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Sample records for accelerator reveals ancient

  1. Archimedes: Accelerator Reveals Ancient Text

    SciTech Connect

    Bergmann, Uwe

    2004-02-24

    Archimedes (287-212 BC), who is famous for shouting 'Eureka' (I found it) is considered one of the most brilliant thinkers of all times. The 10th-century parchment document known as the 'Archimedes Palimpsest' is the unique source for two of the great Greek's treatises. Some of the writings, hidden under gold forgeries, have recently been revealed at the Stanford Synchrotron Radiation Laboratory at SLAC. An intense x-ray beam produced in a particle accelerator causes the iron in original ink, which has been partly erased and covered, to send out a fluorescence glow. A detector records the signal and a digital image showing the ancient writings is produced. Please join us in this fascinating journey of a 1,000-year-old parchment from its origin in the Mediterranean city of Constantinople to a particle accelerator in Menlo Park.

  2. Ancient River revealed

    NASA Astrophysics Data System (ADS)

    Recent flights of the Spaceborne Imaging Radar-C/X-band Synthetic Aperture Radar (SIR-C/X-SAR) mission aboard the space shuttle Endeavour discovered a previously unknown branch of an ancient river. The images, released at AGU's Spring Meeting, show the river channel buried under thousands of years worth of windblown sand in a region of North Africa's Sahara Desert near the Kufra Oasis in southeast Libya, centered at 23.3°N latitude, 22.9°E longitude. The image from the flight last October reveals a system of old, now inactive stream valleys, called “paleodrainage systems,” which carried running water northward across the Sahara during periods of wetter climate.

  3. Ancient Pb and Ti mobilization revealed by Scanning Ion Imaging

    NASA Astrophysics Data System (ADS)

    Kusiak, Monika A.; Whitehouse, Martin J.; Wilde, Simon A.

    2014-05-01

    Zircons from strongly layered early Archean ortho- and paragneisses in ultra-high temperature (UHT) metamorphic rocks of the Napier Complex, Enderby Land, East Antarctica are characterized by complex U-Th-Pb systematics [1,2,3]. A large number of zircons from three samples, Gage Ridge, Mount Sones and Dallwitz Nunatak, are reversely discordant (U/Pb ages older than 207Pb/206Pb ages) with the oldest date of 3.9 Ga [4] (for the grain from Gage Ridge orthogneiss). To further investigate this process, we utilized a novel high spatial resolution Scanning Ion Imaging technique on the CAMECA IMS 1280 at the Natural History Museum in Stockholm. Areas of 70 μm x 70 μm were selected for imaging in mono- and multicollection modes using a ~2 μm rastered primary beam to map out the distribution of 48Ti, 89Y, 180Hf, 232Th, 238U, 204Pb, 206Pb and 207Pb. The ion maps reveal variable distribution of certain elements within analysed grains that can be compared to their CL response. Yttrium, together with U and Th, exhibits zonation visible on the CL images, Hf shows expected minimal variation. Unusual patchiness is visible in the map for Ti and Pb distribution. The bright patches with enhanced signal do not correspond to any zones or to crystal imperfections (e.g. cracks). The presence of patchy titanium is likely to affect Ti-in-zircon thermometry, and patchy Pb affecting 207Pb/206Pb ages, usually considered as more robust for Archean zircons. Using the WinImage program, we produced 207Pb/206Pb ratio maps that allow calculation of 207Pb/206Pb ages for spots of any size within the frame of the picture and at any time after data collection. This provides a new and unique method for obtaining age information from zircon. These maps show areas of enhanced brightness where the 207Pb/206Pb ratio is higher and demonstrate that within these small areas (μm scale) the apparent 207Pb/206Pb age is older, in some of these patches even > 4 Ga. These data are a result of ancient Pb

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

    PubMed Central

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

    2014-01-01

    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. PMID:24573854

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

    PubMed Central

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

    2015-01-01

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

  6. Ancient DNA reveals male diffusion through the Neolithic Mediterranean route.

    PubMed

    Lacan, Marie; Keyser, Christine; Ricaut, François-Xavier; Brucato, Nicolas; Duranthon, Francis; Guilaine, Jean; Crubézy, Eric; Ludes, Bertrand

    2011-06-14

    The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.

  7. Ancient DNA reveals male diffusion through the Neolithic Mediterranean route

    PubMed Central

    Lacan, Marie; Keyser, Christine; Ricaut, François-Xavier; Brucato, Nicolas; Duranthon, Francis; Guilaine, Jean; Crubézy, Eric; Ludes, Bertrand

    2011-01-01

    The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition. PMID:21628562

  8. Ancient DNA sequence revealed by error-correcting codes

    PubMed Central

    Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

    2015-01-01

    A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

  9. Early allelic selection in maize as revealed by ancient DNA.

    PubMed

    Jaenicke-Després, Viviane; Buckler, Ed S; Smith, Bruce D; Gilbert, M Thomas P; Cooper, Alan; Doebley, John; Pääbo, Svante

    2003-11-14

    Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.

  10. Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists.

    PubMed

    Ning, Chao; Gao, Shizhu; Deng, Boping; Zheng, Hongxiang; Wei, Dong; Lv, Haoze; Li, Hongjie; Song, Li; Wu, Yong; Zhou, Hui; Cui, Yinqiu

    2016-02-01

    The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga-Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.

  11. Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots[W

    PubMed Central

    Jiao, Yuannian; Li, Jingping; Tang, Haibao; Paterson, Andrew H.

    2014-01-01

    Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage. PMID:25082857

  12. Determination of the cosmological rate of change of G and the tidal accelerations of earth and moon from ancient and modern astronomical data

    NASA Technical Reports Server (NTRS)

    Muller, P. M.

    1976-01-01

    The theory and numerical analysis of ancient astronomical observations (1374 to 1715) are combined with modern data in a simultaneous solution for: the tidal acceleration of the lunar longitude; the observed apparent acceleration of the earth's rotation; the true nontidal geophysical part of this acceleration; and the rate of change in the gravitational constant. Provided are three independent determinations of a rate of change of G consistent with the Hubble Constant and a near zero nontidal rotational acceleration of the earth. The tidal accelerations are shown to have remained constant during the historical period within uncertainties. Ancient and modern solar system data, and extragalactic observations provided a completely consistent astronomical and cosmological scheme.

  13. Managing shifting species: Ancient DNA reveals conservation conundrums in a dynamic world.

    PubMed

    Waters, Jonathan M; Grosser, Stefanie

    2016-11-01

    The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts.​.

  14. Comparative analysis of teleost fish genomes reveals preservation of different ancient clock duplicates in different fishes.

    PubMed

    Wang, Han

    2008-06-01

    Clock (Circadian locomotor output cycle kaput) was the first vertebrate circadian clock gene identified in a mouse forward genetics mutagenesis screen. It encodes a bHLH-PAS protein that is highly conserved throughout evolution. Tetrapods also have the second Clock gene, Clock2 or Npas2 (Neuronal PAS domain protein 2). Conversely, the fruit fly, an invertebrate, has only one clock gene. Interrogation of the five teleost fish genome databases revealed that the zebrafish and the Japanese pufferfish (fugu) each have three clock genes, whereas the green spotted pufferfish (tetraodon), the Japanese medaka fish and the three-spine stickleback each have two clock genes. Phylogenetic and splice site analyses indicated that zebrafish and fugu each have two clock1 genes, clock1a and clock1b and one clock2; tetraodon also have clock1a and clock1b but do not have clock2; and medaka and stickleback each have clock1b and one clock2. Genome neighborhood analysis further showed that clock1a/clock1b in zebrafish, fugu and tetraodon is an ancient duplicate. While the dN/dS ratios of these three fish clock duplicates are all <1, indicating that purifying selection has acted upon them; the Tajima relative rate test showed that all three fish clock duplicates have asymmetric evolutionary rates, implicating that one of these duplicates have been under positive selection or relaxed functional constraint. These results support the view that teleost fish clock genes were generated from an ancient genome-wide duplication, and differential gene loss after the duplication resulted in retention of different ancient duplicates in different teleost fishes, which could have contributed to the evolution of the distinct fish circadian clock mechanisms.

  15. Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure.

    PubMed

    Galinsky, Kevin J; Loh, Po-Ru; Mallick, Swapan; Patterson, Nick J; Price, Alkes L

    2016-11-03

    Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for using population differentiation to detect selection and enables an analysis of the UK population structure at fine resolution. In this study, analyses of 113,851 UK Biobank samples showed that population structure in the UK is dominated by five principal components (PCs) spanning six clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses of ancient Eurasians revealed that populations in the northern UK have higher levels of Steppe ancestry and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along the top PCs identified a genome-wide-significant signal of selection at the coding variant rs601338 in FUT2 (p = 9.16 × 10(-9)). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified genome-wide-significant (p = 5 × 10(-8)) signals of recent selection at two additional loci: CYP1A2-CSK and F12. We detected strong associations between diastolic blood pressure in the UK Biobank and both the variants with selection signals at CYP1A2-CSK (p = 1.10 × 10(-19)) and the variants with ancient Eurasian selection signals at the ATXN2-SH2B3 locus (p = 8.00 × 10(-33)), implicating recent adaptation related to blood pressure.

  16. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea.

    PubMed

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-02-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics.

  17. Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea

    PubMed Central

    Rascovan, Nicolás; Maldonado, Javier; Vazquez, Martín P; Eugenia Farías, María

    2016-01-01

    Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics. PMID:26140530

  18. An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile.

    PubMed

    Hekkala, Evon; Shirley, Matthew H; Amato, George; Austin, James D; Charter, Suellen; Thorbjarnarson, John; Vliet, Kent A; Houck, Marlys L; Desalle, Rob; Blum, Michael J

    2011-10-01

    The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the 'true crocodiles' of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers, as well as karyotype analysis of chromosome number and structure, to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species' taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.

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

    PubMed

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

    2016-02-10

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

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

    PubMed Central

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

    2016-01-01

    The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional ‘cryptic’ invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts. PMID:26842575

  1. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid

    PubMed Central

    Dutta, Moumita; Pollard, Dominic J.; Goldstone, David C.; Ramos, Andres; Müllers, Erik; Stirnnagel, Kristin; Stanke, Nicole; Lindemann, Dirk; Taylor, William R.; Rosenthal, Peter B.

    2016-01-01

    The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. PMID:27829070

  2. Common and unexpected findings in mummies from ancient Egypt and South America as revealed by CT.

    PubMed

    Jackowski, Christian; Bolliger, Stephan; Thali, Michael J

    2008-01-01

    Computed tomography (CT) has proved to be a valuable investigative tool for mummy research and is the method of choice for examining mummies. It allows for noninvasive insight, especially with virtual endoscopy, which reveals detailed information about the mummy's sex, age, constitution, injuries, health, and mummification techniques used. CT also supplies three-dimensional information about the scanned object. Mummification processes can be summarized as "artificial," when the procedure was performed on a body with the aim of preservation, or as "natural," when the body's natural environment resulted in preservation. The purpose of artificial mummification was to preserve that person's morphologic features by delaying or arresting the decay of the body. The ancient Egyptians are most famous for this. Their use of evisceration followed by desiccation with natron (a compound of sodium salts) to halt putrefaction and prevent rehydration was so effective that their embalmed bodies have survived for nearly 4500 years. First, the body was cleaned with a natron solution; then internal organs were removed through the cribriform plate and abdomen. The most important, and probably the most lengthy, phase was desiccation. After the body was dehydrated, the body cavities were rinsed and packed to restore the body's former shape. Finally, the body was wrapped. Animals were also mummified to provide food for the deceased, to accompany the deceased as pets, because they were seen as corporal manifestations of deities, and as votive offerings. Artificial mummification was performed on every continent, especially in South and Central America.

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

    PubMed Central

    Rai, Niraj; Kumar, Giriraj; Pruthi, Parul Aggarwal; Thangaraj, Kumarasamy; Bajpai, Sunil; Pruthi, Vikas

    2017-01-01

    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. PMID:28273082

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

    PubMed

    Jain, Sonal; Rai, Niraj; Kumar, Giriraj; Pruthi, Parul Aggarwal; Thangaraj, Kumarasamy; Bajpai, Sunil; Pruthi, Vikas

    2017-01-01

    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.

  5. Ancient collagen reveals evolutionary history of the endemic South American ‘ungulates’

    PubMed Central

    Buckley, Michael

    2015-01-01

    Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs. PMID:25833851

  6. Discovery of methylfarnesoate as the annelid brain hormone reveals an ancient role of sesquiterpenoids in reproduction

    PubMed Central

    Schenk, Sven; Krauditsch, Christian; Frühauf, Peter; Gerner, Christopher; Raible, Florian

    2016-01-01

    Animals require molecular signals to determine when to divert resources from somatic functions to reproduction. This decision is vital in animals that reproduce in an all-or-nothing mode, such as bristle worms: females committed to reproduction spend roughly half their body mass for yolk and egg production; following mass spawning, the parents die. An enigmatic brain hormone activity suppresses reproduction. We now identify this hormone as the sesquiterpenoid methylfarnesoate. Methylfarnesoate suppresses transcript levels of the yolk precursor Vitellogenin both in cell culture and in vivo, directly inhibiting a central energy–costly step of reproductive maturation. We reveal that contrary to common assumptions, sesquiterpenoids are ancient animal hormones present in marine and terrestrial lophotrochozoans. In turn, insecticides targeting this pathway suppress vitellogenesis in cultured worm cells. These findings challenge current views of animal hormone evolution, and indicate that non-target species and marine ecosystems are susceptible to commonly used insect larvicides. DOI: http://dx.doi.org/10.7554/eLife.17126.001 PMID:27894418

  7. Structural and functional analysis of amphioxus HIFα reveals ancient features of the HIFα family.

    PubMed

    Gao, Shan; Lu, Ling; Bai, Yan; Zhang, Peng; Song, Weibo; Duan, Cunming

    2014-04-01

    Hypoxia-inducible factors (HIFs) are master regulators of the transcriptional response to hypoxia. To gain insight into the structural and functional evolution of the HIF family, we characterized the HIFα gene from amphioxus, an invertebrate chordate, and identified several alternatively spliced HIFα isoforms. Whereas HIFα Ia, the full-length isoform, contained a complete oxygen-dependent degradation (ODD) domain, the isoforms Ib, Ic, and Id had 1 or 2 deletions in the ODD domain. When tagged with GFP and tested in mammalian cells, the amphioxus HIFα Ia protein level increased in response to hypoxia or CoCl2 treatment, whereas HIFα Ib, Ic, and Id showed reduced or no hypoxia regulation. Deletion of the ODD sequence in HIFα Ia up-regulated the HIFα Ia levels under normoxia. Gene expression analysis revealed HIFα Ic to be the predominant isoform in embryos and larvae, whereas isoform Ia was the most abundant form in the adult stage. The expression levels of Ib and Id were very low. Hypoxia treatment of adults had no effect on the mRNA levels of these HIFα isoforms. Functional analyses in mammalian cells showed all 4 HIFα isoforms capable of entering the nucleus and activating hypoxia response element-dependent reporter gene expression. The functional nuclear location signal (NLS) mapped to 3 clusters of basic residues. (775)KKARL functioned as the primary NLS, but (737)KRK and (754)KK also contributed to the nuclear localization. All amphioxus HIFα isoforms had 2 functional transactivation domains (TADs). Its C-terminal transactivation (C-TAD) shared high sequence identity with the human HIF-1α and HIF-2α C-TAD. This domain contained a conserved asparagine, and its mutation resulted in an increase in transcriptional activity. These findings reveal many ancient features of the HIFα family and provide novel insights into the evolution of the HIFα family.

  8. Accurate 3d Scanning of Damaged Ancient Greek Inscriptions for Revealing Weathered Letters

    NASA Astrophysics Data System (ADS)

    Papadaki, A. I.; Agrafiotis, P.; Georgopoulos, A.; Prignitz, S.

    2015-02-01

    In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and "hidden" letters.

  9. Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community

    PubMed Central

    2012-01-01

    Background A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves. Results The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y–chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave. Conclusions Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site

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

    PubMed

    Haile, James; Froese, Duane G; Macphee, Ross D E; Roberts, Richard G; Arnold, Lee J; Reyes, Alberto V; Rasmussen, Morten; Nielsen, Rasmus; Brook, Barry W; Robinson, Simon; Demuro, Martina; Gilbert, M Thomas P; Munch, Kasper; Austin, Jeremy J; Cooper, Alan; Barnes, Ian; Möller, Per; Willerslev, Eske

    2009-12-29

    Causes of late Quaternary extinctions of large mammals ("megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or confined to refugia. Here we report an alternative approach to detect 'ghost ranges' of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.

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

    PubMed Central

    Haile, James; Froese, Duane G.; MacPhee, Ross D. E.; Roberts, Richard G.; Arnold, Lee J.; Reyes, Alberto V.; Rasmussen, Morten; Nielsen, Rasmus; Brook, Barry W.; Robinson, Simon; Demuro, Martina; Gilbert, M. Thomas P.; Munch, Kasper; Austin, Jeremy J.; Cooper, Alan; Barnes, Ian; Möller, Per; Willerslev, Eske

    2009-01-01

    Causes of late Quaternary extinctions of large mammals (“megafauna”) continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000–13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or confined to refugia. Here we report an alternative approach to detect ‘ghost ranges’ of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene. PMID:20018740

  12. Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age.

    PubMed

    Gao, Shi-Zhu; Zhang, Ye; Wei, Dong; Li, Hong-Jie; Zhao, Yong-Bin; Cui, Yin-Qiu; Zhou, Hui

    2015-05-01

    Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.

  13. Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.

    PubMed

    Cappellini, Enrico; Jensen, Lars J; Szklarczyk, Damian; Ginolhac, Aurélien; da Fonseca, Rute A R; Stafford, Thomas W; Holen, Steven R; Collins, Matthew J; Orlando, Ludovic; Willerslev, Eske; Gilbert, M Thomas P; Olsen, Jesper V

    2012-02-03

    We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43 000 year old woolly mammoth ( Mammuthus primigenius ) bone preserved in the Siberian permafrost. For the first time, 126 unique protein accessions, mostly low-abundance extracellular matrix and plasma proteins, were confidently identified by solid molecular evidence. Among the best characterized was the carrier protein serum albumin, presenting two single amino acid substitutions compared to extant African ( Loxodonta africana ) and Indian ( Elephas maximus ) elephants. Strong evidence was observed of amino acid modifications due to post-mortem hydrolytic and oxidative damage. A consistent subset of this permafrost bone proteome was also identified in more recent Columbian mammoth ( Mammuthus columbi ) samples from temperate latitudes, extending the potential of the approach described beyond subpolar environments. Mass spectrometry-based ancient protein sequencing offers new perspectives for future molecular phylogenetic inference and physiological studies on samples not amenable to ancient DNA investigation. This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics.

  14. Amy2B copy number variation reveals starch diet adaptations in ancient European dogs

    PubMed Central

    Tresset, Anne; Bastian, Fabiola; Lagoutte, Laetitia; Arendt, Maja-Louise; Bălăşescu, Adrian; Marshour, Marjan; Sablin, Mikhail V.; Salanova, Laure; Vigne, Jean-Denis; Hitte, Christophe; Hänni, Catherine

    2016-01-01

    Extant dog and wolf DNA indicates that dog domestication was accompanied by the selection of a series of duplications on the Amy2B gene coding for pancreatic amylase. In this study, we used a palaeogenetic approach to investigate the timing and expansion of the Amy2B gene in the ancient dog populations of Western and Eastern Europe and Southwest Asia. Quantitative polymerase chain reaction was used to estimate the copy numbers of this gene for 13 ancient dog samples, dated to between 15 000 and 4000 years before present (cal. BP). This evidenced an increase of Amy2B copies in ancient dogs from as early as the 7th millennium cal. BP in Southeastern Europe. We found that the gene expansion was not fixed across all dogs within this early farming context, with ancient dogs bearing between 2 and 20 diploid copies of the gene. The results also suggested that selection for the increased Amy2B copy number started 7000 years cal. BP, at the latest. This expansion reflects a local adaptation that allowed dogs to thrive on a starch rich diet, especially within early farming societies, and suggests a biocultural coevolution of dog genes and human culture. PMID:28018628

  15. REVEALING COMPANIONS TO NEARBY STARS WITH ASTROMETRIC ACCELERATION

    SciTech Connect

    Tokovinin, Andrei; Hartung, Markus; Hayward, Thomas L.; Makarov, Valeri V. E-mail: mhartung@gemini.edu E-mail: valeri.makarov@usno.navy.mil

    2012-07-15

    A subset of 51 Hipparcos astrometric binaries among FG dwarfs within 67 pc has been surveyed with the Near-Infrared Coronagraphic Imager adaptive optics system at Gemini-S, directly resolving for the first time 17 subarcsecond companions and 7 wider ones. Using these data together with published speckle interferometry of 57 stars, we compare the statistics of resolved astrometric companions with those of a simulated binary population. The fraction of resolved companions is slightly lower than expected from binary statistics. About 10% of astrometric companions could be 'dark' (white dwarfs and close pairs of late M-dwarfs). To our surprise, several binaries are found with companions too wide to explain the acceleration. Re-analysis of selected intermediate astrometric data shows that some acceleration solutions in the original Hipparcos catalog are spurious.

  16. Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals.

    PubMed

    Beck, Robin M D; Lee, Michael S Y

    2014-10-22

    Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic-Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.

  17. Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

    PubMed Central

    Beck, Robin M. D.; Lee, Michael S. Y.

    2014-01-01

    Analyses of a comprehensive morphological character matrix of mammals using ‘relaxed’ clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic–Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the ‘explosive’ palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates. PMID:25165770

  18. [Different uses of Fagopyrum esculentum Moench (buckwheat) in Japan and China: what ancient medical documents reveal].

    PubMed

    Tatsumi, Nami; Marui, Eiji

    2012-03-01

    The purpose of this thesis is to demonstrate that buckwheat has been recognized, both in Japan and China, as a crop that is useful in many ways: as an agricultural crop, and for the healing powers and properties that, according to traditional Chinese medicine, it has. A comparative study of ancient documents pertaining to medicine in these countries has made it clear that this is the case. Buckwheat, however, has been used quite differently in each country. As is shown in some ancient Chinese documents pertaining to medicine, China has treated buckwheat primarily as a medicine for clinical use rather than as an edible crop. Nowadays, buckwheat is eaten only in some regions of China. Although it came to Japan from China as a medicine, in Japan buckwheat gradually became a popular food crop. It has become an important component of traditional Japanese cuisine thanks in part to government support and the strong demand that developed in Japanese society.

  19. Molecular degradation of ancient documents revealed by 1H HR-MAS NMR spectroscopy

    PubMed Central

    Corsaro, Carmelo; Mallamace, Domenico; Łojewska, Joanna; Mallamace, Francesco; Pietronero, Luciano; Missori, Mauro

    2013-01-01

    For centuries mankind has stored its knowledge on paper, a remarkable biomaterial made of natural cellulose fibers. However, spontaneous cellulose degradation phenomena weaken and discolorate paper over time. The detailed knowledge of products arising from cellulose degradation is essential in understanding deterioration pathways and in improving durability of cultural heritage. In this study, for the first time, products of cellulose degradation were individually detected in solid paper samples by means of an extremely powerful proton HR-MAS NMR set-up, in combination to a wise use of both ancient and, as reference, artificially aged paper samples. Carboxylic acids, in addition to more complex dicarboxylic and hydroxy-carboxylic acids, were found in all samples studied. Since these products can catalyze further degradation, their knowledge is fundamental to improve conservation strategies of historical documents. Furthermore, the identification of compounds used in ancient production techniques, also suggests for artifacts dating, authentication and provenance. PMID:24104201

  20. Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis.

    PubMed

    Lertrit, Patcharee; Poolsuwan, Samerchai; Thosarat, Rachanie; Sanpachudayan, Thitima; Boonyarit, Hathaichanoke; Chinpaisal, Chatchai; Suktitipat, Bhoom

    2008-12-01

    The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.

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

    PubMed

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

    2016-06-14

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

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

    PubMed

    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.

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

    PubMed

    Lira, Jaime; Linderholm, Anna; Olaria, Carmen; Brandström Durling, Mikael; Gilbert, M Thomas P; Ellegren, Hans; Willerslev, Eske; Lidén, Kerstin; Arsuaga, Juan Luis; Götherström, Anders

    2010-01-01

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

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

    PubMed Central

    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

  5. The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment

    PubMed Central

    Alcaraz, Luis David; Olmedo, Gabriela; Bonilla, Germán; Cerritos, René; Hernández, Gustavo; Cruz, Alfredo; Ramírez, Enrique; Putonti, Catherine; Jiménez, Beatriz; Martínez, Eva; López, Varinia; Arvizu, Jacqueline L.; Ayala, Francisco; Razo, Francisco; Caballero, Juan; Siefert, Janet; Eguiarte, Luis; Vielle, Jean-Philippe; Martínez, Octavio; Souza, Valeria; Herrera-Estrella, Alfredo; Herrera-Estrella, Luis

    2008-01-01

    The Cuatro Ciénegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico) hosts a wide diversity of microorganisms contained within springs thought to be geomorphological relics of an ancient sea. A major question remaining to be answered is whether bacteria from CCB are ancient marine bacteria that adapted to an oligotrophic system poor in NaCl, rich in sulfates, and with extremely low phosphorus levels (<0.3 μM). Here, we report the complete genome sequence of Bacillus coahuilensis, a sporulating bacterium isolated from the water column of a desiccation lagoon in CCB. At 3.35 Megabases this is the smallest genome sequenced to date of a Bacillus species and provides insights into the origin, evolution, and adaptation of B. coahuilensis to the CCB environment. We propose that the size and complexity of the B. coahuilensis genome reflects the adaptation of an ancient marine bacterium to a novel environment, providing support to a “marine isolation origin hypothesis” that is consistent with the geology of CCB. This genomic adaptation includes the acquisition through horizontal gene transfer of genes involved in phosphorous utilization efficiency and adaptation to high-light environments. The B. coahuilensis genome sequence also revealed important ecological features of the bacterial community in CCB and offers opportunities for a unique glimpse of a microbe-dominated world last seen in the Precambrian. PMID:18408155

  6. Ancient DNA Reveals Matrilineal Continuity in Present-Day Poland over the Last Two Millennia

    PubMed Central

    Juras, Anna; Dabert, Miroslawa; Kushniarevich, Alena; Malmström, Helena; Raghavan, Maanasa; Kosicki, Jakub Z.; Metspalu, Ene; Willerslev, Eske; Piontek, Janusz

    2014-01-01

    While numerous ancient human DNA datasets from across Europe have been published till date, modern-day Poland in particular, remains uninvestigated. Besides application in the reconstruction of continent-wide human history, data from this region would also contribute towards our understanding of the history of the Slavs, whose origin is hypothesized to be in East or Central Europe. Here, we present the first population-scale ancient human DNA study from the region of modern-day Poland by establishing mitochondrial DNA profiles for 23 samples dated to 200 BC – 500 AD (Roman Iron Age) and for 20 samples dated to 1000–1400 AD (Medieval Age). Our results show that mitochondrial DNA sequences from both periods belong to haplogroups that are characteristic of contemporary West Eurasia. Haplotype sharing analysis indicates that majority of the ancient haplotypes are widespread in some modern Europeans, including Poles. Notably, the Roman Iron Age samples share more rare haplotypes with Central and Northeast Europeans, whereas the Medieval Age samples share more rare haplotypes with East-Central and South-East Europeans, primarily Slavic populations. Our data demonstrates genetic continuity of certain matrilineages (H5a1 and N1a1a2) in the area of present-day Poland from at least the Roman Iron Age until present. As such, the maternal gene pool of present-day Poles, Czechs and Slovaks, categorized as Western Slavs, is likely to have descended from inhabitants of East-Central Europe during the Roman Iron Age. PMID:25337992

  7. Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide

    PubMed Central

    Young, J. N.; Rickaby, R. E. M.; Kapralov, M. V.; Filatov, D. A.

    2012-01-01

    Rubisco, the most abundant enzyme on the Earth and responsible for all photosynthetic carbon fixation, is often thought of as a highly conserved and sluggish enzyme. Yet, different algal Rubiscos demonstrate a range of kinetic properties hinting at a history of evolution and adaptation. Here, we show that algal Rubisco has indeed evolved adaptively during ancient and distinct geological periods. Using DNA sequences of extant marine algae of the red and Chromista lineage, we define positive selection within the large subunit of Rubisco, encoded by rbcL, to occur basal to the radiation of modern marine groups. This signal of positive selection appears to be responding to changing intracellular concentrations of carbon dioxide (CO2) triggered by physiological adaptations to declining atmospheric CO2. Within the ecologically important Haptophyta (including coccolithophores) and Bacillariophyta (diatoms), positive selection occurred consistently during periods of falling Phanerozoic CO2 and suggests emergence of carbon-concentrating mechanisms. During the Proterozoic, a strong signal of positive selection after secondary endosymbiosis occurs at the origin of the Chromista lineage (approx. 1.1 Ga), with further positive selection events until 0.41 Ga, implying a significant and continuous decrease in atmospheric CO2 encompassing the Cryogenian Snowball Earth events. We surmise that positive selection in Rubisco has been caused by declines in atmospheric CO2 and hence acts as a proxy for ancient atmospheric CO2. PMID:22232761

  8. Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception

    PubMed Central

    Kang, Kyeongjin; Pulver, Stefan R.; Panzano, Vincent C.; Chang, Elaine C.; Griffith, Leslie C.; Theobald, Douglas L.; Garrity, Paul A.

    2010-01-01

    Chemical nociception, the detection of tissue-damaging chemicals, is important for animal survival and causes human pain and inflammation, but its evolutionary origins are largely unknown. Reactive electrophiles are a class of noxious compounds humans find pungent and irritating, like allyl isothiocyanate (in wasabi) and acrolein (in cigarette smoke)1–3. Insects to humans find reactive electrophiles aversive1–3, but whether this reflects conservation of an ancient sensory modality has been unclear. Here we identify the molecular basis of reactive electrophile detection in flies. We demonstrate that dTRPA1, the Drosophila melanogaster ortholog of the human irritant sensor, acts in gustatory chemosensors to inhibit reactive electrophile ingestion. We show that fly and mosquito TRPA1 orthologs are molecular sensors of electrophiles, using a mechanism conserved with vertebrate TRPA1s. Phylogenetic analyses indicate invertebrate and vertebrate TRPA1s share a common ancestor that possessed critical characteristics required for electrophile detection. These findings support emergence of TRPA1-based electrophile detection in a common bilaterian ancestor, with widespread conservation throughout vertebrate and invertebrate evolution. Such conservation contrasts with the evolutionary divergence of canonical olfactory and gustatory receptors and may relate to electrophile toxicity. We propose human pain perception relies on an ancient chemical sensor conserved across ~500 million years of animal evolution. PMID:20237474

  9. Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

  11. Revealing Companions to Nearby Stars with Astrometric Acceleration

    DTIC Science & Technology

    2012-07-01

    of 57 stars, we compare the statistics of resolved astrometric companions with those of a simulated binary population. The fraction of resolved...frequency of supernovae, blue stragglers, X-ray binaries, etc. The statistical properties of binaries strongly depend on stellar mass. Only for nearby solar ...a large fraction of these stars by the Geneva-Copenhagen Sur- vey of the Solar neighborhood, GCS (Nordströem et al. 2004), revealing short-period

  12. Low-altitude magnetic field measurements by MESSENGER reveal Mercury’s ancient crustal field

    NASA Astrophysics Data System (ADS)

    Johnson, Catherine L.; Phillips, Roger J.; Purucker, Michael E.; Anderson, Brian J.; Byrne, Paul K.; Denevi, Brett W.; Feinberg, Joshua M.; Hauck, Steven A.; Head, James W.; Korth, Haje; James, Peter B.; Mazarico, Erwan; Neumann, Gregory A.; Philpott, Lydia C.; Siegler, Matthew A.; Tsyganenko, Nikolai A.; Solomon, Sean C.

    2015-05-01

    Magnetized rocks can record the history of the magnetic field of a planet, a key constraint for understanding its evolution. From orbital vector magnetic field measurements of Mercury taken by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft at altitudes below 150 kilometers, we have detected remanent magnetization in Mercury’s crust. We infer a lower bound on the average age of magnetization of 3.7 to 3.9 billion years. Our findings indicate that a global magnetic field driven by dynamo processes in the fluid outer core operated early in Mercury’s history. Ancient field strengths that range from those similar to Mercury’s present dipole field to Earth-like values are consistent with the magnetic field observations and with the low iron content of Mercury’s crust inferred from MESSENGER elemental composition data.

  13. Transmissible [corrected] dog cancer genome reveals the origin and history of an ancient cell lineage.

    PubMed

    Murchison, Elizabeth P; Wedge, David C; Alexandrov, Ludmil B; Fu, Beiyuan; Martincorena, Inigo; Ning, Zemin; Tubio, Jose M C; Werner, Emma I; Allen, Jan; De Nardi, Andrigo Barboza; Donelan, Edward M; Marino, Gabriele; Fassati, Ariberto; Campbell, Peter J; Yang, Fengtang; Burt, Austin; Weiss, Robin A; Stratton, Michael R

    2014-01-24

    Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions. More than 10,000 genes carry nonsynonymous variants, and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived about 11,000 years ago. The cancer spawned by this individual dispersed across continents about 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  15. Vortex magnetic structure in framboidal magnetite reveals existence of water droplets in an ancient asteroid

    NASA Astrophysics Data System (ADS)

    Kimura, Yuki; Sato, Takeshi; Nakamura, Norihiro; Nozawa, Jun; Nakamura, Tomoki; Tsukamoto, Katsuo; Yamamoto, Kazuo

    2013-10-01

    The majority of water has vanished from modern meteorites, yet there remain signatures of water on ancient asteroids. How and when water disappeared from the asteroids is important, because the final fluid-concentrated chemical species played critical roles in the early evolution of organics and in the final minerals in meteorites. Here we show evidence of vestigial traces of water based on a nanometre-scale palaeomagnetic method, applying electron holography to the framboids in the Tagish Lake meteorite. The framboids are colloidal crystals composed of three-dimensionally ordered magnetite nanoparticles and therefore are only able to form against the repulsive force induced by the surface charge of the magnetite as a water droplet parches in microgravity. We demonstrate that the magnetites have a flux closure vortex structure, a unique magnetic configuration in nature that permits the formation of colloidal crystals just before exhaustion of water from a local system within a hydrous asteroid.

  16. Mixture model of pottery decorations from Lake Chad Basin archaeological sites reveals ancient segregation patterns

    PubMed Central

    O'Brien, John D.; Lin, Kathryn; MacEachern, Scott

    2016-01-01

    We present a new statistical approach to analysing an extremely common archaeological data type—potsherds—that infers the structure of cultural relationships across a set of excavation units (EUs). This method, applied to data from a set of complex, culturally heterogeneous sites around the Mandara mountains in the Lake Chad Basin, helps elucidate cultural succession through the Neolithic and Iron Age. We show how the approach can be integrated with radiocarbon dates to provide detailed portraits of cultural dynamics and deposition patterns within single EUs. In this context, the analysis supports ancient cultural segregation analogous to historical ethnolinguistic patterning in the region. We conclude with a discussion of the many possible model extensions using other archaeological data types. PMID:27009217

  17. Ancient igneous intrusions and early expansion of the Moon revealed by GRAIL gravity gradiometry.

    PubMed

    Andrews-Hanna, Jeffrey C; Asmar, Sami W; Head, James W; Kiefer, Walter S; Konopliv, Alexander S; Lemoine, Frank G; Matsuyama, Isamu; Mazarico, Erwan; McGovern, Patrick J; Melosh, H Jay; Neumann, Gregory A; Nimmo, Francis; Phillips, Roger J; Smith, David E; Solomon, Sean C; Taylor, G Jeffrey; Wieczorek, Mark A; Williams, James G; Zuber, Maria T

    2013-02-08

    The earliest history of the Moon is poorly preserved in the surface geologic record due to the high flux of impactors, but aspects of that history may be preserved in subsurface structures. Application of gravity gradiometry to observations by the Gravity Recovery and Interior Laboratory (GRAIL) mission results in the identification of a population of linear gravity anomalies with lengths of hundreds of kilometers. Inversion of the gravity anomalies indicates elongated positive-density anomalies that are interpreted to be ancient vertical tabular intrusions or dikes formed by magmatism in combination with extension of the lithosphere. Crosscutting relationships support a pre-Nectarian to Nectarian age, preceding the end of the heavy bombardment of the Moon. The distribution, orientation, and dimensions of the intrusions indicate a globally isotropic extensional stress state arising from an increase in the Moon's radius by 0.6 to 4.9 kilometers early in lunar history, consistent with predictions of thermal models.

  18. Planetary science. Low-altitude magnetic field measurements by MESSENGER reveal Mercury's ancient crustal field.

    PubMed

    Johnson, Catherine L; Phillips, Roger J; Purucker, Michael E; Anderson, Brian J; Byrne, Paul K; Denevi, Brett W; Feinberg, Joshua M; Hauck, Steven A; Head, James W; Korth, Haje; James, Peter B; Mazarico, Erwan; Neumann, Gregory A; Philpott, Lydia C; Siegler, Matthew A; Tsyganenko, Nikolai A; Solomon, Sean C

    2015-05-22

    Magnetized rocks can record the history of the magnetic field of a planet, a key constraint for understanding its evolution. From orbital vector magnetic field measurements of Mercury taken by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft at altitudes below 150 kilometers, we have detected remanent magnetization in Mercury's crust. We infer a lower bound on the average age of magnetization of 3.7 to 3.9 billion years. Our findings indicate that a global magnetic field driven by dynamo processes in the fluid outer core operated early in Mercury's history. Ancient field strengths that range from those similar to Mercury's present dipole field to Earth-like values are consistent with the magnetic field observations and with the low iron content of Mercury's crust inferred from MESSENGER elemental composition data.

  19. Ancient DNA reveals Holocene loss of genetic diversity in a South American rodent.

    PubMed

    Chan, Yvonne L; Lacey, Eileen A; Pearson, Oliver P; Hadly, Elizabeth A

    2005-12-22

    Understanding how animal populations have evolved in response to palaeoenvironmental conditions is essential for predicting the impact of future environmental change on current biodiversity. Analyses of ancient DNA provide a unique opportunity to track population responses to prehistoric environments. We explored the effects of palaeoenvironmental change on the colonial tuco-tuco (Ctenomys sociabilis), a highly endemic species of Patagonian rodent that is currently listed as threatened by the IUCN. By combining surveys of modern genetic variation from throughout this species' current geographic range with analyses of DNA samples from fossil material dating back to 10,000 ybp, we demonstrate a striking decline in genetic diversity that is concordant with environmental events in the study region. Our results highlight the importance of non-anthropogenic factors in loss of diversity, including reductions in smaller mammals such as rodents.

  20. Mixture model of pottery decorations from Lake Chad Basin archaeological sites reveals ancient segregation patterns.

    PubMed

    O'Brien, John D; Lin, Kathryn; MacEachern, Scott

    2016-03-30

    We present a new statistical approach to analysing an extremely common archaeological data type--potsherds--that infers the structure of cultural relationships across a set of excavation units (EUs). This method, applied to data from a set of complex, culturally heterogeneous sites around the Mandara mountains in the Lake Chad Basin, helps elucidate cultural succession through the Neolithic and Iron Age. We show how the approach can be integrated with radiocarbon dates to provide detailed portraits of cultural dynamics and deposition patterns within single EUs. In this context, the analysis supports ancient cultural segregation analogous to historical ethnolinguistic patterning in the region. We conclude with a discussion of the many possible model extensions using other archaeological data types.

  1. Chemical profiling of ancient hearths reveals recurrent salmon use in Ice Age Beringia

    PubMed Central

    Choy, Kyungcheol; Potter, Ben A.; McKinney, Holly J.; Reuther, Joshua D.; Wang, Shiway W.; Wooller, Matthew J.

    2016-01-01

    Current approaches to reconstruct subsistence and dietary trends in ancient hunter-gatherer societies include stable isotope analyses, but these have focused on human remains, cooking pottery, and food residues, which are relatively rare in the archaeological record. In contrast, short-term hearths are more ubiquitous worldwide, and these features can provide valuable evidence for ancient subsistence practices, particularly when faunal remains are not preserved. To test the suitability of hearths for this purpose, we conducted multiple chemical analyses: stable carbon and nitrogen isotope analyses of total organic matter (expressed as δ13C and δ15N values) and compound-specific carbon isotope analyses of individual fatty acids (δ13C16:0 and δ13C18:0) from 17 well-preserved hearths present in three occupations dating between ∼13,200–11,500 calibrated years B.P. at the Upward Sun River (USR) site in central Alaska. We combined δ15N and δ13CFA data in a Bayesian mixing model (stable isotope analysis in R) with concentration dependency to each hearth. Our model values were tested against faunal indices, indicating a strong positive relationship between marine proportional contributions to each hearth and salmon abundance. Results of the models show substantial anadromous salmon use in multiple USR components, indicating recurrent use of the site for salmon processing during the terminal Pleistocene. Our results demonstrate that salmonid and freshwater resources were more important for late Pleistocene hunter-gatherers than previously thought and highlight the potential of chemical profiling of hearth organic residues for providing greater geographic and temporal insights into resource use by prepottery societies. PMID:27573838

  2. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

    PubMed

    Miller, Webb; Schuster, Stephan C; Welch, Andreanna J; Ratan, Aakrosh; Bedoya-Reina, Oscar C; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C; Drautz, Daniela I; Wittekindt, Nicola E; Tomsho, Lynn P; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K; Rode, Karyn; Obbard, Martyn; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Olafur; Aars, Jon; Mailund, Thomas; Wiig, Oystein; Talbot, Sandra L; Lindqvist, Charlotte

    2012-09-04

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  3. Chemical profiling of ancient hearths reveals recurrent salmon use in Ice Age Beringia.

    PubMed

    Choy, Kyungcheol; Potter, Ben A; McKinney, Holly J; Reuther, Joshua D; Wang, Shiway W; Wooller, Matthew J

    2016-08-30

    Current approaches to reconstruct subsistence and dietary trends in ancient hunter-gatherer societies include stable isotope analyses, but these have focused on human remains, cooking pottery, and food residues, which are relatively rare in the archaeological record. In contrast, short-term hearths are more ubiquitous worldwide, and these features can provide valuable evidence for ancient subsistence practices, particularly when faunal remains are not preserved. To test the suitability of hearths for this purpose, we conducted multiple chemical analyses: stable carbon and nitrogen isotope analyses of total organic matter (expressed as δ(13)C and δ(15)N values) and compound-specific carbon isotope analyses of individual fatty acids (δ(13)C16:0 and δ(13)C18:0) from 17 well-preserved hearths present in three occupations dating between ∼13,200-11,500 calibrated years B.P. at the Upward Sun River (USR) site in central Alaska. We combined δ(15)N and δ(13)CFA data in a Bayesian mixing model (stable isotope analysis in R) with concentration dependency to each hearth. Our model values were tested against faunal indices, indicating a strong positive relationship between marine proportional contributions to each hearth and salmon abundance. Results of the models show substantial anadromous salmon use in multiple USR components, indicating recurrent use of the site for salmon processing during the terminal Pleistocene. Our results demonstrate that salmonid and freshwater resources were more important for late Pleistocene hunter-gatherers than previously thought and highlight the potential of chemical profiling of hearth organic residues for providing greater geographic and temporal insights into resource use by prepottery societies.

