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Sample records for ancient insect dna

  1. Non-destructive sampling of ancient insect DNA

    DEFF Research Database (Denmark)

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

    2009-01-01

    BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological...... of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost......-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient...

  2. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    David Penney

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

  4. 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 ...

  5. Ancient DNA from marine mammals

    DEFF Research Database (Denmark)

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

    2012-01-01

    such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an oppor- tunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have...... focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes...... in distribution and range of marine mammal species; we review these studies and discuss the limitations of such ‘presence only’ studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also...

  6. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

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

    2013-01-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences...... 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....

  7. Ancient and modern environmental DNA

    Science.gov (United States)

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

    2015-01-01

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

  8. 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...

  9. Paleo-Environmental Reconstruction Using Ancient DNA

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther

    The aim of this thesis has been to investigate and expand the methodology and applicability for using ancient DNA deposited in lake sediments to detect and determine its genetic sources for paleo-environmental reconstruction. The aim was furthermore to put this tool into an applicable context...... solving other scientifically interesting questions. Still in its childhood, ancient environmental DNA research has a large potential for still developing, improving and discovering its possibilities and limitations in different environments and for identifying various organisms, both in terms...... research on ancient and modern environmental DNA (Paper 1), secondly by setting up a comparative study (Paper 2) to investigate how an ancient plant DNA (mini)-barcode can reflect other traditional methods (e.g. pollen and macrofossils) for reconstructing floristic history. In prolongation of the results...

  10. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders

    2005-01-01

    degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes...... such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics......, and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived...

  11. Ancient DNA analysis of dental calculus.

    Science.gov (United States)

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

    2015-02-01

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

  12. Ancient and modern environmental DNA

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  13. Fossil avian eggshell preserves ancient DNA

    DEFF Research Database (Denmark)

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

    2010-01-01

    Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful...... isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids......, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has...

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

    African Journals Online (AJOL)

    Quantification and presence of human ancient DNA in burial place remains of Turkey using real time polymerase chain reaction. ... A published real-time PCR assay, which allows for the combined analysis of nuclear or ancient DNA and mitochondrial DNA, was modified. This approach can be used for recovering DNA from ...

  15. Ancient bacteria show evidence of DNA repair

    DEFF Research Database (Denmark)

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

    2007-01-01

    -term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence...... geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long...... that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability....

  16. Evolution of DNA Methylation across Insects.

    Science.gov (United States)

    Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

    2017-03-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. 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.

  18. Ancient pathogen DNA in human teeth and petrous bones

    DEFF Research Database (Denmark)

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

    2018-01-01

    Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petro...

  19. Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives

    Directory of Open Access Journals (Sweden)

    Michael Knapp

    2010-07-01

    Full Text Available The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA  research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA...... to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons...

  1. Using Ancient DNA to Understand Evolutionary and Ecological Processes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Cooper, Alan

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

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

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both...... quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when...

  4. 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.

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

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    with fullgenome comparisons that the process has general relevance in extant bacteria. Our findings reveal that the large environmental reservoir of short and damaged DNA retains capacity for natural transformation, even after thousands of years. This describes for the first time a process by which cells can...... transfer playing an important role early in the evolution of life. The published article explains the chemical structure behind an observed degradation difference between the two purine-nucleotides guanosine and adenosine in ancient DNA. We also point at new uses for high-through-put DNA sequencing...

  6. Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.

    Directory of Open Access Journals (Sweden)

    Henrik B Hansen

    Full Text Available Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively than parietal skull bone (average of 2.2%. Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001. This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA. In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.

  7. Ancient DNA (aDNA): What is it? Why is it important?- Fact Sheet

    OpenAIRE

    Alexa Walker; George Nicholas; Daryl Pullman; Alan Goodman; Bioarchaeology and Genetics Working Group

    2014-01-01

    As genetic research is increasingly applied to new areas of study, including in archaeological and heritage contexts, a range of questions arise concerning the social, ethical, legal, and political implications of ancient DNA. This fact sheet explains the nature and challenges of aDNA research, and why information from it is important and relevant to people today.  

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

    Directory of Open Access Journals (Sweden)

    Jessica I Rivera-Perez

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

  9. Recombinant DNA technology and insect control

    International Nuclear Information System (INIS)

    Seawright, J.A.; Cockburn, Andrew F.

    1989-01-01

    In the past, the most successful avenue for the use of genetics in insect control has been the employment of the sterile insect technique, in which huge numbers of a species are produced in a factory, sterilized by exposure to ionizing radiation and released into the native habitat. this method is suitable for some species, but for logistical, economical, and biological reasons this control technique is not suitable for many economically important species. Our ability to use genetic approaches to cope with the myriad of insect pests will improve in the near future because of progress in the biochemical manipulation of genes. Molecular geneticists have created bacteria, plants, animals, and fungi that have useful new properties, and many of these are being used or tested for commercial use. A reasonable forecast is that a virtual revolution will occur in the way that we currently practice and perceive the genetic control of insects. Using genetic engineering manipulations to develop control techniques for insects of agricultural and public health importance is an exciting prospect and a highly desirable goal

  10. Recombinant DNA technology and insect control

    Energy Technology Data Exchange (ETDEWEB)

    Seawright, J A; Cockburn, Andrew F [Insects Affecting Man and Animals Laboratory, Agric. Res. Serv., U.S. Department of Agriculture, Gainesville, FL (United States)

    1989-08-01

    In the past, the most successful avenue for the use of genetics in insect control has been the employment of the sterile insect technique, in which huge numbers of a species are produced in a factory, sterilized by exposure to ionizing radiation and released into the native habitat. this method is suitable for some species, but for logistical, economical, and biological reasons this control technique is not suitable for many economically important species. Our ability to use genetic approaches to cope with the myriad of insect pests will improve in the near future because of progress in the biochemical manipulation of genes. Molecular geneticists have created bacteria, plants, animals, and fungi that have useful new properties, and many of these are being used or tested for commercial use. A reasonable forecast is that a virtual revolution will occur in the way that we currently practice and perceive the genetic control of insects. Using genetic engineering manipulations to develop control techniques for insects of agricultural and public health importance is an exciting prospect and a highly desirable goal.

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

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2006-01-01

    cloning. Yet these studies have used mobile insertion elements (e.g. IS 6110 in tuberculosis) or conserved loci (e.g. 16S) to detect the presence of pathogens, and very similar or identical sequences have been reported from environmental bacteria (Gilbert et al. 2004). For example, Rollo & Marota (1999......We agree with Donoghue & Spigelman (2005) that, although pathogen studies hold great potential, any discussion requires a critical assessment of the results to date. However, we did note, as did Pääbo et al. (2004), that the field of ancient pathogen DNA still lacks a series of well......-controlled and rigorous studies that address technical issues and reliability criteria. This is unfortunate, as the rapid evolutionary rate of many pathogens offers a unique means to establish the authenticity of ancient pathogen sequences-since they should clearly be ancestral to modern genetic diversity (e.g. Reid et...

  12. High-Throughput DNA sequencing of ancient wood.

    Science.gov (United States)

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

    2018-03-01

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

  13. Wolbachia and DNA barcoding insects: patterns, potential, and problems.

    Science.gov (United States)

    Smith, M Alex; Bertrand, Claudia; Crosby, Kate; Eveleigh, Eldon S; Fernandez-Triana, Jose; Fisher, Brian L; Gibbs, Jason; Hajibabaei, Mehrdad; Hallwachs, Winnie; Hind, Katharine; Hrcek, Jan; Huang, Da-Wei; Janda, Milan; Janzen, Daniel H; Li, Yanwei; Miller, Scott E; Packer, Laurence; Quicke, Donald; Ratnasingham, Sujeevan; Rodriguez, Josephine; Rougerie, Rodolphe; Shaw, Mark R; Sheffield, Cory; Stahlhut, Julie K; Steinke, Dirk; Whitfield, James; Wood, Monty; Zhou, Xin

    2012-01-01

    Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein--wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor--which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Sandoval Velasco, Marcela

    As one of a limited number of biomolecules recording evolutionary events, DNA provides an unparalleled means of investigating genetic processes. Over three decades, ancient DNA research has matured in many ways, growing alongside technological and methodological advancements. However, due to DNA...... means of investigating genetic processes. Over three decades, ancient DNA research has matured in many ways, growing alongside technological and methodological advancements. However, due to DNA preservation, degradation and contamination, ancient DNA research presents significant limitations...... preservation, degradation and contamination, ancient DNA research presents significant limitations and challenges. Until recently, it was thought that DNA did not survive more than few hundred thousand years, and that it was impossible to retrieve whole genome data from ancient samples preserved under...

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    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 phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from...... adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nu...

  17. Ancient DNA and the rewriting of human history: be sparing with Occam's razor.

    Science.gov (United States)

    Haber, Marc; Mezzavilla, Massimo; Xue, Yali; Tyler-Smith, Chris

    2016-01-11

    Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.

  18. 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.

  19. Ancient bacterial endosymbionts of insects: Genomes as sources of insight and springboards for inquiry.

    Science.gov (United States)

    Wernegreen, Jennifer J

    2017-09-15

    Ancient associations between insects and bacteria provide models to study intimate host-microbe interactions. Currently, a wealth of genome sequence data for long-term, obligately intracellular (primary) endosymbionts of insects reveals profound genomic consequences of this specialized bacterial lifestyle. Those consequences include severe genome reduction and extreme base compositions. This minireview highlights the utility of genome sequence data to understand how, and why, endosymbionts have been pushed to such extremes, and to illuminate the functional consequences of such extensive genome change. While the static snapshots provided by individual endosymbiont genomes are valuable, comparative analyses of multiple genomes have shed light on evolutionary mechanisms. Namely, genome comparisons have told us that selection is important in fine-tuning gene content, but at the same time, mutational pressure and genetic drift contribute to genome degradation. Examples from Blochmannia, the primary endosymbiont of the ant tribe Camponotini, illustrate the value and constraints of genome sequence data, and exemplify how genomes can serve as a springboard for further comparative and experimental inquiry. Copyright © 2017. Published by Elsevier Inc.

  20. Setting the stage - building and working in an ancient DNA laboratory.

    Science.gov (United States)

    Knapp, Michael; Clarke, Andrew C; Horsburgh, K Ann; Matisoo-Smith, Elizabeth A

    2012-01-20

    With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process. Copyright © 2011 Elsevier GmbH. All rights reserved.

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

    Science.gov (United States)

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

    2009-12-22

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

  2. Supercoiled circular DNA of an insect granulosis virus.

    Science.gov (United States)

    Tweeten, K A; Bulla, L A; Consigli, R A

    1977-08-01

    The DNA of the granulosis virus of the Indian meal moth, Plodia interpunctella, was characterized by physical chemical and electron microscopic techniques. Twenty-five percent of the DNA extracted from purified virus was isolated as supercoiled circular molecules. The remaining 75% consisted of relaxed circular molecules. These molecular forms were indicated by the production of two radioactive bands during sedimentation of (3)H-labeled granulosis virus DNA in alkaline sucrose gradients or in equilibrium density gradients of neutral cesium chloride/propidium iodide. Electron microscopic visualization of the DNA that banded at the higher density in the latter gradients revealed supercoiled structures whereas that of DNA that banded at the lower density demonstrated relaxed circular molecules. The superhelical molecules were converted to relaxed circles by treatment with pancreatic DNase. The molecular weight of the viral DNA was calculated to be 81 x 10(6) by sedimentation in neutral sucrose and 78 x 10(6) by sedimentation in alkaline sucrose. The molecular weight estimated from length measurements in electron micrographs was 76 x 10(6). The buoyant density of the granulosis virus DNA was 1.703 g/cm(3) and that of its insect host DNA was 1.697 g/cm(3). Equilibrium sedimentation in cesium chloride and thermal denaturation indicated G + C contents of 44% and 39% for the viral and host DNA, respectively.

  3. 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.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail...... 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...

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions....

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

    Science.gov (United States)

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

  7. Experimental conditions improving in-solution target enrichment for ancient DNA

    DEFF Research Database (Denmark)

    Cruz-Dávalos, Diana I.; Llamas, Bastien; Gaunitz, Charleen

    2017-01-01

    High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods ...

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

    Science.gov (United States)

    Yoshida, Kentaro; Sasaki, Eriko; Kamoun, Sophien

    2015-01-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    , and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate about hundred times faster than single stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen...... conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost...

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

    Directory of Open Access Journals (Sweden)

    Andaine Seguin-Orlando

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

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

    Directory of Open Access Journals (Sweden)

    Chang Seok Oh

    2010-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Cristian M. Crespo

    2010-12-01

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

  13. Fact Sheet- Ancient DNA: What is it? Why is it Important?

    OpenAIRE

    Alexa Walker; George Nicholas; Daryl Pullman; Alan Goodman; Bioarchaeology and Genetics Working Group

    2016-01-01

    As genetic research is increasingly applied to new areas of study, including in archaeological and heritage contexts, a range of questions arise concerning the social, ethical, legal, and political implications of ancient DNA. This fact sheet explains the nature and challenges of aDNA research, and why information from it is important and relevant to people today. 

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

    Science.gov (United States)

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

    2010-04-01

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

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates o...... for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution....

  16. Development of identification process for insect group using radiation marker DNA

    International Nuclear Information System (INIS)

    Muraji, M.; Tamura, T.

    2004-01-01

    Detection of a band pattern for insect groups was tried by using radiation marked DNA clone. A rapid segregation process for poly-type DNA segment was investigated. A band pattern of silkworm was detected by analysis using DNA type transposon, K1.4. The exon regions on genes of hemiptera insect were segregated by in vitro cloning. Band patterns of the silkworm and the other insects were detected by identification process of DNA clone and radiation marker. Family singularity mutation existed in the inserted position of transposon. The family of insect was identified easily by the difference of the detection band patterns. Effective band pattern for family discrimination were obtained by analysis for a part of mitochondria DNA and ribosomal DNA. DNA segregation process was investigated by using the enriched library, also. (M. Suetake)

  17. Early history of European domestic cattle as revealed by ancient DNA.

    Science.gov (United States)

    Bollongino, R; Edwards, C J; Alt, K W; Burger, J; Bradley, D G

    2006-03-22

    We present an extensive ancient DNA analysis of mainly Neolithic cattle bones sampled from archaeological sites along the route of Neolithic expansion, from Turkey to North-Central Europe and Britain. We place this first reasonable population sample of Neolithic cattle mitochondrial DNA sequence diversity in context to illustrate the continuity of haplotype variation patterns from the first European domestic cattle to the present. Interestingly, the dominant Central European pattern, a starburst phylogeny around the modal sequence, T3, has a Neolithic origin, and the reduced diversity within this cluster in the ancient samples accords with their shorter history of post-domestic accumulation of mutation.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains...... aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high...

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

    Directory of Open Access Journals (Sweden)

    F. Balzano

    2011-01-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation. Furthermore, although DNA can be PCR-amplified from wool dyed with one of four common plant dyes (tansy, woad, madder, weld), the use of mordants such as alum or iron leads...... and content of DNA in hair shafts are known to vary, and it is possible that common treatments of wool such as dyeing may negatively impact the DNA. Using quantitative real-time polymerase chain reaction (PCR), we demonstrate that in general, short fragments of both mitochondrial and single-copy nuclear DNA...

  2. Ancient pathogen DNA in human teeth and petrous bones

    DEFF Research Database (Denmark)

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

    2018-01-01

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

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... burial place remains of Turkey using real time ... DNA was isolaled from fossil bone tissue remains with Bio Robot EZ1 and ... the increase in the amount of DNA as it is amplified. The ... species or human blood in this work.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  6. A proteomic approach for studying insect phylogeny: CAPA peptides of ancient insect taxa (Dictyoptera, Blattoptera as a test case

    Directory of Open Access Journals (Sweden)

    Gäde Gerd

    2009-03-01

    Full Text Available Abstract Background Neuropeptide ligands have to fit exactly into their respective receptors and thus the evolution of the coding regions of their genes is constrained and may be strongly conserved. As such, they may be suitable for the reconstruction of phylogenetic relationships within higher taxa. CAPA peptides of major lineages of cockroaches (Blaberidae, Blattellidae, Blattidae, Polyphagidae, Cryptocercidae and of the termite Mastotermes darwiniensis were chosen to test the above hypothesis. The phylogenetic relationships within various groups of the taxon Dictyoptera (praying mantids, termites and cockroaches are still highly disputed. Results Tandem mass spectrometry of neuropeptides from perisympathetic organs was used to obtain sequence data of CAPA peptides from single specimens; the data were analysed by Maximum Parsimony and Bayesian Interference. The resulting cladograms, taking 61 species into account, show a topology which is in general agreement with recent molecular and morphological phylogenetic analyses, including the recent phylogenetic arrangement placing termites within the cockroaches. When sequence data sets from other neuropeptides, viz. adipokinetic hormones and sulfakinins, were included, the general topology of the cladogram did not change but bootstrap values increased considerably. Conclusion This study represents the first comprehensive survey of neuropeptides of insects for solely phylogenetic purposes and concludes that sequences of short neuropeptides are suitable to complement molecular biological and morphological data for the reconstruction of phylogenetic relationships.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 16000-32000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS...

  8. Ancient DNA: Saber-Toothed Cats Are the Same Beasts After All.

    Science.gov (United States)

    Meachen, Julie A

    2017-11-06

    Ancient DNA from the saber-toothed cat Homotherium reveals that the late Pleistocene species from Europe and North America were the same. Homotherium turns out to be only distantly related to the well-known saber-toothed Smilodon. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    Seguin-Orlando, Andaine; Gamba, Cristina; Sarkissian, Clio Der; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D.; Lopez, Patricio; McDonald, H. Gregory; Scott, Eric; Tikhonov, Alexei; Stafford,, Thomas W.; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A. S.; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. PMID:26134828

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

    Indian Academy of Sciences (India)

    Navya

    nucleotide substitutions per nucleotide site per year for mitochondrial DNA. DISCUSSION ... Despite the nature of mutations, we think the degree of variability in mutation rates is still an ..... Saccharomyces cerevisiae. Microbiology. 150 ...

  11. A new model for ancient DNA decay based on paleogenomic meta-analysis.

    Science.gov (United States)

    Kistler, Logan; Ware, Roselyn; Smith, Oliver; Collins, Matthew; Allaby, Robin G

    2017-06-20

    The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Parasitic infections and resource economy of Danish Iron Age settlement through ancient DNA sequencing.

    Science.gov (United States)

    Tams, Katrine Wegener; Jensen Søe, Martin; Merkyte, Inga; Valeur Seersholm, Frederik; Henriksen, Peter Steen; Klingenberg, Susanne; Willerslev, Eske; Kjær, Kurt H; Hansen, Anders Johannes; Kapel, Christian Moliin Outzen

    2018-01-01

    In this study, we screen archaeological soil samples by microscopy and analyse the samples by next generation sequencing to obtain results with parasites at species level and untargeted findings of plant and animal DNA. Three separate sediment layers of an ancient man-made pond in Hoby, Denmark, ranging from 100 BC to 200 AD, were analysed by microscopy for presence of intestinal worm eggs and DNA analysis were performed to identify intestinal worms and dietary components. Ancient DNA of parasites, domestic animals and edible plants revealed a change in use of the pond over time reflecting the household practice in the adjacent Iron Age settlement. The most abundant parasite found belonged to the Ascaris genus, which was not possible to type at species level. For all sediment layers the presence of eggs of the human whipworm Trichuris trichiura and the beef tapeworm Taenia saginata suggests continuous disposal of human faeces in the pond. Moreover, the continuous findings of T. saginata further imply beef consumption and may suggest that cattle were living in the immediate surrounding of the site throughout the period. Findings of additional host-specific parasites suggest fluctuating presence of other domestic animals over time: Trichuris suis (pig), Parascaris univalens (horse), Taenia hydatigena (dog and sheep). Likewise, alternating occurrence of aDNA of edible plants may suggest changes in agricultural practices. Moreover, the composition of aDNA of parasites, plants and vertebrates suggests a significant change in the use of the ancient pond over a period of three centuries.

  13. Ancient pests: the season of the Santorini Minoan volcanic eruption and a date from insect chitin

    Science.gov (United States)

    Panagiotakopulu, Eva; Higham, Thomas; Sarpaki, Anaya; Buckland, Paul; Doumas, Christos

    2013-07-01

    Attributing a season and a date to the volcanic eruption of Santorini in the Aegean has become possible by using preserved remains of the bean weevil, Bruchus rufipes, pests of pulses, from the storage jars of the West House, in the Bronze Age settlement at Akrotiri. We have applied an improved pre-treatment methodology for dating the charred insects, and this provides a date of 1744-1538 BC. This date is within the range of others obtained from pulses from the same context and confirms the utility of chitin as a dating material. Based on the nature of the insect material and the life cycle of the species involved, we argue for a summer eruption, which took place after harvest, shortly after this material was transported into the West House storeroom.

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Indian Academy of Sciences (India)

    lated strains was extracted by using a Fast DNA kit for soil (BIO 101, Vista, USA) based .... lites, but its movement is extremely slow (Burt and Williams. 1976). A bacterium of ... Despite the nature of mutations, we think the degree of variability in ...

  16. Ancient DNA: Would the Real Neandertal Please Stand up?

    DEFF Research Database (Denmark)

    Cooper, Alan; Drummond, Alexei J.; Willerslev, Eske

    2004-01-01

    Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contri...

  17. Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo.

    Science.gov (United States)

    González-Oliver, A; Márquez-Morfín, L; Jiménez, J C; Torre-Blanco, A

    2001-11-01

    Ancient DNA from the bone remains of 25 out of 28 pre-Columbian individuals from the Late Classic-Postclassic Maya site of Xcaret, Quintana Roo, was recovered, and mitochondrial DNA (mtDNA) was amplified by using the polymerase chain reaction. The presence of the four founding Amerindian mtDNA lineages was investigated by restriction analysis and by direct sequencing in selected individuals. The mtDNA lineages A, B, and C were found in this population. Eighty-four percent of the individuals were lineage A, whereas lineages B and C were present at low frequencies, 4% and 8%, respectively. Lineage D was absent from our sample. One individual did not possess any of the four lineages. Six skeletons out of 7 dated from the Late Classic period were haplotype A, whereas 11 skeletons out of 16 dated from the Postclassic period were also haplotype A. The distribution of mtDNA lineages in the Xcaret population contrasts sharply with that found in ancient Maya from Copán, which lack lineages A and B. On the other hand, our results resemble more closely the frequencies of mtDNA lineages found in contemporary Maya from the Yucatán Peninsula and in other Native American contemporary populations of Mesoamerican origin. Copyright 2001 Wiley-Liss, Inc.

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

    Science.gov (United States)

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

    2007-07-07

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro...... extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure......, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    study of genetic variation of Danish aurochs. In addition, for all specimens we address correlations between the ability to obtain DNA sequences and various parameters such as the age of the sample, the collagen content, the museum storage period, Danish geography and whether the specimens were found...... in an archeological or geological context. We find that aurochs from southern Scandinavia display a star-shaped population genetic structure, that is indicative of a local and relatively recent diversification from a few ancestral haplotypes that may have originated in the ancestral Western European population before...... migration northwards during the retreat of the glaciers. Scenarios suggesting several invasions of genetically distinct aurochs are not supported by these analyses. Rather, our results suggest that a single continuous migration northward occurred. Our findings also suggest, although with only limited...

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

    DEFF Research Database (Denmark)

    Lira, Jaime; Linderholm, Anna; Olaria, Carmen

    2010-01-01

    Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group...... wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times....

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

    Science.gov (United States)

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

    2014-11-30

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern......]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations....

  4. Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction.

    Directory of Open Access Journals (Sweden)

    Vincent Croset

    2010-08-01

    Full Text Available Ionotropic glutamate receptors (iGluRs are a highly conserved family of ligand-gated ion channels present in animals, plants, and bacteria, which are best characterized for their roles in synaptic communication in vertebrate nervous systems. A variant subfamily of iGluRs, the Ionotropic Receptors (IRs, was recently identified as a new class of olfactory receptors in the fruit fly, Drosophila melanogaster, hinting at a broader function of this ion channel family in detection of environmental, as well as intercellular, chemical signals. Here, we investigate the origin and evolution of IRs by comprehensive evolutionary genomics and in situ expression analysis. In marked contrast to the insect-specific Odorant Receptor family, we show that IRs are expressed in olfactory organs across Protostomia--a major branch of the animal kingdom that encompasses arthropods, nematodes, and molluscs--indicating that they represent an ancestral protostome chemosensory receptor family. Two subfamilies of IRs are distinguished: conserved "antennal IRs," which likely define the first olfactory receptor family of insects, and species-specific "divergent IRs," which are expressed in peripheral and internal gustatory neurons, implicating this family in taste and food assessment. Comparative analysis of drosophilid IRs reveals the selective forces that have shaped the repertoires in flies with distinct chemosensory preferences. Examination of IR gene structure and genomic distribution suggests both non-allelic homologous recombination and retroposition contributed to the expansion of this multigene family. Together, these findings lay a foundation for functional analysis of these receptors in both neurobiological and evolutionary studies. Furthermore, this work identifies novel targets for manipulating chemosensory-driven behaviours of agricultural pests and disease vectors.

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

    Science.gov (United States)

    Slatkin, Montgomery

    2016-01-01

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

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

    Science.gov (United States)

    Sankaranarayanan, Krithivasan; Timofeeff, Michael N; Spathis, Rita; Lowenstein, Tim K; Lum, J Koji

    2011-01-01

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

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

    Science.gov (United States)

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

    2016-10-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  9. 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.

  10. 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

  11. Dichlorvos exposure impedes extraction and amplification of DNA from insects in museum collections

    Directory of Open Access Journals (Sweden)

    Åkerlund Monika

    2010-01-01

    Full Text Available Abstract Background The insecticides dichlorvos, paradichlorobenzene and naphthalene have been commonly used to eradicate pest insects from natural history collections. However, it is not known how these chemicals affect the DNA of the specimens in the collections. We thus tested the effect of dichlorvos, paradichlorobenzene and naphthalene on DNA of insects (Musca domestica by extracting and amplifying DNA from specimens exposed to insecticides in two different concentrations over increasing time intervals. Results The results clearly show that dichlorvos impedes both extraction and amplification of mitochondrial and nuclear DNA after relatively short time, whereas paradichlorobenzene and naphthalene do not. Conclusion Collections treated with paradichlorobenzene and naphthalene, are better preserved concerning DNA, than those treated with dichlorvos. Non toxic pest control methods should, however, be preferred due to physical damage of specimens and putative health risks by chemicals.

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

    Science.gov (United States)

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

    2012-08-23

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

  13. 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

    , 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......). This is the first ancient nuclear SNP typed from a Native population in the Americas. In addition, using the same teeth we conducted a stable isotopes analysis of collagen and dentine to show that both individuals relied on marine sources (fresh and salt water fish, seals) with no hierarchy seen between them......, 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...

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

    Directory of Open Access Journals (Sweden)

    Treena Swanston

    2011-02-01

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

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

    Science.gov (United States)

    Lech, T

    2016-05-06

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

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

    Science.gov (United States)

    Müller, Romy; Roberts, Charlotte A; Brown, Terence A

    2014-02-01

    Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st-19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as "probable" or "possible." None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB. Copyright © 2013 Wiley Periodicals, Inc.

  17. 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.

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

    Science.gov (United States)

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

    2017-12-04

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

  19. 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

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

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

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

    Directory of Open Access Journals (Sweden)

    Dan Bar Yaacov

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

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

    Directory of Open Access Journals (Sweden)

    Lumibao Candice Y

    2011-01-01

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

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

    Science.gov (United States)

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

    2014-04-01

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

  4. Association of insect life stages using DNA sequences : the larvae of Philodytes umbrinus (Motschulsky) (Coleoptera : Dytiscidae)

    NARCIS (Netherlands)

    Miller, KB; Alarie, Y; Wolfe, GW; Whiting, MF

    2005-01-01

    Insect life stages are known imperfectly in many cases, and classifications are based often on only one or a few semaphoronts of a species. This is unfortunate as information in alternative life stages often is useful for scientific study. Although recent examples of DNA in taxonomy have emphasized

  5. Qualitative evaluation of the DNA degradation in plague insects exposed to gamma radiation

    International Nuclear Information System (INIS)

    Ortega, Yuriko; Agapito, Juan; Vargas, Johnny; Vivanco, Monica; Martinez, Norberta

    2014-01-01

    Insects produce large losses in stored grain depending on the type of cereal and storage time and other factors. The rice weevil Sitophilus oryzae L and the false flour beetle Tribolium confusum are important pests of stored grain. The study aimed to qualitatively evaluate the effect of gamma radiation on the DNA of two species of insect pests from samples stored Chullpi and white corn infested with adult weevils. Samples were treated with radiation doses of 100, 400, 1000 and 2000 Gy and DNA extraction was obtained by three methods: TNES-urea, CTAB and NaOH. The DNA damage induced by gamma radiation in weevils was determined by gel electrophoresis. As a result, it was found that exposure of adult weevils to a radiation dose of 100 Gy and 400 caused an average mortality of the insects, showing a degree of resistance to gamma radiation. However, radiation doses of 1000 and 2000 Gy caused 100 % mortality of insects. Preliminary results show that DNA damage is proportional to the amount of gamma radiation. (authors).

