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Sample records for bantu expansions mtdna

  1. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

    OpenAIRE

    Beleza Sandra; Luiselli Donata; Sequeira Fernando; Coelho Margarida; Rocha Jorge

    2009-01-01

    Abstract Background Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyanek...

  2. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

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    Beleza Sandra

    2009-04-01

    Full Text Available Abstract Background Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale. We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations. Results Correspondence analysis, lineage sharing patterns and admixture estimates indicate that the gene pool from southwestern Angola is predominantly derived from West-Central Africa. The pastoralist Herero-speaking Kuvale people were additionally characterized by relatively high frequencies of Y-chromosome (12% and mtDNA (22% Khoe-San lineages, as well as by the presence of the -14010C lactase persistence mutation (6%, which likely originated in non-Bantu pastoralists from East Africa. Inferred demographic parameters show that both male and female populations underwent significant size growth after the split between the western and eastern branches of Bantu expansions occurring 4000 years ago. However, males had lower population sizes and migration rates than females throughout the Bantu dispersals. Conclusion Genetic variation in southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa with autochthonous Khoisan-speaking peoples from the south. Interactions between the Bantus

  3. The analysis of variation of mtDNA hypervariable region 1 suggests that Eastern and Western Pygmies diverged before the Bantu expansion.

    Science.gov (United States)

    Destro-Bisol, Giovanni; Coia, Valentina; Boschi, Ilaria; Verginelli, Fabio; Cagliá, Alessandra; Pascali, Vincenzo; Spedini, Gabriella; Calafell, Francesc

    2004-02-01

    The Eastern Pygmies from Zaire and Western Pygmies from Cameroon, Congo, and the Central African Republic represent the two principal groups of African Pygmies. In the "recent divergence" hypothesis in which Western Pygmies are thought to be the result of hybridization between the ancestors of Eastern Pygmies and Bantu farmers who penetrated the equatorial belt and came into contact with Pygmies around 2-3 kiloyears ago. On the basis of recent archaeological research in the tropical rain forest, we propose a "pre-Bantu divergence" hypothesis, which posits the separation between the ancestors of Eastern and Western Pygmies earlier than 18 kiloyears ago. In order to test the two hypotheses, we analyzed the variation of the hypervariable region 1 of the mitochondrial DNA in the Mbenzele, Western Pygmies of the Central African Republic, and compared our results with those of previous mtDNA and Y chromosome studies. Distribution, sequence variation, and age of haplogroups along with genetic distances among populations, estimates of divergence times, and simulations based on the coalescent approach were found to be congruent with the pre-Bantu divergence but failed to support the recent divergence hypothesis.

  4. Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.

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    Chiara Barbieri

    Full Text Available Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000-5000 years, reaching different parts of southern Africa 1200-2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift, while the similarity of the Herero, Himba, and Damara probably reflects admixture, as also suggested by linguistic analyses.

  5. At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes.

    Science.gov (United States)

    Rowold, Diane; Garcia-Bertrand, Ralph; Calderon, Silvia; Rivera, Luis; Benedico, David Perez; Alfonso Sanchez, Miguel A; Chennakrishnaiah, Shilpa; Varela, Mangela; Herrera, Rene J

    2014-12-01

    Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific.

  6. At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

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    Diane Rowold

    2014-12-01

    Full Text Available Here, we present 12 loci paternal haplotypes (Y-STR profiles against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150 and Pygmy (B2b-M112 lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1 the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2 only traces of Khoisan (1.3% and Pygmy (1.3% markers persist in the Maputo Province Bantu gene pool, 3 the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4 the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west may have impacted the paternal landscape of sub-Saharan Africa, 5 the admixture and assimilation processes of Bantu elements were both highly complex and region-specific.

  7. Climate-induced vegetation dynamics and the Bantu Expansion: Evidence from Bantu names for pioneer trees (Elaeis guineensis, Canarium schweinfurthii, and Musanga cecropioides)

    Science.gov (United States)

    Bostoen, Koen; Grollemund, Rebecca; Koni Muluwa, Joseph

    2013-07-01

    The present article examines whether Late Holocene climate-induced vegetation changes in the Central African forest block may have facilitated the Bantu Expansion. This is done through a body of evidence that is not commonly used for the reconstruction of vegetation dynamics, i.e. language data. The article focuses on common Bantu vocabulary for three pioneer species abundantly present in the Central African pollen record between ca. 2500 and 2000 BP: Musanga cecropioides, Elaeis guineensis, and Canarium schweinfurthii. The geographical distribution patterns of the vernacular names for these pioneer trees add weight to the hypothesis according to which the rainforest contraction that emerged in the first millennium BC had an impact on the way Bantu languages dispersed.

  8. Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa

    OpenAIRE

    Chiara Barbieri; Mário Vicente; Sandra Oliveira; Koen Bostoen; Jorge Rocha; Mark Stoneking; Brigitte Pakendorf

    2014-01-01

    Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000-5000 years, reaching different parts of southern Africa 1200-2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speak...

  9. Bantu expansion shows that habitat alters the route and pace of human dispersals.

    Science.gov (United States)

    Grollemund, Rebecca; Branford, Simon; Bostoen, Koen; Meade, Andrew; Venditti, Chris; Pagel, Mark

    2015-10-27

    Unlike most other biological species, humans can use cultural innovations to occupy a range of environments, raising the intriguing question of whether human migrations move relatively independently of habitat or show preferences for familiar ones. The Bantu expansion that swept out of West Central Africa beginning ∼5,000 y ago is one of the most influential cultural events of its kind, eventually spreading over a vast geographical area a new way of life in which farming played an increasingly important role. We use a new dated phylogeny of ∼400 Bantu languages to show that migrating Bantu-speaking populations did not expand from their ancestral homeland in a "random walk" but, rather, followed emerging savannah corridors, with rainforest habitats repeatedly imposing temporal barriers to movement. When populations did move from savannah into rainforest, rates of migration were slowed, delaying the occupation of the rainforest by on average 300 y, compared with similar migratory movements exclusively within savannah or within rainforest by established rainforest populations. Despite unmatched abilities to produce innovations culturally, unfamiliar habitats significantly alter the route and pace of human dispersals.

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

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    Hong-Xiang Zheng

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

  11. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion

    DEFF Research Database (Denmark)

    Saillard, J; Forster, P; Lynnerup, N;

    2000-01-01

    characterization of Eskimos in general and Greenlanders in particular, we have sequenced hypervariable segment I (HVS-I) of the mitochondrial DNA (mtDNA) control region and typed relevant RFLP sites in the mtDNA of 82 Eskimos from Greenland. A comparison of our data with published sequences demonstrates major mtDNA...... types shared between Na Dene and Eskimo, indicating a common Beringian history within the Holocene. We further confirm the presence of an Eskimo-specific mtDNA subgroup characterized by nucleotide position 16265G within mtDNA group A2. This subgroup is found in all Eskimo groups analyzed so far and is...... estimated to have originated <3,000 years ago. A founder analysis of all Eskimo and Chukchi A2 types indicates that the Siberian and Greenland ancestral mtDNA pools separated around the time when the Neo-Eskimo culture emerged. The Greenland mtDNA types are a subset of the Alaskan mtDNA variation: they lack...

  12. Cladistic analysis of Bantu languages: a new tree based on combined lexical and grammatical data

    Science.gov (United States)

    Rexová, Kateřina; Bastin, Yvonne; Frynta, Daniel

    2006-04-01

    The phylogeny of the Bantu languages is reconstructed by application of the cladistic methodology to the combined lexical and grammatical data (87 languages, 144 characters). A maximum parsimony tree and Bayesian analysis supported some previously recognized clades, e.g., that of eastern and southern Bantu languages. Moreover, the results revealed that Bantu languages south and east of the equatorial forest are probably monophyletic. It suggests an unorthodox scenario of Bantu expansion including (after initial radiation in their homelands and neighboring territories) just a single passage through rainforest areas followed by a subsequent divergence into major clades. The likely localization of this divergence is in the area west of the Great Lakes. It conforms to the view that demographic expansion and dispersal throughout the dry-forests and savanna regions of subequatorial Africa was associated with the acquisition of new technologies (iron metallurgy and grain cultivation).

  13. The making of the African mtDNA landscape.

    Science.gov (United States)

    Salas, Antonio; Richards, Martin; De la Fe, Tomás; Lareu, María-Victoria; Sobrino, Beatriz; Sánchez-Diz, Paula; Macaulay, Vincent; Carracedo, Angel

    2002-11-01

    Africa presents the most complex genetic picture of any continent, with a time depth for mitochondrial DNA (mtDNA) lineages >100,000 years. The most recent widespread demographic shift within the continent was most probably the Bantu dispersals, which archaeological and linguistic evidence suggest originated in West Africa 3,000-4,000 years ago, spreading both east and south. Here, we have carried out a thorough phylogeographic analysis of mtDNA variation in a total of 2,847 samples from throughout the continent, including 307 new sequences from southeast African Bantu speakers. The results suggest that the southeast Bantu speakers have a composite origin on the maternal line of descent, with approximately 44% of lineages deriving from West Africa, approximately 21% from either West or Central Africa, approximately 30% from East Africa, and approximately 5% from southern African Khoisan-speaking groups. The ages of the major founder types of both West and East African origin are consistent with the likely timing of Bantu dispersals, with those from the west somewhat predating those from the east. Despite this composite picture, the southeastern African Bantu groups are indistinguishable from each other with respect to their mtDNA, suggesting that they either had a common origin at the point of entry into southeastern Africa or have undergone very extensive gene flow since.

  14. The Somali Bantu: Their History and Culture. Culture Profile.

    Science.gov (United States)

    Lehman, Dan Van; Eno, Omar

    This booklet is a basic introduction to the people, history, and cultures of the Somali Bantu. It is designed primarily for service providers and others assisting Somali Bantu refugees in their new communities in the United States. It focuses on: "Introduction"; "Land"; "People" (place in society and social structures); "History" (colonial period,…

  15. Expanding Our Understanding of mtDNA Deletions.

    Science.gov (United States)

    Picard, Martin; Vincent, Amy E; Turnbull, Doug M

    2016-07-12

    Clonal expansion of mtDNA deletions compromises mitochondrial function in human disease and aging, but how deleterious mtDNA genomes propagate has remained unclear. In this issue (Gitschlag et al., 2016) and in a recent Nature publication, C. elegans studies implicate the mitochondrial unfolded protein response (UPR(mt)) and offer mechanistic insights into this process. PMID:27411002

  16. Melanesian mtDNA complexity.

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    Jonathan S Friedlaender

    Full Text Available Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA sequences from hypervariable regions 1 and 2 (HVR1 and HVR2 from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups. Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP, and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal Austronesian influence in this region remains unresolved.

  17. From Bantu Education to the Fight for Socially Just Education

    Science.gov (United States)

    Ndimande, Bekisizwe S.

    2013-01-01

    This article illustrates the transition from Bantu Education to social justice education in South Africa. I argue that education reform in post-apartheid South Africa has made important changes during this transition, although inequalities persist. Large disparities in resources between black township (still segregated) and formerly white (now…

  18. Tone and Syntax in Rutooro, a Toneless Bantu Language of Western Uganda

    Science.gov (United States)

    Kaji, Shigeki

    2009-01-01

    This paper explores the interaction of tone and syntax in Rutooro, a Bantu language of Western Uganda. Rutooro has lost its lexical tone but retains a phrasally defined high pitch that appears on the penultimate syllable--the default position in Bantu. This high pitch can work grammatically and in fact distinguishes between the noun phrase vs.…

  19. Définition de l'adjectif en langues bantu

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    J. Baka

    1998-01-01

    Full Text Available In Bantu, as in other language groups, the definition of the adjective depends on the type of criteria that one uses. Some authors make use of morphological criteria, some of syntactic criteria and others of semantic criteria. From this variety of criteria there follows a diversity of definitions. One can reach, nevertheless, a more appropriate definition, by having recourse to the whole set of possible criteria but giving primacy to the syntactic ones. Such definition allows us - on the one hand - to bypass the dichotomy between nouns and pronouns which is founded on a purely morphological criterion « the form of the prefix » and - on the other hand - to restrict the meaning of the word 'adjective' to a purely semantic notion.

  20. Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia.

    Science.gov (United States)

    Barbieri, Chiara; Butthof, Anne; Bostoen, Koen; Pakendorf, Brigitte

    2013-04-01

    Some Bantu languages spoken in southwestern Zambia and neighboring regions of Botswana, Namibia, and Angola are characterized by the presence of click consonants, whereas their closest linguistic relatives lack such clicks. As clicks are a typical feature not of the Bantu language family, but of Khoisan languages, it is highly probable that the Bantu languages in question borrowed the clicks from Khoisan languages. In this paper, we combine complete mitochondrial genome sequences from a representative sample of populations from the Western Province of Zambia speaking Bantu languages with and without clicks, with fine-scaled analyses of Y-chromosomal single nucleotide polymorphisms and short tandem repeats to investigate the prehistoric contact that led to this borrowing of click consonants. Our results reveal complex population-specific histories, with female-biased admixture from Khoisan-speaking groups associated with the incorporation of click sounds in one Bantu-speaking population, while concomitant levels of potential Khoisan admixture did not result in sound change in another. Furthermore, the lack of sequence sharing between the Bantu-speaking groups from southwestern Zambia investigated here and extant Khoisan populations provides an indication that there must have been genetic substructure in the Khoisan-speaking indigenous groups of southern Africa that did not survive until the present or has been substantially reduced.

  1. Revolutionizing Bantu Lexicography — A Zulu Case Study

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    Gilles-Maurice de Schryver

    2011-10-01

    Full Text Available

    ABSTRACT: Zulu uses a conjunctive writing system, that is, a system whereby relatively short linguistic words are joined together to form long orthographic words with complex morphological structures. This has led to the so-called 'stem tradition' in dictionary making — for Zulu, as well as for most other Bantu languages. Given this lemmatization approach has been found to be inadequate for young learners (who fail to isolate stems, the development of a new approach was imperative for them, but until recently deemed impossible to implement. In this paper it is argued that it is now perfectly possible to reverse the unproductive trend, and to opt for the lemmatization of full words for all but one of the word classes in Bantu. This revolution is made possible thanks to the recent availability of relatively large corpora, with which the really frequent citation options may be pinpointed. Rather than a mission statement, this paper offers the result for all word classes. To do so, an actual guide to the use of a Zulu dictionary is re-represented and annotated.

    SAMENVATTING: Bantoe lexicografie radicaal omgooien — een gevalsanalyse voor Zoeloe. Zoeloe maakt gebruik van een conjunctief schrijfsysteem, d.w.z. een systeem waarbij relatief korte linguïstische woorden vast aan elkaar geschreven worden met lange orthografische woorden tot gevolg, die ook nog complexe morfologische structuren vertonen. Dit heeft geleid tot wat men de 'stam traditie' in de lexicografie is gaan noemen — voor Zoeloe, alsook voor de meeste andere Bantoetalen. Aangezien deze lemmatisatieaanpak ongeschikt is gebleken voor jonge gebruikers (die woordstammen maar niet kunnen isoleren, moest voor hen een nieuwe aanpak ontwikkeld worden. Tot voor kort werd zo'n aanpak echter als niet-implementeerbaar beschouwd. In dit artikel wordt geargumenteerd dat het vandaag de dag perfect mogelijk is om de onproductieve trend om te keren, en om te kiezen voor het lemmatiseren

  2. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes.

    Science.gov (United States)

    Wood, Elizabeth T; Stover, Daryn A; Ehret, Christopher; Destro-Bisol, Giovanni; Spedini, Gabriella; McLeod, Howard; Louie, Leslie; Bamshad, Mike; Strassmann, Beverly I; Soodyall, Himla; Hammer, Michael F

    2005-07-01

    To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

  3. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

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    Andres Gomez

    2016-03-01

    Full Text Available To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.

  4. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.

    Science.gov (United States)

    Gomez, Andres; Petrzelkova, Klara J; Burns, Michael B; Yeoman, Carl J; Amato, Katherine R; Vlckova, Klara; Modry, David; Todd, Angelique; Jost Robinson, Carolyn A; Remis, Melissa J; Torralba, Manolito G; Morton, Elise; Umaña, Juan D; Carbonero, Franck; Gaskins, H Rex; Nelson, Karen E; Wilson, Brenda A; Stumpf, Rebecca M; White, Bryan A; Leigh, Steven R; Blekhman, Ran

    2016-03-01

    To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.

  5. Humeral cortical thickness in female Bantu - its relationship to the incidence of femoral neck fracture

    Energy Technology Data Exchange (ETDEWEB)

    Bloom, R.A.; Pogrund, H.

    1982-03-01

    Measurements of the humeral cortical thickness demonstrate that generalised osteoporosis in female Bantu commences in the fifth decade and gradually increases until, in the ninth decade, all subjects are osteoporotic. The combined cortical thickness (CCT) of the humerus in young adults is very similar to that found previously in a white London population and the loss of cortex with age is very similar. It is concluded that the known low incidence of femoral neck fracture in Bantu is not due to a lower incidence of generalised osteoporosis but to environmental factors. The chief environmental factor postulated is the greater amount of physical work performed by the Bantu. A more careful mode of walking is suggested as a subsidiary cause.

  6. Occlusal characteristics during different emergence stages of the permanent dentition in Tanzanian Bantu and finnish children.

    NARCIS (Netherlands)

    Mugonzibwa, E.A.; Eskeli, R.; Kuijpers-Jagtman, A.M.; Laine-Alava, M.T.; Hof, M.A. van 't

    2004-01-01

    Occlusal characteristics and anomalies were studied among 869 (428 boys, 441 girls) Tanzanian Bantu children aged 3.5-16 years and 706 (319 boys, 387 girls) Finnish children aged 5-11 years during different emergence stages of the permanent dentition. Various occlusal variables were registered accor

  7. "Where to Start": Learning from Somali Bantu Refugee Students and Families

    Science.gov (United States)

    Roxas, Kevin; Roy, Laura

    2012-01-01

    This article provides an overview of research conducted with Somali Bantu refugee students in two contexts: Michigan and South Texas. We provide recommendations for outreach to refugee families and their families, for instruction in the classroom, for advising and support for these children, and for implementing school and district policy as it…

  8. Review Article: Second Language Acquisition of Bantu Languages--A (Mostly) Untapped Research Opportunity

    Science.gov (United States)

    Spinner, Patti

    2011-01-01

    This review article presents a summary of research on the second language acquisition of Bantu languages, including Swahili, Zulu, Xhosa and Lingala. Although second language (L2) research on these languages is currently very limited, work in morphosyntax and phonology suggests promising directions for future study, particularly on noun class,…

  9. Inheritance of the Bantu/Benin haplotype causes less severe hemolytic and oxidative stress in sickle cell anemia patients treated with hydroxycarbamide.

    Science.gov (United States)

    Okumura, Jéssika V; Silva, Danilo G H; Torres, Lidiane S; Belini-Junior, Edis; Barberino, Willian M; Oliveira, Renan G; Carrocini, Gisele C S; Gelaleti, Gabriela B; Lobo, Clarisse L C; Bonini-Domingos, Claudia R

    2016-07-01

    Beta S-globin gene cluster haplotypes (β(S)-haplotypes) can modulate the response to hydroxycarbamide (HC) treatment in sickle cell anemia (SCA) patients. In Brazil, the most common haplotypes are Bantu and Benin, and both confer a poor prognosis for patients when untreated with HC. We evaluated oxidative and hemolytic biomarkers in 48 SCA patients undergoing HC treatment separated in three subgroups: Bantu/Bantu, Bantu/Benin and Benin/Benin haplotype. On the basis of reduced haptoglobin (HP) levels, patients with Bantu/Bantu haplotypes had 3.0% higher hemolysis degree when compared with those with Bantu/Benin haplotypes (P=0.01). The Benin/Benin patients had 53.6% greater lipid peroxidation index than the Bantu/Bantu patients (P=0.01) because of evaluated thiobarbituric acid reactive species levels. The Bantu/Benin subgroup had intermediate levels of hemolytic and oxidative stress markers compared with the homozygous subgroups. Through strict inclusion criteria adopted, as well as consolidated and well-described hemolytic and the oxidative parameters evaluated, we suggest a haplotype-interaction response to HC treatment mediated by a 'balance' between the genetic factors of each haplotype studied. PMID:26961071

  10. Diversidade clínica e laboratorial no haplótipo bantu da anemia falciforme Clinical and laboratorial diversity in the bantu haplotype of sickle cell anemia

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    Paulo J. M. S. Costa

    2006-03-01

    Full Text Available Muitos fatores são responsáveis pela diversidade de sintomas nos pacientes de anemia falciforme, entre eles: sexo, idade, haplótipos e nível de hemoglobina fetal. O objetivo deste estudo foi verificar a diversidade clínica e laboratorial dentro do haplótipo bantu. Realizou-se um estudo descritivo onde foram avaliados 18 crianças e adolescentes portadores de anemia falciforme e homozigóticos para o haplótipo bantu, relacionando sexo e idade com as características clínicas e laboratoriais, além de relacioná-las diretamente entre si. As amostras foram do tipo casuais simples. O tamanho da amostra teve uma variação de freqüência para o evento de 30% a 65% e nível de confiança de 99,9%. As análises estatísticas foram realizadas através do programa EPIINFO, versão 6.04b, com erro a de 5%. A faixa etária de 01 a 11 anos teve um maior número de infecções que a faixa de 12 a 19, além de níveis mais altos de hemoglobina fetal. Os valores do hematócrito foram maiores no sexo feminino. Níveis mais elevados de hemoglobina A2 foram relacionados com maior número de infecções, enquanto níveis mais elevados de hemo­globina fetal foram relacionados com maiores valores de hematócrito e menor número de crises álgicas/ano de acompanhamento. O número de transfusões/ano teve correlação positiva com o número de crises álgicas, de infecções e de inter­namentos. Este estudo sugere que há uma diversidade clínica e laboratorial dentro do haplótipo bantu e possivelmente está relacionado com o sexo, a idade e os níveis de hemoglobina fetal e A2 dos pacientes.Several factors have been identified as possibly being responsible for the diversity of sickle cell anemia patients’ symptoms, including gender, age, haplotypes and hemoglobin F levels. The aim of this paper is to verify the clinical and laboratorial diversity of the Bantu haplotype. A descriptive study was performed of eighteen children and adolescents with sickle

  11. Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population

    OpenAIRE

    Wilson, J F; Goldstein, D. B.

    2000-01-01

    Both the optimal marker density for genome scans in case-control association studies and the appropriate study design for the testing of candidate genes depend on the genomic pattern of linkage disequilibrium (LD). In this study, we provide the first conclusive demonstration that the diverse demographic histories of human populations have produced dramatic differences in genomewide patterns of LD. Using a panel of 66 markers spanning the X chromosome, we show that, in the Lemba, a Bantu-Semit...

  12. Molecular epidemiology of human polyomavirus JC in the Biaka Pygmies and Bantu of Central Africa.

    Science.gov (United States)

    Chima, S C; Ryschkewitsch, C F; Stoner, G L

    1998-01-01

    Polyomavirus JC (JCV) is ubiquitous in humans and causes a chronic demyelinating disease of the central nervous system, progressive multifocal leukoencephalopathy which is common in AIDS. JCV is excreted in urine of 30-70% of adults worldwide. Based on sequence analysis of JCV complete genomes or fragments thereof, JCV can be classified into geographically derived genotypes. Types 1 and 2 are of European and Asian origin respectively while Types 3 and 6 are African in origin. Type 4, a possible recombinant of European and African genotypes (1 and 3) is common in the USA. To delineate the JCV genotypes in an aboriginal African population, random urine samples were collected from the Biaka Pygmies and Bantu from the Central African Republic. There were 43 males and 25 females aged 4-55 years, with an average age of 26 years. After PCR amplification of JCV in urine, products were directly cycle sequenced. Five of 23 Pygmy adults (22%) and four of 20 Bantu adults (20%) were positive for JC viruria. DNA sequence analysis revealed JCV Type 3 (two), Type 6 (two) and one Type 1 variant in Biaka Pygmies. All the Bantu strains were Type 6. Type 3 and 6 strains of JCV are the predominant strains in central Africa. The presence of multiple subtypes of JCV in Biaka Pygmies may be a result of extensive interactions of Pygmies with their African tribal neighbors during their itinerant movements in the equatorial forest.