  4. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

    PubMed Central

    2014-01-01

    Background Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Results Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes. Conclusions Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species. PMID:24987520

  5. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

    USGS Publications Warehouse

    Miller, Webb; Schuster, Stephan C.; Welch, Andreanna J.; Ratan, Aakrosh; Bedoya-Reina, Oscar C.; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C.; Drautz, Daniela I.; Wittekindt, Nicola E.; Tomsho, Lynn P.; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K.; Rode, Karyn; Obbard, Martyn E.; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Ólafur; Aars, Jon; Mailund, Thomas; Wiig, Øystein; Talbot, Sandra L.; Lindqvist, Charlotte

    2012-01-01

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

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

    PubMed Central

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

    2013-01-01

    Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages. PMID:23180578

  7. Ancient DNA Analyses Reveal Contrasting Phylogeographic Patterns amongst Kiwi (Apteryx spp.) and a Recently Extinct Lineage of Spotted Kiwi

    PubMed Central

    Shepherd, Lara D.; Worthy, Trevor H.; Tennyson, Alan J. D.; Scofield, R. Paul; Ramstad, Kristina M.; Lambert, David M.

    2012-01-01

    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. PMID:22876319

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

    PubMed

    Shepherd, Lara D; Worthy, Trevor H; Tennyson, Alan J D; Scofield, R Paul; Ramstad, Kristina M; Lambert, David M

    2012-01-01

    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.

  9. The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

    PubMed Central

    Gui, Songtao; Wu, Zhihua; Zhang, Hongyuan; Zheng, Yinzhen; Zhu, Zhixuan; Liang, Dequan; Ding, Yi

    2016-01-01

    Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots. PMID:27444405

  10. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox

    PubMed Central

    Dalén, Love; Nyström, Veronica; Valdiosera, Cristina; Germonpré, Mietje; Sablin, Mikhail; Turner, Elaine; Angerbjörn, Anders; Arsuaga, Juan Luis; Götherström, Anders

    2007-01-01

    How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures. PMID:17420452

  11. Ancient DNA from Coral-Hosted Symbiodinium Reveal a Static Mutualism over the Last 172 Years

    PubMed Central

    Baker, David M.; Weigt, Lee; Fogel, Marilyn; Knowlton, Nancy

    2013-01-01

    Ancient DNA (aDNA) provides powerful evidence for detecting the genetic basis for adaptation to environmental change in many taxa. Among the greatest of changes in our biosphere within the last century is rapid anthropogenic ocean warming. This phenomenon threatens corals with extinction, evidenced by the increasing observation of widespread mortality following mass bleaching events. There is some evidence and conjecture that coral-dinoflagellate symbioses change partnerships in response to changing external conditions over ecological and evolutionary timescales. Until now, we have been unable to ascertain the genetic identity of Symbiodinium hosted by corals prior to the rapid global change of the last century. Here, we show that Symbiodinium cells recovered from dry, century old specimens of 6 host species of octocorals contain sufficient DNA for amplification of the ITS2 subregion of the nuclear ribosomal DNA, commonly used for genotyping within this genus. Through comparisons with modern specimens sampled from similar locales we show that symbiotic associations among several species have been static over the last century, thereby suggesting that adaptive shifts to novel symbiont types is not common among these gorgonians, and perhaps, symbiotic corals in general. PMID:23405111

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

    PubMed

    Malmström, Helena; Gilbert, M Thomas P; Thomas, Mark G; Brandström, Mikael; Storå, Jan; Molnar, Petra; Andersen, Pernille K; Bendixen, Christian; Holmlund, Gunilla; Götherström, Anders; Willerslev, Eske

    2009-11-03

    The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence 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 Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.

  13. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox.

    PubMed

    Dalén, Love; Nyström, Veronica; Valdiosera, Cristina; Germonpré, Mietje; Sablin, Mikhail; Turner, Elaine; Angerbjörn, Anders; Arsuaga, Juan Luis; Götherström, Anders

    2007-04-17

    How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.

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

    PubMed

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

    2017-01-11

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

  15. Ancient Genetic Signatures of Orang Asli Revealed by Killer Immunoglobulin-Like Receptor Gene Polymorphisms

    PubMed Central

    NurWaliyuddin, Hanis Z. A.; Norazmi, Mohd N.; Edinur, Hisham A.; Chambers, Geoffrey K.; Panneerchelvam, Sundararajulu; Zafarina, Zainuddin

    2015-01-01

    The aboriginal populations of Peninsular Malaysia, also known as Orang Asli (OA), comprise three major groups; Semang, Senoi and Proto-Malays. Here, we analyzed for the first time KIR gene polymorphisms for 167 OA individuals, including those from four smallest OA subgroups (Che Wong, Orang Kanaq, Lanoh and Kensiu) using polymerase chain reaction-sequence specific primer (PCR-SSP) analyses. The observed distribution of KIR profiles of OA is heterogenous; Haplotype B is the most frequent in the Semang subgroups (especially Batek) while Haplotype A is the most common type in the Senoi. The Semang subgroups were clustered together with the Africans, Indians, Papuans and Australian Aborigines in a principal component analysis (PCA) plot and shared many common genotypes (AB6, BB71, BB73 and BB159) observed in these other populations. Given that these populations also display high frequencies of Haplotype B, it is interesting to speculate that Haplotype B may be generally more frequent in ancient populations. In contrast, the two Senoi subgroups, Che Wong and Semai are displaced toward Southeast Asian and African populations in the PCA scatter plot, respectively. Orang Kanaq, the smallest and the most endangered of all OA subgroups, has lost some degree of genetic variation, as shown by their relatively high frequency of the AB2 genotype (0.73) and a total absence of KIR2DL2 and KIR2DS2 genes. Orang Kanaq tradition that strictly prohibits intermarriage with outsiders seems to have posed a serious threat to their survival. This present survey is a demonstration of the value of KIR polymorphisms in elucidating genetic relationships among human populations. PMID:26565719

  16. Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations.

    PubMed

    Goldberg, Amy; Günther, Torsten; Rosenberg, Noah A; Jakobsson, Mattias

    2017-03-07

    Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic Steppe during the late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

  17. Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics.

    PubMed

    Spyrou, Maria A; Tukhbatova, Rezeda I; Feldman, Michal; Drath, Joanna; Kacki, Sacha; Beltrán de Heredia, Julia; Arnold, Susanne; Sitdikov, Airat G; Castex, Dominique; Wahl, Joachim; Gazimzyanov, Ilgizar R; Nurgaliev, Danis K; Herbig, Alexander; Bos, Kirsten I; Krause, Johannes

    2016-06-08

    Ancient DNA analysis has revealed an involvement of the bacterial pathogen Yersinia pestis in several historical pandemics, including the second plague pandemic (Europe, mid-14(th) century Black Death until the mid-18(th) century AD). Here we present reconstructed Y. pestis genomes from plague victims of the Black Death and two subsequent historical outbreaks spanning Europe and its vicinity, namely Barcelona, Spain (1300-1420 cal AD), Bolgar City, Russia (1362-1400 AD), and Ellwangen, Germany (1485-1627 cal AD). Our results provide support for (1) a single entry of Y. pestis in Europe during the Black Death, (2) a wave of plague that traveled toward Asia to later become the source population for contemporary worldwide epidemics, and (3) the presence of an historical European plague focus involved in post-Black Death outbreaks that is now likely extinct.

  18. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

    PubMed

    Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

    2015-05-01

    The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies.

  19. Ancient DNA

    PubMed Central

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564

  20. Pth4, an ancient parathyroid hormone lost in eutherian mammals, reveals a new brain-to-bone signaling pathway.

    PubMed

    Suarez-Bregua, Paula; Torres-Nuñez, Eva; Saxena, Ankur; Guerreiro, Pedro; Braasch, Ingo; Prober, David A; Moran, Paloma; Cerda-Reverter, Jose Miguel; Du, Shao Jun; Adrio, Fatima; Power, Deborah M; Canario, Adelino V M; Postlethwait, John H; Bronner, Marianne E; Cañestro, Cristian; Rotllant, Josep

    2017-02-01

    Regulation of bone development, growth, and remodeling traditionally has been thought to depend on endocrine and autocrine/paracrine modulators. Recently, however, brain-derived signals have emerged as key regulators of bone metabolism, although their mechanisms of action have been poorly understood. We reveal the existence of an ancient parathyroid hormone (Pth)4 in zebrafish that was secondarily lost in the eutherian mammals' lineage, including humans, and that is specifically expressed in neurons of the hypothalamus and appears to be a central neural regulator of bone development and mineral homeostasis. Transgenic fish lines enabled mapping of axonal projections leading from the hypothalamus to the brainstem and spinal cord. Targeted laser ablation demonstrated an essential role for of pth4-expressing neurons in larval bone mineralization. Moreover, we show that Runx2 is a direct regulator of pth4 expression and that Pth4 can activate cAMP signaling mediated by Pth receptors. Finally, gain-of-function experiments show that Pth4 can alter calcium/phosphorus levels and affect expression of genes involved in phosphate homeostasis. Based on our discovery and characterization of Pth4, we propose a model for evolution of bone homeostasis in the context of the vertebrate transition from an aquatic to a terrestrial lifestyle.-Suarez-Bregua, P., Torres-Nuñez, E., Saxena, A., Guerreiro, P., Braasch, I., Prober, D. A., Moran, P., Cerda-Reverter, J. M., Du, S. J., Adrio, F., Power, D. M., Canario, A. V. M., Postlethwait, J. H., Bronner, M E., Cañestro, C., Rotllant, J. Pth4, an ancient parathyroid hormone lost in eutherian mammals, reveals a new brain-to-bone signaling pathway.

  1. Paleotopographic Reconstruction of the Tharsis Magmatic Complex Reveals Potential Ancient Drainage Basin/Aquifer System

    NASA Technical Reports Server (NTRS)

    Dohm, J. M.; Ferris, J.; Anderson, R. C.; Baker, V.; Hare, T.; Barlow, N. G.; Strom, R. G.; Tanaka, K. L.; Scott, D. H.

    2001-01-01

    Paleotopographic reconstructions reveal the potential existence of an enormous Noachian drainage basin in the eastern part of the Tharsis region of significant geologic and paleohydrologic implications. Additional information is contained in the original extended abstract.

  2. Redox-controlled U Cycle in Ancient Oceans Revealed by Black Shale Records

    NASA Astrophysics Data System (ADS)

    Partin, C. A.; Bekker, A.; Scott, C. T.; Gill, B.; Lyons, T. W.

    2009-05-01

    Redox-sensitive elements, such as U and Mo, are valuable proxies for oxygen availability in the ancient atmosphere and ocean. Scott et al. (2008) inferred three stages from the secular trend of Mo concentrations in organic matter-rich shales: 1) shales older than 2.2 Ga have low but above crustal average Mo concentrations; 2) shales ca. 2.2 Ga show a dramatic increase in Mo concentrations after the rise of atmospheric oxygen; 3) shales straddling the Precambrian-Cambrian boundary show a second rise in Mo concentrations. Both Mo and U are released during oxidative continental weathering but removed via different pathways from the ocean; Mo is predominantly enriched in shales deposited under euxinic conditions, whereas U only requires anoxic conditions to be scavenged from the water column. These elements therefore can provide complementary, but independent, information about the redox state of the ocean and atmosphere. Our compilation of U concentrations from >2.2 Ga organic matter-rich shales shows minor enrichments relative to average crust, consistent with the Mo trend. This observation is intriguing because neither U nor Mo would be carried to the ocean under fully anoxic conditions. However, under an Archean oxygen-free atmosphere, the fraction of oxygen produced by cyanobacteria would be consumed by oxidative crustal weathering. Thus, our data are relevant to the continuing debate over the timing of the first appearance of oxygenic photosynthesis and the transient presence of photosynthetically-produced oxygen in the Archean. Similar to trends in the Mo record, U concentrations increased in response to the rise of atmospheric oxygen, and once more close to the Precambrian-Cambrian boundary, reaching the highest enrichments seen in the geologic record. While the first increase in U concentrations likely reflects atmospheric oxygenation, the second rise possibly corresponds with deep-ocean ventilation and restriction of the areal extent of anoxic and euxinic

  3. Third-harmonic generation microscopy reveals dental anatomy in ancient fossils.

    PubMed

    Chen, Yu-Cheng; Lee, Szu-Yu; Wu, Yana; Brink, Kirstin; Shieh, Dar-Bin; Huang, Timothy D; Reisz, Robert R; Sun, Chi-Kuang

    2015-04-01

    Fossil teeth are primary tools in the study of vertebrate evolution, but standard imaging modalities have not been capable of providing high-quality images in dentin, the main component of teeth, owing to small refractive index differences in the fossilized dentin. Our first attempt to use third-harmonic generation (THG) microscopy in fossil teeth has yielded significant submicrometer level anatomy, with an unexpectedly strong signal contrasting fossilized tubules from the surrounding dentin. Comparison between fossilized and extant teeth of crocodilians reveals a consistent evolutionary signature through time, indicating the great significance of THG microscopy in the evolutionary studies of dental anatomy in fossil teeth.

  4. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity.

    PubMed

    Buckley, Thomas R; James, Sam; Allwood, Julia; Bartlam, Scott; Howitt, Robyn; Prada, Diana

    2011-01-01

    We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota.

  5. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province.

    PubMed

    Bryson, Robert W; Savary, Warren E; Zellmer, Amanda J; Bury, R Bruce; McCormack, John E

    2016-08-01

    The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species distribution models (SDMs) to determine climatically suitable areas for Uroctonus both now and during the Last Glacial Maximum. Based on our analyses, Uroctonus is composed of two major genetic groups that likely diverged over 2 million years ago. Each of these groups itself contains numerous genetic groups that reveal a pattern of vicariance and microendemism across the CFP. Migration rates among these populations are low. SDMs suggest forest scorpion habitat has remained relatively stable over the last 21 000 years, consistent with the genetic data. Our results suggest tectonic plate rafting, mountain uplift, river drainage formation and climate-induced habitat fragmentation have all likely played a role in the diversification of Uroctonus. The intricate pattern of genetic fragmentation revealed across a temporal continuum highlights the potential of low-dispersing species to shed light on small-scale patterns of biodiversity and the underlying processes that have generated this diversity in biodiversity hotspots.

  6. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity.

    PubMed

    Brandt, Guido; Haak, Wolfgang; Adler, Christina J; Roth, Christina; Szécsényi-Nagy, Anna; Karimnia, Sarah; Möller-Rieker, Sabine; Meller, Harald; Ganslmeier, Robert; Friederich, Susanne; Dresely, Veit; Nicklisch, Nicole; Pickrell, Joseph K; Sirocko, Frank; Reich, David; Cooper, Alan; Alt, Kurt W

    2013-10-11

    The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.

  7. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution.

    PubMed

    Mitchell, Kieren J; Llamas, Bastien; Soubrier, Julien; Rawlence, Nicolas J; Worthy, Trevor H; Wood, Jamie; Lee, Michael S Y; Cooper, Alan

    2014-05-23

    The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.

  8. Ancient DNA reveals key stages in the formation of Central European mitochondrial genetic diversity

    PubMed Central

    Brandt, Guido; Haak, Wolfgang; Adler, Christina J.; Roth, Christina; Szécsényi-Nagy, Anna; Karimnia, Sarah; Möller-Rieker, Sabine; Meller, Harald; Ganslmeier, Robert; Friederich, Susanne; Dresely, Veit; Nicklisch, Nicole; Pickrell, Joseph K.; Sirocko, Frank; Reich, David; Cooper, Alan; Alt, Kurt W.

    2014-01-01

    The processes which shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42kyrs ago and the immigration of Neolithic farmers into Europe ~8kyrs ago appear to have played important roles, but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5,500–1,550 cal BC). We use this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity. PMID:24115443

  9. Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication

    PubMed Central

    Speller, Camilla F.; Kemp, Brian M.; Wyatt, Scott D.; Monroe, Cara; Lipe, William D.; Arndt, Ursula M.; Yang, Dongya Y.

    2010-01-01

    Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC–AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices. PMID:20133614

  10. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

    PubMed Central

    Kippes, Nestor; Debernardi, Juan M.; Vasquez-Gross, Hans A.; Akpinar, Bala A.; Budak, Hikment; Kato, Kenji; Chao, Shiaoman; Akhunov, Eduard; Dubcovsky, Jorge

    2015-01-01

    Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in four vernalization genes regulating this requirement has favored wheat adaptation to different environments. The first three genes (VRN1–VRN3) have been cloned and characterized before. Here we show that the fourth gene, VRN-D4, originated by the insertion of a ∼290-kb region from chromosome arm 5AL into the proximal region of chromosome arm 5DS. The inserted 5AL region includes a copy of VRN-A1 that carries distinctive mutations in its coding and regulatory regions. Three lines of evidence confirmed that this gene is VRN-D4: it cosegregated with VRN-D4 in a high-density mapping population; it was expressed earlier than other VRN1 genes in the absence of vernalization; and induced mutations in this gene resulted in delayed flowering. VRN-D4 was found in most accessions of the ancient subspecies Triticum aestivum ssp. sphaerococcum from South Asia. This subspecies showed a significant reduction of genetic diversity and increased genetic differentiation in the centromeric region of chromosome 5D, suggesting that VRN-D4 likely contributed to local adaptation and was favored by positive selection. Three adjacent SNPs in a regulatory region of the VRN-D4 first intron disrupt the binding of GLYCINE-RICH RNA-BINDING PROTEIN 2 (TaGRP2), a known repressor of VRN1 expression. The same SNPs were identified in VRN-A1 alleles previously associated with reduced vernalization requirement. These alleles can be used to modulate vernalization requirements and to develop wheat varieties better adapted to different or changing environments. PMID:26324889

  11. Making teeth to order: conserved genes reveal an ancient molecular pattern in paddlefish (Actinopterygii)

    PubMed Central

    Smith, Moya M.; Johanson, Zerina; Butts, Thomas; Ericsson, Rolf; Modrell, Melinda; Tulenko, Frank J.; Davis, Marcus C.; Fraser, Gareth J.

    2015-01-01

    Ray-finned fishes (Actinopterygii) are the dominant vertebrate group today (+30 000 species, predominantly teleosts), with great morphological diversity, including their dentitions. How dental morphological variation evolved is best addressed by considering a range of taxa across actinopterygian phylogeny; here we examine the dentition of Polyodon spathula (American paddlefish), assigned to the basal group Acipenseriformes. Although teeth are present and functional in young individuals of Polyodon, they are completely absent in adults. Our current understanding of developmental genes operating in the dentition is primarily restricted to teleosts; we show that shh and bmp4, as highly conserved epithelial and mesenchymal genes for gnathostome tooth development, are similarly expressed at Polyodon tooth loci, thus extending this conserved developmental pattern within the Actinopterygii. These genes map spatio-temporal tooth initiation in Polyodon larvae and provide new data in both oral and pharyngeal tooth sites. Variation in cellular intensity of shh maps timing of tooth morphogenesis, revealing a second odontogenic wave as alternate sites within tooth rows, a dental pattern also present in more derived actinopterygians. Developmental timing for each tooth field in Polyodon follows a gradient, from rostral to caudal and ventral to dorsal, repeated during subsequent loss of teeth. The transitory Polyodon dentition is modified by cessation of tooth addition and loss. As such, Polyodon represents a basal actinopterygian model for the evolution of developmental novelty: initial conservation, followed by tooth loss, accommodating the adult trophic modification to filter-feeding. PMID:25788604

  12. Secrets in the Ancient Goatskins: X-Rays Reveal Archimedes' Oldest Writings

    SciTech Connect

    Bergmann, Uwe

    2008-04-02

    Archimedes of Syracruse (287 - 212 B.C.) is considered one of the most brilliant thinkers of all time. The tenth-century parchment known as the Archimedes Palimpsest is by far the oldest surviving manuscript containing works of Archimedes. it is also the unique source for three of the Greek's treatises: the Stomachion, the Method of Mechanical Theorems, and the Greek version of On Floating Bodies. The privately owned palimpsest is the subject of a integrated campaign of conservation, imaging, and scholarship being undertaken at the Walters Art Museum in Baltimore. Much of the text has been imaged by various optical techniques, but significant gaps in our knowledge of the writing of Archimedes remained. A breakthrough in uncovering the missing Archimedes writings was achieved at the Stanford Synchrotron Radiation Laboratory. Using x-ray fluorescence imaging, writings from faint traces of the partly erased iron gall ink were brought to light. The x-ray image revealed Archimedes writings from some of his most important works covered by twelfth-century biblical texts and twentieth-century gold forgeries. This talk will focus on the fascinating journal of a 1,000 year old parchment from its origin in the Mediterranean city of Constantinople to an x-ray beamline at SLAC.

  13. Secrets in the Ancient Goatskins: X-Rays Reveal archimedes' Oldest Writings

    SciTech Connect

    Bergmann, Uwe

    2008-04-02

    Archimedes of Syracruse (287 - 212 B.C.) is considered one of the most brilliant thinkers of all time. The tenth-century parchment known as the Archimedes Palimpsest is by far the oldest surviving manuscript containing works of Archimedes. it is also the unique source for three of the Greek's treatises: the Stomachion, the Method of Mechanical Theorems, and the Greek version of On Floating Bodies. The privately owned palimpsest is the subject of a integrated campaign of conservation, imaging, and scholarship being undertaken at the Walters Art Museum in Baltimore. Much of the text has been imaged by various optical techniques, but significant gaps in our knowledge of the writing of Archimedes remained. A breakthrough in uncovering the missing Archimedes writings was achieved at the Stanford Synchrotron Radiation Laboratory. Using x-ray fluorescence imaging, writings from faint traces of the partly erased iron gall ink were brought to light. The x-ray image revealed Archimedes writings from some of his most important works covered by twelfth-century biblical texts and twentieth-century gold forgeries. This talk will focus on the fascinating journal of a 1,000 year old parchment from its origin in the Mediterranean city of Constantinople to an x-ray beamline at SLAC.

  14. Bacterial discrimination by Dictyostelid amoebae reveals the complexity of ancient interspecies interactions

    PubMed Central

    Nasser, Waleed; Santhanam, Balaji; Miranda, Edward Roshan; Parikh, Anup; Juneja, Kavina; Rot, Gregor; Dinh, Chris; Chen, Rui; Zupan, Blaz; Shaulsky, Gad; Kuspa, Adam

    2014-01-01

    Background Amoebae and bacteria interact within predator/prey and host/pathogen relationships, but the general response of amoeba to bacteria is not well understood. The amoeba Dictyostelium discoideum feeds on, and is colonized by diverse bacterial species including Gram-positive [Gram(+)] and Gram-negative [Gram(−)] bacteria, two major groups of bacteria that differ in structure and macromolecular composition. Results Transcriptional profiling of D. discoideum revealed sets of genes whose expression is enriched in amoebae interacting with different species of bacteria, including sets that appear specific to amoebae interacting with Gram(+), or with Gram(−) bacteria. In a genetic screen utilizing the growth of mutant amoebae on a variety of bacteria as a phenotypic readout, we identified amoebal genes that are only required for growth on Gram(+) bacteria, including one that encodes the cell surface protein gp130, as well as several genes that are only required for growth on Gram(−) bacteria including one that encodes a putative lysozyme, AlyL. These genes are required for parts of the transcriptional response of wild-type amoebae, and this allowed their classification into potential response pathways. Conclusions We have defined genes that are critical for amoebal survival during feeding on Gram(+), or Gram(−), bacteria which we propose form part of a regulatory network that allows D. discoideum to elicit specific cellular responses to different species of bacteria in order to optimize survival. PMID:23664307

  15. Transcriptional Control of an Essential Ribozyme in Drosophila Reveals an Ancient Evolutionary Divide in Animals

    PubMed Central

    Manivannan, Sathiya N.; Lai, Lien B.; Gopalan, Venkat; Simcox, Amanda

    2015-01-01

    Ribonuclease P (RNase P) is an essential enzyme required for 5′-maturation of tRNA. While an RNA-free, protein-based form of RNase P exists in eukaryotes, the ribonucleoprotein (RNP) form is found in all domains of life. The catalytic component of the RNP is an RNA known as RNase P RNA (RPR). Eukaryotic RPR genes are typically transcribed by RNA polymerase III (pol III). Here we showed that the RPR gene in Drosophila, which is annotated in the intron of a pol II-transcribed protein-coding gene, lacks signals for transcription by pol III. Using reporter gene constructs that include the RPR-coding intron from Drosophila, we found that the intron contains all the sequences necessary for production of mature RPR but is dependent on the promoter of the recipient gene for expression. We also demonstrated that the intron-coded RPR copurifies with RNase P and is required for its activity. Analysis of RPR genes in various animal genomes revealed a striking divide in the animal kingdom that separates insects and crustaceans into a single group in which RPR genes lack signals for independent transcription and are embedded in different protein-coding genes. Our findings provide evidence for a genetic event that occurred approximately 500 million years ago in the arthropod lineage, which switched the control of the transcription of RPR from pol III to pol II. PMID:25569672

  16. Lamprey type II collagen and Sox9 reveal an ancient origin of the vertebrate collagenous skeleton.

    PubMed

    Zhang, Guangjun; Miyamoto, Michael M; Cohn, Martin J

    2006-02-28

    Type II collagen is the major cartilage matrix protein in the jawed vertebrate skeleton. Lampreys and hagfishes, by contrast, are thought to have noncollagenous cartilage. This difference in skeletal structure has led to the hypothesis that the vertebrate common ancestor had a noncollagenous skeleton, with type II collagen becoming the predominant cartilage matrix protein after the divergence of jawless fish from the jawed vertebrates approximately 500 million years ago. Here we report that lampreys have two type II collagen (Col2alpha1) genes that are expressed during development of the cartilaginous skeleton. We also demonstrate that the adult lamprey skeleton is rich in Col2alpha1 protein. Furthermore, we have isolated a lamprey orthologue of Sox9, a direct transcriptional regulator of Col2alpha1 in jawed vertebrates, and show that it is coexpressed with both Col2alpha1 genes during skeletal development. These results reveal that the genetic pathway for chondrogenesis in lampreys and gnathostomes is conserved through the activation of cartilage matrix molecules and suggest that a collagenous skeleton evolved surprisingly early in vertebrate evolution.

  17. Secrets in the Ancient Goatskins: X-Rays Reveal Archimedes' Oldest Writings

    ScienceCinema

    Bergmann, Uwe [SLAC Linear Accelerator Center, United States

    2016-07-12

    Archimedes of Syracruse (287 - 212 B.C.) is considered one of the most brilliant thinkers of all time. The tenth-century parchment known as the Archimedes Palimpsest is by far the oldest surviving manuscript containing works of Archimedes. it is also the unique source for three of the Greek's treatises: the Stomachion, the Method of Mechanical Theorems, and the Greek version of On Floating Bodies. The privately owned palimpsest is the subject of a integrated campaign of conservation, imaging, and scholarship being undertaken at the Walters Art Museum in Baltimore. Much of the text has been imaged by various optical techniques, but significant gaps in our knowledge of the writing of Archimedes remained. A breakthrough in uncovering the missing Archimedes writings was achieved at the Stanford Synchrotron Radiation Laboratory. Using x-ray fluorescence imaging, writings from faint traces of the partly erased iron gall ink were brought to light. The x-ray image revealed Archimedes writings from some of his most important works covered by twelfth-century biblical texts and twentieth-century gold forgeries. This talk will focus on the fascinating journal of a 1,000 year old parchment from its origin in the Mediterranean city of Constantinople to an x-ray beamline at SLAC.

  18. Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya

    PubMed Central

    Mbole-Kariuki, M N; Sonstegard, T; Orth, A; Thumbi, S M; Bronsvoort, B M de C; Kiara, H; Toye, P; Conradie, I; Jennings, A; Coetzer, K; Woolhouse, M E J; Hanotte, O; Tapio, M

    2014-01-01

    The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (⩾12.5%), moderate (1.56%ancient zebu × AT admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression. PMID:24736786

  19. Phylogeographic, ancient DNA, fossil and morphometric analyses reveal ancient and modern introductions of a large mammal: the complex case of red deer (Cervus elaphus) in Ireland

    NASA Astrophysics Data System (ADS)

    Carden, Ruth F.; McDevitt, Allan D.; Zachos, Frank E.; Woodman, Peter C.; O'Toole, Peter; Rose, Hugh; Monaghan, Nigel T.; Campana, Michael G.; Bradley, Daniel G.; Edwards, Ceiridwen J.

    2012-05-01

    The problem of how and when the island of Ireland attained its contemporary fauna has remained a key question in understanding Quaternary faunal assemblages. We assessed the complex history and origins of the red deer (Cervus elaphus) in Ireland using a multi-disciplinary approach. Mitochondrial sequences of contemporary and ancient red deer (dating from c 30,000 to 1700 cal. yr BP) were compared to decipher possible source populations of red deer in Ireland, in addition to craniometric analyses of skulls from candidate regions to distinguish between different colonization scenarios. Radiocarbon dating was undertaken on all bone fragments that were previously undated. Finally, a comprehensive review of the scientific literature, unpublished reports and other sources of data were also searched for red deer remains within Irish palaeontological and archaeological contexts. Despite being present in Ireland prior to the Last Glacial Maximum (LGM), there is a notable scarcity of red deer from the Younger Dryas stadial period until the Neolithic. The presence of red deer in Irish archaeological sites then occurs more frequently relative to other species. One population in the southwest of Ireland (Co. Kerry) shared haplotypes with the ancient Irish specimens and molecular dating and craniometric analysis suggests its persistence in Ireland since the Neolithic period. The synthesis of the results from this multi-disciplinary study all indicate that red deer were introduced by humans during the Irish Neolithic period and that one of these populations persists today. In conjunction with recent results from other species, Neolithic people from Ireland's nearest landmass, Britain, played a vital role in establishing its contemporary fauna and flora.

  20. Ancient astronomy revealed

    NASA Astrophysics Data System (ADS)

    Steele, John

    2009-03-01

    In the autumn of 1900 a team of sponge divers from the small Greek island of Symi, just north of Rhodes, made one of the most spectacular underwater discoveries of modern times. After being blown off course on their journey back to Symi from the southern Mediterranean sponge-fishing grounds, they sheltered near the island of Antikythera, located between the southern tip of the Greek mainland and the north-west corner of Crete. When the winds died down, the team's captain, Dimitrios Kontos, decided to send the divers down in the hope of adding some final sponges to their catch. Instead, Elias Stadiatis, the first diver into the water, spotted a shipwreck on the sea bed.

  1. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence 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, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  2. Ancient genomics.

    PubMed

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence 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, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  3. [Genetic diversity of ancient tea gardens and tableland tea gardens from Yunnan Province as revealed by AFLP marker].

    PubMed

    Ji, Peng-Zhang; Jiang, Hui-Bing; Huang, Xing-Qi; Zhang, Jun; Liang, Min-Zhi; Wang, Ping-Sheng

    2009-01-01

    This study was conducted to evaluate the genetic diversity within and among the plants of four ancient tea gardens and two tableland tea gardens form Yunnan Province, China by AFLP technique. The percentage of polymorphic loci (P) of the plants from six tea gardens was 92.31%. The genetic diversity within the six gardens demonstrated by Nei cents genetic diversity (He) was estimated to be 0.1366, while Shannon indices (Ho) were 0.2323. The percentage of polymorphic loci of the four ancient tea populations was 45.55% on average, with a range of 36.44% (Mengsong) to 59.11% (Mengla). But the percentages of polymorphic loci of the plants from two tableland gardens were 13.77% (Yunkang 10) and 24.2% (Menghai Daye), respectively. There was a great genetic difference between ancient tea gardens and tableland tea gardens. The genetic diversity among the plants of the ancient tea garden was higher than those of the sexual tableland tea garden and the clone tableland tea garden based on P valve. The four ancient tea gardens and two tableland gardens could be differentiated with AFLP markers. The results show that AFLP marker is an effective tool in the discrimination of tea germplasm, as well as sundried green tea.

  4. Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (hypericaceae).

    PubMed

    Meseguer, Andrea S; Lobo, Jorge M; Ree, Richard; Beerling, David J; Sanmartín, Isabel

    2015-03-01

    integrative approach to historical biogeography-that combines sources of evidence as diverse as paleontology, ecology, and phylogenetics-could help us obtain more accurate reconstructions of ancient evolutionary history. It also reveals the confounding effect different rates of extinction across regions have in biogeography, sometimes leading to ancestral areas being erroneously inferred as recent colonization events.

  5. Integrating Fossils, Phylogenies, and Niche Models into Biogeography to Reveal Ancient Evolutionary History: The Case of Hypericum (Hypericaceae)

    PubMed Central

    Meseguer, Andrea S.; Lobo, Jorge M.; Ree, Richard; Beerling, David J.; Sanmartín, Isabel

    2015-01-01

    integrative approach to historical biogeography—that combines sources of evidence as diverse as paleontology, ecology, and phylogenetics—could help us obtain more accurate reconstructions of ancient evolutionary history. It also reveals the confounding effect different rates of extinction across regions have in biogeography, sometimes leading to ancestral areas being erroneously inferred as recent colonization events. PMID:25398444

  6. Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses

    PubMed Central

    2011-01-01

    Background Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. Results We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Conclusion Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic

  7. Characteristics of ancient Egyptian glazed ceramic objects from Fatimid and Mamluk periods as revealed by ion beam analysis

    NASA Astrophysics Data System (ADS)

    Sadek, Hamada; M, Abd El Hady M.

    2012-07-01

    Ion beam analysis (PIXE, μPIXE) has been successfully applied in analysis of archaeological materials, it has many advantages. In this work Ion Beam Analysis (IBA) used in analysis of ancient Egyptian glazed ceramic from 10th to the 16th centuries (Fatimid and Mamluk periods). Glazed ceramic samples from Al-Fustat Excavation store have been chosen to represent different colours (green, blue, brown, black ...etc), the colours of glaze depend on many factors such as oxides present in the glaze layer, fluxes and the conditions in which objects had been manufactured in the past. Ion Beam allows the identification of elemental composition of the glaze layer i.e., the information about colorants used in glaze, which is of great importance for compositional data play a key role in solving questions concerning dating, provenance, technology, use and the relationship between ancient cultures with the environment.

  8. 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

    NASA Astrophysics Data System (ADS)

    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.

  9. Epoch-based likelihood models reveal no evidence for accelerated evolution of viviparity in squamate reptiles in response to cenozoic climate change.

    PubMed

    King, Benedict; Lee, Michael S Y

    2015-09-01

    A broad scale analysis of the evolution of viviparity across nearly 4,000 species of squamates revealed that origins increase in frequency toward the present, raising the question of whether rates of change have accelerated. We here use simulations to show that the increased frequency is within the range expected given that the number of squamate lineages also increases with time. Novel, epoch-based methods implemented in BEAST (which allow rates of discrete character evolution to vary across time-slices) also give congruent results, with recent epochs having very similar rates to older epochs. Thus, contrary to expectations, there was no accelerated burst of origins of viviparity in response to global cooling during the Cenozoic or glacial cycles during the Plio-Pleistocene. However, if one accepts the conventional view that viviparity is more likely to evolve than to be lost, and also the evidence here that viviparity has evolved with similar regularity throughout the last 200 Ma, then the absence of large, ancient clades of viviparous squamates (analogs to therian mammals) requires explanation. Viviparous squamate lineages might be more prone to extinction than are oviparous lineages, due to their prevalance at high elevations and latitudes and thus greater susceptibility to climate fluctuations. If so, the directional bias in character evolution would be offset by the bias in extinction rates.

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

    PubMed Central

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

    2011-01-01

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

  11. Oceanic mantle rocks reveal evidence for an ancient, 1.2-1.3 Ga global melting event

    NASA Astrophysics Data System (ADS)

    Dijkstra, A. H.; Sergeev, D.; McTaminey, L.; Dale, C. W.; Meisel, T. C.

    2011-12-01

    It is now increasingly being recognized that many oceanic peridotites are refertilized harzburgites, and that the refertilization often masks an extremely refractory character of the original mantle rock 'protolith'. Oceanic peridotites are, when the effects of melt refertilization are undone, often too refractory to be simple mantle melting residues after the extraction of mid-ocean ridge basalts at a spreading center. Rhenium-osmium isotope analysis is a powerful method to look through the effects of refertilization and to obtain constraints on the age of the melting that produced the refractory mantle protolith. Rhenium-depletion model ages of such anomalously refractory oceanic mantle rocks - found as abyssal peridotites or as mantle xenoliths on ocean islands - are typically >1 Ga, i.e., much older than the ridge system at which they were emplaced. In my contribution I will show results from two case studies of refertilized anciently depleted mantle rocks (Macquarie Island 'abyssal' peridotites and Lanzarote mantle xenoliths). Interestingly, very refractory oceanic mantle rocks from sites all around the world show recurring evidence for a Mesoproterozoic (~1.2-1.3 Ga) melting event [1]. Therefore, oceanic mantle rocks seem to preserve evidence for ancient melting events of global significance. Alternatively, such mantle rocks may be samples of rafts of ancient continental lithospheric mantle. Laser-ablation osmium isotope 'dating' of large populations of individual osmium-bearing alloys from mantle rocks is the key to better constrain the nature and significance of these ancient depletion events. Osmium-bearing alloys form when mantle rocks are melted to high-degrees. We have now extracted over >250 detrital osmium alloys from placer gold occurrences in the river Rhine. These alloys are derived from outcrops of ophiolitic mantle rocks in the Alps, which include blocks of mantle rocks emplaced within the Tethys Ocean, and ultramafic lenses of unknown

  12. Origins of enigmatic C-3 methyl and C-3 H porphyrins in ancient sediments revealed from formation of pyrophaeophorbide d in simulation experiments

    NASA Astrophysics Data System (ADS)

    Pickering, Matthew D.; Keely, Brendan J.

    2013-03-01

    The reaction of methyl pyrophaeophorbide a with hydrogen sulfide and oxygen under mild conditions (low temperature, moderate pH), which resemble those in certain natural environments, leads to its near quantitative conversion into methyl pyrophaeophorbide d (82-89%). The transformation, via oxidative cleavage of the C-3 vinyl substituent of pyrophaeophorbide a to afford an aldehyde at C-3, results from co-oxidation of the vinyl group and hydrogen sulfide by molecular oxygen. The co-oxidation transformation pathway operating on vinyl substituted chlorophyll derivatives can explain the origins of C-3 methyl and C-3 H porphyrins in ancient sediments and oils, structures for which the origins were previously unresolved. Evaluation of previous reports of C-3 methyl and C-3 H porphyrins in ancient sediments and oils reveals that their distributions are consistent with insights provided from analysis of the reaction mechanisms revealed by the laboratory studies. Thus, the sedimentary distributions reveal key features of the depositional settings, in particular the presence of a deep or a shallow chemocline. The oxidative cleavage of the C-3 vinyl group also provides insight into the biosynthesis of chlorophyll d by the cyanobacterium Acaryochloris marina, and offers a mild alternative to classical methods for the synthetic manipulation of the vinyl substituents of tetrapyrroles.

  13. Bacteriophage P23-77 capsid protein structures reveal the archetype of an ancient branch from a major virus lineage.

    PubMed

    Rissanen, Ilona; Grimes, Jonathan M; Pawlowski, Alice; Mäntynen, Sari; Harlos, Karl; Bamford, Jaana K H; Stuart, David I

    2013-05-07

    It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor.

  14. Broad taxonomic characterization of Verticillium wilt resistance genes reveals an ancient origin of the tomato Ve1 immune receptor.

    PubMed

    Song, Yin; Zhang, Zhao; Seidl, Michael F; Majer, Aljaz; Jakse, Jernej; Javornik, Branka; Thomma, Bart P H J

    2017-02-01

    Plant-pathogenic microbes secrete effector molecules to establish themselves on their hosts, whereas plants use immune receptors to try and intercept such effectors in order to prevent pathogen colonization. The tomato cell surface-localized receptor Ve1 confers race-specific resistance against race 1 strains of the soil-borne vascular wilt fungus Verticillium dahliae which secrete the Ave1 effector. Here, we describe the cloning and characterization of Ve1 homologues from tobacco (Nicotiana glutinosa), potato (Solanum tuberosum), wild eggplant (Solanum torvum) and hop (Humulus lupulus), and demonstrate that particular Ve1 homologues govern resistance against V. dahliae race 1 strains through the recognition of the Ave1 effector. Phylogenetic analysis shows that Ve1 homologues are widely distributed in land plants. Thus, our study suggests an ancient origin of the Ve1 immune receptor in the plant kingdom.

  15. Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor.

    PubMed

    Decker, Brennan; Davis, Brian W; Rimbault, Maud; Long, Adrienne H; Karlins, Eric; Jagannathan, Vidhya; Reiman, Rebecca; Parker, Heidi G; Drögemüller, Cord; Corneveaux, Jason J; Chapman, Erica S; Trent, Jeffery M; Leeb, Tosso; Huentelman, Matthew J; Wayne, Robert K; Karyadi, Danielle M; Ostrander, Elaine A

    2015-11-01

    Canine transmissible venereal tumor (CTVT) is a parasitic cancer clone that has propagated for thousands of years via sexual transfer of malignant cells. Little is understood about the mechanisms that converted an ancient tumor into the world's oldest known continuously propagating somatic cell lineage. We created the largest existing catalog of canine genome-wide variation and compared it against two CTVT genome sequences, thereby separating alleles derived from the founder's genome from somatic mutations that must drive clonal transmissibility. We show that CTVT has undergone continuous adaptation to its transmissible allograft niche, with overlapping mutations at every step of immunosurveillance, particularly self-antigen presentation and apoptosis. We also identified chronologically early somatic mutations in oncogenesis- and immune-related genes that may represent key initiators of clonal transmissibility. Thus, we provide the first insights into the specific genomic aberrations that underlie CTVT's dogged perseverance in canids around the world.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    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.

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

    PubMed

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

    2017-04-04

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

  19. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in the vernalization genes regulating this requirement has favored wheat adaptation to different environments. The main wheat vernalization genes VRN1, V...