  6. Ancient DNA analysis suggests negligible impact of the Wari Empire expansion in Peru's central coast during the Middle Horizon

    OpenAIRE

    Valverde, G.; Romero, M.; Espinoza, I.; Cooper, A.; Fehren-Schmitz, L.; Llamas, B.; Haak, W.

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650?1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, wh...

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Bobbi M Johnson

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

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

    Directory of Open Access Journals (Sweden)

    Sonal Jain

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-04-29

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

  12. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

    Science.gov (United States)

    Weyrich, Laura S; Duchene, Sebastian; Soubrier, Julien; Arriola, Luis; Llamas, Bastien; Breen, James; Morris, Alan G; Alt, Kurt W; Caramelli, David; Dresely, Veit; Farrell, Milly; Farrer, Andrew G; Francken, Michael; Gully, Neville; Haak, Wolfgang; Hardy, Karen; Harvati, Katerina; Held, Petra; Holmes, Edward C; Kaidonis, John; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Semal, Patrick; Soltysiak, Arkadiusz; Townsend, Grant; Usai, Donatella; Wahl, Joachim; Huson, Daniel H; Dobney, Keith; Cooper, Alan

    2017-04-20

    Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

  13. 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.

  14. Prehistoric introduction of domestic pigs onto the Okinawa Islands: ancient mitochondrial DNA evidence.

    Science.gov (United States)

    Watanobe, Takuma; Ishiguro, Naotaka; Nakano, Masuo; Takamiya, Hiroto; Matsui, Akira; Hongo, Hitomi

    2002-08-01

    Ancient DNAs of Sus scrofa specimens excavated from archaeological sites on the Okinawa islands were examined to clarify the genetic relationships among prehistoric Sus scrofa, modern wild boars and domestic pigs inhabiting the Ryukyu archipelago, the Japanese islands, and the Asian continent. We extracted remain DNA from 161 bone specimens excavated from 12 archaeological sites on the Okinawa islands and successfully amplified mitochondrial DNA control region fragments from 33 of 161 specimens. Pairwise difference between prehistoric and modern S. scrofa nucleotide sequences showed that haplotypes of the East Asian domestic pig lineage were found from archaeological specimens together with Ryukyu wild boars native to the Ryukyu archipelago. Phylogenetic analysis of 14 ancient sequences (11 haplotypes; 574 bp) indicated that S. scrofa specimens from two Yayoi-Heian sites (Kitahara and Ara shellmiddens) and two Recent Times sites (Wakuta Kiln and Kiyuna sites) are grouped with modern East Asian domestic pigs. Sus scrofa specimens from Shimizu shellmidden (Yayoi-Heian Period) were very closely related to modern Sus scrofa riukiuanus but had a unique nucleotide insertion, indicating that the population is genetically distinct from the lineage of modern Ryukyu wild boars. This genetic evidence suggests that domestic pigs from the Asian continent were introduced to the Okinawa islands in the early Yayoi-Heian period (1700-2000 BP), or earlier.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified....

  17. Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna.

    Science.gov (United States)

    Volkov, Roman A; Panchuk, Irina I; Borisjuk, Nikolai V; Hosiawa-Baranska, Marta; Maluszynska, Jolanta; Hemleben, Vera

    2017-01-23

    inheritance from the tetraploid progenitor. The obtained molecular, cytogenetic and phylogenetic data demonstrate complex evolutionary dynamics of rDNA loci in allohexaploid species of Atropa belladonna. The high level of sequence unification revealed in 45S and 5S rDNA loci of this ancient hybrid species have been seemingly achieved by different molecular mechanisms.

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

    Directory of Open Access Journals (Sweden)

    Sarit Suissa

    2009-05-01

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

  19. 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...... selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura, using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology...

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

    Directory of Open Access Journals (Sweden)

    Krithivasan Sankaranarayanan

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

  1. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

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

    Science.gov (United States)

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

    2018-02-01

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

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

    Science.gov (United States)

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

    2017-08-22

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

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

    Science.gov (United States)

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

    2011-01-07

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

  5. 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

  6. Ancient mitogenomics

    DEFF Research Database (Denmark)

    Ho, Simon Y. W.; Gilbert, Tom

    2010-01-01

    the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.......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...... obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe...

  7. Display of a Maize cDNA library on baculovirus infected insect cells

    Directory of Open Access Journals (Sweden)

    Jones Ian M

    2008-08-01

    Full Text Available Abstract Background Maize is a good model system for cereal crop genetics and development because of its rich genetic heritage and well-characterized morphology. The sequencing of its genome is well advanced, and new technologies for efficient proteomic analysis are needed. Baculovirus expression systems have been used for the last twenty years to express in insect cells a wide variety of eukaryotic proteins that require complex folding or extensive posttranslational modification. More recently, baculovirus display technologies based on the expression of foreign sequences on the surface of Autographa californica (AcMNPV have been developed. We investigated the potential of a display methodology for a cDNA library of maize young seedlings. Results We constructed a full-length cDNA library of young maize etiolated seedlings in the transfer vector pAcTMVSVG. The library contained a total of 2.5 × 105 independent clones. Expression of two known maize proteins, calreticulin and auxin binding protein (ABP1, was shown by western blot analysis of protein extracts from insect cells infected with the cDNA library. Display of the two proteins in infected insect cells was shown by selective biopanning using magnetic cell sorting and demonstrated proof of concept that the baculovirus maize cDNA display library could be used to identify and isolate proteins. Conclusion The maize cDNA library constructed in this study relies on the novel technology of baculovirus display and is unique in currently published cDNA libraries. Produced to demonstrate proof of principle, it opens the way for the development of a eukaryotic in vivo display tool which would be ideally suited for rapid screening of the maize proteome for binding partners, such as proteins involved in hormone regulation or defence.

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

    Science.gov (United States)

    Bennett, Casey C; Kaestle, Frederika A

    2010-04-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  10. A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects.

    Science.gov (United States)

    Schlipalius, D I; Waldron, J; Carroll, B J; Collins, P J; Ebert, P R

    2001-12-01

    Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability in three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced approximately 50 scoreable polymorphic DNA markers, between individuals of three independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from individual DNA samples that had been combined to create the bulked samples.

  11. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... 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...

  12. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2016-04-01

    Full Text Available Cytochrome c oxidase I (COI is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

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

    Science.gov (United States)

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

    2017-07-26

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

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

    Science.gov (United States)

    Søe, Martin Jensen; Nejsum, Peter; Fredensborg, Brian Lund; Kapel, Christian Moliin Outzen

    2015-02-01

    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 selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced 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.

  15. The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups

    Directory of Open Access Journals (Sweden)

    David G. Mahal

    2018-01-01

    Full Text Available Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree. A total of 2,504 Y-DNA haplotypes, representing 50 different ethnic groups in the Indian subcontinent, were analyzed. The results identified 14 different haplogroups with 14 geographic origins for these people. Moreover, every ethnic group had representation in more than one haplogroup, indicating multiple geographic origins for these communities. The results also showed that despite their varied languages and cultural differences, most ethnic groups shared some common ancestors because of admixture in the past. These findings provide new insights into the ancient geographic origins of ethnic groups in the Indian subcontinent. With about 2,000 other ethnic groups and tribes in the region, it is expected that more scientific discoveries will follow, providing insights into how, from where, and when the ancestors of these people arrived in the subcontinent to create so many different communities.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2014-04-01

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

  18. Ancient Resistome.

    Science.gov (United States)

    Olaitan, Abiola Olumuyiwa; Rolain, Jean-Marc

    2016-08-01

    Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides. The investigation of the resistome of ancient bacteria is a recent and emerging field of research, and technological advancements such as next-generation sequencing will further contribute to its growth. It is hoped that the knowledge gained from this research will help us to better understand the evolution of antibiotic resistance genes and will also be used in drug design as a proactive measure against antibiotic resistance.

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Wolfgang Haak

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

  1. 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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

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

    1995-06-01

    Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.

  4. Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA.

    Science.gov (United States)

    Marr, Melissa M; Brace, Selina; Schreve, Danielle C; Barnes, Ian

    2018-02-09

    Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.

  5. Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Nejsum, Peter; Seersholm, Frederik Valeur

    2018-01-01

    , vertebrate and plant DNA proved highly informative in the study of ancient health, human-animal interactions as well as animal and plant dietary components. Most prominent were finding of soil-borne parasites transmitted directly between humans, but also meat-borne parasites that require consumption of raw...... or undercooked fish and pork. The detection of parasites for which sheep, horse, dog, pig, and rodents serves as definitive hosts are clear markers of domestic and synanthropic animals living in closer proximity of the respective sites. Finally, the reconstruction of full mitochondrial parasite genomes from...

  6. Effect of UV on DNA synthesis in UV-resistant insect cells

    International Nuclear Information System (INIS)

    Styer, S.C.; Meechan, P.J.; Griffiths, T.D.

    1987-01-01

    Insect cells are most resistant to killing by 254 nm ultraviolet light (UV) than mammalian cells. Because they have an active photolyase, it may be possible to generate a higher number of [6-4] PyC lesions per genome, allowing the possibility to distinguish between the effects of [5-6] pyrimidine lesions and the nonphotoreactable [6-4] lesions on DNA replication. IAL-PID2 cells, derived from imaginal wing discs of the Indian meal moth were exposed to UV followed by photoreactivating light (PR) or sham treatment and then analyzed by measuring the incorporation of [/sup 3/H]-thymidine into acid precipitable form. As expected, there was a fluence-dependent decrease in the amount of thymidine incorporated after exposure to UV. The response was similar to that observed in wild type CHO cells (AAS) except that the rate of decline was more rapid. When PR followed UV, there was less of a decline in thymidine incorporation and a more rapid recovery. However, thymidine incorporation did not return to control levels as rapidly as expected if [5-6] lesions were the only lesions involved in the disruption of DNA synthesis after exposure to UV

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2018-04-06

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

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

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    Gui-Lian Sheng

    2018-04-01

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

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

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    Lara D Shepherd

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

  11. 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.

  12. All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality

    Directory of Open Access Journals (Sweden)

    JinHee Choi

    2015-07-01

    Full Text Available More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about “old” samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the “fresh” specimens.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2010-02-01

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

  16. Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus complex.

    Directory of Open Access Journals (Sweden)

    Xiuguang Mao

    Full Text Available The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2 and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.

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

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    Nadezhda V Vorobieva

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Guido Valverde

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

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

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    Esther J Lee

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

  1. Genetic polymorphisms in prehistoric Pacific islanders determined by analysis of ancient bone DNA.

    Science.gov (United States)

    Hagelberg, E; Clegg, J B

    1993-05-22

    A previously characterized Asian-specific mitochondrial DNA (mtDNA) length mutation has been detected in DNA isolated from prehistoric human bones from Polynesia, including Hawaii, Chatham Islands and Society Islands. In contrast, the Asian mutation was absent in skeletal samples from the Melanesian archipelagos of New Britain and Vanuatu and in the oldest samples from Fiji, Tonga and Samoa in the central Pacific (2700-1600 years BP) although it was present in a more recent prehistoric sample from Tonga. These results, augmented by informative DNA sequence data from the hypervariable region of mtDNA, fail to support current views that the central Pacific was settled directly by voyagers from island Southeast Asia, the putative ancestors of modern Polynesians. An earlier occupation by peoples from the neighbouring Melanesian archipelagos seems more likely.

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

    DEFF Research Database (Denmark)

    Dissing, Jørgen; Binladen, Jonas; Hansen, Anders

    2006-01-01

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

  3. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA.

    Science.gov (United States)

    Bennett, E Andrew; Champlot, Sophie; Peters, Joris; Arbuckle, Benjamin S; Guimaraes, Silvia; Pruvost, Mélanie; Bar-David, Shirli; Davis, Simon J M; Gautier, Mathieu; Kaczensky, Petra; Kuehn, Ralph; Mashkour, Marjan; Morales-Muñiz, Arturo; Pucher, Erich; Tournepiche, Jean-François; Uerpmann, Hans-Peter; Bălăşescu, Adrian; Germonpré, Mietje; Gündem, Can Y; Hemami, Mahmoud-Reza; Moullé, Pierre-Elie; Ötzan, Aliye; Uerpmann, Margarete; Walzer, Chris; Grange, Thierry; Geigl, Eva-Maria

    2017-01-01

    Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into eleven clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent mitochondrial introgression between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly-endangered species.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    DNA analysis identified unreported plant and animal taxa, some of which are locally extinct or endemic. The survival and preservation of DNA in hot, arid environments is a complex and poorly understood process that is both sporadic and rare, but the survival of DNA through desiccation may be important......The study of arid palaeoenvironments is often frustrated by the poor or non-existent preservation of plant and animal material, yet these environments are of considerable environmental importance. The analysis of pollen and macrofossils isolated from herbivore middens has been an invaluable source...

  5. 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

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

    Science.gov (United States)

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

    2011-09-01

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

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

    Science.gov (United States)

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

    2012-01-20

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

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

    Science.gov (United States)

    Dissing, Jørgen; Binladen, Jonas; Hansen, Anders; Sejrsen, Birgitte; Willerslev, Eske; Lynnerup, Niels

    2007-02-14

    The last of the Danish Viking Kings, Sven Estridsen, died in a.d. 1074 and is entombed in Roskilde Cathedral with other Danish kings and queens. Sven's mother, Estrid, is entombed in a pillar across the chancel. However, while there is no reasonable doubt about the identity of Sven, there have been doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D-loop were PCR amplified, cloned and a number of clones with each segment were sequenced. Also a segment containing the H/non-H specific nucleotide 7028 was sequenced. Consensus sequences were determined and D-loop results were replicated in an independent laboratory. This allowed the assignment of King Sven Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases where the sequence has been altered by a germ line mutation. Therefore, the observation of two sequence differences makes it highly unlikely that the entombed woman was the mother of Sven. In addition, physical examination of the skeleton and the teeth strongly indicated that this woman was much younger (approximately 35 years) at the time of death than the 70 years history records tell. Although the entombed woman cannot be the Estrid, she may well be one of Sven's two daughters-in-law who were also called Estrid and who both became queens.

  9. Chromatin condensation and differential sensitivity of mammalian and insect cells to DNA strand breaks induced by bleomycin

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Larraza, Daniel M. [IMBICE, C.C. 403, 1900 La Plata (Argentina)]. E-mail: danielop@imbice.org.ar; Padron, Juan [IMBICE, C.C. 403, 1900 La Plata (Argentina); Ronci, Natalia E. [IMBICE, C.C. 403, 1900 La Plata (Argentina); Vidal Rioja, Lidia A. [IMBICE, C.C. 403, 1900 La Plata (Argentina)

    2006-08-30

    Bleomycin (BLM) induces DNA damage in living cells. In this report we analyzed the role of chromatin compactness in the differential response of mosquito (ATC-15) and mammalian (CHO) cells to DNA strand breaks induced by BLM. We used cells unexposed and exposed to sodium butyrate (NaB), which induces chromatin decondensation. By nucleoid sedimentation assay and digestions of nuclei with DNAse I, untreated mosquito cells (no BLM; no NaB) were shown to have more chromatin condensation than untreated CHO cells. By alkaline unwinding ATC-15 cells treated with NaB showed more BLM-induced DNA strand breaks than NaB-untreated CHO cells. The time-course of BLM-induced DNA damage to nuclear DNA was similar for NaB-untreated mammalian and insect cells, but with mosquito cells showing less DNA strand breaks, both at physiological temperatures and at 4 {sup o}C. However, when DNA repair was inhibited by low temperatures and chromatin was decondensed by NaB treatments, differences in BLM-induced DNA damage between these cells lines were no longer observed. In both cell lines, NaB did not affect BLM action on cell growth and viability. On the other hand, the low sensitivity of ATC-15 cells to BLM was reflected in their better growth efficiency. These cells exhibited a satisfactory growth at BLM doses that produced a permanent arrest of growth in CHO cells. The data suggest that mosquito cells might have linker DNAs shorter than those of mammalian cells, which would result in the observed both greater chromatin condensation and greater resistance to DNA damage induced by BLM as compared to CHO cells.

  10. Chromatin condensation and differential sensitivity of mammalian and insect cells to DNA strand breaks induced by bleomycin

    International Nuclear Information System (INIS)

    Lopez-Larraza, Daniel M.; Padron, Juan; Ronci, Natalia E.; Vidal Rioja, Lidia A.

    2006-01-01

    Bleomycin (BLM) induces DNA damage in living cells. In this report we analyzed the role of chromatin compactness in the differential response of mosquito (ATC-15) and mammalian (CHO) cells to DNA strand breaks induced by BLM. We used cells unexposed and exposed to sodium butyrate (NaB), which induces chromatin decondensation. By nucleoid sedimentation assay and digestions of nuclei with DNAse I, untreated mosquito cells (no BLM; no NaB) were shown to have more chromatin condensation than untreated CHO cells. By alkaline unwinding ATC-15 cells treated with NaB showed more BLM-induced DNA strand breaks than NaB-untreated CHO cells. The time-course of BLM-induced DNA damage to nuclear DNA was similar for NaB-untreated mammalian and insect cells, but with mosquito cells showing less DNA strand breaks, both at physiological temperatures and at 4 o C. However, when DNA repair was inhibited by low temperatures and chromatin was decondensed by NaB treatments, differences in BLM-induced DNA damage between these cells lines were no longer observed. In both cell lines, NaB did not affect BLM action on cell growth and viability. On the other hand, the low sensitivity of ATC-15 cells to BLM was reflected in their better growth efficiency. These cells exhibited a satisfactory growth at BLM doses that produced a permanent arrest of growth in CHO cells. The data suggest that mosquito cells might have linker DNAs shorter than those of mammalian cells, which would result in the observed both greater chromatin condensation and greater resistance to DNA damage induced by BLM as compared to CHO cells

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

    Science.gov (United States)

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

    1998-10-13

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

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

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic Antoine Alexandre

    2013-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Annina Krüttli

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

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

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    Alcover Josep Antoni

    2005-12-01

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

  16. Brief communication: Ancient nuclear DNA and kinship analysis: the case of a medieval burial in San Esteban Church in Cuellar (Segovia, Central Spain).

    Science.gov (United States)

    Gamba, Cristina; Fernández, Eva; Tirado, Mirian; Pastor, Francisco; Arroyo-Pardo, Eduardo

    2011-03-01

    The aim of this work was to investigate a very common situation in the archaeological and anthropological context: the study of a burial site containing several individuals, probably related genetically, using ancient DNA techniques. We used available ancient DNA and forensic protocols to obtain reliable results on archaeological material. The results also enabled molecular sex determination to be compared with osteological data. Specifically, a modified ancient DNA extraction method combined with the amplification of nuclear markers with the AmpFlSTR®MiniFiler™ kit(Applied Biosystems) was used. Seven medieval individuals buried in four niches dated in the 15th Century at San Esteban Church in Cuellar (Segovia, Central Spain) were analyzed by the proposed method, and four of seven provided complete autosomal short tandem repeat (STRs) profiles. Kinship analyses comprising paternity and sibship relations were carried out with pedigree-specific software used in forensic casework. A 99.98% paternity probability was established between two individuals, although lower percentages (68%) were obtained in other cases, and some hypothetical kinship relations were excluded. The overall results could eventually provide evidence for reconstructing the historical record. Copyright © 2010 Wiley-Liss, Inc.

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

    Directory of Open Access Journals (Sweden)

    Mu-Yeong Lee

    2012-01-01

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

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

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    Brenna A McLeod

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

  19. Vaccination of carp against SVCV with an oral DNA vaccine or an insect cells-based subunit vaccine.

    Science.gov (United States)

    Embregts, C W E; Rigaudeau, D; Tacchi, L; Pijlman, G P; Kampers, L; Veselý, T; Pokorová, D; Boudinot, P; Wiegertjes, G F; Forlenza, M

    2018-03-19

    We recently reported on a successful vaccine for carp against SVCV based on the intramuscular injection of a DNA plasmid encoding the SVCV glycoprotein (SVCV-G). This shows that the intramuscular (i.m.) route of vaccination is suitable to trigger protective responses against SVCV, and that the SVCV G-protein is a suitable vaccine antigen. Yet, despite the general success of DNA vaccines, especially against fish rhabdoviruses, their practical implementation still faces legislative as well as consumer's acceptance concerns. Furthermore, the i.m. route of plasmid administration is not easily combined with most of the current vaccination regimes largely based on intraperitoneal or immersion vaccination. For this reason, in the current study we evaluated possible alternatives to a DNA-based i.m. injectable vaccine using the SVCV-G protein as the vaccine antigen. To this end, we tested two parallel approaches: the first based on the optimization of an alginate encapsulation method for oral delivery of DNA and protein antigens; the second based on the baculovirus recombinant expression of transmembrane SVCV-G protein in insect cells, administered as whole-cell subunit vaccine through the oral and injection route. In addition, in the case of the oral DNA vaccine, we also investigated the potential benefits of the mucosal adjuvants Escherichia coli lymphotoxin subunit B (LTB). Despite the use of various vaccine types, doses, regimes, and administration routes, no protection was observed, contrary to the full protection obtained with our reference i.m. DNA vaccine. The limited protection observed under the various conditions used in this study, the nature of the host, of the pathogen, the type of vaccine and encapsulation method, will therefore be discussed in details to provide an outlook for future vaccination strategies against SVCV. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. 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.

  1. Leprosy in a Lombard-Avar cemetery in central Italy (Campochiaro, Molise, 6th-8th century AD): ancient DNA evidence and demography.

    Science.gov (United States)

    Rubini, Mauro; Zaio, Paola; Spigelman, Mark; Donoghue, Helen D

    2017-09-01

    The study of past infectious diseases increases knowledge of the presence, impact and spread of pathogens within ancient populations. Polymerase chain reaction (PCR) was used to examine bones for the presence of Mycobacterium leprae ancient DNA (aDNA) as, even when leprosy is present, bony changes are not always pathognomonic of the disease. This study also examined the demographic profile of this population and compared it with two other populations to investigate any changes in mortality trends between different infectious diseases and between the pre-antibiotic and antibiotic eras. The individuals were from a site in Central Italy (6th-8th CE) and were examined for the presence of Mycobacterium leprae aDNA. In addition, an abridged life mortality table was constructed. Two individuals had typical leprosy palaeopathology, and one was positive for Mycobacterium leprae aDNA. However, the demographic profile shows a mortality curve similar to that of the standard, in contrast to a population that had been subjected to bubonic plague. This study shows that, in the historical population with leprosy, the risk factors for health seem to be constant and distributed across all age classes, similar to what is found today in the antibiotic era. There were no peaks of mortality equivalent to those found in fatal diseases such as the plague, probably due to the long clinical course of leprosy.

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

    Science.gov (United States)

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

    2015-01-01

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

  3. DNA microarrays of baculovirus genomes: differential expression of viral genes in two susceptible insect cell lines.

    Science.gov (United States)

    Yamagishi, J; Isobe, R; Takebuchi, T; Bando, H

    2003-03-01

    We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the best-studied members of the family Baculoviridae, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Bombyx mori nucleopolyhedrovirus (BmNPV). In this study, a viral DNA chip (Ac-BmNPV chip) was fabricated and used to characterize the viral gene expression profile for AcMNPV in different cell types. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of PCR-amplified viral DNA fragments on glass for ORFs in the NPV genome. Viral gene expression was monitored by hybridization to the DNA fragment microarrays with fluorescently labeled cDNAs prepared from infected Spodoptera frugiperda, Sf9 cells and Trichoplusia ni, TnHigh-Five cells, the latter a major producer of baculovirus and recombinant proteins. A comparison of expression profiles of known ORFs in AcMNPV elucidated six genes (ORF150, p10, pk2, and three late gene expression factor genes lef-3, p35 and lef- 6) the expression of each of which was regulated differently in the two cell lines. Most of these genes are known to be closely involved in the viral life cycle such as in DNA replication, late gene expression and the release of polyhedra from infected cells. These results imply that the differential expression of these viral genes accounts for the differences in viral replication between these two cell lines. Thus, these fabricated microarrays of NPV DNA which allow a rapid analysis of gene expression at the viral genome level should greatly speed the functional analysis of large genomes of NPV.

  4. Identifying insects with incomplete DNA barcode libraries, African fruit flies (Diptera: Tephritidae) as a test case.

    Science.gov (United States)

    Virgilio, Massimiliano; Jordaens, Kurt; Breman, Floris C; Backeljau, Thierry; De Meyer, Marc

    2012-01-01

    We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.

  5. 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.

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

    Science.gov (United States)

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

    2015-01-01

    A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts. PMID:26473047

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

    Science.gov (United States)

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

    2015-09-01

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

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

    OpenAIRE

    Fehren-Schmitz, Lars

    2012-01-01

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

  9. Insect barcode information system.

    Science.gov (United States)

    Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

    2014-01-01

    Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. http://www.nabg-nbaii.res.in/barcode.

  10. Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect.

    Science.gov (United States)

    Standage, Daniel S; Berens, Ali J; Glastad, Karl M; Severin, Andrew J; Brendel, Volker P; Toth, Amy L

    2016-04-01

    Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of caste-related transcriptome and methylome sequence data for adult queens and workers. Polistes dominula possesses a fairly typical hymenopteran genome, but shows very low genomewide GC content and some evidence of reduced genome size. We found numerous caste-related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these -omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects: DNA methylation. Along with a conspicuous loss of a key gene associated with environmentally responsive DNA methylation (the de novo DNA methyltransferase Dnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative -omics data for this important behavioural and evolutionary model system call into question the general importance of DNA methylation in caste differences and evolution in social insects. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  11. DNA Barcoding for Species Identification of Insect Skins: A Test on Chironomidae (Diptera) Pupal Exuviae

    Science.gov (United States)

    Ekrem, Torbjørn; Stur, Elisabeth

    2017-01-01

    Abstract Chironomidae (Diptera) pupal exuviae samples are commonly used for biological monitoring of aquatic habitats. DNA barcoding has proved useful for species identification of chironomid life stages containing cellular tissue, but the barcoding success of chironomid pupal exuviae is unknown. We assessed whether standard DNA barcoding could be efficiently used for species identification of chironomid pupal exuviae when compared with morphological techniques and if there were differences in performance between temperate and tropical ecosystems, subfamilies, and tribes. PCR, sequence, and identification success differed significantly between geographic regions and taxonomic groups. For Norway, 27 out of 190 (14.2%) of pupal exuviae resulted in high-quality chironomid sequences that match species. For Costa Rica, 69 out of 190 (36.3%) Costa Rican pupal exuviae resulted in high-quality sequences, but none matched known species. Standard DNA barcoding of chironomid pupal exuviae had limited success in species identification of unknown specimens due to contaminations and lack of matching references in available barcode libraries, especially from Costa Rica. Therefore, we recommend future biodiversity studies that focus their efforts on understudied regions, to simultaneously use morphological and molecular identification techniques to identify all life stages of chironomids and populate the barcode reference library with identified sequences.

  12. Anhydrobiotic insect Polypedilum vanderplanki: molecular mechanisms of DNA and protein protection against extreme environments.

    Science.gov (United States)

    Gusev, Oleg; Nakahara, Yuichi; Kikawada, Takahiro; Levinskikh, Margarita; Sychev, Vladimir; Okuda, Takashi

    Some organisms showing no sign of living due to complete desiccation are nevertheless able to resume active life after rehydration. This peculiar biological state is referred to as "anhydrobiosis". Larvae of the sleeping chironomid, P. vanderplanki living in temporary pools in semi-arid areas on the African continent become completely desiccated upon drought, but can revive after water becomes available upon the next rain. The dried larvae can stand other extreme conditions, such as exposure to 100˚C, -270˚C, 100We have adopted several methods to evaluated DNA damage in cells of P. vanderplanki and cloned and analyzed expression of the main agent of genetic stress response showing that the larvae possess highly developed anti-stress genetic system, involving anti-oxidative stress genes, hsp and DNA reparation enzymes acting together to provide stability of proteins and DNA in the absence of water. From 2005, dried larvae were included in a number of research programs, including exposition to space environments onboard ISS and long-term exposure to outer space environment outside of ISS ("Expose-R" and"Biorisk" projects) and now are being considered for including into the Phobos-Grunt mission as a testing organism to analyze capability of resting stages of multicellular organism to interplanetary flights.