  13. Molecular Epidemiology of Human Polyomavirus JC in the Biaka Pygmies and Bantu of Central Africa

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    Sylvester C Chima

    1998-09-01

    Full Text Available Polyomavirus JC (JCV is ubiquitous in humans and causes a chronic demyelinating disease of the central nervous system , progressive multifocal leukoencephalopathy which is common in AIDS. JCV is excreted in urine of 30-70% of adults worldwide. Based on sequence analysis of JCV complete genomes or fragments thereof, JCV can be classified into geographically derived genotypes. Types 1 and 2 are of European and Asian origin respectively while Types 3 and 6 are African in origin. Type 4, a possible recombinant of European and African genotypes (1 and 3 is common in the USA. To delineate the JCV genotypes in an aboriginal African population, random urine samples were collected from the Biaka Pygmies and Bantu from the Central African Republic. There were 43 males and 25 females aged 4-55 years, with an average age of 26 years. After PCR amplification of JCV in urine, products were directly cycle sequenced. Five of 23 Pygmy adults (22% and four of 20 Bantu adults (20% were positive for JC viruria. DNA sequence analysis revealed JCV Type 3 (two, Type 6 (two and one Type 1 variant in Biaka Pygmies. All the Bantu strains were Type 6. Type 3 and 6 strains of JCV are the predominant strains in central Africa. The presence of multiple subtypes of JCV in Biaka Pygmies may be a result of extensive interactions of Pygmies with their African tribal neighbors during their itinerant movements in the equatorial forest.

  14. Psychoactive ubulawu spiritual medicines and healing dynamics in the initiation process of Southern Bantu diviners.

    Science.gov (United States)

    Sobiecki, Jean-Francois

    2012-01-01

    The use of psychoactive plants by traditional healers in southern Africa appears to be a neglected area of ethnobotanical research. This article explores the healing dynamics involved in the use of popular psychoactive plant preparations known as ubulawu in the initiation rituals of Southern Bantu diviners. Research methods include a review of the literature, fieldwork interviews with Southern Bantu diviners, and an analysis of experiential accounts from diverse informants on their use of ubulawu. Findings reveal that there is widespread reliance on ubulawu as psychoactive spiritual medicines by the indigenous people of southern Africa to communicate with their ancestral spirits--so as to bring luck, and to treat mental disturbances. In the case of the Southern Bantu diviners, ubulawu used in a ritual initiation process acts as a mnemonic aid and medicine to familiarize the initiates with enhanced states of awareness and related psychospiritual phenomena such as enhanced intuition and dreams of the ancestral spirits, who teach the initiates how to find and use medicinal plants. The progression of the latter phenomena indicates the steady success of the initiates' own healing integration. Various factors such as psychological attitude and familiarization, correct plant combinations/synergy and a compatible healer-initiate relationship influence ubulawu responsiveness. PMID:23061321

  15. Bantu language trees reflect the spread of farming across sub-Saharan Africa: a maximum-parsimony analysis.

    Science.gov (United States)

    Holden, Clare Janaki

    2002-04-22

    Linguistic divergence occurs after speech communities divide, in a process similar to speciation among isolated biological populations. The resulting languages are hierarchically related, like genes or species. Phylogenetic methods developed in evolutionary biology can thus be used to infer language trees, with the caveat that 'borrowing' of linguistic elements between languages also occurs, to some degree. Maximum-parsimony trees for 75 Bantu and Bantoid African languages were constructed using 92 items of basic vocabulary. The level of character fit on the trees was high (consistency index was 0.65), indicating that a tree model fits Bantu language evolution well, at least for the basic vocabulary. The Bantu language tree reflects the spread of farming across this part of sub-Saharan Africa between ca. 3000 BC and AD 500. Modern Bantu subgroups, defined by clades on parsimony trees, mirror the earliest farming traditions both geographically and temporally. This suggests that the major subgroups of modern Bantu stem from the Neolithic and Early Iron Age, with little subsequent movement by speech communities.

  16. Pushing Back the Origin of Bantu Lexicography: The Vocabularium Congense of 1652, 1928, 2012.

    Science.gov (United States)

    De Kind, Jasper; de Schryver, Gilles-Maurice; Bostoen, Koen

    2012-12-01

    In this article, the oldest Bantu dictionary hitherto known is explored, that is the Vocabularium Latinum, Hispanicum, e Congense, handed down to us through a manuscript from 1652 by the Flemish Capuchin Joris van Gheel, missionary in the Kongo (present-day north-western Angola and the southern part of the Lower Congo Province of the DRC). The manuscript was heavily reworked by the Belgian Jesuits Joseph van Wing and Constant Penders, and published in 1928. Both works are currently being digitized, linked and added to an interlingual and multimedia database that revolves around Kikongo and the early history of the Kongo kingdom. In Sections 1 and 2 the origins of Bantu lexicography in general and of Kikongo metalexicography in particular are revisited. Sections 3 and 4 are devoted to a study of Van Gheel's manuscript and an analysis of Van Wing and Penders' rework. In Sections 5 and 6 translation equivalence and lexicographical structure in both dictionaries are scrutinized and compared. In Section 7, finally, all the material is brought together.

  17. Tense, Aspect and Case in Bantu and significance in Translation- The Case of Lulogooli Bible

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    Joyce Imali Wangia

    2014-06-01

    Full Text Available Tense and Aspect are morphological features and in some languages like English, they are marked mainly by inflection on the verb. In Bantu languages, the verbal element is characteristically conflated to mark tense and aspect and more often than not, the morphemes marking tense and aspect cannot be isolated. In many instances, they are tonally marked. Thus, a lexical verb may mark three or even more distinctions whose semantic realization is only through tonal variation. Similarly, Case realization is unique compared to for example English that marks possession on the noun and gender distinction on pronouns. This study will examine these features in Lulogooli, a Bantu language spoken in Western Kenya. Lulogooli has only two gender distinctions; male and female but does not use pronouns to mark them. This study proposes to sample data from the Lulogooli bible translation to show why and how improper use of these three grammatical categories leads to mistranslation. The analysis will also contribute to the significance of understanding language typology to translators so as to aid accuracy and effectiveness in translation. The study posits the significance of aspects of linguistic analysis to translation.

  18. Beyond Time: Temporal and Extra-Temporal Functions of Tense and Aspect Marking in Totela, a Bantu Language of Zambia

    Science.gov (United States)

    Crane, Thera Marie

    2011-01-01

    This dissertation aims to characterize the relationship between the temporal and information-structuring functions of tense and aspect marking in Totela, an endangered Bantu language of Zambia and Namibia. To that end, I investigate and describe in detail the semantics and pragmatics of selected tense and aspect markers, showing for each that a…

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

    OpenAIRE

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

    2009-01-01

    Although the functional consequences of mitochondrial DNA ( mtDNA) genetic backgrounds (haplotypes, haplogroups) have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are "evolutionary silent hitchhikers''. We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcri...

  20. Epidemiology and genetic variability of HHV-8/KSHV in Pygmy and Bantu populations in Cameroon.

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    Edouard Betsem

    2014-05-01

    Full Text Available BACKGROUND: Kaposi's sarcoma associated herpesvirus (KSHV/HHV-8 is the causal agent of all forms of Kaposi sarcoma. Molecular epidemiology of the variable K1 region identified five major subtypes exhibiting a clear geographical clustering. The present study is designed to gain new insights into the KSHV epidemiology and genetic diversity in Cameroon. METHODOLOGY/PRINCIPAL FINDINGS: Bantu and Pygmy populations from remote rural villages were studied. Antibodies directed against latent nuclear antigens (LANA were detected by indirect immunofluorescence using BC3 cells. Peripheral blood cell DNAs were subjected to a nested PCR amplifying a 737 bp K1 gene fragment. Consensus sequences were phylogenetically analyzed. We studied 2,063 persons (967 females, 1,096 males, mean age 39 years, either Bantus (1,276 or Pygmies (787. The Bantu group was older (42 versus 35 years: P<10(-4. KSHV anti-LANA seroprevalence was of 37.2% (768/2063, with a significant increase with age (P<10(-4 but no difference according to sex. Seroprevalence, as well as the anti-LANA antibodies titres, were higher in Bantus (43.2% than in Pygmies (27.6% (P<10(-4, independently of age. We generated 29 K1 sequences, comprising 24 Bantus and five Pygmies. These sequences belonged to A5 (24 cases or B (five cases subtypes. They exhibited neither geographical nor ethnic aggregation. A5 strains showed a wide genetic diversity while the B strains were more homogenous and belonged to the B1 subgroup. CONCLUSION: These data demonstrate high KSHV seroprevalence in the two major populations living in Southern and Eastern Cameroon with presence of mostly genetically diverse A5 but also B K1 subtypes.

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

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    Sarit Suissa

    2009-05-01

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

  2. Diet-related buccal dental microwear patterns in Central African Pygmy foragers and Bantu-speaking farmer and pastoralist populations.

    Science.gov (United States)

    Romero, Alejandro; Ramírez-Rozzi, Fernando V; De Juan, Joaquín; Pérez-Pérez, Alejandro

    2013-01-01

    Pygmy hunter-gatherers from Central Africa have shared a network of socioeconomic interactions with non-Pygmy Bantu speakers since agropastoral lifestyle spread across sub-Saharan Africa. Ethnographic studies have reported that their diets differ in consumption of both animal proteins and starch grains. Hunted meat and gathered plant foods, especially underground storage organs (USOs), are dietary staples for pygmies. However, scarce information exists about forager-farmer interaction and the agricultural products used by pygmies. Since the effects of dietary preferences on teeth in modern and past pygmies remain unknown, we explored dietary history through quantitative analysis of buccal microwear on cheek teeth in well-documented Baka pygmies. We then determined if microwear patterns differ among other Pygmy groups (Aka, Mbuti, and Babongo) and between Bantu-speaking farmer and pastoralist populations from past centuries. The buccal dental microwear patterns of Pygmy hunter-gatherers and non-Pygmy Bantu pastoralists show lower scratch densities, indicative of diets more intensively based on nonabrasive foodstuffs, compared with Bantu farmers, who consume larger amounts of grit from stoneground foods. The Baka pygmies showed microwear patterns similar to those of ancient Aka and Mbuti, suggesting that the mechanical properties of their preferred diets have not significantly changed through time. In contrast, Babongo pygmies showed scratch densities and lengths similar to those of the farmers, consistent with sociocultural contacts and genetic factors. Our findings support that buccal microwear patterns predict dietary habits independent of ecological conditions and reflect the abrasive properties of preferred or fallback foods such as USOs, which may have contributed to the dietary specializations of ancient human populations.

  3. Diet-related buccal dental microwear patterns in Central African Pygmy foragers and Bantu-speaking farmer and pastoralist populations.

    Directory of Open Access Journals (Sweden)

    Alejandro Romero

    Full Text Available Pygmy hunter-gatherers from Central Africa have shared a network of socioeconomic interactions with non-Pygmy Bantu speakers since agropastoral lifestyle spread across sub-Saharan Africa. Ethnographic studies have reported that their diets differ in consumption of both animal proteins and starch grains. Hunted meat and gathered plant foods, especially underground storage organs (USOs, are dietary staples for pygmies. However, scarce information exists about forager-farmer interaction and the agricultural products used by pygmies. Since the effects of dietary preferences on teeth in modern and past pygmies remain unknown, we explored dietary history through quantitative analysis of buccal microwear on cheek teeth in well-documented Baka pygmies. We then determined if microwear patterns differ among other Pygmy groups (Aka, Mbuti, and Babongo and between Bantu-speaking farmer and pastoralist populations from past centuries. The buccal dental microwear patterns of Pygmy hunter-gatherers and non-Pygmy Bantu pastoralists show lower scratch densities, indicative of diets more intensively based on nonabrasive foodstuffs, compared with Bantu farmers, who consume larger amounts of grit from stoneground foods. The Baka pygmies showed microwear patterns similar to those of ancient Aka and Mbuti, suggesting that the mechanical properties of their preferred diets have not significantly changed through time. In contrast, Babongo pygmies showed scratch densities and lengths similar to those of the farmers, consistent with sociocultural contacts and genetic factors. Our findings support that buccal microwear patterns predict dietary habits independent of ecological conditions and reflect the abrasive properties of preferred or fallback foods such as USOs, which may have contributed to the dietary specializations of ancient human populations.

  4. Redesign Alat Bantu Pengutip Brondolan Kelapa Sawit Secara Ergonomis Guna Peningkatan Produktivitas. (Kasus: PT. Perkebunan Nusantara III Kebun Rambutan)

    OpenAIRE

    Pasaribu, Donny Heri

    2014-01-01

    Pengutipan brondolan kelapa sawit dilakukan para buruh panen (BP) secara manual atau tidak menggunakan alat bantu. Posisi kerja para BP tersebut umumnya dalam keadaan jongkok dan membungkuk yang dilakukan secara berulang-ulang mulai dari jam 7 pagi sampai jam 1 siang. Sikap kerja dari berbagai postur tersebut cenderung menyebabkan timbulnya kelelahan pada beberapa anggota tubuh dan merupakan penyebab terjadinya gangguan musculoskeletal. Oleh karena itu, postur tubuh dari berbagai sikap kerja ...

  5. HLA class II polymorphism in Aka Pygmies and Bantu Congolese and a reassessment of HLA-DRB1 African diversity.

    Science.gov (United States)

    Renquin, J; Sanchez-Mazas, A; Halle, L; Rivalland, S; Jaeger, G; Mbayo, K; Bianchi, F; Kaplan, C

    2001-10-01

    HLA-DRB1, -DQB1 and -DPB1 polymorphisms were investigated in two African populations, the Basse Lobaye Aka Pygmies of the Central African Republic, and a Bantu-speaking group from the Democratic Republic of Congo Kinshasa. Allelic and haplotypic frequency distributions reveal marked differences between the two populations in spite of their geographical proximity: the Aka exhibit high frequencies for several alleles, especially at the DPB1 locus (0.695 for DPB1*0402), probably due to rapid genetic drift, while the Bantu distributions are more even. Genetic distances computed from DRB1 allelic frequencies among 21 populations from North and sub-Saharan Africa were applied to a multidimensional scaling analysis. African populations genetic structure is significantly shaped by linguistic differentiation, as confirmed by an analysis of molecular variance. However, selective neutrality tests indicate that many African populations exhibit an excess of heterozygotes for DRB1, which is likely to explain the genetic similarity observed between some North African and Bantu populations. Overall, this study shows that natural selection must be taken into account when interpreting the patterns of HLA diversity, but that this effect is probably minor in relation to the stochastic events of human population differentiations.

  6. A Phylogenetic Comparative Study of Bantu Kinship Terminology Finds Limited Support for Its Co-Evolution with Social Organisation.

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    Myrtille Guillon

    Full Text Available The classification of kin into structured groups is a diverse phenomenon which is ubiquitous in human culture. For populations which are organized into large agropastoral groupings of sedentary residence but not governed within the context of a centralised state, such as our study sample of 83 historical Bantu-speaking groups of sub-Saharan Africa, cultural kinship norms guide all aspects of everyday life and social organization. Such rules operate in part through the use of differing terminological referential systems of familial organization. Although the cross-cultural study of kinship terminology was foundational in Anthropology, few modern studies have made use of statistical advances to further our sparse understanding of the structuring and diversification of terminological systems of kinship over time. In this study we use Bayesian Markov Chain Monte Carlo methods of phylogenetic comparison to investigate the evolution of Bantu kinship terminology and reconstruct the ancestral state and diversification of cousin terminology in this family of sub-Saharan ethnolinguistic groups. Using a phylogenetic tree of Bantu languages, we then test the prominent hypothesis that structured variation in systems of cousin terminology has co-evolved alongside adaptive change in patterns of descent organization, as well as rules of residence. We find limited support for this hypothesis, and argue that the shaping of systems of kinship terminology is a multifactorial process, concluding with possible avenues of future research.

  7. A Phylogenetic Comparative Study of Bantu Kinship Terminology Finds Limited Support for Its Co-Evolution with Social Organisation.

    Science.gov (United States)

    Guillon, Myrtille; Mace, Ruth

    2016-01-01

    The classification of kin into structured groups is a diverse phenomenon which is ubiquitous in human culture. For populations which are organized into large agropastoral groupings of sedentary residence but not governed within the context of a centralised state, such as our study sample of 83 historical Bantu-speaking groups of sub-Saharan Africa, cultural kinship norms guide all aspects of everyday life and social organization. Such rules operate in part through the use of differing terminological referential systems of familial organization. Although the cross-cultural study of kinship terminology was foundational in Anthropology, few modern studies have made use of statistical advances to further our sparse understanding of the structuring and diversification of terminological systems of kinship over time. In this study we use Bayesian Markov Chain Monte Carlo methods of phylogenetic comparison to investigate the evolution of Bantu kinship terminology and reconstruct the ancestral state and diversification of cousin terminology in this family of sub-Saharan ethnolinguistic groups. Using a phylogenetic tree of Bantu languages, we then test the prominent hypothesis that structured variation in systems of cousin terminology has co-evolved alongside adaptive change in patterns of descent organization, as well as rules of residence. We find limited support for this hypothesis, and argue that the shaping of systems of kinship terminology is a multifactorial process, concluding with possible avenues of future research.

  8. Les proverbes dans Kongo Proverbs and the Origins of Bantu Wisdom par Mukumbuta Lisimba

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    Ludwine Mabika Mbokou

    2011-10-01

    Full Text Available

    Résumé: On emploie tous les jours des proverbes, des maximes, des devinettes et des dictons.Malgré les progrès techniques des denières décénies en matière d'outils didactiques, le proverbefait partie du quotidien des sociétés africaines en particulier et de celles du monde en général. Ilreste un instrument d'éducation indispensable et vital pour les générations futures, et quiconquedésire un conseil ou une orientation dans une certaine situation s'y réfère. Il fait partie intégrantede l'acte de communication.À la lumière des analyses du Dr Lisimba de certains proverbes de la famille bantu, nousdécouvrons l'importance que revêt la dynamique du langage offert par les proverbes. Ils peuventainsi être employés comme données dans la compilation de dictionnaires. En effet, pour la disciplinedes sciences du langage qu'est la lexicographie, le traitement des proverbes et idiomes estd'une importance capitale parce que ces derniers sont le véhicule de la culture et des moeurs d'unpeuple. Ainsi, pour mener à bien une telle entreprise, le lexicographe devra choisir le traitement àl'intérieur de la liste centrale, sinon à l'extérieur de la liste centrale, l'option la plus profitable pourlui restant une classification thématique qui tient compte non seulement de l'aspect sémantique duproverbe, mais aussi de son aspect formel.

    Mots-clés: ANALYSE FORMELLE, ANALYSE SÉMANTIQUE, CLASSIFICATION THÉMATIQUE,DIDACTIQUE, DICTIONNAIRE, GENRE PROVERBIAL, IDIOMES, LEXICOGRAPHE,LEXICOGRAPHIE, LISTE CENTRALE, LITTÉRATURE ORALE, PRÉ-TEXTES, POST-TEXTES,PROVERBES

    Abstract: Proverbs according to Kongo Proverbs and the Origins of Bantu Wisdom by Mukumbuta Lisimba. Proverbs, maxims, riddles and sayings are used every day. In spite of the technical progress during the last decades as far as didactic tools are concerned, the proverb forms part of the daily life of African societies in particular and those of the world in

  9. Homopolymeric tract heteroplasmy in mtDNA from tissues and single oocytes: Support for a genetic bottleneck

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    Marchington, D.R.; Hartshorne, G.M.; Barlow, D.; Poulton, J. [Univ. of Oxford (United Kingdom)

    1997-02-01

    While mtDNA polymorphisms at single base positions are common, the overwhelming majority of the mitochondrial genomes within a single individual are usually identical. When there is a point-mutation difference between a mother and her offspring, there may be a complete switching of mtDNA type within a single generation. It is generally assumed that there is a genetic bottleneck whereby a single or small number of founder mtDNA(s) populate the organism, but it is not known at which stages the restriction/amplification of mtDNA subtype(s) occur, and this uncertainty impedes antenatal diagnosis for mtDNA disorders. Length polymorphisms in homopolymeric tracts have been demonstrated in the large noncoding region of mtDNA. We have developed a new method, T-PCR (trimmed PCR), to quantitate heteroplasmy for two of these tracts (D310 and D16189). D310 variation is sufficient to indicate clonal origins of tissues and single oocytes. Tissues from normal individuals often possessed more than one length variant (heteroplasmy). However, there was no difference in the pattern of the length variants between somatic tissues in any control individual when bulk samples were taken. Oocytes from normal women undergoing in vitro fertilization were frequently heteroplasmic for length variants, and in two cases the modal length of the D310 tract differed in individual oocytes from the same woman. These data suggest that a restriction/amplification event, which we attribute to clonal expansion of founder mtDNA(s), has occurred by the time oocytes are mature, although further segregation may occur at a later stage. In contrast to controls, the length distribution of the D310 tract varied between tissues in a patient with heteroplasmic mtDNA rearrangements, suggesting that these mutants influence segregation. These findings have important implications for the genetic counselling of patients with pathogenic mtDNA mutations. 21 refs., 5 figs., 1 tab.

  10. Keeping mtDNA in shape between generations.

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    James B Stewart

    2014-10-01

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

  11. ANALISIS DAN PEMODELAN PROSES BISNIS PROSEDUR PELAKSANAAN PROYEK AKHIR SEBAGAI ALAT BANTU IDENTIFIKASI KEBUTUHAN SISTEM

    Directory of Open Access Journals (Sweden)

    Siska Komala Sari

    2015-11-01

    Full Text Available Proyek Akhir (PA adalah mata kuliah yang diajukan untuk memenuhi persyaratan studi Diploma di suatu Perguruan Tinggi. Mata kuliah ini dilaksanakan pada Semester 6 (enam atau tingkat akhir dari perkuliahan studi Diploma. Sebuah proses bisnis dapat dijelaskan dengan sederhana sebagai aliran aktifitas kegiatan. Proses bisnis adalah kumpulan dari tugas atau aktivitas yang terstruktur yang dapat menghasilkan layanan atau produk tertentu untuk satu atau banyak konsumen. Pada penelitian ini dilakukan analisis dan pemodelan proses bisnis dalam pelaksanaan proyek akhir. Hasil analisis dan pemodelan proses bisnis ini digunakan untuk memperbaiki alur kerja dan sebagai dasar pengembangan sistem informasi manajemen proyek akhir yang mampu mendukung alur pelaksanaan proyek akhir meliputi pengajuan topik, penentuan pembimbing, pelaksanaan seminar dan pelaksanaan sidang. Dalam analisa proses bisnis pelaksanaan proyek akhir ini kita dapat mengidentifikasi bahwa ada kasus yang dapat dimodelkan dengan BPMN (Business Process Modelling & Notation dan ada kasus yang cukup dimodelkan dengan notasi swimlanes s dimana masing-masing model memiliki kelebihan dan kekurangan masing-masing. Analisis dan pemodelan proses bisnis pelaksanaan proyek akhir ini dapat digunakan sebagai alat bantu untuk mengidentifikasi kebutuhan sistem

  12. Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA.

    Science.gov (United States)

    Melton, Phillip E; Briceño, I; Gómez, A; Devor, E J; Bernal, J E; Crawford, M H

    2007-05-01

    We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present. PMID:17340631

  13. Modelling the spread of farming in the Bantu-speaking regions of Africa: an archaeology-based phylogeography.

    Science.gov (United States)

    Russell, Thembi; Silva, Fabio; Steele, James

    2014-01-01

    We use archaeological data and spatial methods to reconstruct the dispersal of farming into areas of sub-Saharan Africa now occupied by Bantu language speakers, and introduce a new large-scale radiocarbon database and a new suite of spatial modelling techniques. We also introduce a method of estimating phylogeographic relationships from archaeologically-modelled dispersal maps, with results produced in a format that enables comparison with linguistic and genetic phylogenies. Several hypotheses are explored. The 'deep split' hypothesis suggests that an early-branching eastern Bantu stream spread around the northern boundary of the equatorial rainforest, but recent linguistic and genetic work tends not to support this. An alternative riverine/littoral hypothesis suggests that rivers and coastlines facilitated the migration of the first farmers/horticulturalists, with some extending this to include rivers through the rainforest as conduits to East Africa. More recently, research has shown that a grassland corridor opened through the rainforest at around 3000-2500 BP, and the possible effect of this on migrating populations is also explored. Our results indicate that rivers and coasts were important dispersal corridors, but do not resolve the debate about a 'Deep Split'. Future work should focus on improving the size, quality and geographical coverage of the archaeological (14)C database; on augmenting the information base to establish descent relationships between archaeological sites and regions based on shared material cultural traits; and on refining the associated physical geographical reconstructions of changing land cover.

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  15. Transcriptional quiescence of paternal mtDNA in cyprinid fish embryos.

