonio

    2006-02-01

    Seventy individuals from two African and four black Brazilian populations were studied for the first hypervariable segment of mtDNA. To delineate a more complete phylogeographic scenario of the African mtDNA haplogroups in Brazil and to provide additional information on the nature of the Atlantic slave trade, we analyzed our data together with previously published data. The results indicate different sources of African slaves for the four major Brazilian regions. In addition, the data revealed patterns that differ from those expected on the basis of historical registers, thus suggesting the role of ethnic sex differences in the slave trade.

  8. Post-bottleneck mtDNA diversity in a free-living population of European bison: implications for conservation

    DEFF Research Database (Denmark)

    Wojcik, J. M.; Kawalko, A.; Tokarska, M.

    2009-01-01

    genetic diversity. We studied a total of 195 individuals (127 males and 68 females). A 1429 bp fragment of mitochondrial DNA (mtDNA) including the D-loop region was analyzed in 87 individuals and revealed only three distinct haplotypes. Nucleotide (pi) and haplotype (H-d) diversity values were estimated...... for the European bison and were compared with pi and H-d estimated from three individuals of American bison Bison bison. Very low diversity values were found in the European bison in comparison with the diversity values found in the American bison. The low mtDNA variability in the European bison is in concordance...

  9. Genetic differentiation in the striped dolphin Stenella coeruleoalba from European waters according to mitochondrial DNA (mtDNA) restriction analysis.

    Science.gov (United States)

    García-Martínez, J; Moya, A; Raga, J A; Latorre, A

    1999-06-01

    We used mitochondrial DNA (mtDNA) restriction analysis to study genetic variation in 98 striped dolphins (Stenella coeruleoalba) stranded on coasts from different European countries and from animals caught by fisheries. A total of 63 different restriction sites was mapped after digestion of mtDNA with 15 restriction endonucleases that yielded a total of 27 haplotypes. No haplotype was shared between Mediterranean and Atlantic areas. All the analyses indicate the existence of two different populations with a very limited gene flow across the Strait of Gibraltar.

  10. Mental health and sexual activity according to ancient Greek physicians.

    Science.gov (United States)

    Laios, K; Tsoucalas, G; Kontaxaki, Μ-Ι; Karamanou, Μ; Sgantzos, Μ; Androutsos, G

    2015-01-01

    The ancient Greek physicians have not failed in their studies to indicate the beneficial role of sexual activity in human health. They acknowledged that sex helps to maintain mental balance. Very interesting is their observation that sex may help mental patients to recover. Nevertheless they stressed emphatically that sex is beneficial only when there is a measure in it, so they believed that sexual abstinence or excessive sexual activity affect negatively the mental and physical health of man. Ancient Greek physicians reached this conclusion by empirical observation. They tried to justify the mental imbalance, as the potential physical problems, which probably will be listed today in the psychosomatic manifestations, of people with long-term sexual abstinence or hyperactivity, based on the theory of humors which was the main methodological tool of ancient Greek medicine. Their fundamental idea was that the four humors of the body (blood, phlegm, yellow and black bile) should be in balance. Therefore they believed that the loss and the exchange of bodily fluids during sex help body's humors to maintain their equilibrium which in turn will form the basis for the physical and mental health. Although in ancient medical texts the irrationality presented by people in the aforementioned conditions was not attributed in any of the major mental illnesses recognized in antiquity, as mania, melancholy and phrenitis, our belief is that their behavior is more suited to the characteristics of melancholy, while according to modern medicine it should be classified in the depressive disorders. We have come to this conclusion, because common characteristics of people who either did not have sexual life or was overactive, was sadness, lack of interest and hope, as well as paranoid thinking that can reach up to suicide. Regarding the psychosomatic problems, which could occur in these people, they were determined by the ancient Greek physicians in the following; continuous headaches

  11. Diagnosis and management of retroperitoneal ancient schwannomas

    Directory of Open Access Journals (Sweden)