  20. Convergence and Divergence in the Evolution of the APOBEC3G-Vif Interaction Reveal Ancient Origins of Simian Immunodeficiency Viruses

    PubMed Central

    Compton, Alex A.; Emerman, Michael

    2013-01-01

    Naturally circulating lentiviruses are abundant in African primate species today, yet their origins and history of transmitting between hosts remain obscure. As a means to better understand the age of primate lentiviruses, we analyzed primate genomes for signatures of lentivirus-driven evolution. Specifically, we studied the adaptive evolution of host restriction factor APOBEC3G (A3G) in Old World Monkey (OWM) species. We find recurrent mutation of A3G in multiple primate lineages at sites that determine susceptibility to antagonism by the lentiviral accessory protein Vif. Using a broad panel of SIV Vif isolates, we demonstrate that natural variation in OWM A3G confers resistance to Vif-mediated degradation, suggesting that adaptive variants of the host factor were selected upon exposure to pathogenic lentiviruses at least 5–6 million years ago (MYA). Furthermore, in members of the divergent Colobinae subfamily of OWM, a multi-residue insertion event in A3G that arose at least 12 MYA blocks the activity of Vif, suggesting an even more ancient origin of SIV. Moreover, analysis of the lentiviruses associated with Colobinae monkeys reveal that the interface of the A3G-Vif interaction has shifted and given rise to a second genetic conflict. Our analysis of virus-driven evolution describes an ancient yet ongoing genetic conflict between simian primates and lentiviruses on a million-year time scale. PMID:23359341

  1. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.

    PubMed

    Wood, Hannah Marie; Matzke, Nicholas J; Gillespie, Rosemary G; Griswold, Charles E

    2013-03-01

    Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the diversification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.

  2. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds.

    PubMed

    Skoglund, Pontus; Ersmark, Erik; Palkopoulou, Eleftheria; Dalén, Love

    2015-06-01

    The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

  3. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.

    PubMed

    Statham, Mark J; Murdoch, James; Janecka, Jan; Aubry, Keith B; Edwards, Ceiridwen J; Soulsbury, Carl D; Berry, Oliver; Wang, Zhenghuan; Harrison, David; Pearch, Malcolm; Tomsett, Louise; Chupasko, Judith; Sacks, Benjamin N

    2014-10-01

    Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Cloning the uteroglobin gene promoter from the relic volcano rabbit (Romerolagus diazi) reveals an ancient estrogen-response element.

    PubMed

    Acosta-MontesdeOca, Adriana; Zariñán, Teresa; Macías, Héctor; Pérez-Solís, Marco A; Ulloa-Aguirre, Alfredo; Gutiérrez-Sagal, Rubén

    2012-05-01

    To gain further insight on the estrogen-dependent transcriptional regulation of the uteroglobin (UG) gene, we cloned the 5'-flanking region of the UG gene from the phylogenetically ancient volcano rabbit (Romerolagus diazi; Rd). The cloned region spans 812 base pairs (bp; -812/-1) and contains a noncanonical TATA box (TACA). The translation start site is 48 bp downstream from the putative transcription initiation site (AGA), and is preceded by a consensus Kozak box. Comparison of the Rd-UG gene with that previously isolated from rabbits (Oryctolagus cuniculus) showed 93% in sequence identity as well as a number of conserved cis-acting elements, including the estrogen-response element (ERE; -265/-251), which differs from the consensus by two nucleotides. In MCF-7 cells, 17β-estradiol (E(2)) induced transcription of a luciferase reporter driven by the Rd-UG promoter in a similar manner as in an equivalent rabbit UG reporter; the Rd-UG promoter was 30% more responsive to E(2) than the rabbit promoter. Mutagenesis studies on the Rd-ERE confirmed this cis-element as a target of E(2) as two luciferase mutant reporters of the Rd-promoter, one with the rabbit and the other with the consensus ERE, were more responsive to the hormone than the wild-type reporter. Gel shift and super-shift assays showed that estrogen receptor-α indeed binds to the imperfect palindromic sequence of the Rd-ERE.

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

    USGS Publications Warehouse

    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.

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

    PubMed

    Jørgensen, Tina; Haile, James; Möller, Per; Andreev, Andrei; Boessenkool, Sanne; Rasmussen, Morten; Kienast, Frank; Coissac, Eric; Taberlet, Pierre; Brochmann, Christian; Bigelow, Nancy H; Andersen, Kenneth; Orlando, Ludovic; Gilbert, M Thomas P; Willerslev, Eske

    2012-04-01

    Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46-12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping and, in combination, reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation into temporal changes in species composition 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.

  8. Ancient Egyptian herbal wines

    PubMed Central

    McGovern, Patrick E.; Mirzoian, Armen; Hall, Gretchen R.

    2009-01-01

    Chemical analyses of ancient organics absorbed into pottery jars from the beginning of advanced ancient Egyptian culture, ca. 3150 B.C., and continuing for millennia have revealed that a range of natural products—specifically, herbs and tree resins—were dispensed by grape wine. These findings provide chemical evidence for ancient Egyptian organic medicinal remedies, previously only ambiguously documented in medical papyri dating back to ca. 1850 B.C. They illustrate how humans around the world, probably for millions of years, have exploited their natural environments for effective plant remedies, whose active compounds have recently begun to be isolated by modern analytical techniques. PMID:19365069

  9. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

    PubMed Central

    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

  10. Mitochondrial DNA Reveals the Trace of the Ancient Settlers of a Violently Devastated Late Bronze and Iron Ages Village

    PubMed Central

    Núñez, Carolina; Baeta, Miriam; Cardoso, Sergio; Palencia-Madrid, Leire; García-Romero, Noemí; Llanos, Armando; M. de Pancorbo, Marian

    2016-01-01

    La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iron Ages of the north of the Iberian Peninsula, until it was violently devastated around the 4th century and abandoned in the 3rd century B.C. Archaeological evidences suggest that descendants from La Hoya placed their new settlement in a nearby hill, which gave rise to the current village of Laguardia. In this study, we have traced the genetic imprints of the extinct inhabitants of La Hoya through the analysis of maternal lineages. In particular, we have analyzed the mitochondrial DNA (mtDNA) control region of 41 human remains recovered from the archaeological site for comparison with a sample of 51 individuals from the geographically close present-day population of Laguardia, as well as 56 individuals of the general population of the province of Alava, where the archaeological site and Laguardia village are located. MtDNA haplotypes were successfully obtained in 25 out of 41 ancient samples, and 14 different haplotypes were identified. The major mtDNA subhaplogroups observed in La Hoya were H1, H3, J1 and U5, which show a distinctive frequency pattern in the autochthonous populations of the north of the Iberian Peninsula. Approximate Bayesian Computation analysis was performed to test the most likely model for the local demographic history. The results did not sustain a genealogical continuity between Laguardia and La Hoya at the haplotype level, although factors such as sampling effects, recent admixture events, and genetic bottlenecks need to be considered. Likewise, the highly similar subhaplogroup composition detected between La Hoya and Laguardia and Alava populations do not allow us to reject a maternal genetic continuity in the human groups of the area since at least the Iron Age to present times. Broader analyses, based on a larger collection of samples and genetic markers, would be required to study fine-scale population events in these human groups. PMID

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

    PubMed

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

    2012-12-01

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

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

    PubMed

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

    2014-01-01

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

  13. Mitochondrial DNA Reveals the Trace of the Ancient Settlers of a Violently Devastated Late Bronze and Iron Ages Village.

    PubMed

    Núñez, Carolina; Baeta, Miriam; Cardoso, Sergio; Palencia-Madrid, Leire; García-Romero, Noemí; Llanos, Armando; M de Pancorbo, Marian

    2016-01-01

    La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iron Ages of the north of the Iberian Peninsula, until it was violently devastated around the 4th century and abandoned in the 3rd century B.C. Archaeological evidences suggest that descendants from La Hoya placed their new settlement in a nearby hill, which gave rise to the current village of Laguardia. In this study, we have traced the genetic imprints of the extinct inhabitants of La Hoya through the analysis of maternal lineages. In particular, we have analyzed the mitochondrial DNA (mtDNA) control region of 41 human remains recovered from the archaeological site for comparison with a sample of 51 individuals from the geographically close present-day population of Laguardia, as well as 56 individuals of the general population of the province of Alava, where the archaeological site and Laguardia village are located. MtDNA haplotypes were successfully obtained in 25 out of 41 ancient samples, and 14 different haplotypes were identified. The major mtDNA subhaplogroups observed in La Hoya were H1, H3, J1 and U5, which show a distinctive frequency pattern in the autochthonous populations of the north of the Iberian Peninsula. Approximate Bayesian Computation analysis was performed to test the most likely model for the local demographic history. The results did not sustain a genealogical continuity between Laguardia and La Hoya at the haplotype level, although factors such as sampling effects, recent admixture events, and genetic bottlenecks need to be considered. Likewise, the highly similar subhaplogroup composition detected between La Hoya and Laguardia and Alava populations do not allow us to reject a maternal genetic continuity in the human groups of the area since at least the Iron Age to present times. Broader analyses, based on a larger collection of samples and genetic markers, would be required to study fine-scale population events in these human groups.

  14. Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell.

    PubMed

    Grealy, Alicia; Phillips, Matthew; Miller, Gifford; Gilbert, M Thomas P; Rouillard, Jean-Marie; Lambert, David; Bunce, Michael; Haile, James

    2017-04-01

    Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable. Here, we use ancient DNA (aDNA) extracted from fossil eggshell, together with target enrichment and next-generation sequencing techniques, to reconstruct an additional new mitogenome from Aepyornis sp. with 33.5X coverage. We also recover the first elephant bird nuclear aDNA, represented by 12,500bp of exonic information. While we confirm that elephant birds are sister taxa to the kiwi, our data suggests that, like neognaths, palaeognaths underwent an explosive radiation between 69 and 52Ma-well after the break-up of Gondwana, and more rapidly than previously estimated from mitochondrial data alone. These results further support the idea that ratites primarily diversified immediately following the Cretaceous-Palaeogene mass extinction and convergently evolved flightlessness. Our study reinforces the importance of including information from the nuclear genome of extinct taxa for recovering deep evolutionary relationships. Furthermore, with approximately 3% endogenous aDNA retrieved, avian eggshell can be a valuable substrate for recovering high quality aDNA. We suggest that elephant bird whole genome recovery is ultimately achievable, and will provide future insights into the evolution these birds.

  15. Sequencing of Pax6 Loci from the Elephant Shark Reveals a Family of Pax6 Genes in Vertebrate Genomes, Forged by Ancient Duplications and Divergences

    PubMed Central

    Gautier, Philippe; Loosli, Felix; Tay, Boon-Hui; Tay, Alice; Murdoch, Emma; Coutinho, Pedro; van Heyningen, Veronica; Brenner, Sydney; Venkatesh, Byrappa; Kleinjan, Dirk A.

    2013-01-01

    Pax6 is a developmental control gene essential for eye development throughout the animal kingdom. In addition, Pax6 plays key roles in other parts of the CNS, olfactory system, and pancreas. In mammals a single Pax6 gene encoding multiple isoforms delivers these pleiotropic functions. Here we provide evidence that the genomes of many other vertebrate species contain multiple Pax6 loci. We sequenced Pax6-containing BACs from the cartilaginous elephant shark (Callorhinchus milii) and found two distinct Pax6 loci. Pax6.1 is highly similar to mammalian Pax6, while Pax6.2 encodes a paired-less Pax6. Using synteny relationships, we identify homologs of this novel paired-less Pax6.2 gene in lizard and in frog, as well as in zebrafish and in other teleosts. In zebrafish two full-length Pax6 duplicates were known previously, originating from the fish-specific genome duplication (FSGD) and expressed in divergent patterns due to paralog-specific loss of cis-elements. We show that teleosts other than zebrafish also maintain duplicate full-length Pax6 loci, but differences in gene and regulatory domain structure suggest that these Pax6 paralogs originate from a more ancient duplication event and are hence renamed as Pax6.3. Sequence comparisons between mammalian and elephant shark Pax6.1 loci highlight the presence of short- and long-range conserved noncoding elements (CNEs). Functional analysis demonstrates the ancient role of long-range enhancers for Pax6 transcription. We show that the paired-less Pax6.2 ortholog in zebrafish is expressed specifically in the developing retina. Transgenic analysis of elephant shark and zebrafish Pax6.2 CNEs with homology to the mouse NRE/Pα internal promoter revealed highly specific retinal expression. Finally, morpholino depletion of zebrafish Pax6.2 resulted in a “small eye” phenotype, supporting a role in retinal development. In summary, our study reveals that the pleiotropic functions of Pax6 in vertebrates are served by a divergent

  16. Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu (EASZ)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Indigenous zebu cattle are widespread across East Africa owing to their tropically-adapted physiology. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at the genome-wide level th...

  17. Ancient Egypt.

    ERIC Educational Resources Information Center

    Evers, Virginia

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

  18. Physicians of ancient India

    PubMed Central

    Saini, Anu

    2016-01-01

    A survey of Indian medical historiography will reveal no dearth of work on the systems of medicine and medical literature of ancient India. However, the people who were responsible for the healing have not received much attention. This article traces the evolution of the physician as a professional in ancient India. This article reviews the secondary literature on healing and medical practice in India, specifically pertaining to the individual medical practitioner, drawing from varied sources. The healers of ancient India hailed from different castes and classes. They were well-respected and enjoyed state patronage. They were held to the highest ethical standards of the day and were bound by a strict code of conduct. They underwent rigorous training in both medicine and surgery. Most physicians were multi-skilled generalists, and expected to be skilled in elocution and debate. They were reasonably well-off financially. The paper also briefly traces the evolution of medicinal ideas in ancient India. PMID:27843823

  19. The function of the RNA-binding protein TEL1 in moss reveals ancient regulatory mechanisms of shoot development.

    PubMed

    Vivancos, Julien; Spinner, Lara; Mazubert, Christelle; Charlot, Florence; Paquet, Nicolas; Thareau, Vincent; Dron, Michel; Nogué, Fabien; Charon, Céline

    2012-03-01

    The shoot represents the basic body plan in land plants. It consists of a repeated structure composed of stems and leaves. Whereas vascular plants generate a shoot in their diploid phase, non-vascular plants such as mosses form a shoot (called the gametophore) in their haploid generation. The evolution of regulatory mechanisms or genetic networks used in the development of these two kinds of shoots is unclear. TERMINAL EAR1-like genes have been involved in diploid shoot development in vascular plants. Here, we show that disruption of PpTEL1 from the moss Physcomitrella patens, causes reduced protonema growth and gametophore initiation, as well as defects in gametophore development. Leafy shoots formed on ΔTEL1 mutants exhibit shorter stems with more leaves per shoot, suggesting an accelerated leaf initiation (shortened plastochron), a phenotype shared with the Poaceae vascular plants TE1 and PLA2/LHD2 mutants. Moreover, the positive correlation between plastochron length and leaf size observed in ΔTEL1 mutants suggests a conserved compensatory mechanism correlating leaf growth and leaf initiation rate that would minimize overall changes in plant biomass. The RNA-binding protein encoded by PpTEL1 contains two N-terminus RNA-recognition motifs, and a third C-terminus non-canonical RRM, specific to TEL proteins. Removal of the PpTEL1 C-terminus (including this third RRM) or only 16-18 amino acids within it seriously impairs PpTEL1 function, suggesting a critical role for this third RRM. These results show a conserved function of the RNA-binding PpTEL1 protein in the regulation of shoot development, from early ancestors to vascular plants, that depends on the third TEL-specific RRM.

  20. Synergistic interaction between ankle and knee during hopping revealed through induced acceleration analysis.

    PubMed

    João, Filipa; Veloso, António; Cabral, Sílvia; Moniz-Pereira, Vera; Kepple, Thomas

    2014-02-01

    The forces produced by the muscles can deliver energy to a target segment they are not attached to, by transferring this energy throughout the other segments in the chain. This is a synergistic way of functioning, which allows muscles to accelerate or decelerate segments in order to reach the target one. The purpose of this study was to characterize the contribution of each lower extremity joint to the vertical acceleration of the body's center of mass during a hopping exercise. To accomplish this, an induced acceleration analysis was performed using a model with eight segments. The results indicate that the strategies produced during a hopping exercise rely on the synergy between the knee and ankle joints, with most of the vertical acceleration being produced by the knee extensors, while the ankle plantar flexors act as stabilizers of the foot. This synergy between the ankle and the knee is perhaps a mechanism that allows the transfer of power from the knee muscles to the ground, and we believe that in this particular task the net action of the foot and ankle moments is to produce a stable foot with little overall acceleration.

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

    PubMed

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

    2016-07-01

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

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

    PubMed Central

    Bover, Pere; Soibelzon, Leopoldo; Schubert, Blaine W.; Prevosti, Francisco; Prieto, Alfredo; Martin, Fabiana; Austin, Jeremy J.; Cooper, Alan

    2016-01-01

    The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American short-faced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses. PMID:27095265

  3. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

    PubMed Central

    Ottoni, Claudio; Willet, Rinse; Claeys, Johan; Talloen, Peter; Van de Vijver, Katrien; Chikhi, Lounès; Poblome, Jeroen; Decorte, Ronny

    2016-01-01

    More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake. PMID:26998313

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

    PubMed

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

    2016-04-01

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

  5. As Old as the Hills: Montane Scorpions in Southwestern North America Reveal Ancient Associations between Biotic Diversification and Landscape History

    PubMed Central

    Bryson, Robert W.; Riddle, Brett R.; Graham, Matthew R.; Smith, Brian Tilston; Prendini, Lorenzo

    2013-01-01

    Background The age of lineages has become a fundamental datum in studies exploring the interaction between geological transformation and biotic diversification. However, phylogeographical studies are often biased towards lineages that are younger than the geological features of the landscapes they inhabit. A temporally deeper historical biogeography framework may be required to address episodes of biotic diversification associated with geologically older landscape changes. Signatures of such associations may be retained in the genomes of ecologically specialized (stenotopic) taxa with limited vagility. In the study presented here, genetic data from montane scorpions in the Vaejovis vorhiesi group, restricted to humid rocky habitats in mountains across southwestern North America, were used to explore the relationship between scorpion diversification and regional geological history. Results Strong phylogeographical signal was evident within the vorhiesi group, with 27 geographically cohesive lineages inferred from a mitochondrial phylogeny. A time-calibrated multilocus species tree revealed a pattern of Miocene and Pliocene (the Neogene period) lineage diversification. An estimated 21 out of 26 cladogenetic events probably occurred prior to the onset of the Pleistocene, 2.6 million years ago. The best-fit density-dependent model suggested diversification rate in the vorhiesi group gradually decreased through time. Conclusions Scorpions of the vorhiesi group have had a long history in the highlands of southwestern North America. Diversification among these stenotopic scorpions appears to have occurred almost entirely within the Neogene period, and is temporally consistent with the dynamic geological history of the Basin and Range, and Colorado Plateau physiographical provinces. The persistence of separate lineages at small spatial scales suggests that a combination of ecological stenotopy and limited vagility may make these scorpions particularly valuable indicators

  6. Acceleration Data Reveal Highly Individually Structured Energetic Landscapes in Free-Ranging Fishers (Pekania pennanti)

    PubMed Central

    Scharf, Anne K.; LaPoint, Scott; Wikelski, Martin; Safi, Kamran

    2016-01-01

    Investigating animal energy expenditure across space and time may provide more detailed insight into how animals interact with their environment. This insight should improve our understanding of how changes in the environment affect animal energy budgets and is particularly relevant for animals living near or within human altered environments where habitat change can occur rapidly. We modeled fisher (Pekania pennanti) energy expenditure within their home ranges and investigated the potential environmental and spatial drivers of the predicted spatial patterns. As a proxy for energy expenditure we used overall dynamic body acceleration (ODBA) that we quantified from tri-axial accelerometer data during the active phases of 12 individuals. We used a generalized additive model (GAM) to investigate the spatial distribution of ODBA by associating the acceleration data to the animals' GPS-recorded locations. We related the spatial patterns of ODBA to the utilization distributions and habitat suitability estimates across individuals. The ODBA of fishers appears highly structured in space and was related to individual utilization distribution and habitat suitability estimates. However, we were not able to predict ODBA using the environmental data we selected. Our results suggest an unexpected complexity in the space use of animals that was only captured partially by re-location data-based concepts of home range and habitat suitability. We suggest future studies recognize the limits of ODBA that arise from the fact that acceleration is often collected at much finer spatio-temporal scales than the environmental data and that ODBA lacks a behavioral correspondence. Overcoming these limits would improve the interpretation of energy expenditure in relation to the environment. PMID:26840399

  7. Dust Production and Particle Acceleration in Supernova 1987A Revealed with ALMA

    NASA Technical Reports Server (NTRS)

    Indebetouw, R.; Matsuura, M.; Dwek, E.; Zanardo, G.; Barlow, M. J.; Baes, M.; Bouchet, P.; Burrows, D. N.; Chevalier, R.; Clayton, G. C.; Fransson, C.; Gaensler, B.; Kirshner, R.; Lakicevic, M.; Long, K. S.; Lundqvist, P.; Marti-Vidal, I.; Marcaide, J.; McCray, R.; Meixner, M.; Ng, C.-Y.; Park, S.; Sonneborn, G.; Staveley-Smith, L.; vanLoon, J.

    2014-01-01

    Supernova (SN) explosions are crucial engines driving the evolution of galaxies by shock heating gas, increasing the metallicity, creating dust, and accelerating energetic particles. In 2012 we used the Atacama Large Millimeter/ Submillimeter Array to observe SN1987A, one of the best-observed supernovae since the invention of the telescope. We present spatially resolved images at 450 µm, 870 µm, 1.4 mm, and 2.8 mm, an important transition wavelength range. Longer wavelength emission is dominated by synchrotron radiation from shock-accelerated particles, shorter wavelengths by emission from the largest mass of dust measured in a supernova remnant (>0.2 Solar Mass). For the first time we show unambiguously that this dust has formed in the inner ejecta (the cold remnants of the exploded star's core). The dust emission is concentrated at the center of the remnant, so the dust has not yet been affected by the shocks. If a significant fraction survives, and if SN 1987A is typical, supernovae are important cosmological dust producers.

  8. Dust Production and Particle Acceleration in Supernova 1987A Revealed with ALMA

    NASA Astrophysics Data System (ADS)

    Indebetouw, R.; Matsuura, M.; Dwek, E.; Zanardo, G.; Barlow, M. J.; Baes, M.; Bouchet, P.; Burrows, D. N.; Chevalier, R.; Clayton, G. C.; Fransson, C.; Gaensler, B.; Kirshner, R.; Lakićević, M.; Long, K. S.; Lundqvist, P.; Martí-Vidal, I.; Marcaide, J.; McCray, R.; Meixner, M.; Ng, C.-Y.; Park, S.; Sonneborn, G.; Staveley-Smith, L.; Vlahakis, C.; van Loon, J.

    2014-02-01

    Supernova (SN) explosions are crucial engines driving the evolution of galaxies by shock heating gas, increasing the metallicity, creating dust, and accelerating energetic particles. In 2012 we used the Atacama Large Millimeter/Submillimeter Array to observe SN 1987A, one of the best-observed supernovae since the invention of the telescope. We present spatially resolved images at 450 μm, 870 μm, 1.4 mm, and 2.8 mm, an important transition wavelength range. Longer wavelength emission is dominated by synchrotron radiation from shock-accelerated particles, shorter wavelengths by emission from the largest mass of dust measured in a supernova remnant (>0.2 M ⊙). For the first time we show unambiguously that this dust has formed in the inner ejecta (the cold remnants of the exploded star's core). The dust emission is concentrated at the center of the remnant, so the dust has not yet been affected by the shocks. If a significant fraction survives, and if SN 1987A is typical, supernovae are important cosmological dust producers.

  9. DUST PRODUCTION AND PARTICLE ACCELERATION IN SUPERNOVA 1987A REVEALED WITH ALMA

    SciTech Connect

    Indebetouw, R.; Chevalier, R.; Matsuura, M.; Barlow, M. J.; Dwek, E.; Zanardo, G.; Baes, M.; Bouchet, P.; Burrows, D. N.; Clayton, G. C.; Fransson, C.; Lundqvist, P.; Gaensler, B.; Kirshner, R.; Lakićević, M.; Long, K. S.; Meixner, M.; Martí-Vidal, I.; Marcaide, J.; and others

    2014-02-10

    Supernova (SN) explosions are crucial engines driving the evolution of galaxies by shock heating gas, increasing the metallicity, creating dust, and accelerating energetic particles. In 2012 we used the Atacama Large Millimeter/Submillimeter Array to observe SN 1987A, one of the best-observed supernovae since the invention of the telescope. We present spatially resolved images at 450 μm, 870 μm, 1.4 mm, and 2.8 mm, an important transition wavelength range. Longer wavelength emission is dominated by synchrotron radiation from shock-accelerated particles, shorter wavelengths by emission from the largest mass of dust measured in a supernova remnant (>0.2 M {sub ☉}). For the first time we show unambiguously that this dust has formed in the inner ejecta (the cold remnants of the exploded star's core). The dust emission is concentrated at the center of the remnant, so the dust has not yet been affected by the shocks. If a significant fraction survives, and if SN 1987A is typical, supernovae are important cosmological dust producers.

  10. 30-Year Satellite Record Reveals Accelerated Arctic Sea Ice Loss, Antarctic Sea Ice Trend Reversal

    NASA Technical Reports Server (NTRS)

    Cavalieri, Donald J.; Parkinson, C. L.; Vinnikov, K. Y.

    2003-01-01

    Arctic sea ice extent decreased by 0.30 plus or minus 0.03 x 10(exp 6) square kilometers per decade from 1972 through 2002, but decreased by 0.36 plus or minus 0.05 x 10(exp 6) square kilometers per decade from 1979 through 2002, indicating an acceleration of 20% in the rate of decrease. In contrast to the Arctic, the Antarctic sea ice extent decreased dramatically over the period 1973-1977, then gradually increased, with an overall 30-year trend of -0.15 plus or minus 0.08 x 10(exp 6) square kilometers per 10yr. The trend reversal is attributed to a large positive anomaly in Antarctic sea ice extent observed in the early 1970's.

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

  12. Vibrotactile masking experiments reveal accelerated somatosensory processing in congenitally blind braille readers.

    PubMed

    Bhattacharjee, Arindam; Ye, Amanda J; Lisak, Joy A; Vargas, Maria G; Goldreich, Daniel

    2010-10-27

    Braille reading is a demanding task that requires the identification of rapidly varying tactile patterns. During proficient reading, neighboring characters impact the fingertip at ∼100 ms intervals, and adjacent raised dots within a character at 50 ms intervals. Because the brain requires time to interpret afferent sensorineural activity, among other reasons, tactile stimuli separated by such short temporal intervals pose a challenge to perception. How, then, do proficient Braille readers successfully interpret inputs arising from their fingertips at such rapid rates? We hypothesized that somatosensory perceptual consolidation occurs more rapidly in proficient Braille readers. If so, Braille readers should outperform sighted participants on masking tasks, which demand rapid perceptual processing, but would not necessarily outperform the sighted on tests of simple vibrotactile sensitivity. To investigate, we conducted two-interval forced-choice vibrotactile detection, amplitude discrimination, and masking tasks on the index fingertips of 89 sighted and 57 profoundly blind humans. Sighted and blind participants had similar unmasked detection (25 ms target tap) and amplitude discrimination (compared with 100 μm reference tap) thresholds, but congenitally blind Braille readers, the fastest readers among the blind participants, exhibited significantly less masking than the sighted (masker, 50 Hz, 50 μm; target-masker delays, ±50 and ±100 ms). Indeed, Braille reading speed correlated significantly and specifically with masking task performance, and in particular with the backward masking decay time constant. We conclude that vibrotactile sensitivity is unchanged but that perceptual processing is accelerated in congenitally blind Braille readers.

  13. Foreign exchange market data analysis reveals statistical features that predict price movement acceleration

    NASA Astrophysics Data System (ADS)

    Nacher, Jose C.; Ochiai, Tomoshiro

    2012-05-01

    Increasingly accessible financial data allow researchers to infer market-dynamics-based laws and to propose models that are able to reproduce them. In recent years, several stylized facts have been uncovered. Here we perform an extensive analysis of foreign exchange data that leads to the unveiling of a statistical financial law. First, our findings show that, on average, volatility increases more when the price exceeds the highest (or lowest) value, i.e., breaks the resistance line. We call this the breaking-acceleration effect. Second, our results show that the probability P(T) to break the resistance line in the past time T follows power law in both real data and theoretically simulated data. However, the probability calculated using real data is rather lower than the one obtained using a traditional Black-Scholes (BS) model. Taken together, the present analysis characterizes a different stylized fact of financial markets and shows that the market exceeds a past (historical) extreme price fewer times than expected by the BS model (the resistance effect). However, when the market does, we predict that the average volatility at that time point will be much higher. These findings indicate that any Markovian model does not faithfully capture the market dynamics.

  14. In Silico and In Vivo Experiments Reveal M-CSF Injections Accelerate Regeneration Following Muscle Laceration.

    PubMed

    Martin, Kyle S; Kegelman, Christopher D; Virgilio, Kelley M; Passipieri, Julianna A; Christ, George J; Blemker, Silvia S; Peirce, Shayn M

    2017-03-01

    Numerous studies have pharmacologically modulated the muscle milieu in the hopes of promoting muscle regeneration; however, the timing and duration of these interventions are difficult to determine. This study utilized a combination of in silico and in vivo experiments to investigate how inflammation manipulation improves muscle recovery following injury. First, we measured macrophage populations following laceration injury in the rat tibialis anterior (TA). Then we calibrated an agent-based model (ABM) of muscle injury to mimic the observed inflammation profiles. The calibrated ABM was used to simulate macrophage and satellite stem cell (SC) dynamics, and suggested that delivering macrophage colony stimulating factor (M-CSF) prior to injury would promote SC-mediated injury recovery. Next, we performed an experiment wherein 1 day prior to injury, we injected M-CSF into the rat TA muscle. M-CSF increased the number of macrophages during the first 4 days post-injury. Furthermore, treated muscles experienced a swifter increase in the appearance of PAX7(+) SCs and regenerating muscle fibers. Our study suggests that computational models of muscle injury provide novel insights into cellular dynamics during regeneration, and further, that pharmacologically altering inflammation dynamics prior to injury can accelerate the muscle regeneration process.

  15. Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus.

    PubMed

    Yang, Liandong; Wang, Ying; Zhang, Zhaolei; He, Shunping

    2014-12-26

    Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes.

  16. Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus

    PubMed Central

    Yang, Liandong; Wang, Ying; Zhang, Zhaolei; He, Shunping

    2015-01-01

    Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes. PMID:25543049

  17. Isolation of Hox Cluster Genes from Insects Reveals an Accelerated Sequence Evolution Rate

    PubMed Central

    Hadrys, Heike; Simon, Sabrina; Kaune, Barbara; Schmitt, Oliver; Schöner, Anja; Jakob, Wolfgang; Schierwater, Bernd

    2012-01-01

    Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution. PMID:22685537

  18. The long-period eccentric orbit of the particle accelerator HD 167971 revealed by long baseline interferometry

    NASA Astrophysics Data System (ADS)

    De Becker, M.; Sana, H.; Absil, O.; Le Bouquin, J.-B.; Blomme, R.

    2012-07-01

    Using optical long baseline interferometry, we resolved for the first time the two wide components of HD 167971, a candidate hierarchical triple system known to efficiently accelerate particles. Our multi-epoch Very Large Telescope Interferometer observations provide direct evidence for a gravitational link between the O8 supergiant and the close eclipsing O + O binary. The separation varies from 8 to 15 mas over the 3-year baseline of our observations, suggesting that the components evolve on a wide and very eccentric orbit (most probably e > 0.5). These results provide evidence that the wide orbit revealed by our study is not coplanar with the orbit of the inner eclipsing binary. From our measurements of the near-infrared luminosity ratio, we constrain the spectral classification of the components in the close binary to be O6-O7, and confirm that these stars are likely main-sequence objects. Our results are discussed in the context of the bright non-thermal radio emission already reported for this system, and we provide arguments in favour of a maximum radio emission coincident with periastron passage. HD 167971 turns out to be an efficient O-type particle accelerator that constitutes a valuable target for future high angular resolution radio imaging using Very Long Baseline Interferometry facilities. Based on observations collected at the European Southern Observatory, Paranal, Chile, under the programme IDs 381.D-0095, 086.D-0586 and 087.D-0264.

  19. Continuously accelerating ice loss over Amundsen Sea catchment, West Antarctica, revealed by integrating altimetry and GRACE data

    NASA Astrophysics Data System (ADS)

    Lee, Hyongki; Shum, C. K.; Howat, Ian M.; Monaghan, Andrew; Ahn, Yushin; Duan, Jianbin; Guo, Jun-Yi; Kuo, Chung-Yen; Wang, Lei

    2012-03-01

    Satellite altimetry and Gravity Recovery and Climate Experiment (GRACE) measurements have provided contemporary, but substantially different Antarctic ice sheet mass balance estimates. Altimetry provides no information about firn density while GRACE data is significantly impacted by poorly constrained glacial isostatic adjustment signals. Here, we combine Envisat radar altimetry and GRACE data over the Amundsen Sea (AS) sector, West Antarctica, to estimate the basin-wide averaged snow and firn column density over a seasonal time scale. Removing the firn variability signal from Envisat-observed ice-sheet elevation changes reveals more rapid dynamic thinning of underlying ice. We report that the net AS sector mass change rates are estimated to be - 47 ± 8 Gt yr- 1 between 2002 and 2006, and - 80 ± 4 Gt yr- 1 between2007 and 2009, equivalent to a sea level rise of 0.13 and 0.22 mm yr- 1, respectively. The acceleration is due to a combination of decreased snowfall accumulation (+ 13 Gt yr- 1 in 2002-2006, and - 6 Gt yr- 1 in 2007-2009) and enhanced ice dynamic thinning (- 60 ± 10 Gt yr- 1 in 2002-2006, and - 74 ± 11 Gt yr- 1 in 2007-2009) after 2007. Because there is no significant snowfall trend over the past 21 yr (1989-2009) and an increase in ice flow speed (2003-2010), the accelerated mass loss is likely to continue.

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

    PubMed Central

    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

  1. DNA analysis of a 30,000-year-old Urocitellus glacialis from northeastern Siberia reveals phylogenetic relationships between ancient and present-day arctic ground squirrels

    PubMed Central

    Faerman, Marina; Bar-Gal, Gila Kahila; Boaretto, Elisabetta; Boeskorov, Gennady G.; Dokuchaev, Nikolai E.; Ermakov, Oleg A.; Golenishchev, Fedor N.; Gubin, Stanislav V.; Mintz, Eugenia; Simonov, Evgeniy; Surin, Vadim L.; Titov, Sergei V.; Zanina, Oksana G.; Formozov, Nikolai A.

    2017-01-01

    In contrast to the abundant fossil record of arctic ground squirrels, Urocitellus parryii, from eastern Beringia, only a limited number of fossils is known from its western part. In 1946, unnamed GULAG prisoners discovered a nest with three mummified carcasses of arctic ground squirrels in the permafrost sediments of the El’ga river, Yakutia, Russia, that were later attributed to a new species, Citellus (Urocitellus) glacialis Vinogr. To verify this assignment and to explore phylogenetic relationships between ancient and present-day arctic ground squirrels, we performed 14C dating and ancient DNA analyses of one of the El’ga mummies and four contemporaneous fossils from Duvanny Yar, northeastern Yakutia. Phylogenetic reconstructions, based on complete cytochrome b gene sequences of five Late Pleistocene arctic ground squirrels and those of modern U. parryii from 21 locations across western Beringia, provided no support for earlier proposals that ancient arctic ground squirrels from Siberia constitute a distinct species. In fact, we observed genetic continuity of the glacialis mitochondrial DNA lineage in modern U. parryii of the Kamchatka peninsula. When viewed in a broader geographic perspective, our findings provide new insights into the genetic history of U. parryii in Late Pleistocene Beringia. PMID:28205612

  2. Ancient Egypt

    NASA Astrophysics Data System (ADS)

    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.

  3. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns.

    PubMed

    Shao, Zhu-Qing; Xue, Jia-Yu; Wu, Ping; Zhang, Yan-Mei; Wu, Yue; Hang, Yue-Yu; Wang, Bin; Chen, Jian-Qun

    2016-04-01

    Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.

  4. Microfluidic Platform for Studying Chemotaxis of Adhesive Cells Revealed a Gradient-Dependent Migration and Acceleration of Cancer Stem Cells.

    PubMed

    Zou, Heng; Yue, Wanqing; Yu, Wai-Kin; Liu, Dandan; Fong, Chi-Chun; Zhao, Jianlong; Yang, Mengsu

    2015-07-21

    Recent studies reveal that solid tumors consist of heterogeneous cells with distinct phenotypes and functions. However, it is unclear how different subtypes of cancer cells migrate under chemotaxis. Here, we developed a microfluidic device capable of generating multiple stable gradients, culturing cells on-chip, and monitoring single cell migratory behavior. The microfluidic platform was used to study gradient-induced chemotaxis of lung cancer stem cell (LCSC) and differentiated LCSC (dLCSC) in real time. Our results showed the dynamic and differential response of both LCSC and dLCSC to chemotaxis, which was regulated by the β-catenin dependent Wnt signaling pathway. The microfluidic analysis showed that LCSC and dLCSC from the same origin behaved differently in the same external stimuli, suggesting the importance of cancer cell heterogeneity. We also observed for the first time the acceleration of both LCSC and dLCSC during chemotaxis caused by increasing local concentration in different gradients, which could only be realized through the microfluidic approach. The capability to analyze single cell chemotaxis under spatially controlled conditions provides a novel analytical platform for the study of cellular microenvironments and cancer cell metastasis.

  5. Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen-Ning; Freitas, Beatriz C.; Qian, Hao; Lux, Jacques; Acab, Allan; Trujillo, Cleber A.; Herai, Roberto H.; Nguyen Huu, Viet Anh; Wen, Jessica H.; Joshi-Barr, Shivanjali; Karpiak, Jerome V.; Engler, Adam J.; Fu, Xiang-Dong; Muotri, Alysson R.; Almutairi, Adah

    2016-03-01

    Probing a wide range of cellular phenotypes in neurodevelopmental disorders using patient-derived neural progenitor cells (NPCs) can be facilitated by 3D assays, as 2D systems cannot entirely recapitulate the arrangement of cells in the brain. Here, we developed a previously unidentified 3D migration and differentiation assay in layered hydrogels to examine how these processes are affected in neurodevelopmental disorders, such as Rett syndrome. Our soft 3D system mimics the brain environment and accelerates maturation of neurons from human induced pluripotent stem cell (iPSC)-derived NPCs, yielding electrophysiologically active neurons within just 3 wk. Using this platform, we revealed a genotype-specific effect of methyl-CpG-binding protein-2 (MeCP2) dysfunction on iPSC-derived neuronal migration and maturation (reduced neurite outgrowth and fewer synapses) in 3D layered hydrogels. Thus, this 3D system expands the range of neural phenotypes that can be studied in vitro to include those influenced by physical and mechanical stimuli or requiring specific arrangements of multiple cell types.

  6. Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction.

    PubMed

    Zhang, Zhen-Ning; Freitas, Beatriz C; Qian, Hao; Lux, Jacques; Acab, Allan; Trujillo, Cleber A; Herai, Roberto H; Nguyen Huu, Viet Anh; Wen, Jessica H; Joshi-Barr, Shivanjali; Karpiak, Jerome V; Engler, Adam J; Fu, Xiang-Dong; Muotri, Alysson R; Almutairi, Adah

    2016-03-22

    Probing a wide range of cellular phenotypes in neurodevelopmental disorders using patient-derived neural progenitor cells (NPCs) can be facilitated by 3D assays, as 2D systems cannot entirely recapitulate the arrangement of cells in the brain. Here, we developed a previously unidentified 3D migration and differentiation assay in layered hydrogels to examine how these processes are affected in neurodevelopmental disorders, such as Rett syndrome. Our soft 3D system mimics the brain environment and accelerates maturation of neurons from human induced pluripotent stem cell (iPSC)-derived NPCs, yielding electrophysiologically active neurons within just 3 wk. Using this platform, we revealed a genotype-specific effect of methyl-CpG-binding protein-2 (MeCP2) dysfunction on iPSC-derived neuronal migration and maturation (reduced neurite outgrowth and fewer synapses) in 3D layered hydrogels. Thus, this 3D system expands the range of neural phenotypes that can be studied in vitro to include those influenced by physical and mechanical stimuli or requiring specific arrangements of multiple cell types.

  7. Visualization of in vivo metabolic flows reveals accelerated utilization of glucose and lactate in penumbra of ischemic heart

    PubMed Central

    Sugiura, Yuki; Katsumata, Yoshinori; Sano, Motoaki; Honda, Kurara; Kajimura, Mayumi; Fukuda, Keiichi; Suematsu, Makoto

    2016-01-01

    Acute ischemia produces dynamic changes in labile metabolites. To capture snapshots of such acute metabolic changes, we utilized focused microwave treatment to fix metabolic flow in vivo in hearts of mice 10 min after ligation of the left anterior descending artery. The left ventricle was subdivided into short-axis serial slices and the metabolites were analyzed by capillary electrophoresis mass spectrometry and matrix-assisted laser desorption/ionization imaging mass spectrometry. These techniques allowed us to determine the fate of exogenously administered 13C6-glucose and 13C3-lactate. The penumbra regions, which are adjacent to the ischemic core, exhibited the greatest adenine nucleotide energy charge and an adenosine overflow extending from the ischemic core, which can cause ischemic hyperemia. Imaging analysis of metabolic pathway flows revealed that the penumbra executes accelerated glucose oxidation, with remaining lactate utilization for tricarboxylic acid cycle for energy compensation, suggesting unexpected metabolic interplays of the penumbra with the ischemic core and normoxic regions. PMID:27581923

  8. Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction

    PubMed Central

    Zhang, Zhen-Ning; Freitas, Beatriz C.; Qian, Hao; Lux, Jacques; Acab, Allan; Trujillo, Cleber A.; Herai, Roberto H.; Nguyen Huu, Viet Anh; Wen, Jessica H.; Joshi-Barr, Shivanjali; Karpiak, Jerome V.; Engler, Adam J.; Fu, Xiang-Dong; Muotri, Alysson R.; Almutairi, Adah

    2016-01-01

    Probing a wide range of cellular phenotypes in neurodevelopmental disorders using patient-derived neural progenitor cells (NPCs) can be facilitated by 3D assays, as 2D systems cannot entirely recapitulate the arrangement of cells in the brain. Here, we developed a previously unidentified 3D migration and differentiation assay in layered hydrogels to examine how these processes are affected in neurodevelopmental disorders, such as Rett syndrome. Our soft 3D system mimics the brain environment and accelerates maturation of neurons from human induced pluripotent stem cell (iPSC)-derived NPCs, yielding electrophysiologically active neurons within just 3 wk. Using this platform, we revealed a genotype-specific effect of methyl-CpG-binding protein-2 (MeCP2) dysfunction on iPSC-derived neuronal migration and maturation (reduced neurite outgrowth and fewer synapses) in 3D layered hydrogels. Thus, this 3D system expands the range of neural phenotypes that can be studied in vitro to include those influenced by physical and mechanical stimuli or requiring specific arrangements of multiple cell types. PMID:26944080

  9. Revised 14C dating of ice wedge growth in interior Alaska (USA) to MIS 2 reveals cold paleoclimate and carbon recycling in ancient permafrost terrain

    NASA Astrophysics Data System (ADS)

    Lachniet, Matthew S.; Lawson, Daniel E.; Sloat, Alison R.