    Science.gov (United States)

    Wen, Ming; Peng, Liangyue; Hu, Xinjiang; Zhao, Yuling; Liu, Shaojun; Hong, Yunhan

    2016-01-01

    Mitochondrial homoplasmy signifies the existence of identical copies of mitochondrial DNA (mtDNA) and is essential for normal development, as heteroplasmy causes abnormal development and diseases in human. Homoplasmy in many organisms is ensured by maternal mtDNA inheritance through either absence of paternal mtDNA delivery or early elimination of paternal mtDNA. However, whether paternal mtDNA is transcribed has remained unknown. Here we report that paternal mtDNA shows late elimination and transcriptional quiescence in cyprinid fishes. Paternal mtDNA was present in zygotes but absent in larvae and adult organs of goldfish and blunt-snout bream, demonstrating paternal mtDNA delivery and elimination for maternal mtDNA inheritance. Surprisingly, paternal mtDNA remained detectable up to the heartbeat stage, suggesting its late elimination leading to embryonic heteroplasmy up to advanced embryogenesis. Most importantly, we never detected the cytb RNA of paternal mtDNA at all stages when paternal mtDNA was easily detectable, which reveals that paternal mtDNA is transcriptionally quiescent and thus excludes its effect on the development of heteroplasmic embryos. Therefore, paternal mtDNA in cyprinids shows late elimination and transcriptional quiescence. Clearly, transcriptional quiescence of paternal mtDNA represents a new mechanism for maternal mtDNA inheritance and provides implications for treating mitochondrion-associated diseases by mitochondrial transfer or replacement. PMID:27334806

  16. Random Genetic Drift Determines the Level of Mutant mtDNA in Human Primary Oocytes

    OpenAIRE

    Brown, D T; Samuels, D C; Michael, E. M.; Turnbull, D.M.; Chinnery, P F

    2000-01-01

    We measured the proportion of mutant mtDNA (mutation load) in 82 primary oocytes from a woman who harbored the A3243G mtDNA mutation. The frequency distribution of mutation load indicates that random drift is the principal mechanism that determines the level of mutant mtDNA within individual oocytes.

  17. Pitfalls in the analysis of ancient human mtDNA

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

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

  18. The matrilocal tribe: an organization of demic expansion.

    Science.gov (United States)

    Jones, Doug

    2011-07-01

    This article integrates (1) research in the historical dynamics of state societies relating group solidarity and group expansion to cultural frontiers, (2) comparative research in anthropology relating matrilocality to a particular variety of internal politics and a particular form of warfare, and (3) interdisciplinary reconstructions of large-scale "demic expansions" and associated kinship systems in prehistory. The argument is that "metaethnic frontiers," where very different cultures clash, are centers for the formation of larger, more enduring, and more militarily effective groups. In small-scale non-state societies, the major path toward the formation of such groups is the establishment of cross-cutting ties among men. This often involves the adoption of matrilocal norms. The current distribution of matrilocality and matrilineality around the world may be partly a residue of major demic expansions in prehistory involving matrilocal tribes. This hypothesis is evaluated with a range of evidence, including information regarding the spread of two language families, Bantu and Austronesian. PMID:22388807

  19. ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells.

    Science.gov (United States)

    Lewis, Samantha C; Uchiyama, Lauren F; Nunnari, Jodi

    2016-07-15

    Mitochondrial DNA (mtDNA) encodes RNAs and proteins critical for cell function. In human cells, hundreds to thousands of mtDNA copies are replicated asynchronously, packaged into protein-DNA nucleoids, and distributed within a dynamic mitochondrial network. The mechanisms that govern how nucleoids are chosen for replication and distribution are not understood. Mitochondrial distribution depends on division, which occurs at endoplasmic reticulum (ER)-mitochondria contact sites. These sites were spatially linked to a subset of nucleoids selectively marked by mtDNA polymerase and engaged in mtDNA synthesis--events that occurred upstream of mitochondrial constriction and division machine assembly. Our data suggest that ER tubules proximal to nucleoids are necessary but not sufficient for mtDNA synthesis. Thus, ER-mitochondria contacts coordinate licensing of mtDNA synthesis with division to distribute newly replicated nucleoids to daughter mitochondria.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-07-01

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

  1. Geographic Patterns of mtDNA Diversity in Europe

    OpenAIRE

    Simoni, Lucia; Calafell, Francesc; Pettener, Davide; Bertranpetit, Jaume; Barbujani, Guido

    1999-01-01

    Genetic diversity in Europe has been interpreted as a reflection of phenomena occurring during the Paleolithic (∼45,000 years before the present [BP]), Mesolithic (∼18,000 years BP), and Neolithic (∼10,000 years BP) periods. A crucial role of the Neolithic demographic transition is supported by the analysis of most nuclear loci, but the interpretation of mtDNA evidence is controversial. More than 2,600 sequences of the first hypervariable mitochondrial control region were analyzed for geograp...

  2. Cellular Heterogeneity in the Level of mtDNA Heteroplasmy in Mouse Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Jitesh Neupane

    2015-11-01

    Full Text Available Variation in the level of mtDNA heteroplasmy in adult tissues is commonly seen in patients with a mixture of wild-type and mutant mtDNA. A mixture of different mtDNA variants may influence such variation and cause mtDNA segregation bias. We analyzed cellular heterogeneity in embryonic stem cells (ESCs derived from a polymorphic mouse model containing NZB and BALB mtDNA genotypes. In ESCs, inter-colony heterogeneity varied up to 61%, whereas intra-colony heterogeneity varied up to 100%. Three out of five cell lines displayed nearly homoplasmic BALB and NZB mtDNA haplotypes in differentiated single cells. The proportion of NZB mtDNA genotype increased with progressive passaging (0.39%; p = 0.002. These results demonstrate the bimodal segregation of mtDNA haplotypes, indicating the occurrence of tissues with variable levels of heteroplasmies in individuals with mtDNA mutations. Furthermore, proliferation of one mtDNA genotype over another may pose the risk of accumulating mutant mtDNAs during subsequent cell divisions.

  3. Cellular Heterogeneity in the Level of mtDNA Heteroplasmy in Mouse Embryonic Stem Cells.

    Science.gov (United States)

    Neupane, Jitesh; Ghimire, Sabitri; Vandewoestyne, Mado; Lu, Yuechao; Gerris, Jan; Van Coster, Rudy; Deroo, Tom; Deforce, Dieter; Vansteelandt, Stijn; De Sutter, Petra; Heindryckx, Björn

    2015-11-17

    Variation in the level of mtDNA heteroplasmy in adult tissues is commonly seen in patients with a mixture of wild-type and mutant mtDNA. A mixture of different mtDNA variants may influence such variation and cause mtDNA segregation bias. We analyzed cellular heterogeneity in embryonic stem cells (ESCs) derived from a polymorphic mouse model containing NZB and BALB mtDNA genotypes. In ESCs, inter-colony heterogeneity varied up to 61%, whereas intra-colony heterogeneity varied up to 100%. Three out of five cell lines displayed nearly homoplasmic BALB and NZB mtDNA haplotypes in differentiated single cells. The proportion of NZB mtDNA genotype increased with progressive passaging (0.39%; p = 0.002). These results demonstrate the bimodal segregation of mtDNA haplotypes, indicating the occurrence of tissues with variable levels of heteroplasmies in individuals with mtDNA mutations. Furthermore, proliferation of one mtDNA genotype over another may pose the risk of accumulating mutant mtDNAs during subsequent cell divisions.

  4. Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup

    OpenAIRE

    Emery, Leslie S.; Magnaye, Kevin M.; Bigham, Abigail W.; Akey, Joshua M.; Bamshad, Michael J.

    2015-01-01

    The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual’s place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ances...

  5. Quantitative Analysis of mtDNA Content in Formalin-Fixed Paraffin-Embedded Muscle Tissue

    OpenAIRE

    Font, Aida; Tort, Frederic; Navarro-Sastre, Aleix; Cusí, Victòria; García-Villoria, Judit; Briones, Paz; Ribes, Antonia

    2011-01-01

    Quantification of mitochondrial DNA (mtDNA) content is an essential tool for the diagnosis of mtDNA depletion syndrome (MDS). Samples collected and processed for anatomopathology studies represent a unique source of archived biological material. Thus, the possibility to study mtDNA copy number in these specimens would be a useful way to screen for MDS. In this study, we designed and validated the methodology to determine mtDNA content by quantitative real-time polymerase chain reaction (qRT-P...

  6. Genetic characterization of Clupisoma garua (Hamilton 1822) from six Indian populations using mtDNA cytochrome b gene.

    Science.gov (United States)

    Saraswat, Darpan; Lakra, W S; Nautiyal, Prakash; Goswami, Mukunda; Shyamakant, Komal; Malakar, Abhishekh

    2014-02-01

    Clupisoma garua (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. This study investigates the genetic diversity and population structure of six Indian populations of C. garua using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). We sequenced cyt b gene of 64 individuals collected from five distant rivers: Ganga, Gomti, Betwa, Gandak and Brahmaputra. Sequencing of 1054 bp cyt b mtDNA fragment revealed the presence of 19 haplotypes with a haplotype diversity value of 1.000 and a nucleotide diversity value of 0.0258 ± 0.00164. The Gandak river fish population showed highest nucleotide diversity. The fixation index analysis indicated significant genetic divergence among populations from different geographical areas. Both the neighbor-joining tree and median-joining network analysis of the haplotype data showed distinct patterns of phylo-geographic structure. The hierarchical analysis of molecular variance revealed that intra-group variation among populations was highly significant. The results of this study suggest that C. garua populations, especially geographically isolated groups, have developed significant genetic structures within the population. In addition, tests of neutrality suggest that C. garua may have experienced a population expansion. The study results establish cyt b as polymorphic and a potential marker to determine the population structure of C. garua. Information of genetic variation and population structure generated from this study would be useful for planning effective strategies for the conservation and rehabilitation of Schilibid cat fishes.

  7. Genetic characterization of Clupisoma garua (Hamilton 1822) from six Indian populations using mtDNA cytochrome b gene.

    Science.gov (United States)

    Saraswat, Darpan; Lakra, W S; Nautiyal, Prakash; Goswami, Mukunda; Shyamakant, Komal; Malakar, Abhishekh

    2014-02-01

    Clupisoma garua (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. This study investigates the genetic diversity and population structure of six Indian populations of C. garua using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). We sequenced cyt b gene of 64 individuals collected from five distant rivers: Ganga, Gomti, Betwa, Gandak and Brahmaputra. Sequencing of 1054 bp cyt b mtDNA fragment revealed the presence of 19 haplotypes with a haplotype diversity value of 1.000 and a nucleotide diversity value of 0.0258 ± 0.00164. The Gandak river fish population showed highest nucleotide diversity. The fixation index analysis indicated significant genetic divergence among populations from different geographical areas. Both the neighbor-joining tree and median-joining network analysis of the haplotype data showed distinct patterns of phylo-geographic structure. The hierarchical analysis of molecular variance revealed that intra-group variation among populations was highly significant. The results of this study suggest that C. garua populations, especially geographically isolated groups, have developed significant genetic structures within the population. In addition, tests of neutrality suggest that C. garua may have experienced a population expansion. The study results establish cyt b as polymorphic and a potential marker to determine the population structure of C. garua. Information of genetic variation and population structure generated from this study would be useful for planning effective strategies for the conservation and rehabilitation of Schilibid cat fishes. PMID:23676141

  8. Sequence-length variation of mtDNA HVS-IC-stretch in Chinese ethnic groups

    Institute of Scientific and Technical Information of China (English)

    Feng CHEN; Yong-hui DANG; Chun-xia YAN; Yan-ling LIU; Ya-jun DENG; David J. R. FULTON; Teng CHEN

    2009-01-01

    The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing ap-proaches. Thirty eight C-stretch haplotypes were identified, and some novel and population specific haplotypes were also detected. The C-stretch genetic diversity (GD) values were relatively high, and probability (P) values were low. Additionally, C-stretch length heteroplasmy was observed in approximately 9% of individuals studied. There was a significant correlation (r=-0.961, P<0.01) between the expansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of up-stream adenines. These results indicate that the C-stretch could be a useful genetic maker in forensic identification of Chinese populations. The results from the Fst and dA genetic distance matrix, neighbor-joining tree, and principal component map also suggest that C-stretch could be used as a reliable genetic marker in population genetics.

  9. Regional Variation in mtDNA of the Lesser Prairie-Chicken

    Science.gov (United States)

    Hagen, Christian A.; Pitman, James C.; Sandercock, Brett K.; Wolfe, Don H.; Robel, Robel J.; Applegate, Roger D.; Oyler-McCance, Sara J.

    2010-01-01

    Cumulative loss of habitat and long-term decline in the populations of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) have led to concerns for the species' viability throughout its range in the southern Great Plains. For more efficient conservation past and present distributions of genetic variation need to be understood. We examined the distribution of mitochondrial DNA (mtDNA) variation in the Lesser Prairie-Chicken across Kansas, Colorado, Oklahoma, and New Mexico. Throughout the range we found little genetic differentiation except for the population in New Mexico, which was significantly different from most other publications. We did, however, find significant isolation by distance at the rangewide scale (r=0.698). We found no relationship between haplotype phylogeny and geography, and our analyses provide evidence for a post-glacial population expansion within the species that is consistent with the idea that speciation within Tympanuchus is recent. Conservation actions that increase the likelihood of genetically viable populations in the future should be evaluated for implementation.

  10. Quality matters: how does mitochondrial network dynamics and quality control impact on mtDNA integrity?

    NARCIS (Netherlands)

    Busch, K.B.; Kowald, A.; Spelbrink, H.

    2014-01-01

    Mammalian mtDNA encodes for 13 core proteins of oxidative phosphorylation. Mitochondrial DNA mutations and deletions cause severe myopathies and neuromuscular diseases. Thus, the integrity of mtDNA is pivotal for cell survival and health of the organism. We here discuss the possible impact of mitoch

  11. Replication factors transiently associate with mtDNA at the mitochondrial inner membrane to facilitate replication

    NARCIS (Netherlands)

    Rajala, N.; Gerhold, J.M.; Martinsson, P.; Klymov, A.; Spelbrink, H.

    2014-01-01

    Mitochondrial DNA (mtDNA) is organized in discrete protein-DNA complexes, nucleoids, that are usually considered to be mitochondrial-inner-membrane associated. Here we addressed the association of replication factors with nucleoids and show that endogenous mtDNA helicase Twinkle and single-stranded

  12. Mitochondrial DNA (mtDNA) biogenesis: visualization and duel incorporation of BrdU and EdU into newly synthesized mtDNA in vitro.

    Science.gov (United States)

    Lentz, Stephen I; Edwards, James L; Backus, Carey; McLean, Lisa L; Haines, Kristine M; Feldman, Eva L

    2010-02-01

    Mitochondria are key regulators of cellular energy and are the focus of a large number of studies examining the regulation of mitochondrial dynamics and biogenesis in healthy and diseased conditions. One approach to monitoring mitochondrial biogenesis is to measure the rate of mitochondrial DNA (mtDNA) replication. We developed a sensitive technique to visualize newly synthesized mtDNA in individual cells to study mtDNA replication within subcellular compartments of neurons. The technique combines the incorporation of 5-bromo-2-deoxyuridine (BrdU) and/or 5-ethynyl-2'-deoxyuridine (EdU) into mtDNA, together with a tyramide signal amplification protocol. Employing this technique, we visualized and measured mtDNA biogenesis in individual cells. The labeling procedure for EdU allows for more comprehensive results by allowing the comparison of its incorporation with other intracellular markers, because it does not require the harsh acid or enzyme digests necessary to recover the BrdU epitope. In addition, the utilization of both BrdU and EdU permits sequential pulse-chase experiments to follow the intracellular localization of mtDNA replication. The ability to quantify mitochondrial biogenesis provides an essential tool for investigating the alterations in mitochondrial dynamics involved in the pathogenesis of multiple cellular disorders, including neuropathies and neurodegenerative diseases. PMID:19875847

  13. Biomarker Validation for Aging: Lessons from mtDNA Heteroplasmy Analyses in Early Cancer Detection

    Directory of Open Access Journals (Sweden)

    Peter E. Barker

    2009-11-01

    Full Text Available The anticipated biological and clinical utility of biomarkers has attracted significant interest recently. Aging and early cancer detection represent areas active in the search for predictive and prognostic biomarkers. While applications differ, overlapping biological features, analytical technologies and specific biomarker analytes bear comparison. Mitochondrial DNA (mtDNA as a biomarker in both biological models has been evaluated. However, it remains unclear whether mtDNA changes in aging and cancer represent biological relationships that are causal, incidental, or a combination of both. This article focuses on evaluation of mtDNA-based biomarkers, emerging strategies for quantitating mtDNA admixtures, and how current understanding of mtDNA in aging and cancer evolves with introduction of new technologies. Whether for cancer or aging, lessons from mtDNA based biomarker evaluations are several. Biological systems are inherently dynamic and heterogeneous. Detection limits for mtDNA sequencing technologies differ among methods for low-level DNA sequence admixtures in healthy and diseased states. Performance metrics of analytical mtDNA technology should be validated prior to application in heterogeneous biologically-based systems. Critical in evaluating biomarker performance is the ability to distinguish measurement system variance from inherent biological variance, because it is within the latter that background healthy variability as well as high-value, disease-specific information reside.

  14. The role of the mtDNA set point in differentiation, development and tumorigenesis.

    Science.gov (United States)

    Sun, Xin; St John, Justin C

    2016-10-01

    Mitochondrial DNA replication is critical for maintaining mtDNA copy number to generate sufficient cellular energy that is required for development and for functional cells. In early development, mtDNA copy number is strictly regulated at different stages, and, as a result, the establishment of the mtDNA set point is required for sequential cell lineage commitment. The failure to establish the mtDNA set point results in incomplete differentiation or embryonic arrest. The regulation of mtDNA copy number during differentiation is closely associated with cellular gene expression, especially with the pluripotency network, and DNA methylation profiles. The findings from cancer research highlight the relationship between mitochondrial function, mtDNA copy number and DNA methylation in regulating differentiation. DNA methylation at exon 2 of DNA polymerase gamma subunit A (POLGA) has been shown to be a key factor, which can be modulated to change the mtDNA copy number and cell fate of differentiating and tumour cells. The present review combines multi-disciplinary data from mitochondria, development, epigenetics and tumorigenesis, which could provide novel insights for further research, especially for developmental disorders and cancers. PMID:27679856

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

    OpenAIRE

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

    2009-01-01

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

  16. Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing.

    NARCIS (Netherlands)

    Greaves, L.C.; Nooteboom, M.; Elson, J.L.; Tuppen, H.A.; Taylor, G.A.; Commane, D.M.; Arasaradnam, R.P.; Khrapko, K.; Taylor, R.W.; Kirkwood, T.B.; Mathers, J.C.; Turnbull, D.M.

    2014-01-01

    Age-related decline in the integrity of mitochondria is an important contributor to the human ageing process. In a number of ageing stem cell populations, this decline in mitochondrial function is due to clonal expansion of individual mitochondrial DNA (mtDNA) point mutations within single cells. Ho

  17. Improvement and Check on the mtDNA extract techniques for termites%白蚁 mtDNA 提取方法改良及检测

    Institute of Scientific and Technical Information of China (English)

    姜丽红; 邹湘武; 宁涤非; 席在星

    2013-01-01

      利用mtDNA多态性进行种类鉴定是一种分子生物学常用方法,从DNA水平对白蚁进行物种鉴别并探讨物种的进化,其必要前提是提取到一定数量和质量的mtDNA.在分离得到线粒体后,分别采用CTAB、SDS 2种方法提取mtDNA.紫外分光光度计检测DNA纯度及浓度,用mtDNA 特异性引物进行PCR 扩增检测.试验证明2种方法均能成功提取白蚁的mtDNA, SDS法提取效果较好.%Species identification with mtDNA polymorphisms is an usual method in molecular biology. To identify the species and to explore the evolution of the termites from the DNA level, it is necessary to extract the mtDNA with enough quantity and good quality. In this study, mitochondria of termites is firstly isolated, then CTAB and SDS methods were employed for the extraction of mtDNA, respectively. Purity and concentration of mtDNA were determined by UV spectrophotometer. PCR amplification of mtDNA was executed by specific primers. Results shows that both CTAB the SDS methods can successfully extracted termite mtDNA, but SDS method shows better performance than CTAB method.

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

    Directory of Open Access Journals (Sweden)

    Juan J. Yunis

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Candela L Hernández

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

  20. Evolution of Bombina bombina and Bombina variegata (Anura: Discoglossidae) in the Carpathian Basin: a history of repeated mt-DNA introgression across species.

    Science.gov (United States)

    Vörös, Judit; Alcobendas, Marina; Martínez-Solano, Iñigo; García-París, Mario

    2006-03-01

    The structure and geographic location of hybrid zones change through time. Current patterns result from present and historical population-environment interactions that act on each of the hybridizing taxa. This is particularly evident for species involved in complex hybrid zones, such as that formed by the toad species Bombina bombina and Bombina variegata (Anura: Discoglossidae), which interact along extensive areas in Central Europe. We used data on external morphology and partial sequences of the cytochrome oxidase I (cox1) and nicotinamide adenine dinucleotid dehydrogenase subunit 4 (nad4) mitochondrial DNA (mt-DNA) genes to analyze the current patterns of genetic structure shown by both species of Bombina along their contact zone in Hungary. Phylogenetic, phylogeographic, and historical demography analyses were applied to 1.5kb mt-DNA obtained from 119 individuals representing 24 populations from Hungary and additional specimens from Slovakia, Albania, and Bosnia-Herzegovina. We use these data to infer the evolutionary history of the isolated populations of B. variegata in Hungary and to discriminate between competing biogeographic scenarios accounting for the historical interactions between species in this region. Results from the inferred phylogenetic branching pattern and sequence divergence among species and populations support the following: (i) recent population expansion has occurred in Hungarian populations of B. bombina, which are genetically very homogeneous; (ii) the Hungarian populations of B. variegata correspond to two distinct mitochondrial lineages (Carpathian and Alpine, respectively); average maximum-likelihood-corrected sequence divergence between these lineages is 8.96% for cox1 and 10.85% for nad4; (iii) mt-DNA divergence among the three isolated western populations of B. variegata from Transdanubia is low, with four closely related haplotypes, which suggests that the isolation between these populations is the result of a recent process

  1. Exercise-induced mitochondrial p53 repairs mtDNA mutations in mutator mice

    OpenAIRE

    Safdar, Adeel; Khrapko, Konstantin; Flynn, James M.; Saleem, Ayesha; De Lisio, Michael; Johnston, Adam P. W.; Kratysberg, Yevgenya; Samjoo, Imtiaz A.; Kitaoka, Yu; Ogborn, Daniel I.; Little, Jonathan P.; Raha, Sandeep; Parise, Gianni; Akhtar, Mahmood; Bart P Hettinga

    2016-01-01

    Background Human genetic disorders and transgenic mouse models have shown that mitochondrial DNA (mtDNA) mutations and telomere dysfunction instigate the aging process. Epidemiologically, exercise is associated with greater life expectancy and reduced risk of chronic diseases. While the beneficial effects of exercise are well established, the molecular mechanisms instigating these observations remain unclear. Results Endurance exercise reduces mtDNA mutation burden, alleviates multisystem pat...

  2. Reduced mtDNA copy number increases the sensitivity of tumor cells to chemotherapeutic drugs.

    Science.gov (United States)

    Mei, H; Sun, S; Bai, Y; Chen, Y; Chai, R; Li, H

    2015-04-02

    Many cancer drugs are toxic to cells by activating apoptotic pathways. Previous studies have shown that mitochondria have key roles in apoptosis in mammalian cells, but the role of mitochondrial DNA (mtDNA) copy number variation in the pathogenesis of tumor cell apoptosis remains largely unknown. We used the HEp-2, HNE2, and A549 tumor cell lines to explore the relationship between mtDNA copy number variation and cell apoptosis. We first induced apoptosis in three tumor cell lines and one normal adult human skin fibroblast cell line (HSF) with cisplatin (DDP) or doxorubicin (DOX) treatment and found that the mtDNA copy number significantly increased in apoptotic tumor cells, but not in HSF cells. We then downregulated the mtDNA copy number by transfection with shRNA-TFAM plasmids or treatment with ethidium bromide and found that the sensitivity of tumor cells to DDP or DOX was significantly increased. Furthermore, we observed that levels of reactive oxygen species (ROS) increased significantly in tumor cells with lower mtDNA copy numbers, and this might be related to a low level of antioxidant gene expression. Finally, we rescued the increase of ROS in tumor cells with lipoic acid or N-acetyl-L-cysteine and found that the apoptosis rate decreased. Our studies suggest that the increase of mtDNA copy number is a self-protective mechanism of tumor cells to prevent apoptosis and that reduced mtDNA copy number increases ROS levels in tumor cells, increases the tumor cells' sensitivity to chemotherapeutic drugs, and increases the rate of apoptosis. This research provides evidence that mtDNA copy number variation might be a promising new therapeutic target for the clinical treatment of tumors.