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

    Science.gov (United States)

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

    2013-09-01

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

  14. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region

    Science.gov (United States)

    Delfin, Frederick; Min-Shan Ko, Albert; Li, Mingkun; Gunnarsdóttir, Ellen D; Tabbada, Kristina A; Salvador, Jazelyn M; Calacal, Gayvelline C; Sagum, Minerva S; Datar, Francisco A; Padilla, Sabino G; De Ungria, Maria Corazon A; Stoneking, Mark

    2014-01-01

    The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago. PMID:23756438

  15. Ancient Biomolecules and Evolutionary Inference

    DEFF Research Database (Denmark)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando

    2018-01-01

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleo...

  16. Reconstructing ancient genomes and epigenomes

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  17. 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.

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

    Science.gov (United States)

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

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650–1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region’s demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500–700 AD), Wari (Middle Horizon, 800–1000 AD) and Ychsma (Late Intermediate Period, 1000–1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast. PMID:27248693

  19. Genetic Engineering of Insects

    Indian Academy of Sciences (India)

    wild-type DNA resulted in the production of adults with wing ... using conventional method of breeding and selection. .... insects, birds, and other animals .... used to derive the expression of the antibiotic, tetracycline repressible transactivator.

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

    Directory of Open Access Journals (Sweden)

    Heike H. Zimmermann

    2017-10-01

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

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

    Science.gov (United States)

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

    2010-09-01

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

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

    Directory of Open Access Journals (Sweden)

    S Elizabeth Alter

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

  3. Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.

    Science.gov (United States)

    Loog, Liisa; Thomas, Mark G; Barnett, Ross; Allen, Richard; Sykes, Naomi; Paxinos, Ptolemaios D; Lebrasseur, Ophélie; Dobney, Keith; Peters, Joris; Manica, Andrea; Larson, Greger; Eriksson, Anders

    2017-08-01

    Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

    NARCIS (Netherlands)

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

    1995-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Scott D Hamilton-Brehm

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

  6. A guide to ancient protein studies

    DEFF Research Database (Denmark)

    Hendy, Jessica; Welker, Frido; Demarchi, Beatrice

    2018-01-01

    Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from....... Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research...

  7. Nucleotide sequence of a cDNA coding for the barley seed protein CMa: an inhibitor of insect α-amylase

    DEFF Research Database (Denmark)

    Rasmussen, Søren Kjærsgård; Johansson, A.

    1992-01-01

    The primary structure of the insect alpha-amylase inhibitor CMa of barley seeds was deduced from a full-length cDNA clone pc43F6. Analysis of RNA from barley endosperm shows high levels 15 and 20 days after flowering. The cDNA predicts an amino acid sequence of 119 residues preceded by a signal...... peptide of 25 amino acids. Ala and Leu account for 55% of the signal peptide. CMa is 60-85% identical with alpha-amylase inhibitors of wheat, but shows less than 50% identity to trypsin inhibitors of barley and wheat. The 10 Cys residues are located in identical positions compared to the cereal inhibitor...

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

    Science.gov (United States)

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

    2014-04-02

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

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

    Science.gov (United States)

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

    2011-12-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

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

    OpenAIRE

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

    1998-01-01

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

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

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand

    Due to the recent advances in DNA sequencing technology genomic data are being generated at an unprecedented rate and we are gaining access to entire genomes at population level. The technology does, however, not give direct access to the genetic variation and the many levels of preprocessing...... that is required before being able to make inferences from the data introduces multiple levels of uncertainty, especially for low-depth data. Therefore methods that take into account the inherent uncertainty are needed for being able to make robust inferences in the downstream analysis of such data. This poses...... a problem for a range of key summary statistics within populations genetics where existing methods are based on the assumption that the true genotypes are known. Motivated by this I present: 1) a new method for the estimation of relatedness between pairs of individuals, 2) a new method for estimating...

  13. 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.

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

    Science.gov (United States)

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

    2017-11-01

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

  15. Marine insects

    National Research Council Canada - National Science Library

    Cheng, Lanna

    1976-01-01

    .... Not only are true insects, such as the Collembola and insect parasites of marine birds and mammals, considered, but also other kinds of intertidal air-breathing arthropods, notably spiders, scorpions...

  16. Edible Insects

    NARCIS (Netherlands)

    Huis, van A.; Dunkel, F.V.

    2016-01-01

    The interest in insects as human food in the Western world is increasingly considered as a viable alternative to other protein sources. In tropical countries it is common practice and about 2000 insect species are eaten. Insects emit low levels of greenhouse gases, need little water, and require

  17. Consuming insects

    NARCIS (Netherlands)

    Roos, N.; Huis, van A.

    2017-01-01

    How healthy are insects? This is a highly relevant question in view of the global interest in the potential of insects as a sustainable food source in food systems and diets. Edible insects, like other foods, can provide nutrients and dietary energy to meet the requirements of the human body as a

  18. Siberian population of the New Stone Age: mtDNA haplotype diversity in the ancient population from the Ust'-Ida I burial ground, dated 4020-3210 BC by 14C.

    Science.gov (United States)

    Naumova O, Y u; Rychkov S, Y u

    1998-03-01

    On the basis of analysis of mtDNA from skeletal remains, dated by 14C 4020-3210 BC, from the Ust'-Ida I Neolithic burial ground in Cis-Baikal area of Siberia, we obtained genetic characteristics of the ancient Mongoloid population. Using the 7 restriction enzymes for the analysis of site's polymorphism in 16,106-16,545 region of mtDNA, we studied the structure of the most frequent DNA haplotypes, and estimated the intrapopulational nucleotide diversity of the Neolithic population. Comparison of the Neolithic and modern indigeneous populations from Siberia, Mongolia and Ural showed, that the ancient Siberian population is one of the ancestors of the modern population of Siberia. From genetic distance, in the assumption of constant nucleotide substitution rate, we estimated the divergence time between the Neolithic and the modern Siberian population. This divergence time (5572 years ago) is conformed to the age of skeletal remains (5542-5652 years). With use of the 14C dates of the skeletal remains, nucleotide substitution rate in mtDNA was estimated as 1% sequence divergence for 8938-9115 years.

  19. Ancient Egypt

    Science.gov (United States)

    Swamy, Ashwin Balegar

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

  20. 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 sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results......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...

  1. Insect Detectives

    Indian Academy of Sciences (India)

    2002-08-01

    Aug 1, 2002 ... all life stages of insects from and around the corpse. The collected specimens are subjected to further analysis either in the field itself or in the laboratory. A forensic entomologist has three main objectives in his mind while analyzing the insect data: determination of place, time and mode of death, each of.

  2. Insect Keepers

    Science.gov (United States)

    Moore, Virginia J.; Chessin, Debby A.; Theobald, Becky

    2010-01-01

    Insects are fascinating creatures--especially when you and your students get up close and personal with them! To that end, the authors facilitated an inquiry-based investigation with an emphasis on identification of the different types of insects found in the school yard, their characteristics, their habitat, and what they eat, while engaging the…

  3. Edible insects

    NARCIS (Netherlands)

    Huis, van A.

    2017-01-01

    Is it an impossible task to convince consumers to eat insects? This does not only apply to western consumers who are less familiar with this food habit than consumers in tropical countries. In the tropics too, many people do not consume insects, even though they are easier to collect as food than

  4. Eating insects

    NARCIS (Netherlands)

    Tan, Hui Shan Grace

    2017-01-01

    In recent years, edible insects have gained global attention due to their nutritional and environmental advantages over conventional meat. While numerous species of edible insects are enjoyed in various cultures around the world, most Western consumers react with disgust and aversion towards

  5. Solar ultraviolet-B radiation affects seedling emergence, DNA integrity, plant morphology, growth rate, and attractiveness to herbivore insects in Datura ferox

    International Nuclear Information System (INIS)

    Ballare, C.L.; Scopel, A.L.; Stapleton, A.E.

    1996-01-01

    To study functional relationships between the effects of solar ultraviolet-B radiation (UV0B) on different aspects of the physiology of a wild plant, we carried out exclusion experiments in the field with the summer annual Datura ferrox L. Solar UV-B incident over Buenos Aires reduced daytime seedling emergence, inhibited stem elongation and leaf expansion, and tended to reduce biomass accumulation during early growth. However, UV-B had no effect on calculated net assimilation rate. Using a monoclonal antibody specific to the cyclobutane-pyrimidine dimer (CPD), we found that plants receiving full sunlight had more CPDs per unit of DNA than plants shielded from solar UV-B, but the positive correlation between UV-B and CPD burden tended to level off at high (near solar) UV-B levels. At our field site, Datura plants were consumed by leaf beetles (Coleoptera), and the proportion of plants attacked by insects declined with the amount of UV-B received during growth. Field experiments showed that plant exposure to solar UV-B reduced the likelihood of leaf beetle attack by one-half. Our results highlight the complexities associated with scaling plant responses to solar UV-B, because they show: (a) a lack of correspondence between UV-B effects on net assimilation rate and whole-plant growth rate, (b) nonlinear UV-B dose-response curves, and (c) UV-B effects of plant attractiveness to natural herbivores. 56 refs., 7 figs

  6. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

    DEFF Research Database (Denmark)

    Campos, Paula; Kristensen, Tommy; Orlando, Ludovic Antoine Alexandre

    2010-01-01

    of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two...... well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals...... and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate...

  7. Marketing insects

    DEFF Research Database (Denmark)

    Schiemer, Carolin; Halloran, Afton Marina Szasz; Jespersen, Kristjan

    2018-01-01

    In entering Western markets, edible insects are typically framed as the ‘solution’ to a number of challenges caused by unsustainable global food systems, such as climate change and global health issues. In addition, some media outlets also frame insects as the next ‘superfood’. Superfood is a mar......In entering Western markets, edible insects are typically framed as the ‘solution’ to a number of challenges caused by unsustainable global food systems, such as climate change and global health issues. In addition, some media outlets also frame insects as the next ‘superfood’. Superfood...... is a marketing term for nutrient-packed foods, which are successfully promoted to Western consumers with the promises of health, well-being and beauty. However, the increase in the demand in the West is argued to cause negative social, environmental, economic and cultural consequences – externalities – felt...

  8. Insect Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Records of past temperature and environment derived from beetle and other insect fossils. Parameter keywords describe what was measured in this data set. Additional...

  9. Insect Detectives

    Indian Academy of Sciences (India)

    2002-08-01

    Aug 1, 2002 ... He writes popular science articles in ... science, English poetry is his area of ... A fascinating branch of insect science (ento- ... Methods in Forensic Entomology .... bullet wound to the right temple, and a substantial pooling of.

  10. Eating insects

    OpenAIRE

    Tan, Hui Shan Grace

    2017-01-01

    In recent years, edible insects have gained global attention due to their nutritional and environmental advantages over conventional meat. While numerous species of edible insects are enjoyed in various cultures around the world, most Western consumers react with disgust and aversion towards eating creatures that are not regarded as food. The low consumer acceptance of this culturally inappropriate food is currently considered to be one of the key barriers to attaining the benefits of this po...

  11. Deciphering Equine Evolution and Spatial Ancestry with Ancient Data

    DEFF Research Database (Denmark)

    Jónsson, Hákon

    High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored to the s......High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored...... in the analysis of environmental bacterial sequences, which generally dominate ancient DNA extracts, and in the first pipeline completely devoted to the computational analysis of raw ancient DNA sequences. We then develop a spatially explicit method for determining which extant populations show the greatest...... genetic anity to ancient individuals, which often represents the key question in human paleogenomic projects. We applied the computational infrastructure developed to complete the genomic characterization of extant members of the genus Equus, which is composed of horses, asses and zebras. We sequenced...

  12. Insects vis a vis radiations

    International Nuclear Information System (INIS)

    Srivastava, Meera

    2014-01-01

    , although the dominant theory is that it relates to the relatively small amount of DNA in insect cells. One of the difficulties is assessing possible mechanisms is that very little work on insect radiobiology is being carried out?

  13. Ancient Biomolecules and Evolutionary Inference.

    Science.gov (United States)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando; Welker, Frido; Pedersen, Mikkel Winther; Allentoft, Morten E; de Barros Damgaard, Peter; Gutenbrunner, Petra; Dunne, Julie; Hammann, Simon; Roffet-Salque, Mélanie; Ilardo, Melissa; Moreno-Mayar, J Víctor; Wang, Yucheng; Sikora, Martin; Vinner, Lasse; Cox, Jürgen; Evershed, Richard P; Willerslev, Eske

    2018-04-25

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  14. 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…

  15. Molecules in the mud: Combining ancient DNA and lipid biomarkers to reconstruct vegetation response to climate variability during the Last Interglacial and the Holocene on Baffin Island, Arctic Canada

    Science.gov (United States)

    Crump, S. E.; Sepúlveda, J.; Bunce, M.; Miller, G. H.

    2017-12-01

    Modern ecological studies are revealing that the "greening" of the Arctic, resulting from a poleward shift in woody vegetation ranges, is already underway. The increasing abundance of shrubs in tundra ecosystems plays an important role in the global climate system through multiple positive feedbacks, yet uncertainty in future predictions of terrestrial vegetation means that climate models are likely not capturing these feedbacks accurately. Recently developed molecular techniques for reconstructing past vegetation and climate allow for a closer look at the paleo-record in order to improve our understanding of tundra community responses to climate variability; our current research focus is to apply these tools to both Last Interglacial and Holocene warm times. Here we present initial results from a small lake on southern Baffin Island spanning the last 7.2 ka. We reconstruct climate with both bulk geochemical and biomarker proxies, primarily using biogenic silica and branched glycerol dialkyl glycerol tetraethers (brGDGTs) as temperature indicators. We assess shifts in plant community using multivariate analysis of sedimentary ancient DNA (sedaDNA) metabarcoding data. This combination of approaches reveals that the vegetation community has responded sensitively to early Holocene warmth, Neoglacial cooling, and possibly modern anthropogenic warming. To our knowledge, this represents the first combination of a quantitative, biomarker-based climate reconstruction with a sedaDNA-based paleoecological reconstruction, and offers a glimpse at the potential of these molecular techniques used in tandem.

  16. Consuming insects

    DEFF Research Database (Denmark)

    Roos, Nanna; van Huis, A.

    2017-01-01

    as a part of a varied diet. They also have the potential to provide bioactive compounds that have health benefits beyond simple nutritional values, as is the case for other food groups such as fruits and vegetables. Various recent studies have indicated such bioactivity in different insect species....... The enormous number of edible insect species may be a source of novel bioactive compounds with health benefits addressing global health challenges. However, any identified health benefits need to be confirmed in human studies or in standardised assays accepted in health research prior to making health claims....

  17. Insect Capital

    Directory of Open Access Journals (Sweden)

    Andrew Pilsch

    2015-12-01

    Full Text Available In this note, Pilsch address William Gibson’s use of insect imagery in to trouble the common understanding of the novel Neuromancer, its commentary on corporate culture, and its relationship to a then-emergent posthumanism. Further, he concludes by suggesting that, for Gibson, the insect hive as an image for the corporate body shows that corporate culture is, in contrast to the banal image the term brings to mind, a set of nefarious cultural techniques derived for interfacing human bodies with the corporation’s native environment in the postmodern era: the abstractions of data.

  18. Stinging Insect Matching Game

    Science.gov (United States)

    ... for Kids ▸ Stinging Insect Matching Game Share | Stinging Insect Matching Game Stinging insects can ruin summer fun for those who are ... the difference between the different kinds of stinging insects in order to keep your summer safe and ...

  19. Ancient DNA Investigation of a Medieval German Cemetery Confirms Long-Term Stability of CCR5-Δ32 Allele Frequencies in Central Europe.

    Science.gov (United States)

    Bouwman, Abigail; Shved, Natallia; Akgül, Gülfirde; Rühli, Frank; Warinner, Christina

    2017-04-01

    The CCR5-Δ32 mutation present in European populations is among the most prominently debated cases of recent positive selection in humans. This allele, a 32-bp deletion that renders the T-cell CCR5 receptor nonfunctional, has important epidemiological and public health significance, as homozygous carriers are resistant to several HIV strains. However, although the function of this allele in preventing HIV infection is now well described, its human evolutionary origin is poorly understood. Initial attempts to determine the emergence of the CCR5-Δ32 allele pointed to selection during the 14th-century Black Death pandemic; however, subsequent analyses suggest that the allele rose in frequency more than 5,000 years ago, possibly through drift. Recently, three studies have identified populations predating the 14th century CE that are positive for the CCR5-Δ32 allele, supporting the claim for a more ancient origin. However, these studies also suggest poorly understood regional differences in the recent evolutionary history of the CCR5-Δ32 allele. Here a new hydrolysis-probe-based real-time PCR assay was designed to ascertain CCR5 allele frequency in 53 individuals from a 10th- to 12th-century CE church and convent complex in central Germany that predates outbreaks of the Black Death pandemic. High-confidence genotypes were obtained for 32 individuals, and results show that CCR5-Δ32 allele frequency has remained unchanged in this region of Central Europe over the last millennium, suggesting that there has been no strong positive selective pressure over this time period and confirming a more ancient origin for the allele.

  20. Insects: A nutritional alternative

    Science.gov (United States)

    Dufour, P. A.

    1981-01-01

    Insects are considered as potential food sources in space. Types of insects consumed are discussed. Hazards of insect ingestion are considered. Insect reproduction, requirements, and raw materials conversion are discussed. Nutrition properties and composition of insects are considered. Preparation of insects as human food is discussed.

  1. Social insects and selfish genes.

    Science.gov (United States)

    Bourke, A F

    2001-10-01

    Sometimes science advances because of a new idea. Sometimes, it's because of a new technique. When both occur together, exciting times result. In the study of social insects, DNA-based methods for measuring relatedness now allow increasingly detailed tests of Hamilton's theory of kin selection.

  2. The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th-17th century burial population from the Canary Islands, Spain.

    Science.gov (United States)

    Santana, Jonathan; Fregel, Rosa; Lightfoot, Emma; Morales, Jacob; Alamón, Martha; Guillén, José; Moreno, Marco; Rodríguez, Amelia

    2016-02-01

    The Canary Islands are considered one of the first places where Atlantic slave plantations with labourers of African origin were established, during the 15th century AD. In Gran Canaria (Canary Islands, Spain), a unique cemetery dated to the 15th and 17th centuries was discovered adjacent to an ancient sugar plantation with funerary practices that could be related to enslaved people. In this article, we investigate the origin and possible birthplace of each individual buried in this cemetery, as well as the identity and social status of these people. The sample consists of 14 individuals radiocarbon dated to the 15th and 17th centuries AD. We have employed several methods, including the analysis of ancient human DNA, stable isotopes, and skeletal markers of physical activity. 1) the funerary practices indicate a set of rituals not previously recorded in the Canary Islands; 2) genetic data show that some people buried in the cemetery could have North-African and sub-Saharan African lineages; 3) isotopic results suggest that some individuals were born outside Gran Canaria; and 4) markers of physical activity show a pattern of labour involving high levels of effort. This set of evidence, along with information from historical sources, suggests that Finca Clavijo was a cemetery for a multiethnic marginalized population that had being likely enslaved. Results also indicate that this population kept practicing non-Christian rituals well into the 17th century. We propose that this was possible because the location of the Canaries, far from mainland Spain and the control of the Spanish Crown, allowed the emergence of a new society with multicultural origins that was more tolerant to foreign rituals and syncretism. © 2015 Wiley Periodicals, Inc.

  3. Genetic continuity after the collapse of the Wari empire: mitochondrial DNA profiles from Wari and post-Wari populations in the ancient Andes.

    Science.gov (United States)

    Kemp, Brian M; Tung, Tiffiny A; Summar, Marshall L

    2009-09-01

    The Wari empire flourished in the central, highland Peruvian Andes from AD 600-1000, and although the events that led to its demise are unknown, archaeological evidence indicates that Wari control waned at the end of the first millennium. Here, we test the hypothesis that, despite the major shift in social and political organization at the fall of the Wari empire, the mitochondrial DNA (mtDNA) composition of populations from the Ayacucho Basin, the former imperial heartland of the empire, remained essentially unchanged. Results show that mtDNA haplogroup frequencies among the Wari and post-Wari groups differ, but the difference is not statistically significant (chi2 = 5.886, df = 3, P = 0.1172). This is the first study in the Andes to use haplotypic data to evaluate the observed genetic distance between two temporally distinct prehispanic populations (F(ST) = 0.029) against modeled expectations of four possible evolutionary scenarios. None of these simulations allowed the rejection of continuity. In total, at both the haplogroup and haplotype levels these data do not allow us to reject the hypothesis that post-Wari individuals sampled in this study are the maternal descendants of those sampled from the Wari era site of Conchopata. However, genetic homogeneity in the mitochondrial gene pool, as seen in the late prehispanic southern Andes, may also characterize our study region. But, prior to this research, this was unknown. If our new data show mtDNA homogeneity, then this could limit the detection of female migration if, in fact, it occurred. Nonetheless, the novel mtDNA data presented here currently do not support the hypothesis that there was an influx of genetically distinct females into the former Wari heartland after the Wari collapse. Copyright 2009 Wiley-Liss, Inc.

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

    Directory of Open Access Journals (Sweden)

    Montserrat Hervella

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

  5. 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...

  6. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations.

    Science.gov (United States)

    Elkamel, Sarra; Boussetta, Sami; Khodjet-El-Khil, Houssein; Benammar Elgaaied, Amel; Cherni, Lotfi

    2018-05-01

    Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE. © 2018 Wiley Periodicals, Inc.

  7. Insect Cell Culture

    NARCIS (Netherlands)

    Oers, van M.M.; Lynn, D.E.

    2010-01-01

    Insect cell cultures are widely used in studies on insect cell physiology, developmental biology and microbial pathology. In particular, insect cell culture is an indispensable tool for the study of insect viruses. The first continuously growing insect cell cultures were established from

  8. Ancient DNA unravels the truth behind the controversial GUS Greenlandic Norse fur samples: the bison was a horse, and the muskox and beats were goats

    DEFF Research Database (Denmark)

    Sinding, Mikkel-Holger; Arneborg, Jette; Nyegaard, Georg

    2015-01-01

    The Norse Greenlandic archaeological site known as ‘the Farm Beneath the Sand’ (GUS) has sourced many well-preserved and unique archaeological artefacts. Some of the most controversial finds are tufts of hair, which previous morphological-based examination concluded derive from bison, black bear...... mitochondrial 16S DNA analysis. The results revealed that the putative bison was, in fact horse, while the bears and muskox were goat. The results demonstrate the importance of using genetic analyses to validate results derived from morphological analyses on hair, in particular where such studies lead...

  9. Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

    Science.gov (United States)

    Doerr, Daniel; Chauve, Cedric

    2017-01-01

    Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains. PMID:29114402

  10. Insects and Scorpions

    Science.gov (United States)

    ... insects or scorpions can be hazardous to outdoor workers. Stinging or biting insects include bees, wasps, hornets, and fire ants. The health effects of stinging or biting insects or scorpions range ...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    and the determination of indicator species to describe environmental changes. Combining data from all three proxies reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place...... in the Northern Hemisphere during this time, with changes in average annual temperatures of >22 °C. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals...... the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and adds to the increasing evidence suggesting large areas of the Northern Hemisphere remained ecologically stable during the Late Pleistocene....

  12. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

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

    2010-01-01

    , the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two...... 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...

  13. 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)

  14. Endocrinology in ancient Sparta.

    Science.gov (United States)

    Tsoulogiannis, Ioannis N; Spandidos, Demetrios A

    2007-01-01

    This article attempts to analyze the crucial link between the plant Agnus castus and human health, particularly hormonal status, with special reference to the needs of the society of ancient Sparta. The ancient Spartans used Agnus both as a cure for infertility and as a remedy to treat battle wounds. These special properties were recognized by the sanctuary of Asclepios Agnita, which was located in Sparta, as well as by medical practitioners in Sparta during the classical, Hellenistic and Roman ages.

  15. Repair of UV-induced DNA damage and its inhibition by etoposide in Sf9 insect cells: comparison with human cells

    International Nuclear Information System (INIS)

    Chandna, Sudhir; Dwarakanath, B.S.; Moorthy, Ganesh; Jain, Charu

    2004-01-01

    In the present investigation, the kinetics of DNA repair in a lepidopteran cell line Sf9 (derived from the ovaries of Spodoptera frugiperda) following UV-irradiation was compared with the responses in a human embryonic kidney cell. DNA repair was studied by analyzing the kinetics of induction and removal of repair related strand breaks using the alkaline single cell gel electrophoresis and Halo assays. Since topoisomerases play important roles in the cellular responses to UV-induced damage, the effects of etoposideon DNA repair kinetics was also studied

  16. Comparison of four species-delimitation methods applied to a DNA barcode data set of insect larvae for use in routine bioassessment for use in routine bioassessment

    Science.gov (United States)

    Species delimitation (grouping individuals into distinct taxonomic groups) is an essential part of evolutionary, conservation, and molecular ecology. Deoxyribonucleic acid (DNA) barcodes, short fragments of the cytochrome c oxidase subunit I (COI) gene, are being used in environm...

  17. Insects, isotopes and radiation

    International Nuclear Information System (INIS)

    Lindquist, D.A.

    1987-01-01

    The article describes the increased use of nuclear techniques in controlling harmful insects. The sterile insect technique (SIT), which uses radiation to sexually sterilize insects and prevent reproduction, is particularly effective in eradication programmes. At the present time, there are approximately 10 species of insect pests being attacked by the SIT. Research and development is being conducted on other insect species and it is anticipated that the technology will be more widely used in the future

  18. fruitless alternative splicing and sex behaviour in insects: an ancient ...

    Indian Academy of Sciences (India)

    2010-09-06

    Sep 6, 2010 ... gifts, physical touch, and even the use of aphrodisiac sub- stances. ..... male aggressive interaction' behaviour in D. melanogaster. (Lee and Hall 2000; ..... In conclusion, fru with its complex system of multi-level regulation is ...

  19. Debris-carrying camouflage among diverse lineages of Cretaceous insects.

    Science.gov (United States)

    Wang, Bo; Xia, Fangyuan; Engel, Michael S; Perrichot, Vincent; Shi, Gongle; Zhang, Haichun; Chen, Jun; Jarzembowski, Edmund A; Wappler, Torsten; Rust, Jes

    2016-06-01

    Insects have evolved diverse methods of camouflage that have played an important role in their evolutionary success. Debris-carrying, a behavior of actively harvesting and carrying exogenous materials, is among the most fascinating and complex behaviors because it requires not only an ability to recognize, collect, and carry materials but also evolutionary adaptations in related morphological characteristics. However, the fossil record of such behavior is extremely scarce, and only a single Mesozoic example from Spanish amber has been recorded; therefore, little is known about the early evolution of this complicated behavior and its underlying anatomy. We report a diverse insect assemblage of exceptionally preserved debris carriers from Cretaceous Burmese, French, and Lebanese ambers, including the earliest known chrysopoid larvae (green lacewings), myrmeleontoid larvae (split-footed lacewings and owlflies), and reduviids (assassin bugs). These ancient insects used a variety of debris material, including insect exoskeletons, sand grains, soil dust, leaf trichomes of gleicheniacean ferns, wood fibers, and other vegetal debris. They convergently evolved their debris-carrying behavior through multiple pathways, which expressed a high degree of evolutionary plasticity. We demonstrate that the behavioral repertoire, which is associated with considerable morphological adaptations, was already widespread among insects by at least the Mid-Cretaceous. Together with the previously known Spanish specimen, these fossils are the oldest direct evidence of camouflaging behavior in the fossil record. Our findings provide a novel insight into early evolution of camouflage in insects and ancient ecological associations among plants and insects.

  20. Resurrecting ancient animal genomes: the extinct moa and more.

    Science.gov (United States)

    Huynen, Leon; Millar, Craig D; Lambert, David M

    2012-08-01

    Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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.

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

    DEFF Research Database (Denmark)

    Mouatt, Julia Thidamarth Vilstrup

    enrichment methods and the massive throughput and latest advances within DNA sequencing, the field of ancient DNA has flourished in later years. Those advances have even enabled the sequencing of complete genomes from the past, moving the field into genomic sciences. In this thesis we have used these latest......The sequencing of ancient DNA provides perspectives on the genetic history of past populations and extinct species. However, ancient DNA research presents specific limitations mostly due to DNA survival, damage and contamination. Yet with stringent laboratory procedures, the sensitivity of target...... developments within ancient DNA research, including target enrichment capture and Next-Generation Sequencing, to address a range of evolutionary questions related to two major mammalian groups, equids and rodents. In particular we have resolved phylogenetic relationships within equids using complete mitochond...