    2012-09-01

    Establishing firm radiocarbon chronologies for Quaternary permafrost sequences remains a challenge because of the persistence of old carbon in younger deposits. To investigate carbon dynamics and establish ice wedge formation ages in Interior Alaska, we dated a late Pleistocene ice wedge, formerly assigned to Marine Isotope Stage (MIS) 3, and host sediments near Fairbanks, Alaska, with 24 radiocarbon analyses on wood, particulate organic carbon (POC), air-bubble CO2, and dissolved organic carbon (DOC). Our new CO2 and DOC ages are up to 11,170 yr younger than ice wedge POC ages, indicating that POC is detrital in origin. We conclude an ice wedge formation age between 28 and 22 cal ka BP during cold stadial conditions of MIS 2 and solar insolation minimum, possibly associated with Heinrich event 2 or the last glacial maximum. A DOC age for an ice lens in a thaw unconformity above the ice wedge returned a maximum age of 21,470 ± 200 cal yr BP. Our variable 14C data indicate recycling of older carbon in ancient permafrost terrain, resulting in radiocarbon ages significantly older than the period of ice-wedge activity. Release of ancient carbon with climatic warming will therefore affect the global 14C budget.

  10. Structural and functional characterization of a TGFβ molecule from amphioxus reveals an ancient origin of both immune-enhancing and -inhibitory functions.

    PubMed

    Wang, Shengnan; Li, Fengzhen; Hu, Lili; Liu, Shousheng; Li, Hongyan; Zhang, Shicui

    2014-08-01

    Transforming growth factor beta (TGFβ) is a pleiotropic cytokine with important roles in mediating inflammatory response. TGFβ has been shown to be widely present in invertebrates, but little is known about its functions in immune and inflammatory responses. Moreover, structural and functional insights into TGFβ molecules in invertebrates remain completely lacking. Here we demonstrate the presence of a single TGFβ-like gene in the amphioxus Branchiostoma japonicum, Bjtgfβ, which represents the archetype of vertebrate TGFβ proteins, and displays a higher expression in the hind-gut, hepatic caecum, ovary, and gill. We also show that amphioxus TGFβ exerts both enhancing and suppressing effects on the migration of macrophages like RAW264.7, and the motif WSTD is important for TGFβ in inducing or inhibiting the migration of macrophages. Altogether, these data suggest that amphioxus TGFβ is phylogenetically and functionally similar to vertebrate TGFβ, suggesting an ancient origin of bipolar function of TGFβ proteins.

  11. Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars

    PubMed Central

    Terral, Jean-Frédéric; Tabard, Elidie; Bouby, Laurent; Ivorra, Sarah; Pastor, Thierry; Figueiral, Isabel; Picq, Sandrine; Chevance, Jean-Baptiste; Jung, Cécile; Fabre, Laurent; Tardy, Christophe; Compan, Michel; Bacilieri, Roberto; Lacombe, Thierry; This, Patrice

    2010-01-01

    Background and Aims In spite of the abundance of archaeological, bio-archaeological, historical and genetic data, the origins, historical biogeography, identity of ancient grapevine cultivars and mechanisms of domestication are still largely unknown. Here, analysis of variation in seed morphology aims to provide accurate criteria for the discrimination between wild grapes and modern cultivars and to understand changes in functional traits in relation to the domestication process. This approach is also used to quantify the phenotypic diversity in the wild and cultivated compartments and to provide a starting point for comparing well-preserved archaeological material, in order to elucidate the history of grapevine varieties. Methods Geometrical analysis (elliptic Fourier transform method) was applied to grapevine seed outlines from modern wild individuals, cultivars and well-preserved archaeological material from southern France, dating back to the first to second centuries. Key Results and Conclusions Significant relationships between seed shape and taxonomic status, geographical origin (country or region) of accessions and parentage of varieties are highlighted, as previously noted based on genetic approaches. The combination of the analysis of modern reference material and well-preserved archaeological seeds provides original data about the history of ancient cultivated forms, some of them morphologically close to the current ‘Clairette’ and ‘Mondeuse blanche’ cultivars. Archaeobiological records seem to confirm the complexity of human contact, exchanges and migrations which spread grapevine cultivation in Europe and in Mediterranean areas, and argue in favour of the existence of local domestication in the Languedoc (southern France) region during Antiquity. PMID:20034966

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

    PubMed Central

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

    2016-01-01

    The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A. PMID:27741281

  13. Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)

    NASA Astrophysics Data System (ADS)

    Hildegard Zimmermann, Heike; Raschke, Elena; Saskia Epp, Laura; Rosmarie Stoof-Leichsenring, Kathleen; Schwamborn, Georg; Schirrmeister, Lutz; Overduin, Pier Paul; Herzschuh, Ulrike

    2017-02-01

    Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4-11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Ancient DNA reveals selection acting on genes associated with hypoxia response in pre-Columbian Peruvian Highlanders in the last 8500 years

    PubMed Central

    Fehren-Schmitz, Lars; Georges, Lea

    2016-01-01

    Archaeological evidence shows that humans began living in the high altitude Andes approximately 12,000 years ago. Andean highlanders are known to have developed the most complex societies of pre-Columbian South America despite challenges to their health and reproductive success resulting from chronic exposure to hypoxia. While the physiological adaptations to this environmental stressor are well studied in contemporary Andean highlanders, the molecular evolutionary processes associated with such adaptations remain unclear. We aim to better understand how humans managed to demographically establish in this harsh environment by addressing a central question: did exposure to hypoxia drive adaptation via natural selection within Andean populations or did an existing phenotype –characterized by reduced susceptibility to hypoxic stress–enable human settlement of the Andes? We genotyped three variable loci within the NOS3 and EGLN1 genes previously associated with adaptation to high altitude in 150 ancient human DNA samples from Peruvian high altitude and coastal low altitude sites in a time frame between ~8500–560 BP. We compare the data of 109 successful samples to forward simulations of genetic drift with natural selection and find that selection, rather than drift, explains the gradual frequency changes observed in the highland populations for two of the three SNPs. PMID:26996763

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

    PubMed

    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.

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

    PubMed

    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.

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

    PubMed Central

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

    2013-01-01

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

  20. Apps for Ancient Civilizations

    ERIC Educational Resources Information Center

    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…

  1. Evidence for Ancient Mesoamerican Earthquakes

    NASA Astrophysics Data System (ADS)

    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

  2. Progress on plasma accelerators

    SciTech Connect

    Chen, P.

    1986-05-01

    Several plasma accelerator concepts are reviewed, with emphasis on the Plasma Beat Wave Accelerator (PBWA) and the Plasma Wake Field Accelerator (PWFA). Various accelerator physics issues regarding these schemes are discussed, and numerical examples on laboratory scale experiments are given. The efficiency of plasma accelerators is then revealed with suggestions on improvements. Sources that cause emittance growth are discussed briefly.

  3. Skeletal dysplasia in ancient Egypt.

    PubMed

    Kozma, Chahira

    2008-12-01

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

  4. Ground-penetrating radar survey on the island of Pantelleria (Italy) reveals an ancient architectural complex with likely Punic and Roman components

    NASA Astrophysics Data System (ADS)

    Urban, Thomas M.; Murray, Carrie Ann; Vella, Clive; Lahikainen, Amanda

    2015-12-01

    A ground-penetrating radar (GPR) survey conducted on the small volcanic island of Pantelleria, in the Strait of Sicily, south-central Mediterranean, revealed an apparent complex of Punic/Roman architecture. The survey focused on the Lago di Venere area, where a previously investigated ritual Punic site was built alongside a brackish volcanic lake. The site also exhibits evidence of earlier Eneolithic components and later Roman components. The full extent of the site has remained undetermined, however, with only the small area of the Punic ritual complex having been excavated from 1996 to 2002. The GPR survey was intended to explore whether additional architecture remained unseen in surrounding areas, thus taking a first step toward determining the site's full spatial extent and archaeological potential. This survey revealed a complex of architectural ruins beneath an active agricultural field immediately west of the previously excavated features, and extending to a depth of approximately 2 m. These newly discovered features expand the known architectural footprint of the immediate site by three-fold. This GPR study is the first published archaeo-geophysical investigation on the island.

  5. Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface

    PubMed Central

    McCarthy, Kevin R.; Kirmaier, Andrea; Autissier, Patrick; Johnson, Welkin E.

    2015-01-01

    The widespread distribution of lentiviruses among African primates, and the lack of severe pathogenesis in many of these natural reservoirs, are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses (SIVs) and their primate hosts. Evidence for positive selection acting on antiviral restriction factors is consistent with virus-host interactions spanning millions of years of primate evolution. However, many restriction mechanisms are not virus-specific, and selection cannot be unambiguously attributed to any one type of virus. We hypothesized that the restriction factor TRIM5, because of its unique specificity for retrovirus capsids, should accumulate adaptive changes in a virus-specific fashion, and therefore, that phylogenetic reconstruction of TRIM5 evolution in African primates should reveal selection by lentiviruses closely related to modern SIVs. We analyzed complete TRIM5 coding sequences of 22 Old World primates and identified a tightly-spaced cluster of branch-specific adaptions appearing in the Cercopithecinae lineage after divergence from the Colobinae around 16 million years ago. Functional assays of both extant TRIM5 orthologs and reconstructed ancestral TRIM5 proteins revealed that this cluster of adaptations in TRIM5 specifically resulted in the ability to restrict Cercopithecine lentiviruses, but had no effect (positive or negative) on restriction of other retroviruses, including lentiviruses of non-Cercopithecine primates. The correlation between lineage-specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of Cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity. PMID:26291613

  6. Ancient DNA and human history

    PubMed Central

    Slatkin, Montgomery; Racimo, Fernando

    2016-01-01

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. PMID:27274045

  7. Ancient DNA and human history.

    PubMed

    Slatkin, Montgomery; Racimo, Fernando

    2016-06-07

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.

  8. Ancient DNA of the Extinct Lava Shearwater (Puffinus olsoni) from the Canary Islands Reveals Incipient Differentiation within the P. puffinus Complex

    PubMed Central

    Ramirez, Oscar; Illera, Juan Carlos; Rando, Juan Carlos; Gonzalez-Solis, Jacob; Alcover, Josep Antoni; Lalueza-Fox, Carles

    2010-01-01

    Background The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae) the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands. Methodology/Principal Findings We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae) to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA) cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni) from Fuerteventura (Canary Islands), the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species. Conclusions The phylogenetic analyses based on the DNA data reveal that: (i) the “Puffinus puffinus complex”, an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae), shows unresolved phylogenetic relationships; (ii) despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus. PMID:21209838

  9. Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene.

    PubMed

    Pérez, Trinidad; Fernández, Margarita; Hammer, Sabine E; Domínguez, Ana

    2017-01-01

    The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.

  10. Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene

    PubMed Central

    Pérez, Trinidad; Fernández, Margarita; Hammer, Sabine E.

    2017-01-01

    The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms. PMID:28146581

  11. Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single nucleotide polymorphism was employed in the construction of a high-resolution, expressed sequence tag (EST) map of Aegilops tauschii, the diploid source of the wheat D genome. Comparison of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and...

  12. Studying Ancient History.

    ERIC Educational Resources Information Center

    Barrow, Robin

    1982-01-01

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

  13. Ancient Astronomy in Armenia

    NASA Astrophysics Data System (ADS)

    Parsamian, Elma S.

    2007-08-01

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

  14. Ancient Maya Mercury

    NASA Astrophysics Data System (ADS)

    Pendergast, David M.

    1982-08-01

    Discovery of mercury in an ancient Maya offering at Lamanai, Belize, has stimulated examination of possible sources of the material in the Maya area. Two zones of cinnabar and native mercury deposits can be defined in the Maya highlands, and the presence of the native metal suggests that the ancient Maya collected rather than extracted the mercury from ore.

  15. Dental health and disease in ancient Egypt.

    PubMed

    Forshaw, R J

    2009-04-25

    In ancient Egypt the exceptionally dry climate together with the unique burial customs has resulted in the survival of large numbers of well-preserved skeletal and mummified remains. Examinations of these remains together with an analysis of the surviving documentary, archaeological and ethnographic evidence has enabled a detailed picture of the dental health of these ancient people to be revealed, perhaps more so than for any other civilisation in antiquity. In this, the first of two articles, the dental pathological conditions that afflicted the ancient Egyptians is considered. The commonest finding is that of tooth wear, which was often so excessive that it resulted in pulpal exposure. Multiple abscesses were frequently seen, but caries was not a significant problem. Overall the findings indicate that the various pathological conditions and non-pathological abnormalities of teeth evident in dentitions in the twenty-first century were also manifest in ancient Egypt, although the incidences of these conditions varies considerably between the civilisations.

  16. Evolutionary biology. Chewed leaves reveal ancient relationship.

    PubMed

    Pennisi, E

    2000-07-14

    On page 291, researchers describe a new beetle fossil based not on traces of the insect skeleton but on the distinctive gouges the beetles left when they munched on 11 ginger leaves many millions of years ago. The chew marks of the newly described Cephaloleichnites strongi prove that leaf beetles underwent rapid evolution and diversification more than 65 million years ago, possibly taking advantage of (and perhaps influencing) the rapid diversification among flowering plants occurring at the same time. What's more, C. strongi represents the earliest known rolled-leaf beetle species, hundreds of which today still prefer just one of the ginger- and heliconia-like plants in the Zingiberales order.

  17. The salivary gland transcriptome of the neotropical malaria vector Anopheles darlingi reveals accelerated evolution of genes relevant to hematophagy

    PubMed Central

    Calvo, Eric; Pham, Van M; Marinotti, Osvaldo; Andersen, John F; Ribeiro, José MC

    2009-01-01

    Background Mosquito saliva, consisting of a mixture of dozens of proteins affecting vertebrate hemostasis and having sugar digestive and antimicrobial properties, helps both blood and sugar meal feeding. Culicine and anopheline mosquitoes diverged ~150 MYA, and within the anophelines, the New World species diverged from those of the Old World ~95 MYA. While the sialotranscriptome (from the Greek sialo, saliva) of several species of the Cellia subgenus of Anopheles has been described thoroughly, no detailed analysis of any New World anopheline has been done to date. Here we present and analyze data from a comprehensive salivary gland (SG) transcriptome of the neotropical malaria vector Anopheles darlingi (subgenus Nyssorhynchus). Results A total of 2,371 clones randomly selected from an adult female An. darlingi SG cDNA library were sequenced and used to assemble a database that yielded 966 clusters of related sequences, 739 of which were singletons. Primer extension experiments were performed in selected clones to further extend sequence coverage, allowing for the identification of 183 protein sequences, 114 of which code for putative secreted proteins. Conclusion Comparative analysis of sialotranscriptomes of An. darlingi and An. gambiae reveals significant divergence of salivary proteins. On average, salivary proteins are only 53% identical, while housekeeping proteins are 86% identical between the two species. Furthermore, An. darlingi proteins were found that match culicine but not anopheline proteins, indicating loss or rapid evolution of these proteins in the old world Cellia subgenus. On the other hand, several well represented salivary protein families in old world anophelines are not expressed in An. darlingi. PMID:19178717

  18. Ancient Egyptian Astronomical Calander

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

  19. Reconstructing an Ancient Wonder.

    ERIC Educational Resources Information Center

    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)

  20. Endocrinology in ancient Sparta.

    PubMed

    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.

  1. Archaeology Informs Our Understanding of Ancient Texts.

    ERIC Educational Resources Information Center

    Mull, Kenneth V.

    1990-01-01

    Recognizes the importance and utility of archaeology for understanding ancient texts and revealing how they illuminate biblical meaning and history. Presents guidelines showing classroom teachers how to incorporate archaeological knowledge into their lessons. Describes current Middle Eastern excavation sites, using Jerusalem as a case study.…

  2. Tapping Ancient Roots: Plaited Paper Baskets

    ERIC Educational Resources Information Center

    Patrick, Jane

    2011-01-01

    With ancient roots, basket making has been practiced since the earliest civilizations, and according to textile experts, probably pre-dates pottery. This is partly conjecture since few baskets remain. It is through evidence found in clay impressions that the earliest baskets reveal themselves. Basically, basketry construction is like flat weaving.…

  3. Pectus excavatum in mummies from ancient Egypt.

    PubMed

    Kwiecinski, Jakub

    2016-12-01

    Pectus excavatum is one of the common congenital anomalies, yet there seems to be a suspicious absence of any cases or descriptions of this deformity from antiquity. This could represent a real change in disease prevalence but is more likely just due to an inadequate reporting in medico-historical literature. The current study reviews reports of computed tomography (CT) scans of 217 ancient Egyptian mummies, revealing 3 presumed cases of this deformity. Therefore, pectus excavatum was in fact present already in ancient times, with prevalence roughly similar to the modern one.

  4. Discovering the Ancient Maya From Space

    NASA Technical Reports Server (NTRS)

    Sever, T. L.

    2007-01-01

    The Peten region of northern Guatemala contains some of the most significant Mayan archeological sites in Latin America. It was in this region that the Maya civilization began, flourished, and abruptly disappeared. Remote sensing technology is helping to locate and map ancient Maya sites that are threatened today by accelerating deforestation and looting. Thematic Mapper, IKONOS, and QuickBird satellite, and airborne STAR-3i and AIRSAR radar data, combined with Global Positioning System (GPS) technology, are successfully detecting ancient Maya features such as sites, roadways, canals, and water reservoirs. Satellite imagery is also being used to map the bajos, which are seasonally flooded swamps that cover over 40% of the land surface. Through the use of various airborne and satellite sensor systems we have been able to detect and map ancient causeways, temples, reservoirs, and land forms, and locate these features on the ground through GPS technology. Recently, we have discovered that there is a strong relationship between a tropical forest vegetation signature in satellite imagery and the location of archeological sites. We believe that the use o f limestone and lime plasters in ancient Maya construction affects the moisture, nutrition, and plant species of the surface vegetation. We have mapped these vegetation signatures in the imagery and verified through field survey that they are indicative of archeological sites. Through the use of remote sensing and GIS technology it is possible to identify unrecorded archeological features in a dense tropical forest environment and monitor these cultural features for their protection.

  5. Discovering the Ancient Maya from Space

    NASA Technical Reports Server (NTRS)

    Sever, T. L.

    2008-01-01

    The Pet6n region of northern Guatemala contains some of the most significant Mayan archeological sites in Latin America. It was in this region that the Maya civilization began, flourished, and abruptly disappeared. Remote sensing technology is helping to locate and map ancient Maya sites that are threatened today by accelerating deforestation and looting. Thematic Mapper, IKONOS, and QuickBird satellite, and airborne STAR-3i and AIRSAR radar data, combined with Global Positioning System (GPS) technology, are successfully detecting ancient Maya features such as sites, roadways, canals, and water reservoirs. Satellite imagery is also being used to map the bajos, which are seasonally flooded swamps that cover over 40% of the land surface. Through the use of various airborne and satellite sensor systems we have been able to detect and map ancient causeways, temples, reservoirs, and land forms, and locate these features on the ground through GPS technology. Recently, we have discovered that there is a strong relationship between a tropical forest vegetation signature in satellite imagery and the location of archeological sites. We believe that the use of limestone and lime plasters in ancient Maya construction affects the moisture, nutrition, and plant species of the surface vegetation. We have mapped these vegetation signatures in the imagery and verified through field survey that they are indicative of archeological sites. Through the use of remote sensing and GIS technology it is possible to identify unrecorded archeological features in a dense tropical forest environment and monitor these cultural features for their protection.

  6. Dwarfs in ancient Egypt.

    PubMed

    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.

  7. Identification of ancient remains through genomic sequencing

    PubMed Central

    Blow, Matthew J.; Zhang, Tao; Woyke, Tanja; Speller, Camilla F.; Krivoshapkin, Andrei; Yang, Dongya Y.; Derevianko, Anatoly; Rubin, Edward M.

    2008-01-01

    Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla. PMID:18426903

  8. [Psychiatry in ancient Mexico].

    PubMed

    Calderón Narváez, G

    1992-12-01

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

  9. Ancient Egypt: Personal Perspectives.

    ERIC Educational Resources Information Center

    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…

  10. Creative Ventures: Ancient Civilizations.

    ERIC Educational Resources Information Center

    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…

  11. Ancient Egypt: History 380.

    ERIC Educational Resources Information Center

    Turk, Laraine D.

    "Ancient Egypt," an upper-division, non-required history course covering Egypt from pre-dynastic time through the Roman domination is described. General descriptive information is presented first, including the method of grading, expectation of student success rate, long-range course objectives, procedures for revising the course, major…

  12. Ancient deforestation revisited.

    PubMed

    Hughes, J Donald

    2011-01-01

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

  13. Printing Ancient Terracotta Warriors

    ERIC Educational Resources Information Center

    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…

  14. [Midwifes in ancient Greece].

    PubMed

    Arata, Luigi

    2009-01-01

    The article deals with the evidence about obstetrics and in particular midwifes in ancient Greece. The substantives which mean "obstetrician" in Greek are quite numerous, but the most attested and common is [see text]. This work examines all the tasks which were connected with this profession (e.g. in the legal field).

  15. Linear Accelerators

    NASA Astrophysics Data System (ADS)

    Sidorin, Anatoly

    2010-01-01

    In linear accelerators the particles are accelerated by either electrostatic fields or oscillating Radio Frequency (RF) fields. Accordingly the linear accelerators are divided in three large groups: electrostatic, induction and RF accelerators. Overview of the different types of accelerators is given. Stability of longitudinal and transverse motion in the RF linear accelerators is briefly discussed. The methods of beam focusing in linacs are described.

  16. Ancient Sedimentary Rocks

    NASA Technical Reports Server (NTRS)

    2003-01-01

    MGS MOC Release No. MOC2-469, 31 August 2003

    The terraced area in this Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image is an outcropping of ancient, sedimentary rock. It occurs in a crater in western Arabia Terra near 10.8oN, 4.5oW. Sedimentary rocks provide a record of past environments on Mars. Field work will likely be required to begin to get a good understanding of the nature of the record these rocks contain. Their generally uniform thickness and repeated character suggests that deposition of fine sediment in this crater was episodic, if not cyclic. These rocks might be indicators of an ancient lake, or they might have been deposited from grains settling out of an earlier, thicker, martian atmosphere. This image covers an area 3 km (1.9 mi) across and is illuminated from the lower left.

  17. Ancient human microbiomes

    PubMed Central

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

    2015-01-01

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

  18. Ancient human microbiomes.

    PubMed

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

    2015-02-01

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

  19. No rheumatoid arthritis in ancient Egypt: a reappraisal.

    PubMed

    Kwiecinski, Jakub; Rothschild, Bruce M

    2016-06-01

    Antiquity of rheumatoid arthritis (RA) remains controversial, and its origins in Americas or in the Old World are disputed. Proponents of the latter frequently refer to RA in ancient Egypt, but validity of those claims has never been examined. Review of all reported RA cases from ancient Egypt revealed that none of them represent real RA, instead being either examples of changing naming conventions or of imprecise diagnostic criteria. Most cases represented osteoarthritis or spondyloarthropathies. Also review of preserved ancient Egyptian medical writings revealed many descriptions of musculoskeletal disorders, but none of them resembled RA. This suggests that RA was absent in ancient Egypt and supports the hypothesis of the New World origin of RA and its subsequent global spread in the last several centuries.

  20. Case report 872. "Ancient" schwannoma (degenerated neurilemoma).

    PubMed

    Schultz, E; Sapan, M R; McHeffey-Atkinson, B; Naidich, J B; Arlen, M

    1994-10-01

    A case of an ancient schwannoma was presented. The rare occurrence of this tumor has resulted in only a few reported cases with descriptions of its features on imaging. Our patient's tumor, like one previously reported case, demonstrated calcification on the plain film - a finding not associated with other histologic types of schwannomas. Angiography revealed the tumor to be hypervascular. Evaluation by MRI demonstrated a lobulated, encapsulated soft tissue mass containing several cystic areas that corresponded histologically to areas of necrosis. Hypertrophied blood vessels were seen in the periphery of the tumoral mass. Too few ancient schwannomas have been reported to conclude whether or not radiographic evidence of soft tissue calcification is characteristic of this histologically distinctive subtype of schwannoma. However, since calcification is seen histologically as part of the degenerating process, its presence on plain films could be a feature of this tumor. Furthermore, the presence of cystic areas on MRI is not surprising given the pathological changes that occur in this tumor. We suggest that a diagnosis of ancient schwannoma be considered when a patient presents with a hypervascular soft tissue mass containing amorphous calcification on plain films and cystic areas on MRI. Despite the nonspecificity of these imaging findings, this point is relevant because each of these features suggests the presence of a malignant mass. Awareness of the possibility of a benign ancient schwannoma could obviate unnecessary radical surgery.

  1. Genomic correlates of atherosclerosis in ancient humans.

    PubMed

    Zink, Albert; Wann, L Samuel; Thompson, Randall C; Keller, Andreas; Maixner, Frank; Allam, Adel H; Finch, Caleb E; Frohlich, Bruno; Kaplan, Hillard; Lombardi, Guido P; Sutherland, M Linda; Sutherland, James D; Watson, Lucia; Cox, Samantha L; Miyamoto, Michael I; Narula, Jagat; Stewart, Alexandre F R; Thomas, Gregory S; Krause, Johannes

    2014-06-01

    Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world.

  2. Suicide in ancient Greece.

    PubMed

    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. Can Accelerators Accelerate Learning?

    NASA Astrophysics Data System (ADS)

    Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.

    2009-03-01

    The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ) [1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

  4. PARTICLE ACCELERATOR

    DOEpatents

    Teng, L.C.

    1960-01-19

    ABS>A combination of two accelerators, a cyclotron and a ring-shaped accelerator which has a portion disposed tangentially to the cyclotron, is described. Means are provided to transfer particles from the cyclotron to the ring accelerator including a magnetic deflector within the cyclotron, a magnetic shield between the ring accelerator and the cyclotron, and a magnetic inflector within the ring accelerator.

  5. Hsp90 inhibition accelerates cell lysis. Anti-Hsp90 ribozyme reveals a complex mechanism of Hsp90 inhibitors involving both superoxide- and Hsp90-dependent events.

    PubMed

    Sreedhar, Amere Subbarao; Mihály, Katalin; Pató, Bálint; Schnaider, Tamás; Steták, Attila; Kis-Petik, Katalin; Fidy, Judit; Simonics, Tibor; Maraz, Anna; Csermely, Péter

    2003-09-12

    The 90 kDa heat shock protein, Hsp90, is an abundant molecular chaperone participating in the cytoprotection of eukaryotic cells. Here we analyzed the involvement of Hsp90 in the maintenance of cellular integrity using partial cell lysis as a measure. Inhibition of Hsp90 by geldanamycin, radicicol, cisplatin, and novobiocin induced a significant acceleration of detergent- and hypotonic shock-induced cell lysis. The concentration and time dependence of cell lysis acceleration was in agreement with the Hsp90 inhibition characteristics of the N-terminal inhibitors, geldanamycin and radicicol. Glutathione and other reducing agents partially blocked geldanamycin-induced acceleration of cell lysis but were largely ineffective with other inhibitors. Indeed, geldanamycin treatment led to superoxide production and a change in membrane fluidity. When Hsp90 content was diminished using anti-Hsp90 hammerhead ribozymes, an accelerated cell lysis was also observed. Hsp90 inhibition-induced cell lysis was more pronounced in eukaryotic (yeast, mouse red blood, and human T-lymphoma) cells than in bacteria. Our results indicate that besides the geldanamycin-induced superoxide production, and a consequent increase in cell lysis, inhibition or lack of Hsp90 alone can also compromise cellular integrity. Moreover, cell lysis after hypoxia and complement attack was also enhanced by any type of Hsp90 inhibition used, which shows that the maintenance of cellular integrity by Hsp90 is important in physiologically relevant lytic conditions of tumor cells.

  6. Infectious diseases in ancient Egypt.

    PubMed

    Brier, Bob

    2004-03-01

    Techniques for studying infectious disease in the ancient world are discussed. A brief survey of infectious diseases, such as schistosomiasis and malaria, in ancient Egypt is presented, and the physical traces of these diseases are examined. A discussion of the ancient Egyptian physician's response to infectious disease is included. There are two substantial sources of evidence for infectious diseases-physical remains and descriptions in Egyptian medical papyri. This preliminary survey suggests that ancient Egypt was far from the idyllic paradise on the Nile that some historians would like to imagine.

  7. Gnomons in Ancient China

    NASA Astrophysics Data System (ADS)

    Li, Geng

    Gnomon shadow measurement was one of the most fundamental astronomical observations in ancient China. It was crucial for calendar making, which constituted an important aspect of imperial governance. A painted stick discovered from a prehistoric (2300 BC) astronomical site of Taosi (see Chap. 201, "Taosi Observatory", 10.1007/978-1-4614-6141-8_215") is the oldest gnomon known of China. From second century BC onward, gnomon shadow measurements have been essential part of calendrical practice. Various historical measurements are discussed in this chapter.

  8. Tracheostomy in ancient Egypt.

    PubMed

    Blomstedt, Patric

    2014-08-01

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

  9. Urology in ancient India

    PubMed Central

    Das, Sakti

    2007-01-01

    The practice of medical and surgical measures in the management of urological ailments prevailed in ancient India from the Vedic era around 3000 BC. Subsequently in the Samhita period, the two stalwarts - Charaka in medicine and Susruta in surgery elevated the art of medicine in India to unprecedented heights. Their elaboration of the etiopathological hypothesis and the medical and surgical treatments of various urological disorders of unparalleled ingenuity still remain valid to some extent in our contemporary understanding. The new generation of accomplished Indian urologists should humbly venerate the legacy of the illustrious pioneers in urology of our motherland. PMID:19675749

  10. Ancient and Medieval Cosmology in Armenian Highland

    NASA Astrophysics Data System (ADS)

    Farmanyan, Sona V.; Mickaelian, Areg M.

    2016-12-01

    Humankind has always sought to recognize the nature of various sky related phenomena and tried to give them explanations. It is especially vivid in ancient cultures, many of which are related to the Middle East. The purpose of this study is to identify ancient Armenian's pantheistic and cosmological perceptions, world view, notions and beliefs. By this study we answer the question "How did the Universe work in Ancient Armenian Highland?" The paper focuses on the structure of the Universe and many phenomena of nature that have always had major influence on ancient Armenians thinking. Here we weave together astronomy, anthropology and mythology of Armenia, and scientific thinking revealed in local astronomy traditions. The initial review of the study covers Moses of Khoren, Yeznik of Koghb, Anania Shirakatsi and other 5th-7th centuries historians' and scientists' records about the Universe related superstitious beliefs and cosmological understanding. By discussing and comparing Universe structure in various regional traditions, myths, folk songs and phraseological units we very often came across "seven worlds", "seven earths" and "seven layers" concepts. We draw parallels between scientific and mythological Earth and Heaven and thus find similar number of layers on both of the ancient and modern thinking. In the article we also give some details about the tripartite structure of the Universe and how these parts are connected with axis. This axis is either a column or a Cosmic Tree (Kenatz Tsar). In Armenian culture the preliminary meanings of the Kenatz Tsar are more vivid in folk songs (Jan gyulums), plays, epic, and so on, which was subsequently mixed with religious and spiritual views. We conclude that the perception of the Universe structure and celestial objects had a significant impact on culture and worldview of the people of the Armenian Highland; particularly it was one of the bases of the regional cultural diversity.

  11. Ancient and modern environmental DNA.

    PubMed

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

    2015-01-19

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

  12. Ancient and modern environmental DNA

    PubMed Central

    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

  13. Epigenetics of Ancient DNA

    PubMed Central

    Zhenilo, S. V.; Sokolov, A.S.; Prokhortchouk, E. B.

    2016-01-01

    Initially, the study of DNA isolated from ancient specimens had been based on the analysis of the primary nucleotide sequence. This approach has allowed researchers to study the evolutionary changes that occur in different populations and determine the influence of the environment on genetic selection. However, the improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression. It was discovered recently that the methylation status of the regulatory elements of the HOXD cluster and MEIS1 gene changed during human evolution. Epigenetic changes in these genes played a key role in the evolution of the limbs of modern humans. Recent works have demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes. In the nearest future, if a preserved fossils brain is found, it will be possible to identify the evolutionary changes in the higher nervous system associated with epigenetic differences. PMID:27795845

  14. Ancient celtic horns

    NASA Astrophysics Data System (ADS)

    Campbell, Murray

    2002-11-01

    There is considerable evidence from iconographic and documentary sources that musical lip-reed instruments were important in the early celtic communities of Scotland and Ireland. In recent years several studies have been undertaken with the aim of gaining a better understanding of the musical nature of these ancient horns, and of their place in the life and culture of the time. A valuable source of tangible evidence is to be found in the archaeological remains deposited across Scotland and the whole of Ireland. A project is now under way, under the auspices of the Kilmartin House Trust and the general direction of John Purser, which has brought together an international team of musicians, craftsmen, archaeologists, musicologists and physicists with the aim of analyzing ancient musical artifacts, reconstructing some of the original instruments, and analyzing the sounds they produce. This paper describes acoustical studies carried out on a number of recent reconstructions of wooden and bronze instruments, and discusses the role of acoustics in this type of investigation. [Work supported by Sciart and EPSRC.

  15. Communication Media in Ancient Cultures.

    ERIC Educational Resources Information Center

    Jabusch, David M.

    Interest in early means of communication and in the uses and kinds of media that existed in ancient cultures is starting to grow among communication scholars. Conversation analysis of these cultures is obviously impossible, so that the emphasis must rest with material cultural artifacts. Many ancient cultures used non-verbal codes for dyadic…

  16. The Ancients' Appliance of Science

    ERIC Educational Resources Information Center

    Stephenson, Philip; Sword, Frances

    2004-01-01

    An innovative collaboration between the Fitzwilliam Museum in Cambridge and the University of Cambridge Faculty of Education encourages new questions to be asked of ancient objects. In the museum galleries children work directly from ancient Egyptian objects through activities designed to encourage questioning that unpicks the technologies of the…

  17. Tamil merchant in ancient Mesopotamia.

    PubMed

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

    2014-01-01

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

  18. Ancient Chinese Sundials

    NASA Astrophysics Data System (ADS)

    Deng, Kehui

    Timekeeping was essential in the agricultural society of ancient China. The use of sundials for timekeeping was associated with the use of the gnomon, which had its origin in remote antiquity. This chapter studies three sundials (guiyi 晷仪) from the Qin and Han dynasties, the shorter shadow plane sundial (duanying ping yi 短影平仪) invented by Yuan Chong in the Sui Dynasty, and the sundial chart (guiyingtu 晷影图) invented by Zeng Minxing in the Southern Song dynasty. This chapter also introduces Guo Shoujing's hemispherical sundial (yang yi 仰仪). A circular stone sundial discovered at the Small Wild Goose Pagoda in Xi'an is also mentioned. It is dated from the Sui and Tang dynasties. A brief survey of sundials from the Qing dynasty shows various types of sundials.

  19. Speciation in ancient lakes.

    PubMed

    Martens, K

    1997-05-01

    About a dozen lakes in the world are up to three orders of magnitude older than most others. Lakes Tanganyika (East Africa) and Baikal (Siberia) have probably existed in some form for 12-20 million years, maybe more. Such lakes can have different origins, sizes, shapes, depths and limnologies, but, in contrast to short-lived (mostly post-glacial) lakes, they have exceptionally high faunal diversity and levels of endemicity. A multitude of and processes accounting for these explosive radiations have recently been documented, most of them based on particular groups in certain lakes, but comparative research can detect repeated patterns. No special speciafion mechanism, exclusive to ancient lakes has been demonstrated, although cases of ultra-rapid speciation have been documented. Extant diversity results not by simple accumulation, but by a complex process of immigration, speciation and extinction.

  20. Reanimation of Ancient Bacteria

    SciTech Connect

    Vreeland, Russell H.

    2009-01-09

    Recent highly publicized experiments conducted on salt crystals taken from the Permian Salado Formation in Southeastern New Mexico have shown that some ancient crystals contain viable microorganisms trapped within fluid inclusions. Stringent geological and microbiological selection criteria were used to select crystals and conduct all sampling. This talk will focus on how each of these lines of data support the conclusion that such isolated bacteria are as old as the rock in which they are trapped. In this case, the isolated microbes are salt tolerant bacilli that grow best in media containing 8% NaCl, and respond to concentrated brines by forming spores. One of the organisms is phylogenetically related to several bacilli, but does have several unique characteristics. This talk will trace the interdisciplinary data and procedures supporting these discoveries, and describe the various isolated bacteria.

  1. Reanimation of Ancient Bacteria

    SciTech Connect

    Vreeland, Russell H.

    2002-01-09

    Recent highly publicized experiments conducted on salt crystals taken from the Permian Salado Formation in Southeastern New Mexico have shown that some ancient crystals contain viable microorganisms trapped within fluid inclusions. Stringent geological and microbiological selection criteria were used to select crystals and conduct all sampling. This talk will focus on how each of these lines of data support the conclusion that such isolated bacteria are as old as the rock in which they are trapped. In this case, the isolated microbes are salt tolerant bacilli that grow best in media containing 8% NaCl, and respond to concentrated brines by forming spores. One of the organisms is phylogenetically related to several bacilli, but does have several unique characteristics. This talk will trace the interdisciplinary data and procedures supporting these discoveries, and describe the various isolated bacteria.

  2. Characterization of Ancient Tripitaka

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  3. Senenmut: An Ancient Egyptian Astronomer

    NASA Astrophysics Data System (ADS)

    Novakovic, B.

    2008-10-01

    The celestial phenomena have always been a source of wonder and interest to people, even as long ago as the ancient Egyptians. While the ancient Egyptians did not know all the things about astronomy that we do now, they had a good understanding of some celestial phenomena. The achievements in astronomy of ancient Egyptians are relatively well known, but we know very little about the people who made these achievements. The goal of this paper is to bring some light on the life of Senenmut, the chief architect and astronomer during the reign of Queen Hatshepsut.

  4. Ancient Astronomy in Ukraine

    NASA Astrophysics Data System (ADS)

    Artemenko, Tatyana G.; Vavilova, Iryna B.

    2007-08-01

    Astronomical culture and research have long-standing traditions in Ukraine. The first signs of astronomical knowledge were found in archaeological excavations and records. The most ancient find (dated as 15,000 B.C.) is a mammoth tusk with a fretwork image of a table of lunar phases found in the Poltava region. The so-called Trypillya culture (dated 4,000 - 3,000 B.C) had numerous examples of ornaments at the howls, distaffs, wheels and other everyday articles with symbolic images of zodiac constellations, and vessel-calendars indicating the vernal/autumnal equinoxes and the motion of the Sun. Some of such unique exhibits stored at the National Museum of History of Ukraine will be described in details in this paper. For example, the vessel calendar dating by IV century of our era (from village Romashki, Kyiv region). This image was interpreted by B. Rybakov as an agricultural calendar from May to August (time of harvesting). Most of exhibits of Museum were founded by archaeologist Vikenty Khvoyko and presented by him to Museum in 1905. Description and pictures of vessels and cups from Chernyahiv, Trypillya IV century B.C. with the Solar signs and tusk of the mammoth from Kyrilovska parking with notches interpreted as a calendar as well as tree-storied pictures of vessel from Trypillya interpreted as a “vertical cross section of the world” in dynamics will be also given. Another unique historical record relates to the times of the powerful state of the Kievan Rus' (X- XIII centuries), when astronomical observations were conducted mainly in cloisters. For example, the authors of the Lavrentievska chronicle describe the solar eclipses of the years 1064, 1091, and 1115 A.D. and the lunar eclipses of 1161 A.D. At that times some natural cataclysms have been connected with eclipses that, for example, was described in “The Word about Igor's shelf” by Nestor Letopisec. Thus, facts discussed in paper pointed out once more that astronomy is one of the most ancient

  5. Research on the Ancient Mongolian Place-Name Along the Silk Road

    NASA Astrophysics Data System (ADS)

    Nashunwuritu; Baiyinbateer; Duoxi

    2016-06-01

    "Silk Road" is an ancient commercial trade channel connecting China with Asia, Africa and Europe and a major link of the economy, politics and culture of the East and West as well. In the 13th Century, with the westward expedition of Mongolian, the communication and integration of culture among different countries was accelerated, which led to many Mongolian place-names scattered in the countries along the silk-road, such as Khwarezmia, Armenia, Mesopotamia, Kipchak, Persian, involving today's Russia, Poland, Ukraine, Bulgaria, Hungary, Austria, Italy, Serbia, Syria, Iran, Afghanistan, Iraq, Uzbekistan, Turkmenistan, India and many other countries and regions. The place-name is a kind of important factor that can represent the changes of culture, economic in history. We analyzed the current place-names in different countries or regions with different language to find out ancient Mongolian place-names, and marked the names on the digital map. Through the changes and transition of the place-name, we explored the development of Mongolian language changes itself, Mongolian blends with other languages, and furtherly reveal information of culture exchange.

  6. Astronomical Significance of Ancient Monuments

    NASA Astrophysics Data System (ADS)

    Simonia, I.

    2011-06-01

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

  7. Ancient Astronomical Monuments of Athens

    NASA Astrophysics Data System (ADS)

    Theodossiou, E.; Manimanis, V. N.

    2010-07-01

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

  8. Layout of Ancient Maya Cities

    NASA Astrophysics Data System (ADS)

    Aylesworth, Grant R.

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

  9. Ancient Astronomers Along the Nile.

    ERIC Educational Resources Information Center

    Reed, George

    1986-01-01

    Discussed contributions to the field of astronomy made by ancient Egyptians. Provides examples of how some of the observations made were applied to science. The use of geometry is illustrated by several calculations of celestial alignment. (TW)

  10. Future accelerators (?)

    SciTech Connect

    John Womersley

    2003-08-21

    I describe the future accelerator facilities that are currently foreseen for electroweak scale physics, neutrino physics, and nuclear structure. I will explore the physics justification for these machines, and suggest how the case for future accelerators can be made.

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

    PubMed

    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.

  12. Hippocrates, Galen, and the uses of trepanation in the ancient classical world.

    PubMed

    Missios, Symeon

    2007-01-01

    Trepanation is the process by which a hole is drilled into the skull, exposing the intracranial contents for either medical or mystical purposes. It represents one of the oldest surgical procedures, and its practice was widespread in many ancient cultures and several parts of the world. Trepanation was used in ancient Greece and Rome, as described in several ancient texts. Hippocrates and Galen are two of the most prominent ancient Greek medical writers, and their works have influenced the evolution of medicine and neurosurgery across the centuries. The purpose of this paper is to examine Hippocrates' and Galen's written accounts of the technique and use of trepanation in the ancient Greek and Roman world. Examination of those records reveals the ancient knowledge of neurological anatomy, physiology, and therapeutics, and illustrates the state and evolution of neurosurgery in the classical world.