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

    Directory of Open Access Journals (Sweden)

    Horst Jürgen

    2011-02-01

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

  4. Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder.

    Science.gov (United States)

    Cai, Na; Li, Yihan; Chang, Simon; Liang, Jieqin; Lin, Chongyun; Zhang, Xiufei; Liang, Lu; Hu, Jingchu; Chan, Wharton; Kendler, Kenneth S; Malinauskas, Tomas; Huang, Guo-Jen; Li, Qibin; Mott, Richard; Flint, Jonathan

    2015-12-21

    Control over the number of mtDNA molecules per cell appears to be tightly regulated, but the mechanisms involved are largely unknown. Reversible alterations in the amount of mtDNA occur in response to stress suggesting that control over the amount of mtDNA is involved in stress-related diseases including major depressive disorder (MDD). Using low-coverage sequence data from 10,442 Chinese women to compute the normalized numbers of reads mapping to the mitochondrial genome as a proxy for the amount of mtDNA, we identified two loci that contribute to mtDNA levels: one within the TFAM gene on chromosome 10 (rs11006126, p value = 8.73 × 10(-28), variance explained = 1.90%) and one over the CDK6 gene on chromosome 7 (rs445, p value = 6.03 × 10(-16), variance explained = 0.50%). Both loci replicated in an independent cohort. CDK6 is thus a new molecule involved in the control of mtDNA. We identify increased rates of heteroplasmy in women with MDD, and show from an experimental paradigm using mice that the increase is likely due to stress. Furthermore, at least one heteroplasmic variant is significantly associated with changes in the amount of mtDNA (position 513, p value = 3.27 × 10(-9), variance explained = 0.48%) suggesting site-specific heteroplasmy as a possible link between stress and increase in amount of mtDNA. These findings indicate the involvement of mitochondrial genome copy number and sequence in an organism's response to stress.

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

    OpenAIRE

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

    1998-01-01

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

  6. Porcine oocyte mtDNA copy number is high or low depending on the donor.

    Science.gov (United States)

    Pedersen, Hanne Skovsgaard; Løvendahl, Peter; Larsen, Knud; Madsen, Lone Bruhn; Callesen, Henrik

    2016-08-01

    Oocyte capacity is relevant in understanding decreasing female fertility and in the use of assisted reproductive technologies in human and farm animals. Mitochondria are important to the development of a functionally good oocyte and the oocyte mtDNA copy number has been introduced as a useful parameter for prediction of oocyte competence. The aim of this study was to investigate: (i) if the oocyte donor has an influence on its oocyte's mtDNA copy number; and (ii) the relation between oocyte size and mtDNA copy number using pre- and postpubertal pig oocytes. Cumulus-oocyte complexes were collected from individual donor pigs. The oocytes were allocated into different size-groups, snap-frozen and single-oocyte mtDNA copy number was estimated by quantitative real-time PCR using the genes ND1 and COX1. Results showed that mean mtDNA copy number in oocytes from any individual donor could be categorized as either 'high' (≥100,000) or 'low' (difference in threshold between pre- and postpubertal oocytes. No linear correlation was detected between oocyte size and mtDNA copy number within pre- and postpubertal oocytes. This study demonstrates the importance of the oocyte donor in relation to oocyte mtDNA copy number, irrespectively of the donor's puberty status and the oocyte's growth stage. Observations from this study facilitate both further investigations of the importance of mtDNA copy number and the unravelling of relations between different mitochondrial parameters and oocyte competence. PMID:26679989

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

    International Nuclear Information System (INIS)

    Highlights: → Increased mtDNA mutations in MEFs lead to high level of spontaneous immortalization. → This process is independent of endogenous ROS production. → Aerobic glycolysis significantly contributes to spontaneous immortalization of MEFs. -- Abstract: An increase in mtDNA mutation load leads to a loss of critical cells in different tissues thereby contributing to the physiological process of organismal ageing. Additionally, the accumulation of senescent cells that display changes in metabolic function might act in an active way to further disrupt the normal tissue function. We believe that this could be the important link missing in our understanding of the molecular mechanisms of premature ageing in the mtDNA mutator mice. We tested proliferation capacity of mtDNA mutator cells in vitro. When cultured in physiological levels of oxygen (3%) their proliferation capacity is somewhat lower than wild-type cells. Surprisingly, in conditions of increased oxidative stress (20% O2) mtDNA mutator mouse embryonic fibroblasts exhibit continuous proliferation due to spontaneous immortalization, whereas the same conditions promote senescence in wild-type cells. We believe that an increase in aerobic glycolysis observed in mtDNA mutator mice is a major mechanism behind this process. We propose that glycolysis promotes proliferation and allows a fast turnover of metabolites, but also leads to energy crisis due to lower ATP production rate. This could lead to compromised replication and/or repair and therefore, in rare cases, might lead to mutations in tumor suppressor genes and spontaneous immortalization.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-10

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

  9. The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants.

    Science.gov (United States)

    Goremykin, Vadim V; Lockhart, Peter J; Viola, Roberto; Velasco, Riccardo

    2012-08-01

    Mitochondrial genomes of spermatophytes are the largest of all organellar genomes. Their large size has been attributed to various factors; however, the relative contribution of these factors to mitochondrial DNA (mtDNA) expansion remains undetermined. We estimated their relative contribution in Malus domestica (apple). The mitochondrial genome of apple has a size of 396 947 bp and a one to nine ratio of coding to non-coding DNA, close to the corresponding average values for angiosperms. We determined that 71.5% of the apple mtDNA sequence was highly similar to sequences of its nuclear DNA. Using nuclear gene exons, nuclear transposable elements and chloroplast DNA as markers of promiscuous DNA content in mtDNA, we estimated that approximately 20% of the apple mtDNA consisted of DNA sequences imported from other cell compartments, mostly from the nucleus. Similar marker-based estimates of promiscuous DNA content in the mitochondrial genomes of other species ranged between 21.2 and 25.3% of the total mtDNA length for grape, between 23.1 and 38.6% for rice, and between 47.1 and 78.4% for maize. All these estimates are conservative, because they underestimate the import of non-functional DNA. We propose that the import of promiscuous DNA is a core mechanism for mtDNA size expansion in seed plants. In apple, maize and grape this mechanism contributed far more to genome expansion than did homologous recombination. In rice the estimated contribution of both mechanisms was found to be similar.

  10. Ancient mtDNA sequences from the First Australians revisited.

    Science.gov (United States)

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

    2016-06-21

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

  11. POLRMT regulates the switch between replication primer formation and gene expression of mammalian mtDNA.

    Science.gov (United States)

    Kühl, Inge; Miranda, Maria; Posse, Viktor; Milenkovic, Dusanka; Mourier, Arnaud; Siira, Stefan J; Bonekamp, Nina A; Neumann, Ulla; Filipovska, Aleksandra; Polosa, Paola Loguercio; Gustafsson, Claes M; Larsson, Nils-Göran

    2016-08-01

    Mitochondria are vital in providing cellular energy via their oxidative phosphorylation system, which requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes (mtDNA). Transcription of the circular mammalian mtDNA depends on a single mitochondrial RNA polymerase (POLRMT). Although the transcription initiation process is well understood, it is debated whether POLRMT also serves as the primase for the initiation of mtDNA replication. In the nucleus, the RNA polymerases needed for gene expression have no such role. Conditional knockout of Polrmt in the heart results in severe mitochondrial dysfunction causing dilated cardiomyopathy in young mice. We further studied the molecular consequences of different expression levels of POLRMT and found that POLRMT is essential for primer synthesis to initiate mtDNA replication in vivo. Furthermore, transcription initiation for primer formation has priority over gene expression. Surprisingly, mitochondrial transcription factor A (TFAM) exists in an mtDNA-free pool in the Polrmt knockout mice. TFAM levels remain unchanged despite strong mtDNA depletion, and TFAM is thus protected from degradation of the AAA(+) Lon protease in the absence of POLRMT. Last, we report that mitochondrial transcription elongation factor may compensate for a partial depletion of POLRMT in heterozygous Polrmt knockout mice, indicating a direct regulatory role of this factor in transcription. In conclusion, we present in vivo evidence that POLRMT has a key regulatory role in the replication of mammalian mtDNA and is part of a transcriptional mechanism that provides a switch between primer formation for mtDNA replication and mitochondrial gene expression. PMID:27532055

  12. Evidence of animal mtDNA recombination between divergent populations of the potato cyst nematode Globodera pallida.

    Science.gov (United States)

    Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

    2012-03-01

    Recombination is typically assumed to be absent in animal mitochondrial genomes (mtDNA). However, the maternal mode of inheritance means that recombinant products are indistinguishable from their progenitor molecules. The majority of studies of mtDNA recombination assess past recombination events, where patterns of recombination are inferred by comparing the mtDNA of different individuals. Few studies assess contemporary mtDNA recombination, where recombinant molecules are observed as direct mosaics of known progenitor molecules. Here we use the potato cyst nematode, Globodera pallida, to investigate past and contemporary recombination. Past recombination was assessed within and between populations of G. pallida, and contemporary recombination was assessed in the progeny of experimental crosses of these populations. Breeding of genetically divergent organisms may cause paternal mtDNA leakage, resulting in heteroplasmy and facilitating the detection of recombination. To assess contemporary recombination we looked for evidence of recombination between the mtDNA of the parental populations within the mtDNA of progeny. Past recombination was detected between a South American population and several UK populations of G. pallida, as well as between two South American populations. This suggests that these populations may have interbred, paternal mtDNA leakage occurred, and the mtDNA of these populations subsequently recombined. This evidence challenges two dogmas of animal mtDNA evolution; no recombination and maternal inheritance. No contemporary recombination between the parental populations was detected in the progeny of the experimental crosses. This supports current arguments that mtDNA recombination events are rare. More sensitive detection methods may be required to adequately assess contemporary mtDNA recombination in animals.

  13. Decreased mtDNA Copy Number of Gastric Cancer: a New Tumor Marker?

    Institute of Scientific and Technical Information of China (English)

    FanLi; XiaosongWang; ChengboHan; JieLin

    2004-01-01

    OBJECTIVE To explore the relationship between mtDNA (mitochondrial DNA) and gastric cancer by comparing the difference of mtDNA copy number in gastric cancers and paracancerous tissues.METHODS The HV1 (hypervariable region) and HV2 of the mitochondrial Dloop region from 20 cases of gastric cancer and 20 paracancerous tissues were amplified by PCR with 13-actin serving as a quantitative standard marker. The products were separated by polyacrylamide gel electrophoresis (PAGE) and silver stained in order to compare the difference in mtDNA copy number between gastric cancers and paracancerous tissues. The mtDNA copy number was determined for gastric cancer shaving various pathological characteristics and the results compared with previous immunohistochemical staininq of the tumors,RESULTS There was a significantly quantitative difference in HV1, HV2 (standardized with β-actin) between gastric cancers and paracancerous tissues (P0.05).CONCLUSION The occurrence of gastric cancer was closely associated with decreased mtDNA copy number, which may be a new tumor marker.

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

    Science.gov (United States)

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

    2001-07-01

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

  15. Contribution of non-reference alleles in mtDNA of Alzheimer's disease patients.

    Science.gov (United States)

    Casoli, Tiziana; Di Stefano, Giuseppina; Spazzafumo, Liana; Balietti, Marta; Giorgetti, Belinda; Giuli, Cinzia; Postacchini, Demetrio; Fattoretti, Patrizia; Conti, Fiorenzo

    2014-04-01

    Many observations suggest that mutations of mitochondrial DNA (mtDNA) could be responsible for the neurodegenerative changes of Alzheimer's disease (AD). Here we examined the signal intensity of the four alleles of each mtDNA nucleotide position (np) in whole blood of AD patients and age-matched controls using MitoChip v2.0 array. Our analysis identified 270 significantly different nps which, with one exception, showed an increased contribution of non-reference alleles in AD patients. Principal component analysis (PCA) and cluster analysis showed that five of these nps could discriminate AD from control subjects with 80% of cases correctly classified. Our data support the hypothesis of mtDNA alterations as an important factor in the etiology of AD. PMID:25590040

  16. mtDNA D-loop of Chinese main indigenous sheep breeds using PCR-RFLP

    Institute of Scientific and Technical Information of China (English)

    LI Xianglong; ZHANG Zengli; GONG Yuanfang; LIU Zhengzhu; JIA Qing; WANG Lize

    2007-01-01

    The polymorphism of mitochondrial DNA (mtDNA) D-loop of 83 individuals from nine Chinese indigenous sheep breeds and two imported sheep breeds was studied with five endonucleases,Hinf I,Msp I,Sau3A I,Xsp I and Taq I,using PCR-RFLP.The results indicated that there existed two basic haplotypes in the region ofmtDNA D-loop.It couldbe inferred that Chinese indigenous sheep breeds originated from two maternal ancestors.The average polymorphic degree (π value=0.0421%) of mtDNA D-loop showed that the genetic diversity of mtDNA of Chinese indigenous sheep breeds was very low.

  17. Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant's gazelles

    DEFF Research Database (Denmark)

    Lorenzen, Eline Deidre; Arctander, Peter; Siegismund, Hans Redlef

    2008-01-01

    net nucleotide distances of 8-12%. The three lineages-notata, granti and petersii-grouped populations according to their geographic origin, encompassing populations in the north, southwest, and east, respectively. The mtDNA lineages reflected distinct evolutionary trajectories, and the data are...... discussed in reference to the four currently recognised subspecies. We suggest Grant's gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite their...

  18. Non-randomized mtDNA damage after ionizing radiation via charge transport

    OpenAIRE

    Xin Zhou; Xinguo Liu; Xin Zhang; Rong Zhou; Yang He; Qiang Li; Zhenhua Wang; Hong Zhang

    2012-01-01

    Although it is well known that there are mutation hot spots in mtDNA, whether there are damage hot spots remain elusive. In this study, the regional DNA damage of mitochondrial genome after ionizing radiation was determined by real-time quantitative PCR. The mtDNA damage level was found to be dose-dependent and regional unequal. The control region was the most susceptible region to oxidative damage. GGG, as an typical hole trap during charge transport, was found to be disproportionally enrich...

  19. The African Origin of mtDNA Haplogroup M1

    Directory of Open Access Journals (Sweden)

    Clyde Winters

    2010-11-01

    Full Text Available The aim of this study is to determine the geographical origin of haplogroup M1. Controversy surrounds the origin and expansion of the M1 haplogroup (hg. Some researchers believe that the M1 macrohaplogroup originated in Asia and represents a backflow to Africa, while other researchers believe hg M1 is of African origin. The analysis of M1 clades in Africa and Eurasia illustrate a high frequency for hg M1 in Sub Saharan A frica instead of A sia and the Near East; and the distribution of haplogroups L3(M and LOd across Sub Saharan Africa dating back to the Sangoan period make a 'back migration' of M1 to Africa highly unlikely.

  20. Mechanisms of mtDNA segregation and mitochondrial signalling in cells with the pathogenic A3243G mutation

    NARCIS (Netherlands)

    Jahangir Tafrechi, Roshan Sakineh

    2008-01-01

    Using newly developed single cell A3243G mutation load assays a novel mechanism of mtDNA segregation was identified in which the multi-copy mtDNA nucleoid takes a central position. Furthermore, likely due to low level changes in gene expression, no genes or gene sets could be identified with gene wi

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

    Directory of Open Access Journals (Sweden)

    Auke B.C. Otten

    2016-07-01

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

  2. Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

    Directory of Open Access Journals (Sweden)

    Schneider Horacio

    2011-09-01

    Full Text Available Abstract Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3 we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB, while R. marina sequences from the left Amazon bank (LAB are monophyletic. An Isolation-with-Migration (IM analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene, while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene. This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr, which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these

  3. Forensic and phylogeographic characterization of mtDNA lineages from northern Thailand (Chiang Mai).

    Science.gov (United States)

    Zimmermann, Bettina; Bodner, Martin; Amory, Sylvain; Fendt, Liane; Röck, Alexander; Horst, David; Horst, Basil; Sanguansermsri, Torpong; Parson, Walther; Brandstätter, Anita

    2009-11-01

    The immigration of diverse ethnic groups over the past centuries from surrounding countries into Thailand left footprints in the genetic composition of Thai mitochondrial DNA (mtDNA) lineages. The entire mtDNA control region (1,122 bp) was typed in 190 unrelated male volunteers from the northern Thailand province of Chiang Mai following highest quality standards. For a more precise haplogroup classification, selected single nucleotide polymorphisms from the mtDNA coding region were genotyped. We found several new, so far undescribed mtDNA lineages. Quasi-median networks were constructed for visualisation of character conflicts. The data were put into population-genetic relationships with other Southeast Asian populations. Although the frequencies of the Thai haplogroups were characteristic for Southeast Asia in terms of haplotype composition and genetic structure, the Thai population was significantly different from other Southeast Asian populations. This necessitates establishing regional databases, especially for forensic applications. The population data have been submitted to the EMPOP database (www.empop.org) and will be available on publication. PMID:19727793

  4. Advances Achieved on Studies of East Asian mtDNA Phylogeny

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Agroup of geneticists at the CAS Kunming Institute of Zoology (KIZ)succeeded in advancing out knowledge on the East Asian phylogeny of human mitochondrial DNA (mtDNA). Their work, which was finished by Dr. Kong Qingpeng under the guidance of ZHANG Yaping, was published by the journal Human Molecular Genetics.

  5. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia.

    Science.gov (United States)

    Loogväli, Eva-Liis; Roostalu, Urmas; Malyarchuk, Boris A; Derenko, Miroslava V; Kivisild, Toomas; Metspalu, Ene; Tambets, Kristiina; Reidla, Maere; Tolk, Helle-Viivi; Parik, Jüri; Pennarun, Erwan; Laos, Sirle; Lunkina, Arina; Golubenko, Maria; Barac, Lovorka; Pericic, Marijana; Balanovsky, Oleg P; Gusar, Vladislava; Khusnutdinova, Elsa K; Stepanov, Vadim; Puzyrev, Valery; Rudan, Pavao; Balanovska, Elena V; Grechanina, Elena; Richard, Christelle; Moisan, Jean-Paul; Chaventré, André; Anagnou, Nicholas P; Pappa, Kalliopi I; Michalodimitrakis, Emmanuel N; Claustres, Mireille; Gölge, Mukaddes; Mikerezi, Ilia; Usanga, Esien; Villems, Richard

    2004-11-01

    It has been often stated that the overall pattern of human maternal lineages in Europe is largely uniform. Yet this uniformity may also result from an insufficient depth and width of the phylogenetic analysis, in particular of the predominant western Eurasian haplogroup (Hg) H that comprises nearly a half of the European mitochondrial DNA (mtDNA) pool. Making use of the coding sequence information from 267 mtDNA Hg H sequences, we have analyzed 830 mtDNA genomes, from 11 European, Near and Middle Eastern, Central Asian, and Altaian populations. In addition to the seven previously specified subhaplogroups, we define fifteen novel subclades of Hg H present in the extant human populations of western Eurasia. The refinement of the phylogenetic resolution has allowed us to resolve a large number of homoplasies in phylogenetic trees of Hg H based on the first hypervariable segment (HVS-I) of mtDNA. As many as 50 out of 125 polymorphic positions in HVS-I were found to be mutated in more than one subcluster of Hg H. The phylogeographic analysis revealed that sub-Hgs H1*, H1b, H1f, H2a, H3, H6a, H6b, and H8 demonstrate distinct phylogeographic patterns. The monophyletic subhaplogroups of Hg H provide means for further progress in the understanding of the (pre)historic movements of women in Eurasia and for the understanding of the present-day genetic diversity of western Eurasians in general.

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

    Science.gov (United States)

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

    2007-06-01

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

  7. Absence of mtDNA mutations in leukocytes of CADASIL patients

    Directory of Open Access Journals (Sweden)

    Hellani Ali

    2008-05-01

    Full Text Available Abstract Background Ultrastructural and biochemical abnormalities of mitochondria have been reported in skeletal muscle biopsies of CADASIL patients with mutations in the NOTCH3 nuclear gene. Additionally, it was proposed that NOTCH3 gene mutations may predispose the mitochondrial DNA (mtDNA to mutations. Methods We sequenced the entire mitochondrial genome in five Arab patients affected by CADASIL. Results The mean number of mtDNA sequence variants (synonymous and nonsynonymous in CADASIL patients was not statistically significantly different from that in controls (p = 0.378. After excluding haplogroup specific single nucleotide polymorphisms (SNPs and proved silent polymorphisms, no known or novel pathologic mtDNA mutation(s could be detected in any patient. Additionally, there was no difference in the prevalence of different mitochondrial haplogroups between patients and controls. Conclusion Our study group is too small for any valid conclusion to be made. However, if our observation is confirmed in larger study group, then mtDNA mutations or mitochondrial haplogroups may not be important in the pathogenesis of CADASIL.