  3. Genomic gigantism: DNA loss is slow in mountain grasshoppers.

    Science.gov (United States)

    Bensasson, D; Petrov, D A; Zhang, D X; Hartl, D L; Hewitt, G M

    2001-02-01

    Several studies have shown DNA loss to be inversely correlated with genome size in animals. These studies include a comparison between Drosophila and the cricket, Laupala, but there has been no assessment of DNA loss in insects with very large genomes. Podisma pedestris, the brown mountain grasshopper, has a genome over 100 times as large as that of Drosophila and 10 times as large as that of Laupala. We used 58 paralogous nuclear pseudogenes of mitochondrial origin to study the characteristics of insertion, deletion, and point substitution in P. pedestris and Italopodisma. In animals, these pseudogenes are "dead on arrival"; they are abundant in many different eukaryotes, and their mitochondrial origin simplifies the identification of point substitutions accumulated in nuclear pseudogene lineages. There appears to be a mononucleotide repeat within the 643-bp pseudogene sequence studied that acts as a strong hot spot for insertions or deletions (indels). Because the data for other insect species did not contain such an unusual region, hot spots were excluded from species comparisons. The rate of DNA loss relative to point substitution appears to be considerably and significantly lower in the grasshoppers studied than in Drosophila or Laupala. This suggests that the inverse correlation between genome size and the rate of DNA loss can be extended to comparisons between insects with large or gigantic genomes (i.e., Laupala and Podisma). The low rate of DNA loss implies that in grasshoppers, the accumulation of point mutations is a more potent force for obscuring ancient pseudogenes than their loss through indel accumulation, whereas the reverse is true for Drosophila. The main factor contributing to the difference in the rates of DNA loss estimated for grasshoppers, crickets, and Drosophila appears to be deletion size. Large deletions are relatively rare in Podisma and Italopodisma.

  4. A nuclear insect appears

    International Nuclear Information System (INIS)

    Shin, Gi Hwal

    1989-06-01

    This book is dairy of a nuclear insect in A. F. era. It consists of 6 parts, which have fun pictures and titles. The contents are the letter that is sent the Homo sapiens by insect, exodus of nuclear insect F 100 years latter. The time that a nuclear insect is attacked in F 101, the time that a nuclear dinosaur is beat in AF 102, the time that a nuclear insect struggles in AF 104 and the time that a nuclear insect drifts in AF 104.

  5. 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...

  6. Printing Ancient Terracotta Warriors

    Science.gov (United States)

    Gadecki, Victoria L.

    2010-01-01

    Standing in awe in Xian, China, at the Terra Cotta warrior archaeological site, the author thought of sharing this experience and excitement with her sixth-grade students. She decided to let her students carve patterns of the ancient soldiers to understand their place in Chinese history. They would make block prints and print multiple soldiers on…

  7. Trepanation in Ancient China.

    Science.gov (United States)

    Hobert, Leah; Binello, Emanuela

    2017-05-01

    Trepanation, the process of making a burr hole in the skull to access the brain, is an ancient form of a primitive craniotomy. There is widespread evidence of contributions made to this practice by ancient civilizations in Europe, Africa, and South America, where archaeologists have unearthed thousands of trepanned skulls dating back to the Neolithic period. Little is known about trepanation in China, and it is commonly believed that the Chinese used only traditional Chinese medicine and nonsurgical methods for treating brain injuries. However, a thorough analysis of the available archeological and literary evidence reveals that trepanation was widely practiced throughout China thousands of years ago. A significant number of trepanned Chinese skulls have been unearthed showing signs of healing and suggesting that patients survived after surgery. Trepanation was likely performed for therapeutic and spiritual reasons. Medical and historical works from Chinese literature contain descriptions of primitive neurosurgical procedures, including stories of surgeons, such as the legendary Hua Tuo, and surgical techniques used for the treatment of brain pathologies. The lack of translation of Chinese reports into the English language and the lack of publications on this topic in the English language may have contributed to the misconception that ancient China was devoid of trepanation. This article summarizes the available evidence attesting to the performance of successful primitive cranial surgery in ancient China. Copyright © 2016 Elsevier Inc. All rights reserved.

  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. 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…

  10. Ancient ports of Kalinga

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    which plied between Kalinga and south east Asian countries. Nanda Raja, is said to have attacked Kalinga with the intention of getting access to the sea for the landlocked Kingdom of Magadha (Bihar). The ancient texa Artha Sastra (3rd-4th century B...

  11. DNA sequences of troglobitic nicoletiid insects support Sierra de El Abra and the Sierra de Guatemala as a single biogeographical area: Implications for Astyanax

    Directory of Open Access Journals (Sweden)

    Luis Espinasa

    2014-03-01

    Full Text Available The blind Mexican tetra fish, Astyanax mexicanus, has become the most influential model for research of cave adapted organisms. Many authors assume that the Sierra de Guatemala populations and the Sierra de El Abra populations are derived from two independent colonizations. This assumption arises in part from biogeography. The 100 m high, 100 m wide Servilleta Canyon of the Boquillas River separates both mountain ranges and is an apparent barrier for troglobite dispersion. Anelpistina quinterensis (Nicoletiidae, Zygentoma, Insecta is one of the most troglomorphic nicoletiid silverfish insects ever described. 16S rRNA sequences support that this species migrated underground to reach both mountain ranges within less than 12,000 years. Furthermore, literature shows a plethora of aquatic and terrestrial cave restricted species that inhabit both mountain ranges. Thus, the Servilleta canyon has not been an effective biological barrier that prevented underground migration of troglobites between the Sierra de Guatemala and the Sierra de El Abra. The Boquillas River has changed its course throughout time. Caves that in the past connected the two Sierras were only recently geologically truncated by the erosion of the new river course. It is likely that, with the geological changes of the area and throughout the 2-8 million years of evolutionary history of cave Astyanax, there have been opportunities to migrate across the Servilleta canyon.

  12. Respiration in Aquatic Insects.

    Science.gov (United States)

    MacFarland, John

    1985-01-01

    This article: (1) explains the respiratory patterns of several freshwater insects; (2) describes the differences and mechanisms of spiracular cutaneous, and gill respiration; and (3) discusses behavioral aspects of selected aquatic insects. (ML)

  13. Insect Bites and Stings

    Science.gov (United States)

    Most insect bites are harmless, though they sometimes cause discomfort. Bee, wasp, and hornet stings and fire ant bites usually hurt. Mosquito and flea bites usually itch. Insects can also spread diseases. In the United States, ...

  14. Insects: An Interdisciplinary Unit

    Science.gov (United States)

    Leger, Heather

    2007-01-01

    The author talks about an interdisciplinary unit on insects, and presents activities that can help students practice communication skills (interpersonal, interpretive, and presentational) and learn about insects with hands-on activities.

  15. Insects of the riparian

    Science.gov (United States)

    Terrence J. Rogers

    1996-01-01

    This paper describes life histories, defoliation problems and other activities of insects associated with forest tree species growing along high elevation streams and river banks. In addition, examples of insects and diseases associated with lower elevation riparian areas are given.

  16. Radioactive labelling of insects

    International Nuclear Information System (INIS)

    Thygesen, Th.

    Experiments are described with the internal contamination of insects with phosphorus 32 introduced previously in plants of the brassica type using three different techniques. The intake of radioactivity from the plants to the insects is shown. (L.O.)

  17. Exploring Sound with Insects

    Science.gov (United States)

    Robertson, Laura; Meyer, John R.

    2010-01-01

    Differences in insect morphology and movement during singing provide a fascinating opportunity for students to investigate insects while learning about the characteristics of sound. In the activities described here, students use a free online computer software program to explore the songs of the major singing insects and experiment with making…

  18. Insects and human nutrition

    DEFF Research Database (Denmark)

    Roos, Nanna

    2018-01-01

    Despite high diversity in species as well as metamorphological life-­stages, edible insects are essentially an animal-source food contributing high quality protein and fat when viewed in the context of human nutrition. The nutritional contribution of insects to diets in populations where insects ...

  19. Ligation bias in Illumina next-generation DNA libraries

    DEFF Research Database (Denmark)

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

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products,...... for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.......Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by......-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate...

  20. PLEIADES IN ANCIENT MESOPOTAMIA

    OpenAIRE

    Verderame, L.

    2016-01-01

    In this paper I will analyse the different features of the Pleiades in the astronomical, astrological, and calendrical interpretation as well as their mythical and cultural background in ancient Mesopotamia. According to cuneiform sources, the Pleiades are among the most important stars. They are simply known in Sumerian as ―the Stars‖ (MUL.MUL), while their Akkadian name, ―the Bristle‖ (zappu), links them to the imagery and the cultural context of the ―Bull of Heaven‖ constellation (Taurus),...

  1. Linen in Ancient Egypt

    Directory of Open Access Journals (Sweden)

    dr.Rehab Mahmoud Ahmed Elsharnouby

    2014-01-01

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

  2. 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

  3. DNA sequence and prokaryotic expression analysis of vitellogenin ...

    African Journals Online (AJOL)

    USER

    2010-02-08

    Feb 8, 2010 ... 2Laboratory of Silkworm Genetics and Pathology, Faculty of Textile Science and Technology, ... tera insects Bombyx mori (Yano et al., 1994a; Yano et al., ... To investigate the evolutionary ..... reveals ancient common ancestry.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  5. 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...

  6. 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.

  7. 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

  8. Musical ensembles in Ancient Mesapotamia

    NARCIS (Netherlands)

    Krispijn, T.J.H.; Dumbrill, R.; Finkel, I.

    2010-01-01

    Identification of musical instruments from ancient Mesopotamia by comparing musical ensembles attested in Sumerian and Akkadian texts with depicted ensembles. Lexicographical contributions to the Sumerian and Akkadian lexicon.

  9. Endocrinology of insects

    National Research Council Canada - National Science Library

    Downer, Roger G. H; Laufer, Hans

    1983-01-01

    Contents: Organization of the neuroendocrine system - Chemistry of insect hormones and neurohormones - Regulation of metamorphosis - Regulation of reproduction - Regulation of growth and development...

  10. Detecting Ancient Tuberculosis

    Directory of Open Access Journals (Sweden)

    Angela M. Gernaey

    1998-12-01

    Full Text Available Some diseases have played a more significant role in human development than others. Here we describe the results of a trial to diagnose ancient tuberculosis using chemical methods. Palaeo-epidemiological studies of the disease are compromised, but it has become apparent that tuberculosis (TB is a 'population-density dependent' disease. From modern studies, it is also apparent that the prevalence of TB can be used as an indicator of the level of poverty within the studied population. Mid-shaft rib samples from articulated individuals recovered from the former Newcastle Infirmary Burial Ground (1753-1845 AD were examined for mycolic acids that are species-specific for Mycobacterium tuberculosis. The 24% of ribs positive for mycolic acids correlated with the documented 27% tuberculosis prevalence. Mycolic acid biomarkers have the potential to provide an accurate trace of the palaeo-epidemiology of tuberculosis in ancient populations, thereby providing an indication of the overall level of poverty - a useful adjunct for archaeology.

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

    CERN Document Server

    Kelley, David H

    2011-01-01

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

  12. The role of birds and insects in pollination shifts of Scrophularia (Scrophulariaceae).

    Science.gov (United States)

    Navarro-Pérez, María L; López, Josefa; Fernández-Mazuecos, Mario; Rodríguez-Riaño, Tomás; Vargas, Pablo; Ortega-Olivencia, Ana

    2013-10-01

    The mixed vertebrate-insect pollination system is rare in Holarctic plants. Phylogenetic relationships of 116 Scrophularia taxa were investigated based on two plastid (ndhF and trnL-trnF) and one nuclear (ITS) DNA regions. A wider time-calibrated analysis of ndhF sequences of the Lamiales revealed that Scrophularia diverged as early as in the Miocene (<22 Ma). Results of maximum-likelihood optimizations supported wasp pollination as the ancestral pollination system from which other systems derived (hoverfly, mixed vertebrate-insect and bird systems). Four origins for a mixed vertebrate-insect (MVI) pollination system were inferred, in which two western Mediterranean species (S. sambucifolia and S. grandiflora) and two island species (the Tirrenian S. trifoliata and the Canarian S. calliantha) were involved. S. calliantha is the only species in which a more complex MVI system, including pollination by the lizard Gallotia stehlini, has evolved. In addition, bird (hummingbird) floral traits found in the New Mexican S. macrantha appear to have been independently acquired. In contrast, we failed to find evidence for an ancient role of hummingbirds in the evolution of European Scrophularia. Indeed, paleontological data revealed that extinction of European hummingbirds (30-32 Ma) occurred earlier than the divergence of European MVI lineages of Scrophularia. In conclusion, our results showed that a role of birds in pollination of Scrophularia may not have been effective in the Miocene-Pliocene, but bird pollination that shows its origin in the Pliocene-Pleistocene is still operating independently in different islands and continents. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Perspectives for DNA studies on polar ice cores

    DEFF Research Database (Denmark)

    Hansen, Anders J.; Willerslev, E.

    2002-01-01

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

  14. Insects and diseases

    Science.gov (United States)

    John W. Couston

    2009-01-01

    Insects and diseases are a natural part of forested ecosystems. Their activity is partially regulated by biotic factors, e.g., host abundance, host quality; physical factors, e.g., soil, climate; and disturbances (Berryman 1986). Insects and diseases can influence both forest patterns and forest processes by causing, for example, defoliation and mortality. These...

  15. Insects: Bugged Out!

    Science.gov (United States)

    Piehl, Kathy

    2011-01-01

    Insects really need no introduction. They have lived on earth much longer than humans and vastly outnumber people and all other animal species combined. People encounter them daily in their houses and yards. Yet, when children want to investigate insects, books can help them start their explorations. "Paleo Bugs" carries readers back to the time…

  16. Insects and Bugs

    Science.gov (United States)

    Sutherland, Karen

    2009-01-01

    They have been around for centuries. They sting, they bite. They cause intense itching or painful sores. They even cause allergic reactions and sometimes death. There are two types of insects that are pests to humans--those that sting and those that bite. The insects that bite do so with their mouths and include mosquitoes, chiggers, and ticks.…

  17. Helminthes and insects: maladies or therapies.

    Science.gov (United States)

    El-Tantawy, Nora L

    2015-02-01

    By definition, parasites cause harm to their hosts. But, considerable evidence from ancient traditional medicine has supported the theory of using parasites and their products in treating many diseases. Maggots have been used successfully to treat chronic, long-standing, infected wounds which failed to respond to conventional treatment by many beneficial effects on the wound including debridement, disinfection, and healing enhancement. Maggots are also applied in forensic medicine to estimate time between the death and discovery of a corpse and in entomotoxicology involving the potential use of insects as alternative samples for detecting drugs and toxins in death investigations. Leeches are segmented invertebrates, famous by their blood-feeding habits and used in phlebotomy to treat various ailments since ancient times. Leech therapy is experiencing resurgence nowadays in health care principally in plastic and reconstructive surgery. Earthworms provide a source of medicinally useful products with potential antimicrobial, antiviral, and anticancer properties. Lumbrokinases are a group of fibrinolytic enzymes isolated and purified from earthworms capable of degrading plasminogen-rich and plasminogen-free fibrin and so can be used to treat various conditions associated with thrombotic diseases. Helminth infection has been proved to have therapeutic effects in both animal and human clinical trials with promising evidence in treating many allergic diseases and can block the induction of or reduce the severity of some autoimmune disorders as Crohn's disease or ulcerative colitis. What is more, venomous arthropods such as scorpions, bees, wasps, spiders, ants, centipedes, snail, beetles, and caterpillars. The venoms and toxins from these arthropods provide a promising source of natural bioactive compounds which can be employed in the development of new drugs to treat diseases as cancer. The possibility of using these active molecules in biotechnological processes can

  18. 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.

  19. 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.

  20. Insect cell transformation vectors that support high level expression and promoter assessment in insect cell culture

    Science.gov (United States)

    A somatic transformation vector, pDP9, was constructed that provides a simplified means of producing permanently transformed cultured insect cells that support high levels of protein expression of foreign genes. The pDP9 plasmid vector incorporates DNA sequences from the Junonia coenia densovirus th...

  1. Ancient symbiosis confers desiccation resistance to stored grain pest beetles.

    Science.gov (United States)

    Engl, Tobias; Eberl, Nadia; Gorse, Carla; Krüger, Theresa; Schmidt, Thorsten H P; Plarre, Rudy; Adler, Cornel; Kaltenpoth, Martin

    2017-11-08

    Microbial symbionts of insects provide a range of ecological traits to their hosts that are beneficial in the context of biotic interactions. However, little is known about insect symbiont-mediated adaptation to the abiotic environment, for example, temperature and humidity. Here, we report on an ancient clade of intracellular, bacteriome-located Bacteroidetes symbionts that are associated with grain and wood pest beetles of the phylogenetically distant families Silvanidae and Bostrichidae. In the saw-toothed grain beetle Oryzaephilus surinamensis, we demonstrate that the symbionts affect cuticle thickness, melanization and hydrocarbon profile, enhancing desiccation resistance and thereby strongly improving fitness under dry conditions. Together with earlier observations on symbiont contributions to cuticle biosynthesis in weevils, our findings indicate that convergent acquisitions of bacterial mutualists represented key adaptations enabling diverse pest beetle groups to survive and proliferate under the low ambient humidity that characterizes dry grain storage facilities. © 2017 John Wiley & Sons Ltd.

  2. Beneficial Insects and Insect Pollinators on Milkweed in South Georgia

    Science.gov (United States)

    Insect pollinators are essential for the reproduction of more than two-thirds of the world’s crops, and beneficial insects play an important role in managing pest insects in agricultural farmscapes. These insects depend on nectar for their survival in these farmscapes. The flowers of tropical milkwe...

  3. 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

  4. Evolutionary conservation and changes in insect TRP channels.

    Science.gov (United States)

    Matsuura, Hironori; Sokabe, Takaaki; Kohno, Keigo; Tominaga, Makoto; Kadowaki, Tatsuhiko

    2009-09-10

    TRP (Transient Receptor Potential) channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP channels and the mechanisms of integrating sensory inputs in insects, we have identified and compared TRP channel genes in Drosophila melanogaster, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, and Pediculus humanus genomes as part of genome sequencing efforts. All the insects examined have 2 TRPV, 1 TRPN, 1 TRPM, 3 TRPC, and 1 TRPML subfamily members, demonstrating that these channels have the ancient origins in insects. The common pattern also suggests that the mechanisms for detecting mechanical and visual stimuli and maintaining lysosomal functions may be evolutionarily well conserved in insects. However, a TRPP channel, the most ancient TRP channel, is missing in B. mori, A. mellifera, and N. vitripennis. Although P. humanus and D. melanogaster contain 4 TRPA subfamily members, the other insects have 5 TRPA subfamily members. T. castaneum, A. mellifera, and N. vitripennis contain TRPA5 channels, which have been specifically retained or gained in Coleoptera and Hymenoptera. Furthermore, TRPA1, which functions for thermotaxis in Drosophila, is missing in A. mellifera and N. vitripennis; however, they have other Hymenoptera-specific TRPA channels (AmHsTRPA and NvHsTRPA). NvHsTRPA expressed in HEK293 cells is activated by temperature increase, demonstrating that HsTRPAs function as novel thermal sensors in Hymenoptera. The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP family members. As shown for mammalian TRP channels, this

  5. Evolutionary conservation and changes in insect TRP channels

    Directory of Open Access Journals (Sweden)

    Tominaga Makoto

    2009-09-01

    Full Text Available Abstract Background TRP (Transient Receptor Potential channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP channels and the mechanisms of integrating sensory inputs in insects, we have identified and compared TRP channel genes in Drosophila melanogaster, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, and Pediculus humanus genomes as part of genome sequencing efforts. Results All the insects examined have 2 TRPV, 1 TRPN, 1 TRPM, 3 TRPC, and 1 TRPML subfamily members, demonstrating that these channels have the ancient origins in insects. The common pattern also suggests that the mechanisms for detecting mechanical and visual stimuli and maintaining lysosomal functions may be evolutionarily well conserved in insects. However, a TRPP channel, the most ancient TRP channel, is missing in B. mori, A. mellifera, and N. vitripennis. Although P. humanus and D. melanogaster contain 4 TRPA subfamily members, the other insects have 5 TRPA subfamily members. T. castaneum, A. mellifera, and N. vitripennis contain TRPA5 channels, which have been specifically retained or gained in Coleoptera and Hymenoptera. Furthermore, TRPA1, which functions for thermotaxis in Drosophila, is missing in A. mellifera and N. vitripennis; however, they have other Hymenoptera-specific TRPA channels (AmHsTRPA and NvHsTRPA. NvHsTRPA expressed in HEK293 cells is activated by temperature increase, demonstrating that HsTRPAs function as novel thermal sensors in Hymenoptera. Conclusion The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP

  6. [Ancient Egyptian Odontology].

    Science.gov (United States)

    Berghult, B

    1999-01-01

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

  7. Feeding the insect industry

    Science.gov (United States)

    This article reports the use of insect colloidal artificial diets suitable for the rearing of economically important arthropods, such as Lygus lineolaris, Lygus hesperus, Coleomegilla maculata, and Phytoseiulus persimilis The different diets contain key nutrients such as proteins, carbohydrates, vit...

  8. Allergies to Insect Venom

    Science.gov (United States)

    ... insects (as might be the case when a nest is disturbed, or when Africanized honeybees are involved); ... test with the five commercially available venoms; honey bee, paper wasp, yellow jacket, yellow hornet and white- ...

  9. Evolution of the Insects

    Science.gov (United States)

    Grimaldi, David; Engel, Michael S.

    2005-05-01

    This book chronicles the complete evolutionary history of insects--their living diversity and relationships as well as 400 million years of fossils. Introductory sections cover the living species diversity of insects, methods of reconstructing evolutionary relationships, basic insect structure, and the diverse modes of insect fossilization and major fossil deposits. Major sections then explore the relationships and evolution of each order of hexapods. The volume also chronicles major episodes in the evolutionary history of insects from their modest beginnings in the Devonian and the origin of wings hundreds of millions of years before pterosaurs and birds to the impact of mass extinctions and the explosive radiation of angiosperms on insects, and how they evolved into the most complex societies in nature. Whereas other volumes focus on either living species or fossils, this is the first comprehensive synthesis of all aspects of insect evolution. Illustrated with 955 photo- and electron- micrographs, drawings, diagrams, and field photos, many in full color and virtually all of them original, this reference will appeal to anyone engaged with insect diversity--professional entomologists and students, insect and fossil collectors, and naturalists. David Grimaldi and Michael S. Engel have collectively published over 200 scientific articles and monographs on the relationships and fossil record of insects, including 10 articles in the journals Science, Nature, and Proceedings of the National Academy of Sciences. David Grimaldi is curator in the Division of Invertebrate Zoology, American Museum of Natural History and adjunct professor at Cornell University, Columbia University, and the City University of New York. David Grimaldi has traveled in 40 countries on 6 continents, collecting and studying recent species of insects and conducting fossil excavations. He is the author of Amber: Window to the Past (Abrams, 2003). Michael S. Engel is an assistant professor in the

  10. Insects and other invertebrates

    Science.gov (United States)

    John R. Jones; Norbert V. DeByle; Diane M. Bowers

    1985-01-01

    Quaking aspen throughout its range appears to be host to several insect and other invertebrate pests (fig. 1). It is a short-lived species that is palatable to a large variety of animals. Furniss and Carolin (1977) listed 33 insect species that use aspen as a food source. Some are quite damaging and may kill otherwise healthy stands of aspen; others feed on weakened or...

  11. Insect immunology and hematopoiesis

    OpenAIRE

    Hillyer, Julián F.

    2015-01-01

    Insects combat infection by mounting powerful immune responses that are mediated by hemocytes, the fat body, the midgut, the salivary glands and other tissues. Foreign organisms that have entered the body of an insect are recognized by the immune system when pathogen-associated molecular patterns bind host-derived pattern recognition receptors. This, in turn, activates immune signaling pathways that amplify the immune response, induce the production of factors with antimicrobial activity, and...

  12. Beneficial Insects: Beetles

    OpenAIRE

    Hodgson, Erin W.; Patterson, Ron

    2007-01-01

    There are many beneficial beetles in Utah besides lady beetles or ladybugs. Beetles can significantly reduce common insect and weed problems and in some cases eliminate the need for chemical control. Examples of beneficial beetles include: ground beetles, rove beetles, tiger beetles and tortoise beetles. Many of these beetles are native to Utah, while others have been purposely introduced to help control damage from exotic insect and weed pests.

  13. 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.

  14. Insect immunology and hematopoiesis.

    Science.gov (United States)

    Hillyer, Julián F

    2016-05-01

    Insects combat infection by mounting powerful immune responses that are mediated by hemocytes, the fat body, the midgut, the salivary glands and other tissues. Foreign organisms that have entered the body of an insect are recognized by the immune system when pathogen-associated molecular patterns bind host-derived pattern recognition receptors. This, in turn, activates immune signaling pathways that amplify the immune response, induce the production of factors with antimicrobial activity, and activate effector pathways. Among the immune signaling pathways are the Toll, Imd, Jak/Stat, JNK, and insulin pathways. Activation of these and other pathways leads to pathogen killing via phagocytosis, melanization, cellular encapsulation, nodulation, lysis, RNAi-mediated virus destruction, autophagy and apoptosis. This review details these and other aspects of immunity in insects, and discusses how the immune and circulatory systems have co-adapted to combat infection, how hemocyte replication and differentiation takes place (hematopoiesis), how an infection prepares an insect for a subsequent infection (immune priming), how environmental factors such as temperature and the age of the insect impact the immune response, and how social immunity protects entire groups. Finally, this review highlights some underexplored areas in the field of insect immunobiology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Insect bite reactions

    Directory of Open Access Journals (Sweden)

    Sanjay Singh

    2013-01-01

    Full Text Available Insects are a class of living creatures within the arthropods. Insect bite reactions are commonly seen in clinical practice. The present review touches upon the medically important insects and their places in the classification, the sparse literature on the epidemiology of insect bites in India, and different variables influencing the susceptibility of an individual to insect bites. Clinical features of mosquito bites, hypersensitivity to mosquito bites Epstein-Barr virus NK (HMB-EBV-NK disease, eruptive pseudoangiomatosis, Skeeter syndrome, papular pruritic eruption of HIV/AIDS, and clinical features produced by bed bugs, Mexican chicken bugs, assassin bugs, kissing bugs, fleas, black flies, Blandford flies, louse flies, tsetse flies, midges, and thrips are discussed. Brief account is presented of the immunogenic components of mosquito and bed bug saliva. Papular urticaria is discussed including its epidemiology, the 5 stages of skin reaction, the SCRATCH principle as an aid in diagnosis, and the recent evidence supporting participation of types I, III, and IV hypersensitivity reactions in its causation is summarized. Recent developments in the treatment of pediculosis capitis including spinosad 0.9% suspension, benzyl alcohol 5% lotion, dimethicone 4% lotion, isopropyl myristate 50% rinse, and other suffocants are discussed within the context of evidence derived from randomized controlled trials and key findings of a recent systematic review. We also touch upon a non-chemical treatment of head lice and the ineffectiveness of egg-loosening products. Knockdown resistance (kdr as the genetic mechanism making the lice nerves insensitive to permethrin is discussed along with the surprising contrary clinical evidence from Europe about efficacy of permethrin in children with head lice carrying kdr-like gene. The review also presents a brief account of insects as vectors of diseases and ends with discussion of prevention of insect bites and some

  16. Mitochondrial phylogenomics of modern and ancient equids.

    Science.gov (United States)

    Vilstrup, Julia T; Seguin-Orlando, Andaine; Stiller, Mathias; Ginolhac, Aurelien; Raghavan, Maanasa; Nielsen, Sandra C A; Weinstock, Jacobo; Froese, Duane; Vasiliev, Sergei K; Ovodov, Nikolai D; Clary, Joel; Helgen, Kristofer M; Fleischer, Robert C; Cooper, Alan; Shapiro, Beth; Orlando, Ludovic

    2013-01-01

    The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).

  17. Mitochondrial Phylogenomics of Modern and Ancient Equids

    Science.gov (United States)

    Vilstrup, Julia T.; Seguin-Orlando, Andaine; Stiller, Mathias; Ginolhac, Aurelien; Raghavan, Maanasa; Nielsen, Sandra C. A.; Weinstock, Jacobo; Froese, Duane; Vasiliev, Sergei K.; Ovodov, Nikolai D.; Clary, Joel; Helgen, Kristofer M.; Fleischer, Robert C.; Cooper, Alan; Shapiro, Beth; Orlando, Ludovic

    2013-01-01

    The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya). PMID:23437078

  18. Mitochondrial phylogenomics of modern and ancient equids.

    Directory of Open Access Journals (Sweden)

    Julia T Vilstrup

    Full Text Available The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga. Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya.

  19. 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.

  20. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

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

    Directory of Open Access Journals (Sweden)

    Yeşim Doğan Alakoç

    2011-12-01

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

  2. The Sterile Insect Technique

    International Nuclear Information System (INIS)

    Kiragu, J.