  13. Vascular plants promote ancient peatland carbon loss with climate warming.

    PubMed

    Walker, Tom N; Garnett, Mark H; Ward, Susan E; Oakley, Simon; Bardgett, Richard D; Ostle, Nicholas J

    2016-05-01

    Northern peatlands have accumulated one third of the Earth's soil carbon stock since the last Ice Age. Rapid warming across northern biomes threatens to accelerate rates of peatland ecosystem respiration. Despite compensatory increases in net primary production, greater ecosystem respiration could signal the release of ancient, century- to millennia-old carbon from the peatland organic matter stock. Warming has already been shown to promote ancient peatland carbon release, but, despite the key role of vegetation in carbon dynamics, little is known about how plants influence the source of peatland ecosystem respiration. Here, we address this issue using in situ (14)C measurements of ecosystem respiration on an established peatland warming and vegetation manipulation experiment. Results show that warming of approximately 1 °C promotes respiration of ancient peatland carbon (up to 2100 years old) when dwarf-shrubs or graminoids are present, an effect not observed when only bryophytes are present. We demonstrate that warming likely promotes ancient peatland carbon release via its control over organic inputs from vascular plants. Our findings suggest that dwarf-shrubs and graminoids prime microbial decomposition of previously 'locked-up' organic matter from potentially deep in the peat profile, facilitating liberation of ancient carbon as CO2. Furthermore, such plant-induced peat respiration could contribute up to 40% of ecosystem CO2 emissions. If consistent across other subarctic and arctic ecosystems, this represents a considerable fraction of ecosystem respiration that is currently not acknowledged by global carbon cycle models. Ultimately, greater contribution of ancient carbon to ecosystem respiration may signal the loss of a previously stable peatland carbon pool, creating potential feedbacks to future climate change.

  14. Neonatal medicine in ancient art.

    PubMed

    Yurdakök, Murat

    2010-01-01

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

  15. Ancient "Observatories" - A Relevant Concept?

    NASA Astrophysics Data System (ADS)

    Belmonte, Juan Antonio

    It is quite common, when reading popular books on astronomy, to see a place referred to as "the oldest observatory in the world". In addition, numerous books on archaeoastronomy, of various levels of quality, frequently refer to the existence of "prehistoric" or "ancient" observatories when describing or citing monuments that were certainly not built with the primary purpose of observing the skies. Internet sources are also guilty of this practice. In this chapter, the different meanings of the word observatory will be analyzed, looking at how their significances can be easily confused or even interchanged. The proclaimed "ancient observatories" are a typical result of this situation. Finally, the relevance of the concept of the ancient observatory will be evaluated.

  16. Improving ancient DNA genome assembly

    PubMed Central

    Nieselt, Kay

    2017-01-01

    Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions. PMID:28392981

  17. Ancient suture zones within continents.

    PubMed

    Moores, E M

    1981-07-03

    Ancient suture belts within continents are deformed regions which contain the remnants of former ocean basins. They form when two continents or island arcs that earlier were separated by an ocean basin converge and collide during plate tectonic activity. These belts provide the only record we have of deep oceanic crust and of ancient sea-floor processes for the first 94 percent of the earth's history, that is, prior to the oldest preserved crust in the oceans. Ten criteria for the recognition and interpretation of these ancient belts are discussed. A comprehensive program for the study of these belts should have great scientific and economic benefit for the United States and would be relatively cheap compared to other large national scientific efforts.

  18. Night Blindness and Ancient Remedy

    PubMed Central

    Al Binali, H.A. Hajar

    2014-01-01

    The aim of this article is to briefly review the history of night blindness and its treatment from ancient times until the present. The old Egyptians, the Babylonians, the Greeks and the Arabs used animal liver for treatment and successfully cured the disease. The author had the opportunity to observe the application of the old remedy to a patient. Now we know what the ancients did not know, that night blindness is caused by Vitamin A deficiency and the animal liver is the store house for Vitamin A. PMID:25774260

  19. Assessing the maximum contribution from ancient populations.

    PubMed

    Sjödin, Per; Skoglund, Pontus; Jakobsson, Mattias

    2014-05-01

    Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).

  20. Mapping The Ancient Maya Landscape From Space

    NASA Technical Reports Server (NTRS)

    Sever, Tom; Arnold, James E. (Technical Monitor)

    2002-01-01

    The Peten region of northern Guatemala is one of the last places on earth where major archeological sites remain to be discovered. It was in this region that the Maya civilization began, flourished, and abruptly disappeared. Remote sensing technology is helping to locate and map ancient Maya sites that are threatened today by accelerating deforestation and looting. Thematic Mapper and IKONOS satellite and airborne Star3-I radar data, combined with Global Positioning System (GPS) technology, are successfully detecting ancient Maya features such as cities, roadways, canals, and water reservoirs. Satellite imagery is also being used to map the bajos, which are seasonally flooded swamps that cover over 40% of the land surface. The use of bajos for farming has been a source of debate within the professional community for many years. But the recent detection and verification of cultural features within the bajo system by our research team are providing conclusive evidence that the ancient Maya had adapted well to wetland environments from the earliest times and utilized them until the time of the Maya collapse. The use of the bajos for farming is also an important resource for the future of the current inhabitants who are experiencing rapid population growth. Remote sensing imagery is also demonstrating that in the Preclassic period (600 BC- AD 250), the Maya had already achieved a high organizational level as evidenced by the construction of massive temples and an elaborate inter-connecting roadway system. Although they experienced several setbacks such as droughts and hurricanes, the Maya nevertheless managed the delicate forest ecosystem successfully for several centuries. However, around AD 800, something happened to the Maya to cause their rapid decline and eventual disappearance from the region. The evidence indicates that at this time there was increased climatic dryness, extensive deforestation, overpopulation, and widespread warfare. This raises a question that

  1. Astronomical Deities in Ancient Mesoamerica

    NASA Astrophysics Data System (ADS)

    Milbrath, Susan

    The best known astronomical deities in ancient Mesoamerica are the sun, moon, and Venus. The Milky Way was also deified, and its constellations were visualized as celestial animals or locations. The sun and Venus were male deities, but the moon had both male and female aspects. Some of these concepts survive today in Mesoamerican ethnographic accounts referencing different transformations of the moon.

  2. The ancient name of rose.

    PubMed

    Dalby, A

    2001-01-01

    The article is a survey of plants foods and drugs that Greeks and Romans thought to be aphrodisiac and to have a specific effect on the male libido. The article is a useful support to study the sexual therapy in ancient world.

  3. Ancient medicine--a review.

    PubMed

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

    2008-01-01

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

  4. Discovering the Ancient Temperate Rainforest.

    ERIC Educational Resources Information Center

    Lindsay, Anne

    1997-01-01

    Two activities for grades 3 through 8 explore species adaptation and forestry issues in the North American rainforests. In one activity, students create imaginary species of plants or animals that are adapted for life in an ancient temperate rainforest. In the second activity, students role play groups affected by plans to log an area of the…

  5. Drinking habits in ancient India

    PubMed Central

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

    2016-01-01

    Consumption of one or other form of intoxicating substances has been present throughout the history of the world. This article traces such use in the Indian subcontinent, both in North and South India. References to the use of intoxicants are to be found in the Vedas, the Great Epics, and the ancient Tamil literature. PMID:26985113

  6. Drinking habits in ancient India.

    PubMed

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

    2016-01-01

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

  7. The Echoes of Ancient Humans

    ERIC Educational Resources Information Center

    Watzman, Haim

    2006-01-01

    Several artifacts found at the Gesher Benot Ya'aqov, or Daughters of Jacob Bridge, archaeological site in Israel provide a picture of ancient human ancestors that is different from the once accepted by most scholars. The discoveries by Israeli archaeologist Naama Goren-Inbar suggest that humans developed language and other key abilities far…

  8. Ancient and Modern Coins Unit Plans.

    ERIC Educational Resources Information Center

    United States Mint (Dept. of Treasury), Washington, DC.

    Ancient times comes to life when a student can hold in his/her hand or read about an artifact, such as a coin of the Greek or Roman era. Students are familiar with coins, and this commonality helps them understand the similarities and differences between their lives and times in ancient Greece or Rome. Many symbols on the ancient coins can be…

  9. LINEAR ACCELERATOR

    DOEpatents

    Colgate, S.A.

    1958-05-27

    An improvement is presented in linear accelerators for charged particles with respect to the stable focusing of the particle beam. The improvement consists of providing a radial electric field transverse to the accelerating electric fields and angularly introducing the beam of particles in the field. The results of the foregoing is to achieve a beam which spirals about the axis of the acceleration path. The combination of the electric fields and angular motion of the particles cooperate to provide a stable and focused particle beam.

  10. [Microbial communities of ancient seeds derived from permanently frozen Pleistocene deposits].

    PubMed

    Stakhov, V L; Gubin, S V; Maksimovich, S V; Rebrikov, D V; Savilova, A M; Kochkina, G A; Ozerskaia, S M; Ivanushkina, N E; Vorob'eva, E A

    2008-01-01

    Microbial communities from the surface of ancient seeds of higher plants and embedding frozen material dated to the late Pleistocene (formed about 30 thousand years ago) were studied by various methods: scanning electron microscopy, epifluorescence microscopy, and inoculation of nutrient media, followed by identification of isolated cultures. Both prokaryotic and eukaryotic microorganisms were found on the surface of ancient seeds. The total quantity of bacterial cells determined by direct counting and dilution plating (CFU) for the samples of ancient seeds exceeded the value in the embedding frozen material by one to two orders of magnitude. This pattern was not maintained for mycelial fungi; their quantity in the embedding material was also rather high. A significant difference was revealed between the microbial communities of ancient seeds and embedding frozen material. These findings suggest that ancient plant seeds are a particular ecological niche for microorganisms existing in permafrost and require individual detailed study.

  11. Comparing the Dimensions of Modern and Ancient Barrier Island Systems to Understand Controls on Preservation

    NASA Astrophysics Data System (ADS)

    Mulhern, J.; Johnson, C. L.; Stright, L.

    2015-12-01

    supply control resulting deposits when accommodation is sufficient for preservation. Future consideration of other parameters, including tectonic setting, latitude, and climate may reveal paleomorphodynamic relationships between modern and ancient barriers and improve predictions for ancient barrier dimensions.

  12. Acceleration switch

    DOEpatents

    Abbin, Jr., Joseph P.; Devaney, Howard F.; Hake, Lewis W.

    1982-08-17

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  13. Acceleration switch

    DOEpatents

    Abbin, J.P. Jr.; Devaney, H.F.; Hake, L.W.

    1979-08-29

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  14. ION ACCELERATOR

    DOEpatents

    Bell, J.S.

    1959-09-15

    An arrangement for the drift tubes in a linear accelerator is described whereby each drift tube acts to shield the particles from the influence of the accelerating field and focuses the particles passing through the tube. In one embodiment the drift tube is splii longitudinally into quadrants supported along the axis of the accelerator by webs from a yoke, the quadrants. webs, and yoke being of magnetic material. A magnetic focusing action is produced by energizing a winding on each web to set up a magnetic field between adjacent quadrants. In the other embodiment the quadrants are electrically insulated from each other and have opposite polarity voltages on adjacent quadrants to provide an electric focusing fleld for the particles, with the quadrants spaced sufficienily close enough to shield the particles within the tube from the accelerating electric field.

  15. LINEAR ACCELERATOR

    DOEpatents

    Christofilos, N.C.; Polk, I.J.

    1959-02-17

    Improvements in linear particle accelerators are described. A drift tube system for a linear ion accelerator reduces gap capacity between adjacent drift tube ends. This is accomplished by reducing the ratio of the diameter of the drift tube to the diameter of the resonant cavity. Concentration of magnetic field intensity at the longitudinal midpoint of the external sunface of each drift tube is reduced by increasing the external drift tube diameter at the longitudinal center region.

  16. Dreams in ancient Greek Medicine.

    PubMed

    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

  17. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals

    PubMed Central

    2011-01-01

    Background Scleractinian corals are currently a focus of major interest because of their ecological importance and the uncertain fate of coral reefs in the face of increasing anthropogenic pressure. Despite this, remarkably little is known about the evolutionary origins of corals. The Scleractinia suddenly appear in the fossil record about 240 Ma, but the range of morphological variation seen in these Middle Triassic fossils is comparable to that of modern scleractinians, implying much earlier origins that have so far remained elusive. A significant weakness in reconstruction(s) of early coral evolution is that deep-sea corals have been poorly represented in molecular phylogenetic analyses. Results By adding new data from a large and representative range of deep-water species to existing molecular datasets and applying a relaxed molecular clock, we show that two exclusively deep-sea families, the Gardineriidae and Micrabaciidae, diverged prior to the Complexa/Robusta coral split around 425 Ma, thereby pushing the evolutionary origin of scleractinian corals deep into the Paleozoic. Conclusions The early divergence and distinctive morphologies of the extant gardineriid and micrabaciid corals suggest a link with Ordovician "scleractiniamorph" fossils that were previously assumed to represent extinct anthozoan skeletonized lineages. Therefore, scleractinian corals most likely evolved from Paleozoic soft-bodied ancestors. Modern shallow-water Scleractinia, which are dependent on symbionts, appear to have had several independent origins from solitary, non-symbiotic precursors. The Scleractinia have survived periods of massive climate change in the past, suggesting that as a lineage they may be less vulnerable to future changes than often assumed. PMID:22034946

  18. Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase

    PubMed Central

    Dean, Antony M.; Golding, G. Brian

    1997-01-01

    Evolutionary analysis indicates that eubacterial NADP-dependent isocitrate dehydrogenases (EC 1.1.1.42) first evolved from an NAD-dependent precursor about 3.5 billion years ago. Selection in favor of utilizing NADP was probably a result of niche expansion during growth on acetate, where isocitrate dehydrogenase provides 90% of the NADPH necessary for biosynthesis. Amino acids responsible for differing coenzyme specificities were identified from x-ray crystallographic structures of Escherichia coli isocitrate dehydrogenase and the distantly related Thermus thermophilus NAD-dependent isopropylmalate dehydrogenase. Site-directed mutagenesis at sites lining the coenzyme binding pockets has been used to invert the coenzyme specificities of both enzymes. Reconstructed ancestral sequences indicate that these replacements are ancestral. Hence the adaptive history of molecular evolution is amenable to experimental investigation. PMID:9096353

  19. Genomics reveal ancient forms of stanniocalcin in amphioxus and tunicate.

    PubMed

    Roch, Graeme J; Sherwood, Nancy M

    2010-07-01

    Stanniocalcin (STC) is present throughout vertebrates, including humans, but a structure for STC has not been identified in animals that evolved before bony fish. The origin of this pleiotropic hormone known to regulate calcium is not clear. In the present study, we have cloned three stanniocalcins from two invertebrates, the tunicate Ciona intestinalis and the amphioxus Branchiostoma floridae. Both species are protochordates with the tunicates as the closest living relatives to vertebrates. Amphioxus are basal to both tunicates and vertebrates. The genes and predicted proteins of tunicate and amphioxus share several key structural features found in all previously described homologs. Both the invertebrate and vertebrate genes have four conserved exons. The predicted length of the single pro-STC in Ciona is 237 amino acids and the two pro-hormones in amphioxus are 207 and 210 residues, which is shorter than human pro-STCs at 247 and 302 residues due to expansion of the C-terminal region in vertebrate forms. The conserved pattern of 10 cysteines in all chordate STCs is crucial for identification as amphioxus and tunicate amino acids are only 14-23% identical with human STC1 and STC2. The 11th cysteine, which is the cysteine shown to form a homodimer in vertebrates, is present only in amphioxus STCa, but not in amphioxus STCb or tunicate STC, suggesting the latter two are monomers. The expression of stanniocalcin in Ciona is widespread as shown by RT-PCR and by quantitative PCR. The latter method shows that the highest amount of STC mRNA is in the heart with lower amounts in the neural complex, branchial basket, and endostyle. A widespread distribution is present also in mammals and fish for both STC1 and STC2. Stanniocalcin is a presumptive regulator of calcium in both Ciona and amphioxus, although the structure of a STC receptor remains to be identified in any organism. Our data suggest that amphioxus STCa is most similar to the common ancestor of vertebrate STCs because it has an 11th cysteine necessary for dimerization, an N-glycosylation motif, although not the canonical one in vertebrate STCs, and similar gene organization. Tunicate and amphioxus STCs are more similar in structure to vertebrate STC1 than to vertebrate STC2. The unique features of STC2, including 14 instead of 11 cysteines and a cluster of histidines in the C-terminal region, appear to be found exclusively in vertebrates.

  20. Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton

    PubMed Central

    Sattlegger, Evelyn; Chernova, Tatiana A.; Gogoi, Neeku M.; Pillai, Indu V.; Chernoff, Yury O.; Munn, Alan L.

    2014-01-01

    Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organisation of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes. PMID:25138357

  1. Ancient DNA extraction from plants.

    PubMed

    Kistler, Logan

    2012-01-01

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

  2. Molecular analysis of ancient caries

    PubMed Central

    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

  3. Molecular analysis of ancient caries.

    PubMed

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

    2014-09-07

    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.

  4. Psychiatric Thoughts in Ancient India*

    PubMed Central

    Abhyankar, Ravi

    2015-01-01

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

  5. Nanoscience of an ancient pigment.

    PubMed

    Johnson-McDaniel, Darrah; Barrett, Christopher A; Sharafi, Asma; Salguero, Tina T

    2013-02-06

    We describe monolayer nanosheets of calcium copper tetrasilicate, CaCuSi(4)O(10), which have strong near-IR luminescence and are amenable to solution processing methods. The facile exfoliation of bulk CaCuSi(4)O(10) into nanosheets is especially surprising in view of the long history of this material as the colored component of Egyptian blue, a well-known pigment from ancient times.

  6. Eclipses and Ancient Greek Philosophers

    NASA Astrophysics Data System (ADS)

    Rovithis-Livaniou, H.; Rovithis, P.

    2007-05-01

    Eclipses had attracted the interest of many ancient Greek philosophers, independently where they lived: on the mainland, or in the Greek colonies. In this short review their opinions are presented together with some predicted or registered solar or lunar eclipses. Moreover, the way of prediction as well as some other observations -like occultations by the Moon- are noted. Other findings -like the spherical shape of the Earth, the dimensions and the distances of the Moon and the Sun- are also mentioned.

  7. Dental surgery in ancient Egypt.

    PubMed

    Blomstedt, Patric

    2013-01-01

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

  8. Orthopedic surgery in ancient Egypt

    PubMed Central

    Blomstedt, Patric

    2014-01-01

    Background — Ancient Egypt might be considered the cradle of medicine. The modern literature is, however, sometimes rather too enthusiastic regarding the procedures that are attributed an Egyptian origin. I briefly present and analyze the claims regarding orthopedic surgery in Egypt, what was actually done by the Egyptians, and what may have been incorrectly ascribed to them. Methods — I reviewed the original sources and also the modern literature regarding surgery in ancient Egypt, concentrating especially on orthopedic surgery. Results — As is well known, both literary sources and the archaeological/osteological material bear witness to treatment of various fractures. The Egyptian painting, often claimed to depict the reduction of a dislocated shoulder according to Kocher’s method, is, however, open to interpretation. Therapeutic amputations are never depicted or mentioned in the literary sources, while the specimens suggested to demonstrate such amputations are not convincing. Interpretation — The ancient Egyptians certainly treated fractures of various kinds, and with varying degrees of success. Concerning the reductions of dislocated joints and therapeutic amputations, there is no clear evidence for the existence of such procedures. It would, however, be surprising if dislocations were not treated, even though they have not left traces in the surviving sources. Concerning amputations, the general level of Egyptian surgery makes it unlikely that limb amputations were done, even if they may possibly have been performed under extraordinary circumstances. PMID:25140982

  9. Screening ancient tuberculosis with qPCR: challenges and opportunities

    PubMed Central

    Harkins, Kelly M.; Buikstra, Jane E.; Campbell, Tessa; Bos, Kirsten I.; Johnson, Eric D.; Krause, Johannes; Stone, Anne C.

    2015-01-01

    The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies. PMID:25487341

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

    PubMed

    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.

  11. Acceleration Studies

    NASA Technical Reports Server (NTRS)

    Rogers, Melissa J. B.

    1993-01-01

    Work to support the NASA MSFC Acceleration Characterization and Analysis Project (ACAP) was performed. Four tasks (analysis development, analysis research, analysis documentation, and acceleration analysis) were addressed by parallel projects. Work concentrated on preparation for and implementation of near real-time SAMS data analysis during the USMP-1 mission. User support documents and case specific software documentation and tutorials were developed. Information and results were presented to microgravity users. ACAP computer facilities need to be fully implemented and networked, data resources must be cataloged and accessible, future microgravity missions must be coordinated, and continued Orbiter characterization is necessary.

  12. Functional and RNA-Sequencing Analysis Revealed Expression of a Novel Stay-Green Gene from Zoysia japonica (ZjSGR) Caused Chlorophyll Degradation and Accelerated Senescence in Arabidopsis

    PubMed Central

    Teng, Ke; Chang, Zhihui; Li, Xiao; Sun, Xinbo; Liang, Xiaohong; Xu, Lixin; Chao, Yuehui; Han, Liebao

    2016-01-01

    Senescence is not only an important developmental process, but also a responsive regulation to abiotic and biotic stress for plants. Stay-green protein plays crucial roles in plant senescence and chlorophyll degradation. However, the underlying mechanisms were not well-studied, particularly in non-model plants. In this study, a novel stay-green gene, ZjSGR, was isolated from Zoysia japonica. Subcellular localization result demonstrated that ZjSGR was localized in the chloroplasts. Quantitative real-time PCR results together with promoter activity determination using transgenic Arabidopsis confirmed that ZjSGR could be induced by darkness, ABA and MeJA. Its expression levels could also be up-regulated by natural senescence, but suppressed by SA treatments. Overexpression of ZjSGR in Arabidopsis resulted in a rapid yellowing phenotype; complementary experiments proved that ZjSGR was a functional homolog of AtNYE1 from Arabidopsis thaliana. Over expression of ZjSGR accelerated chlorophyll degradation and impaired photosynthesis in Arabidopsis. Transmission electron microscopy observation revealed that overexpression of ZjSGR decomposed the chloroplasts structure. RNA sequencing analysis showed that ZjSGR could play multiple roles in senescence and chlorophyll degradation by regulating hormone signal transduction and the expression of a large number of senescence and environmental stress related genes. Our study provides a better understanding of the roles of SGRs, and new insight into the senescence and chlorophyll degradation mechanisms in plants. PMID:28018416

  13. Characterization of multiple SPS knockout mutants reveals redundant functions of the four Arabidopsis sucrose phosphate synthase isoforms in plant viability, and strongly indicates that enhanced respiration and accelerated starch turnover can alleviate the blockage of sucrose biosynthesis.

    PubMed

    Bahaji, Abdellatif; Baroja-Fernández, Edurne; Ricarte-Bermejo, Adriana; Sánchez-López, Ángela María; Muñoz, Francisco José; Romero, Jose M; Ruiz, María Teresa; Baslam, Marouane; Almagro, Goizeder; Sesma, María Teresa; Pozueta-Romero, Javier

    2015-09-01

    We characterized multiple knock-out mutants of the four Arabidopsis sucrose phosphate synthase (SPSA1, SPSA2, SPSB and SPSC) isoforms. Despite their reduced SPS activity, spsa1/spsa2, spsa1/spsb, spsa2/spsb, spsa2/spsc, spsb/spsc, spsa1/spsa2/spsb and spsa2/spsb/spsc mutants displayed wild type (WT) vegetative and reproductive morphology, and showed WT photosynthetic capacity and respiration. In contrast, growth of rosettes, flowers and siliques of the spsa1/spsc and spsa1/spsa2/spsc mutants was reduced compared with WT plants. Furthermore, these plants displayed a high dark respiration phenotype. spsa1/spsb/spsc and spsa1/spsa2/spsb/spsc seeds poorly germinated and produced aberrant and sterile plants. Leaves of all viable sps mutants, except spsa1/spsc and spsa1/spsa2/spsc, accumulated WT levels of nonstructural carbohydrates. spsa1/spsc leaves possessed high levels of metabolic intermediates and activities of enzymes of the glycolytic and tricarboxylic acid cycle pathways, and accumulated high levels of metabolic intermediates of the nocturnal starch-to-sucrose conversion process, even under continuous light conditions. Results presented in this work show that SPS is essential for plant viability, reveal redundant functions of the four SPS isoforms in processes that are important for plant growth and nonstructural carbohydrate metabolism, and strongly indicate that accelerated starch turnover and enhanced respiration can alleviate the blockage of sucrose biosynthesis in spsa1/spsc leaves.

  14. Volatiles and Isotopes and the Exploration of Ancient and Modern Martian Habitability with the Curiosity Rover

    NASA Technical Reports Server (NTRS)

    Mhaffy, P. R.

    2015-01-01

    The Mars Science Laboratory Mission was designed to pave the way for the study of life beyond Earth through a search for a habitable environment in a carefully selected landing site on Mars. Its ongoing exploration of Gale Crater with the Curiosity Rover has provided a rich data set that revealed such an environment in an ancient lakebed [1]. Volatile and isotope measurements of both the atmosphere and solids contribute to our growing understanding of both modern and ancient environments.

  15. Information about Macedonian medicine in ancient Greece.

    PubMed

    Giannouli, Vaitsa; Syrmos, Nikolaos

    2011-01-01

    Ancient Greek Macedonians were highly interested in the improvement of their physical and psychological health. At first, they worshiped the mythical god Asclepius and his daughter Hygieia. In at least 24 places in northern Greece, in Halkidiki, Thessaloniki, Kozani, Kavala, Thassos, Serres and other places, archaelogical findings were related to Asclepius. Macedonian kings were also interested in the development of medicine, for the sake of their fellow citizens and their soldiers. Characteristic examples are the close relations of Hippocrates with king Perdikas (5(th) century B.C.) and of Nicomachus (Aristotle's father being a physician) with king Amintas. Alexander the Great had as his personal physician, the famous physician Philippos of Acarnania. An incident between Alexander and Philippos of Acarnania shows the respect of Macedonian kings to their doctors: Alexander became ill after a bath in the frozen river Cydnus (near ancient Tarsus). At this time he received a letter from his general Parmenion for not to trust his physician. Alexander gave this letter to Philippos to read it and while Philippos was reading it and was rather frightened, he saw Alexander drinking the medicine he had given him. We may note that Alexander the Great as a student of Aristotle had a general education about medicine. Archaeological findings revealed two funerary monuments of physicians: a doctor from Thasos, who practiced in Pella as a public physician during the 3rd quarter of the 4(th) century B.C. and a physician named Alexander, who lived in the 1rst half of the 5(th) century A.D. The tomb of a third physician, probably a surgeon, excavated in Pydna, near mount Olympus (3(rd) century BC)also indicates the importance of physicians in Macedonia. Archaeological findings, like surgical knives, from the Hellinistic and Roman periods, found in the city of Veria, also showed the respect of Ancient Greeks to medicine and to their physicians. An example is the skeleton of a young

  16. Particle acceleration

    NASA Technical Reports Server (NTRS)

    Vlahos, L.; Machado, M. E.; Ramaty, R.; Murphy, R. J.; Alissandrakis, C.; Bai, T.; Batchelor, D.; Benz, A. O.; Chupp, E.; Ellison, D.

    1986-01-01

    Data is compiled from Solar Maximum Mission and Hinothori satellites, particle detectors in several satellites, ground based instruments, and balloon flights in order to answer fundamental questions relating to: (1) the requirements for the coronal magnetic field structure in the vicinity of the energization source; (2) the height (above the photosphere) of the energization source; (3) the time of energization; (4) transistion between coronal heating and flares; (5) evidence for purely thermal, purely nonthermal and hybrid type flares; (6) the time characteristics of the energization source; (7) whether every flare accelerates protons; (8) the location of the interaction site of the ions and relativistic electrons; (9) the energy spectra for ions and relativistic electrons; (10) the relationship between particles at the Sun and interplanetary space; (11) evidence for more than one acceleration mechanism; (12) whether there is single mechanism that will accelerate particles to all energies and also heat the plasma; and (13) how fast the existing mechanisms accelerate electrons up to several MeV and ions to 1 GeV.

  17. Plasma accelerator

    DOEpatents

    Wang, Zhehui; Barnes, Cris W.

    2002-01-01

    There has been invented an apparatus for acceleration of a plasma having coaxially positioned, constant diameter, cylindrical electrodes which are modified to converge (for a positive polarity inner electrode and a negatively charged outer electrode) at the plasma output end of the annulus between the electrodes to achieve improved particle flux per unit of power.

  18. Accelerated Achievement

    ERIC Educational Resources Information Center

    Ford, William J.

    2010-01-01

    This article focuses on the accelerated associate degree program at Ivy Tech Community College (Indiana) in which low-income students will receive an associate degree in one year. The three-year pilot program is funded by a $2.3 million grant from the Lumina Foundation for Education in Indianapolis and a $270,000 grant from the Indiana Commission…

  19. ACCELERATION INTEGRATOR

    DOEpatents

    Pope, K.E.

    1958-01-01

    This patent relates to an improved acceleration integrator and more particularly to apparatus of this nature which is gyrostabilized. The device may be used to sense the attainment by an airborne vehicle of a predetermined velocitv or distance along a given vector path. In its broad aspects, the acceleration integrator utilizes a magnetized element rotatable driven by a synchronous motor and having a cylin drical flux gap and a restrained eddy- current drag cap deposed to move into the gap. The angular velocity imparted to the rotatable cap shaft is transmitted in a positive manner to the magnetized element through a servo feedback loop. The resultant angular velocity of tae cap is proportional to the acceleration of the housing in this manner and means may be used to measure the velocity and operate switches at a pre-set magnitude. To make the above-described dcvice sensitive to acceleration in only one direction the magnetized element forms the spinning inertia element of a free gyroscope, and the outer housing functions as a gimbal of a gyroscope.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  1. Ancient Chinese Astronomy - An Overview

    NASA Astrophysics Data System (ADS)

    Shi, Yunli

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

  2. [Urinary schistosomiasis in ancient Egypt].

    PubMed

    Ziskind, Bernard

    2009-12-01

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

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

    PubMed

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

    2014-03-01

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

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

    PubMed Central

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

    2014-01-01

    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 of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics. PMID:24299735

  5. Particle Accelerators in China

    NASA Astrophysics Data System (ADS)

    Zhang, Chuang; Fang, Shouxian

    As the special machines that can accelerate charged particle beams to high energy by using electromagnetic fields, particle accelerators have been widely applied in scientific research and various areas of society. The development of particle accelerators in China started in the early 1950s. After a brief review of the history of accelerators, this article describes in the following sections: particle colliders, heavy-ion accelerators, high-intensity proton accelerators, accelerator-based light sources, pulsed power accelerators, small scale accelerators, accelerators for applications, accelerator technology development and advanced accelerator concepts. The prospects of particle accelerators in China are also presented.

  6. Compact accelerator

    DOEpatents

    Caporaso, George J.; Sampayan, Stephen E.; Kirbie, Hugh C.

    2007-02-06

    A compact linear accelerator having at least one strip-shaped Blumlein module which guides a propagating wavefront between first and second ends and controls the output pulse at the second end. Each Blumlein module has first, second, and third planar conductor strips, with a first dielectric strip between the first and second conductor strips, and a second dielectric strip between the second and third conductor strips. Additionally, the compact linear accelerator includes a high voltage power supply connected to charge the second conductor strip to a high potential, and a switch for switching the high potential in the second conductor strip to at least one of the first and third conductor strips so as to initiate a propagating reverse polarity wavefront(s) in the corresponding dielectric strip(s).

  7. [Biological evolution and ancient DNA].

    PubMed

    Debruyne, Régis; Barriel, Véronique

    2006-05-01

    Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.

  8. [Ancient history of Indian pharmacy].

    PubMed

    Okuda, Jun; Natsume, Yohko

    2010-01-01

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

  9. Laser acceleration

    NASA Astrophysics Data System (ADS)

    Tajima, T.; Nakajima, K.; Mourou, G.

    2017-02-01

    The fundamental idea of Laser Wakefield Acceleration (LWFA) is reviewed. An ultrafast intense laser pulse drives coherent wakefield with a relativistic amplitude robustly supported by the plasma. While the large amplitude of wakefields involves collective resonant oscillations of the eigenmode of the entire plasma electrons, the wake phase velocity ˜ c and ultrafastness of the laser pulse introduce the wake stability and rigidity. A large number of worldwide experiments show a rapid progress of this concept realization toward both the high-energy accelerator prospect and broad applications. The strong interest in this has been spurring and stimulating novel laser technologies, including the Chirped Pulse Amplification, the Thin Film Compression, the Coherent Amplification Network, and the Relativistic Mirror Compression. These in turn have created a conglomerate of novel science and technology with LWFA to form a new genre of high field science with many parameters of merit in this field increasing exponentially lately. This science has triggered a number of worldwide research centers and initiatives. Associated physics of ion acceleration, X-ray generation, and astrophysical processes of ultrahigh energy cosmic rays are reviewed. Applications such as X-ray free electron laser, cancer therapy, and radioisotope production etc. are considered. A new avenue of LWFA using nanomaterials is also emerging.

  10. BICEP's acceleration

    SciTech Connect

    Contaldi, Carlo R.

    2014-10-01

    The recent Bicep2 [1] detection of, what is claimed to be primordial B-modes, opens up the possibility of constraining not only the energy scale of inflation but also the detailed acceleration history that occurred during inflation. In turn this can be used to determine the shape of the inflaton potential V(φ) for the first time — if a single, scalar inflaton is assumed to be driving the acceleration. We carry out a Monte Carlo exploration of inflationary trajectories given the current data. Using this method we obtain a posterior distribution of possible acceleration profiles ε(N) as a function of e-fold N and derived posterior distributions of the primordial power spectrum P(k) and potential V(φ). We find that the Bicep2 result, in combination with Planck measurements of total intensity Cosmic Microwave Background (CMB) anisotropies, induces a significant feature in the scalar primordial spectrum at scales k∼ 10{sup -3} Mpc {sup -1}. This is in agreement with a previous detection of a suppression in the scalar power [2].

  11. Ancient Cosmology, superfine structure of the Universe and Anthropological Principle

    NASA Astrophysics Data System (ADS)

    Arakelyan, Hrant; Vardanyan, Susan

    2015-07-01

    The modern cosmology by its spirit, conception of the Big Bang is closer to the ancient cosmology, than to the cosmological paradigm of the XIX century. Repeating the speculations of the ancients, but using at the same time subtle mathematical methods and relying on the steadily accumulating empirical material, the modern theory tends to a quantitative description of nature, in which increasing role are playing the numerical ratios between the physical constants. The detailed analysis of the influence of the numerical values -- of physical quantities on the physical state of the universe revealed amazing relations called fine and hyperfine tuning. In order to explain, why the observable universe comes to be a certain set of interrelated fundamental parameters, in fact a speculative anthropic principle was proposed, which focuses on the fact of the existence of sentient beings.

  12. A Case for the Ancient Origin of Coronaviruses

    PubMed Central

    Chu, Daniel K. W.; Peiris, Joseph S. M.; Kosakovsky Pond, Sergei L.

    2013-01-01

    Coronaviruses are found in a diverse array of bat and bird species, which are believed to act as natural hosts. Molecular clock dating analyses of coronaviruses suggest that the most recent common ancestor of these viruses existed around 10,000 years ago. This relatively young age is in sharp contrast to the ancient evolutionary history of their putative natural hosts, which began diversifying tens of millions of years ago. Here, we attempted to resolve this discrepancy by applying more realistic evolutionary models that have previously revealed the ancient evolutionary history of other RNA viruses. By explicitly modeling variation in the strength of natural selection over time and thereby improving the modeling of substitution saturation, we found that the time to the most recent ancestor common for all coronaviruses is likely far greater (millions of years) than the previously inferred range. PMID:23596293

  13. Giant ancient schwannoma of the pelvis.

    PubMed

    Hide, I G; Baudouin, C J; Murray, S A; Malcolm, A J

    2000-09-01

    A 43-year-old man with a large ancient schwannoma of the pelvis, presenting with varicose veins, is reported. Ancient schwannoma (neurilemmoma) is a benign tumour of nerve sheath origin characterised histologically by features of severe degeneration and which rarely can grow to a large size. Malignant transformation, though reported, is extremely rare.

  14. Women--Sex Objects in Ancient Egypt.

    ERIC Educational Resources Information Center

    Mutimer, Brian T. P.

    Although it has been said that the women in Ancient Egypt enjoyed a reasonable state of social and professional equality with men, this paper presents an alternate theory--that women were second-class citizens whose physical prowess was secondary to their role as sex objects. It appears that men and women in Ancient Egypt often participated in the…

  15. Computed tomography of an ancient Egyptian cat.

    PubMed

    Falke, T H; Zweypfenning-Snijders, M C; Zweypfenning, R C; James, A E

    1987-01-01

    The use of CT in the documentation of ancient Egyptian mummified human remains has previously been described in this and other journals. We recently applied this technique to a collection of ancient Egyptian mummified fauna and sarcophagi. We selected an example to illustrate that CT is also uniquely suitable for the study of such specimens in a noninvasive way.

  16. Magnetite biomineralization and ancient life on Mars.

    PubMed

    Frankel, R B; Buseck, P R

    2000-04-01

    Certain chemical and mineral features of the Martian meteorite ALH84001 were reported in 1996 to be probable evidence of ancient life on Mars. In spite of new observations and interpretations, the question of ancient life on Mars remains unresolved. Putative biogenic, nanometer magnetite has now become a leading focus in the debate.

  17. Contemporary Greek Presentations of Ancient Greek Theatre.

    ERIC Educational Resources Information Center

    Metallinos, Nikos

    Confronted with the problems imposed by the stage presentation and interpretation of ancient Greek theatre to contemporary audiences, scholars have developed four major approaches to the presentation of Greek drama over the past 70 years. The first approach, referred to as modificationist or realist, claims that communicating ancient Greek drama…

  18. The building stones of ancient Egypt a gift of its geology

    NASA Astrophysics Data System (ADS)

    Klemm, Dietrich D.; Klemm, Rosemarie

    2001-08-01

    Building stones and clay-rich Nile mud were ancient Egypt's main raw construction materials. While the mud was easily accessible along the Nile river valley, the immense quantities of the different stone materials used for construction of the famous pyramids, precious temples and tombs needed a systematic quarrying organization, well arranged transport logistics over extreme distances and a high standard of stone masonry. The petrography, occurrence, and main applications of the 11 most popular stone types used in ancient Egypt are described in this contribution. Rough estimates of the scale of this mining activity, based on the volume of many different ancient quarry sites, all over Egypt, reveal that the monuments known today represent only a small fraction of the amount of building stones mined during the long, ancient Egyptian history.

  19. Ancient DNA analysis of human remains from the Upper Capital City of Kublai Khan.

    PubMed

    Fu, Yuqin; Xie, Chengzhi; Xu, Xuelian; Li, Chunxiang; Zhang, Quanchao; Zhou, Hui; Zhu, Hong

    2009-01-01

    Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons.

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

    PubMed

    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.

  1. A Swarm of Ancient Stars

    NASA Astrophysics Data System (ADS)

    2010-12-01

    We know of about 150 of the rich collections of old stars called globular clusters that orbit our galaxy, the Milky Way. This sharp new image of Messier 107, captured by the Wide Field Imager on the 2.2-metre telescope at ESO's La Silla Observatory in Chile, displays the structure of one such globular cluster in exquisite detail. Studying these stellar swarms has revealed much about the history of our galaxy and how stars evolve. The globular cluster Messier 107, also known as NGC 6171, is a compact and ancient family of stars that lies about 21 000 light-years away. Messier 107 is a bustling metropolis: thousands of stars in globular clusters like this one are concentrated into a space that is only about twenty times the distance between our Sun and its nearest stellar neighbour, Alpha Centauri, across. A significant number of these stars have already evolved into red giants, one of the last stages of a star's life, and have a yellowish colour in this image. Globular clusters are among the oldest objects in the Universe. And since the stars within a globular cluster formed from the same cloud of interstellar matter at roughly the same time - typically over 10 billion years ago - they are all low-mass stars, as lightweights burn their hydrogen fuel supply much more slowly than stellar behemoths. Globular clusters formed during the earliest stages in the formation of their host galaxies and therefore studying these objects can give significant insights into how galaxies, and their component stars, evolve. Messier 107 has undergone intensive observations, being one of the 160 stellar fields that was selected for the Pre-FLAMES Survey - a preliminary survey conducted between 1999 and 2002 using the 2.2-metre telescope at ESO's La Silla Observatory in Chile, to find suitable stars for follow-up observations with the VLT's spectroscopic instrument FLAMES [1]. Using FLAMES, it is possible to observe up to 130 targets at the same time, making it particularly well suited

  2. Advanced concepts for acceleration

    SciTech Connect

    Keefe, D.

    1986-07-01

    Selected examples of advanced accelerator concepts are reviewed. Such plasma accelerators as plasma beat wave accelerator, plasma wake field accelerator, and plasma grating accelerator are discussed particularly as examples of concepts for accelerating relativistic electrons or positrons. Also covered are the pulsed electron-beam, pulsed laser accelerator, inverse Cherenkov accelerator, inverse free-electron laser, switched radial-line accelerators, and two-beam accelerator. Advanced concepts for ion acceleration discussed include the electron ring accelerator, excitation of waves on intense electron beams, and two-wave combinations. (LEW)

  3. Accelerators and the Accelerator Community

    SciTech Connect

    Malamud, Ernest; Sessler, Andrew

    2008-06-01

    In this paper, standing back--looking from afar--and adopting a historical perspective, the field of accelerator science is examined. How it grew, what are the forces that made it what it is, where it is now, and what it is likely to be in the future are the subjects explored. Clearly, a great deal of personal opinion is invoked in this process.

  4. Impact accelerations

    NASA Technical Reports Server (NTRS)

    Vongierke, H. E.; Brinkley, J. W.

    1975-01-01

    The degree to which impact acceleration is an important factor in space flight environments depends primarily upon the technology of capsule landing deceleration and the weight permissible for the associated hardware: parachutes or deceleration rockets, inflatable air bags, or other impact attenuation systems. The problem most specific to space medicine is the potential change of impact tolerance due to reduced bone mass and muscle strength caused by prolonged weightlessness and physical inactivity. Impact hazards, tolerance limits, and human impact tolerance related to space missions are described.

  5. [Notes on ancient Islamic medicine].