  8. Analysis of mtDNA variant segregation during early human embryonic development: a tool for successful NARP preimplantation diagnosis

    Science.gov (United States)

    Steffann, J; Frydman, N; Gigarel, N; Burlet, P; Ray, P F; Fanchin, R; Feyereisen, E; Kerbrat, V; Tachdjian, G; Bonnefont, J‐P; Frydman, R; Munnich, A

    2006-01-01

    Background Diseases arising from mitochondrial DNA (mtDNA) mutations are usually serious pleiotropic disorders with maternal inheritance. Owing to the high recurrence risk in the progeny of carrier females, “at‐risk” couples often ask for prenatal diagnosis. However, reliability of such practices remains under debate. Preimplantation diagnosis (PGD), a theoretical alternative to conventional prenatal diagnosis, requires that the mutant load measured in a single cell from an eight cell embryo accurately reflects the overall heteroplasmy of the whole embryo, but this is not known to be the case. Objective To investigate the segregation of an mtDNA length polymorphism in blastomeres of 15 control embryos from four unrelated couples, the NARP mutation in blastomeres of three embryos from a carrier of this mutation. Results Variability of the mtDNA polymorphism heteroplasmy among blastomeres from each embryo was limited, ranging from zero to 19%, with a mean of 7%. PGD for the neurogenic ataxia retinitis pigmentosa (NARP) mtDNA mutation (8993T→G) was therefore carried out in the carrier mother of an affected child. One of three embryos was shown to carry 100% of mutant mtDNA species while the remaining two were mutation‐free. These two embryos were transferred, resulting in a singleton pregnancy with delivery of a healthy child. Conclusions This PGD, the first reported for a mtDNA mutation, illustrates the skewed meiotic segregation of the NARP mtDNA mutation in early human development. However, discrepancies between the segregation patterns of the NARP mutation and the HV2 polymorphism indicate that a particular mtDNA nucleotide variant might differentially influenced the mtDNA segregation, precluding any assumption on feasibility of PGD for other mtDNA mutations. PMID:16155197

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-04-14

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

  10. Locativos preposicionados em posição de sujeito : uma possivel contribuição da línguas Bantu à sintaxe do português brasileiro

    Directory of Open Access Journals (Sweden)

    Juanito Avelar

    2008-01-01

    Full Text Available We observe the existing contrast between Brazilian and European Portuguese in relation to prepositional locatives in embedded sentences, and we argue that those constituents can occupy the grammatical subject position in transitive sentences in Brazilian Portuguese. After examining the so-called locative inversion (in which a non-argumental locative constituent may be in subject position found in various languages, we focus on the cases of the construction in the Bantu languages, since some of them were spoken by the majority of slaves brought to Brazil between the 16th and 19th centuries. We suggest that the Brazilian Portuguese innovations are the result of the Portuguese used as a second language by Bantu languages native speakers. The possibility for a locative to be pre-verbal and agree with the predicate in those languages combined with the impoverishment of the inflectional paradigm present in the primary linguistic data generated ambiguity for the child acquiring Portuguese as her first language. The pre-verbal locative phrase, which was in a peripheral position in Portuguese, is reanalized as possible in the position of grammatical subject in Brazilian Portuguese

  11. Extracellular mtDNA activates NF-κB via toll-like receptor 9 and induces cell death in cardiomyocytes.

    Science.gov (United States)

    Bliksøen, Marte; Mariero, Lars Henrik; Torp, May Kristin; Baysa, Anton; Ytrehus, Kirsti; Haugen, Fred; Seljeflot, Ingebjørg; Vaage, Jarle; Valen, Guro; Stensløkken, Kåre-Olav

    2016-07-01

    Acute myocardial infarction (AMI) causes sterile inflammation, which exacerbates tissue injury. Elevated levels of circulating mitochondrial DNA (mtDNA) have been associated with AMI. We hypothesized that mtDNA triggers an innate immune response via TLR9 and NF-κB activation, causing cardiomyocyte injury. Murine cardiomyocytes express TLR9 mRNA and protein and were able to internalize fluorescently labeled mouse mtDNA. Incubation of human embryonic kidney cells with serum from AMI patients containing naturally elevated levels of mtDNA induced TLR9-dependent NF-κB activity. This effect was mimicked by isolated mtDNA. mtDNA activated NF-κB in reporter mice both in vivo and in isolated cardiomyocytes. Moreover, incubation of isolated cardiomyocytes with mtDNA induced cell death after 4 and 24 h. Laser confocal microscopy showed that incubation of cardiomyocytes with mtDNA accelerated mitochondrial depolarization induced by reactive oxygen species. In contrast to mtDNA, isolated total DNA did not activate NF-κB nor induce cell death. In conclusion, mtDNA can induce TLR9-dependent NF-κB activation in reporter cells and activate NF-κB in cardiomyocytes. In cardiomyocytes, mtDNA causes mitochondrial dysfunction and death. Endogenous mtDNA in the extracellular space is a danger signal with direct detrimental effects on cardiomyocytes. PMID:27164906

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  13. Parkinson's disease brain mitochondria have impaired respirasome assembly, age-related increases in distribution of oxidative damage to mtDNA and no differences in heteroplasmic mtDNA mutation abundance

    Directory of Open Access Journals (Sweden)

    Keeney Paula M

    2009-09-01

    Full Text Available Abstract Background Sporadic Parkinson's disease (sPD is a nervous system-wide disease that presents with a bradykinetic movement disorder and is frequently complicated by depression and cognitive impairment. sPD likely has multiple interacting causes that include increased oxidative stress damage to mitochondrial components and reduced mitochondrial bioenergetic capacity. We analyzed mitochondria from postmortem sPD and CTL brains for evidence of oxidative damage to mitochondrial DNA (mtDNA, heteroplasmic mtDNA point mutations and levels of electron transport chain proteins. We sought to determine if sPD brains possess any mtDNA genotype-respiratory phenotype relationships. Results Treatment of sPD brain mtDNA with the mitochondrial base-excision repair enzyme 8-oxyguanosine glycosylase-1 (hOGG1 inhibited, in an age-dependent manner, qPCR amplification of overlapping ~2 kbase products; amplification of CTL brain mtDNA showed moderate sensitivity to hOGG1 not dependent on donor age. hOGG1 mRNA expression was not different between sPD and CTL brains. Heteroplasmy analysis of brain mtDNA using Surveyor nuclease® showed asymmetric distributions and levels of heteroplasmic mutations across mtDNA but no patterns that statistically distinguished sPD from CTL. sPD brain mitochondria displayed reductions of nine respirasome proteins (respiratory complexes I-V. Reduced levels of sPD brain mitochondrial complex II, III and V, but not complex I or IV proteins, correlated closely with rates of NADH-driven electron flow. mtDNA levels and PGC-1α expression did not differ between sPD and CTL brains. Conclusion PD brain mitochondria have reduced mitochondrial respiratory protein levels in complexes I-V, implying a generalized defect in respirasome assembly. These deficiencies do not appear to arise from altered point mutational burden in mtDNA or reduction of nuclear signaling for mitochondrial biogenesis, implying downstream etiologies. The origin of age

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

    Directory of Open Access Journals (Sweden)

    Scalais Emmanuel

    2009-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Xiujuan Wang

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

  16. Two distinct mtDNA lineages among captive African penguins in Japan.

    Science.gov (United States)

    Murata, Michiko; Murakami, Masaru

    2014-04-01

    The African penguin (Spheniscus demersus) is one of the world's most endangered seabirds. In Japan, although the number of African penguins in captivity continues to increase, genetic data have not been collected for either wild or captive populations. To reveal genetic diversity and characterization in captive African penguins, we analyzed the nucleotide sequences of mitochondrial DNA (mtDNA) from a sample of 236 African penguins. Analysis of 433 bp of the control region and 1,140 bp of cytochrome b sequences revealed the existence of two mtDNA clades. Control region haplotypes were much more divergent (d=3.39%) between the two clades than within each clade. The divergence of these clades may reflect differences at the subspecies or geographical population level in African penguins. These findings suggest that at least two distinct maternal lineages exist in the wild populations of the African penguin.

  17. MtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints.

    Science.gov (United States)

    Zhidkov, Ilia; Livneh, Erez A; Rubin, Eitan; Mishmar, Dan

    2009-04-01

    Multiple human mutational landscapes of normal and cancer conditions are currently available. However, while the unique mutational patterns of tumors have been extensively studied, little attention has been paid to similarities between malignant and normal conditions. Here we compared the pattern of mutations in the mitochondrial genomes (mtDNAs) of cancer (98 sequences) and natural populations (2400 sequences). De novo mtDNA mutations in cancer preferentially colocalized with ancient variants in human phylogeny. A significant portion of the cancer mutations was organized in recurrent combinations (COMs), reaching a length of seven mutations, which also colocalized with ancient variants. Thus, by analyzing similarities rather than differences in patterns of mtDNA mutations in tumor and human evolution, we discovered evidence for similar selective constraints, suggesting a functional potential for these mutations.

  18. Non-randomized mtDNA damage after ionizing radiation via charge transport

    Science.gov (United States)

    Zhou, Xin; Liu, Xinguo; Zhang, Xin; Zhou, Rong; He, Yang; Li, Qiang; Wang, Zhenhua; Zhang, Hong

    2012-10-01

    Although it is well known that there are mutation hot spots in mtDNA, whether there are damage hot spots remain elusive. In this study, the regional DNA damage of mitochondrial genome after ionizing radiation was determined by real-time quantitative PCR. The mtDNA damage level was found to be dose-dependent and regional unequal. The control region was the most susceptible region to oxidative damage. GGG, as an typical hole trap during charge transport, was found to be disproportionally enriched in the control region. A total of 107 vertebrate mitochondrial genomes were then analyzed to testify whether the GGG enrichment in control region was evolutionary conserved. Surprisingly, the triple G enrichment can be observed in most of the homeothermal animals, while the majority of heterothermic animals showed no triple G enrichment. These results indicated that the triple G enrichment in control region was related to the mitochondrial metabolism during evolution.

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

    Science.gov (United States)

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

    2012-02-01

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

  20. Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing

    OpenAIRE

    Eduardoff, Mayra; Huber, Gabriela; Bayer, Birgit; Schmid, Dagmar; Anslinger, Katja; Göbel, Tanja; Zimmermann, Bettina; Schneider, Peter M; Röck, Alexander W; Parson, Walther

    2013-01-01

    In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results. Among these are methods that involve mass-spectrometry resulting in base composition profiles that are, by definition, less informative than the full nucleotide sequence. Here, we applied a highly automated electrospray ionization mass spectrometry ...

  1. Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi.

    Science.gov (United States)

    Nadimi, Maryam; Daubois, Laurence; Hijri, Mohamed

    2016-05-01

    Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293bp and 69,505bp with G+C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as "supergenes" (16 concatenated coding genes), using Shimodaira-Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis 'species complex'. PMID:26868331

  2. Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data

    OpenAIRE

    Gissi, Carmela; Pesole, Graziano

    2003-01-01

    Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to analyze processing and mapping of the mitochondrial transcripts and to investigate the gene organization of a previously uncharacterized mitochondrial genome (mtDNA). This new strategy would greatly facilitate the sequencing and annotation of mtDNAs. In Ciona intestinalis, the assembled mt-...

  3. Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation

    OpenAIRE

    Hoda, Anila; Biçoku, Ylli; Dobi, Petrit

    2014-01-01

    Albanian farmers have a long tradition in goat farming. Recently, several studies were carried out to determine genetic diversity of local goat populations, using molecular markers such as SNP (Single Nucleotide Polymorphisms), microsatellites and AFLP (Amplified Fragment Length Polymorphism). In the present study 77 mtDNA D-loop sequences from six different goat breeds were analysed. The results revealed 67 different haplotypes, with haplotype diversity ranging from 0.864 to 1 and nucleotide...

  4. Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker

    Directory of Open Access Journals (Sweden)

    Tike Sartika

    2000-06-01

    Full Text Available Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5'-CATCTTGGCATCTTCAGTGCC-3' and DNA Light stranded Ll6750 (5'-AGGACTACGGCTTGAAAAGC-3' was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT, Hpall (C↓CGG, Mbol (↓GATC, Rsal (GT↓AC, NlaIII (CATG↓ and HaeIII (GG↓CC were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.

  5. A new mtDNA mutation showing accumulation with time and restriction to skeletal muscle

    Energy Technology Data Exchange (ETDEWEB)

    Weber, K.; Wilson, J.N.; Taylor, L. [Middlesbrough General Hospital (United Kingdom)] [and others

    1997-02-01

    We have identified a new mutation in mtDNA, involving tRNA{sup Leu(CUN)} in a patient manifesting an isolated skeletal myopathy. This heteroplasmic A{r_arrow}G transition at position 12320 affects the T{Psi}C loop at a conserved site and was not found in 120 controls. Analysis of cultured fibroblasts, white blood cells/platelets, and skeletal muscle showed that only skeletal muscle contained the mutation and that only this tissue demonstrated a biochemical defect of respiratory-chain activity. In a series of four muscle-biopsy specimens taken over a 12-year period, there was a gradual increase, from 70% to 90%, in the overall level of mutation, as well as a marked clinical deterioration. Single-fiber PCR confirmed that the proportion of mutant mtDNA was highest in cytochrome c oxidase-negative fibers. This study, which reports a mutation involving tRNA{sup Leu(CUN)}, demonstrates clearly that mtDNA point mutations can accumulate over time and may be restricted in their tissue distribution. Furthermore, clinical deterioration seemed to follow the increase in the level of mutation, although, interestingly, the appearance of fibers deficient in respiratory-chain activity showed a lag period. 32 refs., 4 figs., 1 tab.

  6. mtDNA copy number in oocytes of different sizes from individual pre- and post-pubertal pigs

    DEFF Research Database (Denmark)

    Pedersen, Hanne Skovsgaard; Løvendahl, Peter; Larsen, Knud Erik;

    2014-01-01

    .99–1.00) and amplification efficiencies (COX1, 91–104%; ND1, 84–92%). As inter-assay control, standard curves were compared using interaction with dates, showing no differences. mtDNA copy number between groups was compared by ANOVA after log-transformation of data. Relationship between oocyte size and mtDNA copy number......- and postpubertal oocytes (r2 = 0.00). The donor has a strong influence on oocyte mtDNA copy number in pre- and postpubertal pigs, which could influence individual fertility. mtDNA copy number does not seem to explain the higher developmental competence of neither post- compared to prepubertal pigs nor large...

  7. Role of direct repeat and stem-loop motifs in mtDNA deletions: cause or coincidence?

    Directory of Open Access Journals (Sweden)

    Lakshmi Narayanan Lakshmanan

    Full Text Available Deletion mutations within mitochondrial DNA (mtDNA have been implicated in degenerative and aging related conditions, such as sarcopenia and neuro-degeneration. While the precise molecular mechanism of deletion formation in mtDNA is still not completely understood, genome motifs such as direct repeat (DR and stem-loop (SL have been observed in the neighborhood of deletion breakpoints and thus have been postulated to take part in mutagenesis. In this study, we have analyzed the mitochondrial genomes from four different mammals: human, rhesus monkey, mouse and rat, and compared them to randomly generated sequences to further elucidate the role of direct repeat and stem-loop motifs in aging associated mtDNA deletions. Our analysis revealed that in the four species, DR and SL structures are abundant and that their distributions in mtDNA are not statistically different from randomized sequences. However, the average distance between the reported age associated mtDNA breakpoints and their respective nearest DR motifs is significantly shorter than what is expected of random chance in human (p10 bp tend to decrease with increasing lifespan among the four mammals studied here, further suggesting an evolutionary selection against stable mtDNA misalignments associated with long DRs in long-living animals. In contrast to the results on DR, the probability of finding SL motifs near a deletion breakpoint does not differ from random in any of the four mtDNA sequences considered. Taken together, the findings in this study give support for the importance of stable mtDNA misalignments, aided by long DRs, as a major mechanism of deletion formation in long-living, but not in short-living mammals.

  8. Multipole expansions in magnetostatics

    International Nuclear Information System (INIS)

    Multipole expansions of the magnetic field of a spatially restricted system of stationary currents and those for the potential function of such currents in an external magnetic field are studied using angular momentum algebraic techniques. It is found that the expansion for the magnetic induction vector is made identical to that for the electric field strength of a neutral system of charges by substituting electric for magnetic multipole moments. The toroidal part of the multipole expansion for the magnetic field vector potential can, due to its potential nature, be omitted in the static case. Also, the potential function of a system of currents in an external magnetic field and the potential energy of a neutral system of charges in an external electric field have identical multipole expansions. For axisymmetric systems, the expressions for the field and those for the potential energy of electric and magnetic multipoles are reduced to simple forms, with symmetry axis orientation dependence separated out. (methodological notes)

  9. Multipole expansions in magnetostatics

    Energy Technology Data Exchange (ETDEWEB)

    Agre, Mark Ya [National University of ' Kyiv-Mohyla Academy' , Kyiv (Ukraine)

    2011-02-28

    Multipole expansions of the magnetic field of a spatially restricted system of stationary currents and those for the potential function of such currents in an external magnetic field are studied using angular momentum algebraic techniques. It is found that the expansion for the magnetic induction vector is made identical to that for the electric field strength of a neutral system of charges by substituting electric for magnetic multipole moments. The toroidal part of the multipole expansion for the magnetic field vector potential can, due to its potential nature, be omitted in the static case. Also, the potential function of a system of currents in an external magnetic field and the potential energy of a neutral system of charges in an external electric field have identical multipole expansions. For axisymmetric systems, the expressions for the field and those for the potential energy of electric and magnetic multipoles are reduced to simple forms, with symmetry axis orientation dependence separated out. (methodological notes)

  10. Alterations of mtDNA number and 4977 bp deletion induced by ionizing radiation in human peripheral blood

    International Nuclear Information System (INIS)

    Alterations of mitochondria DNA (mtDNA) 4977 bp common deletion (CD) and mtDNA copy number induced by ionizing radiation were observed in human different cell lines and total body irradiation patients. However, only few experiments have evaluated the levels of the CD and mtDNA copy number in human peripheral blood exposed to ionizing radiation till now. The aim of this study is to analyze the mtDNA alterations in irradiated human peripheral blood from healthy donors as well as to explore their feasibility as biomarkers for constructing new biodosimeter. Peripheral blood samples were collected from six healthy donors, and exposed to 60Co gamma ray with the doses of 0 Gy, 1 Gy, 2 Gy, 3 Gy, 4 Gy and 5 Gy. Levels of the CD and mtDNA copy number in irradiated samples after 2h or 24 h incubation were detected using TaqMan real-time PCR, and the CD ratio was calculated. The results showed that the mean of the CD ratio and the CD copy number exhibited a dose-dependent increase 2 h in the dose range from 0-5 Gy, and of the mtDNA copy number significantly increased 24 h in irradiated groups compared with 0 Gy group after irradiation. It indicates that the parameters in human peripheral blood may be considered as molecular biomarkers to applying construction of new biodosimeter. (authors)

  11. MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation

    Directory of Open Access Journals (Sweden)

    Santa-Rita Pedro

    2005-06-01

    Full Text Available Abstract Background The picture of dog mtDNA diversity, as obtained from geographically wide samplings but from a small number of individuals per region or breed, has revealed weak geographic correlation and high degree of haplotype sharing between very distant breeds. We aimed at a more detailed picture through extensive sampling (n = 143 of four Portuguese autochthonous breeds – Castro Laboreiro Dog, Serra da Estrela Mountain Dog, Portuguese Sheepdog and Azores Cattle Dog-and comparatively reanalysing published worldwide data. Results Fifteen haplotypes belonging to four major haplogroups were found in these breeds, of which five are newly reported. The Castro Laboreiro Dog presented a 95% frequency of a new A haplotype, while all other breeds contained a diverse pool of existing lineages. The Serra da Estrela Mountain Dog, the most heterogeneous of the four Portuguese breeds, shared haplotypes with the other mainland breeds, while Azores Cattle Dog shared no haplotypes with the other Portuguese breeds. A review of mtDNA haplotypes in dogs across the world revealed that: (a breeds tend to display haplotypes belonging to different haplogroups; (b haplogroup A is present in all breeds, and even uncommon haplogroups are highly dispersed among breeds and continental areas; (c haplotype sharing between breeds of the same region is lower than between breeds of different regions and (d genetic distances between breeds do not correlate with geography. Conclusion MtDNA haplotype sharing occurred between Serra da Estrela Mountain dogs (with putative origin in the centre of Portugal and two breeds in the north and south of the country-with the Castro Laboreiro Dog (which behaves, at the mtDNA level, as a sub-sample of the Serra da Estrela Mountain Dog and the southern Portuguese Sheepdog. In contrast, the Azores Cattle Dog did not share any haplotypes with the other Portuguese breeds, but with dogs sampled in Northern Europe. This suggested that the

  12. Resonant state expansions

    International Nuclear Information System (INIS)

    The completeness properties of the discrete set of bound state, virtual states and resonances characterizing the system of a single nonrelativistic particle moving in a central cutoff potential is investigated. From a completeness relation in terms of these discrete states and complex scattering states one can derive several Resonant State Expansions (RSE). It is interesting to obtain purely discrete expansion which, if valid, would significantly simplify the treatment of the continuum. Such expansions can be derived using Mittag-Leffler (ML) theory for a cutoff potential and it would be nice to see if one can obtain the same expansions starting from an eigenfunction theory that is not restricted to a finite sphere. The RSE of Greens functions is especially important, e.g. in the continuum RPA (CRPA) method of treating giant resonances in nuclear physics. The convergence of RSE is studied in simple cases using square well wavefunctions in order to achieve high numerical accuracy. Several expansions can be derived from each other by using the theory of analytic functions and one can the see how to obtain a natural discretization of the continuum. Since the resonance wavefunctions are oscillating with an exponentially increasing amplitude, and therefore have to be interpreted through some regularization procedure, every statement made about quantities involving such states is checked by numerical calculations.Realistic nuclear wavefunctions, generated by a Wood-Saxon potential, are used to test also the usefulness of RSE in a realistic nuclear calculation. There are some fundamental differences between different symmetries of the integral contour that defines the continuum in RSE. One kind of symmetry is necessary to have an expansion of the unity operator that is idempotent. Another symmetry must be used if we want purely discrete expansions. These are found to be of the same form as given by ML. (29 refs.)

  13. Constraints on Cardassian Expansion

    CERN Document Server

    Frith, W J

    2004-01-01

    High redshift supernovae and Cosmic Microwave Background data are used to constrain the Cardassian expansion model (Freese & Lewis 2002), a cosmology in which a modification to the Friedmann equation gives rise to a flat, matter-dominated Universe which is currently undergoing a phase of accelerated expansion. In particular, the precision of the positions of the Doppler peaks in the CMB angular power spectrum provided by WMAP tightly constrains the cosmology. The available parameter space is further constrained by various high redshift supernova datasets taken from Tonry et al. (2003), a sample of 230 supernovae collated from the literature, in which fits to the distance and extinction have been recomputed where possible and a consistent zero-point has been applied. In addition, the Cardassian model can also be loosely constrained by inferred upper limits on the epoch at which the Cardassian term in the modified Friedmann equation begins to dominate the expansion (z_eq). Using these methods, a Cardassian ...

  14. Novel Foraminal Expansion Technique

    Science.gov (United States)

    Senturk, Salim; Ciplak, Mert; Oktenoglu, Tunc; Sasani, Mehdi; Egemen, Emrah; Yaman, Onur; Suzer, Tuncer

    2016-01-01

    The technique we describe was developed for cervical foraminal stenosis for cases in which a keyhole foraminotomy would not be effective. Many cervical stenosis cases are so severe that keyhole foraminotomy is not successful. However, the technique outlined in this study provides adequate enlargement of an entire cervical foraminal diameter. This study reports on a novel foraminal expansion technique. Linear drilling was performed in the middle of the facet joint. A small bone graft was placed between the divided lateral masses after distraction. A lateral mass stabilization was performed with screws and rods following the expansion procedure. A cervical foramen was linearly drilled medially to laterally, then expanded with small bone grafts, and a lateral mass instrumentation was added with surgery. The patient was well after the surgery. The novel foraminal expansion is an effective surgical method for severe foraminal stenosis. PMID:27559460

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

    Science.gov (United States)

    Delgado, Ana M; Cook, James M

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Cook James M

    2009-03-01

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

  17. Clustering of Caucasian Leber hereditary optic neuropathy patients containing the 11778 or 14484 mutations on an mtDNA lineage

    Energy Technology Data Exchange (ETDEWEB)

    Brown, M.D.; Sun, F.; Wallace, D.C. [Emory Univ. School of Medicine, Atlanta, GA (United States)

    1997-02-01

    Leber hereditary optic neuropathy (LHON) is a type of blindness caused by mtDNA mutations. Three LHON mtDNA mutations at nucleotide positions 3460, 11778, and 14484 are specific for LHON and account for 90% of worldwide cases and are thus designated as {open_quotes}primary{close_quotes} LHON mutations. Fifteen other {open_quotes}secondary{close_quotes} LHON mtDNA mutations have been identified, but their pathogenicity is unclear. mtDNA haplotype and phylogenetic analysis of the primary LHON mutations in North American Caucasian patients and controls has shown that, unlike the 3460 and 11778 mutations, which are distributed throughout the European-derived (Caucasian) mtDNA phylogeny, patients containing the 14484 mutation tended to be associated with European mtDNA haplotype J. To investigate this apparent clustering, we performed {chi}{sup 2}-based statistical analyses to compare the distribution of LHON patients on the Caucasian phylogenetic tree. Our results indicate that, unlike the 3460 and 11778 mutations, the 14484 mutation was not distributed on the phylogeny in proportion to the frequencies of the major Caucasian mtDNA haplogroups found in North America. The 14484 mutation was next shown to occur on the haplogroup J background more frequently that expected, consistent with the observation that {approximately}75% of worldwide 14484-positive LHON patients occur in association with haplogroup J. The 11778 mutation also exhibited a moderate clustering on haplogroup J. These observations were supported by statistical analysis using all available mutation frequencies reported in the literature. This paper thus illustrates the potential importance of genetic background in certain mtDNA-based diseases, speculates on a pathogenic role for a subset of LHON secondary mutations and their interaction with primary mutations, and provides support for a polygenic model for LHON expression in some cases. 18 refs., 3 tabs.

  18. Uniform gradient expansions

    Energy Technology Data Exchange (ETDEWEB)

    Giovannini, Massimo, E-mail: massimo.giovannini@cern.ch [Department of Physics, Theory Division, CERN, 1211 Geneva 23 (Switzerland); INFN, Section of Milan-Bicocca, 20126 Milan (Italy)

    2015-06-30

    Cosmological singularities are often discussed by means of a gradient expansion that can also describe, during a quasi-de Sitter phase, the progressive suppression of curvature inhomogeneities. While the inflationary event horizon is being formed the two mentioned regimes coexist and a uniform expansion can be conceived and applied to the evolution of spatial gradients across the protoinflationary boundary. It is argued that conventional arguments addressing the preinflationary initial conditions are necessary but generally not sufficient to guarantee a homogeneous onset of the conventional inflationary stage.

  19. Deep mtDNA divergences indicate cryptic species in a fig-pollinating wasp

    Directory of Open Access Journals (Sweden)

    Martin Joanne

    2006-10-01

    Full Text Available Abstract Background Figs and fig-pollinating wasps are obligate mutualists that have coevolved for ca 90 million years. They have radiated together, but do not show strict cospeciation. In particular, it is now clear that many fig species host two wasp species, so there is more wasp speciation than fig speciation. However, little is known about how fig wasps speciate. Results We studied variation in 71 fig-pollinating wasps from across the large geographic range of Ficus rubiginosa in Australia. All wasps sampled belong to one morphological species (Pleistodontes imperialis, but we found four deep mtDNA clades that differed from each other by 9–17% nucleotides. As these genetic distances exceed those normally found within species and overlap those (10–26% found between morphologically distinct Pleistodontes species, they strongly suggest cryptic fig wasp species. mtDNA clade diversity declines from all four present in Northern Queensland to just one in Sydney, near the southern range limit. However, at most sites multiple clades coexist and can be found in the same tree or even the same fig fruit and there is no evidence for parallel sub-division of the host fig species. Both mtDNA data and sequences from two nuclear genes support the monophyly of the "P. imperialis complex" relative to other Pleistodontes species, suggesting that fig wasp divergence has occurred without any host plant shift. Wasps in clade 3 were infected by a single strain (W1 of Wolbachia bacteria, while those in other clades carried a double infection (W2+W3 of two other strains. Conclusion Our study indicates that cryptic fig-pollinating wasp species have developed on a single host plant species, without the involvement of host plant shifts, or parallel host plant divergence. Despite extensive evidence for coevolution between figs and fig wasps, wasp speciation may not always be linked strongly with fig speciation.