    2006-01-01

    Insect pests have caused an increasing problem in agriculture and human health through crop losses and disease transmission to man and livestock. Intervention to ensure food security and human health has relied on Integrated Pest Management (IPM) strategies to keep the pests population below economic injury levels. IPM integrate a variety of methods, but there has been over-reliance on chemical control following the discovery of insecticidal properties of DDT. It is now realized that, maintaining pest populations at controlled levels is unsustainable and eradication options is now being considered. Although the Sterile Insect Technique(SIT) could be used for insect suppression, it is gaining favour in the elimination (eradication) of the target pest population through Areawide-based IPM (Author)

  3. Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea

    Directory of Open Access Journals (Sweden)

    Urban Julie M

    2012-06-01

    Full Text Available Abstract Background Members of the hemipteran suborder Auchenorrhyncha (commonly known as planthoppers, tree- and leafhoppers, spittlebugs, and cicadas are unusual among insects known to harbor endosymbiotic bacteria in that they are associated with diverse assemblages of bacterial endosymbionts. Early light microscopic surveys of species representing the two major lineages of Auchenorrhyncha (the planthopper superfamily Fulgoroidea; and Cicadomorpha, comprising Membracoidea [tree- and leafhoppers], Cercopoidea [spittlebugs], and Cicadoidea [cicadas], found that most examined species harbored at least two morphologically distinct bacterial endosymbionts, and some harbored as many as six. Recent investigations using molecular techniques have identified multiple obligate bacterial endosymbionts in Cicadomorpha; however, much less is known about endosymbionts of Fulgoroidea. In this study, we present the initial findings of an ongoing PCR-based survey (sequencing 16S rDNA of planthopper-associated bacteria to document endosymbionts with a long-term history of codiversification with their fulgoroid hosts. Results Results of PCR surveys and phylogenetic analyses of 16S rDNA recovered a monophyletic clade of Betaproteobacteria associated with planthoppers; this clade included Vidania fulgoroideae, a recently described bacterium identified in exemplars of the planthopper family Cixiidae. We surveyed 77 planthopper species representing 18 fulgoroid families, and detected Vidania in 40 species (representing 13 families. Further, we detected the Sulcia endosymbiont (identified as an obligate endosymbiont of Auchenorrhyncha in previous studies in 30 of the 40 species harboring Vidania. Concordance of the Vidania phylogeny with the phylogeny of the planthopper hosts (reconstructed based on sequence data from five genes generated from the same insect specimens from which the bacterial sequences were obtained was supported by statistical tests of

  4. Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea).

    Science.gov (United States)

    Urban, Julie M; Cryan, Jason R

    2012-06-14

    Members of the hemipteran suborder Auchenorrhyncha (commonly known as planthoppers, tree- and leafhoppers, spittlebugs, and cicadas) are unusual among insects known to harbor endosymbiotic bacteria in that they are associated with diverse assemblages of bacterial endosymbionts. Early light microscopic surveys of species representing the two major lineages of Auchenorrhyncha (the planthopper superfamily Fulgoroidea; and Cicadomorpha, comprising Membracoidea [tree- and leafhoppers], Cercopoidea [spittlebugs], and Cicadoidea [cicadas]), found that most examined species harbored at least two morphologically distinct bacterial endosymbionts, and some harbored as many as six. Recent investigations using molecular techniques have identified multiple obligate bacterial endosymbionts in Cicadomorpha; however, much less is known about endosymbionts of Fulgoroidea. In this study, we present the initial findings of an ongoing PCR-based survey (sequencing 16S rDNA) of planthopper-associated bacteria to document endosymbionts with a long-term history of codiversification with their fulgoroid hosts. Results of PCR surveys and phylogenetic analyses of 16S rDNA recovered a monophyletic clade of Betaproteobacteria associated with planthoppers; this clade included Vidania fulgoroideae, a recently described bacterium identified in exemplars of the planthopper family Cixiidae. We surveyed 77 planthopper species representing 18 fulgoroid families, and detected Vidania in 40 species (representing 13 families). Further, we detected the Sulcia endosymbiont (identified as an obligate endosymbiont of Auchenorrhyncha in previous studies) in 30 of the 40 species harboring Vidania. Concordance of the Vidania phylogeny with the phylogeny of the planthopper hosts (reconstructed based on sequence data from five genes generated from the same insect specimens from which the bacterial sequences were obtained) was supported by statistical tests of codiversification. Codiversification tests also

  5. Insect Repellents: Protect Your Child from Insect Bites

    Science.gov (United States)

    ... Español Text Size Email Print Share Choosing an Insect Repellent for Your Child Page Content Mosquitoes, biting ... sunscreen needs to be reapplied often. Reactions to Insect Repellents If you suspect that your child is ...

  6. Sterile insect technique and radiation in insect control

    International Nuclear Information System (INIS)

    1982-01-01

    Out of 39 papers and 6 summaries of the poster presentations published in this proceeding series, 23 respectively fall within the INIS subject scope. Four main topics were covered: a review of the sterile insect technique against various insect pests; its application to tsetse flies in eradication programmes; quality control of mass-reared insects for release; and the development of genetic approaches to insect mass rearing and control. Other topics emphasized integrated pest management, computer models and radioisotope labelling

  7. 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

  8. Diversity and survivability of microbial community in ancient permafrost sediment of northeast Siberia

    Science.gov (United States)

    Liang, R.; Lau, M.; Vishnivetskaya, T. A.; Lloyd, K. G.; Pfiffner, S. M.; Rivkina, E.; Onstott, T. C.

    2017-12-01

    The prevalence of microorganisms in frozen permafrost has been well documented in ancient sediment up to several million years old. However, the long term survivability and metabolic activity of microbes over geological timespans remain underexplored. Siberian permafrost sediment was collected at various depths (1.4m, 11.8 m and 24.8m) to represent a wide range of geological time from thousands to millions of years. Extracellular (eDNA) and intracellular DNA (iDNA) was simultaneously recovered for sequencing to characterize the potentially extinct and extant microbial community. Additionally, aspartic acid racemization assay (D/L Asp) was used to infer the metabolic activity of microbes in ancient permafrost. As compared with the young sample (1.4m), DNA yield and content of aspartic acid dramatically decreased in old samples (11.8m and 24.8m). However, D/L Asp and eDNA/iDNA significantly increased with the geological age. Such findings suggested that ancient microbiomes might be subjected to racemization or even DNA/proteins degradation at subzero temperature over the wide geological time scale. Preliminary characterization of microbial community indicated that the majority of sequences in old samples were identified as bacteria and only a small fraction was identified as archaea from the iDNA pool. While the eDNA and iDNA fractions shared similar dominant taxa at phylum level, the relative abundance of Proteobacteria in eDNA library was much higher than iDNA. By contrast, the phylum affiliated with Firmicutes was more numerically abundant in the iDNA fraction. More dramatic differences were observed between eDNA and iDNA library at lower taxonomic levels. Particularly, the microbial lineages affiliated with the genera Methanoregula, Desulfosporosinus and Syntrophomonas were only detected in the iDNA library. Such taxonomic difference between the relic eDNA and iDNA suggested that numerous species become locally "extinct" whereas many other taxa might survive in

  9. Flying insects and Campylobacter

    DEFF Research Database (Denmark)

    Hald, Birthe; Sommer, Helle Mølgaard; Skovgård, Henrik

    Campylobacter in flies Flies of the Muscidae family forage on all kind of faeces – various fly species have different preferences. M domestica prefer pigs, horses and cattle faeces, animals which are all known to frequently excrete Campylobacter. As a result, the insects pick up pathogenic micro...

  10. Insects and sex

    NARCIS (Netherlands)

    Beukeboom, Leo

    2005-01-01

    Most organisms reproduce sexually, but the evolution of sexual reproduction is not yet well understood. Sexual reproduction leads to new variation and adaptations to the environment, but sex is also costly. Some insects reproduce without sex through parthenogenesis or paedogenesis. Almost all sexual

  11. Dispersal of forest insects

    Science.gov (United States)

    Mcmanus, M. L.

    1979-01-01

    Dispersal flights of selected species of forest insects which are associated with periodic outbreaks of pests that occur over large contiguous forested areas are discussed. Gypsy moths, spruce budworms, and forest tent caterpillars were studied for their massive migrations in forested areas. Results indicate that large dispersals into forested areas are due to the females, except in the case of the gypsy moth.

  12. Investigation--Insects!

    Science.gov (United States)

    Fay, Janice

    2000-01-01

    Presents activities on insects for second grade students. In the first activity, students build a butterfly garden. In the second activity, students observe stimuli reactions with mealworms in the larval stage. Describes the assessment process and discusses the effects of pollution on living things. (YDS)

  13. Insect flight muscle metabolism

    NARCIS (Netherlands)

    Horst, D.J. van der; Beenakkers, A.M.Th.; Marrewijk, W.J.A. van

    1984-01-01

    The flight of an insect is of a very complicated and extremely energy-demanding nature. Wingbeat frequency may differ between various species but values up to 1000 Hz have been measured. Consequently metabolic activity may be very high during flight and the transition from rest to flight is

  14. Insects, isotopes and radiations

    International Nuclear Information System (INIS)

    Lingkvist, D.A.

    1987-01-01

    The IAEA activity on coordinating the IAEA member-state efforts in the field of pest control is considered. A complex program of agricultural pest control (IPM), applied in many parts of the world is developed. The program provides for the use of natural means of control and cases of critical pest numbers-the use of insecticides. When controlling certain types of insects it is advisable to apply the 'large area control' methods which provide for the insect destruction in places of their concentration prior to migration. Methods of pest control over large areas also include radiation sexual sterilization method (SSM), application of insect phoromons (sexual attractants) to prevent mating, other types of chemical attractants, traps, mass cultivation and reproduction of parasite plants and animals, destroying insects, as well as improvement of host-plant resistance. A great attention is paid to isotope and radiation application in pest control (labelling, sexual sterilization using ionising radiation, radiation application in genetic engineering, mutant plant cultivation)

  15. Anaphylaxis and insect allergy.

    Science.gov (United States)

    Demain, Jeffrey G; Minaei, Ashley A; Tracy, James M

    2010-08-01

    Anaphylaxis is an acute-onset and potentially life-threatening allergic reaction that can be caused by numerous allergic triggers including stinging insects. This review focuses on recent advances, natural history, risk factors and therapeutic considerations. Recent work suggests that concerns over insect allergy diagnosis continue to exist. This is especially true with individuals who have a convincing history of a serious life-threatening anaphylactic event, but lack the necessary diagnostic criteria of venom-specific IgE by skin test or in-vitro diagnostic methods to confirm the diagnosis. The role of occult mastocytosis or increased basophile reactivity may play a role in this subset population. Additionally, epinephrine continues to be underutilized as the primary acute intervention for an anaphylactic reaction in the emergent setting. The incidence of anaphylaxis continues to rise across all demographic groups, especially those less than 20 years of age. Fortunately, the fatalities related to anaphylaxis appear to have decreased over the past decades. Our understanding of various triggers, associated risk factors, as well as an improved understanding and utilization of biological markers such as serum tryptase have improved. Our ability to treat insect anaphylaxis by venom immunotherapy is highly effective. Unfortunately, anaphylaxis continues to be underappreciated and undertreated especially in regard to insect sting anaphylaxis. This includes the appropriate use of injectable epinephrine as the primary acute management tool. These findings suggest that continued education of the general population, primary care healthcare providers and emergency departments is required.

  16. Broadening insect gastronomy

    DEFF Research Database (Denmark)

    Halloran, Afton Marina Szasz; Münke, Christopher; Vantomme, Paul

    2015-01-01

    In recent years there has been a trend among chefs to diversify their ingredients and techniques, drawing inspiration from other cultures and creating new foods by blending this knowledge with the flavours of their local region. Edible insects, with their plethora of taste, aromatic, textural and...

  17. Culture of insect tissues

    International Nuclear Information System (INIS)

    Cestari, A.N.; Simoes, L.C.G.

    1978-01-01

    Several aspects are discussed related to the behavior of politenic chromosomes from Rhyncosciara salivary glands kept in culture during different periods of time, without interference of insect hormones. Nucleic acid-and protein synthesis in isolated nuclei and chromosomes are also investigated. Autoradiographic techniques and radioactive precursors for nucleic acids and proteins are used in the research. (M.A.) [pt

  18. Insect (food) allergy and allergens.

    Science.gov (United States)

    de Gier, Steffie; Verhoeckx, Kitty

    2018-05-03

    Insects represent an alternative for meat and fish in satisfying the increasing demand for sustainable sources of nutrition. Approximately two billion people globally consume insects. They are particularly popular in Asia, Latin America, and Africa. Most research on insect allergy has focussed on occupational or inhalation allergy. Research on insect food safety, including allergenicity, is therefore of great importance. The objective of this review is to provide an overview of cases reporting allergy following insect ingestion, studies on food allergy to insects, proteins involved in insect allergy including cross-reactive proteins, and the possibility to alter the allergenic potential of insects by food processing and digestion. Food allergy to insects has been described for silkworm, mealworm, caterpillars, Bruchus lentis, sago worm, locust, grasshopper, cicada, bee, Clanis bilineata, and the food additive carmine, which is derived from female Dactylopius coccus insects. For cockroaches, which are also edible insects, only studies on inhalation allergy have been described. Various insect allergens have been identified including tropomyosin and arginine kinase, which are both pan-allergens known for their cross-reactivity with homologous proteins in crustaceans and house dust mite. Cross-reactivity and/or co-sensitization of insect tropomyosin and arginine kinase has been demonstrated in house dust mite and seafood (e.g. prawn, shrimp) allergic patients. In addition, many other (allergenic) species (various non-edible insects, arachnids, mites, seafoods, mammals, nematoda, trematoda, plants, and fungi) have been identified with sequence alignment analysis to show potential cross-reactivity with allergens of edible insects. It was also shown that thermal processing and digestion did not eliminate insect protein allergenicity. Although purified natural allergens are scarce and yields are low, recombinant allergens from cockroach, silkworm, and Indian mealmoth are

  19. Edible insects of Northern Angola

    OpenAIRE

    Lautenschläger,Thea; Neinhuis,Christoph; Monizi,Mawunu; Mandombe,José Lau; Förster,Anke; Henle,Thomas; Nuss,Matthias

    2017-01-01

    From 2013–2017, we accompanied and interviewed local people harvesting edible insects in the Northern Angolan province of Uíge. Insect and host plant samples were collected for species identification and nutritive analyses. Additionally, live caterpillars were taken to feed and keep until pupation and eclosion of the imago, necessary for morphological species identification. Altogether, 18 insect species eaten by humans were recorded. Twenty four edible insect species were formerly known from...

  20. Pathogen avoidance by insect predators

    OpenAIRE

    Meyling, Nicolai V.; Ormond, Emma; Roy, Helen E.; Pell, Judith K.

    2008-01-01

    Insects can detect cues related to the risk of attack by their natural enemies. Pathogens are among the natural enemies of insects and entomopathogenic fungi attack a wide array of host species. Evidence documents that social insects in particular have adapted behavioural mechanisms to avoid infection by fungal pathogens. These mechanisms are referred to as 'behavioural resistance'. However, there is little evidence for similar adaptations in non-social insects. We have conducted experime...

  1. Protecting Yourself from Stinging Insects

    Science.gov (United States)

    ... from St ing in g In sect s Flying Insects Outdoor workers are at risk of being stung by flying insects (bees, wasps, and hornets) and fire ants. While ... If a worker is stung by a stinging insect: ■■ Have someone stay with the worker to be ...

  2. The promise of insect genomics

    DEFF Research Database (Denmark)

    Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael

    2007-01-01

    Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts...

  3. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence ...

  4. On Ancient Babylonian Algebra and Geometry

    Indian Academy of Sciences (India)

    ber system prevalent during the ancient Mesopotamian civilization. In this article, we study the ... civilization provides a better insight into the thought processes of the ancient Babylonian mathematicians. In this context, consider the following ...

  5. Ancient woodland boundaries in Europe

    Czech Academy of Sciences Publication Activity Database

    Szabó, Péter

    2010-01-01

    Roč. 36, č. 2 (2010), s. 205-214 ISSN 0305-7488 R&D Projects: GA AV ČR IAA600050812 Institutional research plan: CEZ:AV0Z60050516 Keywords : ancient woodland * historical ecology * landscape archaeology Subject RIV: EF - Botanics Impact factor: 0.983, year: 2010

  6. Insect herbivory and plant adaptation in an early successional community.

    Science.gov (United States)

    Agrawal, Anurag A; Hastings, Amy P; Fines, Daniel M; Bogdanowicz, Steve; Huber, Meret

    2018-05-01

    To address the role of insect herbivores in adaptation of plant populations and the persistence of selection through succession, we manipulated herbivory in a long-term field experiment. We suppressed insects in half of 16 plots over nine years and examined the genotypic structure and chemical defense of common dandelion (Taraxacum officinale), a naturally colonizing perennial apomictic plant. Insect suppression doubled dandelion abundance in the first few years, but had negligible effects thereafter. Using microsatellite DNA markers, we genotyped >2500 plants and demonstrate that insect suppression altered the genotypic composition of plots in both sampling years. Phenotypic and genotypic estimates of defensive terpenes and phenolics from the field plots allowed us to infer phenotypic plasticity and the response of dandelion populations to insect-mediated natural selection. The effects of insect suppression on plant chemistry were, indeed, driven both by plasticity and plant genotypic identity. In particular, di-phenolic inositol esters were more abundant in plots exposed to herbivory (due to the genotypic composition of the plots) and were also induced in response to herbivory. This field experiment thus demonstrates evolutionary sorting of plant genotypes in response to insect herbivores that was in same direction as the plastic defensive response within genotypes. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

  7. 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...

  8. Cleptobiosis in Social Insects

    Directory of Open Access Journals (Sweden)

    Michael D. Breed

    2012-01-01

    Full Text Available In this review of cleptobiosis, we not only focus on social insects, but also consider broader issues and concepts relating to the theft of food among animals. Cleptobiosis occurs when members of a species steal food, or sometimes nesting materials or other items of value, either from members of the same or a different species. This simple definition is not universally used, and there is some terminological confusion among cleptobiosis, cleptoparasitism, brood parasitism, and inquilinism. We first discuss the definitions of these terms and the confusion that arises from varying usage of the words. We consider that cleptobiosis usually is derived evolutionarily from established foraging behaviors. Cleptobionts can succeed by deception or by force, and we review the literature on cleptobiosis by deception or force in social insects. We focus on the best known examples of cleptobiosis, the ectatommine ant Ectatomma ruidum, the harvester ant Messor capitatus, and the stingless bee Lestrimellita limão. Cleptobiosis is facilitated either by deception or physical force, and we discuss both mechanisms. Part of this discussion is an analysis of the ecological implications (competition by interference and the evolutionary effects of cleptobiosis. We conclude with a comment on how cleptobiosis can increase the risk of disease or parasite spread among colonies of social insects.

  9. 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

  10. Chemical signaling and insect attraction is a conserved trait in yeasts.

    Science.gov (United States)

    Becher, Paul G; Hagman, Arne; Verschut, Vasiliki; Chakraborty, Amrita; Rozpędowska, Elżbieta; Lebreton, Sébastien; Bengtsson, Marie; Flick, Gerhard; Witzgall, Peter; Piškur, Jure

    2018-03-01

    Yeast volatiles attract insects, which apparently is of mutual benefit, for both yeasts and insects. However, it is unknown whether biosynthesis of metabolites that attract insects is a basic and general trait, or if it is specific for yeasts that live in close association with insects. Our goal was to study chemical insect attractants produced by yeasts that span more than 250 million years of evolutionary history and vastly differ in their metabolism and lifestyle. We bioassayed attraction of the vinegar fly Drosophila melanogaster to odors of phylogenetically and ecologically distinct yeasts grown under controlled conditions. Baker's yeast Saccharomyces cerevisiae , the insect-associated species Candida californica , Pichia kluyveri and Metschnikowia andauensis , wine yeast Dekkera bruxellensis , milk yeast Kluyveromyces lactis , the vertebrate pathogens Candida albicans and Candida glabrata , and oleophilic Yarrowia lipolytica were screened for fly attraction in a wind tunnel. Yeast headspace was chemically analyzed, and co-occurrence of insect attractants in yeasts and flowering plants was investigated through a database search. In yeasts with known genomes, we investigated the occurrence of genes involved in the synthesis of key aroma compounds. Flies were attracted to all nine yeasts studied. The behavioral response to baker's yeast was independent of its growth stage. In addition to Drosophila , we tested the basal hexapod Folsomia candida (Collembola) in a Y-tube assay to the most ancient yeast, Y. lipolytica, which proved that early yeast signals also function on clades older than neopteran insects. Behavioral and chemical data and a search for selected genes of volatile metabolites underline that biosynthesis of chemical signals is found throughout the yeast clade and has been conserved during the evolution of yeast lifestyles. Literature and database reviews corroborate that yeast signals mediate mutualistic interactions between insects and yeasts

  11. Insights into Modern Human Prehistory Using Ancient Genomes.

    Science.gov (United States)

    Yang, Melinda A; Fu, Qiaomei

    2018-03-01

    The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. [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.

  13. Insect symbiotic bacteria harbour viral pathogens for transovarial transmission.

    Science.gov (United States)

    Jia, Dongsheng; Mao, Qianzhuo; Chen, Yong; Liu, Yuyan; Chen, Qian; Wu, Wei; Zhang, Xiaofeng; Chen, Hongyan; Li, Yi; Wei, Taiyun

    2017-03-06

    Many insects, including mosquitoes, planthoppers, aphids and leafhoppers, are the hosts of bacterial symbionts and the vectors for transmitting viral pathogens 1-3 . In general, symbiotic bacteria can indirectly affect viral transmission by enhancing immunity and resistance to viruses in insects 3-5 . Whether symbiotic bacteria can directly interact with the virus and mediate its transmission has been unknown. Here, we show that an insect symbiotic bacterium directly harbours a viral pathogen and mediates its transovarial transmission to offspring. We observe rice dwarf virus (a plant reovirus) binding to the envelopes of the bacterium Sulcia, a common obligate symbiont of leafhoppers 6-8 , allowing the virus to exploit the ancient oocyte entry path of Sulcia in rice leafhopper vectors. Such virus-bacterium binding is mediated by the specific interaction of the viral capsid protein and the Sulcia outer membrane protein. Treatment with antibiotics or antibodies against Sulcia outer membrane protein interferes with this interaction and strongly prevents viral transmission to insect offspring. This newly discovered virus-bacterium interaction represents the first evidence that a viral pathogen can directly exploit a symbiotic bacterium for its transmission. We believe that such a model of virus-bacterium communication is a common phenomenon in nature.

  14. 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

  15. Edible insects are the future?

    Science.gov (United States)

    van Huis, Arnold

    2016-08-01

    The global increase in demand for meat and the limited land area available prompt the search for alternative protein sources. Also the sustainability of meat production has been questioned. Edible insects as an alternative protein source for human food and animal feed are interesting in terms of low greenhouse gas emissions, high feed conversion efficiency, low land use, and their ability to transform low value organic side streams into high value protein products. More than 2000 insect species are eaten mainly in tropical regions. The role of edible insects in the livelihoods and nutrition of people in tropical countries is discussed, but this food source is threatened. In the Western world, there is an increasing interest in edible insects, and examples are given. Insects as feed, in particular as aquafeed, have a large potential. Edible insects have about the same protein content as conventional meat and more PUFA. They may also have some beneficial health effects. Edible insects need to be processed and turned into palatable dishes. Food safety may be affected by toxicity of insects, contamination with pathogens, spoilage during conservation and allergies. Consumer attitude is a major issue in the Western world and a number of strategies are proposed to encourage insect consumption. We discuss research pathways to make insects a viable sector in food and agriculture: an appropriate disciplinary focus, quantifying its importance, comparing its nutritional value to conventional protein sources, environmental benefits, safeguarding food safety, optimising farming, consumer acceptance and gastronomy.

  16. 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.

  17. ANCIENT BREAD STAMPS FROM JORDAN

    OpenAIRE

    Kakish, Randa

    2014-01-01

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

  18. ORAL INSECT REPELLENTS - INSECT TASTE RECEPTORS AND THEIR ACTION,

    Science.gov (United States)

    CULICIDAE, * CHEMORECEPTORS ), INSECT REPELLENTS, ELECTROPHYSIOLOGY, STIMULATION(PHYSIOLOGY), ELECTROLYTES(PHYSIOLOGY), BLOOD, INGESTION(PHYSIOLOGY), REPRODUCTION(PHYSIOLOGY), NUTRITION, ENTOMOLOGY, AEDES, MOUTH

  19. 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.

  20. Sterilizing insects with ionizing radiation

    International Nuclear Information System (INIS)

    Bakri, A.; Mehta, K.; Lance, D.R.

    2005-01-01

    Exposure to ionizing radiation is currently the method of choice for rendering insects reproductively sterile for area-wide integrated pest management (AW-IPM) programmes that integrate the sterile insect technique (SIT). Gamma radiation from isotopic sources (cobalt-60 or caesium-137) is most often used, but high-energy electrons and X-rays are other practical options. Insect irradiation is safe and reliable when established safety and quality-assurance guidelines are followed. The key processing parameter is absorbed dose, which must be tightly controlled to ensure that treated insects are sufficiently sterile in their reproductive cells and yet able to compete for mates with wild insects. To that end, accurate dosimetry (measurement of absorbed dose) is critical. Irradiation data generated since the 1950s, covering over 300 arthropod species, indicate that the dose needed for sterilization of arthropods varies from less than 5 Gy for blaberid cockroaches to 300 Gy or more for some arctiid and pyralid moths. Factors such as oxygen level, and insect age and stage during irradiation, and many others, influence both the absorbed dose required for sterilization and the viability of irradiated insects. Consideration of these factors in the design of irradiation protocols can help to find a balance between the sterility and competitiveness of insects produced for programmes that release sterile insects. Many programmes apply 'precautionary' radiation doses to increase the security margin of sterilization, but this overdosing often lowers competitiveness to the point where the overall induced sterility in the wild population is reduced significantly. (author)

  1. 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.

  2. Photorhabdus luminescens genes induced upon insect infection

    Directory of Open Access Journals (Sweden)

    Jung Kirsten

    2008-05-01

    Full Text Available Abstract Background Photorhabdus luminescens is a Gram-negative luminescent enterobacterium and a symbiote to soil nematodes belonging to the species Heterorhabditis bacteriophora. P.luminescens is simultaneously highly pathogenic to insects. This bacterium exhibits a complex life cycle, including one symbiotic stage characterized by colonization of the upper nematode gut, and a pathogenic stage, characterized by release from the nematode into the hemocoel of insect larvae, resulting in rapid insect death caused by bacterial toxins. P. luminescens appears to sense and adapt to the novel host environment upon changing hosts, which facilitates the production of factors involved in survival within the host, host-killing, and -exploitation. Results A differential fluorescence induction (DFI approach was applied to identify genes that are up-regulated in the bacterium after infection of the insect host Galleria mellonella. For this purpose, a P. luminescens promoter-trap library utilizing the mCherry fluorophore as a reporter was constructed, and approximately 13,000 clones were screened for fluorescence induction in the presence of a G. mellonella larvae homogenate. Since P. luminescens has a variety of regulators that potentially sense chemical molecules, like hormones, the screen for up-regulated genes or operons was performed in vitro, excluding physicochemical signals like oxygen, temperature or osmolarity as variables. Clones (18 were obtained exhibiting at least 2.5-fold induced fluorescence and regarded as specific responders to insect homogenate. In combination with a bioinformatics approach, sequence motifs were identified in these DNA-fragments that are similar to 29 different promoters within the P. luminescens genome. By cloning each of the predicted promoters upstream of the reporter gene, induction was verified for 27 promoters in vitro, and for 24 promoters in viable G. mellonella larvae. Among the validated promoters are some known

  3. 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.

  4. Hydrodynamics of insect spermatozoa

    Science.gov (United States)

    Pak, On Shun; Lauga, Eric

    2010-11-01

    Microorganism motility plays important roles in many biological processes including reproduction. Many microorganisms propel themselves by propagating traveling waves along their flagella. Depending on the species, propagation of planar waves (e.g. Ceratium) and helical waves (e.g. Trichomonas) were observed in eukaryotic flagellar motion, and hydrodynamic models for both were proposed in the past. However, the motility of insect spermatozoa remains largely unexplored. An interesting morphological feature of such cells, first observed in Tenebrio molitor and Bacillus rossius, is the double helical deformation pattern along the flagella, which is characterized by the presence of two superimposed helical flagellar waves (one with a large amplitude and low frequency, and the other with a small amplitude and high frequency). Here we present the first hydrodynamic investigation of the locomotion of insect spermatozoa. The swimming kinematics, trajectories and hydrodynamic efficiency of the swimmer are computed based on the prescribed double helical deformation pattern. We then compare our theoretical predictions with experimental measurements, and explore the dependence of the swimming performance on the geometric and dynamical parameters.

  5. Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.

    Science.gov (United States)

    Yang, Yunxia; Xu, Shixia; Xu, Junxiao; Guo, Yan; Yang, Guang

    2014-01-01

    Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.