    PubMed

    de Micheli-Serra, Alfredo

    2002-01-01

    Arab medicine arose as a consequence of the assimilation and breeding of Hellenistic medicine, particularly of Galenic medicine. It reached its high point between the X and XII centuries and, after the XIII century, lost all creative capabilities. Nevertheless, it achieved the status of being an incentive for European medieval medicine. Some aspects of the medical teaching and publications of the most distinguished Moslem physicians, such as Rhazes (865-932), Avicenna (980-1037), and Averroës (1126-1198) are described. The main characteristics of Moslem medical institutions such as guilds, hospitals, and organizations of professional practice also are discussed. Although Arab medicine essentially constituted a transmission vehicle of master ideas of ancient medical thought, this medicine awoke the interest and initiative of the medieval physicians of western Europe, for example, those at the medical school of Salerno.

  6. Topochemical investigation of ancient manuscripts.

    PubMed

    Wagner, B; Bulska, E; Hulanicki, A; Heck, M; Ortner, H M

    2001-04-01

    Various modern instrumental techniques for surface analysis were applied for the non-destructive physicochemical examination of works of art. As samples, pieces of ancient manuscripts endangered by iron-gall ink corrosion were used. Surface characterisation of the morphology of the cellulose fibres within corroded and non-corroded parts of the manuscript performed by scanning electron microscopy (SEM) showed seriously damaged cellulose fibres in the written parts. The elemental composition of selected parts of the manuscript was determined by energy dispersive X-ray fluorescence analysis (EDX). A more detailed study of the paper surface was then performed by electron probe microanalysis (EPMA). This technique yields the morphological characteristics of the surface as well as element distribution maps over the written area of the investigated manuscript.

  7. Ancient aqueous sedimentation on Mars

    SciTech Connect

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

    1991-02-01

    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.

  8. Sacred psychiatry in ancient Greece

    PubMed Central

    2014-01-01

    From the ancient times, there are three basic approaches for the interpretation of the different psychic phenomena: the organic, the psychological, and the sacred approach. The sacred approach forms the primordial foundation for any psychopathological development, innate to the prelogical human mind. Until the second millennium B.C., the Great Mother ruled the Universe and shamans cured the different mental disorders. But, around 1500 B.C., the predominance of the Hellenic civilization over the Pelasgic brought great changes in the theological and psychopathological fields. The Hellenes eliminated the cult of the Great Mother and worshiped Dias, a male deity, the father of gods and humans. With the Father's help and divinatory powers, the warrior-hero made diagnoses and found the right therapies for mental illness; in this way, sacerdotal psychiatry was born. PMID:24725988

  9. Sacred psychiatry in ancient Greece.

    PubMed

    Tzeferakos, Georgios; Douzenis, Athanasios

    2014-04-12

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

  10. GPR prospection in ancient Ephesos

    NASA Astrophysics Data System (ADS)

    Hruska, Jiri; Fuchs, Gerald

    1999-03-01

    Urban area of ancient Ephesos (present Turkey) is too large to be fully excavated, so geophysical prospection and mapping can help with the investigation. Georadar is one of the most effective tools for it. Two different tasks solved by georadar are presented. The first problem was the interconnection between the city and the temple of Artemis. By historical records, it was made by two sacred procession roads, which had character of Graeco-Roman stoa, i.e., a roofed road. Only small parts of these roads were discovered in ruins or excavated. Some hundreds of metres from total length of a few kilometres became known, but the questions above were not solved. Then, the area was prospected by georadar. Series of GPR lines were scanned gradually from the last known points and evaluated right on the spot. As a result, a plan of georadar indications could be drawn. These indications created two lines tracing unknown parts of both roads joining together and then continuing till the entry of the temple. The results were confirmed by two boreholes. The second task was mapping of Hellenistic level of Tetragonos agora. At present, it is under the Roman level, and is visible only in some excavation pits. About a half the square was covered by detailed georadar survey. Numerous anomalies indicated presence of underground objects. Compared with the results of excavations, they were interpreted as ancient remains in several levels. Then plans of these indications were compiled for separated levels. Hellenistic buildings remains were mapped, forming an older agora, smaller and slightly different by its shape from the Roman building plan. Besides it, uncovered parts of Roman ruins were detected, as well as some remains of Classic and Archaic settlement levels. Some traces of even older human presence were found under them. Georadar results will serve as a guideline for future excavations.

  11. HIV thrives in ancient traditions.

    PubMed

    Shreedhar, J

    1995-01-01

    Participation in ancient traditions is facilitating the current spread of HIV through India. For most of the year, Koovagam is a typical Indian village. Each April on the night of the full moon, however, the Chittirai-Pournami festival is held in Koovagam, a celebration in homage to Aravan during which up to 2000 pilgrims from across the country engage in thousands of acts of unprotected sexual intercourse. Aravan is a man depicted in a Hindu tale who asked to experience sexual bliss before being sacrificed to the gods. To fulfill this last wish, the god Krishna is said to have assumed the form of a beautiful woman and had sexual intercourse with Aravan. Many of the festival participants are hijras, eunuchs and transsexuals who sell sex for a living. Hijras may be accompanied by men who serve as their sex partners and bodyguards. Surveys suggest that one-third of the 10,000 hijras in New Delhi may be infected with HIV. Other participants are known as dangas, men who are either married or single and appear to lead strictly heterosexual lives throughout the year except during the Chittirai-Pournami festival when they dress as women and sell sex to other men attending the festival. The panthis comprise another group of participants and tend to be either single or married men who attend the festival to have sex with the hijras and dangas for fees up to ten rupees, approximately US$0.50, per sexual encounter. Prostitution within the devadasi sect and the sale of young, virgin girls in the state of Andhra Pradesh to the highest male bidders are other examples of how ancient traditions are facilitating the current spread of HIV in India.

  12. Astronomy and its role in ancient Mesoamerica

    NASA Astrophysics Data System (ADS)

    Šprajc, Ivan

    2011-06-01

    The observation of the sky had an important rôle among the Maya, Aztecs and other prehispanic peoples of Mesoamerica. Their familiarity with the regularities of the apparent motion of the Sun, the Moon and bright planets is attested in a large amount of astronomical data contained in codices and monumental hieroglyphic inscriptions, as well as in their sophisticated calendrical system. On the other hand, the study of architectural alignments has disclosed that civic and ceremonial buildings were largely oriented on astronomical grounds, mostly to sunrises and sunsets on certain dates, allowing the use of observational calendars that facilitated a proper scheduling of agricultural and the associated ritual activities in the yearly cycle. Both accurate knowledge and other astronomically-derived concepts reveal that the significance attributed to certain celestial events by the ancient Mesoamericans can be explained in terms of the relationship of these phenomena with specific environmental and cultural facts, such as seasonal climatic changes and subsistence strategies. It was particularly due to its practical utility that astronomy, intertwined with religious ideas and practices, had such an important place in the worldview and, consequently, in the cosmologically substantiated political ideology of Mesoamerican societies

  13. Ancient DNA studies: new perspectives on old samples

    PubMed Central

    2012-01-01

    In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field. PMID:22697611

  14. Evolutionary history and metabolic insights of ancient mammalian uricases

    PubMed Central

    Kratzer, James T.; Lanaspa, Miguel A.; Murphy, Michael N.; Cicerchi, Christina; Graves, Christina L.; Tipton, Peter A.; Ortlund, Eric A.; Johnson, Richard J.; Gaucher, Eric A.

    2014-01-01

    Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients. PMID:24550457

  15. Accelerator system and method of accelerating particles

    NASA Technical Reports Server (NTRS)

    Wirz, Richard E. (Inventor)

    2010-01-01

    An accelerator system and method that utilize dust as the primary mass flux for generating thrust are provided. The accelerator system can include an accelerator capable of operating in a self-neutralizing mode and having a discharge chamber and at least one ionizer capable of charging dust particles. The system can also include a dust particle feeder that is capable of introducing the dust particles into the accelerator. By applying a pulsed positive and negative charge voltage to the accelerator, the charged dust particles can be accelerated thereby generating thrust and neutralizing the accelerator system.

  16. gargammel: a sequence simulator for ancient DNA.

    PubMed

    Renaud, Gabriel; Hanghøj, Kristian; Willerslev, Eske; Orlando, Ludovic

    2016-10-29

    Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico, we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.

  17. Seeking Ancient Microbial Biosignatures With PIXL on Mars 2020

    NASA Astrophysics Data System (ADS)

    Allwood, A.; Hurowitz, J.; Wade, L. W. A.; Hodyss, R. P.; Flannery, D.

    2014-12-01

    Identifying ancient microbial biosignatures in the geologic record requires an assemblage of evidence, and almost never results from a single "smoking gun". When a potential biosignature such as a microfossil, organic deposit or stromatolite is found, sources of evidence for testing the biogenic hypothesis include the inherent properties of the feature itself, the assemblage characteristics of multiple candidate features, the geologic context of the features, and the relationship between changes in the features and changes in the geologic context. Given these diverse sources of evidence, multiple analytical techniques necessarily come into play. Some of the most powerful techniques emerging for ancient biosignature investigations are those that detailed, spatially correlated observations of fine texture, microstructure and composition (mineralogy, chemistry, organics etc). MicroX-ray fluorescence is a significant new method for in situ compositional analysis at sub-millimeter scales. Micro-XRF scans a focused X-ray beam across the surface of a rock to create a map of elemental composition at mm-cm scales, comprising individual spot measurements of 100 microns diameter. A micro-XRF instrument, PIXL (Planetary Instrument for X-ray Lithochemistry) was selected for flight aboard the Mars 2020 rover. We have used PIXL to analyze to diverse geological samples including ancient stromatolites, reduction spots, ooids, altered basalts, concretions and shales, and found that PIXL element maps are not only a highly effective way to quickly ascertain the compositional variability of the sample, but also that unexpected features typically emerge that can be critical for interpreting sedimentary, diagenetic and biological processes. For example, in two different stromatolite cases, elemental distribution revealed sedimentary and diagenetic textures that constrained the processes of stromatolite formation and implied biological influence. These textures were invisible in reflected

  18. Earthquake Archaeology: a case study from Ancient Cnidus

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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

  19. Ancient mines of the Farah Garan area, southwestern Saudi Arabia

    USGS Publications Warehouse

    Smith, C.W.; Blank, H. Richard

    1979-01-01

    Ancient miners, in quest of oxidized copper minerals, gold, silver, and possibly zinc, mined gossans to approximately 20 m depth in an area 1.1 by 0.5 km in extent at Farah Garan. The gossans, derived from sulfides, are ordinarily found at contacts between marble lenses and metavolcanic-metasedimentary rocks, but in the southern part of the mined area, gossans are also within marbles. The gossans are generally lensoidal and discontinuous along strike. The same type of metallization, in similar rocks, was found at the Hemair ancient workings, about 3 km southeast. Both deposits are thought to be of epigenetic origin, and ore deposition was controlled by shearing along marble contacts. Drilling is recommended at Farah Garan. Al Ashyab is 4 km south of Farah Garan, and similar rocks and structures extend through both areas but there are no ancient workings at Al Ashyab. The dominant geologic feature in the area is a high, narrow, light-colored ridge consisting of intensely silicified quartz porphyry. Pyritized metavolcanic rocks envelope the silicified rock, and geochemical sampling revealed weakly anomalous, erratically spaced concentrations of copper and zinc within these rocks. No further work is recommended for the area. Quartz-filled fractures containing gold were mapped at Al Asharfat, Lejourah, and other locations where ancient miners worked the veins. The gold-bearing quartz veins are narrow and have short strike lengths, and potential tonnages are thought to be small. The veins are in younger, more massive rocks than the enclosing metamorphic rocks and are thought to be younger than the adjacent sulfide deposits. No further work is recommended. Pyritized zones and associated sparse copper oxides extend intermittently about 6 km south of Hemair in metasedimentary rocks of the Jiddah group. Similar zones, associated quartz vein swarms, and minor magnetite and gold are found in mafic metavolcanic rocks adjacent to the contact with quartz porphyry about 1 km west

  20. Tyrannosaur paleobiology: new research on ancient exemplar organisms.

    PubMed

    Brusatte, Stephen L; Norell, Mark A; Carr, Thomas D; Erickson, Gregory M; Hutchinson, John R; Balanoff, Amy M; Bever, Gabe S; Choiniere, Jonah N; Makovicky, Peter J; Xu, Xing

    2010-09-17

    Tyrannosaurs, the group of dinosaurian carnivores that includes Tyrannosaurus rex and its closest relatives, are icons of prehistory. They are also the most intensively studied extinct dinosaurs, and thanks to large sample sizes and an influx of new discoveries, have become ancient exemplar organisms used to study many themes in vertebrate paleontology. A phylogeny that includes recently described species shows that tyrannosaurs originated by the Middle Jurassic but remained mostly small and ecologically marginal until the latest Cretaceous. Anatomical, biomechanical, and histological studies of T. rex and other derived tyrannosaurs show that large tyrannosaurs could not run rapidly, were capable of crushing bite forces, had accelerated growth rates and keen senses, and underwent pronounced changes during ontogeny. The biology and evolutionary history of tyrannosaurs provide a foundation for comparison with other dinosaurs and living organisms.

  1. Ancient Dry Spells Offer Clues About Drought

    NASA Video Gallery

    New research indicates that the ancient Mesoamerican civilizations of the Mayans and Aztecs amplified droughts in the Yucatán and southern Mexico by clearing rainforests to make room for pastures ...

  2. Ancient Magnetic Reversals: Clues to the Geodynamo.

    ERIC Educational Resources Information Center

    Hoffman, Kenneth A.

    1988-01-01

    Discusses the question posed by some that the earth's magnetic field may reverse. States that rocks magnetized by ancient fields may offer clues to the underlying reversal mechanism in the earth's core. (TW)

  3. Vascular medicine and surgery in ancient Egypt.

    PubMed

    Barr, Justin

    2014-07-01

    Lauded alike by ancient civilizations and modern society, pharaonic Egyptian medicine remains an object of fascination today. This article discusses its surprisingly sophisticated understanding of a cardiovascular system. The term "cardiovascular system," however, carries assumptions and meanings to a modern audience, especially readers of this journal, which simply do not apply when considering ancient conceptions of the heart and vessels. For lack of better language, this article will use "cardiovascular" and similar terms while recognizing the anachronistic inaccuracy. After briefly summarizing ancient Egyptian medicine generally, it will review the anatomy, pathology, and treatment of the vasculature. The practice of mummification in ancient Egypt provides a unique opportunity for paleopathology, and the conclusion will explore evidence of arterial disease from a modern scientific perspective.

  4. Ancient history of congenital adrenal hyperplasia.

    PubMed

    New, Maria I

    2011-01-01

    Although there are many erudite reports on the history of endocrinology and endocrine disorders, the history of congenital adrenal hyperplasia has not been published. I have tried to review ancient as well as modern history of CAH.

  5. VRIKSHAYURVEDA (Arboreal Medicine in Ancient India)

    PubMed Central

    Ramachanran, C.K.

    1984-01-01

    This paper discusses the special branch of the Ancient Indian science on plant life as depicted by Vrikshayurveda, and the obvious relevance of the insights these provide to enrich our knowledge and practice in this field PMID:22557461

  6. Ancient wolf lineages in India.

    PubMed Central

    Sharma, Dinesh K; Maldonado, Jesus E; Jhala, Yadrendradev V; Fleischer, Robert C

    2004-01-01

    All previously obtained wolf (Canis lupus) and dog (Canis familiaris) mitochondrial (mt) DNA sequences fall within an intertwined and shallow clade (the 'wolf-dog' clade). We sequenced mtDNA of recent and historical samples from 45 wolves from throughout lowland peninsular India and 23 wolves from the Himalayas and Tibetan Plateau and compared these sequences with all available wolf and dog sequences. All 45 lowland Indian wolves have one of four closely related haplotypes that form a well-supported, divergent sister lineage to the wolf-dog clade. This unique lineage may have been independent for more than 400,000 years. Although seven Himalayan wolves from western and central Kashmir fall within the widespread wolf-dog clade, one from Ladakh in eastern Kashmir, nine from Himachal Pradesh, four from Nepal and two from Tibet form a very different basal clade. This lineage contains five related haplotypes that probably diverged from other canids more than 800,000 years ago, but we find no evidence of current barriers to admixture. Thus, the Indian subcontinent has three divergent, ancient and apparently parapatric mtDNA lineages within the morphologically delineated wolf. No haplotypes of either novel lineage are found within a sample of 37 Indian (or other) dogs. Thus, we find no evidence that these two taxa played a part in the domestication of canids. PMID:15101402

  7. Ancient origin of mast cells

    PubMed Central

    Wong, G. William; Zhuo, Lisheng; Kimata, Koji; Lam, Bing K.; Satoh, Nori; Stevens, Richard L.

    2014-01-01

    The sentinel roles of mammalian mast cells (MCs) in varied infections raised the question of their evolutionary origin. We discovered that the test cells in the sea squirt Ciona intestinalis morphologically and histochemically resembled cutaneous human MCs. Like the latter, C. intestinalis test cells stored histamine and varied heparin•serine protease complexes in their granules. Moreover, they exocytosed these preformed mediators when exposed to compound 48/80. In support of the histamine data, a C. intestinalis-derived cDNA was isolated that resembled that which encodes histidine decarboxylase in human MCs. Like heparin-expressing mammalian MCs, activated test cells produced prostaglandin D2 and contained cDNAs that encode a protein that resembles the synthase needed for its biosynthesis in human MCs. The accumulated morphological, histochemical, biochemical, and molecular biology data suggest that the test cells in C. intestinalis are the counterparts of mammalian MCs that reside in varied connective tissues. The accumulated data point to an ancient origin of MCs that predates the emergence of the chordates >500 million years ago, well before the development of adaptive immunity. The remarkable conservation of MCs throughout evolution is consistent with their importance in innate immunity. PMID:25094046

  8. Ancient history of flatfish research

    NASA Astrophysics Data System (ADS)

    Berghahn, Rüdiger; Bennema, Floris Pieter

    2013-01-01

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

  9. Recognizing characters of ancient manuscripts

    NASA Astrophysics Data System (ADS)

    Diem, Markus; Sablatnig, Robert

    2010-02-01

    Considering printed Latin text, the main issues of Optical Character Recognition (OCR) systems are solved. However, for degraded handwritten document images, basic preprocessing steps such as binarization, gain poor results with state-of-the-art methods. In this paper ancient Slavonic manuscripts from the 11th century are investigated. In order to minimize the consequences of false character segmentation, a binarization-free approach based on local descriptors is proposed. Additionally local information allows the recognition of partially visible or washed out characters. The proposed algorithm consists of two steps: character classification and character localization. Initially Scale Invariant Feature Transform (SIFT) features are extracted which are subsequently classified using Support Vector Machines (SVM). Afterwards, the interest points are clustered according to their spatial information. Thereby, characters are localized and finally recognized based on a weighted voting scheme of pre-classified local descriptors. Preliminary results show that the proposed system can handle highly degraded manuscript images with background clutter (e.g. stains, tears) and faded out characters.

  10. Ancient Admixture in Human History

    PubMed Central

    Patterson, Nick; Moorjani, Priya; Luo, Yontao; Mallick, Swapan; Rohland, Nadin; Zhan, Yiping; Genschoreck, Teri; Webster, Teresa; Reich, David

    2012-01-01

    Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.” PMID:22960212

  11. Ancient technology in contemporary surgery.

    PubMed

    Buck, B A

    1982-03-01

    Archaeologists have shown that ancient man developed the ability to produce cutting blades of an extreme degree of sharpness from volcanic glass. The finest of these prismatic blades were produced in Mesoamerica about 2,500 years ago. The technique of production of these blades was rediscovered 12 years ago by Dr. Don Crabtree, who suggested possible uses for the blades in modern surgery. Blades produced by Dr. Crabtree have been used in experimental microsurgery with excellent results. Animal experiments have shown the tensile strength of obsidian produced wounds to be equal to or greater than that of wounds produced by steel scalpels after 14 days of healing. We have been able to demonstrate neither flaking of glass blades into the wounds nor any foreign body reaction in healed wounds. Skin incisions in human patients have likewise healed well without complications. The prismatic glass blade is infinitely sharper than a honed steel edge, and these blades can be produced in a wide variety of shapes and sizes. It is therefore suggested that this type of blade may find an appropriate use in special areas of modern surgery.

  12. Rethinking the Ancient Sulfur Cycle

    NASA Astrophysics Data System (ADS)

    Fike, David A.; Bradley, Alexander S.; Rose, Catherine V.

    2015-05-01

    The sulfur biogeochemical cycle integrates the metabolic activity of multiple microbial pathways (e.g., sulfate reduction, disproportionation, and sulfide oxidation) along with abiotic reactions and geological processes that cycle sulfur through various reservoirs. The sulfur cycle impacts the global carbon cycle and climate primarily through the remineralization of organic carbon. Over geological timescales, cycling of sulfur is closely tied to the redox state of Earth's exosphere through the burial of oxidized (sulfate) and reduced (sulfide) sulfur species in marine sediments. Biological sulfur cycling is associated with isotopic fractionations that can be used to trace the fluxes through various metabolic pathways. The resulting isotopic data provide insights into sulfur cycling in both modern and ancient environments via isotopic signatures in sedimentary sulfate and sulfide phases. Here, we review the deep-time δ34S record of marine sulfates and sulfides in light of recent advances in understanding how isotopic signatures are generated by microbial activity, how these signatures are encoded in marine sediments, and how they may be altered following deposition. The resulting picture shows a sulfur cycle intimately coupled to ambient carbon cycling, where sulfur isotopic records preserved in sedimentary rocks are critically dependent on sedimentological and geochemical conditions (e.g., iron availability) during deposition.

  13. Leprosy and its socio-cultural perception in Indian religions and ancient texts.

    PubMed

    Sinha, A K; Banerjee, B G; Singh, S

    2010-01-01

    Leprosy is one of the oldest ailments known to the mankind. Many of the ancient texts and scriptures reveal that leprosy was not categorised as a specified disease but was grouped along with other skin diseases. However, in certain texts categorical mention of this disease does exist. The prime objective of this article is to highlight the age old traditional line of perception about this disease. A literature review was done to up-date the socio-cultural perception of leprosy in Indian religions and ancient texts. References were obtained through examining relevant bibliographies and the views/suggestions of eminent scholars engaged in this field were also included. An analysis of the secondary sources of data, particularly the ancient texts reveals that in good old days, leprosy had been considered to be an infliction of wrong-doings and sins. This viewpoint has been significantly reflected in these texts.

  14. Ancient administrative handwritten documents: X-ray analysis and imaging.

    PubMed

    Albertin, F; Astolfo, A; Stampanoni, M; Peccenini, Eva; Hwu, Y; Kaplan, F; Margaritondo, G

    2015-03-01

    Handwritten characters in administrative antique documents from three centuries have been detected using different synchrotron X-ray imaging techniques. Heavy elements in ancient inks, present even for everyday administrative manuscripts as shown by X-ray fluorescence spectra, produce attenuation contrast. In most cases the image quality is good enough for tomography reconstruction in view of future applications to virtual page-by-page `reading'. When attenuation is too low, differential phase contrast imaging can reveal the characters from refractive index effects. The results are potentially important for new information harvesting strategies, for example from the huge Archivio di Stato collection, objective of the Venice Time Machine project.

  15. Ancient administrative handwritten documents: X-ray analysis and imaging

    PubMed Central

    Albertin, F.; Astolfo, A.; Stampanoni, M.; Peccenini, Eva; Hwu, Y.; Kaplan, F.; Margaritondo, G.

    2015-01-01

    Handwritten characters in administrative antique documents from three centuries have been detected using different synchrotron X-ray imaging techniques. Heavy elements in ancient inks, present even for everyday administrative manuscripts as shown by X-ray fluorescence spectra, produce attenuation contrast. In most cases the image quality is good enough for tomography reconstruction in view of future applications to virtual page-by-page ‘reading’. When attenuation is too low, differential phase contrast imaging can reveal the characters from refractive index effects. The results are potentially important for new information harvesting strategies, for example from the huge Archivio di Stato collection, objective of the Venice Time Machine project. PMID:25723946

  16. Acceleration modules in linear induction accelerators

    NASA Astrophysics Data System (ADS)

    Wang, Shao-Heng; Deng, Jian-Jun

    2014-05-01

    The Linear Induction Accelerator (LIA) is a unique type of accelerator that is capable of accelerating kilo-Ampere charged particle current to tens of MeV energy. The present development of LIA in MHz bursting mode and the successful application into a synchrotron have broadened LIA's usage scope. Although the transformer model is widely used to explain the acceleration mechanism of LIAs, it is not appropriate to consider the induction electric field as the field which accelerates charged particles for many modern LIAs. We have examined the transition of the magnetic cores' functions during the LIA acceleration modules' evolution, distinguished transformer type and transmission line type LIA acceleration modules, and re-considered several related issues based on transmission line type LIA acceleration module. This clarified understanding should help in the further development and design of LIA acceleration modules.

  17. Transnasal excerebration surgery in ancient Egypt.

    PubMed

    Fanous, Andrew A; Couldwell, William T

    2012-04-01

    Ancient Egyptians were pioneers in many fields, including medicine and surgery. Our modern knowledge of anatomy, pathology, and surgical techniques stems from discoveries and observations made by Egyptian physicians and embalmers. In the realm of neurosurgery, ancient Egyptians were the first to elucidate cerebral and cranial anatomy, the first to describe evidence for the role of the spinal cord in the transmission of information from the brain to the extremities, and the first to invent surgical techniques such as trepanning and stitching. In addition, the transnasal approach to skull base and intracranial structures was first devised by Egyptian embalmers to excerebrate the cranial vault during mummification. In this historical vignette, the authors examine paleoradiological and other evidence from ancient Egyptian skulls and mummies of all periods, from the Old Kingdom to Greco-Roman Egypt, to shed light on the development of transnasal surgery in this ancient civilization. The authors confirm earlier observations concerning the laterality of this technique, suggesting that ancient Egyptian excerebration techniques penetrated the skull base mostly on the left side. They also suggest that the original technique used to access the skull base in ancient Egypt was a transethmoidal one, which later evolved to follow a transsphenoidal route similar to the one used today to gain access to pituitary lesions.

  18. Proton Acceleration at Oblique Shocks

    NASA Astrophysics Data System (ADS)

    Galinsky, V. L.; Shevchenko, V. I.

    2011-06-01

    Acceleration at the shock waves propagating oblique to the magnetic field is studied using a recently developed theoretical/numerical model. The model assumes that resonant hydromagnetic wave-particle interaction is the most important physical mechanism relevant to motion and acceleration of particles as well as to excitation and damping of waves. The treatment of plasma and waves is self-consistent and time dependent. The model uses conservation laws and resonance conditions to find where waves will be generated or damped, and hence particles will be pitch-angle-scattered. The total distribution is included in the model and neither introduction of separate population of seed particles nor some ad hoc escape rate of accelerated particles is needed. Results of the study show agreement with diffusive shock acceleration models in the prediction of power spectra for accelerated particles in the upstream region. However, they also reveal the presence of spectral break in the high-energy part of the spectra. The role of the second-order Fermi-like acceleration at the initial stage of the acceleration is discussed. The test case used in the paper is based on ISEE-3 data collected for the shock of 1978 November 12.

  19. PROTON ACCELERATION AT OBLIQUE SHOCKS

    SciTech Connect

    Galinsky, V. L.; Shevchenko, V. I.

    2011-06-20

    Acceleration at the shock waves propagating oblique to the magnetic field is studied using a recently developed theoretical/numerical model. The model assumes that resonant hydromagnetic wave-particle interaction is the most important physical mechanism relevant to motion and acceleration of particles as well as to excitation and damping of waves. The treatment of plasma and waves is self-consistent and time dependent. The model uses conservation laws and resonance conditions to find where waves will be generated or damped, and hence particles will be pitch-angle-scattered. The total distribution is included in the model and neither introduction of separate population of seed particles nor some ad hoc escape rate of accelerated particles is needed. Results of the study show agreement with diffusive shock acceleration models in the prediction of power spectra for accelerated particles in the upstream region. However, they also reveal the presence of spectral break in the high-energy part of the spectra. The role of the second-order Fermi-like acceleration at the initial stage of the acceleration is discussed. The test case used in the paper is based on ISEE-3 data collected for the shock of 1978 November 12.

  20. New perspectives on ancient Mars.

    PubMed

    Solomon, Sean C; Aharonson, Oded; Aurnou, Jonathan M; Banerdt, W Bruce; Carr, Michael H; Dombard, Andrew J; Frey, Herbert V; Golombek, Matthew P; Hauck, Steven A; Head, James W; Jakosky, Bruce M; Johnson, Catherine L; McGovern, Patrick J; Neumann, Gregory A; Phillips, Roger J; Smith, David E; Zuber, Maria T

    2005-02-25

    Mars was most active during its first billion years. The core, mantle, and crust formed within approximately 50 million years of solar system formation. A magnetic dynamo in a convecting fluid core magnetized the crust, and the global field shielded a more massive early atmosphere against solar wind stripping. The Tharsis province became a focus for volcanism, deformation, and outgassing of water and carbon dioxide in quantities possibly sufficient to induce episodes of climate warming. Surficial and near-surface water contributed to regionally extensive erosion, sediment transport, and chemical alteration. Deep hydrothermal circulation accelerated crustal cooling, preserved variations in crustal thickness, and modified patterns of crustal magnetization.

  1. Burns treatment in ancient times.

    PubMed

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

    2013-01-01

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

  2. Ancient dna from pleistocene fossils: Preservation, recovery, and utility of ancient genetic information for quaternary research

    NASA Astrophysics Data System (ADS)

    Yang, Hong

    Until recently, recovery and analysis of genetic information encoded in ancient DNA sequences from Pleistocene fossils were impossible. Recent advances in molecular biology offered technical tools to obtain ancient DNA sequences from well-preserved Quaternary fossils and opened the possibilities to directly study genetic changes in fossil species to address various biological and paleontological questions. Ancient DNA studies involving Pleistocene fossil material and ancient DNA degradation and preservation in Quaternary deposits are reviewed. The molecular technology applied to isolate, amplify, and sequence ancient DNA is also presented. Authentication of ancient DNA sequences and technical problems associated with modern and ancient DNA contamination are discussed. As illustrated in recent studies on ancient DNA from proboscideans, it is apparent that fossil DNA sequence data can shed light on many aspects of Quaternary research such as systematics and phylogeny. conservation biology, evolutionary theory, molecular taphonomy, and forensic sciences. Improvement of molecular techniques and a better understanding of DNA degradation during fossilization are likely to build on current strengths and to overcome existing problems, making fossil DNA data a unique source of information for Quaternary scientists.

  3. New interpretation of the ancient constellations

    NASA Astrophysics Data System (ADS)

    Dementev, M. S.

    New method of study of the ancient constellations and mythes is discussed. It is based on the comparison of two maps - the sky and the Earth. The Stellar map is built in an equatorial system of coordinates, the geografic map - in the Mercator's projection and of the same scale. The former map is put on the laster one. The constellation of Pleiades (seven daughter of Atlant) is placed on the meridian of Atlant (Western coast of Africa). If the Stellar map is constructed for a epoch J-3000 (3000 years up to B.C.) then we could found the following. The constellations Andromeda (the daughter of the Ethiopian tsar), Cetus, Perseus and Cassiopeia (mother of Andromeda) are projected on the centre, south and west of Ancient Ethiopia and Mediterranean Sea, respectively. That is all the constellations fall to the places, where events described in mythes occured. A constellation Cepheus (Arabian name is "Burning") covers the Caucasus. Possibly, before a epoch J-1000 this group of stars was connected with Prometheus. It is known Prometheus was chained to the Caucasian rock because of stealing of a fire. Ancient Chineses divided the sky in other way. They called "The Heavenly Town" the area of sky consisting of stars in Herculis, Aquilae and Ophiuchi. Parts of the mentioned constellation were called as a provinces in Ancient China. If the Heavenly Town locate near the Ancient China then the Greek constellations (Andromeda, Perseus and Cetus) will appear over Africa. Three important conclusions follow from this: (i) the geography of the Earth is reflected on the sky; (ii) the ancient astronomers were investigating a connection between the sky and Earth; (iii) the ancient peoples exchanged by the information about a construction of the world.

  4. [Light and blindness in ancient Egypt].

    PubMed

    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.

  5. First images of respiratory system in ancient Egypt: Trachea, bronchi and pulmonary lobes.

    PubMed

    Kwiecinski, Jakub

    2012-01-01

    Examination of ancient Egyptians' depictions of the respiratory tract, dating back to the 30th century BC, reveals their awareness of the pulmonary anatomy: reinforced with cartilaginous rings, the trachea is split into two main bronchi, which then enter the lungs (lungs being divided into pulmonary lobes).

  6. Low-temperature thermochronology applied to ancient settings

    NASA Astrophysics Data System (ADS)

    Enkelmann, Eva; Garver, John I.

    2016-01-01

    Low-temperature thermochronometric dating techniques are commonly used to reveal and quantify the spatial and temporal pattern of cooling and exhumation in many active mountain belts. These methods illuminate the relationship between rock exhumation, and the processes that bring rock to the surface, including climate-driven surface processes. Thermochronological studies on rocks in ancient settings (Precambrian and Paleozoic) are far more complicated, and in general have largely failed to reveal exhumation processes in orogenic belts, mainly due to imprecision of the technique, complications from radiation damage, and subsequent resetting. However, in a few locations, remnants of the exhumation record of ancient orogens may be studied with low-temperature dating techniques and in these cases we can gather first-order information on tectonics, thermal events, and exhumation processes that have occurred in the deep past. Here we provide an overview of the most common low-temperature thermochronology methods of fission-track and (U-Th)/He dating of apatite and zircon and discuss methodological challenges in their application to old settings. We review several case studies from the Northern Appalachians, central Argentina, the Canadian Shield, central Wyoming, and the European Variscides where thermochronology data have been successful in reconstructing geologic processes in deep-time that have affected the upper crust. With these examples we provide sampling strategies and analytical approaches that partly circumvent issues related to radiation damage in old mineral grains that result in changes in the retention of helium and fission tracks.

  7. The Ancient Martian Climate System

    NASA Technical Reports Server (NTRS)

    Haberle, Robert M.

    2014-01-01

    Today Mars is a cold, dry, desert planet. The atmosphere is thin and liquid water is not stable. But there is evidence that very early in its history it was warmer and wetter. Since Mariner 9 first detected fluvial features on its ancient terrains researchers have been trying to understand what climatic conditions could have permitted liquid water to flow on the surface. Though the evidence is compelling, the problem is not yet solved. The main issue is coping with the faint young sun. During the period when warmer conditions prevailed 3.5-3.8 Gy the sun's luminosity was approximately 25% less than it is today. How can we explain the presence of liquid water on the surface of Mars under such conditions? A similar problem exists for Earth, which would have frozen over under a faint sun even though the evidence suggests otherwise. Attempts to solve the "Faint Young Sun Paradox" rely on greenhouse warming from an atmosphere with a different mass and composition than we see today. This is true for both Mars and Earth. However, it is not a straightforward solution. Any greenhouse theory must (a) produce the warming and rainfall needed, (b) have a plausible source for the gases required, (c) be sustainable, and (d) explain how the atmosphere evolved to its present state. These are challenging requirements and judging from the literature they have yet to be met. In this talk I will review the large and growing body of work on the early Mars climate system. I will take a holistic approach that involves many disciplines since our goal is to present an integrated view that touches on each of the requirements listed in the preceding paragraph. I will begin with the observational evidence, which comes from the geology, mineralogy, and isotopic data. Each of the data sets presents a consistent picture of a warmer and wetter past with a thicker atmosphere. How much warmer and wetter and how much thicker is a matter of debate, but conditions then were certainly different than

  8. Magnetic Strips Preserve Record of Ancient Mars

    NASA Technical Reports Server (NTRS)

    1999-01-01

    magnetic interference, and they do not have the resolution to detect these features,' Acuna noted. 'We began with misfortune, and ended up winning the lottery.'

    The bands of magnetized crust apparently formed in the distant past when Mars had an active dynamo, or hot core of molten metal, which generated a global magnetic field. Mars was geologically active, with molten rock rising from below cooling at the surface and forming new crust. As the new crust solidified, the magnetic field that permeated the rock was 'frozen' in the crust. Periodically, conditions in the dynamo changed and the global magnetic field reversed direction. The oppositely directed magnetic field was then frozen into newer crust.

    [figure removed for brevity, see original site] (P50331,MRPS94770)

    Above: These images are an artist's concept of the process that may have generated magnetic stripes in the crust of ancient Mars. In the left image, the blue arrows and compass needle indicate the direction of the magnetic field. The yellow-orange shape represents a pool of molten rock (magma)upwelling beneath the Martian crust. The red and blue bands are magnetized crust on either side of a spreading center, or rift.

    'Like a Martian tape recorder, the crust has preserved a fossil record of the magnetic field directions that prevailed at different times in the ancient past,' Connerney said. When the planet's hot core cooled, the dynamo ceased and the global magnetic field of Mars vanished. However, a record of the magnetic field was preserved in the crust and detected by the Global Surveyor instrument.

    The mission's map of Martian magnetic regions may help solve another mystery -- the origin of a striking difference in appearance between the smooth, sparsely cratered northern lowlands of Mars and the heavily cratered southern highlands. The map reveals that the northern regions are largely free of magnetism, indicating the northern crust formed after the dynamo died. 'The dynamo likely

  9. Medical science in ancient Indian culture with special reference to Atharvaveda.

    PubMed

    Narayana, A

    1995-01-01

    A high quality of Medical Knowledge was prevalent in ancient India. The present day Archaeological evidences of Mohenjo-daro and Harappa imparts the high civilization in matters of sanitation and hygiene. An analysis of the material in the Vedas reveals that, all the four Vedas replete the references regarding various aspects of medicine. The Atharva Veda is deemed to be an encyclopaedia for medicine "Interalia", and Ayurveda (the science of life) is considered as Upa Veda (supplementary subject) of the Atharva Veda. A few glimpses of medical Science as prevalent in the ancient India have been presented here.

  10. Determination and Radiocarbon Dating of Marine Mollusc Fossils in Ancient Sea Shelf of Central Java Indonesia

    NASA Astrophysics Data System (ADS)

    Aisyah, S.; Pringgenies, D.; Hartoko, A.; Sumantyo, J. T. S.; Matsuzaki, H.

    2017-02-01

    Mollusc phylum is one of the most adaptive animal groups on Earth. They occupy and thrive in incredibly diverse habitats. Their distribution in the fossil record is equally diverse. Indonesia is one of the country with marine mollusc fossil variety, such as in the archaeological site of Sangiran, Patiayam (Ancient Muria Strait) and Grobogan – Central Java. Radiocarbon Dating is the method for dating analysis using 14C. By measuring 14C content, we can estimate how long ago the fossils died. Radiocarbon dating is an extremely useful technique for determining the ages of geological materials (that have some organic-derived carbon in them). Field sampling had found variety of marine mollusc fossils such us 1) Sangiran: Dosinia sp., Telescopium telescopium, Anadara sp., and Dosinia insularum; 2) Patiayam (Ancient Muria Strait): Pseudodon vondenbuschianus, Elongaria orientalis, Conus (Pionoconus) sp., Ampullina bandongensis, Anadara pilula and Filopaludina javanica; 3) Grobogan: Antigona chemnitzii, Cultelus dilatatus, Plotia scabra and Tibia modesta. Mollusc fossils sample was analysed using Accelerator Mass Spectrometer (AMS) radiocarbon system. It is a good method for dating specific samples. The result showed that Sangiran as an ancient deepsea has fossils age 38710 – 31947 years, then Patiayam (Ancient Muria Strait) with fossils age 26248 – 11994. Mollusc fossils from Grobogan was the youngest area has fossils age 25692 – 6479 years.

  11. Faunal histories from Holocene ancient DNA.

    PubMed

    de Bruyn, Mark; Hoelzel, A Rus; Carvalho, Gary R; Hofreiter, Michael

    2011-08-01

    Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.

  12. The practice of dentistry in ancient Egypt.

    PubMed

    Forshaw, R J

    2009-05-09

    This paper addresses the questions of whether a dental profession existed in ancient Egypt and if it did then considers whether these practitioners were operative dental surgeons as we know them today or whether they were pharmacists. Evidence from hieroglyphic inscriptions, from the dentitions of the surviving mummified and skeletal remains, and from ancient documents and artefacts are examined. The conclusion would suggest that operative dental treatment if it did exist at all was extremely limited. The dental treatment that appears to have been provided was mainly restricted to pharmaceutical preparations that were either applied to the gingival and mucosal tissues or used as mouthwashes, and these at best may only have provided some short term relief. It seems apparent that many ancient Egyptians suffered from widespread and painful dental disease, which the available treatments can have done relatively little to alleviate.

  13. Did the ancient egyptians discover Algol?

    NASA Astrophysics Data System (ADS)

    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).

  14. Twins in Ancient Greece: a synopsis.

    PubMed

    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.

  15. Prehistoric polymers: rubber processing in ancient mesoamerica

    PubMed

    Hosler; Burkett; Tarkanian

    1999-06-18

    Ancient Mesoamerican peoples harvested latex from Castilla elastica, processed it using liquid extracted from Ipomoea alba (a species of morning glory vine), and fashioned rubber balls, hollow rubber figurines, and other rubber artifacts from the resulting material. Chemical and mechanical analyses of the latex and of the processed rubber indicate that the enhanced elastic behavior of the rubber relative to the unprocessed latex is due to purification of the polymer component and to an increase in the strength and number of interchain interactions that are induced by organic compounds present in I. alba. These ancient peoples' control over the properties of latex and processed rubber gave rise to the Mesoamerican ball game, a central ritual element in all ancient Mesoamerican societies.

  16. Palaeoparasitology - Human Parasites in Ancient Material.

    PubMed

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

    2015-01-01

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

  17. Ancient Greek psychotherapy for contemporary nurses.

    PubMed

    Kourkouta, Lambrini

    2002-08-01

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

  18. Finding Ancient Supernovae at 5 < z < 12 with Frontier Fields

    NASA Astrophysics Data System (ADS)

    Whalen, Daniel J.

    Supernovae are important probes of the properties of stars at high redshifts because they can be detected at early epochs and their masses can be inferred from their light curves. Direct detection of the first cosmic explosions in the universe will only be possible with JWST, WFIRST and the next generation of extremely large telescopes. But strong gravitational lensing by massive clusters, like those in the Frontier Fields, could reveal supernovae at slightly lower redshifts now by magnifying their flux by factors of 10 or more. We find that Frontier Fields will likely discover dozens of core-collapse supernovae at 5 < z < 12. Future surveys of cluster lenses similar in scope to Frontier Fields by JWST might find hundreds of these events out to z ~ 15 - 17. Besides revealing the masses of early stars, these ancient supernovae could also constrain cosmic star formation rates in the era of first galaxy formation.