  20. MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders

    Science.gov (United States)

    Kang, Longli; Zheng, Hong-Xiang; Zhang, Menghan; Yan, Shi; Li, Lei; Liu, Lijun; Liu, Kai; Hu, Kang; Chen, Feng; Ma, Lifeng; Qin, Zhendong; Wang, Yi; Wang, Xiaofeng; Jin, Li

    2016-01-01

    Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10−8). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10−4). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation. PMID:27498855

  1. Autosomal microsatellite and mtDNA genetic analysis in Sicily (Italy).

    Science.gov (United States)

    Romano, V; Calì, F; Ragalmuto, A; D'Anna, R P; Flugy, A; De Leo, G; Giambalvo, O; Lisa, A; Fiorani, O; Di Gaetano, C; Salerno, A; Tamouza, R; Charron, D; Zei, G; Matullo, G; Piazza, A

    2003-01-01

    DNA samples from 465 blood donors living in 7 towns of Sicily, the largest island of Italy, have been collected according to well defined criteria, and their genetic heterogeneity tested on the basis of 9 autosomal microsatellite and mitochondrial DNA polymorphisms for a total of 85 microsatellite allele and 10 mtDNA haplogroup frequencies. A preliminary account of the results shows that: a) the samples are genetically heterogeneous; b) the first principal coordinates of the samples are correlated more with their longitude than with their latitude, and this result is even more remarkable when one outlier sample (Butera) is not considered; c) distances among samples calculated from allele and haplogroup frequencies and from the isonymy matrix are weakly correlated (r = 0.43, P = 0.06) but such correlation disappears (r = 0.16) if the mtDNA haplogroups alone are taken into account; d) mtDNA haplogroups and microsatellite distances suggest settlements of people occurred at different times: divergence times inferred from microsatellite data seem to describe a genetic composition of the town of Sciacca mainly derived from settlements after the Roman conquest of Sicily (First Punic war, 246 BC), while all other divergence times take root from the second to the first millennium BC, and therefore seem to backdate to the pre-Hellenistic period. A more reliable association of these diachronic genetic strata to different historical populations (e.g. Sicani, Elymi, Siculi), if possible, must be postponed to the analysis of more samples and hopefully more informative uniparental DNA markers such as the recently available DHPLC-SNP polymorphisms of the Y chromosome. PMID:12556234

  2. mtDNA haplogroup J Modulates telomere length and Nitric Oxide production

    Directory of Open Access Journals (Sweden)

    Fernández-Moreno Mercedes

    2011-12-01

    Full Text Available Abstract Background Oxidative stress due to the overproduction of nitric oxide (NO and other oxygen reactive species (ROS, play a main role in the initiation and progression of the OA disease and leads to the degeneration of mitochondria. Therefore, the goal of this work is to describe the difference in telomere length of peripheral blood leukocytes (PBLs and Nitric Oxide (NO production between mitochondrial DNA (mtDNA haplogroup J and non-J carriers, as indirect approaches of oxidative stress. Methods The telomere length of PBL was analyzed in DNA samples from 166 healthy controls (114 J and 52 non-J and 79 OA patients (41 J and 38 non-J by means of a validated qPCR method. The NO production was assessed in 7 carriers of the haplogroup J and 27 non-J carriers, by means of the colorimetric reaction of the Griess reagent in supernatants of cultured chondrocytes. Inducible nitric oxide synthase (iNOS mRNA from these samples was analyzed by qPCR. Appropiated statistical analyses were performed Results Carriers of the haplogroup J showed a significantly longer telomere length of PBLs than non-J carriers, regardless of age, gender and diagnosis (p = 0.025. Cultured chondrocytes carrying the mtDNA haplogroup J also showed a lower NO production than non-J carriers (p = 0.043. No significant correlations between age and telomore length of PBLs were detected neither for carriers of the haplogroup J nor for non-J carriers. A strong positive correlation between NO production and iNOS expression was also observed (correlation coefficient = 0.791, p Conclusion The protective effect of the mtDNA haplogroup J in the OA disease arise from a lower oxidative stress in carriers of this haplogroup, since this haplogroup is related to lower NO production and hence longer telomere length of PBLs too.

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

    DEFF Research Database (Denmark)

    Gonçalves, V.F.; Stenderup, J.; Rodrigues-Carvalho, C.;

    2013-01-01

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

  4. Typing of 24 mtDNA SNPs in a Chinese Population Using SNaPshot Minisequencing

    Institute of Scientific and Technical Information of China (English)

    黄代新; 桂程; 易少华; 杨庆恩; 杨荣芝; 梅焜

    2010-01-01

    Three SNaPshot multiplex assays were developed to test 23 coding region single nucleotide polymorphisms(SNPs) and one control region SNP outside hypervariable regions(HVR)Ⅰand Ⅱ,which was aimed at increasing the discrimination power of the mitochondrial DNA(mtDNA) typing in forensic casework,and confirming haplogroup assignments of mtDNA profiles in both human population studies and medical research.The selected SNPs targeted the East Asian phylogeny.These multiplex assays were validated by comparing with t...

  5. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage.

    Science.gov (United States)

    Sardina, M T; Ballester, M; Marmi, J; Finocchiaro, R; van Kaam, J B C H M; Portolano, B; Folch, J M

    2006-08-01

    The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.

  6. Complete genome sequence of mitochondrial DNA (mtDNA) of Chlorella sorokiniana.

    Science.gov (United States)

    Orsini, Massimiliano; Costelli, Cristina; Malavasi, Veronica; Cusano, Roberto; Concas, Alessandro; Angius, Andrea; Cao, Giacomo

    2016-01-01

    The complete sequence of mitochondrial genome of the Chlorella sorokiniana strain (SAG 111-8 k) is presented in this work. Within the Chlorella genus, it represents the second species with a complete sequenced and annotated mitochondrial genome (GenBank accession no. KM241869). The genome consists of circular chromosomes of 52,528 bp and encodes a total of 31 protein coding genes, 3 rRNAs and 26 tRNAs. The overall AT contents of the C. sorokiniana mtDNA is 70.89%, while the coding sequence is of 97.4%.

  7. THESAURUS AND QUERY EXPANSION

    Directory of Open Access Journals (Sweden)

    Hazra Imran

    2009-11-01

    Full Text Available The explosive growth of the World Wide Web is making it difficult for a user to locate information that isrelevant to his/her interest. Though existing search engines work well to a certain extent but they still faceproblems like word mismatch which arises because the majority of information retrieval systemscompare query and document terms on lexical level rather than on semantic level and short query: theaverage length of queries by the user is less than two words. Short queries and the incompatibilitybetween the terms in user queries and documents strongly affect the retrieval of relevant document.Query expansion has long been suggested as a technique to increase the effectiveness of the informationretrieval. Query expansion is the process of supplementing additional terms or phrases to the originalquery to improve the retrieval performance. The central problem of query expansion is the selection ofthe expansion terms based on which user’s original query is expanded. Thesaurus helps to solve thisproblem. Thesaurus have frequently been incorporated in information retrieval system for identifying thesynonymous expressions and linguistic entities that are semantically similar. Thesaurus has been widelyused in many applications, including information retrieval and natural language processing.

  8. Expansion of Pannes

    Science.gov (United States)

    For the Long Island, New Jersey, and southern New England region, one facet of marsh drowning as a result of accelerated sea level rise is the expansion of salt marsh ponds and pannes. Over the past century, marsh ponds and pannes have formed and expanded in areas of poor drainag...

  9. Natural underlying mtDNA heteroplasmy as a potential source of intra-person hiPSC variability.

    Science.gov (United States)

    Perales-Clemente, Ester; Cook, Alexandra N; Evans, Jared M; Roellinger, Samantha; Secreto, Frank; Emmanuele, Valentina; Oglesbee, Devin; Mootha, Vamsi K; Hirano, Michio; Schon, Eric A; Terzic, Andre; Nelson, Timothy J

    2016-09-15

    Functional variability among human clones of induced pluripotent stem cells (hiPSCs) remains a limitation in assembling high-quality biorepositories. Beyond inter-person variability, the root cause of intra-person variability remains unknown. Mitochondria guide the required transition from oxidative to glycolytic metabolism in nuclear reprogramming. Moreover, mitochondria have their own genome (mitochondrial DNA [mtDNA]). Herein, we performed mtDNA next-generation sequencing (NGS) on 84 hiPSC clones derived from a cohort of 19 individuals, including mitochondrial and non-mitochondrial patients. The analysis of mtDNA variants showed that low levels of potentially pathogenic mutations in the original fibroblasts are revealed through nuclear reprogramming, generating mutant hiPSCs with a detrimental effect in their differentiated progeny. Specifically, hiPSC-derived cardiomyocytes with expanded mtDNA mutations non-related with any described human disease, showed impaired mitochondrial respiration, being a potential cause of intra-person hiPSC variability. We propose mtDNA NGS as a new selection criterion to ensure hiPSC quality for drug discovery and regenerative medicine. PMID:27436875

  10. Can the occurrence of rare insertion/deletion polymor-phisms in human mtDNA beverified from phylogeny?

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Due to its specific characteristics, such as maternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it harbors. Rare mutation (excluding parallel mutation) occurring at multiple times in different haplogroups could thus be a potential reading error according to the mtDNA phylogeny. This experience has been widely used in double-checking the credibility of the rare mutations in human mtDNA sequences. However, no test has been performed so far for the feasibility of applying this strategy to the rare insertion/deletion (indel) events in mtDNA sequences. In this study, we attempted to relate the rare indels in mtDNAs to their haplogroup status in a total of 2352 individuals from 50 populations in China. Our results show that the insertion of A at position 16259 is restricted to a subclade of haplogroup C and can be verified. The other indel polymorphisms, which occur in the repeat of the deleted or inserted nucleotide(s), may not be distinguished from phantom mutations from a phylogenetic point of view. Independently and multiply sequencing the fragment with the indel is the best and the most reliable way for confirmation.

  11. Cladistic analysis of Heliconius butterflies and relatives (Nymphalidae: Heliconiiti): a revised phylogenetic position for Eueides based on sequences from mtDNA and a nuclear gene

    Science.gov (United States)

    Brower, A. V. Z.; Egan, M. G.

    1997-01-01

    A new phylogenetic hypothesis for Heliconius and related genera is presented, based on DNA sequence data from mtDNA combined with a region of the wingless gene. This study also adds eight new taxa to a previous cladistic hypothesis based on the mtDNA alone. Simultaneous phylogenetic analysis of the two gene regions together supports a topology largely in agreement with traditional views of heliconiine relationships based on morphology and suggests that the mtDNA support for the sister relationship between Eueides and H. charithonia is due to convergent evolution of homoplasious mtDNA sites.

  12. Mitochondrial, Y-chromosomal and autosomal variation in Mbenzele Pygmies from the Central African Republic.

    Science.gov (United States)

    Anagnostou, Paolo; Coia, Valentina; Spedini, Gabriella; Destro-Bisol, Giovanni

    2010-06-01

    In this paper, we carry out a combined analysis of autosomal (ten microsatellites and an Alu insertion), mitochondrial (HVR-1 sequence, 360 nucleotides) and Y-chromosomal (seven microsatellites) variation in the Mbenzele Pygmies from the Central African Republic. This study focuses on two important questions concerning the admixture and origin of African Pygmies. Ethnographic observations suggest a sex-biased gene flow between the Bantus and Pygmies, an issue which could be clarified through genetic analyses may shed light. A study of intrapopulational variation of mtDNA and Y-chromosome produces results in accordance with the hypothesized matrimonial behaviour. In fact, while shared mitochondrial haplotypes belonging to the L1c5 (or L1c1a1 clade) sub-haplogroup provides evidence of a Pygmy-to-Bantu female biased gene flow, a male biased gene flow from Bantu to Pygmies is supported by the distribution of the Y-chromosomes bearing M2 mutation. The second part of our study regards the question of the genetic relationships between Western and Eastern Pygmies. Our results favour the pre-Bantu hypothesis which suggests that the two Pygmy groups separated in ancient times (at least 18,000 years ago), whereas they do not support the recent divergence and differential admixture hypothesis which posits their separation as a consequence of the Bantu expansion (2,000-3,000 years ago).

  13. A new view on dam lines in Polish Arabian horses based on mtDNA analysis

    Directory of Open Access Journals (Sweden)

    Sell Jerzy

    2007-09-01

    Full Text Available Abstract Polish Arabian horses are one of the oldest and the most important Arab populations in the world. The Polish Arabian Stud Book and the Genealogical Charts by Skorkowski are the main sources of information on the ancestors of Polish Arabs. Both publications were viewed as credible sources of information until the 1990s when the data regarding one of the dam lines was questioned. The aim of the current study was to check the accuracy of the pedigree data of Polish dam lines using mtDNA analysis. The analyses of a 458 bp mtDNA D-loop fragment from representatives of 15 Polish Arabian dam lines revealed 14 distinct haplotypes. The results were inconsistent with pedigree data in the case of two lines. A detailed analysis of the historical sources was performed to explain these discrepancies. Our study revealed that representatives of different lines shared the same haplotypes. We also noted a genetic identity between some lines founded by Polish mares of unknown origin and lines established by desert-bred mares.

  14. Primary Analysis on mtDNA D-loop Hypervariable Region in Eutamias sibiricus

    Institute of Scientific and Technical Information of China (English)

    LI Shipeng; BAI Xiujuan

    2008-01-01

    This study analyzed the mitochondrial DNA D-loop hypervariable region 601 bp sequence in 12 Eutamias sibiricus from Heilongjiang area.The result showed that the average contents of A,T,G and C were 33.2%, 30.5%, 11.8% and 24.5% respectively, the A+T content (63.7%) was obviously higher than the G+C content (36.3%).Thirty-six, mutation (approximately 6.0%) sites.were found and 9 haplotypes were defined.The mutations types,including transition,transversion and deletion were all found in the detected mtDNA D-loop regions,most of which was transition.The average nucleotide mutational ratio was 1.22%.The nucleotide mutation sites affected the restriction site appearance or disappearance of the restriction site. The research on mtDNA D-loop is focused on the domestic animals and there is no report on Eutamias sibiricus.This study analyzed the mitochondrial DNA D-loop hypervariable in Eutamias sibiricus so as to provide some useful informations for related research in the future.

  15. Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop

    Science.gov (United States)

    Wani, Charles E.; Yousif, Ibrahim A.; Ibrahim, Muntasir E.; Musa, Hassan H.

    2014-01-01

    The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise Fst showed high genetic difference between Betwil populations and the rest with Fst ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm = 4.622). PMID:25535590

  16. Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop

    Directory of Open Access Journals (Sweden)

    Charles E. Wani

    2014-01-01

    Full Text Available The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise Fst showed high genetic difference between Betwil populations and the rest with Fst ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm=4.622.

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

    Directory of Open Access Journals (Sweden)

    Siôn L Williams

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

  18. Frequent mtDNA mutations and its role in gastric carcino-genesis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In order to disclose the relationship between mutations of mitochondrial DNA (mtDNA) and gastric carcinogenesis, we screened the entire mtDNA sequence in 30 cases of human gastric cancer and matched normal tissues by using denaturing high-performance liquid chromatography (DHPLC) and DNA sequencing. Our data showed that high frequency (66.7%, 20/30) of mitochondrial genome mutation occur red in gastric cancer. Among these variants, 17 cases (56.7%, 17/30) were identified to be somatic mutation. High level mutant frequency was found in ND4, ND5 c oding genes and D-loop control region, which was 36.7%, 26.7% and 30% respective ly. Comparing with complexes Ⅲ, Ⅳ and Ⅴof the electron transport chain, we found that variants appeared to be more frequent in the subunit genes of complexⅠ . Most of mutations were base substitutions (85.4%, 41/48). Our results suggested that mutations of subunit genes encoding complex Ⅰ, especially ND3, ND4 and N D5 genes, might contribute to human gastric carcinogenesis.

  19. mtDNA variation in Inuit populations of Greenland and Canada: migration history and population structure.

    Science.gov (United States)

    Helgason, Agnar; Pálsson, Gísli; Pedersen, Henning Sloth; Angulalik, Emily; Gunnarsdóttir, Ellen Dröfn; Yngvadóttir, Bryndís; Stefánsson, Kári

    2006-05-01

    We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.

  20. Genetic variations in two seahorse species (Hippocampus mohnikei and Hippocampus trimaculatus: evidence for middle Pleistocene population expansion.

    Directory of Open Access Journals (Sweden)

    Yanhong Zhang

    Full Text Available Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb and control region (CR were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments.

  1. Expansion at Olympic Dam

    International Nuclear Information System (INIS)

    The Olympic Dam orebody is the 6th largest copper and the single largest uranium orebody in the world. Mine production commenced in June 1988, at an annual production rate of around 45,000 tonnes of copper and 1,000 tonnes of uranium. Western Mining Corporation announced in 1996 a proposed $1.25 billion expansion of the Olympic Dam operation to raise the annual production capacity of the mine to 200,000 tonnes of copper, approximately 3,700 tonnes of uranium, 75,000 ounces of gold and 950,000 ounces of silver by 2001. Further optimisation work has identified a faster track expansion route, with an increase in the capital cost to $1.487 billion but improved investment outcome, a new target completion date of end 1999, and a new uranium output of 4,600 tonnes per annum from that date

  2. Operator product expansion algebra

    Energy Technology Data Exchange (ETDEWEB)

    Holland, Jan [CPHT, Ecole Polytechnique, Paris-Palaiseau (France)

    2014-07-01

    The Operator Product Expansion (OPE) is a theoretical tool for studying the short distance behaviour of products of local quantum fields. Over the past 40 years, the OPE has not only found widespread computational application in high-energy physics, but, on a more conceptual level, it also encodes fundamental information on algebraic structures underlying quantum field theories. I review new insights into the status and properties of the OPE within Euclidean perturbation theory, addressing in particular the topics of convergence and ''factorisation'' of the expansion. Further, I present a formula for the ''deformation'' of the OPE algebra caused by a quartic interaction. This formula can be used to set up a novel iterative scheme for the perturbative computation of OPE coefficients, based solely on the zeroth order coefficients (and renormalisation conditions) as initial input.

  3. Overexpression of TFAM or twinkle increases mtDNA copy number and facilitates cardioprotection associated with limited mitochondrial oxidative stress.

    Directory of Open Access Journals (Sweden)

    Masataka Ikeda

    Full Text Available Mitochondrial DNA (mtDNA copy number decreases in animal and human heart failure (HF, yet its role in cardiomyocytes remains to be elucidated. Thus, we investigated the cardioprotective function of increased mtDNA copy number resulting from the overexpression of human transcription factor A of mitochondria (TFAM or Twinkle helicase in volume overload (VO-induced HF.Two strains of transgenic (TG mice, one overexpressing TFAM and the other overexpressing Twinkle helicase, exhibit an approximately 2-fold equivalent increase in mtDNA copy number in heart. These TG mice display similar attenuations in eccentric hypertrophy and improved cardiac function compared to wild-type (WT mice without any deterioration of mitochondrial enzymatic activities in response to VO, which was accompanied by a reduction in matrix-metalloproteinase (MMP activity and reactive oxygen species after 8 weeks of VO. Moreover, acute VO-induced MMP-2 and MMP-9 upregulation was also suppressed at 24 h in both TG mice. In isolated rat cardiomyocytes, mitochondrial reactive oxygen species (mitoROS upregulated MMP-2 and MMP-9 expression, and human TFAM (hTFAM overexpression suppressed mitoROS and their upregulation. Additionally, mitoROS were equally suppressed in H9c2 rat cardiomyoblasts that overexpress hTFAM or rat Twinkle, both of which exhibit increased mtDNA copy number. Furthermore, mitoROS and mitochondrial protein oxidation from both TG mice were suppressed compared to WT mice.The overexpression of TFAM or Twinkle results in increased mtDNA copy number and facilitates cardioprotection associated with limited mitochondrial oxidative stress. Our findings suggest that increasing mtDNA copy number could be a useful therapeutic strategy to target mitoROS in HF.

  4. IKEA's International Expansion

    OpenAIRE

    Harapiak, Clayton

    2013-01-01

    This case concerns a global retailing firm that is dealing with strategic management and marketing issues. Applying a scenario of international expansion, this case provides a thorough analysis of the current business environment for IKEA. Utilizing a variety of methods (e.g. SWOT, PESTLE, McKinsey Matrix) the overall objective is to provide students with the opportunity to apply their research skills and knowledge regarding a highly competitive industry to develop strategic marketing strateg...

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

    OpenAIRE

    Anderson Nonato do Rosário Marinho; Milene Raiol de Moraes; Sidney Santos; Ândrea Ribeiro-dos- Santos

    2011-01-01

    The accumulation of somatic mutations in mtDNA is correlated with aging. In this work, we sought to identify somatic mutations in the HVS-1 region (D-loop) of mtDNA that might be associated with aging. For this, we compared 31 grandmothers (mean age: 63 ± 2.3 years) and their 62 grandchildren (mean age: 15 ± 4.1 years), the offspring of their daughters. Direct DNA sequencing showed that mutations absent in the grandchildren were detected in a presumably homoplasmic state in three grandmothers...

  6. VARIATION IN MITOCHONDRIAL-DNA LEVELS IN MUSCLE FROM NORMAL CONTROLS - IS DEPLETION OF MTDNA IN PATIENTS WITH MITOCHONDRIAL MYOPATHY A DISTINCT CLINICAL SYNDROME

    NARCIS (Netherlands)

    POULTON, J; SEWRY, C; POTTER, CG; BOUGERON, T; CHRETIEN, D; WIJBURG, FA; MORTEN, KJ; BROWN, G

    1995-01-01

    Recent studies have identified a group of patients with cytochrome oxidase (COX) deficiency presenting in infancy associated with a deficiency of mtDNA in muscle or other affected tissue (Moraes et al 1991). We used a navel approach to compare the level of mitochondrial (mtDNA) compared to nuclear D

  7. Operator product expansion algebra

    Energy Technology Data Exchange (ETDEWEB)

    Holland, Jan [School of Mathematics, Cardiff University, Senghennydd Rd, Cardiff CF24 4AG (United Kingdom); Hollands, Stefan [School of Mathematics, Cardiff University, Senghennydd Rd, Cardiff CF24 4AG (United Kingdom); Institut für Theoretische Physik, Universität Leipzig, Brüderstr. 16, Leipzig, D-04103 (Germany)

    2013-07-15

    We establish conceptually important properties of the operator product expansion (OPE) in the context of perturbative, Euclidean φ{sup 4}-quantum field theory. First, we demonstrate, generalizing earlier results and techniques of hep-th/1105.3375, that the 3-point OPE, =Σ{sub C}C{sub A{sub 1A{sub 2A{sub 3}{sup C}}}}, usually interpreted only as an asymptotic short distance expansion, actually converges at finite, and even large, distances. We further show that the factorization identity C{sub A{sub 1A{sub 2A{sub 3}{sup B}}}}=Σ{sub C}C{sub A{sub 1A{sub 2}{sup C}}}C{sub CA{sub 3}{sup B}} is satisfied for suitable configurations of the spacetime arguments. Again, the infinite sum is shown to be convergent. Our proofs rely on explicit bounds on the remainders of these expansions, obtained using refined versions, mostly due to Kopper et al., of the renormalization group flow equation method. These bounds also establish that each OPE coefficient is a real analytic function in the spacetime arguments for non-coinciding points. Our results hold for arbitrary but finite loop orders. They lend support to proposals for a general axiomatic framework of quantum field theory, based on such “consistency conditions” and akin to vertex operator algebras, wherein the OPE is promoted to the defining structure of the theory.

  8. Rethinking expansive learning

    DEFF Research Database (Denmark)

    Kolbæk, Ditte; Lundh Snis, Ulrika

    discussion forum on Google groups, they created new ways of reflecting and learning. We used netnography to select qualitative postings from the online community and expansive learning concepts for data analysis. The findings show how students changed practices of organisational learning......Abstract: This paper analyses an online community of master’s students taking a course in ICT and organisational learning. The students initiated and facilitated an educational design for organisational learning called Proactive Review in the organisation where they are employed. By using an online...