  6. Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics

    NARCIS (Netherlands)

    Paijmans, Johanna L.A.; Barnett, Ross; Gilbert, M. Thomas P.; Zepeda-Mendoza, M. Lisandra; Reumer, Jelle W.F.; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F.; Leonard, Jennifer A.; Rohland, Nadin; Westbury, Michael V.; Barlow, Axel; Hofreiter, Michael

    2017-01-01

    Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  8. The conscious of Nightmares in ancient China

    OpenAIRE

    西林, 眞紀子

    2006-01-01

    The analaysis concerns Nightmares in ancient China. People in ancient China were very afraid of Nightmares. Nightmares are described in the『春秋左氏傳』etc. The exocis Nightmares is described in the『周禮』. The ceremony "難" of exocis Nightmares in the『禮記』. In the characters Meng (夢) had the conscious of Nightmares in ancient China. The analaysis is about the characters 'Meng', about the characters of the relationship 'Meng'

  9. 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.

  10. Characterization of an ancient lepidopteran lateral gene transfer.

    Directory of Open Access Journals (Sweden)

    David Wheeler

    Full Text Available Bacteria to eukaryote lateral gene transfers (LGT are an important potential source of material for the evolution of novel genetic traits. The explosion in the number of newly sequenced genomes provides opportunities to identify and characterize examples of these lateral gene transfer events, and to assess their role in the evolution of new genes. In this paper, we describe an ancient lepidopteran LGT of a glycosyl hydrolase family 31 gene (GH31 from an Enterococcus bacteria. PCR amplification between the LGT and a flanking insect gene confirmed that the GH31 was integrated into the Bombyx mori genome and was not a result of an assembly error. Database searches in combination with degenerate PCR on a panel of 7 lepidopteran families confirmed that the GH31 LGT event occurred deep within the Order approximately 65-145 million years ago. The most basal species in which the LGT was found is Plutella xylostella (superfamily: Yponomeutoidea. Array data from Bombyx mori shows that GH31 is expressed, and low dN/dS ratios indicates the LGT coding sequence is under strong stabilizing selection. These findings provide further support for the proposition that bacterial LGTs are relatively common in insects and likely to be an underappreciated source of adaptive genetic material.

  11. 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

  12. 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...

  13. 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

  14. 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

  15. Love Games that Insects Play

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 1. Love Games that Insects Play - The Evolution of Sexual Behaviours in Insects ... Author Affiliations. K N Ganeshaiah1. Department of Genetics & Plant Breeding University of Agricultural Sciences, GKVK Bangalore 560 065, India ...

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

    International Nuclear Information System (INIS)

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

    2000-01-01

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

  17. Advances on polyphenism in insects.

    Science.gov (United States)

    Xue, Xian-Ci; Yu, Li

    2017-09-20

    Polyphenism denotes that one genome produces two or more distinct phenotypes due to environmental inductions. Many cases have been reported in insects, for example, metamorphosis, seasonal polyphenism, the caste of eusocial insects and so on. Polyphenism is one of the most important reasons for insects to survive and thrive, because insects can adapt and use the environmental cues around them in order to avoid predators and reproduce by changing their phenotypes. Polyphenism has received growing attentions, ranging from the earlier description of this phenomenon to the exploration of possible inducing factors. With the recent advent of the genomic era, more and more studies based on next generation sequencing, gene knockout and RNA interference have been reported to reveal the molecular mechanism of polyphenism. In this review, we summarize the progresses of the polyphenism in insects and envision prospects of future researches.

  18. Plant defense against insect herbivores

    DEFF Research Database (Denmark)

    Fürstenberg-Hägg, Joel; Zagrobelny, Mika; Bak, Søren

    2013-01-01

    , defense compounds. These bioactive specialized plant defense compounds may repel or intoxicate insects, while defense proteins often interfere with their digestion. Volatiles are released upon herbivory to repel herbivores, attract predators or for communication between leaves or plants, and to induce......Plants have been interacting with insects for several hundred million years, leading to complex defense approaches against various insect feeding strategies. Some defenses are constitutive while others are induced, although the insecticidal defense compound or protein classes are often similar...... defense responses. Plants also apply morphological features like waxes, trichomes and latices to make the feeding more difficult for the insects. Extrafloral nectar, food bodies and nesting or refuge sites are produced to accommodate and feed the predators of the herbivores. Meanwhile, herbivorous insects...

  19. 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.

  20. 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

  1. Insect anaphylaxis: addressing clinical challenges.

    Science.gov (United States)

    Tracy, James M; Lewis, Elena J; Demain, Jeffrey G

    2011-08-01

    Few allergic reactions are as potentially life-threatening, or frightening to the patient, as anaphylaxis. Food, medications, and insect stings are the three most common triggers of anaphylaxis, but insect allergy provides the best opportunity to understand the biology of anaphylaxis. If the physician can establish a diagnosis of insect allergy, treatment with nearly 98% effectiveness can be initiated. However, sometimes patients have a compelling history of insect sting anaphylaxis, but negative skin and blood tests. This situation presents us with a fascinating opportunity to understand the biology of insect anaphylaxis. Recent and ongoing work shows that occult mast cell disease may be critical in insect anaphylaxis. Mastocytosis, serum tryptase and basophil biology are key elements; genetic markers may potentially help us diagnose at-risk individuals and determine proper treatment. Understanding basophil activation may play an additional role both in diagnosis and knowing when therapy might be terminated. Mast cell disease, serum tryptase and basophil biology are providing an opportunity to better understand and manage insect allergy. This evolving understanding should improve long-term management of insect anaphylaxis and help us to better understand the clinical dilemma of appropriate management of the history-positive patient in which testing is unable to detect venom-specific IgE. Furthermore, omalizumab's immunomodulatory effects may play a role in difficult-to-treat insect allergy and mastocytosis. Finally, unrelated to these, but still important as an ongoing risk factor, is the continued underutilization of epinephrine for both acute and long-term management of insect anaphylaxis.

  2. Letter to the editor: Genetics and the archaeology of ancient Israel.

    Science.gov (United States)

    Brody, Aaron J; King, Roy J

    2013-12-01

    This letter is a call for DNA testing on ancient skeletal materials from the southern Levant to begin a database of genetic information of the inhabitants of this crossroads region. In this region, during the Iron I period traditionally dated to circa 1200-1000 BCE, archaeologists and biblical historians view the earliest presence of a group that called itself Israel. They lived in villages in the varied hill countries of the region, contemporary with urban settlements in the coastal plains, inland valleys, and central hill country attributed to varied indigenous groups collectively called Canaanite. The remnants of Egyptian imperial presence in the region lasted until around 1150 BCE, postdating the arrival of an immigrant group from the Aegean called the Philistines circa 1175 BCE. The period that follows in the southern Levant is marked by the development of territorial states throughout the region, circa 1000-800 BCE. These patrimonial kingdoms, including the United Kingdom of Israel and the divided kingdoms of northern Israel and Judah, coalesced varied peoples under central leadership and newly founded administrative and religious bureaucracies. Ancient DNA testing will give us a further refined understanding of the individuals who peopled the region of the southern Levant throughout its varied archaeological and historic periods and provide scientific data that will support, refute, or nuance our sociohistoric reconstruction of ancient group identities. These social identities may or may not map onto genetic data, but without sampling of ancient DNA we may never know. A database of ancient DNA will also allow for comparisons with modern DNA samples collected throughout the greater region and the Mediterranean littoral, giving a more robust understanding of the long historical trajectories of regional human genetics and the genetics of varied ancestral groups of today's Jewish populations and other cultural groups in the modern Middle East and Mediterranean

  3. Environmental manipulation for edible insect procurement: a historical perspective

    Science.gov (United States)

    2012-01-01

    Throughout history humans have manipulated their natural environment for an increased predictability and availability of plant and animal resources. Research on prehistoric diets increasingly includes small game, but edible insects receive minimal attention. Using the anthropological and archaeological literature we show and hypothesize about the existence of such environmental manipulations related to the procurement of edible insects. As examples we use eggs of aquatic Hemiptera in Mexico which are semi-cultivated by water management and by providing egg laying sites; palm weevil larvae in the Amazon Basin, tropical Africa, and New Guinea of which the collection is facilitated by manipulating host tree distribution and abundance and which are semi-cultivated by deliberately cutting palm trees at a chosen time at a chosen location; and arboreal, foliage consuming caterpillars in sub-Saharan Africa for which the collection is facilitated by manipulating host tree distribution and abundance, shifting cultivation, fire regimes, host tree preservation, and manually introducing caterpillars to a designated area. These manipulations improve insect exploitation by increasing their predictability and availability, and most likely have an ancient origin. PMID:22264307

  4. Environmental manipulation for edible insect procurement: a historical perspective.

    Science.gov (United States)

    Van Itterbeeck, Joost; van Huis, Arnold

    2012-01-21

    Throughout history humans have manipulated their natural environment for an increased predictability and availability of plant and animal resources. Research on prehistoric diets increasingly includes small game, but edible insects receive minimal attention. Using the anthropological and archaeological literature we show and hypothesize about the existence of such environmental manipulations related to the procurement of edible insects. As examples we use eggs of aquatic Hemiptera in Mexico which are semi-cultivated by water management and by providing egg laying sites; palm weevil larvae in the Amazon Basin, tropical Africa, and New Guinea of which the collection is facilitated by manipulating host tree distribution and abundance and which are semi-cultivated by deliberately cutting palm trees at a chosen time at a chosen location; and arboreal, foliage consuming caterpillars in sub-Saharan Africa for which the collection is facilitated by manipulating host tree distribution and abundance, shifting cultivation, fire regimes, host tree preservation, and manually introducing caterpillars to a designated area. These manipulations improve insect exploitation by increasing their predictability and availability, and most likely have an ancient origin.

  5. Environmental manipulation for edible insect procurement: a historical perspective

    Directory of Open Access Journals (Sweden)

    Van Itterbeeck Joost

    2012-01-01

    Full Text Available Abstract Throughout history humans have manipulated their natural environment for an increased predictability and availability of plant and animal resources. Research on prehistoric diets increasingly includes small game, but edible insects receive minimal attention. Using the anthropological and archaeological literature we show and hypothesize about the existence of such environmental manipulations related to the procurement of edible insects. As examples we use eggs of aquatic Hemiptera in Mexico which are semi-cultivated by water management and by providing egg laying sites; palm weevil larvae in the Amazon Basin, tropical Africa, and New Guinea of which the collection is facilitated by manipulating host tree distribution and abundance and which are semi-cultivated by deliberately cutting palm trees at a chosen time at a chosen location; and arboreal, foliage consuming caterpillars in sub-Saharan Africa for which the collection is facilitated by manipulating host tree distribution and abundance, shifting cultivation, fire regimes, host tree preservation, and manually introducing caterpillars to a designated area. These manipulations improve insect exploitation by increasing their predictability and availability, and most likely have an ancient origin.

  6. Ancient origin and maternal inheritance of blue cuckoo eggs.

    Science.gov (United States)

    Fossøy, Frode; Sorenson, Michael D; Liang, Wei; Ekrem, Torbjørn; Moksnes, Arne; Møller, Anders P; Rutila, Jarkko; Røskaft, Eivin; Takasu, Fugo; Yang, Canchao; Stokke, Bård G

    2016-01-12

    Maternal inheritance via the female-specific W chromosome was long ago proposed as a potential solution to the evolutionary enigma of co-existing host-specific races (or 'gentes') in avian brood parasites. Here we report the first unambiguous evidence for maternal inheritance of egg colouration in the brood-parasitic common cuckoo Cuculus canorus. Females laying blue eggs belong to an ancient (∼2.6 Myr) maternal lineage, as evidenced by both mitochondrial and W-linked DNA, but are indistinguishable at nuclear DNA from other common cuckoos. Hence, cuckoo host races with blue eggs are distinguished only by maternally inherited components of the genome, which maintain host-specific adaptation despite interbreeding among males and females reared by different hosts. A mitochondrial phylogeny suggests that blue eggs originated in Asia and then expanded westwards as female cuckoos laying blue eggs interbred with the existing European population, introducing an adaptive trait that expanded the range of potential hosts.

  7. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

    Science.gov (United States)

    Stata, Matt; Wang, Wei; White, Merlin M.; Moncalvo, Jean-Marc

    2018-01-01

    ABSTRACT Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects. PMID:29764946

  8. 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...

  9. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

    Science.gov (United States)

    Müller, Romy; Roberts, Charlotte A; Brown, Terence A

    2014-04-22

    The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

  11. Ancient aqueous sedimentation on Mars

    International Nuclear Information System (INIS)

    Goldspiel, J.M.; Squyres, S.W.

    1991-01-01

    Viking orbiter images are presently used to calculate approximate volumes for the inflow valleys of the ancient cratered terrain of Mars; a sediment-transport model is then used to conservatively estimate the amount of water required for the removal of this volume of debris from the valleys. The results obtained for four basins with well-developed inflow networks indicate basin sediment thicknesses of the order of tens to hundreds of meters. The calculations further suggest that the quantity of water required to transport the sediment is greater than that which could be produced by a single discharge of the associated aquifer, unless the material of the Martian highlands was very fine-grained and noncohesive to depths of hundreds of meters. 48 refs

  12. Ergonomic design in ancient Greece.

    Science.gov (United States)

    Marmaras, N; Poulakakis, G; Papakostopoulos, V

    1999-08-01

    Although the science of ergonomics did not actually emerge until the 20th century, there is evidence to suggest that ergonomic principles were in fact known and adhered to 25 centuries ago. The study reported here is a first attempt to research the ergonomics concerns of ancient Greeks, on both a conceptual and a practical level. On the former we present a collection of literature references to the concepts of usability and human-centred design. On the latter, examples of ergonomic design from a variety of fields are analysed. The fields explored here include the design of everyday utensils, the sculpture and manipulation of marble as a building material and the design of theatres. Though hardly exhaustive, these examples serve to demonstrate that the ergonomics principles, in content if not in name, actually emerged a lot earlier than is traditionally thought.

  13. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted

    2011-01-01

    Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient...... genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little...... systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear...

  14. Inherited sterility in insects

    International Nuclear Information System (INIS)

    Carpenter, J.E.; Marec, F.; Bloem, S.

    2005-01-01

    The unique genetic phenomena responsible for inherited sterility (IS) in Lepidoptera and some other arthropods, as compared with full sterility, provide advantages for pest control. Lepidopteran females are usually more sensitive to radiation than males of the same species. This allows the radiation dose to be adjusted to suit programme requirements. When partially sterile males mate with wild females, the radiation-induced deleterious effects are inherited by the F 1 generation. As a result, egg hatch is reduced and the resulting offspring are both highly sterile and predominately male. Compared with the high radiation required to achieve full sterility in Lepidoptera, the lower dose of radiation used to induce F 1 sterility increases the quality and competitiveness of the released insects as measured by improved dispersal after release, increased mating ability, and superior sperm competition. F 1 sterile progeny produced in the field enhance the efficacy of released partially sterile males, and improve compatibility with other pest control strategies. In addition, F 1 sterile progeny can be used to increase the production of natural enemies, and to study the potential host and geographical ranges of exotic lepidopteran pests. (author)

  15. Mycoplasmas, plants, insect vectors: a matrimonial triangle.

    Science.gov (United States)

    Garnier, M; Foissac, X; Gaurivaud, P; Laigret, F; Renaudin, J; Saillard, C; Bové, J M

    2001-10-01

    Plant pathogenic mycoplasmas were discovered by electron microscopy, in 1967, long after the discovery and culture in 1898 of the first pathogenic mycoplasma of animal origin, Mycoplasma mycoides. Mycoplasmas are Eubacteria of the class Mollicutes, a group of organisms phylogenetically related to Gram-positive bacteria. Their more characteristic features reside in the small size of their genomes, the low guanine (G) plus cytosine (C) content of their genomic DNA and the lack of a cell wall. Plant pathogenic mycoplasmas are responsible for several hundred diseases and belong to two groups: the phytoplasmas and the spiroplasmas. The phytoplasmas (previously called MLOs, for mycoplasma like organisms) were discovered first; they are pleiomorphic, and have so far resisted in vitro cultivation. Phytoplasmas represent the largest group of plant pathogenic Mollicutes. Only three plant pathogenic spiroplasmas are known today. Spiroplasma citri, the agent of citrus stubborn was discovered and cultured in 1970 and shown to be helical and motile. S. kunkelii is the causal agent of corn stunt. S. phoeniceum, responsible for periwinkle yellows, was discovered in Syria. There are many other spiroplasmas associated with insects and ticks. Plant pathogenic mycoplasmas are restricted to the phloem sieve tubes in which circulates the photosynthetically-enriched sap, the food for many phloem-feeding insects (aphids, leafhoppers, psyllids, etc.). Interestingly, phytopathogenic mycoplasmas are very specifically transmitted by leafhoppers or psyllid species. In this paper, the most recent knowledge on phytopathogenic mycoplasmas in relation with their insect and plant habitats is presented as well as the experiments carried out to control plant mycoplasma diseases, by expression of mycoplasma-directed-antibodies in plants (plantibodies).

  16. Insect neuropeptides regulating substrate mobilisation

    African Journals Online (AJOL)

    1997-09-25

    Sep 25, 1997 ... Insect flight muscles perform their work completely aerobically, and working flight musdes are ... locusts where they are involved in the control of carbohydrate ... the vertebrate hypothalamo/hypophyseal system, and it can.

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

    African Journals Online (AJOL)

    She obained a master degree in Molecular Anthropology at the university of the .... the presence of compounds which nature is still unclear although some studies could .... which is a matter of continuous scientific debate in archaeology, anthropology and .... and cattle as an estimate of antemortem serum chemistry profiles.

  18. Proper Authentication of Ancient DNA Is Still Essential

    Directory of Open Access Journals (Sweden)

    Raphael Eisenhofer

    2018-02-01

    Full Text Available Santiago-Rodriguez et al. [1] report on the putative gut microbiome and resistome of Inca and Italian mummies, and find that Italian mummies exhibit higher bacterial diversity compared to the Inca mummies.[...

  19. Ancient DNA reveals past existence of Eurasian lynx in Spain

    DEFF Research Database (Denmark)

    Rodríguez-Varela, R.; García, N.; Nores, C.

    2016-01-01

    . The paleontological record and our data indicate a population replacement of the Iberian lynx by the Eurasian lynx during the Pleistocene/Holocene transition in the Cantabrian cornice of Spain. Phylogeographic patterns of Late Pleistocene and Holocene Eurasian lynx from Iberia, France, Italy and Denmark show...

  20. Ancient DNA Tells Story of Giant Eagle Evolution

    OpenAIRE

    Bunce, Michael; Szulkin, Marta; Lerner, Heather R. L; Barnes, Ian; Shapiro, Beth; Cooper, Alan; Holdaway, Richard N

    2005-01-01

    Prior to human settlement 700 years ago New Zealand had no terrestrial mammals--apart from three species of bats--instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10-15 kg; 2-3 m wingspan) was 30%-40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja), and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase...

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

    Indian Academy of Sciences (India)

    ANATOLI

    2Earth Cryosphere Institute, Siberian Branch of Russian Academy of Sciences, Tyumen, 86 Malygina, ... 3State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region 142279, Russia ..... In other words, the energy flux quanta .... Nickle D. C., Learn G. H., Rain M. W., Mullins J. I. and Mittler.

  2. Environmental RNAi in herbivorous insects.

    Science.gov (United States)

    Ivashuta, Sergey; Zhang, Yuanji; Wiggins, B Elizabeth; Ramaseshadri, Partha; Segers, Gerrit C; Johnson, Steven; Meyer, Steve E; Kerstetter, Randy A; McNulty, Brian C; Bolognesi, Renata; Heck, Gregory R

    2015-05-01

    Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a receptive organism by exogenous double-stranded RNA (dsRNA). Although demonstrated under artificial dietary conditions and via transgenic plant presentations in several herbivorous insects, the magnitude and consequence of exogenous dsRNA uptake and the role of eRNAi remains unknown under natural insect living conditions. Our analysis of coleopteran insects sensitive to eRNAi fed on wild-type plants revealed uptake of plant endogenous long dsRNAs, but not small RNAs. Subsequently, the dsRNAs were processed into 21 nt siRNAs by insects and accumulated in high quantities in insect cells. No accumulation of host plant-derived siRNAs was observed in lepidopteran larvae that are recalcitrant to eRNAi. Stability of ingested dsRNA in coleopteran larval gut followed by uptake and transport from the gut to distal tissues appeared to be enabling factors for eRNAi. Although a relatively large number of distinct coleopteran insect-processed plant-derived siRNAs had sequence complementarity to insect transcripts, the vast majority of the siRNAs were present in relatively low abundance, and RNA-seq analysis did not detect a significant effect of plant-derived siRNAs on insect transcriptome. In summary, we observed a broad genome-wide uptake of plant endogenous dsRNA and subsequent processing of ingested dsRNA into 21 nt siRNAs in eRNAi-sensitive insects under natural feeding conditions. In addition to dsRNA stability in gut lumen and uptake, dosage of siRNAs targeting a given insect transcript is likely an important factor in order to achieve measurable eRNAi-based regulation in eRNAi-competent insects that lack an apparent silencing amplification mechanism. © 2015 Ivashuta et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  3. Social insects inspire human design

    Science.gov (United States)

    Holbrook, C. Tate; Clark, Rebecca M.; Moore, Dani; Overson, Rick P.; Penick, Clint A.; Smith, Adrian A.

    2010-01-01

    The international conference ‘Social Biomimicry: Insect Societies and Human Design’, hosted by Arizona State University, USA, 18–20 February 2010, explored how the collective behaviour and nest architecture of social insects can inspire innovative and effective solutions to human design challenges. It brought together biologists, designers, engineers, computer scientists, architects and businesspeople, with the dual aims of enriching biology and advancing biomimetic design. PMID:20392721

  4. Atomic war on insects intensified

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-06-15

    Intensive research work in many countries using nuclear methods aimed at reducing the immense food losses caused by insects have led to a number of important trial operations this year. Some are now in progress in Capri, the famous Italian tourist island, and in Central America. Both are directed against the Mediterranean fruit fly, which attacks most fruit in tropical and sub-tropical countries. Similar methods are also developing to combat other insect pests

  5. Edible insects are the future?

    OpenAIRE

    Huis, van, Arnold

    2016-01-01

    The global increase in demand for meat and the limited land area available prompt the search for alternative protein sources. Also the sustainability of meat production has been questioned. Edible insects as an alternative protein source for human food and animal feed are interesting in terms of low greenhouse gas emissions, high feed conversion efficiency, low land use, and their ability to transform low value organic side streams into high value protein products. More than 2000 insect speci...

  6. An Integrated Molecular Database on Indian Insects.

    Science.gov (United States)

    Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

    2018-01-01

    MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

  7. Detection of Termites and Other Insects Consumed by African Great Apes using Molecular Fecal Analysis

    OpenAIRE

    Ibrahim Hamad; Eric Delaporte; Didier Raoult; Fadi Bittar

    2014-01-01

    The consumption of insects by apes has previously been reported based on direct observations and/or trail signs in feces. However, DNA-based diet analyses may have the potential to reveal trophic links for these wild species. Herein, we analyzed the insect-diet diversity of 9 feces obtained from three species of African great apes, gorilla (Gorilla gorilla gorilla), chimpanzee (Pan troglodytes) and bonobo (Pan paniscus), using two mitochondrial amplifications for arthropods. A total of 1056 c...

  8. 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.

  9. [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.

  10. Problem-oriented approach to Ancient philosophy

    Directory of Open Access Journals (Sweden)

    Berstov, Igor

    2007-06-01

    Full Text Available Igor Berestov and Marina Wolf of the Institute of philosophy and law, Novosibirsk, discuss various methodological difficulties typical of studies in the history of Ancient Greek philosophy and try to develop their own problem-oriented approach.

  11. 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

  12. 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.

  13. NIMI TANTRA (Opthalmology of Ancient India)

    OpenAIRE

    Ramachandran, C.K.

    1984-01-01

    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.

  14. 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. PMID:27732668

  15. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

    Science.gov (United States)

    Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

    2015-11-13

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

  16. Ancient genomics in India: Clarifying the maternal origins of 160-year-old human remains

    Directory of Open Access Journals (Sweden)

    Esha Bandyopadhyay

    2017-10-01

    Full Text Available Sequencing DNA from archaeological remains has opened up new possibilities for furthering our understanding of the origins and evolutionary history of modern humans [1]. However, most ancient DNA (aDNA studies, thus far, have focused on ancient samples obtained from permafrozen and temperate regions, where preservation conditions are better suited for long-term DNA survival. Consequently, this has left a void in aDNA research in tropical regions such as South Asia. The primary aims of the present study were to (a test the feasibility of extracting DNA from historical samples (~160 years old from northern India, and (b correlate obtained mitochondrial DNA (mtDNA signatures with geographical origins of the individuals, as reported in historical records. A total of 30 molars were subjected to DNA extractions and Illumina indexed library preparation. All laboratory work was performed following strict aDNA standards in the clean laboratory at the Centre for Cellular and Molecular Biology, Hyderabad. Complete mtDNA genomes were targeted from all 30 samples following the DNA hybridization method outlined in Maricic et al., 2010 [2]. Captured libraries were sequenced on the Illumina HiSeq 2500 platform (100 bp paired-end mode at MedGenome Inc., Bangalore. Obtained sequences were trimmed for residual adapters using AdapterRemoval and mapped to the revised Cambridge Reference Sequence (rCRS using BWA. HaploGrep2 [3] was used to assign mtDNA haplogroups to each sample. We successfully obtained endogenous mtDNA sequences from all 30 samples, as confirmed by typical aDNA damage (cytosine deamination on the ends of DNA molecules. Coverage and depth of sequencing were in the range of 91-99.5% and 6X-371X, respectively. To ascertain the maternal origins of the individuals, mtDNA haplogroups of our samples were compared to a database compiled from published mtDNA sequences from modern South Asian individuals. Based on this, we were able to confirm northern

  17. From ancient Greek Logos to European rationality

    OpenAIRE

    APOSTOLOPOULOU GEORGIA

    2016-01-01

    Because of history, culture, and politics, European identity has its archetypical elements in ancient Greek culture. Ancient Greek philosophy brought Logos to fore and defined it as the crucial problem and the postulate of the human. We translate the Greek term Logos in English as reason or rationality. These terms, however, do not cover the semantic field of Logos since this includes, among other things, order of being, ground, language, argument etc. The juxtaposition of Logos (reason) to m...

  18. Surgical history of ancient China: Part 2.

    Science.gov (United States)

    Fu, Louis

    2010-03-01

    In this second part of ancient Chinese surgical history, the practice of bone setting in China began around 3000 years ago. Throughout this period, significant progress was made, some highlights of which are cited. These methods, comparable with Western orthopaedic technique, are still being practised today. In conclusion, the possible reasons for the lack of advancement in operative surgery are discussed, within context of the cultural, social and religious background of ancient China.

  19. Ancient Greek in modern language of medicine

    OpenAIRE

    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 analyzed. It may be concluded that the modern language of medicine basically represent...

  20. Social Norms in the Ancient Athenian Courts

    OpenAIRE

    Lanni, Adriaan M.

    2013-01-01

    Ancient Athens was a remarkably peaceful and well-ordered society by both ancient and contemporary standards. Scholars typically attribute Athens’ success to internalized norms and purely informal enforcement mechanisms. This article argues that the formal Athenian court system played a vital role in maintaining order by enforcing informal norms. This peculiar approach to norm enforcement compensated for apparent weaknesses in the state system of coercion. It mitigated the effects of under-e...

  1. Science and Library in the Ancient Age

    Directory of Open Access Journals (Sweden)

    Hasan Sacit Keseroğlu

    2016-09-01

    Full Text Available Science assumes its contemporary identity as a result of the stages of magic, religion and reason. The religious stage starts with the invention of writing and this stage leaves its place to reason with Thales in Ancient Greece. Knowledge eludes from religious beliefs. Ways to reach accurate, reliable and realistic knowledge are sought, along with the answer for what knowledge is. Therefore, beginning of the science is taken into consideration together with science and philosophy. The purpose of this study is to approach knowledge and science of the ancient age in Mesopotamia, Egypt and Ancient Greece in general terms and to determine the relationship between the knowledge produced in those places and libraries established. The hypothesis has been determined as “Egypt and Mesopotamia at the starting point of the history of science and science, and libraries in Ancient Greece have developed parallelly to each other.” The scope of the study has been limited to Mesopotamia, Egypt and Ancient Greece; and Ancient Greece has been explained, with descriptive method, in the frame of the topics of Ionia, Athens, Hellenistic Period and Rome. Many archives and libraries have been established in the ancient age. The difference between an archive and a library has been mentioned first, and then, various libraries have been introduced such as Nineveh in Mesopotamia, Alexandria in Ancient Greece and many others in Egypt. It has been clearly distinguished that there had been a very tight relationship between knowledge production and library, especially with the Library of Alexandria.

  2. Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

    Science.gov (United States)

    Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

    2011-08-01

    Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

  3. All insects are equal, but some insects are more equal than others

    OpenAIRE

    Fischer, Arnout R.H.; Steenbekkers, L.P.A.