  19. Finding Ancient Supernovae at 5 < z < 12 with Frontier Fields

    NASA Astrophysics Data System (ADS)

    Whalen, Daniel

    2015-08-01

    Supernovae are important probes of the properties of stars at high redshifts because they can be detected at early epochs and their masses can be inferred from their light curves. Finding the first cosmic explosions in the universe will only be possible with JWST, the WFIRST and the next generation of extremely large telescopes. But strong gravitational lensing by massive clusters, like those in the Frontier Fields, could reveal supernovae at slightly lower redshifts now by magnifying their flux by factors of 10 or more. We find that Frontier Fields will likely discover dozens of core-collapse supernovae at 5 < z < 12. Future surveys of cluster lenses similar in scope to Frontier Fields by JWST might find hundreds of these events out to z ~ 15 - 17. Besides revealing the masses of early stars, these ancient supernovae could also constrain cosmic star formation rates in the era of first galaxy formation.

  20. Combined geophysical investigation for the detection of ancient metallurgical installations near Keratea City, Greece

    NASA Astrophysics Data System (ADS)

    Apostolopoulos, George V.

    2014-05-01

    Archaeological excavation in an area of Lavrio (mining area from ancient times) has revealed ancient metallurgical installations which offer valuable information on this activity at those times. Within this context, a combined geophysical investigation was carried out in a place near Keratea City to find out whether there are additional installations apart from those that have already been revealed in the immediate area. More importantly, the objective was to locate the ancient tanks which provided water to the installations. Archaeological and geological information have helped in the design of the survey. EMI method measuring apparent conductivity was used to cover the whole area of investigation. Conductivity maps in various investigation depths have positioned the tanks and stacked first derivative maps in two directions (the two directions of the revealed walls) show covered walls. The EMI survey has indicated the position of three (3) ERT profiles made with the dipole-dipole array, which presented the ancient tanks with great detail in depth. GPR profiles for the detection of walls were noisy with the coarse material surface layer but the interrelation with ERT and EMI results confirmed the detected features.

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

    PubMed Central

    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

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

    PubMed

    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.

  3. Ancient mtDNA sequences from the First Australians revisited

    PubMed Central

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

    2016-01-01

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

  4. Ancient mtDNA sequences from the First Australians revisited.

    PubMed

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

    2016-06-21

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

  5. Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

    PubMed Central

    Tito, Raúl Y.; Macmil, Simone; Wiley, Graham; Najar, Fares; Cleeland, Lauren; Qu, Chunmei; Wang, Ping; Romagne, Frederic; Leonard, Sylvain; Ruiz, Agustín Jiménez; Reinhard, Karl; Roe, Bruce A.; Lewis, Cecil M.

    2008-01-01

    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. PMID:19002248

  6. Future accelerator technology

    SciTech Connect

    Sessler, A.M.

    1986-05-01

    A general discussion is presented of the acceleration of particles. Upon this foundation is built a categorization scheme into which all accelerators can be placed. Special attention is devoted to accelerators which employ a wake-field mechanism and a restricting theorem is examined. It is shown how the theorem may be circumvented. Comments are made on various acceleration schemes.

  7. ACCELERATION AND THE GIFTED.

    ERIC Educational Resources Information Center

    GIBSON, ARTHUR R.; STEPHANS, THOMAS M.

    ACCELERATION OF PUPILS AND SUBJECTS IS CONSIDERED A MEANS OF EDUCATING THE ACADEMICALLY GIFTED STUDENT. FIVE INTRODUCTORY ARTICLES PROVIDE A FRAMEWORK FOR THINKING ABOUT ACCELERATION. FIVE PROJECT REPORTS OF ACCELERATED PROGRAMS IN OHIO ARE INCLUDED. ACCELERATION IS NOW BEING REGARDED MORE FAVORABLY THAN FORMERLY, BECAUSE METHODS HAVE BEEN…

  8. Laser driven ion accelerator

    DOEpatents

    Tajima, Toshiki

    2005-06-14

    A system and method of accelerating ions in an accelerator to optimize the energy produced by a light source. Several parameters may be controlled in constructing a target used in the accelerator system to adjust performance of the accelerator system. These parameters include the material, thickness, geometry and surface of the target.

  9. Laser driven ion accelerator

    DOEpatents

    Tajima, Toshiki

    2006-04-18

    A system and method of accelerating ions in an accelerator to optimize the energy produced by a light source. Several parameters may be controlled in constructing a target used in the accelerator system to adjust performance of the accelerator system. These parameters include the material, thickness, geometry and surface of the target.

  10. Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function

    PubMed Central

    Naeem, Villian; Chen, Yanmei; Lee, Terrance; Angeloni, Nicholas; Wang, Yin; Xu, Eugene Yujun

    2010-01-01

    Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. Examination of Boule evolution within insect and mammalian lineages revealed little evidence for accelerated evolution, unlike most reproductive genes. Instead, purifying selection was the major force behind Boule evolution. Furthermore, loss of function of mammalian Boule resulted in male-specific infertility and a global arrest of sperm development remarkably similar to the phenotype in an insect boule mutation. This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis. PMID:20657660

  11. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes.

    PubMed

    Lee, Alison P; Kerk, Sze Yen; Tan, Yue Ying; Brenner, Sydney; Venkatesh, Byrappa

    2011-03-01

    Vertebrate genomes contain thousands of conserved noncoding elements (CNEs) that often function as tissue-specific enhancers. In this study, we have identified CNEs in human, dog, chicken, Xenopus, and four teleost fishes (zebrafish, stickleback, medaka, and fugu) using elephant shark, a cartilaginous vertebrate, as the base genome and investigated the evolution of these ancient vertebrate CNEs (aCNEs) in bony vertebrate lineages. Our analysis shows that aCNEs have been evolving at different rates in different bony vertebrate lineages. Although 78-83% of CNEs have diverged beyond recognition ("lost") in different teleost fishes, only 24% and 40% have been lost in the chicken and mammalian lineages, respectively. Relative rate tests of substitution rates in CNEs revealed that the teleost fish CNEs have been evolving at a significantly higher rate than those in other bony vertebrates. In the ray-finned fish lineage, 68% of aCNEs were lost before the divergence of the four teleosts. This implicates the "fish-specific" whole-genome duplication in the accelerated evolution and the loss of a large number of both copies of duplicated CNEs in teleost fishes. The aCNEs are rich in tissue-specific enhancers and thus many of them are likely to be evolutionarily constrained cis-regulatory elements. The rapid evolution of aCNEs might have affected the expression patterns driven by them. Transgenic zebrafish assay of some human CNE enhancers that have been lost in teleosts has indicated instances of conservation or changes in trans-acting factors between mammals and fishes.

  12. Ancient DNA and Population Turnover in Southern Levantine Pigs- Signature of the Sea Peoples Migration?

    PubMed Central

    Meiri, Meirav; Huchon, Dorothée; Bar-Oz, Guy; Boaretto, Elisabetta; Horwitz, Liora Kolska; Maeir, Aren M.; Sapir-Hen, Lidar; Larson, Greger; Weiner, Steve; Finkelstein, Israel

    2013-01-01

    Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution. PMID:24186332

  13. Accelerated evolution of the Lyα luminosity function at z ≳ 7 revealed by the Subaru ultra-deep survey for Lyα emitters at z = 7.3

    SciTech Connect

    Konno, Akira; Ouchi, Masami; Ono, Yoshiaki; Shibuya, Takatoshi; Naito, Yoshiaki; Momose, Rieko; Yuma, Suraphong; Shimasaku, Kazuhiro; Nakajima, Kimihiko; Furusawa, Hisanori; Iye, Masanori

    2014-12-10

    We present the ultra-deep Subaru narrowband imaging survey for Lyα emitters (LAEs) at z = 7.3 in the Subaru/XMM-Newton Deep Survey (SXDS) and Cosmic Evolution Survey (COSMOS) fields (∼0.5 deg{sup 2}) with a total integration time of 106 hr. Exploiting our new sharp bandwidth filter, NB101, installed on the Suprime-Cam, we have reached L(Lyα) = 2.4 × 10{sup 42} erg s{sup –1} (5σ) for z = 7.3 LAEs, about four times deeper than previous Subaru z ≳ 7 studies, which allows us to reliably investigate the evolution of the Lyα luminosity function (LF) for the first time down to the luminosity limit same as those of Subaru z = 3.1-6.6 LAE samples. Surprisingly, we only find three and four LAEs in the SXDS and COSMOS fields, respectively, while one expects a total of ∼65 LAEs by our survey in the case of no Lyα LF evolution from z = 6.6 to 7.3. We identify a decrease of the Lyα LF from z = 6.6 to 7.3 at the >90% confidence level from our z = 7.3 Lyα LF with the best-fit Schechter parameters of L{sub Lyα}{sup ∗}=2.7{sub −1.2}{sup +8.0}×10{sup 42} erg s{sup −1} and ϕ{sup ∗}=3.7{sub −3.3}{sup +17.6}×10{sup −4} Mpc{sup −3} for a fixed α = –1.5. Moreover, the evolution of the Lyα LF is clearly accelerated at z > 6.6 beyond the measurement uncertainties including cosmic variance. Because no such accelerated evolution of the UV-continuum LF or the cosmic star formation rate (SFR) is found at z ∼ 7, but suggested only at z > 8, this accelerated Lyα LF evolution is explained by physical mechanisms different from a pure SFR decrease but related to the Lyα production and escape in the process of cosmic reionization. Because a simple accelerating increase of intergalactic medium neutral hydrogen absorbing Lyα cannot be reconciled with Thomson scattering of optical depth measurements from WMAP and Planck, our findings may support new physical pictures suggested by recent theoretical studies, such as the existence of HI clumpy clouds within

  14. Understanding projectile acceleration.

    PubMed

    Hecht, H; Bertamini, M

    2000-04-01

    Throwing and catching balls or other objects is a generally highly practiced skill; however, conceptual as well as perceptual understanding of the mechanics that underlie this skill is surprisingly poor. In 5 experiments, we investigated conceptual and perceptual understanding of simple ballistic motion. Paper-and-pencil tests revealed that up to half of all participants mistakenly believed that a ball would continue to accelerate after it left the thrower's hand. Observers also showed a remarkable tolerance for anomalous trajectory shapes. Perceptual judgments based on graphics animations replicated these erroneous beliefs for shallow release angles. Observers' tolerance for anomalies tended to decrease with their distance from the actor. The findings are at odds with claims of the naive physics literature that liken intuitive understanding to Aristotelian or medieval physics theories. Instead, observers seem to project their intentions to the ball itself (externalization) or even feel that they have power over the ball when it is still close.

  15. Pulsed electromagnetic acceleration

    NASA Technical Reports Server (NTRS)

    Jahn, R. G.; Vonjaskowsky, W. F.; Clark, K. E.

    1973-01-01

    Direct measurements of the power deposited in the anode of a multimegawatt MPD accelerator using thermocouples attached to a thin shell anode reveal a dramatic decrease in the fractional anode power from 50% at 200 KW input power to less than 10% at 20 MW power. The corresponding local power flux peak at a value of 10,000 W/sq cm at the lip of the anode exhaust orifice, a distribution traced to a corresponding peak in the local current density at the anode. A comparison of voltage-current characteristics and spectral photographs of the MPD discharge using quartz, boron nitride and plexiglas insulators with various mass injection configurations led to the identification of different voltage modes and regions of ablation free operation. The technique of piezoelectric impact pressure measurement in the MPD exhaust flow was refined to account for the effects due to probe yaw angle.

  16. Unlocking the Mysteries of Ancient Egypt.

    ERIC Educational Resources Information Center

    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…

  17. Ancient DNA analysis of dental calculus.

    PubMed

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

    2015-02-01

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

  18. Communication Arts in the Ancient World.

    ERIC Educational Resources Information Center

    Havelock, Eric A., Ed.; Hershbell, Jackson P., Ed.

    Intended for both classicists and nonclassicists, this volume explores the beginnings of literacy in ancient Greece and Rome and examines the effects of written communication on these cultures. The nine articles, written by classical scholars and educators in the field of communication, discuss the following: the superiority of the alphabet over…

  19. The ancient history of Halley's comet.

    NASA Astrophysics Data System (ADS)

    Stephenson, F. R.

    Contents: The accuracy of orbital parameters. The apparition in 12 B.C. Chinese references to comets around 87 and 164 B.C. Cometary records from ancient China. Late Babylonian cometary records. The apparition of 87 B.C. The apparition of 164 B.C. The apparition of 240 B.C. Conclusion.

  20. Ancient science in a digital age.

    PubMed

    Lehoux, Daryn

    2013-03-01

    Technology is rapidly changing our understanding of ancient science. New methods of visualization are bringing to light important texts we could not previously read; changes in online publishing are allowing unprecedented access to difficult-to-find materials; and online mapping tools are offering new pictures of lost spaces, connectivities, and physical objects.

  1. Defining Astrology in Ancient and Classical History

    NASA Astrophysics Data System (ADS)

    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.

  2. Ancient Human Parasites in Ethnic Chinese Populations

    PubMed Central

    Yeh, Hui-Yuan; Mitchell, Piers D.

    2016-01-01

    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. PMID:27853113

  3. Ancient whole grain gluten-free flatbreads

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA food guide recommends that at least ½ of all the grains eaten should be whole grains. The FDA allows food Health Claim labels for food containing 51% whole gains and 11 g of dietary fiber. This is the only report demonstrating innovative ancient whole grain gluten-free (no yeast or chemical...

  4. The Study of Women in Ancient Society.

    ERIC Educational Resources Information Center

    Moscovich, M. James

    1982-01-01

    Presents ideas for teaching about the roles of women in ancient Greek and Roman societies for undergraduate history and sociology classes. The discussion covers the roots of misogyny in Western culture, parallels between mythologies and sociocultural patterns, and the legal status of women in antiquity. (AM)

  5. Geoscience: Fossil raindrops and ancient air

    NASA Astrophysics Data System (ADS)

    Cassata, William S.; Renne, Paul R.

    2012-04-01

    An analysis of fossil imprints of ancient raindrops suggests that the density of the atmosphere 2.7 billion years ago was much the same as that today. This result casts fresh light on a long-standing palaeoclimate paradox. See Letter p.359

  6. NIMI TANTRA (Opthalmology of Ancient India)

    PubMed Central

    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. PMID:22557403

  7. Perry: american renaissance of an ancient beverage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Burgeoning world interest in cider and perry (pear cider, which is an alcoholic beverage) has created a strong demand for unique perry pear (Pyrus L.) cultivars. The history of perry dates to the ancient Romans. This beverage has been very popular through the centuries in Europe. The U.S. Department...

  8. Women of Ancient Greece: Participating in Sport?

    ERIC Educational Resources Information Center

    Mills, Brett D.

    Based on evidence obtained from Greek literature and artifacts, this paper examines the extent to which women in ancient Greece participated in physical activity, sports, and games. Homer's "Odyssey" describes women playing ball and driving chariots; vases dating back to 700-675 B.C. portray women driving light chariots in a procession;…

  9. Myths and Gods of Ancient Mexico.

    ERIC Educational Resources Information Center

    Rascon, Vincent P.

    Intended to help Americans of Mexican descent understand their rich cultural heritage, this portfolio contains 12 full-color drawings of the myths and gods of the Olmecs and Toltecs of Ancient Mexico. These original drawings are by Vincent P. Rascon. Information captions in English and Spanish are given for each drawing which is printed on heavy…

  10. Microscopical Examination of Ancient Silver Coins

    SciTech Connect

    Pistofidis, N.; Vourlias, G.; Pavlidou, El.; Stergioudis, G.; Polychroniadis, E. K.; Dilo, T.; Prifti, I.; Bilani, O.; Civici, N.; Stamati, F.; Gjongecaj, Sh.

    2007-04-23

    The microstructure of three silver coins of the IIId century B.C. from the Illyrian king Monounios, the ancient Greek city of Dyrrachion and of Korkyra was studied with XRF and microscopy. From this investigation it turned out that these coins have different chemical composition and microstructure that imply different minting method.

  11. Ancient Pyramids Help Students Learn Math Concepts

    ERIC Educational Resources Information Center

    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…

  12. Precursors of Vocational Psychology in Ancient Civilizations.

    ERIC Educational Resources Information Center

    Dumont, Frank; Carson, Andrew D.

    1995-01-01

    Examines philosophical theories produced by two ancient civilizations (Eastern Mediterranean and Chinese) for applications to an applied psychology of work. Includes analysis of Egyptians, Semites, and Greeks, with a special emphasis on Plato. Suggests that many basic elements of vocational psychology were present during the first millennium B.C.…

  13. The Challenges of Qualitatively Coding Ancient Texts

    ERIC Educational Resources Information Center

    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,…

  14. Outreach Testing of Ancient Astronomy

    NASA Astrophysics Data System (ADS)

    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

  15. Comparison of modern Mississippi fan with selected ancient fans

    SciTech Connect

    Shanmugam, G.; Moiola, R.J.; McPherson, J.G.; O'Connell, S.

    1988-09-01

    A comparison of the modern passive-margin Mississippi fan (DSDP Leg 96) with selected ancient active-margin fans reveals major differences in turbidite facies associations and seismic characteristics of the lower fan area. The lower Mississippi fan is composed of channel (facies B and F) and nonchannel sequences (facies C. and D), whereas lower fan areas of ancient active-margin fans are characterized by nonchannelized, thickening-upward depositional lobes (facies C and D) with sheetlike geometry. An absence of depositional lobes in the lower Mississippi fan is also suggested by a lack of mounded seismic reflections. Continuous and parallel seismic reflections of the lower Mississippi fan may represent sheet sands, but not those of true depositional lobes. In mature passive-margin fans, long, sinuous channels develop as a consequence of low gradients and the transport of sediment with a relatively low sand/mud ratio, and these channels develop lenticular sand bodies. In contrast, channels in active-margin fans are short and commonly braided as a result of high gradients and the transport of sediment with a relatively high sand/mud ratio. Braided channels characteristically develop sheetlike sand bodies.

  16. Characterization and Discrimination of Ancient Grains: A Metabolomics Approach.

    PubMed

    Righetti, Laura; Rubert, Josep; Galaverna, Gianni; Folloni, Silvia; Ranieri, Roberto; Stranska-Zachariasova, Milena; Hajslova, Jana; Dall'Asta, Chiara

    2016-07-27

    Hulled, or ancient, wheats were the earliest domesticated wheats by mankind and the ancestors of current wheats. Their cultivation drastically decreased during the 1960s; however, the increasing demand for a healthy and equilibrated diet led to rediscovering these grains. Our aim was to use a non-targeted metabolomic approach to discriminate and characterize similarities and differences between ancient Triticum varieties. For this purpose, 77 hulled wheat samples from three different varieties were collected: Garfagnana T. turgidum var. dicoccum L. (emmer), ID331 T. monococcum L. (einkorn) and Rouquin T. spelta L. (spelt). The ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-QTOF) metabolomics approach highlighted a pronounced sample clustering according to the wheat variety, with an excellent predictability (Q²), for all the models built. Fifteen metabolites were tentatively identified based on accurate masses, isotopic pattern, and product ion spectra. Among these, alkylresorcinols (ARs) were found to be significantly higher in spelt and emmer, showing different homologue composition. Furthermore, phosphatidylcholines (PC) and lysophosphatidylcholines (lysoPC) levels were higher in einkorn variety. The results obtained in this study confirmed the importance of ARs as markers to distinguish between Triticum species and revealed their values as cultivar markers, being not affected by the environmental influences.

  17. [DNA analysis in the anthropological approach of ancient populations].

    PubMed

    Keyser, Christine; Crubézy, Eric; Ludes, Bertrand

    2013-01-01

    The authors highlight the opportunities to reconstruct the human Eurasian steppe migration movements with the analyses of nuclear DNA markers (short tandem repeats on autosomal DNA and on the Y chromosome) as well as mitochondrial DNA markers. They studied 26 ancient human samples from the Krasnoyarsk area (Southern Siberia). The specimens were dated from the middle of the second millennium BC to the fourth century AD. The Y chromosome and the mitochondrial analyses revealed that few of them seem to be related matrilineally or patrilineally, but all subjects belong to Y haplogroup R1a1a-M17 which is known as a marker of the eastward migration of the early Indo-Europeans. Their results are in accordance with the hypothesis that at the Bronze and Iron Ages south Siberia was settled predominantly by European subjects suggesting an eastward migration of kurgan people across the Russo-Kazakh steppe. The single nucleotide polymorphisms (SNP) analyses on the physical traits indicate that the ancient studied specimens were blue or green eyed, fair skinned and light-haired.

  18. Ancient Blacksmiths, The Iron Age, Damascus Steels, and Modern Metallurgy

    SciTech Connect

    Sherby, O.D.; Wadsworth, J.

    2000-09-11

    The history of iron and Damascus steels is described through the eyes of ancient blacksmiths. For example, evidence is presented that questions why the Iron Age could not have begun at about the same time as the early Bronze Age (i.e. approximately 7000 B.C.). It is also clear that ancient blacksmiths had enough information from their forging work, together with their observation of color changes during heating and their estimate of hardness by scratch tests, to have determined some key parts of the present-day iron-carbon phase diagram. The blacksmiths' greatest artistic accomplishments were the Damascus and Japanese steel swords. The Damascus sword was famous not only for its exceptional cutting edge and toughness, but also for its beautiful surface markings. Damascus steels are ultrahigh carbon steels (UHCSs) that contain from 1.0 to 2.1%. carbon. The modern metallurgical understanding of UHCSs has revealed that remarkable properties can be obtained in these hypereutectoid steels. The results achieved in UHCSs are attributed to the ability to place the carbon, in excess of the eutectoid composition, to do useful work that enhances the high temperature processing of carbon steels and that improves the low and intermediate temperature mechanical properties.

  19. Characterization and Discrimination of Ancient Grains: A Metabolomics Approach

    PubMed Central

    Righetti, Laura; Rubert, Josep; Galaverna, Gianni; Folloni, Silvia; Ranieri, Roberto; Stranska-Zachariasova, Milena; Hajslova, Jana; Dall’Asta, Chiara

    2016-01-01

    Hulled, or ancient, wheats were the earliest domesticated wheats by mankind and the ancestors of current wheats. Their cultivation drastically decreased during the 1960s; however, the increasing demand for a healthy and equilibrated diet led to rediscovering these grains. Our aim was to use a non-targeted metabolomic approach to discriminate and characterize similarities and differences between ancient Triticum varieties. For this purpose, 77 hulled wheat samples from three different varieties were collected: Garfagnana T. turgidum var. dicoccum L. (emmer), ID331 T. monococcum L. (einkorn) and Rouquin T. spelta L. (spelt). The ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-QTOF) metabolomics approach highlighted a pronounced sample clustering according to the wheat variety, with an excellent predictability (Q2), for all the models built. Fifteen metabolites were tentatively identified based on accurate masses, isotopic pattern, and product ion spectra. Among these, alkylresorcinols (ARs) were found to be significantly higher in spelt and emmer, showing different homologue composition. Furthermore, phosphatidylcholines (PC) and lysophosphatidylcholines (lysoPC) levels were higher in einkorn variety. The results obtained in this study confirmed the importance of ARs as markers to distinguish between Triticum species and revealed their values as cultivar markers, being not affected by the environmental influences. PMID:27472322

  20. Collodictyon—An Ancient Lineage in the Tree of Eukaryotes

    PubMed Central

    Zhao, Sen; Burki, Fabien; Bråte, Jon; Keeling, Patrick J.; Klaveness, Dag; Shalchian-Tabrizi, Kamran

    2012-01-01

    The current consensus for the eukaryote tree of life consists of several large assemblages (supergroups) that are hypothesized to describe the existing diversity. Phylogenomic analyses have shed light on the evolutionary relationships within and between supergroups as well as placed newly sequenced enigmatic species close to known lineages. Yet, a few eukaryote species remain of unknown origin and could represent key evolutionary forms for inferring ancient genomic and cellular characteristics of eukaryotes. Here, we investigate the evolutionary origin of the poorly studied protist Collodictyon (subphylum Diphyllatia) by sequencing a cDNA library as well as the 18S and 28S ribosomal DNA (rDNA) genes. Phylogenomic trees inferred from 124 genes placed Collodictyon close to the bifurcation of the “unikont” and “bikont” groups, either alone or as sister to the potentially contentious excavate Malawimonas. Phylogenies based on rDNA genes confirmed that Collodictyon is closely related to another genus, Diphylleia, and revealed a very low diversity in environmental DNA samples. The early and distinct origin of Collodictyon suggests that it constitutes a new lineage in the global eukaryote phylogeny. Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods. These may therefore be ancient morphological features among eukaryotes. Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution. PMID:22319147

  1. Collodictyon--an ancient lineage in the tree of eukaryotes.

    PubMed

    Zhao, Sen; Burki, Fabien; Bråte, Jon; Keeling, Patrick J; Klaveness, Dag; Shalchian-Tabrizi, Kamran

    2012-06-01

    The current consensus for the eukaryote tree of life consists of several large assemblages (supergroups) that are hypothesized to describe the existing diversity. Phylogenomic analyses have shed light on the evolutionary relationships within and between supergroups as well as placed newly sequenced enigmatic species close to known lineages. Yet, a few eukaryote species remain of unknown origin and could represent key evolutionary forms for inferring ancient genomic and cellular characteristics of eukaryotes. Here, we investigate the evolutionary origin of the poorly studied protist Collodictyon (subphylum Diphyllatia) by sequencing a cDNA library as well as the 18S and 28S ribosomal DNA (rDNA) genes. Phylogenomic trees inferred from 124 genes placed Collodictyon close to the bifurcation of the "unikont" and "bikont" groups, either alone or as sister to the potentially contentious excavate Malawimonas. Phylogenies based on rDNA genes confirmed that Collodictyon is closely related to another genus, Diphylleia, and revealed a very low diversity in environmental DNA samples. The early and distinct origin of Collodictyon suggests that it constitutes a new lineage in the global eukaryote phylogeny. Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods. These may therefore be ancient morphological features among eukaryotes. Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution.

  2. The Ancient Kemetic Roots of Library and Information Science.

    ERIC Educational Resources Information Center

    Zulu, Itibari M.

    This paper argues that the ancient people of Kemet (Egypt), "the black land," built and operated the first major libraries and institutions of higher education in the world. Topics of discussion include the Ancient Egyptians as an African people; a chronology of Ancient Kemet; literature in Kemet; a history of Egyptian Librarianship; the…

  3. The accelerations of the earth and moon from early astronomical observations

    NASA Technical Reports Server (NTRS)

    Muller, P. M.; Stephenson, F. R.

    1975-01-01

    An investigation has compiled a very large amount of data on central or near central solar eclipses as recorded in four principal ancient sources (Greek and Roman classics, medieval European chronicles, Chinese annals and astronomical treatises, and Late Babylonian astronomical texts) and applied careful data selectivity criteria and statistical methods to obtain reliable dates, magnitudes, and places of observation of the events, and thereby made estimates of the earth acceleration and lunar acceleration. The basic conclusion is that the lunar acceleration and both tidal and nontidal earth accelerations have been essentially constant during the period from 1375 B.C. to the present.

  4. Wryneck in the ancient Hawaiians.

    PubMed

    Douglas, M T

    1991-03-01

    A unique cranial asymmetry previously noted in the skeletal remains from Mokapu, O'ahu, Hawai'i, is described. The anomaly involves an indentation of one or both of the occipital condyles and facial and vault asymmetry. This examination of the asymmetry includes a search for other reported occurrences, a detailed description, and a differential diagnosis. A multiple working hypothesis approach is employed. Comparison of the osseous material with the expected clinical pictures in craniosynostosis, Kleippel-Feil syndrome, primary basilar impression, and torticollis results in the most likely explanation of congenital torticollis. A high rate of occurrence of the anomaly (1.8%) is found in the skeletal remains from the Hawaiian Islands, but it has been documented in only two instances outside Hawai'i. A survey of patients seen at The Shriner's Hospital for Crippled Children does not reveal a high rate of occurrence of torticollis in Hawaiians relative to other ethnic groups.

  5. Accelerating Particles with Plasma

    ScienceCinema

    Litos, Michael; Hogan, Mark

    2016-07-12

    Researchers at SLAC explain how they use plasma wakefields to accelerate bunches of electrons to very high energies over only a short distance. Their experiments offer a possible path for the future of particle accelerators.

  6. Peak acceleration limiter

    NASA Technical Reports Server (NTRS)

    Chapman, C. P.

    1972-01-01

    Device is described that limits accelerations by shutting off shaker table power very rapidly in acceleration tests. Absolute value of accelerometer signal is used to trigger electronic switch which terminates test and sounds alarm.

  7. Linear Accelerator (LINAC)

    MedlinePlus

    ... equipment? How is safety ensured? What is this equipment used for? A linear accelerator (LINAC) is the ... Therapy (SBRT) . top of page How does the equipment work? The linear accelerator uses microwave technology (similar ...

  8. Accelerating Particles with Plasma

    SciTech Connect

    Litos, Michael; Hogan, Mark

    2014-11-05

    Researchers at SLAC explain how they use plasma wakefields to accelerate bunches of electrons to very high energies over only a short distance. Their experiments offer a possible path for the future of particle accelerators.

  9. Improved plasma accelerator

    NASA Technical Reports Server (NTRS)

    Cheng, D. Y.

    1971-01-01

    Converging, coaxial accelerator electrode configuration operates in vacuum as plasma gun. Plasma forms by periodic injections of high pressure gas that is ionized by electrical discharges. Deflagration mode of discharge provides acceleration, and converging contours of plasma gun provide focusing.

  10. Accelerator Technology Division

    NASA Astrophysics Data System (ADS)

    1992-04-01

    In fiscal year (FY) 1991, the Accelerator Technology (AT) division continued fulfilling its mission to pursue accelerator science and technology and to develop new accelerator concepts for application to research, defense, energy, industry, and other areas of national interest. This report discusses the following programs: The Ground Test Accelerator Program; APLE Free-Electron Laser Program; Accelerator Transmutation of Waste; JAERI, OMEGA Project, and Intense Neutron Source for Materials Testing; Advanced Free-Electron Laser Initiative; Superconducting Super Collider; The High-Power Microwave Program; (Phi) Factory Collaboration; Neutral Particle Beam Power System Highlights; Accelerator Physics and Special Projects; Magnetic Optics and Beam Diagnostics; Accelerator Design and Engineering; Radio-Frequency Technology; Free-Electron Laser Technology; Accelerator Controls and Automation; Very High-Power Microwave Sources and Effects; and GTA Installation, Commissioning, and Operations.

  11. Genetic mapping of an ancient translocation in the genus Lens.

    PubMed

    Tadmor, Y; Zamir, D; Ladizinsky, G

    1987-04-01

    Segregation of 18 marker genes was monitored in selfed progeny of a Lens culinaris × L. ervoides hybrid; five linkage groups were mapped, one of which contained a reciprocal translocation break-point that differentiates between the parents. Four markers were found to be linked to the translocation break-point: Aco-1 and Pgm-2 on one side and Gs and Got-2 on the other. The gene pairs on both sides of the translocation are not linked in L. culinaris or in L. orientalis. The L. ervoides gene order was also found in L. odemensis but with significantly reduced map distances. Analysis of monogenic segregations in a number of Lens inter-specific crosses revealed some consistent patterns of deviations from the expected Mendelian ratios. The factors responsible for these unequal segregations, genotypic effects on recombination frequencies, negative interference, and the possible ancient origin of the translocation are discussed.

  12. Unwrapping an ancient Egyptian mummy using x-rays

    NASA Astrophysics Data System (ADS)

    Hughes, Stephen W.

    2010-05-01

    This article describes a project of unwrapping an ancient Egyptian mummy using x-ray computed tomography (CT). About 600 x-ray CT images were obtained through the mummified body of a female named Tjetmutjengebtiu (or Jeni for short), who was a singer in the great temple of Karnak in Egypt during the 22nd dynasty (c 945-715 BC). The x-ray CT images reveal details of the remains of body organs, wrappings and jewellery. 3D reconstructions of Jeni's teeth suggest that she was probably only around 20 years old when she died, although the cause of death cannot be ascertained from the CT scans. The CT images were used to build a 3D model of Jeni's head which enabled an artist to paint a picture of what Jeni may have looked like during life. A PowerPoint presentation and movie clips are provided as supplementary material that may be useful for teaching.

  13. Bacillus DNA in fossil bees: an ancient symbiosis?

    PubMed Central

    Cano, R J; Borucki, M K; Higby-Schweitzer, M; Poinar, H N; Poinar, G O; Pollard, K J

    1994-01-01

    We report here the isolation of DNA from abdominal tissue of four extinct stingless bees (Proplebeia dominicana) in Dominican amber, PCR amplification of a 546-bp fragment of the 16S rRNA gene from Bacillus spp., and their corresponding nucleotide sequences. These sequences were used in basic local alignment search tool searches of nonredundant nucleic acid data bases, and the highest scores were obtained with 16S rRNA sequences from Bacillus spp. Phylogenetic inference analysis by the maximum-likelihood method revealed close phylogenetic relationships of the four presumed ancient Bacillus sequences with Bacillus pumilus, B. firmus, B. subtilis, and B. circulans. These four extant Bacillus spp. are commonly isolated from abdominal tissue of stingless bees. The close phylogenetic association of the extracted DNA sequences with these bee colonizers suggests that a similar bee-Bacillus association existed in the extinct species P. dominicana. PMID:8031102

  14. The Crystal Structure of (S)-3-O-geranylgeranylglycerol phosphate synthase Reveals an Ancient Fold for an Ancient Enzyme

    SciTech Connect

    Payandeh, Jian; Fujihashi, Masahiro; Gillon, Wanda; Pai, Emil F.

    2010-12-03

    We report crystal structures of the citrate and sn-glycerol-1-phosphate (G1P) complexes of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Archaeoglobus fulgidus (AfGGGPS) at 1.55 and 2.0 {angstrom} resolution, respectively. AfGGGPS is an enzyme that performs the committed step in archaeal lipid biosynthesis, and it presents the first triose phosphate isomerase (TIM)-barrel structure with a prenyltransferase function. Our studies provide insight into the catalytic mechanism of AfGGGPS and demonstrate how it selects for the sn-G1P isomer. The replacement of 'Helix 3' by a 'strand' in AfGGGPS, a novel modification to the canonical TIM-barrel fold, suggests a model of enzyme adaptation that involves a 'greasy slide' and a 'swinging door.' We propose functions for the homologous PcrB proteins, which are conserved in a subset of pathogenic bacteria, as either prenyltransferases or being involved in lipoteichoic acid biosynthesis. Sequence and structural comparisons lead us to postulate an early evolutionary history for AfGGGPS, which may highlight its role in the emergence of Archaea.

  15. Accelerators, Colliders, and Snakes

    NASA Astrophysics Data System (ADS)

    Courant, Ernest D.

    2003-12-01

    The author traces his involvement in the evolution of particle accelerators over the past 50 years. He participated in building the first billion-volt accelerator, the Brookhaven Cosmotron, which led to the introduction of the "strong-focusing" method that has in turn led to the very large accelerators and colliders of the present day. The problems of acceleration of spin-polarized protons are also addressed, with discussions of depolarizing resonances and "Siberian snakes" as a technique for mitigating these resonances.

  16. Ancient Impact Basin on Europa

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This feature on Europa was seen as a dark, diffuse circular patch on a previous Galileo global image of Europa's leading hemisphere on April 3, 1997. The 'bulls-eye' pattern appears to be a 140- kilometer (86-mile) wide impact scar (about the size of the island of Hawaii) which formed as the surface fractured minutes after a mountain-sized asteroid or comet slammed into the satellite. This approximately 214-kilometer (132-mile) wide picture is the product of three images which have been processed in false color to enhance shapes and compositions.

    North is toward the top of this picture, which is illuminated from sunlight coming from the west. This color composite reveals a sequence of events which have modified the surface of Europa. The earliest event was the impact which formed the Tyre structure at 34 degrees north latitude and 146.5 degrees west longitude. The impact was followed by the formation of the reddish lines superposed on Tyre. The red color designates areas that are probably a dirty water ice mixture. The fine blue-green lines crossing the region from west to east appear to be ridges which formed after the crater.

    The images were taken on April 4, 1997, at a resolution of 595 meters (1950 feet) per picture element and a range of 29,000 kilometers (17,900 miles). The images were taken by Galileo's solid state imaging (CCD) system.

    The Jet Propulsion Laboratory, Pasadena, CA manages the Galileo mission for NASA's Office of Space Science, Washington, DC. JPL is an operating division of California Institute of Technology (Caltech).

    This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at URL http://www.jpl.nasa.gov/galileo/sepo

  17. Acceleration: It's Elementary

    ERIC Educational Resources Information Center

    Willis, Mariam

    2012-01-01

    Acceleration is one tool for providing high-ability students the opportunity to learn something new every day. Some people talk about acceleration as taking a student out of step. In actuality, what one is doing is putting a student in step with the right curriculum. Whole-grade acceleration, also called grade-skipping, usually happens between…

  18. Angular Acceleration without Torque?

    ERIC Educational Resources Information Center

    Kaufman, Richard D.

    2012-01-01

    Hardly. Just as Robert Johns qualitatively describes angular acceleration by an internal force in his article "Acceleration Without Force?" here we will extend the discussion to consider angular acceleration by an internal torque. As we will see, this internal torque is due to an internal force acting at a distance from an instantaneous center.

  19. Accelerated test design

    NASA Technical Reports Server (NTRS)

    Mcdermott, P. P.

    1980-01-01

    The design of an accelerated life test program for electric batteries is discussed. A number of observations and suggestions on the procedures and objectives for conducting an accelerated life test program are presented. Equations based on nonlinear regression analysis for predicting the accelerated life test parameters are discussed.

  20. [Traumatology due to ancient lead missile projectiles].

    PubMed

    Moog, Ferdinand Peter

    2002-01-01

    The lead missiles of slingers in antiquity, known as glans or molybdis, are widely considered to have been very dangerous projectiles of the ancient armies. Ballistic investigations and results of experimental archaeology seem to confirm this. However, the findings of medical history concerning these missiles disagree with this view. In ancient medical texts these missiles are only mentioned sporadically, as in Celsus or Paul of Aigina, and wounds caused by them are merely discussed incidentally. There is so far no evidence at all on them in palaeopathology. It is undisputed however that in individual cases these missiles were able to cause serious injuries, especially when they hit unprotected parts of the body. Accordingly, their main effect seems to have consisted in the intimidation of the enemy.

  1. Lead in ancient Rome's city waters.

    PubMed

    Delile, Hugo; Blichert-Toft, Janne; Goiran, Jean-Philippe; Keay, Simon; Albarède, Francis

    2014-05-06

    It is now universally accepted that utilization of lead for domestic purposes and water distribution presents a major health hazard. The ancient Roman world was unaware of these risks. How far the gigantic network of lead pipes used in ancient Rome compromised public health in the city is unknown. Lead isotopes in sediments from the harbor of Imperial Rome register the presence of a strong anthropogenic component during the beginning of the Common Era and the Early Middle Ages. They demonstrate that the lead pipes of the water distribution system increased Pb contents in drinking water of the capital city by up to two orders of magnitude over the natural background. The Pb isotope record shows that the discontinuities in the pollution of the Tiber by lead are intimately entwined with the major issues affecting Late Antique Rome and its water distribution system.

  2. Human evolution: a tale from ancient genomes.

    PubMed

    Llamas, Bastien; Willerslev, Eske; Orlando, Ludovic

    2017-02-05

    The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

  3. European neolithization and ancient DNA: an assessment.

    PubMed

    Deguilloux, Marie-France; Leahy, Rachael; Pemonge, Marie-Hélène; Rottier, Stéphane

    2012-01-01

    Neolithic processes underlying the distribution of genetic diversity among European populations have been the subject of intense debate since the first genetic data became available. However, patterns observed in the current European gene pool are the outcome of Paleolithic and Neolithic processes, overlaid with four millennia of further developments. This observation encouraged paleogeneticists to contribute to the debate by directly comparing genetic variation from the ancient inhabitants of Europe to their contemporary counterparts. Pre-Neolithic and Neolithic paleogenetic data are becoming increasingly available for north and northwest European populations. Despite the numerous problems inherent in the paleogenetic approach, the accumulation of ancient DNA datasets offers new perspectives from which to interpret the interactions between hunter-gatherer and farming communities. In light of information emerging from diverse disciplines, including recent paleogenetic studies, the most plausible model explaining the movement of Neolithic pioneer groups in central Europe is that of leapfrog migration.

  4. [Concepts of the heart in Ancient Egypt].

    PubMed

    Ziskind, Bernard; Halioua, Bruno

    2004-03-01

    The heart was regarded in Ancient Egypt as the organic motor of the body and also the seat of intelligence, an important religious and spiritual symbol. It was considered as one of the eight parts of human body. Counter to other organs it had to be kept carefully intact in the mummy to ensure its eternal life. In Ancient Egypt, the concept of heart included three constituents: heart-haty, heart-ib, and the spiritual seat of intelligence, emotion and memory. The hieroglyphs representing the heart early in the first dynasty were drawn with eight vessels attached to it. Egyptian doctors have elaborated an original conception of cardiovascular physiology which endured 30 centuries.

  5. Lipids of aquatic sediments, recent and ancient

    NASA Technical Reports Server (NTRS)

    Eglinton, G.; Hajibrahim, S. K.; Maxwell, J. R.; Quirke, J. M. E.; Shaw, G. J.; Volkman, J. K.; Wardroper, A. M. K.

    1979-01-01

    Computerized gas chromatography-mass spectrometry (GC-MS) is now an essential tool in the analysis of the complex mixtures of lipids (geolipids) encountered in aquatic sediments, both 'recent' (less than 1 million years old) and ancient. The application of MS, and particularly GC-MS, has been instrumental in the rapid development of organic geochemistry and environmental organic chemistry in recent years. The techniques used have resulted in the identification of numerous compounds of a variety of types in sediments. Most attention has been concentrated on molecules of limited size, mainly below 500 molecular mass, and of limited functionality, for examples, hydrocarbons, fatty acids and alcohols. Examples from recent studies (at Bristol) of contemporary, 'recent' and ancient sediments are presented and discussed.

  6. Ancient Chinese Observations and Modern Cometary Models

    NASA Technical Reports Server (NTRS)

    Yeomans, D. K.

    1995-01-01

    Ancient astronomical observations, primarily by Chinese, represent the only data source for discerning the long-term behavior of comets. These sky watchers produced astrological forecasts for their emperors. The comets Halley, Swift-Tuttle, and Tempel-Tuttle have been observed for 2000 years. Records of the Leonid meteor showers, starting from A.D.902, are used to guide predictions for the 1998-1999 reoccurrence.

  7. Volatile and Isotopic Imprints of Ancient Mars

    NASA Technical Reports Server (NTRS)

    Mahaffy, Paul R.; Conrad, Pamela G.