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

    Directory of Open Access Journals (Sweden)

    Olivieri Anna

    2011-10-01

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

  10. Variability of the honey bee mite Varroa destructor in Serbia, based on mtDNA analysis.

    Science.gov (United States)

    Gajic, Bojan; Radulovic, Zeljko; Stevanovic, Jevrosima; Kulisic, Zoran; Vucicevic, Milos; Simeunovic, Predrag; Stanimirovic, Zoran

    2013-09-01

    Only two mitochondrial haplotypes (Korea and Japan) of Varroa destructor, the ectoparasitic honey bee mite, are known to be capable of infesting and successfully reproducing in Apis mellifera colonies worldwide. Varroa destructor (then called Varroa jacobsoni) was observed in Serbia for the first time in 1976. In order to obtain insight into the genetic variability of the mites parasitizing A. mellifera we analyzed 45 adult female mites sampled from nine localities dispersed throughout Serbia. Four fragments within cox1, atp6, cox3 and cytb mtDNA genes were sequenced. The Korea haplotype of V. destructor was found to be present at all localities, but also two new haplotypes (Serbia 1 and Peshter 1) were revealed, based on cox1 and cytb sequence variability. The simultaneous occurrence of Korea and Serbia 1 haplotypes was observed at five localities, whereas Peshter 1 haplotype was identifed at only one place. PMID:23471517

  11. Variability of the honey bee mite Varroa destructor in Serbia, based on mtDNA analysis.

    Science.gov (United States)

    Gajic, Bojan; Radulovic, Zeljko; Stevanovic, Jevrosima; Kulisic, Zoran; Vucicevic, Milos; Simeunovic, Predrag; Stanimirovic, Zoran

    2013-09-01

    Only two mitochondrial haplotypes (Korea and Japan) of Varroa destructor, the ectoparasitic honey bee mite, are known to be capable of infesting and successfully reproducing in Apis mellifera colonies worldwide. Varroa destructor (then called Varroa jacobsoni) was observed in Serbia for the first time in 1976. In order to obtain insight into the genetic variability of the mites parasitizing A. mellifera we analyzed 45 adult female mites sampled from nine localities dispersed throughout Serbia. Four fragments within cox1, atp6, cox3 and cytb mtDNA genes were sequenced. The Korea haplotype of V. destructor was found to be present at all localities, but also two new haplotypes (Serbia 1 and Peshter 1) were revealed, based on cox1 and cytb sequence variability. The simultaneous occurrence of Korea and Serbia 1 haplotypes was observed at five localities, whereas Peshter 1 haplotype was identifed at only one place.

  12. A novel mtDNA ND6 gene mutation associated with LHON in a Caucasian family.

    Science.gov (United States)

    Zhadanov, Sergey I; Atamanov, Vasily V; Zhadanov, Nikolay I; Oleinikov, Oleg V; Osipova, Ludmila P; Schurr, Theodore G

    2005-07-15

    Leber's hereditary optic neuropathy (LHON) is a frequent cause of inherited blindness. A routine screening for common mtDNA mutations constitutes an important first in its diagnosis. However, a substantial number of LHON patients do not harbor known variants, both pointing to the genetic heterogeneity of LHON and bringing into question its genetic diagnosis. We report a familial case that exhibited typical features of LHON but lacked any of the common mutations. Genetic analysis revealed a novel pathogenic defect in the ND6 gene at 14279A that was not detected in any haplogroup-matched controls screened for it, nor has it been previously reported. This mutation causes a substantial conformational change in the secondary structure of the polypeptide matrix coil and may explain the LHON expression. Thus, it expands the spectrum of deleterious changes affecting ND6-encoding subunit and further highlights the functional significance of this gene, providing additional clues to the disease pathogenesis.

  13. Clinical Analysis of Leber's Hereditary Optic Neuropathy Harboring mtDNA Mutation at nt11778

    Institute of Scientific and Technical Information of China (English)

    Xinyu Zhang; Qiang Yu; Qingjiong Zhang; Changxian Yi

    2001-01-01

    Purpose: To improve our diagnostic technique through the analysis of clinical features ofLeber's heredita'y optic neuropathy (LHON) harboring mtDNA point mutation at nt11778. Methods: Detection of nt11778 mutation was performed on 38 patients clinically diagnosed as LHON in our ophthalmic center from year 1998 to 2000. Circumstances of onset and family history were obtained and ophthalmoscopy, fundus fluorescein angiography, visual field and visual evoked potential were performed on all 38 patients. Result: 30 In 38 patients (78.95 % ) harbor nt11778 mutation, including 28 male (93.33%) and 2 female (6.67%). The ratio of affected male to female is 14: 1. Patients harboring nt11778 mutation display typical clinical nanifestations. Ccnclusion: Identification of one of the three LHON specifically associated ntDNA mutations is essential to confirm the diagnosis. Eye Science 2001: 17:31 ~ 34.

  14. The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

    Institute of Scientific and Technical Information of China (English)

    WEN; Bo; SHI; Hong; REN; Ling; XI; Huifeng; LI; Kaiyuan; ZHA

    2004-01-01

    The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the genetic relationship between the Mosuo and five other ethnic groups currently residing in northwest Yunnan, i.e. Naxi, Tibetan, Bai, Yi and Pumi, by typing the genetic variations in mtDNA HVS1 and 21 Y chromosome markers (13 SNPs & 8 STR markers). We showed that the maternal lineages of the Mosuo bear the strongest resemblance with those found in Naxi while its paternal lineages are more similar to those that are prevalent in Yunnan Tibetan. The marked difference between paternal and maternal lineages may be attributable to the genetic history, matriarchal structure, and visiting marriage.

  15. Testing Machine for Expansive Mortar

    CERN Document Server

    Silva, Romulo Augusto Ventura

    2011-01-01

    The correct evaluation of a material property is fundamental to, on their application; they met all expectations that were designed for. In development of an expansive cement for ornamental rocks purpose, was denoted the absence of methodologies and equipments to evaluate the expansive pressure and temperature of expansive cement during their expansive process, having that data collected in a static state of the specimen. In that paper, is described equipment designed for evaluation of pressure and temperature of expansive cements applied to ornamental rocks.

  16. Engineering Properties of Expansive Soil

    Institute of Scientific and Technical Information of China (English)

    DAI Shaobin; SONG Minghai; HUANG Jun

    2005-01-01

    The components of expansive soil were analyzed with EDAX, and it is shown that the main contents of expansive soil in the northern Hubei have some significant effects on engineering properties of expansive soil. Furthermore, the soil modified by lime has an obvious increase of Ca2+ and an improvement of connections between granules so as to reduce the expansibility and contractility of soil. And it also has a better effect on the modified expansive soil than the one modified by pulverized fuel ash.

  17. Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups.

    Science.gov (United States)

    Martínez-Cortés, Gabriela; Salazar-Flores, Joel; Haro-Guerrero, Javier; Rubi-Castellanos, Rodrigo; Velarde-Félix, Jésus S; Muñoz-Valle, José F; López-Casamichana, Mavil; Carrillo-Tapia, Eduardo; Canseco-Avila, Luis M; Bravi, Claudio M; López-Armenta, Mauro; Rangel-Villalobos, Héctor

    2013-08-01

    The maternal ancestry (mtDNA) has important applications in different research fields, such as evolution, epidemiology, identification, and human population history. This is particularly interesting in Mestizos, which constitute the main population in Mexico (∼93%) resulting from post-Columbian admixture between Spaniards, Amerindians, and African slaves, principally. Consequently, we conducted minisequencing analysis (SNaPshot) of 11 mitochondrial single-nucleotide polymorphisms in 742 Mestizos of 10 populations from different regions in Mexico. The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively). Conversely, European and African ancestries were less frequent (5.3 and 1.9%, respectively). The main characteristics of the maternal lineages observed in Mexican-Mestizos comprised the following: 1) contrasting geographic gradient of Haplogroups A and C; 2) increase of European lineages toward the Northwest; 3) low or absent, but homogeneous, African ancestry throughout the Mexican territory; 4) maternal lineages in Mestizos roughly represent the genetic makeup of the surrounding Amerindian groups, particularly toward the Southeast, but not in the North and West; 5) continuity over time of the geographic distribution of Amerindian lineages in Mayas; and 6) low but significant maternal population structure (FST  = 2.8%; P = 0.0000). The average ancestry obtained from uniparental systems (mtDNA and Y-chromosome) in Mexican-Mestizos was correlated with previous ancestry estimates based on autosomal systems (genome-wide single-nucleotide polymorphisms and short tandem repeats). Finally, the comparison of paternal and maternal lineages provided additional information concerning the gender bias admixture, mating patterns, and population structure in Mestizos throughout the Mexican territory.

  18. Molecular phylogenetic relationship of Eplnephelus based on sequences of mtDNA Cty b

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae,Epinephelinae and seven endemic species of groupers-Epinephelus awoara,E.brunneus,E.coioides,E.longispinis,E.sexfasciatus,E.spilotoceps and E.tauvina in China.The seven endemic species and other seven foreign species of groupers--E,aeneus,E.caninus,E.drummondhayi,E,haifensis,E.labriformis,E.marginatus and E.multinotatus from the GenBank were combined and analysed as ingroup,while Variola louti was used as outgroup.We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP)and neighbor-joining method (NJ) respectively.The results were as follows:(1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinepkelus,the content of (A + T) was 53.6%,higher than that of (G + C) (46.4%).The transition/transversion ratio was 4.78 with no mutation saturation.(2) The duster relationships between E.awoara and E.sexfasciatus,E.coioides and E.tauvina,E.longispinis and E.spilotoceps were consistent with phenotypes in taxonomy.(3) In the phylogenetic tree,the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean,which suggested that the Cyt b sequences of Epinephelus were highly conserved.This may be attributed to the coordinate evolution.(4) In well-bred mating or heredity management,mating Epinephelus of the same branch should be avoided.It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.

  19. Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes.

    Science.gov (United States)

    Beaudet, Denis; Terrat, Yves; Halary, Sébastien; de la Providencia, Ivan Enrique; Hijri, Mohamed

    2013-01-01

    Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms.AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes (dpo), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp.) with substantial mtDNA synteny divergence,were sequenced and compared with available glomeromycotan mitochondrial genomes. We used an extensive nucleotide/protein similarity network-based approach to investigated podiversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo-induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity.We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.

  20. Mating patterns amongst Siberian reindeer herders: inferences from mtDNA and Y-chromosomal analyses.

    Science.gov (United States)

    Pakendorf, Brigitte; Novgorodov, Innokentij N; Osakovskij, Vladimir L; Stoneking, Mark

    2007-07-01

    The Evenks and Evens, who speak closely related languages belonging to the Northern Tungusic branch of the Tungusic family, are nomadic reindeer herders and hunters. They are spread over an immense territory in northeastern Siberia, and consequently different subgroups are in contact with diverse peoples speaking Samoyedic, Turkic, Mongolic, Chukotka-Kamchatkan, and Yukaghir languages. Nevertheless, the languages and culture of the Evenks and Evens are similar enough for them to have been classified as a single ethnic group in the past. This linguistic and cultural similarity indicates that they may have spread over their current area of habitation relatively recently, and thus may be closely related genetically. On the other hand, the great distances that separate individual groups of Evens and Evenks from each other might have led to preferential mating with geographic neighbors rather than with linguistically related peoples. In this study, we assess the correlation between linguistic and genetic relationship in three different subgroups of Evenks and Evens, respectively, via mtDNA and Y-chromosomal analyses. The results show that there is some evidence of a common origin based on shared mtDNA lineages and relatively similar Y-haplogroup frequencies amongst most of the Evenk and Even subgroups. However, there is little sharing of Y-chromosomal STR haplotypes, indicating that males within Evenk and Even subgroups have remained relatively isolated. There is further evidence of some female admixture in different Even subgroups with their respective geographic neighbors. However, the Tungusic groups, and especially the Evenks, show signs of genetic drift, making inferences about their prehistory difficult. PMID:17492671

  1. HVSI polymorphism indicates multiple origins of mtDNA in the Hazarewal population of Northern Pakistan.

    Science.gov (United States)

    Akbar, N; Ahmad, H; Nadeem, M S; Hemphill, B E; Muhammad, K; Ahmad, W; Ilyas, M

    2016-01-01

    Mitochondrial DNA (mtDNA) is an important tool used to explore ethnogenetics and the evolutionary history of human populations. In this study, hypervariable segment I (HVSI) from mtDNA was analyzed to establish the genetic lineage of the Hazarewal populations residing in the Mansehra and Abbottabad districts of Northern Pakistan. HVSI was extracted from genetic specimens obtained from 225 unrelated male and female individuals belonging to seven distinct Pakistani ethnic groups (31 Abbassis, 44 Awans, 38 Gujars, 16 Jadoons, 23 Karlals, 33 Syeds, and 40 Tanolis). Eighty-three haplogroups, 39 of which were unique, were identified; haplogroup H was predominantly represented (in 40% of the people), followed by haplogroups M (21.78%), R (16.89%), N (15.56%), L (3.11%), and HV (2.67%). The results revealed a sex-biased genetic contribution from putative West Eurasian, South Asian, and Sub-Saharan populations to the genetic lineage of Hazarewal ancestry, with the effect of Eurasians being predominant. The HVSI nucleotide sequences exhibited some characteristic deletion mutations between 16,022 and 16,193 bp, which is characteristic of specific ethnic groups. HVSI sequence homology showed that Hazarewal populations fall into three major clusters: Syeds and Awans sorted out into cluster I; Tanolis, Gujars, and Karlals segregated in cluster II; and Abbassis and Jadoons in cluster III. Here, we have reported the firsthand genetic information and evolutionary sketch of the selected populations residing alongside the historical Silk Route, which provides a baseline for collating the origin, route of migration, and phylogenetics of the population. PMID:27420957

  2. Identification of an mtDNA mutation hot spot in UV-induced mouse skin tumors producing altered cellular biochemistry.

    Science.gov (United States)

    Jandova, Jana; Eshaghian, Alex; Shi, Mingjian; Li, Meiling; King, Lloyd E; Janda, Jaroslav; Sligh, James E

    2012-02-01

    There is increasing awareness of the role of mtDNA alterations in the development of cancer, as mtDNA point mutations are found at high frequency in a variety of human tumors. To determine the biological effects of mtDNA mutations in UV-induced skin tumors, hairless mice were irradiated to produce tumors, and the tumor mtDNAs were screened for single-nucleotide changes using temperature gradient capillary electrophoresis (TGCE), followed by direct sequencing. A mutation hot spot (9821insA) in the mitochondrially encoded tRNA arginine (mt-Tr) locus (tRNA(Arg)) was discovered in approximately one-third of premalignant and malignant skin tumors. To determine the functional relevance of this particular mutation in vitro, cybrid cell lines containing different mt-Tr (tRNA(Arg)) alleles were generated. The resulting cybrid cell lines contained the same nuclear genotype and differed only in their mtDNAs. The biochemical analysis of the cybrids revealed that the mutant haplotype is associated with diminished levels of complex I protein (CI), resulting in lower levels of baseline oxygen consumption and lower cellular adenosine triphosphate (ATP) production. We hypothesize that this specific mtDNA mutation alters cellular biochemistry, supporting the development of keratinocyte neoplasia.

  3. Chip-based mtDNA mutation screening enables fast and reliable genetic diagnosis of OXPHOS patients

    NARCIS (Netherlands)

    R.G.E. van Eijsden (Rudy); E. Briem (Egill); V. Tiranti (Valeria); H.J.M. Smeets (Hubert); M. Gerards (Mike); L.M.T. Eijssen (Lars); A. Hendrickx (Alexandra); R.J.E. Jongbloed (Roselie); J.H.J. Wokke (John); R.Q. Hintzen (Rogier); M.E. Rubio-Gozalbo (Estela); I.F.M. de Coo (René)

    2006-01-01

    textabstractPURPOSE: Oxidative phosphorylation is under dual genetic control of the nuclear and the mitochondrial DNA (mtDNA). Oxidative phosphorylation disorders are clinically and genetically heterogeneous, which makes it difficult to determine the genetic defect, and symptom-based protocols which

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

    Directory of Open Access Journals (Sweden)

    Anderson Nonato do Rosário Marinho

    2011-01-01

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

  5. Screen for abnormal mitochondrial phenotypes in mouse embryonic stem cells identifies a model for succinyl-CoA ligase deficiency and mtDNA depletion

    Directory of Open Access Journals (Sweden)

    Taraka R. Donti

    2014-02-01

    Full Text Available Mutations in subunits of succinyl-CoA synthetase/ligase (SCS, a component of the citric acid cycle, are associated with mitochondrial encephalomyopathy, elevation of methylmalonic acid (MMA, and mitochondrial DNA (mtDNA depletion. A FACS-based retroviral-mediated gene trap mutagenesis screen in mouse embryonic stem (ES cells for abnormal mitochondrial phenotypes identified a gene trap allele of Sucla2 (Sucla2SAβgeo, which was used to generate transgenic mice. Sucla2 encodes the ADP-specific β-subunit isoform of SCS. Sucla2SAβgeo homozygotes exhibited recessive lethality, with most mutants dying late in gestation (e18.5. Mutant placenta and embryonic (e17.5 brain, heart and muscle showed varying degrees of mtDNA depletion (20–60%. However, there was no mtDNA depletion in mutant liver, where the gene is not normally expressed. Elevated levels of MMA were observed in embryonic brain. SCS-deficient mouse embryonic fibroblasts (MEFs demonstrated a 50% reduction in mtDNA content compared with wild-type MEFs. The mtDNA depletion resulted in reduced steady state levels of mtDNA encoded proteins and multiple respiratory chain deficiencies. mtDNA content could be restored by reintroduction of Sucla2. This mouse model of SCS deficiency and mtDNA depletion promises to provide insights into the pathogenesis of mitochondrial diseases with mtDNA depletion and into the biology of mtDNA maintenance. In addition, this report demonstrates the power of a genetic screen that combines gene trap mutagenesis and FACS analysis in mouse ES cells to identify mitochondrial phenotypes and to develop animal models of mitochondrial dysfunction.

  6. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization.

    Science.gov (United States)

    Turchi, Chiara; Stanciu, Florin; Paselli, Giorgia; Buscemi, Loredana; Parson, Walther; Tagliabracci, Adriano

    2016-09-01

    To evaluate the pattern of Romanian population from a mitochondrial perspective and to establish an appropriate mtDNA forensic database, we generated a high-quality mtDNA control region dataset from 407 Romanian subjects belonging to four major historical regions: Moldavia, Transylvania, Wallachia and Dobruja. The entire control region (CR) was analyzed by Sanger-type sequencing assays and the resulting 306 different haplotypes were classified into haplogroups according to the most updated mtDNA phylogeny. The Romanian gene pool is mainly composed of West Eurasian lineages H (31.7%), U (12.8%), J (10.8%), R (10.1%), T (9.1%), N (8.1%), HV (5.4%),K (3.7%), HV0 (4.2%), with exceptions of East Asian haplogroup M (3.4%) and African haplogroup L (0.7%). The pattern of mtDNA variation observed in this study indicates that the mitochondrial DNA pool is geographically homogeneous across Romania and that the haplogroup composition reveals signals of admixture of populations of different origin. The PCA scatterplot supported this scenario, with Romania located in southeastern Europe area, close to Bulgaria and Hungary, and as a borderland with respect to east Mediterranean and other eastern European countries. High haplotype diversity (0.993) and nucleotide diversity indices (0.00838±0.00426), together with low random match probability (0.0087) suggest the usefulness of this control region dataset as a forensic database in routine forensic mtDNA analysis and in the investigation of maternal genetic lineages in the Romanian population.

  7. Distinct nuclear gene expression profiles in cells with mtDNA depletion and homoplasmic A3243G mutation

    Energy Technology Data Exchange (ETDEWEB)

    Jahangir Tafrechi, Roshan S. [Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden (Netherlands); Svensson, Peter J. [Department of Toxicogenetics, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden (Netherlands); Department of Oncology, Radiology and Clinical Immunology, University Hospital, 75185 Uppsala (Sweden); Janssen, George M.C. [Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden (Netherlands); Szuhai, Karoly [Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden (Netherlands); Maassen, J. Antonie [Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden (Netherlands); Raap, Anton K. [Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9503, 2300 RA Leiden (Netherlands)]. E-mail: A.K.Raap@lumc.nl

    2005-10-15

    The pathobiochemical pathways determining the wide variability in phenotypic expression of mitochondrial DNA (mtDNA) mutations are not well understood. Most pathogenic mtDNA mutations induce a general defect in mitochondrial respiration and thereby ATP synthesis. Yet phenotypic expression of the different mtDNA mutations shows large variations that are difficult to reconcile with ATP depletion as sole pathogenic factor, implying that additional mechanisms contribute to the phenotype. Here, we use DNA microarrays to identify changes in nuclear gene expression resulting from the presence of the A3243G diabetogenic mutation and from a depletion of mtDNA ({rho}{sup 0} cells). We find that cells respond mildly to these mitochondrial states with both general and specific changes in nuclear gene expression. This observation indicates that cells can sense the status of mtDNA. A number of genes show divergence in expression in {rho}{sup 0} cells compared to cells with the A3243G mutation, such as genes involved in oxidative phosphorylation. As a common response in A3243G and {rho}{sup 0} cells, mRNA levels for extracellular matrix genes are up-regulated, while the mRNA levels of genes involved in ubiquitin-mediated protein degradation and in ribosomal protein synthesis is down-regulated. This reduced expression is reflected at the level of cytosolic protein synthesis in both A3243G and {rho}{sup 0} cells. Our finding that mitochondrial dysfunction caused by different mutations affects nuclear gene expression in partially distinct ways suggests that multiple pathways link mitochondrial function to nuclear gene expression and contribute to the development of the different phenotypes in mitochondrial disease.

  8. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization.

    Science.gov (United States)

    Turchi, Chiara; Stanciu, Florin; Paselli, Giorgia; Buscemi, Loredana; Parson, Walther; Tagliabracci, Adriano

    2016-09-01

    To evaluate the pattern of Romanian population from a mitochondrial perspective and to establish an appropriate mtDNA forensic database, we generated a high-quality mtDNA control region dataset from 407 Romanian subjects belonging to four major historical regions: Moldavia, Transylvania, Wallachia and Dobruja. The entire control region (CR) was analyzed by Sanger-type sequencing assays and the resulting 306 different haplotypes were classified into haplogroups according to the most updated mtDNA phylogeny. The Romanian gene pool is mainly composed of West Eurasian lineages H (31.7%), U (12.8%), J (10.8%), R (10.1%), T (9.1%), N (8.1%), HV (5.4%),K (3.7%), HV0 (4.2%), with exceptions of East Asian haplogroup M (3.4%) and African haplogroup L (0.7%). The pattern of mtDNA variation observed in this study indicates that the mitochondrial DNA pool is geographically homogeneous across Romania and that the haplogroup composition reveals signals of admixture of populations of different origin. The PCA scatterplot supported this scenario, with Romania located in southeastern Europe area, close to Bulgaria and Hungary, and as a borderland with respect to east Mediterranean and other eastern European countries. High haplotype diversity (0.993) and nucleotide diversity indices (0.00838±0.00426), together with low random match probability (0.0087) suggest the usefulness of this control region dataset as a forensic database in routine forensic mtDNA analysis and in the investigation of maternal genetic lineages in the Romanian population. PMID:27414754

  9. Conformal expansions and renormalons

    CERN Document Server

    Gardi, E; Gardi, Einan; Grunberg, Georges

    2001-01-01

    The large-order behaviour of QCD is dominated by renormalons. On the other hand renormalons do not occur in conformal theories, such as the one describing the infrared fixed-point of QCD at small beta_0 (the Banks--Zaks limit). Since the fixed-point has a perturbative realization, all-order perturbative relations exist between the conformal coefficients, which are renormalon-free, and the standard perturbative coefficients, which contain renormalons. Therefore, an explicit cancellation of renormalons should occur in these relations. The absence of renormalons in the conformal limit can thus be seen as a constraint on the structure of the QCD perturbative expansion. We show that the conformal constraint is non-trivial: a generic model for the large-order behaviour violates it. We also analyse a specific example, based on a renormalon-type integral over the two-loop running-coupling, where the required cancellation does occur.

  10. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.