    2018-01-01

    Purpose: Lack of acceptance of insects as food is considered a barrier against societal adoption of the potentially valuable contribution of insects to human foods. An underlying barrier may be that insects are lumped together as one group, while consumers typically try specific insects. The purpose of this paper is to investigate the ways in which Dutch consumers, with and without insect tasting experience, are more or less willing to eat different insects. Design/methodology/approach: In a ...

  4. Radiocarbon dating of ancient Japanese documents

    International Nuclear Information System (INIS)

    Oda, H.

    2001-01-01

    History is a reconstruction of past human activity, evidence of which is remained in the form of documents or relics. For the reconstruction of historic period, the radiocarbon dating of ancient documents provides important information. Although radiocarbon age is converted into calendar age with the calibration curve, the calibrated radiocarbon age is still different from the historical age when the document was written. The difference is known as 'old wood effect' for wooden cultural property. The discrepancy becomes more serious problem for recent sample which requires more accurate age determination. Using Tandetron accelerator mass spectrometer at Nagoya University, we have measured radiocarbon ages of Japanese ancient documents, sutras and printed books written dates of which are clarified from the paleographic standpoint. The purpose is to clarify the relation between calibrated radiocarbon age and historical age of ancient Japanese document by AMS radiocarbon dating. This paper reports 23 radiocarbon ages of ancient Japanese documents, sutras and printed books. The calibrated radiocarbon ages are in good agreement with the corresponding historical ages. It was shown by radiocarbon dating of the ancient documents that Japanese paper has little gap by 'old wood effect'; accordingly, ancient Japanese paper is a suitable sample for radiocarbon dating of recent historic period. (author)

  5. Sterile insect supply, emergence, and release

    International Nuclear Information System (INIS)

    Dowell, R.V.; Worley, J.; Gomes, P.J.

    2005-01-01

    Insect mass-rearing for a sterile insect technique (SIT) programme is designed to move beyond the large-scale rearing of insects in a laboratory to the industrial production of consistently high-quality insects for sterilization and release. Each facility reflects the unique biology of the insect reared within it, but there are some generalities for all rearing facilities. Rearing insects in self-contained modules offers flexibility, and increased safety from catastrophic occurrences, compared with using a single building which houses all facets of the rearing process. Although mechanizing certain aspects of the rearing steps helps provide a consistently high-quality insect, successful mass-rearing and delivery depends largely upon the human component. Besides production in centralized facilities, insects can be produced from purchased eggs, or nowadays, adult insects are often obtained from specialized satellite emergence/collection facilities. Interest in commercializing insect production and release is increasing. Shipping sterile insects, sometimes over long distances, is now common practice. Procedures for handling and chilling adult insects, and providing food and water prior to release, are continually being improved. Sterile insects are released via static-release receptacles, ground-release systems, or most commonly from the air. The aerial release of chilled sterile insects is the most efficient method of release, especially when aircraft flight paths are guided by a Global Positioning System (GPS) linked to a computer-controlled release mechanism. (author)

  6. Single origin of the Mascarene stick insects: ancient radiation on sunken islands?

    OpenAIRE

    Bradler, Sven; Cliquennois, Nicolas; Buckley, Thomas R.

    2015-01-01

    Background The study of islands as model systems plays a key role in understanding many evolutionary processes. Knowledge of the historical events leading to present-day island communities is pivotal for exploring fundamental mechanisms of speciation and adaptation. The remote Mascarene archipelago (Mauritius, Réunion, Rodrigues), considered to be the product of an age-progressive trend of north-to-south volcanic activity in the Indian Ocean, hosts a remarkably diverse, endemic and threatened...

  7. Radiations: tool for insect pest management

    International Nuclear Information System (INIS)

    Swami, Kailash Kumar; Kiradoo, M.M.; Srivastava, Meera

    2012-01-01

    The discovery that X-rays or gamma radiation could cause sufficient genetic damage to insect reproductive systems to induce sterility resulted from work conducted by H.J. Muller starting in the 1920s. The sterilizing effect of radiation was noted by scientists of the US Department of Agriculture who had been seeking a method to sterilize insects for many years. These scientists had theorized that if large numbers of the target insect species were reared, sterilized, and released into the field, the sterile insects would mate with the wild insects. These mating would result in no offspring and thus a decline in the population would be obtained. They calculated that if sufficient numbers of sterile insects were released, reproductive rate for the wild population would rapidly decline and reach zero. In simple language, birth control of insects. Radiation sterilization was the answer. In a SIT operation, radiation is used to sexually sterilize insects. Since the SIT is species specific, the selection the insect pest or group of pests on which to work is of primary importance. The Joint Division of the IAEA Food and Agriculture Organization (FAO) has been involved in the use of isotopes and radiation in insect control since 1964. Isotopes are used as tags or markers, for instance, of chemical molecules, insects, or plants. For example, with these tags one can follow the fate of insecticides within insects and the environment; the incorporation of nutrients into the insect; and the movements of insects under field conditions. They also can plants on which insects feed so that the quantity of consumed food can be measured and directly correlated with plant resistance. They can be used as well to follow parasites and predators of insects - for example, their movements, numbers, and ability to help control insect pests. Radiations therefore have come as a novel tool to combat insect pest problem and in future could be very helpful in various other ways, of be it be cost

  8. Insects in fluctuating thermal environments.

    Science.gov (United States)

    Colinet, Hervé; Sinclair, Brent J; Vernon, Philippe; Renault, David

    2015-01-07

    All climate change scenarios predict an increase in both global temperature means and the magnitude of seasonal and diel temperature variation. The nonlinear relationship between temperature and biological processes means that fluctuating temperatures lead to physiological, life history, and ecological consequences for ectothermic insects that diverge from those predicted from constant temperatures. Fluctuating temperatures that remain within permissive temperature ranges generally improve performance. By contrast, those which extend to stressful temperatures may have either positive impacts, allowing repair of damage accrued during exposure to thermal extremes, or negative impacts from cumulative damage during successive exposures. We discuss the mechanisms underlying these differing effects. Fluctuating temperatures could be used to enhance or weaken insects in applied rearing programs, and any prediction of insect performance in the field-including models of climate change or population performance-must account for the effect of fluctuating temperatures.

  9. Spatial distribution of aquatic insects

    DEFF Research Database (Denmark)

    Iversen, Lars Lønsmann

    (time since glacial disturbance and habitat stability) and question the generality of these processes for the understanding of species richness gradients in European rivers. Using regional distributions of European mayflies, stoneflies, and caddisflies this chapter demonstrates that differences...... and shape the habitat requirements and distribution of one of the most affected groups of freshwater species: aquatic insects. It comprises four chapters each addressing different spatial factors in relation to the occurrence of aquatic insects in Europe. Chapter I examine two spatial ecological processes...... niche is derived from local distribution patterns, without incorporating landscape history it can lead to an erroneous niche definition. Chapter III provides some of the first evidence for differences in dispersal phenology related to flight potential in aquatic insects. The chapter highlights...

  10. Biogenic Amines in Insect Antennae

    Directory of Open Access Journals (Sweden)

    Marianna I. Zhukovskaya

    2017-06-01

    Full Text Available Insect antenna is a multisensory organ, each modality of which can be modulated by biogenic amines. Octopamine (OA and its metabolic precursor tyramine (TA affect activity of antennal olfactory receptor neurons. There is some evidence that dopamine (DA modulates gustatory neurons. Serotonin can serve as a neurotransmitter in some afferent mechanosensory neurons and both as a neurotransmitter and neurohormone in efferent fibers targeted at the antennal vessel and mechanosensory organs. As a neurohormone, serotonin affects the generation of the transepithelial potential by sensillar accessory cells. Other possible targets of biogenic amines in insect antennae are hygro- and thermosensory neurons and epithelial cells. We suggest that the insect antenna is partially autonomous in the sense that biologically active substances entering its hemolymph may exert their effects and be cleared from this compartment without affecting other body parts.

  11. My journey to DNA repair.

    Science.gov (United States)

    Lindahl, Tomas

    2013-02-01

    I completed my medical studies at the Karolinska Institute in Stockholm but have always been devoted to basic research. My longstanding interest is to understand fundamental DNA repair mechanisms in the fields of cancer therapy, inherited human genetic disorders and ancient DNA. I initially measured DNA decay, including rates of base loss and cytosine deamination. I have discovered several important DNA repair proteins and determined their mechanisms of action. The discovery of uracil-DNA glycosylase defined a new category of repair enzymes with each specialized for different types of DNA damage. The base excision repair pathway was first reconstituted with human proteins in my group. Cell-free analysis for mammalian nucleotide excision repair of DNA was also developed in my laboratory. I found multiple distinct DNA ligases in mammalian cells, and led the first genetic and biochemical work on DNA ligases I, III and IV. I discovered the mammalian exonucleases DNase III (TREX1) and IV (FEN1). Interestingly, expression of TREX1 was altered in some human autoimmune diseases. I also showed that the mutagenic DNA adduct O(6)-methylguanine (O(6)mG) is repaired without removing the guanine from DNA, identifying a surprising mechanism by which the methyl group is transferred to a residue in the repair protein itself. A further novel process of DNA repair discovered by my research group is the action of AlkB as an iron-dependent enzyme carrying out oxidative demethylation. Copyright © 2013. Production and hosting by Elsevier Ltd.

  12. Ionizing radiation perception by insects

    International Nuclear Information System (INIS)

    Campanhola, C.

    1980-04-01

    The proof of the existence of a perception for ionizing radiation by insects was aimed at, as well as the determination of its processing mechanism. It was tried also to check if such perception induces the insects to keep away from the radiation source, proving therefore a protection against the harms caused by ionizing radiation, or else the stimulus for such behaviour is similar to that caused by light radiations. 60 Co and 241 Am were used as gamma radiation sources, the 60 Co source of 0.435mCi and the 241 Am of 99.68mCi activity. Adult insects were used with the following treatments : exposure to 60 Co and 241 Am radiation and non-exposure (control). A total of approximately 50 insects per replication was released in the central region of an opaque white wooden barrier divided into 3 sections with the same area - 60.0 cm diameter and 7.5 cm height - covered with a nylon screen. 5 replications per treatment were made and the distribution of the insects was evaluated by photographs taken at 15, 30, 45, and 60 minutes after release. Sitophilus oryzae (l., 1763) and Ephestia cautella (Walker, 1864) showed some response to 241 Am gamma radiation, i.e. negative tactism. It was concluded that ionizing radiations can be detected by insects through direct visual stimulus or by visual stimulus reslting from interaction of radiation-Cerenkov radiation - with some other occular component with a refraction index greater than water. Also, the activity of the radioactive source with regard to perception for ionizing radiation, is of relevance in comparison with the energy of the radiation emitted by same, or in other words, what really matters is the radiation dose absorbed. (Author) [pt

  13. Respiratory symptoms in insect breeders.

    Science.gov (United States)

    Harris-Roberts, J; Fishwick, D; Tate, P; Rawbone, R; Stagg, S; Barber, C M; Adisesh, A

    2011-08-01

    A number of specialist food suppliers in the UK breed and distribute insects and insect larvae as food for exotic pets, such as reptiles, amphibians and invertebrates. To investigate the extent of work-related (WR) symptoms and workplace-specific serum IgE in workers potentially exposed to a variety of biological contaminants, including insect and insect larvae allergens, endotoxin and cereal allergens at a UK specialist insect breeding facility. We undertook a study of respiratory symptoms and exposures at the facility, with subsequent detailed clinical assessment of one worker. All 32 workers were assessed clinically using a respiratory questionnaire and lung function. Eighteen workers consented to provide serum for determination of specific IgE to workplace allergens. Thirty-four per cent (11/32) of insect workers reported WR respiratory symptoms. Sensitization, as judged by specific IgE, was found in 29% (4/14) of currently exposed workers. Total inhalable dust levels ranged from 1.2 to 17.9 mg/m(3) [mean 4.3 mg/m(3) (SD 4.4 mg/m(3)), median 2.0 mg/m(3)] and endotoxin levels of up to 29435 EU/m(3) were recorded. Exposure to organic dusts below the levels for which there are UK workplace exposure limits can result in respiratory symptoms and sensitization. The results should alert those responsible for the health of similarly exposed workers to the potential for respiratory ill-health and the need to provide a suitable health surveillance programme.

  14. Conserved genomic organisation of Group B Sox genes in insects.

    Directory of Open Access Journals (Sweden)

    Woerfel Gertrud

    2005-05-01

    Full Text Available Abstract Background Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. Results We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. Conclusion The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and

  15. NIR detects, destroys insect pests

    International Nuclear Information System (INIS)

    McGraw, L.C.

    1998-01-01

    What’s good for Georgia peanuts may also be good for Kansas wheat. An electric eye that scans all food-grade peanuts for visual defects could one day do the same for wheat kernels. For peanuts, it’s a proven method for monitoring quality. In wheat, scanning with near-infrared (NIR) energy can reveal hidden insect infestations that lower wheat quality. ARS entomologists James E. Throne and James E. Baker and ARS agricultural engineer Floyd E. Dowell are the first to combine NIR with an automated grain-handling system to rapidly detect insects hidden in single wheat kernels

  16. ESR signals of irradiated insects

    International Nuclear Information System (INIS)

    Ukai, Mitsuko; Kameya, Hiromi; Imamura, Taro; Miyanoshita, Akihiro; Todoriki, Setsuko; Shimoyama, Yuhei

    2009-01-01

    Analysis of irradiated insects using Electron Spin Resonance (ESR) spectroscopy was reported. The insects were maize weevil, red flour beetle, Indian meal moth and cigarette beetle that are hazardous to crops. The ESR spectra were consisted of a singlet at g=2 and a sextet centered at the similar g-value. The singlet signal is due to an organic free radical. The sextet signal is attributable to the hyperfine interactions from Mn 2+ ions. Upon irradiation, new signals were not detected. The relaxation times, T 1 and T 2 , showed no variations before and after irradiation. (author)

  17. Insects as a Nitrogen Source for Plants

    Directory of Open Access Journals (Sweden)

    Michael J. Bidochka

    2013-07-01

    Full Text Available Many plants have evolved adaptations in order to survive in low nitrogen environments. One of the best-known adaptations is that of plant symbiosis with nitrogen-fixing bacteria; this is the major route by which nitrogen is incorporated into plant biomass. A portion of this plant-associated nitrogen is then lost to insects through herbivory, and insects represent a nitrogen reservoir that is generally overlooked in nitrogen cycles. In this review we show three specialized plant adaptations that allow for the recovery of insect nitrogen; that is, plants gaining nitrogen from insects. First, we show specialized adaptations by carnivorous plants in low nitrogen habitats. Insect carnivorous plants such as pitcher plants and sundews (Nepenthaceae/Sarraceniaceae and Drosera respectively are able to obtain substantial amounts of nitrogen from the insects that they capture. Secondly, numerous plants form associations with mycorrhizal fungi that can provide soluble nitrogen from the soil, some of which may be insect-derived nitrogen, obtained from decaying insects or insect frass. Finally, a specialized group of endophytic, insect-pathogenic fungi (EIPF provide host plants with insect-derived nitrogen. These soil-inhabiting fungi form a remarkable symbiosis with certain plant species. They can infect a wide range of insect hosts and also form endophytic associations in which they transfer insect-derived nitrogen to the plant. Root colonizing fungi are found in disparate fungal phylogenetic lineages, indicating possible convergent evolutionary strategies between taxa, evolution potentially driven by access to carbon-containing root exudates.

  18. 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…

  19. Balancing Acts Between Ancient and Modern Cities: The Ancient Greek Cities Project of C. A. Doxiadis

    Directory of Open Access Journals (Sweden)

    Mantha Zarmakoupi

    2015-12-01

    Full Text Available This paper examines the inception and development of the Ancient Greek Cities (AGC research project (1963–77 of Constantinos A. Doxiadis and addresses the novelty of its methodological approach to the study of classical urbanism. With the AGC project, Doxiadis launched a comprehensive study of the ancient Greek built environment to provide an overview of the factors involved in its shaping. The project produced 24 published volumes — the first two laying out the historical and methodological parameters of the ensuing 22 monographs with case studies — as well as 12 unpublished manuscripts, and through international conferences initiated a wider dialogue on ancient cities beyond the classical Greek world. It was the first interdisciplinary study that attempted to tackle the environmental factors, together with the social and economic ones, underpinning the creation, development and operation of ancient Greek cities. Doxiadis’s innovative approach to the analysis of the ancient city was indebted to his practice as an architect and town planner and was informed by his theory of Ekistics. His purpose was to identify the urban planning principles of ancient Greek settlements in order to employ them in his projects. This paper examines the concept and methodology of the AGC project as well as the ways in which Doxiadis used the study of ancient cities in relation to his contemporary urban/architectural agendas, and explains this important moment in the historiography of ancient Greek urbanism.

  20. Edible insects in China: Utilization and prospects.

    Science.gov (United States)

    Feng, Ying; Chen, Xiao-Ming; Zhao, Min; He, Zhao; Sun, Long; Wang, Cheng-Ye; Ding, Wei-Feng

    2018-04-01

    The use of edible insects has a long history in China, where they have been consumed for more than 2000 years. In general, the level of acceptance is high for the consumption of insects in China. Many studies on edible insects have been conducted in the last 20 years, and the scope of the research includes the culture of entomophagy and the identification, nutritional value, farming and breeding of edible insects, in addition to food production and safety. Currently, 324 species of insects from 11 orders are documented that are either edible or associated with entomophagy in China, which include the common edible species, some less commonly consumed species and some medicinal insects. However, only approximately 10 to 20 types of insects are regularly consumed. The nutritional values for 174 species are available in China, including edible, feed and medicinal species. Although the nutritional values vary among species, all the insects examined contain protein, fat, vitamins and minerals at levels that meet human nutritional requirements. Edible insects were, and continue to be, consumed by different ethnic groups in many parts of China. People directly consume insects or food products made from insects. The processing of products from insect protein powder, oil and chitin, and the development of healthcare foods has been studied in China. People also consume insects indirectly by eating livestock that were fed insects, which may be a more acceptable pathway to use insects in human diets. Although limited, the data on the food safety of insects indicate that insects are safe for food or feed. Incidences of allergic reactions after consuming silkworm pupae, cicadas and crickets have been reported in China. Insect farming is a unique breeding industry in rural China and is a source of income for local people. Insects are reared and bred for human food, medicine and animal feed using two approaches in China: the insects are either fully domesticated and reared

  1. Ancient humans and the origin of modern humans.

    Science.gov (United States)

    Kelso, Janet; Prüfer, Kay

    2014-12-01

    Recent advances in sequencing technologies and molecular methods have facilitated the sequencing of DNA from ancient human remains which has, in turn, provided unprecedented insight into human history. Within the past 4 years the genomes of Neandertals and Denisovans, as well as the genomes of at least two early modern humans, have been sequenced. These sequences showed that there have been several episodes of admixture between modern and archaic groups; including admixture from Neandertals into modern human populations outside of Africa, and admixture from Denisovans into modern human populations in Oceania. Recent results indicate that some of these introgressed regions may have been advantageous for modern humans as they expanded into new regions outside of Africa. Copyright © 2014. Published by Elsevier Ltd.

  2. Detection and analysis of ancient segmental duplications in mammalian genomes.

    Science.gov (United States)

    Pu, Lianrong; Lin, Yu; Pevzner, Pavel A

    2018-05-07

    Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6.05% of the human genome (version hg19), a 17% increase as compared to the previous estimate. Moreover, SDquest classified 6.42% of the latest GRCh38 version of the human genome as SDs, a large increase as compared to previous studies. We thus propose to re-evaluate evolution of SDs based on their accurate representation across multiple genomes. Toward this goal, we analyzed the complex mosaic structure of SDs and decomposed mosaic SDs into elementary SDs, a prerequisite for follow-up evolutionary analysis. We also introduced the concept of the breakpoint graph of mosaic SDs that revealed SD hotspots and suggested that some SDs may have originated from circular extrachromosomal DNA (ecDNA), not unlike ecDNA that contributes to accelerated evolution in cancer. © 2018 Pu et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Evidence for Ancient Mesoamerican Earthquakes

    Science.gov (United States)

    Kovach, R. L.; Garcia, B.

    2001-12-01

    Evidence for past earthquake damage at Mesoamerican ruins is often overlooked because of the invasive effects of tropical vegetation and is usually not considered as a casual factor when restoration and reconstruction of many archaeological sites are undertaken. Yet the proximity of many ruins to zones of seismic activity would argue otherwise. Clues as to the types of damage which should be soughtwere offered in September 1999 when the M = 7.5 Oaxaca earthquake struck the ruins of Monte Alban, Mexico, where archaeological renovations were underway. More than 20 structures were damaged, 5 of them seriously. Damage features noted were walls out of plumb, fractures in walls, floors, basal platforms and tableros, toppling of columns, and deformation, settling and tumbling of walls. A Modified Mercalli Intensity of VII (ground accelerations 18-34 %b) occurred at the site. Within the diffuse landward extension of the Caribbean plate boundary zone M = 7+ earthquakes occur with repeat times of hundreds of years arguing that many Maya sites were subjected to earthquakes. Damage to re-erected and reinforced stelae, walls, and buildings were witnessed at Quirigua, Guatemala, during an expedition underway when then 1976 M = 7.5 Guatemala earthquake on the Motagua fault struck. Excavations also revealed evidence (domestic pttery vessels and skeleton of a child crushed under fallen walls) of an ancient earthquake occurring about the teim of the demise and abandonment of Quirigua in the late 9th century. Striking evidence for sudden earthquake building collapse at the end of the Mayan Classic Period ~A.D. 889 was found at Benque Viejo (Xunantunich), Belize, located 210 north of Quirigua. It is argued that a M = 7.5 to 7.9 earthquake at the end of the Maya Classic period centered in the vicinity of the Chixoy-Polochic and Motagua fault zones cound have produced the contemporaneous earthquake damage to the above sites. As a consequences this earthquake may have accelerated the

  4. The Curious Connection Between Insects and Dreams

    Directory of Open Access Journals (Sweden)

    Barrett A. Klein

    2011-12-01

    Full Text Available A majority of humans spend their waking hours surrounded by insects, so it should be no surprise that insects also appear in humans’ dreams as we sleep. Dreaming about insects has a peculiar history, marked by our desire to explain a dream’s significance and by the tactic of evoking emotions by injecting insects in dream-related works of art, film, music, and literature. I surveyed a scattered literature for examples of insects in dreams, first from the practices of dream interpretation, psychiatry, and scientific study, then from fictional writings and popular culture, and finally in the etymology of entomology by highlighting insects with dream-inspired Latinate names. A wealth of insects in dreams, as documented clinically and culturally, attests to the perceived relevance of dreams and to the ubiquity of insects in our lives.

  5. The Curious Connection Between Insects and Dreams

    Science.gov (United States)

    Klein, Barrett A.

    2011-01-01

    A majority of humans spend their waking hours surrounded by insects, so it should be no surprise that insects also appear in humans’ dreams as we sleep. Dreaming about insects has a peculiar history, marked by our desire to explain a dream’s significance and by the tactic of evoking emotions by injecting insects in dream-related works of art, film, music, and literature. I surveyed a scattered literature for examples of insects in dreams, first from the practices of dream interpretation, psychiatry, and scientific study, then from fictional writings and popular culture, and finally in the etymology of entomology by highlighting insects with dream-inspired Latinate names. A wealth of insects in dreams, as documented clinically and culturally, attests to the perceived relevance of dreams and to the ubiquity of insects in our lives. PMID:26467945

  6. The Curious Connection Between Insects and Dreams.

    Science.gov (United States)

    Klein, Barrett A

    2011-12-21

    A majority of humans spend their waking hours surrounded by insects, so it should be no surprise that insects also appear in humans' dreams as we sleep. Dreaming about insects has a peculiar history, marked by our desire to explain a dream's significance and by the tactic of evoking emotions by injecting insects in dream-related works of art, film, music, and literature. I surveyed a scattered literature for examples of insects in dreams, first from the practices of dream interpretation, psychiatry, and scientific study, then from fictional writings and popular culture, and finally in the etymology of entomology by highlighting insects with dream-inspired Latinate names. A wealth of insects in dreams, as documented clinically and culturally, attests to the perceived relevance of dreams and to the ubiquity of insects in our lives.

  7. Trapping of insects in the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Pathak, S.C.; Parulekar, A.H.

    Some insects caught on RV Gaveshani, while on a cruise in the Arabian Sea in May-June 1986 is reported Of the 23 insects caught, 16 were lepidopterans An interesting flight behaviour of Psychota sp is described...

  8. Towards next-generation biodiversity assessment using DNA metabarcoding

    DEFF Research Database (Denmark)

    Taberlet, Pierre; Coissac, Eric; Pompanon, Francois

    2012-01-01

    Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA (soil......, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next-generation sequencing platforms and the ecologists need for high-throughput taxon identification have facilitated the emergence of DNA metabarcoding. The potential power of DNA...

  9. Aquatic wood -- an insect perspective

    Science.gov (United States)

    Peter S. Cranston; Brendan McKie

    2006-01-01

    Immersed wood provides refugia and substrate for a diverse array of macroinvertebrates, and food for a more restricted genuinely xylophagous fauna. Worldwide, xylophages are found across aquatic insect orders, including Coleoptera, Diptera, Trichoptera and Plecoptera. Xylophages often are specialised, feeding on the wood surface or mining deep within. Many feed...

  10. Developmental constraint of insect audition

    Directory of Open Access Journals (Sweden)

    Strauß Johannes

    2006-12-01

    Full Text Available Abstract Background Insect ears contain very different numbers of sensory cells, from only one sensory cell in some moths to thousands of sensory cells, e.g. in cicadas. These differences still await functional explanation and especially the large numbers in cicadas remain puzzling. Insects of the different orders have distinct developmental sequences for the generation of auditory organs. These sensory cells might have different functions depending on the developmental stages. Here we propose that constraints arising during development are also important for the design of insect ears and might influence cell numbers of the adults. Presentation of the hypothesis We propose that the functional requirements of the subadult stages determine the adult complement of sensory units in the auditory system of cicadas. The hypothetical larval sensory organ should function as a vibration receiver, representing a functional caenogenesis. Testing the hypothesis Experiments at different levels have to be designed to test the hypothesis. Firstly, the neuroanatomy of the larval sense organ should be analyzed to detail. Secondly, the function should be unraveled neurophysiologically and behaviorally. Thirdly, the persistence of the sensory cells and the rebuilding of the sensory organ to the adult should be investigated. Implications of the hypothesis Usually, the evolution of insect ears is viewed with respect to physiological and neuronal mechanisms of sound perception. This view should be extended to the development of sense organs. Functional requirements during postembryonic development may act as constraints for the evolution of adult organs, as exemplified with the auditory system of cicadas.

  11. Edible insects are the future?

    NARCIS (Netherlands)

    Huis, van Arnold

    2016-01-01

    The global increase in demand for meat and the limited land area available prompt the search for alternative protein sources. Also the sustainability of meat production has been questioned. Edible insects as an alternative protein source for human food and animal feed are interesting in terms of

  12. Diversity of insect intestinal microflora

    Czech Academy of Sciences Publication Activity Database

    Mrázek, Jakub; Štrosová, Lenka; Fliegerová, Kateřina; Kott, T.; Kopečný, Jan

    2008-01-01

    Roč. 53, č. 3 (2008), s. 229-233 ISSN 0015-5632 R&D Projects: GA ČR GA303/06/0974 Institutional research plan: CEZ:AV0Z50450515 Keywords : insect intestinal microflora Subject RIV: EE - Microbiology, Virology Impact factor: 1.172, year: 2008

  13. Bug City: Aquatic Insects [Videotape].

    Science.gov (United States)

    1998

    "Bug City" is a video series created to help children learn about insects and other small critters. All aspects of bug life are touched upon including body structure, food, habitat, life cycle, mating habits, camouflage, mutualism (symbiosis), adaptations, social behavior, and more. Each program features dramatic microscopic photography,…

  14. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

    Science.gov (United States)

    Brouchkov, Anatoli; Kabilov, Marsel; Filippova, Svetlana; Baturina, Olga; Rogov, Victor; Galchenko, Valery; Mulyukin, Andrey; Fursova, Oksana; Pogorelko, Gennady

    2017-12-15

    Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Insect pests of stored grain products

    International Nuclear Information System (INIS)

    Chuaqui-Offermanns, N.

    1987-01-01

    The presence of insects in stored products is a worldwide recognized problem. In this report chemical and physical methods to control insect infestations in stored products are discussed. Special attention is given to the use of ionizing radiation to control insect pests in stored grains. The radiosensitivity of the most common insect pests at their different developmental stages is presented and discussed. The conclusions of this review are compiled in an executive summary. 62 refs

  16. All insects are equal, but some insects are more equal than others

    NARCIS (Netherlands)

    Fischer, Arnout R.H.; Steenbekkers, L.P.A.