    Gusani Niraj J

    2009-02-01

    Full Text Available Abstract Background Ancient schwannomas are degenerate peripheral nerve sheath tumors that very rarely occur in the retroperitoneum. They generally reach large proportions before producing symptoms due to mass effect. We describe three cases of retroperitoneal ancient schwannomas and discuss the diagnosis and management of these tumors. Case presentations Three female patients with retroperitoneal ancient schwannomas were reviewed. One patient presented with several weeks of upper abdominal pain and lower chest discomfort, whereas back pain and leg pain with associated weakness were predominant symptoms in the remaining two. Abdominal imaging findings demonstrated heterogeneous masses in the retroperitoneum with demarcated margins, concerning for malignancy. The patients successfully had radical excision of their tumors. Histological examination showed encapsulated tumors that displayed alternating areas of dense cellularity and areas of myxoid matrix consistent with a diagnosis of ancient schwannoma. Conclusion A diagnosis of ancient schwannoma should be entertained for any heterogeneous, well encapsulated mass in the retroperitoneum. In these cases less radical surgical resection should be considered as malignant transformation of these tumors is extremely rare and recurrence is uncommon following excision.

  12. Antické inšpirácie pre hermeneutiku smrti (Ancient Inspirations for Hermeneutics of Death

    Directory of Open Access Journals (Sweden)

    Anton Vydra

    2006-03-01

    Full Text Available The author in this paper investigates ancient understanding of death. There are three interesting problems in ancient thinking. First one, that Greek word sema means a sign but a tombstone, too. It is related to problem of a human memory (a Greek anamnesis. Second one that death is primarily darkening for ancient people. Thanatos – god of death – appears only as a fragment of goddess Night, his mother. Third one, that a fire (or light is import for life of human being. But a fire has symbolical function and it is related to an eternity. There is a light nearby intelligence in ancient world. Desire of philosophers to immortality refers to desire to an eternal intellectual thinking.

  13. Twins in Ancient Greece: a synopsis.

    Science.gov (United States)

    Malamitsi-Puchner, Ariadne

    2016-01-01

    This brief outline associates twins with several aspects of life in Ancient Greece. In Greek mythology twins caused ambivalent reactions and were believed to have ambivalent feelings for each other. Very often, they were viewed as the representatives of the dualistic nature of the universe. Heteropaternal superfecundation, which dominates in ancient myths, explains on one hand, the god-like qualities and, on the other hand, the mortal nature of many twins. An assumption is presented that legends referring to twins might reflect the territorial expansions of Ancient Greeks in Northern Mediterranean, around the Black Sea, in Asia Minor, as well as North East Africa. In conclusion, in Greek antiquity, twins have been used as transitional figures between myth and reality.

  14. Dacic Ancient Astronomical Research in Sarmizegetuza

    Directory of Open Access Journals (Sweden)

    Emanuel George Oprea

    2015-11-01

    Full Text Available The actual Romanian territory belongs to Carpatho-Danubian Space and to Ancient Europe. The Ancient European Society was a vast cultural entity based on a theocratic, matriarchal society, peaceful and art creating.Temples of Sarmizegetusa have given rise to several theories over time, proven by historians with the most diverse arguments. The largest complex of temples and sanctuaries was founded in Sarmizegetusa Regia, the Dacian’s main fortress and ancient capital of Dacia in the time of King Decebalus. The mysterious form of settlements has led researchers to the conclusion that the locations were astronomical observation shrines. Among the places of Dacian worship in Orastie Mountains the most impressive is the Great Circular Sanctuary, used to perform some celestial observations, and also as original solar calendar. This paper had the purpose to re-discover the Dacian Civilization and Dacian cosmogony based on the accumulated knowledge upon our country’s past.

  15. Prehistoric polymers: rubber processing in ancient mesoamerica

    Science.gov (United States)

    Hosler; Burkett; Tarkanian

    1999-06-18

    Ancient Mesoamerican peoples harvested latex from Castilla elastica, processed it using liquid extracted from Ipomoea alba (a species of morning glory vine), and fashioned rubber balls, hollow rubber figurines, and other rubber artifacts from the resulting material. Chemical and mechanical analyses of the latex and of the processed rubber indicate that the enhanced elastic behavior of the rubber relative to the unprocessed latex is due to purification of the polymer component and to an increase in the strength and number of interchain interactions that are induced by organic compounds present in I. alba. These ancient peoples' control over the properties of latex and processed rubber gave rise to the Mesoamerican ball game, a central ritual element in all ancient Mesoamerican societies.