    2015-01-01

    The science investigations enabled by Curiosity rover's instruments focus on identifying and exploring the habitability of the Martian environment. Measurements of noble gases, organic and inorganic compounds, and the isotopes of light elements permit the study of the physical and chemical processes that have transformed Mars throughout its history. Samples of the atmosphere, volatiles released from soils, and rocks from the floor of Gale Crater have provided a wealth of new data and a window into conditions on ancient Mars.

  8. Ancient Chinese Precedents in Chinas National Defense.

    DTIC Science & Technology

    2007-11-02

    period and eventually lead into the Tang Dynasty around 700 AD. ’Ralph D. Sawyer, trans. The Seven Military Classics of Ancient China (Boulder...between emperor Tang Tai Zong of the Tang Dynasty and his chief military advisor Li Wei Gong, but there is debate about the work’s authenticity. While... Tang Tai Zong and Li Wei Gong lived 95 during the early Tang Dynasty , some historians claim the work is a forgery that was constructed in the late

  9. Ancient plant DNA in lake sediments.

    PubMed

    Parducci, Laura; Bennett, Keith D; Ficetola, Gentile Francesco; Alsos, Inger Greve; Suyama, Yoshihisa; Wood, Jamie R; Pedersen, Mikkel Winther

    2017-04-03

    Contents I. II. III. IV. V. VI. VII. VIII. IX. X. XI. References SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.

  10. Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes

    PubMed Central

    Suh, Alexander; Churakov, Gennady; Ramakodi, Meganathan P.; Platt, Roy N.; Jurka, Jerzy; Kojima, Kenji K.; Caballero, Juan; Smit, Arian F.; Vliet, Kent A.; Hoffmann, Federico G.; Brosius, Jürgen; Green, Richard E.; Braun, Edward L.; Ray, David A.; Schmitz, Jürgen

    2015-01-01

    Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians. PMID:25503085

  11. Ancient Venom Systems: A Review on Cnidaria Toxins.

    PubMed

    Jouiaei, Mahdokht; Yanagihara, Angel A; Madio, Bruno; Nevalainen, Timo J; Alewood, Paul F; Fry, Bryan G

    2015-06-18

    Cnidarians are the oldest extant lineage of venomous animals. Despite their simple anatomy, they are capable of subduing or repelling prey and predator species that are far more complex and recently evolved. Utilizing specialized penetrating nematocysts, cnidarians inject the nematocyst content or "venom" that initiates toxic and immunological reactions in the envenomated organism. These venoms contain enzymes, potent pore forming toxins, and neurotoxins. Enzymes include lipolytic and proteolytic proteins that catabolize prey tissues. Cnidarian pore forming toxins self-assemble to form robust membrane pores that can cause cell death via osmotic lysis. Neurotoxins exhibit rapid ion channel specific activities. In addition, certain cnidarian venoms contain or induce the release of host vasodilatory biogenic amines such as serotonin, histamine, bunodosine and caissarone accelerating the pathogenic effects of other venom enzymes and porins. The cnidarian attacking/defending mechanism is fast and efficient, and massive envenomation of humans may result in death, in some cases within a few minutes to an hour after sting. The complexity of venom components represents a unique therapeutic challenge and probably reflects the ancient evolutionary history of the cnidarian venom system. Thus, they are invaluable as a therapeutic target for sting treatment or as lead compounds for drug design.

  12. Ancient Venom Systems: A Review on Cnidaria Toxins

    PubMed Central

    Jouiaei, Mahdokht; Yanagihara, Angel A.; Madio, Bruno; Nevalainen, Timo J.; Alewood, Paul F.; Fry, Bryan G.

    2015-01-01

    Cnidarians are the oldest extant lineage of venomous animals. Despite their simple anatomy, they are capable of subduing or repelling prey and predator species that are far more complex and recently evolved. Utilizing specialized penetrating nematocysts, cnidarians inject the nematocyst content or “venom” that initiates toxic and immunological reactions in the envenomated organism. These venoms contain enzymes, potent pore forming toxins, and neurotoxins. Enzymes include lipolytic and proteolytic proteins that catabolize prey tissues. Cnidarian pore forming toxins self-assemble to form robust membrane pores that can cause cell death via osmotic lysis. Neurotoxins exhibit rapid ion channel specific activities. In addition, certain cnidarian venoms contain or induce the release of host vasodilatory biogenic amines such as serotonin, histamine, bunodosine and caissarone accelerating the pathogenic effects of other venom enzymes and porins. The cnidarian attacking/defending mechanism is fast and efficient, and massive envenomation of humans may result in death, in some cases within a few minutes to an hour after sting. The complexity of venom components represents a unique therapeutic challenge and probably reflects the ancient evolutionary history of the cnidarian venom system. Thus, they are invaluable as a therapeutic target for sting treatment or as lead compounds for drug design. PMID:26094698

  13. Abandonment of terminally ill patients in the Byzantine era. An ancient tradition?

    PubMed Central

    Lascaratos, J; Poulakou-Rebelakou, E; Marketos, S

    1999-01-01

    Our research on the texts of the Byzantine historians and chroniclers revealed an apparently curious phenomenon, namely, the abandonment of terminally ill emperors by their physicians when the latter realised that they could not offer any further treatment. This attitude tallies with the mentality of the ancient Greek physicians, who even in Hippocratic times thought the treatment and care of the terminally ill to be a challenge to nature and hubris to the gods. Nevertheless, it is a very curious attitude in the light of the concepts of the Christian Byzantine physicians who, according to the doctrines of the Christian religion, should have been imbued with the spirit of philanthropy and love for their fellowmen. The meticulous analysis of three examples of abandonment of Byzantine emperors, and especially that of Alexius I Comnenus, by their physicians reveals that this custom, following ancient pagan ethics, in those times took on a ritualised form without any significant or real content. PMID:10390682

  14. Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog

    PubMed Central

    Trifonov, Vladimir A.; Leonard, Jennifer A.; Vorobieva, Nadezhda V.; Ovodov, Nikolai D.; Graphodatsky, Alexander S.; Wayne, Robert K.

    2013-01-01

    The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication. PMID:23483925

  15. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

    PubMed

    Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.

  16. Fiber Accelerating Structures

    SciTech Connect

    Hammond, Andrew P.; /Reed Coll. /SLAC

    2010-08-25

    One of the options for future particle accelerators are photonic band gap (PBG) fiber accelerators. PBG fibers are specially designed optical fibers that use lasers to excite an electric field that is used to accelerate electrons. To improve PBG accelerators, the basic parameters of the fiber were tested to maximize defect size and acceleration. Using the program CUDOS, several accelerating modes were found that maximized these parameters for several wavelengths. The design of multiple defects, similar to having closely bound fibers, was studied to find possible coupling or the change of modes. The amount of coupling was found to be dependent on distance separated. For certain distances accelerating coupled modes were found and examined. In addition, several non-periodic fiber structures were examined using CUDOS. The non-periodic fibers produced several interesting results and promised more modes given time to study them in more detail.

  17. High brightness electron accelerator

    DOEpatents

    Sheffield, Richard L.; Carlsten, Bruce E.; Young, Lloyd M.

    1994-01-01

    A compact high brightness linear accelerator is provided for use, e.g., in a free electron laser. The accelerator has a first plurality of acclerating cavities having end walls with four coupling slots for accelerating electrons to high velocities in the absence of quadrupole fields. A second plurality of cavities receives the high velocity electrons for further acceleration, where each of the second cavities has end walls with two coupling slots for acceleration in the absence of dipole fields. The accelerator also includes a first cavity with an extended length to provide for phase matching the electron beam along the accelerating cavities. A solenoid is provided about the photocathode that emits the electons, where the solenoid is configured to provide a substantially uniform magnetic field over the photocathode surface to minimize emittance of the electons as the electrons enter the first cavity.

  18. Acceleration in astrophysics

    SciTech Connect

    Colgate, S.A.

    1993-12-31

    The origin of cosmic rays and applicable laboratory experiments are discussed. Some of the problems of shock acceleration for the production of cosmic rays are discussed in the context of astrophysical conditions. These are: The presumed unique explanation of the power law spectrum is shown instead to be a universal property of all lossy accelerators; the extraordinary isotropy of cosmic rays and the limited diffusion distances implied by supernova induced shock acceleration requires a more frequent and space-filling source than supernovae; the near perfect adiabaticity of strong hydromagnetic turbulence necessary for reflecting the accelerated particles each doubling in energy roughly 10{sup 5} to {sup 6} scatterings with negligible energy loss seems most unlikely; the evidence for acceleration due to quasi-parallel heliosphere shocks is weak. There is small evidence for the expected strong hydromagnetic turbulence, and instead, only a small number of particles accelerate after only a few shock traversals; the acceleration of electrons in the same collisionless shock that accelerates ions is difficult to reconcile with the theoretical picture of strong hydromagnetic turbulence that reflects the ions. The hydromagnetic turbulence will appear adiabatic to the electrons at their much higher Larmor frequency and so the electrons should not be scattered incoherently as they must be for acceleration. Therefore the electrons must be accelerated by a different mechanism. This is unsatisfactory, because wherever electrons are accelerated these sites, observed in radio emission, may accelerate ions more favorably. The acceleration is coherent provided the reconnection is coherent, in which case the total flux, as for example of collimated radio sources, predicts single charge accelerated energies much greater than observed.

  19. Ancient human disturbances may be skewing our understanding of Amazonian forests.

    PubMed

    McMichael, Crystal N H; Matthews-Bird, Frazer; Farfan-Rios, William; Feeley, Kenneth J

    2017-01-17

    Although the Amazon rainforest houses much of Earth's biodiversity and plays a major role in the global carbon budget, estimates of tree biodiversity originate from fewer than 1,000 forest inventory plots, and estimates of carbon dynamics are derived from fewer than 200 recensus plots. It is well documented that the pre-European inhabitants of Amazonia actively transformed and modified the forest in many regions before their population collapse around 1491 AD; however, the impacts of these ancient disturbances remain entirely unaccounted for in the many highly influential studies using Amazonian forest plots. Here we examine whether Amazonian forest inventory plot locations are spatially biased toward areas with high probability of ancient human impacts. Our analyses reveal that forest inventory plots, and especially forest recensus plots, in all regions of Amazonia are located disproportionately near archaeological evidence and in areas likely to have ancient human impacts. Furthermore, regions of the Amazon that are relatively oversampled with inventory plots also contain the highest values of predicted ancient human impacts. Given the long lifespan of Amazonian trees, many forest inventory and recensus sites may still be recovering from past disturbances, potentially skewing our interpretations of forest dynamics and our understanding of how these forests are responding to global change. Empirical data on the human history of forest inventory sites are crucial for determining how past disturbances affect modern patterns of forest composition and carbon flux in Amazonian forests.

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

    PubMed

    Boessenkool, Sanne; Epp, Laura S; Haile, James; Bellemain, Eva; Edwards, Mary; Coissac, Eric; Willerslev, Eske; Brochmann, Christian

    2012-04-01

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

  1. Microsatellite typing of ancient maize: insights into the history of agriculture in southern South America

    PubMed Central

    Lia, Verónica V; Confalonieri, Viviana A; Ratto, Norma; Hernández, Julián A. Cámara; Alzogaray, Ana M. Miante; Poggio, Lidia; Brown, Terence A

    2006-01-01

    Archaeological maize specimens from Andean sites of southern South America, dating from 400 to 1400 years before present, were tested for the presence of ancient DNA and three microsatellite loci were typed in the specimens that gave positive results. Genotypes were also obtained for 146 individuals corresponding to modern landraces currently cultivated in the same areas and for 21 plants from Argentinian lowland races. Sequence analysis of cloned ancient DNA products revealed a high incidence of substitutions appearing in only one clone, with transitions prevalent. In the archaeological specimens, there was no evidence of polymorphism at any one of the three microsatellite loci: each exhibited a single allelic variant, identical to the most frequent allele found in contemporary populations belonging to races Amarillo Chico, Amarillo Grande, Blanco and Altiplano. Affiliation between ancient specimens and a set of races from the Andean complex was further supported by assignment tests. The striking genetic uniformity displayed by the ancient specimens and their close relationship with the Andean complex suggest that the latter gene pool has predominated in the western regions of southern South America for at least the past 1400 years. The results support hypotheses suggesting that maize cultivation initially spread into South America via a highland route, rather than through the lowlands. PMID:17476775

  2. 2000 Year-old ancient equids: an ancient-DNA lesson from pompeii remains.

    PubMed

    Di Bernardo, Giovanni; Del Gaudio, Stefania; Galderisi, Umberto; Cipollaro, Marilena

    2004-11-15

    Ancient DNA extracted from 2000 year-old equine bones was examined in order to amplify mitochondrial and nuclear DNA fragments. A specific equine satellite-type sequence representing 3.7%-11% of the entire equine genome, proved to be a suitable target to address the question of the presence of aDNA in ancient bones. The PCR strategy designed to investigate this specific target also allowed us to calculate the molecular weight of amplifiable DNA fragments. Sequencing of a 370 bp DNA fragment of mitochondrial control region allowed the comparison of ancient DNA sequences with those of modern horses to assess their genetic relationship. The 16S rRNA mitochondrial gene was also examined to unravel the post-mortem base modification feature and to test the status of Pompeian equids taxon on the basis of a Mae III restriction site polymorphism.

  3. Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation.

    PubMed

    Teske, Andreas; Dhillon, Ashita; Sogin, Mitchell L

    2003-04-01

    Genomic markers for anaerobic microbial processes in marine sediments-sulfate reduction, methanogenesis, and anaerobic methane oxidation-reveal the structure of sulfate-reducing, methanogenic, and methane-oxidizing microbial communities (including uncultured members); they allow inferences about the evolution of these ancient microbial pathways; and they open genomic windows into extreme microbial habitats, such as deep subsurface sediments and hydrothermal vents, that are analogs for the early Earth and for extraterrestrial microbiota.

  4. On relationship between two ancient Chinese algorithms and their application to flash evaporation

    NASA Astrophysics Data System (ADS)

    Liu, Yan-Qing; He, Ji-Huan

    This paper gives a brief introduction to two ancient Chinese methods, Ying Buzu Shu and He Chengtian average. Their relationship is revealed, and it is proved that the two methods are equivalent under some special cases, that means He Chengtian average can be derived from the method of Ying Buzu Shu. Rachford-Rice equation arising in flash evaporation is used as an example for their simple application.

  5. Analysis of Venetian-type glass fragments from the ancient city of Lezha (Albania)

    NASA Astrophysics Data System (ADS)

    Šmit, Ž.; Stamati, F.; Civici, N.; Vevecka-Priftaj, A.; Kos, M.; Jezeršek, D.

    2009-08-01

    A series of glasses excavated in the Albanian city of Lezha (ancient Lissos) were analyzed by the combined PIXE-PIGE method in air and by source-excited XRF. The analysis revealed two types of glass that can be identified as façon de Venise glass and its subsequent younger phase, produced by chemically purer components and using As 2O 3 as decolorant.

  6. The plasma physics of shock acceleration

    NASA Technical Reports Server (NTRS)

    Jones, Frank C.; Ellison, Donald C.

    1991-01-01

    The history and theory of shock acceleration is reviewed, paying particular attention to theories of parallel shocks which include the backreaction of accelerated particles on the shock structure. The work that computer simulations, both plasma and Monte Carlo, are playing in revealing how thermal ions interact with shocks and how particle acceleration appears to be an inevitable and necessary part of the basic plasma physics that governs collisionless shocks is discussed. Some of the outstanding problems that still confront theorists and observers in this field are described.

  7. Baboon palm nut harvesters in ancient Egypt: new (ancient) evidence, new questions.

    PubMed

    Deputte, B L; Anderson, J R

    2009-01-01

    It is well documented that hamadryas baboons were used by the ancient Egyptians to pick fruits, but it is not well known that these baboons were also used to collect palm nuts. We describe this practice as it is depicted on a painting on a rarely exhibited ancient Egyptian artefact. Striking similarities with the modern use of pig-tailed macaques as coconut harvesters are described, raising new questions about the demise of the practice in Africa and its continuation in South-East Asia.

  8. Accessing Surface and Subsurface Habitable Environments of Ancient Mars

    NASA Astrophysics Data System (ADS)

    Mustard, J. F.

    2014-12-01

    The martian Curiosity rover has characterized the Yellowknife Bay region as habitable based on the presence of sedimentary rocks, the array of elements essential to supporting life (CHNOPS), and indications of hydrologic activity either as a shallow stream bed or intermittently wet lake bed. However as an ancient site this surface was challenging for sustained habitability due to the radiation environment and unknown persistence of water. In contrast the shallow subsurface was potentially a longer lived environment sheltered from the harsh surface conditions. Yet our knowledge of subsurface environments is limited. Did the ancient subsurface of Mars encompass the full range of factors needed for habitability, what is the evidence for this, and was this preserved in the geologic record? Syntheses of global 0.4-5.0 μm spectroscopic observations from high (19 m/pixel CRISM) to moderate (1 km/pixel OMEGA) resolution VNIR data show diverse assemblages of aqueous minerals. The most common environment observed from orbit is a subsurface hydrothermal-type environment accounting for more than 70% of observed sites with hydrated silicates. The dominant hydrated mineral phase is smectite clay, implying a moderate pH environment and a thermal environmental <350°C. The heat source to drive hydrothermal systems could be crustal cooling following planet formation, conductive heat flow from the mantle, impact generated heat pulses, deuteric alteration and magmatism. Evidence of relatively rapid cooling of the crust after formation perhaps by hydrothermal circulation is provided by ancient topography preserved by a rigid crust. Exhumation of Noachian-aged phyllosilicate-rich terrains reveal abundant linear ridges resistant to erosion interpreted to be mineralized fraction zones in regional hydrothermal systems. The proposed landing site in Northeast Syrtis provides excellent access to both surface (Late Noachian fluvial systems with standing bodies of water) and subsurface

  9. An introduction to acceleration mechanisms

    SciTech Connect

    Palmer, R.B.

    1987-05-01

    This paper discusses the acceleration of charged particles by electromagnetic fields, i.e., by fields that are produced by the motion of other charged particles driven by some power source. The mechanisms that are discussed include: Ponderamotive Forces, Acceleration, Plasma Beat Wave Acceleration, Inverse Free Electron Laser Acceleration, Inverse Cerenkov Acceleration, Gravity Acceleration, 2D Linac Acceleration and Conventional Iris Loaded Linac Structure Acceleration. (LSP)

  10. Schooling in Times of Acceleration

    ERIC Educational Resources Information Center

    Buddeberg, Magdalena; Hornberg, Sabine

    2017-01-01

    Modern societies are characterised by forms of acceleration, which influence social processes. Sociologist Hartmut Rosa has systematised temporal structures by focusing on three categories of social acceleration: technical acceleration, acceleration of social change, and acceleration of the pace of life. All three processes of acceleration are…

  11. Hydroarchaeology: Measuring the Ancient Human Impact on the Palenque Watershed

    NASA Astrophysics Data System (ADS)

    French, K. D.; Duffy, C. J.

    2010-03-01

    Palenque, one of the best known Classic Maya centers, has what is arguably the most unique and intricate system of water management known anywhere in the Maya Lowlands. Years of archaeological research, including intensive mapping between 1997 and 2000, reveal that this major center, situated on a narrow escarpment at the base of a high mountain range in northern Chiapas, Mexico, began as a modest settlement about AD 100. Then, during the seventh and eighth centuries, Palenque experienced explosive growth, mushrooming into a dense community with an estimated population of 6000 and approximately 1500 structures — residences, palaces, and temples¬ - under a series of powerful rulers. This process of "urban" growth led to obvious changes in landcover. In order to better understand the effects that landcover and climate change have on the availability of water for an ancient city a new approach is required. In this paper we explore a hydroarchaeological approach that utilizes simulated daily paleoclimate data, watershed modeling, and traditional archaeology to view the response of ancient human impact within the watershed surrounding Palenque. There is great potential for watershed-climate modeling in developing plausible scenarios of water use and supply, and the effect of extreme conditions (flood and drought), all of which cannot be fully represented by atmosphere-based climate and weather projections. The first objective of the paper is to test the hypothesis that drought was a major cause for Palenque’s collapse. Did the Maya abandon Palenque in search of water? Secondly, we evaluate the hydraulic design of the water management features at Palenque against extreme meteorological events. How successful was the hydraulic engineering of the Maya in coping with droughts and floods? The archaeological implications for this non-invasive "virtual" method are many, including detecting periods of stress within a community, estimating population by developing caps

  12. Nuclear factor Y regulates ancient budgerigar hepadnavirus core promoter activity.

    PubMed

    Shen, Zhongliang; Liu, Yanfeng; Luo, Mengjun; Wang, Wei; Liu, Jing; Liu, Wei; Pan, Shaokun; Xie, Youhua

    2016-09-16

    Endogenous viral elements (EVE) in animal genomes are the fossil records of ancient viruses and provide invaluable information on the origin and evolution of extant viruses. Extant hepadnaviruses include avihepadnaviruses of birds and orthohepadnaviruses of mammals. The core promoter (Cp) of hepadnaviruses is vital for viral gene expression and replication. We previously identified in the budgerigar genome two EVEs that contain the full-length genome of an ancient budgerigar hepadnavirus (eBHBV1 and eBHBV2). Here, we found eBHBV1 Cp and eBHBV2 Cp were active in several human and chicken cell lines. A region from nt -85 to -11 in eBHBV1 Cp was critical for the promoter activity. Bioinformatic analysis revealed a putative binding site of nuclear factor Y (NF-Y), a ubiquitous transcription factor, at nt -64 to -50 in eBHBV1 Cp. The NF-Y core binding site (ATTGG, nt -58 to -54) was essential for eBHBV1 Cp activity. The same results were obtained with eBHBV2 Cp and duck hepatitis B virus Cp. The subunit A of NF-Y (NF-YA) was recruited via the NF-Y core binding site to eBHBV1 Cp and upregulated the promoter activity. Finally, the NF-Y core binding site is conserved in the Cps of all the extant avihepadnaviruses but not of orthohepadnaviruses. Interestingly, a putative and functionally important NF-Y core binding site is located at nt -21 to -17 in the Cp of human hepatitis B virus. In conclusion, our findings have pinpointed an evolutionary conserved and functionally critical NF-Y binding element in the Cps of avihepadnaviruses.

  13. Interleukin-37 gene variants segregated anciently coexist during hominid evolution.

    PubMed

    Kang, Bin; Cheng, Shimeng; Peng, Jinbiao; Yan, Jingjing; Zhang, Shuye

    2015-10-01

    IL37 is a member of IL-1 cytokine family but conveys anti-inflammatory functions. The biological characteristic and genetic heterogeneity of IL37 are not fully understood yet. Here using the whole-genome sequencing data from 1000 Genomes Project, we performed population and evolutionary genetic analysis of human IL37 gene. First, 2184 IL37 gene sequences from different human populations were retrieved. The IL37 protein sequences were inferred from the coding DNA sequences and multiple species alignment was made. Then, the phylogenetic tree of IL37 was built and dN/dS ratios were calculated for each evolutionary branch, the classic McDonald and Kreitman test was also performed. Next, we conducted intraspecific evolutionary genetic analysis and built the genealogy network of 116 unique IL37 haplotypes through median-joining network analysis. Finally, we compared IL37 sequences between the modern and archaic humans. Our results for the first time provide solid evidence that common IL37 variants other than NCBI reference sequence are present worldwide. Our data also supports that IL37 variants are shaped and maintained by selection instead of neutral evolution. We further identified that human IL37 variants consist of two major haplogroups and their presence in archaic humans corroborates its ancient origin in hominid evolution. In conclusion, these data indicate that common IL37 variants are maintained among human populations by selective force, suggesting their potential involvements in immune regulation and human diseases. In addition, the ancient history of IL37 variants reveals interesting insight into the complicated human evolutionary history.

  14. Is Global Warming Accelerating?

    NASA Astrophysics Data System (ADS)

    Shukla, J.; Delsole, T. M.; Tippett, M. K.

    2009-12-01

    A global pattern that fluctuates naturally on decadal time scales is identified in climate simulations and observations. This newly discovered component, called the Global Multidecadal Oscillation (GMO), is related to the Atlantic Meridional Oscillation and shown to account for a substantial fraction of decadal fluctuations in the observed global average sea surface temperature. IPCC-class climate models generally underestimate the variance of the GMO, and hence underestimate the decadal fluctuations due to this component of natural variability. Decomposing observed sea surface temperature into a component due to anthropogenic and natural radiative forcing plus the GMO, reveals that most multidecadal fluctuations in the observed global average sea surface temperature can be accounted for by these two components alone. The fact that the GMO varies naturally on multidecadal time scales implies that it can be predicted with some skill on decadal time scales, which provides a scientific rationale for decadal predictions. Furthermore, the GMO is shown to account for about half of the warming in the last 25 years and hence a substantial fraction of the recent acceleration in the rate of increase in global average sea surface temperature. Nevertheless, in terms of the global average “well-observed” sea surface temperature, the GMO can account for only about 0.1° C in transient, decadal-scale fluctuations, not the century-long 1° C warming that has been observed during the twentieth century.

  15. Re-discovering ancient wheat varieties as functional foods

    PubMed Central

    Cooper, Raymond

    2015-01-01

    With the gluten-free food market worth almost $1.6 bn in 2011, there is every reason for renewed interest in ancient grains. This resurgent interest is expressed in re-discovering ancient varieties as functional foods. In particular, people affected by celiac disease have to avoid all gluten in their diet and several ancient grains may offer an important alternative. PMID:26151025

  16. Uniformly accelerated black holes

    NASA Astrophysics Data System (ADS)

    Letelier, Patricio S.; Oliveira, Samuel R.

    2001-09-01

    The static and stationary C metric are examined in a generic framework and their interpretations studied in some detail, especially those with two event horizons, one for the black hole and another for the acceleration. We find that (i) the spacetime of an accelerated static black hole is plagued by either conical singularities or a lack of smoothness and compactness of the black hole horizon, (ii) by using standard black hole thermodynamics we show that accelerated black holes have a higher Hawking temperature than Unruh temperature of the accelerated frame, and (iii) the usual upper bound on the product of the mass and acceleration parameters (<1/27) is just a coordinate artifact. The main results are extended to accelerated rotating black holes with no significant changes.

  17. The Dielectric Wall Accelerator

    SciTech Connect

    Caporaso, George J.; Chen, Yu-Jiuan; Sampayan, Stephen E.

    2009-01-01

    The Dielectric Wall Accelerator (DWA), a class of induction accelerators, employs a novel insulating beam tube to impress a longitudinal electric field on a bunch of charged particles. The surface flashover characteristics of this tube may permit the attainment of accelerating gradients on the order of 100 MV/m for accelerating pulses on the order of a nanosecond in duration. A virtual traveling wave of excitation along the tube is produced at any desired speed by controlling the timing of pulse generating modules that supply a tangential electric field to the tube wall. Because of the ability to control the speed of this virtual wave, the accelerator is capable of handling any charge to mass ratio particle; hence it can be used for electrons, protons and any ion. The accelerator architectures, key technologies and development challenges will be described.

  18. Mapping the Ancient Maya Landscape from Space

    NASA Technical Reports Server (NTRS)

    Sever, Tom

    2003-01-01

    This project uses new satellite and airborne imagery in combination with remote sensing, GIS, and GPS technology to understand the dynamics of how the Maya successfully interacted with their karst topographic landscape for several centuries in the northern Peten region of Guatemala. The ancient Maya attained one of the greatest population densities in human history in the tropical forest of the Peten, Guatemala, and it was in this region that the Maya civilization began, flourished, and abruptly disappeared for unknown reasons around AD 800. How the Maya were able to successfully manage water and feed this dense population is not known at this time. However, a recent NASA-funded project was the first to investigate large seasonal swamps (bajos) that make up 40 percent of the landscape. Through the use of remote sensing, ancient Maya features such as cities, roadways, canals and water reservoirs have been detected and verified through ground reconnaissance. The results of this research cast new light on the adaptation of the ancient Maya to their environment. Micro-environmental variation within the wetlands was elucidated and the different vegetational associations identified in the satellite imagery. More than 70 new archeological sites within and at the edges of the bajo were mapped and tested. Modification of the landscape by the Maya in the form of dams and reservoirs in the Holmul River and its tributaries and possible drainage canals in bajos was demonstrated. The recent acquisition of one-meter IKONOS imagery and high resolution STAR-3i radar imagery (2.5m backscatter/ 10m DEM), opens new possibilities for understanding how a civilization was able to survive for centuries upon a karst topographic landscape and their human-induced effects upon the local climate. This understanding is critical for the current population that is presently experiencing rapid population growth and destroying the landscape through non-traditional farming and grazing techniques

  19. [Bow legged adjectives in ancient literature].

    PubMed

    Simon, Frantisek; Steger, Florian

    2011-01-01

    This article addresses the issue of capturing the medical entity called 'curved legs' in a terminologically exact way. In so doing, it refers to the long-lasting process of differentiation of exact nuances of meaning in Ancient Greek and Latin. In the chronological perusal of ancient Greek literature, it becomes evident that the various adjectives employed are often vague when looking at non-medical literature. By contrast, in the Hippocratic corpus these terms are for the first time annotated with explanations intended to lead to a more precise understanding of the described deformity. Further attempts of differentiation can be found in the writings of Galen, who not only distinguishes between outward and inward curvatures, but also between deformities of the thigh and lower leg as well as between pathological and natural curvatures. Latin literature also provides a series of adjectives that were initially often used in the meaning of 'curved' but it was not until Celsus that these were differentiated with respect to the type and direction of the curvature. When comparing Greek and Latin adjectives, it turns out that though the Latin term blaesus can be traced back etymologically to the Greek word beta lambda alpha iota sigma ó zeta, the meaning of beta lambda alpha iota sigma ó zeta does not fully correspond to that of the Latin word. It is not before the later common transliteration of Greek words that this adjective took on the meaning of beta lambda alpha iota sigma ó zeta; however, this was finally lost again. In summary, the article concludes that exact word meanings in ancient literature are often unclear and precise ascriptions of meanings are inconsistent. In the case of "curved legs," this has led to misunderstandings regarding the respective types and directions of the curvature.

  20. Optically pulsed electron accelerator

    DOEpatents

    Fraser, J.S.; Sheffield, R.L.

    1985-05-20

    An optically pulsed electron accelerator can be used as an injector for a free electron laser and comprises a pulsed light source, such as a laser, for providing discrete incident light pulses. A photoemissive electron source emits electron bursts having the same duration as the incident light pulses when impinged upon by same. The photoemissive electron source is located on an inside wall of a radiofrequency-powered accelerator cell which accelerates the electron burst emitted by the photoemissive electron source.

  1. Optically pulsed electron accelerator

    DOEpatents

    Fraser, John S.; Sheffield, Richard L.

    1987-01-01

    An optically pulsed electron accelerator can be used as an injector for a free electron laser and comprises a pulsed light source, such as a laser, for providing discrete incident light pulses. A photoemissive electron source emits electron bursts having the same duration as the incident light pulses when impinged upon by same. The photoemissive electron source is located on an inside wall of a radio frequency powered accelerator cell which accelerates the electron burst emitted by the photoemissive electron source.

  2. ACCELERATION RESPONSIVE SWITCH

    DOEpatents

    Chabrek, A.F.; Maxwell, R.L.

    1963-07-01

    An acceleration-responsive device with dual channel capabilities whereby a first circuit is actuated upon attainment of a predetermined maximum acceleration level and when the acceleration drops to a predetermined minimum acceleriltion level another circuit is actuated is described. A fluid-damped sensing mass slidably mounted in a relatively frictionless manner on a shaft through the intermediation of a ball bushing and biased by an adjustable compression spring provides inertially operated means for actuating the circuits. (AEC)

  3. The foxhole accelerating structure

    SciTech Connect

    Fernow, R.C.; Claus, J.

    1992-07-17

    This report examines some properties of a new type of open accelerating structure. It consists of a series of rectangular cavities, which we call foxholes, joined by a beam channel. The power for accelerating the particles comes from an external radiation source and enters the cavities through their open upper surfaces. Analytic and computer calculations are presented showing that the foxhole is a suitable structure for accelerating relativistic electrons.

  4. Basaltic Volcanism and Ancient Planetary Crusts

    NASA Technical Reports Server (NTRS)

    Shervais, John W.

    1993-01-01

    The purpose of this project is to decipher the origin of rocks which form the ancient lunar crust. Our goal is to better understand how the moon evolved chemically and, more generally, the processes involved in the chemical fractionation of terrestrial planetoids. This research has implications for other planetary bodies besides the Moon, especially smaller planetoids which evolved early in the history of the solar system and are now thermally stable. The three main areas focused on in our work (lunar mare basalts, KREEP basalts, and plutonic rocks of the lunar highlands) provide complementary information on the lunar interior and the processes that formed it.

  5. Modern and ancient alluvial fan deposits

    SciTech Connect

    Nilsen, T.H.

    1985-01-01

    Understanding the structure and depositional processes of alluvial fans (river outwash deposits) has a special interest for those involved with the exploration of petroleum and many minerals. This collection of facsimile reprints of significant and classical research papers sheds new light on the subject. This reference covers the stratigraphy, sedimentology, and depositional processes of modern and ancient alluvial fans. Geographical areas considered include Arctic Canada, the American Southwest, Australia, Wyoming, Norway, and Spain. It includes a state-of-the-art introduction by the editor along with commentaries on all the papers included, a master author citation index and a subject index, and a chronological listing of early studies of alluvial fans.

  6. Extinct 244Pu in ancient zircons.

    PubMed

    Turner, Grenville; Harrison, T Mark; Holland, Greg; Mojzsis, Stephen J; Gilmour, Jamie

    2004-10-01

    We have found evidence, in the form of fissiogenic xenon isotopes, for in situ decay of 244Pu in individual 4.1- to 4.2-billion-year-old zircons from the Jack Hills region of Western Australia. Because of its short half-life, 82 million years, 244Pu was extinct within 600 million years of Earth's formation. Detrital zircons are the only known relics to have survived from this period, and a study of their Pu geochemistry will allow us to date ancient metamorphic events and determine the terrestrial Pu/U ratio for comparison with the solar ratio.

  7. Ancient Indian Astronomy in Introductory Text Books

    NASA Astrophysics Data System (ADS)

    Narahari Achar, B. N.

    1997-11-01

    Introductory survey courses in astronomy usually devote some time to the history of astronomy. Quite often, only the Greek contribution receives any attention in the text books. Some times the contributions from Babylon and China are mentioned. Hardly any account is given of ancient Indian astronomy. Even when one is given, it is usually wrong as shown by examples taken from several current text books. An attempt is made to sketch the contributions from the earliest astronomy of India, namely Vedaanga Jyotisha, to the later Siddhaanta astronomies.

  8. [The patients' view in Ancient Egypt].

    PubMed

    Herrmann, Sabine

    2008-01-01

    Although many medical texts are preserved from Ancient Egypt, these texts are giving only little information about the relationship between the Egyptian doctor and the patient. The aim of this article is to draw the reader's attention to personal documents such as letters between members of the royal court or private persons as well as to literary texts from the New Kingdom until the Roman Period. The article does also focus on Mesopotamian legal texts (Codex Hammurapi) and letters from the kingdom of Mari.

  9. The Ancient Maya Landscape from Space

    NASA Technical Reports Server (NTRS)

    Sever, T.; Arnold, James E. (Technical Monitor)

    1999-01-01

    The Peten, once inhabited by a population of several million before the collapse of the ancient Maya in the 10th and 11th centuries, is being repopulated toward its former demographic peak. Environmental dynamics, however, impose severe constraints to further development. Current practices in subsistence, commercial agriculture, and cattle raising are causing rapid deforestation resulting in the destruction of environmental and archeological resources. The use of remote sensing and Geographic Information Systems (GIS) technology is a cost-effective methodology for addressing issues in Maya archeology as well as monitoring the environmental impacts being experienced by the current population.

  10. Ancient Indian Astronomy in Introductory Texts

    NASA Astrophysics Data System (ADS)

    Narahari Achar, B. N.

    1997-10-01

    It is customary in introductory survey courses in astronomy to devote some time to the history of astronomy. In the available text books only the Greek contribution receives any attention. Apart from Stonehenge and Chichenitza pictures, contributions from Babylon and China are some times mentioned. Hardly any account is given of ancient Indian astronomy. Even when something is mentioned it is incomplete or incorrect or both. Examples are given from several text books currently available. An attempt is made to correct this situation by sketching the contributions from the earliest astronomy of India, namely Vedaanga Jyotisha.

  11. The Astronomical Orientation of Ancient Greek Temples

    PubMed Central

    Salt, Alun M.

    2009-01-01

    Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity. PMID:19936239

  12. The astronomical orientation of ancient Greek temples.

    PubMed

    Salt, Alun M

    2009-11-19

    Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

  13. Particle acceleration in flares

    NASA Technical Reports Server (NTRS)

    Benz, Arnold O.; Kosugi, Takeo; Aschwanden, Markus J.; Benka, Steve G.; Chupp, Edward L.; Enome, Shinzo; Garcia, Howard; Holman, Gordon D.; Kurt, Victoria G.; Sakao, Taro

    1994-01-01

    Particle acceleration is intrinsic to the primary energy release in the impulsive phase of solar flares, and we cannot understand flares without understanding acceleration. New observations in soft and hard X-rays, gamma-rays and coherent radio emissions are presented, suggesting flare fragmentation in time and space. X-ray and radio measurements exhibit at least five different time scales in flares. In addition, some new observations of delayed acceleration signatures are also presented. The theory of acceleration by parallel electric fields is used to model the spectral shape and evolution of hard X-rays. The possibility of the appearance of double layers is further investigated.

  14. Charged particle accelerator grating

    DOEpatents

    Palmer, Robert B.

    1986-01-01

    A readily disposable and replaceable accelerator grating for a relativistic particle accelerator. The grating is formed for a plurality of liquid droplets that are directed in precisely positioned jet streams to periodically dispose rows of droplets along the borders of a predetermined particle beam path. A plurality of lasers are used to direct laser beams into the droplets, at predetermined angles, thereby to excite the droplets to support electromagnetic accelerating resonances on their surfaces. Those resonances operate to accelerate and focus particles moving along the beam path. As the droplets are distorted or destroyed by the incoming radiation, they are replaced at a predetermined frequency by other droplets supplied through the jet streams.

  15. Charged particle accelerator grating

    DOEpatents

    Palmer, Robert B.

    1986-09-02

    A readily disposable and replaceable accelerator grating for a relativistic particle accelerator. The grating is formed for a plurality of liquid droplets that are directed in precisely positioned jet streams to periodically dispose rows of droplets along the borders of a predetermined particle beam path. A plurality of lasers are used to direct laser beams into the droplets, at predetermined angles, thereby to excite the droplets to support electromagnetic accelerating resonances on their surfaces. Those resonances operate to accelerate and focus particles moving along the beam path. As the droplets are distorted or destroyed by the incoming radiation, they are replaced at a predetermined frequency by other droplets supplied through the jet streams.

  16. Accelerator-based BNCT.

    PubMed

    Kreiner, A J; Baldo, M; Bergueiro, J R; Cartelli, D; Castell, W; Thatar Vento, V; Gomez Asoia, J; Mercuri, D; Padulo, J; Suarez Sandin, J C; Erhardt, J; Kesque, J M; Valda, A A; Debray, M E; Somacal, H R; Igarzabal, M; Minsky, D M; Herrera, M S; Capoulat, M E; Gonzalez, S J; del Grosso, M F; Gagetti, L; Suarez Anzorena, M; Gun, M; Carranza, O

    2014-06-01

    The activity in accelerator development for accelerator-based BNCT (AB-BNCT) both worldwide and in Argentina is described. Projects in Russia, UK, Italy, Japan, Israel, and Argentina to develop AB-BNCT around different types of accelerators are briefly presented. In particular, the present status and recent progress of the Argentine project will be reviewed. The topics will cover: intense ion sources, accelerator tubes, transport of intense beams, beam diagnostics, the (9)Be(d,n) reaction as a possible neutron source, Beam Shaping Assemblies (BSA), a treatment room, and treatment planning in realistic cases.

  17. High Gradient Accelerator Research

    SciTech Connect

    Temkin, Richard

    2016-07-12

    The goal of the MIT program of research on high gradient acceleration is the development of advanced acceleration concepts that lead to a practical and affordable next generation linear collider at the TeV energy level. Other applications, which are more near-term, include accelerators for materials processing; medicine; defense; mining; security; and inspection. The specific goals of the MIT program are: • Pioneering theoretical research on advanced structures for high gradient acceleration, including photonic structures and metamaterial structures; evaluation of the wakefields in these advanced structures • Experimental research to demonstrate the properties of advanced structures both in low-power microwave cold test and high-power, high-gradient test at megawatt power levels • Experimental research on microwave breakdown at high gradient including studies of breakdown phenomena induced by RF electric fields and RF magnetic fields; development of new diagnostics of the breakdown process • Theoretical research on the physics and engineering features of RF vacuum breakdown • Maintaining and improving the Haimson / MIT 17 GHz accelerator, the highest frequency operational accelerator in the world, a unique facility for accelerator research • Providing the Haimson / MIT 17 GHz accelerator facility as a facility for outside users • Active participation in the US DOE program of High Gradient Collaboration, including joint work with SLAC and with Los Alamos National Laboratory; participation of MIT students in research at the national laboratories • Training the next generation of Ph. D. students in the field of accelerator physics.

  18. FFAGS for rapid acceleration

    SciTech Connect

    Carol J. Johnstone and Shane Koscielniak

    2002-09-30

    When large transverse and longitudinal emittances are to be transported through a circular machine, extremely rapid acceleration holds the advantage that the beam becomes immune to nonlinear resonances because there is insufficient time for amplitudes to build up. Uncooled muon beams exhibit large emittances and require fast acceleration to avoid decay losses and would benefit from this style of acceleration. The approach here employs a fixed-field alternating gradient or FFAG magnet structure and a fixed frequency acceleration system. Acceptance is enhanced by the use only of linear lattice elements, and fixed-frequency rf enables the use of cavities with large shunt resistance and quality factor.

  19. Acceleration of polarized protons in circular accelerators

    SciTech Connect

    Courant, E.D.; Ruth, R.D.

    1980-09-12

    The theory of depolarization in circular accelerators is presented. The spin equation is first expressed in terms of the particle orbit and then converted to the equivalent spinor equation. The spinor equation is then solved for three different situations: (1) a beam on a flat top near a resonance, (2) uniform acceleration through an isolated resonance, and (3) a model of a fast resonance jump. Finally, the depolarization coefficient, epsilon, is calculated in terms of properties of the particle orbit and the results are applied to a calculation of depolarization in the AGS.

  20. China: A Simulation of Ancient Chung Kuo, the World's Most Ancient Civilization.

    ERIC Educational Resources Information Center

    Sargent, Marcia; Baral, Wanda

    This simulation allows students to participate in the "ways" of ancient Chinese history and culture. The unit is organized into five major phases or "li's." Students may spend about one week on activities in each "li" which focuses on a major aspect of Chinese history, culture, or geography. In each "li"…