    2018-01-01

    Purpose: Lack of acceptance of insects as food is considered a barrier against societal adoption of the potentially valuable contribution of insects to human foods. An underlying barrier may be that insects are lumped together as one group, while consumers typically try specific insects. The purpose

  17. Monitoring Biodiversity using Environmental DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis

    DNA). Especially the advance in DNA sequencing technology has revolutionized this field and opened new frontiers in ecology, evolution and environmental sciences. Also, it is becoming a powerful tool for field biologist, with new and efficient methods for monitoring biodiversity. This thesis focuses on the use...... of eDNA in monitoring of biodiversity in different settings. First, it is shown that a diversity of rare freshwater animals – representing amphibians, fish, mammals, insects and crustaceans – can be detected based on eDNA obtained directly from 15 ml water samples of lakes, ponds and streams...... setting, showing that eDNA obtained directly from ½ l seawater samples can account for marine fish biodiversity using NGS. Promisingly, eDNA covered the fish diversity better than any of 9 methods, conventionally used in marine fish surveys. Additionally, it is shown that even short 100-bp. fish e...

  18. How Insects Survive Winter in the Midwest

    Science.gov (United States)

    Understanding how insects cope with cold temperatures can not only help entomologists more accurately forecast when and where insects are active, but it may also help us understand how climate change will influence insect pests. This newsletter article provides a comprehensive overview of how Midwes...

  19. Plant responses to insect egg deposition

    NARCIS (Netherlands)

    Hilker, M.; Fatouros, N.E.

    2015-01-01

    Plants can respond to insect egg deposition and thus resist attack by herbivorous insects from the beginning of the attack, egg deposition. We review ecological effects of plant responses to insect eggs and differentiate between egg-induced plant defenses that directly harm the eggs and indirect

  20. Radioisotopes and food preservation against insects

    International Nuclear Information System (INIS)

    Hachem Ahmad, M.S.

    1998-01-01

    The book describes how to preserve food from harmful insects by using radioisotopes. It focusses on the impact of ionized radiation on the different stages of insect growth and on its metabolism and immunity. It also discusses the relationship between radiation doses and insect reproduction. It explains the various methods to detect the irradiated foods

  1. 21 CFR 1250.95 - Insect control.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Insect control. 1250.95 Section 1250.95 Food and... SANITATION Sanitation Facilities and Conditions on Vessels § 1250.95 Insect control. Vessels shall be... generally accepted methods of insect control. ...

  2. Eusocial insects as emerging models for behavioural epigenetics.

    Science.gov (United States)

    Yan, Hua; Simola, Daniel F; Bonasio, Roberto; Liebig, Jürgen; Berger, Shelley L; Reinberg, Danny

    2014-10-01

    Understanding the molecular basis of how behavioural states are established, maintained and altered by environmental cues is an area of considerable and growing interest. Epigenetic processes, including methylation of DNA and post-translational modification of histones, dynamically modulate activity-dependent gene expression in neurons and can therefore have important regulatory roles in shaping behavioural responses to environmental cues. Several eusocial insect species - with their unique displays of behavioural plasticity due to age, morphology and social context - have emerged as models to investigate the genetic and epigenetic underpinnings of animal social behaviour. This Review summarizes recent studies in the epigenetics of social behaviour and offers perspectives on emerging trends and prospects for establishing genetic tools in eusocial insects.

  3. Novel insect-specific flavivirus isolated from northern Europe

    Science.gov (United States)

    Huhtamo, Eili; Moureau, Gregory; Cook, Shelley; Julkunen, Ora; Putkuri, Niina; Kurkela, Satu; Uzcátegui, Nathalie Y.; Harbach, Ralph E.; Gould, Ernest A.; Vapalahti, Olli; de Lamballerie, Xavier

    2012-01-01

    Mosquitoes collected in Finland were screened for flaviviral RNA leading to the discovery and isolation of a novel flavivirus designated Hanko virus (HANKV). Virus characterization, including phylogenetic analysis of the complete coding sequence, confirmed HANKV as a member of the “insect-specific” flavivirus (ISF) group. HANKV is the first member of this group isolated from northern Europe, and therefore the first northern European ISF for which the complete coding sequence has been determined. HANKV was not transcribed as DNA in mosquito cell culture, which appears atypical for an ISF. HANKV shared highest sequence homology with the partial NS5 sequence available for the recently discovered Spanish Ochlerotatus flavivirus (SOcFV). Retrospective analysis of mitochondrial sequences from the virus-positive mosquito pool suggested an Ochlerotatus mosquito species as the most likely host for HANKV. HANKV and SOcFV may therefore represent a novel group of Ochlerotatus-hosted insect-specific flaviviruses in Europe and further afield. PMID:22999256

  4. Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling.

    Directory of Open Access Journals (Sweden)

    Thi-Nguyen-Ny Tran

    Full Text Available BACKGROUND: The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. METHODOLOGY/PRINCIPAL FINDINGS: We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279-modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%. Third, we classified 10 of 18 teeth (56% collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I in human ancient and modern dental pulp, respectively. CONCLUSIONS/SIGNIFICANCE: Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.

  5. Classification of Ancient Mammal Individuals Using Dental Pulp MALDI-TOF MS Peptide Profiling

    Science.gov (United States)

    Tran, Thi-Nguyen-Ny; Aboudharam, Gérard; Gardeisen, Armelle; Davoust, Bernard; Bocquet-Appel, Jean-Pierre; Flaudrops, Christophe; Belghazi, Maya; Raoult, Didier; Drancourt, Michel

    2011-01-01

    Background The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. Methodology/Principal Findings We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279–modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively. Conclusions/Significance Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals. PMID:21364886

  6. 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.

  7. Microanalysis study on ancient Wiangkalong Pottery

    Science.gov (United States)

    Won-in, K.; Tancharakorn, S.; Dararutana, P.

    2017-09-01

    Wiangkalong is one of major ceramic production cities in northern of Thailand, once colonized by the ancient Lanna Kingdom (1290 A.D.). Ancient Wiangkalong potteries were produced with shapes and designs as similar as those of the Chinese Yuan and Ming Dynasties. Due to the complex nature of materials and objects, extremely sensitive, spatially resolved, multi-elemental and versatile analytical instruments using non-destructive and non-sampling methods to analyze theirs composition are need. In this work, micro-beam X-ray fluorescence spectroscopy based on synchrotron radiation was firstly used to characterize the elemental composition of the ancient Wiangkalong pottery. The results showed the variations in elemental composition of the body matrix, the glaze and the underglaze painting, such as K, Ca, Ti, V, Cr, Mn and Fe.

  8. Did the ancient egyptians discover Algol?

    Science.gov (United States)

    Jetsu, L.; Porceddu, S.; Porceddu, S.; Lyytinen, J.; Kajatkari, P.; Markkanen, T.; Toivari-Viitala, J.

    2013-02-01

    Fabritius discovered the first variable star, Mira, in 1596. Holwarda determined the 11 months period of Mira in 1638. Montanari discovered the next variable star, Algol, in 1669. Its period, 2.867 days, was determined by Goodricke (178). Algol was associated with demon-like creatures, "Gorgon" in ancient Greek and "ghoul" in ancient Arab mythology. This indicates that its variability was discovered much before 1669 (Wilk 1996), but this mythological evidence is ambiguous (Davis 1975). For thousands of years, the Ancient Egyptian Scribes (AES) observed stars for timekeeping in a region, where there are nearly 300 clear nights a year. We discovered a significant periodicity of 2.850 days in their calendar for lucky and unlucky days dated to 1224 BC, "the Cairo Calendar". Several astrophysical and astronomical tests supported our conclusion that this was the period of Algol three millennia ago. The "ghoulish habits" of Algol could explain this 0.017 days period increase (Battersby 2012).

  9. 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.

  10. Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

    Science.gov (United States)

    Huang, Shi

    2009-01-01

    There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here do not conform to these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils. Far more damaging to the hypothesis than data from extant organisms, which merely question the constancy of mutation rate, the study of ancient fossil organisms here challenges for the first time the fundamental premise of modern evolution theory that genetic distances had always increased with time in the past history of life on Earth. PMID:18600632

  11. Insect biofuel cells using trehalose included in insect hemolymph leading to an insect-mountable biofuel cell.

    Science.gov (United States)

    Shoji, Kan; Akiyama, Yoshitake; Suzuki, Masato; Hoshino, Takayuki; Nakamura, Nobuhumi; Ohno, Hiroyuki; Morishima, Keisuke

    2012-12-01

    In this paper, an insect biofuel cell (BFC) using trehalose included in insect hemolymph was developed. The insect BFC is based on trehalase and glucose oxidase (GOD) reaction systems which oxidize β-glucose obtained by hydrolyzing trehalose. First, we confirmed by LC-MS that a sufficient amount of trehalose was present in the cockroach hemolymph (CHL). The maximum power density obtained using the insect BFC was 6.07 μW/cm(2). The power output was kept more than 10 % for 2.5 h by protecting the electrodes with a dialysis membrane. Furthermore, the maximum power density was increased to 10.5 μW/cm(2) by using an air diffusion cathode. Finally, we succeeded in driving a melody integrated circuit (IC) and a piezo speaker by connecting five insect BFCs in series. The results indicate that the insect BFC is a promising insect-mountable battery to power environmental monitoring micro-tools.

  12. The TL dating of ancient porcelain

    International Nuclear Information System (INIS)

    Leung, P.L.; Stokes, M.J.; Wang Weida; Xia Junding; Zhou Zhixin

    1997-01-01

    The age determination of ancient porcelain using the pre-dose technique in TL dating was reported. The variation of beta dose with depth below the surface of the porcelain slice, the thermal activation characteristic (TAC) for 110 degree C peak, the measurement of paleodose and the estimation of annual dose were studied. The results show that this technique is suitable for authenticity testing of ancient porcelain, but both accuracy and precision for porcelain dating are worse than those for pottery, because porcelain differs from pottery on composition, structure and firing temperature. Besides, some complicated factors in the pre-dose technique would be the possible cause of the greater errors

  13. TREATMENT OF FRACTURES IN ANCIENT EGYPT

    Directory of Open Access Journals (Sweden)

    Z. K. Bashurov

    2012-01-01

    Full Text Available The most complete information about the medicine in Ancient Egypt two papyrus provided: a large medical papyrus of G. Ebers and papyrus about the surgery of E. Smith. Smith’s papyrus is of particular interest as it contains the information on the status of surgery in Ancient Egypt. Papyrus consists of descriptions of the clinical cases. To the present time, 48 cases have survived; it is arranged in order of location - from the head down to the feet. Orthopedic deformities were reflected in the figures on the walls of the pyramids and temples as well as the description of the mummies and archaeological finds.

  14. Insects feeding on cadavers as an alternative source of human genetic material

    Directory of Open Access Journals (Sweden)

    Rafał Skowronek

    2015-03-01

    Full Text Available In some criminal cases, the use of classical sources of human genetic material is difficult or even impossible. One solution may be the use of insects, especially blowfly larvae which feed on corpses. A recent review of case reports and experimental studies available in biomedical databases has shown that insects can be a valuable source of human mitochondrial and genomic deoxyribonucleic acid (DNA, allowing for an effective analysis of hypervariable region (HVR sequences and short tandem repeat (STR profiles, respectively. The optimal source of human DNA is the crop (a part of the gut of active third-instar blowfly larvae. Pupae and insect faeces can be also used in forensic genetic practice instead of the contents of the alimentary tract.

  15. The eukaryotic genome is structurally and functionally more like a social insect colony than a book.

    Science.gov (United States)

    Qiu, Guo-Hua; Yang, Xiaoyan; Zheng, Xintian; Huang, Cuiqin

    2017-11-01

    Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome. Upon comparison with the habitation, sociality and defense mechanisms of a social insect colony, it is found that the genome is similar to a social insect colony in various aspects. A social insect colony may thus be a better metaphor than a book to describe the spatial organization and physical functions of the genome. The potential implications of the metaphor are also discussed.

  16. Phase Coexistence in Insect Swarms

    Science.gov (United States)

    Sinhuber, Michael; Ouellette, Nicholas T.

    2017-10-01

    Animal aggregations are visually striking, and as such are popular examples of collective behavior in the natural world. Quantitatively demonstrating the collective nature of such groups, however, remains surprisingly difficult. Inspired by thermodynamics, we applied topological data analysis to laboratory insect swarms and found evidence for emergent, material-like states. We show that the swarms consist of a core "condensed" phase surrounded by a dilute "vapor" phase. These two phases coexist in equilibrium, and maintain their distinct macroscopic properties even though individual insects pass freely between them. We further define a pressure and chemical potential to describe these phases, extending theories of active matter to aggregations of macroscopic animals and laying the groundwork for a thermodynamic description of collective animal groups.

  17. Prediction of autosomal STR typing success in ancient and Second World War bone samples.

    Science.gov (United States)

    Zupanič Pajnič, Irena; Zupanc, Tomaž; Balažic, Jože; Geršak, Živa Miriam; Stojković, Oliver; Skadrić, Ivan; Črešnar, Matija

    2017-03-01

    Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is

  18. Moessbauer studies on ancient Jizhon plain Temmoku porcelains

    International Nuclear Information System (INIS)

    Yu Zhengfang; Zheng Yufang; Lin Yongqiang

    1994-01-01

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

  19. Nuclear energy against insect pests

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1963-07-15

    The paper presents the main topics discussed at the scientific symposium on the Use and Application of Radioisotopes and Radiation in the Control of Plant and Animal Insect Pests, held in Athens last April, jointly organized by IAEA and FAO with the co-operation of the Greek Government. The sterile male technique is discussed in details and some results from the applications are given

  20. Successes against insects and parasites

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-10-15

    With more and more answers being found to intricate problems which have entailed years of research in many parts of the world, some successes can now be claimed in the fight to control insect threats to crops, animals and human beings. Nuclear techniques are playing an important part in world efforts, and recent reports show that they have been effective in pioneer work against crop pests as well as in finding an answer to some diseases caused by parasites

  1. Outreach Testing of Ancient Astronomy

    Science.gov (United States)

    Sanmartin, J. R. S.; Blanco, M. B. M.

    2015-10-01

    fundamental quantity being given by half the difference between solar distances to vertical at winter and summer solstices, with value about 23.5°. Day and year periods greatly differing by about 2 ½ orders of magnitude, 1 day against 365 days, helps students to correctly visualize and interpret the experimental measurements. Since the gnomon serves to observe at night the moon shadow too, students can also determine the inclination of the lunar orbital plane, as about 5 degrees away from the ecliptic, thus explaining why eclipses are infrequent. Independently, earth taking longer between spring and fall equinoxes than from fall to spring (the solar anomaly), as again verified by the students, was explained in ancient Greek science, which posited orbits universally as circles or their combination, by introducing the eccentric circle, with earth placed some distance away from the orbital centre when considering the relative motion of the sun, which would be closer to the earth in winter. In a sense, this can be seen as hint and approximation of the elliptic orbit proposed by Kepler many centuries later. EPSC Abstracts Vol. 10, EPSC2015-40, 2015 European Planetary Science Congress 2015 c Author(s) 2015 EPSC European Planetary Science Congress Secondly, by observing lunar phases and eclipses from the ground, students could also determine, following Aristarchus of Samos in the 3rd century BC, 4 length ratios involving moon and sun distances to earth, and radii of all three, moon, sun, and earth. The angular width of the moon could be first determined with simplest optical devices as about half a degree; this yields the ratio between moon diameter 2RM and distance DM to earth. Next, eclipses of sun prove its angular width, and thus ratio 2RS/DS, similar to the lunar one, though the relatively high lunar orbital eccentricity, 0.055, does result in not quite a full eclipse if at lunar apogee. Further, at a half-moon phase, when the angle sun-moon-earth is a right one, the angle

  2. Circadian organization in hemimetabolous insects.

    Science.gov (United States)

    Tomioka, Kenji; Abdelsalam, Salaheldin

    2004-12-01

    The circadian system of hemimetabolous insects is reviewed in respect to the locus of the circadian clock and multioscillatory organization. Because of relatively easy access to the nervous system, the neuronal organization of the clock system in hemimetabolous insects has been studied, yielding identification of the compound eye as the major photoreceptor for entrainment and the optic lobe for the circadian clock locus. The clock site within the optic lobe is inconsistent among reported species; in cockroaches the lobula was previously thought to be a most likely clock locus but accessory medulla is recently stressed to be a clock center, while more distal part of the optic lobe including the lamina and the outer medulla area for the cricket. Identification of the clock cells needs further critical studies. Although each optic lobe clock seems functionally identical, in respect to photic entrainment and generation of the rhythm, the bilaterally paired clocks form a functional unit. They interact to produce a stable time structure within individual insects by exchanging photic and temporal information through neural pathways, in which serotonin and pigment-dispersing factor (PDF) are involved as chemical messengers. The mutual interaction also plays an important role in seasonal adaptation of the rhythm.

  3. Stiffness of desiccating insect wings

    International Nuclear Information System (INIS)

    Mengesha, T E; Vallance, R R; Mittal, R

    2011-01-01

    The stiffness of insect wings is typically determined through experimental measurements. Such experiments are performed on wings removed from insects. However, the wings are subject to desiccation which typically leads to an increase in their stiffness. Although this effect of desiccation is well known, a comprehensive study of the rate of change in stiffness of desiccating insect wings would be a significant aid in planning experiments as well as interpreting data from such experiments. This communication presents a comprehensive experimental analysis of the change in mass and stiffness of gradually desiccating forewings of Painted Lady butterflies (Vanessa cardui). Mass and stiffness of the forewings of five butterflies were simultaneously measured every 10 min over a 24 h period. The averaged results show that wing mass declined exponentially by 21.1% over this time period with a time constant of 9.8 h, while wing stiffness increased linearly by 46.2% at a rate of 23.4 μN mm -1 h -1 . For the forewings of a single butterfly, the experiment was performed over a period of 1 week, and the results show that wing mass declined exponentially by 52.2% with a time constant of 30.2 h until it reached a steady-state level of 2.00 mg, while wing stiffness increased exponentially by 90.7% until it reached a steady-state level of 1.70 mN mm -1 . (communication)

  4. Stiffness of desiccating insect wings

    Energy Technology Data Exchange (ETDEWEB)

    Mengesha, T E; Vallance, R R [Department of Mechanical Engineering, The George Washington University, 738 Phillips Hall, 801 22nd St NW, Washington, DC 20052 (United States); Mittal, R, E-mail: vallance@gwu.edu [Department of Mechanical Engineering, Johns Hopkins University, 126 Latrobe Hall, 3400 N Charles Street, Baltimore, MD 21218 (United States)

    2011-03-15

    The stiffness of insect wings is typically determined through experimental measurements. Such experiments are performed on wings removed from insects. However, the wings are subject to desiccation which typically leads to an increase in their stiffness. Although this effect of desiccation is well known, a comprehensive study of the rate of change in stiffness of desiccating insect wings would be a significant aid in planning experiments as well as interpreting data from such experiments. This communication presents a comprehensive experimental analysis of the change in mass and stiffness of gradually desiccating forewings of Painted Lady butterflies (Vanessa cardui). Mass and stiffness of the forewings of five butterflies were simultaneously measured every 10 min over a 24 h period. The averaged results show that wing mass declined exponentially by 21.1% over this time period with a time constant of 9.8 h, while wing stiffness increased linearly by 46.2% at a rate of 23.4 {mu}N mm{sup -1} h{sup -1}. For the forewings of a single butterfly, the experiment was performed over a period of 1 week, and the results show that wing mass declined exponentially by 52.2% with a time constant of 30.2 h until it reached a steady-state level of 2.00 mg, while wing stiffness increased exponentially by 90.7% until it reached a steady-state level of 1.70 mN mm{sup -1}. (communication)

  5. Gut immunity in Lepidopteran insects.

    Science.gov (United States)

    Wu, Kai; Yang, Bing; Huang, Wuren; Dobens, Leonard; Song, Hongsheng; Ling, Erjun

    2016-11-01

    Lepidopteran insects constitute one of the largest fractions of animals on earth, but are considered pests in their relationship with man. Key to the success of this order of insects is its ability to digest food and absorb nutrition, which takes place in the midgut. Because environmental microorganisms can easily enter Lepidopteran guts during feeding, the innate immune response guards against pathogenic bacteria, virus and microsporidia that can be devoured with food. Gut immune responses are complicated by both resident gut microbiota and the surrounding peritrophic membrane and are distinct from immune responses in the body cavity, which depend on the function of the fat body and hemocytes. Due to their relevance to agricultural production, studies of Lepidopteran insect midgut and immunity are receiving more attention, and here we summarize gut structures and functions, and discuss how these confer immunity against different microorganisms. It is expected that increased knowledge of Lepidopteran gut immunity may be utilized for pest biological control in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Ancient Pyramids Help Students Learn Math Concepts

    Science.gov (United States)

    Smith, Courtney D.; Stump, Amanda M.; Lazaros, Edward J.

    2010-01-01

    This article presents an activity that allows students to use mathematics and critical-thinking skills to emulate processes used by the ancient Egyptians to prepare the site for the Pyramids of Giza. To accomplish this, they use three different methods. First, they create a square using only simple technological tools that were available to the…

  7. Modelling human agency in ancient irrigation

    NARCIS (Netherlands)

    Ertsen, M.W.

    2011-01-01

    Human activity is key in understanding ancient irrigation systems. Results of short term actions build up over time, affecting civilizations on larger temporal and spatial scales. Irrigation systems, with their many entities, social and physical, their many interactions within a changing environment

  8. Analysis of ancient pigments by Raman microscopy

    International Nuclear Information System (INIS)

    Zuo Jian; Xu Cunyi

    1999-01-01

    Raman microscopy can be applied for the spatial resolution, and non-destructive in situ analysis of inorganic pigments in pottery, manuscripts and paintings. Compared with other techniques, it is the best single technique for this purpose. An overview is presented of the applications of Raman microscopy in the analysis of ancient pigments

  9. The Roots of Science in Ancient China.

    Science.gov (United States)

    Fisher, Arthur

    1982-01-01

    A 45-year-old research project (culminating in the multivolume "Science and Civilization in China") is examining major scientific innovations in ancient China and attempting to explain why, although the Chinese gained a technological edge in the past, they did not make the forward leap into modern science. (JN)

  10. Cosmic rays and ancient planetary magnetic fields

    International Nuclear Information System (INIS)

    Wesson, P.S.

    1977-01-01

    The possibility is discussed of using the latitude-dependent cutoff in the intensity and flux of cosmic ray particles reaching the surface of a planet to investigate ancient magnetic fields in the Moon, Mars and the Earth. In the last case, the method could provide a validity test for conventional palaeomagnetism. (Auth.)

  11. Unlocking the Mysteries of Ancient Egypt.

    Science.gov (United States)

    Riechers, Maggie

    1995-01-01

    Describes the work of Egyptologist William Murnane who is recording the ritual scenes and inscriptions of a great columned hall from the days of the pharaohs. The 134 columns, covered with divine imagery and hieroglyphic inscriptions represent an unpublished religious text. Briefly discusses ancient Egyptian culture. Includes several photographs…

  12. Truth Obviousness in Ancient Greek Philosophy

    Directory of Open Access Journals (Sweden)

    Halyna I. Budz

    2013-01-01

    Full Text Available 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 something, existing in reality, in other words, something, truly existing, eternal reality. Consequently, to know truth is it to know the substantial reality base. That’s why the justification of the reality origin is the axiomatic doctrine of truth at the same time, because only fundamental principle “truly” exists and is the truth itself. The idea of fundamental principle in ancient Greek philosophy is the axiom, universal principle, which is the base of reality as a substance from ontological perspective and is realized as the truth from gnosiological perspective. Fundamental principle, as Greeks understand it, coincides with the truth, in other words, reality and thinking are identical. The idea of reality source is the universal criterion of world perception at the same time, in other words, it is the truth, which is perceived axiomatically.

  13. Defining Astrology in Ancient and Classical History

    Science.gov (United States)

    Campion, Nicholas

    2015-05-01

    Astrology in the ancient and classical worlds can be partly defined by its role, and partly by the way in which scholars spoke about it. The problem is complicated by the fact that the word is Greek - it has no Babylonian or Egyptian cognates - and even in Greece it was interchangeable with its cousin, 'astronomy'. Yet if we are to understand the role of the sky, stars and planets in culture, debates about the nature of ancient astrology, by both classical and modern scholars, must be taken into account. This talk will consider modern scholars' typologies of ancient astrology, together with ancient debates from Cicero in the 1st century BC, to Plotinus (204/5-270 AD) and Isidore of Seville (c. 560 - 4 April 636). It will consider the implications for our understanding of astronomy's role in culture, and conclude that in the classical period astrology may be best understood through its diversity and allegiance to competing philosophies, and that its functions were therefore similarly varied.

  14. An ancient greek pain remedy for athletes

    DEFF Research Database (Denmark)

    Bartels, Else M.; Swaddling, Judith; Harrison, Adrian Paul

    2006-01-01

    and swellings, which was reserved for use by the winners of Olympic events, the so-called "Fuscum Olympionico inscriptum"-(ointment) entitled "dark Olympic victor's". In a time when the Olympic games have recently returned to their homeland, we examine the potential efficacy of this ancient remedy in terms...

  15. The Cost of Living in Ancient Greece

    Directory of Open Access Journals (Sweden)

    Roberto Morales Harley

    2014-11-01

    Full Text Available The paper focuses on the most relevant economic aspects of Ancient Greece, more specifically, 5th century BC Athens. It explores the Greek notion of economy, the monetary system, the financial administration and the labor market, in order to contextualize the cost of living. The examples on this matter take into account the products’ costs and the people’s wages.

  16. On Ancient Babylonian Algebra and Geometry

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 8; Issue 8. On Ancient Babylonian Algebra and Geometry. Rahul Roy. General Article Volume 8 Issue 8 August 2003 pp 27-42. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/008/08/0027-0042. Keywords.

  17. The Challenges of Qualitatively Coding Ancient Texts

    Science.gov (United States)

    Slingerland, Edward; Chudek, Maciej

    2012-01-01

    We respond to several important and valid concerns about our study ("The Prevalence of Folk Dualism in Early China," "Cognitive Science" 35: 997-1007) by Klein and Klein, defending our interpretation of our data. We also argue that, despite the undeniable challenges involved in qualitatively coding texts from ancient cultures,…

  18. Ancient Human Parasites in Ethnic Chinese Populations.

    Science.gov (United States)

    Yeh, Hui-Yuan; Mitchell, Piers D

    2016-10-01

    Whilst archaeological evidence for many aspects of life in ancient China is well studied, there has been much less interest in ancient infectious diseases, such as intestinal parasites in past Chinese populations. Here, we bring together evidence from mummies, ancient latrines, and pelvic soil from burials, dating from the Neolithic Period to the Qing Dynasty, in order to better understand the health of the past inhabitants of China and the diseases endemic in the region. Seven species of intestinal parasite have been identified, namely roundworm, whipworm, Chinese liver fluke, oriental schistosome, pinworm, Taenia sp. tapeworm, and the intestinal fluke Fasciolopsis buski . It was found that in the past, roundworm, whipworm, and Chinese liver fluke appear to have been much more common than the other species. While roundworm and whipworm remained common into the late 20th century, Chinese liver fluke seems to have undergone a marked decline in its prevalence over time. The iconic transport route known as the Silk Road has been shown to have acted as a vector for the transmission of ancient diseases, highlighted by the discovery of Chinese liver fluke in a 2,000 year-old relay station in northwest China, 1,500 km outside its endemic range.

  19. Ancient Egyptian Medicine: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Samuel Adu-Gyamfi

    2015-12-01

    Full Text Available Our present day knowledge in the area of medicine in Ancient Egypt has been severally sourced from medical papyri several of which have been deduced and analyzed by different scholars. For educational purposes it is always imperative to consult different literature or sources in the teaching of ancient Egypt and medicine in particular. To avoid subjectivity the author has found the need to re-engage the efforts made by several scholars in adducing evidences from medical papyri. In the quest to re-engage the efforts of earlier writers and commentaries on the medical papyri, we are afforded the opportunity to be informed about the need to ask further questions to enable us to construct or reconstruct both past and modern views on ancient Egyptian medical knowledge. It is this vocation the author sought to pursue in the interim, through a preliminary review, to highlight, comment and reinvigorate in the reader or researcher the need for a continuous engagement of some pertinent documentary sources on Ancient Egyptian medical knowledge for educational and research purposes. The study is based on qualitative review of published literature. The selection of those articles as sources was based on the focus of the review, in order to purposively select and comment on articles that were published based either on information from a medical papyrus or focused on medical specialization among the ancient Egyptians as well as ancient Egyptian knowledge on diseases and medicine. It was found that the Egyptians developed relatively sophisticated medical practices covering significant medical fields such as herbal medicine, gynecology and obstetrics, anatomy and physiology, mummification and even the preliminary form of surgery. These practices, perhaps, were developed as remedies for the prevailing diseases and the accidents that might have occurred during the construction of their giant pyramids. It must be stated that they were not without flaws. Also, the

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

    Science.gov (United States)

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

    2016-04-01

    Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations. © 2016 Stichting International Foundation for Animal Genetics.