  16. The practice of dentistry in ancient Egypt.

    Science.gov (United States)

    Forshaw, R J

    2009-05-09

    This paper addresses the questions of whether a dental profession existed in ancient Egypt and if it did then considers whether these practitioners were operative dental surgeons as we know them today or whether they were pharmacists. Evidence from hieroglyphic inscriptions, from the dentitions of the surviving mummified and skeletal remains, and from ancient documents and artefacts are examined. The conclusion would suggest that operative dental treatment if it did exist at all was extremely limited. The dental treatment that appears to have been provided was mainly restricted to pharmaceutical preparations that were either applied to the gingival and mucosal tissues or used as mouthwashes, and these at best may only have provided some short term relief. It seems apparent that many ancient Egyptians suffered from widespread and painful dental disease, which the available treatments can have done relatively little to alleviate.

  17. The Vindolanda Tablets and the Ancient Economy

    DEFF Research Database (Denmark)

    Evers, Kasper Grønlund

    , the aim is to investigate how best to comprehend the economic system attested at Vindolanda and to consider the wider implications for studies of the ancient economy in general. This is accomplished by a three-step approach: first, the nature of the Vindolandan evidence is assessed, and the state...... of research on both studies of the ancient economy and the economy of early Roman Britain is accounted for, so as to highlight the value of the Vindolanda Tablets and lay the ground for the interpretations which follow. Secondly, the economic activities attested by the tablets are analysed in terms of market......, a model is outlined which takes into account the different economic behaviours revealed by the tablets and attempts to fit them together into one coherent, economic system, whilst also relating the activities to questions of scale in the ancient economy; moreover, the conclusions drawn in the study...

  18. A novel mtDNA ND6 gene mutation associated with LHON in a Caucasian family.

    Science.gov (United States)

    Zhadanov, Sergey I; Atamanov, Vasily V; Zhadanov, Nikolay I; Oleinikov, Oleg V; Osipova, Ludmila P; Schurr, Theodore G

    2005-07-15

    Leber's hereditary optic neuropathy (LHON) is a frequent cause of inherited blindness. A routine screening for common mtDNA mutations constitutes an important first in its diagnosis. However, a substantial number of LHON patients do not harbor known variants, both pointing to the genetic heterogeneity of LHON and bringing into question its genetic diagnosis. We report a familial case that exhibited typical features of LHON but lacked any of the common mutations. Genetic analysis revealed a novel pathogenic defect in the ND6 gene at 14279A that was not detected in any haplogroup-matched controls screened for it, nor has it been previously reported. This mutation causes a substantial conformational change in the secondary structure of the polypeptide matrix coil and may explain the LHON expression. Thus, it expands the spectrum of deleterious changes affecting ND6-encoding subunit and further highlights the functional significance of this gene, providing additional clues to the disease pathogenesis.

  19. Pedigrees as a source of information in mtDNA studies of dogs and horses.

    Science.gov (United States)

    Głażewska, I; Prusak, B; Gralak, B

    2013-04-01

    The goal of this study was to demonstrate the usefulness of pedigree data in studies of mitochondrial DNA diversity in dogs and horses. Pedigree information allows for precisely choosing animals with distinct haplotypes for analysis, makes it possible to find rare haplotypes present exclusively in single individuals and helps to evaluate haplotype frequencies at the present and in the past. Estimating founder contributions to gene pools enables evaluating the parts of gene pools observed with the help of mtDNA analysis. An important aspect is also the financial benefits: using pedigree data, researchers can save a significant amount of time and money needed for sample collection and laboratory analysis. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  20. Variability of the honey bee mite Varroa destructor in Serbia, based on mtDNA analysis.

    Science.gov (United States)

    Gajic, Bojan; Radulovic, Zeljko; Stevanovic, Jevrosima; Kulisic, Zoran; Vucicevic, Milos; Simeunovic, Predrag; Stanimirovic, Zoran

    2013-09-01

    Only two mitochondrial haplotypes (Korea and Japan) of Varroa destructor, the ectoparasitic honey bee mite, are known to be capable of infesting and successfully reproducing in Apis mellifera colonies worldwide. Varroa destructor (then called Varroa jacobsoni) was observed in Serbia for the first time in 1976. In order to obtain insight into the genetic variability of the mites parasitizing A. mellifera we analyzed 45 adult female mites sampled from nine localities dispersed throughout Serbia. Four fragments within cox1, atp6, cox3 and cytb mtDNA genes were sequenced. The Korea haplotype of V. destructor was found to be present at all localities, but also two new haplotypes (Serbia 1 and Peshter 1) were revealed, based on cox1 and cytb sequence variability. The simultaneous occurrence of Korea and Serbia 1 haplotypes was observed at five localities, whereas Peshter 1 haplotype was identifed at only one place.