    Science.gov (United States)

    Shaw, Kerry L

    2002-12-10

    It has been asserted that recent mtDNA phylogenies support the plausibility of sympatric speciation, long considered a controversial mechanism of the origin of species. If such inferences are reliable, mtDNA phylogenies should be congruent with phylogenies based on other data. In previous work, a mtDNA phylogeny suggested that diversification of the Hawaiian cricket genus Laupala was initiated by single invasions into each of several Hawaiian islands, followed by multiple sympatric divergences within each island. In contrast, a systematic hypothesis based on morphology argues that speciation in Laupala has occurred primarily in allopatry, with two independent species radiations diversifying across the archipelago. In this study, I analyze nuclear DNA (nDNA) sequences from Laupala to compare with sequences from the mtDNA. The nDNA phylogeny corroborates the hypothesis of allopatric divergence and multiple invasions, and when compared with mtDNA patterns, suggests that interspecific hybridization is a persistent feature of the history of Laupala. The discrepancy between mtDNA and nDNA phylogenies reveals that speciation histories based on mtDNA alone can be extensively misleading. PMID:12451181

  11. Burial Ground Expansion Hydrogeologic Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Gaughan , T.F.

    1999-02-26

    Sirrine Environmental Consultants provided technical oversight of the installation of eighteen groundwater monitoring wells and six exploratory borings around the location of the Burial Ground Expansion.

  12. Analysis of mtDNA sequence variants in colorectal adenomatous polyps

    Directory of Open Access Journals (Sweden)

    Grizzle William

    2010-10-01

    Full Text Available Abstract Colorectal tumors mostly arise from sporadic adenomatous polyps. Polyps are defined as a mass of cells that protrudes into the lumen of the colon. Adenomatous polyps are benign neoplasms that, by definition display some characteristics of dysplasia. It has been shown that polyps were benign tumors which may undergo malignant transformation. Adenomatous polyps have been classified into three histologic types; tubular, tubulovillous, and villous with increasing malignant potential. The ability to differentially diagnose these colorectal adenomatous polyps is important for therapeutic intervention. To date, little efforts have been directed to identifying genetic changes involved in adenomatous polyps. This study was designed to examine the relevance of mitochondrial genome alterations in the three adenomatous polyps. Using high resolution restriction endonucleases and PCR-based sequencing, fifty-seven primary fresh frozen tissues of adenomatous polyps (37 tumors and 20 matched surrounding normal tissues obtained from the southern regional Cooperative Human Tissue Network (CHTN and Grady Memorial Hospital at Atlanta were screened with three mtDNA regional primer pairs that spanned 5.9 kbp. Results from our data analyses revealed the presence of forty-four variants in some of these mitochondrial genes that the primers spanned; COX I, II, III, ATP 6, 8, CYT b, ND 5, 6 and tRNAs. Based on the MITODAT database as a sequence reference, 25 of the 44 (57% variants observed were unreported. Notably, a heteroplasmic variant C8515G/T in the MT-ATP 8 gene and a germline variant 8327delA in the tRNAlys was observed in all the tissue samples of the three adenomatous polyps in comparison to the referenced database sequence. A germline variant G9055A in the MT-ATP 6 gene had a frequency of 100% (17/17 in tubular and 57% (13/23 in villous adenomas; no corresponding variant was in tubulovillous adenomas. Furthermore, A9006G variant at MT-ATP 6 gene was

  13. Parkinson's disease brain mitochondria have impaired respirasome assembly, age-related increases in distribution of oxidative damage to mtDNA and no differences in heteroplasmic mtDNA mutation abundance

    OpenAIRE

    Keeney Paula M; Dunham Lisa D; Morton Stephanie L; Arthur Charles R; Bennett James P

    2009-01-01

    Abstract Background Sporadic Parkinson's disease (sPD) is a nervous system-wide disease that presents with a bradykinetic movement disorder and is frequently complicated by depression and cognitive impairment. sPD likely has multiple interacting causes that include increased oxidative stress damage to mitochondrial components and reduced mitochondrial bioenergetic capacity. We analyzed mitochondria from postmortem sPD and CTL brains for evidence of oxidative damage to mitochondrial DNA (mtDNA...

  14. Asymptotic expansions of Jacobi functions

    International Nuclear Information System (INIS)

    The author presents an asymptotic expansion of the Jacobi polynomials which is based on the fact, that these polynomials are special hypergeometric functions. He uses an integral representation of these functions and expands the integrand in a power series. He derives explicit error bounds on this expansion. (HSI)

  15. Warp Drive With Zero Expansion

    OpenAIRE

    Natario, Jose

    2001-01-01

    It is commonly believed that Alcubierre's warp drive works by contracting space in front of the warp bubble and expanding space behind it. We show that this expansion/contraction is but a marginal consequence of the choice made by Alcubierre, and explicitly construct a similar spacetime where no contraction/expansion occurs. Global and optical properties of warp drive spacetimes are also discussed.

  16. Isotropic Negative Thermal Expansion Metamaterials.

    Science.gov (United States)

    Wu, Lingling; Li, Bo; Zhou, Ji

    2016-07-13

    Negative thermal expansion materials are important and desirable in science and engineering applications. However, natural materials with isotropic negative thermal expansion are rare and usually unsatisfied in performance. Here, we propose a novel method to achieve two- and three-dimensional negative thermal expansion metamaterials via antichiral structures. The two-dimensional metamaterial is constructed with unit cells that combine bimaterial strips and antichiral structures, while the three-dimensional metamaterial is fabricated by a multimaterial 3D printing process. Both experimental and simulation results display isotropic negative thermal expansion property of the samples. The effective coefficient of negative thermal expansion of the proposed models is demonstrated to be dependent on the difference between the thermal expansion coefficient of the component materials, as well as on the circular node radius and the ligament length in the antichiral structures. The measured value of the linear negative thermal expansion coefficient of the three-dimensional sample is among the largest achieved in experiments to date. Our findings provide an easy and practical approach to obtaining materials with tunable negative thermal expansion on any scale.

  17. Genetic architecture of trout from Albania as revealed by mtDNA control region variation

    Directory of Open Access Journals (Sweden)

    Shumka Spase

    2009-02-01

    Full Text Available Abstract To determine the genetic architecture of trout in Albania, 87 individuals were collected from 19 riverine and lacustrine sites in Albania, FYROM and Greece. All individuals were analyzed for sequence variation in the mtDNA control region. Among fourteen haplotypes detected, four previously unpublished haplotypes, bearing a close relationship to haplotypes of the Adriatic and marmoratus lineages of Salmo trutta, were revealed. Ten previously described haplotypes, characteristic of S. ohridanus, S. letnica and the Adriatic and Mediterranean lineages of S. trutta, were also detected. Haplotypes detected in this study were placed in a well supported branch of S. ohridanus, and a cluster of Mediterranean – Adriatic – marmoratus haplotypes, which were further delimited into three subdivisions of Mediterranean, marmoratus, and a previously non-described formation of four Adriatic haplotypes (Balkan cluster. Haplotypes of the Balkan cluster and the other Adriatic haplotypes, do not represent a contiguous haplotype lineage and appear not to be closely related, indicating independent arrivals into the Adriatic drainage and suggesting successive colonization events. Despite the presence of marmoratus haplotypes in Albania, no marbled phenotype was found, confirming previously reported findings that there is no association between this phenotype and marmoratus haplotypes.

  18. Phylogeny of Trachylepis sp. (Reptilia) from Turkey inferred from mtDNA sequences.

    Science.gov (United States)

    Güçlü, Ozgür; Candan, Kamil; Kankiliç, Tolga; Kumlutaş, Yusuf; Durmuş, Salih Hakan; Poulakakis, Nikos; Ilgaz, Cetin

    2014-12-01

    The taxonomic status of the species included into the genus Trachylepis in Turkey are doubtful. So far, three morphological species have been attributed to this genus in Turkey; Trachylepis aurata. T. vittata, and T. septemtaeniata. Here, we investigated the taxonomy of the Turkish Trachylepis species by employing phylogenetic and phylogeographic approaches and using mitochondrial DNA (cytochrome b and 12 S rRNA). In total, 45 Trachylepis and 6 Mabuya specimens were used analyzed. Phylogenetic analyses were carried out using Maximum Likelihood (ML) and Bayesian Inference (BI) methods. The phylogenetic relationships and the genetic distances retrieved, revealed that the Turkish species, which currently recognized as Trachylepis, are highly diversified, forming a distinct clade that shows closer phylogenetic affinity with the species of the genus Mabuya rather than the other Trachylepis species. In this clade, the three Turkish species are monophyletic with T. vittata to branch off first in late Miocene (10.54 Mya). The other two species (T. septemtaeniata and T. aurata) seem to have sister group relationship that diverged at the end of Messinian Salinity Crisis (5.27 Mya). As a whole, the examination of mtDNA lineages in the Turkish lizards of the genus Trachylepis may contribute substantially to the refining of their taxonomic status, since the three species of Turkey, although monophyletic, represent a distinct radiation that would could probably recognized as a different genus in Mabuya sensu lato. PMID:24004307

  19. Cells Lacking mtDNA Display Increased dNTP Pools upon DNA Damage

    DEFF Research Database (Denmark)

    Skovgaard, Tine; Rasmussen, Lene Juel; Munch-Petersen, Birgitte

    and mitochondrial function we have examined the effect of DNA damage on dNTP pools in cells deficient of mtDNA. We show that DNA damage induced by UV irradiation, in a dose corresponding to LD50, induces an S phase delay in different human osteosarcoma cell lines. The UV pulse also has a destabilizing effect......Imbalanced dNTP pools are highly mutagenic due to a deleterious effect on DNA polymerase fidelity. Mitochondrial DNA defects, including mutations and deletions, are commonly found in a wide variety of different cancer types. In order to further study the interconnection between dNTP pools...... of this the rho0 cells have much lower ATP levels than rho+ cells. In order to mimic the ATP situation in rho0 cells the rho+ cells are incubated with the ATP synthase inhibitor, oligomycin. Similar to the rho0 cells the oligomycin incubated rho+ cells display increased dNTP pools upon UV irradiation. Our data...

  20. Cells Lacking mtDNA Display Increased dNTP Pools upon DNA Damage

    DEFF Research Database (Denmark)

    Skovgaard, Tine; Rasmussen, Lene Juel; Munch-Petersen, Birgitte

    and mitochondrial function we have examined the effect of DNA damage on dNTP pools in cells deficient of mtDNA. We show that DNA damage induced by UV irradiation, in a dose corresponding to LD50, induces cell cycle synchronization in different human osteosarcoma cell lines. The UV pulse also has a destabilizing......Imbalanced dNTP pools are highly mutagenic due to a deleterious effect on DNA polymerase fidelity. Mitochondrial DNA defects, including mutations and deletions, are commonly found in a wide variety of different cancer types. In order to further study the interconnection between dNTP pools......-synthase. As a result of this the rho0 cells have much lower ATP levels than rho+ cells. In order to mimic the ATP situation in rho0 cells the rho+ cells are incubated with the ATP synthase inhibitor, oligomycin. Similar to the rho0 cells the oligomycin incubated rho+ cells display destabilized dNTP pools upon UV...

  1. Molecular Identification and Phylogenetic Relationships of Threadfin Breams (Family: Nemipteridae Using mtDNA Marker

    Directory of Open Access Journals (Sweden)

    Vaithilingam RAVITCHANDIRANE

    2012-05-01

    Full Text Available Cytochrome c oxidase-1 gene sequences of mitochondrial genome were analyzed for species identification and phylogenetic relationship among the commercially important Nemipterus species. Sequence analysis of COI gene clearly indicated that all the nine fish species fell into distinct clads, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences provide sufficient phylogenetic information and evolutionary relationship to distinguish the nine Nemipterus species unambiguously. As per the neighbour-joining (NJ and maximum likelihood (ML trees, all the nine species are genetically distant from each other and exhibited identical phylogenetic reservation. Based on the NJ and ML phylogenetic trees N. mesoprion, N. zysron, N. hexodon, N. nematophorus, N. virgatus and N. bipunctatus were closely related with high bootstrap value (97. The overall mean Kimura two parameter (K2P distances between the nine species was 0.109. The intra species K2P distance was high in N. japonicus (0.069 followed by N. peronii (0.050 and N. mesoprion (0.002. This study proves the use of mtDNA COI gene sequence based approach is an alternative tool for identifying fish species at a faster pace.

  2. Forensic and phylogeographic characterisation of mtDNA lineages from Somalia.

    Science.gov (United States)

    Mikkelsen, Martin; Fendt, Liane; Röck, Alexander W; Zimmermann, Bettina; Rockenbauer, Eszter; Hansen, Anders J; Parson, Walther; Morling, Niels

    2012-07-01

    The African mitochondrial (mt) phylogeny is coarsely resolved but the majority of population data generated so far is limited to the analysis of the first hypervariable segment (HVS-1) of the control region (CR). Therefore, this study aimed on the investigation of the entire CR of 190 unrelated Somali individuals to enrich the severely underrepresented African mtDNA pool. The majority (60.5 %) of the haplotypes were of sub-Saharan origin with L0a1d, L2a1h and L3f being the most frequently observed haplogroups. This is in sharp contrast to previous data reported from the Y-chromosome, where only about 5 % of the observed haplogroups were of sub-Saharan provenance. We compared the genetic distances based on population pairwise F (st) values between 11 published East, Central and North African as well as western Asian populations and the Somali sequences and displayed them in a multi-dimensional scaling plot. Genetic proximity evidenced by clustering roughly reflected the relative geographic location of the populations. The sequences will be included in the EMPOP database ( www.empop.org ) under accession number EMP00397 upon publication (Parson and Dür Forensic Sci Int Genet 1:88-92, 2007).

  3. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region.

    Science.gov (United States)

    Kim, Jae-Hwan; Lee, Seong-Su; Kim, Seung Chang; Choi, Seong-Bok; Kim, Su-Hyun; Lee, Chang Woo; Jung, Kyoung-Sub; Kim, Eun Sung; Choi, Young-Sun; Kim, Sung-Bok; Kim, Woo Hyun; Cho, Chang-Yeon

    2016-05-01

    Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds. PMID:26954229

  4. MtDNA variability in whitefly (Bemisia tabaci) populations in Brazil.

    Science.gov (United States)

    Valle, G E; Lourenção, A L; Zucchi, M I; Pinheiro, J B; Abreu, A G

    2011-01-01

    Bemisia tabaci (Hemiptera: Aleyrodidae) consists of a complex of morphologically indistinct biotypes that vary mainly in their capacity to transmit plant viruses and to induce physiological disorders in plants of economic importance. The adaptability of B. tabaci to many regions of the world has fostered the appearance of various biotypes and has resulted in a broad spectrum of host plants. Our goal was to identify which biotypes were present in four B. tabaci populations in Brazil. We quantified genetic variability between and within populations. Three individuals were collected from three host plant species: two populations on soybean (Campinas and Rondonópolis), one on pumpkin (Barreiras) and one on tomato (Cruz das Almas) in three States of Brazil (São Paulo, Mato Grosso, and Bahia). We chose one sequence of the B biotype, obtained from GenBank; the Campinas population, which had been previously characterized as biotype B, was used as a control for this biotype. We also included one sequence of the Q biotype, obtained from GenBank, as an outgroup. The COI region of the mtDNA gene was partially amplified with the CI-J-2195 and L2-N-3014 pair of primers, and the reaction products were sequenced. Based on distance-based algorithm analyses, we found that all haplotypes belong to biotype B, which was confirmed by the haplotype network. Genetic structure analyses showed that the host plant species does not influence population structuring of this pest; only the geographic location mattered. PMID:21968683

  5. Segregation pattern and biochemical effect of the G3460A mtDNA mutation in 27 members of LHON family.

    Science.gov (United States)

    Kaplanová, Vilma; Zeman, Jirí; Hansíková, Hana; Cerná, Leona; Houst'ková, Hana; Misovicová, Nadezda; Houstek, Josef

    2004-08-30

    Inheritance and expression of mitochondrial DNA (mtDNA) mutations are crucial for the pathogenesis of Leber hereditary optic neuropathy (LHON). We have investigated the segregation and functional consequences of G3460A mtDNA mutation in 27 members of a three-generation family with LHON syndrome. Specific activity of respiratory chain complex I in platelets was reduced in average to 56%, but no direct correlation between the mutation load and its biochemical expression was found. Heteroplasmy in blood, platelets and hair follicles varied from 7% to 100%. Segregation pattern exhibited tissue specificity and influence of different nuclear backgrounds in four branches of the pedigree. Longitudinal analysis revealed a significant (p=0.02) decrease in blood mutation load. Although enzyme assay showed reduction of complex I activity, our results give additional support to the hypothesis that expression of LHON mutation depends on complex nuclear-mitochondrial interaction.

  6. Sequence Analysis of mtDNA COIGene and Molecular Phylogeny of Different Geographical Populations of Bemisia tabaci (Gennadius)

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; ZHANG You-jun; CONG Bin; XU Bao-yun; WU Qing-jun; ZHU Guo-ren

    2005-01-01

    Bemisia tabaci(Gennadius) is a serious pest in many cropping systems worldwide and occurs in different biotypes. The mtDNA COI gene of the 12 Bemisia tabaci (Gennadius) populations from different regions and countries were analyzed.Based on mtDNA COI sequences, their biotypes were characterized and phylogenetic relationships among these populations were established with the method of UPGMA. The results indicated the genetic similarity between those populations from Beijing, Zhengzhou, Zaozhuang, Nanjing, Shanghai, Haikou, and the B-biotype populations from California, Texas, Arizona reached 99.8-100%, which meant the nation-wide infested populations of B. tabaci in China in recent years were B-biotypes. Another population collected from Kunming of Yunnan Province showed very high similarity with Q-biotype B. tabaci from Spain and Morocco, which meant the Kunming population was Q-biotype. This is the first report on the invasion of Q-biotype into China.

  7. The impact of the Austronesian expansion: Evidence from mtDNA and Y chromosome diversity in the Admiralty Islands of melanesia

    NARCIS (Netherlands)

    M.H. Kayser (Manfred); Y. Choi (Ying); M. van Oven (Mannis); S. Mona (Stefano); S. Brauer (Silke); R.J. Trent (Ronald); D. Suarkia (Dagwin); W. Schiefenhövel (Wulf); M. Stoneking (Mark)

    2008-01-01

    textabstractThe genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of t

  8. On genus expansion of superpolynomials

    CERN Document Server

    Mironov, A; Sleptsov, A; Smirnov, A

    2013-01-01

    Recently it was shown that the (Ooguri-Vafa) generating function of HOMFLY polynomials is the Hurwitz partition function, i.e. that the dependence of the HOMFLY polynomials on representation is naturally captured by symmetric group characters (cut-and-join eigenvalues). The genus expansion and expansion through Vassiliev invariants explicitly demonstrate this phenomenon. In the present letter we claim that the superpolynomials are not functions of such a type: symmetric group characters do not provide an adequate linear basis for their expansions. Deformation to superpolynomials is, however, straightforward in the multiplicative basis:the Casimir operators are beta-deformed to Hamiltonians of the Calogero-Moser-Sutherland system. Applying this trick to the genus and Vassiliev expansions, we observe that the deformation is rather straightforward only for the thin knots. Beyond this family additional algebraically independent terms appear in the Vassiliev and genus expansions. This can suggest that the superpol...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-01-15

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

  10. Anthropology. Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".

    Science.gov (United States)

    Prüfer, Kay; Meyer, Matthias

    2015-02-20

    Chatters et al. (Reports, 16 May 2014, p. 750) reported the retrieval of DNA sequences from a 12,000- to 13,000-year-old human tooth discovered in an underwater cave in Mexico's Yucatan peninsula. They propose that this ancient human individual's mitochondrial DNA (mtDNA) belongs to haplogroup D1. However, our analysis of postmortem damage patterns finds no evidence for an ancient origin of these sequences.

  11. Multiple hypothesis correction is vital and undermines reported mtDNA links to diseases including AIDS, cancer, and Huntingdon's.

    Science.gov (United States)

    Johnston, Iain G

    2016-09-01

    The ability to sequence mitochondrial genomes quickly and cheaply has led to an explosion in available mtDNA data. As a result, an expanding literature is exploring links between mtDNA features and susceptibility to, or prevalence of, a range of diseases. Unfortunately, this great technological power has not always been accompanied by great statistical responsibility. I will focus on one aspect of statistical analysis, multiple hypothesis correction, that is absolutely required, yet often absolutely ignored, for responsible interpretation of this literature. Many existing studies perform comparisons between incidences of a large number (N) of different mtDNA features and a given disease, reporting all those yielding p values under 0.05 as significant links. But when many comparisons are performed, it is highly likely that several p values under 0.05 will emerge, by chance, in the absence of any underlying link. A suitable correction (for example, Bonferroni correction, requiring p < 0.05/N) must, therefore, be employed to avoid reporting false positive results. The absence of such corrections means that there is good reason to believe that many links reported between mtDNA features and various diseases are false; a state of affairs that is profoundly negative both for fundamental biology and for public health. I will show that statistics matching those claimed to illustrate significant links can arise, with a high probability, when no such link exists, and that these claims should thus be discarded until results of suitable statistical reliability are provided. I also discuss some strategies for responsible analysis and interpretation of this literature. PMID:25884427

  12. Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia).

    Science.gov (United States)

    Sremba, Angela L; Hancock-Hanser, Brittany; Branch, Trevor A; LeDuc, Rick L; Baker, C Scott

    2012-01-01

    The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131° longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968±0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F(ST) = 0.032, p<0.005) and microsatellite alleles (F(ST) = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales. PMID:22412889

  13. Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia)

    OpenAIRE

    Angela L Sremba; Brittany Hancock-Hanser; Branch, Trevor A.; Rick L LeDuc; C Scott Baker

    2012-01-01

    The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genoty...

  14. Phylogenetic Analysis of a Privately-owned Korean Native Chicken Population Using mtDNA D-loop Variations

    OpenAIRE

    Hoque, M. R.; Choi, N. R.; Sultana, H.; Kang, B. S.; Heo, K. N.; Hong, S K; Jo, C.; Lee, J.H.

    2013-01-01

    The use of Korean native chicken is increasing, and the discovery of new genetic resources is very important from both economic and genetic conservation points of view. In this study, mtDNA D-loop sequences from 272 privately-owned Korean native chickens from a Hyunin farm were investigated. Seventeen nucleotide substitutions were identified from the sequence analysis and they were classified as 6 haplotypes. Previously investigated haplotypes in five Korean native chicken populations have be...

  15. Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia.

    Directory of Open Access Journals (Sweden)

    Angela L Sremba

    Full Text Available The Antarctic blue whale (Balaenoptera musculus intermedia was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131° longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86 have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968±0.004, perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F(ST = 0.032, p<0.005 and microsatellite alleles (F(ST = 0.005, p<0.05 among the six Antarctic Areas historically used by the IWC for management of blue whales.

  16. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

    OpenAIRE

    Anne C Stone; Battistuzzi, Fabia U.; Kubatko, Laura S; Perry, George H.; Trudeau, Evan; Lin, Hsiuman; Kumar, Sudhir

    2010-01-01

    Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which ma...

  17. A mitochondrial DNA (mtDNA) mutation associated with maternally inherited Parkinson`s disease (PD) and deafness

    Energy Technology Data Exchange (ETDEWEB)

    Shoffner, J.M.; Brown, M.; Huoponen, K. [Emory Univ., Atlanta, GA (United States)] [and others

    1994-09-01

    A pedigree was characterized in which PD and deafness is expressed along the maternal lineage. The proband is 74 years old and has PD. Her mother and 3 of 7 siblings have PD and a maternal lineage cousin may have early signs of PD. The proband`s mother, a sibling, and all four of her daughters have premature deafness. Since manifestations of PD begin after 50 years of age, the 30-40 year old daughters have not reached an age where extrapyramidal symptoms are likely to appear. Although all 4 daughters have premature deafness, one daughter experienced a rapid reduction of her hearing after receiving a short course during childhood of the aminoglycoside streptomycin. Muscle biopsies from the proband who has PD and 3 daughters with deafness revealed normal histology. Oxidative phosphorylation biochemistry showed Complex I and IV defects in the proband and 2 daughters and a Complex I defect in the other daughter. The proband`s mtDNA was sequenced. Of the nucleotide variants observed, the only significant nucleotide change was a homoplasmic A-to-G point mutation in the 12S rRNA gene at position 1555 of the mtDNA. This site is homologous to the E. coli aminoglycoside binding site and has been found in a large Arab-Israeli pedigree with spontaneously occurring deafness and three Chinese pedigrees with aminoglycoside-induced deafness. Hence, this family shows a direct link between PD, deafness, Complex I and IV defects, and a mutation in a gene that functions in mitochondrial protein synthesis. Furthermore, the interaction between aminoglycosides and the mtDNA in a manner that augments the pathogenic effects of this mutation provides an excellent example of how environmental toxins and mtDNA mutations can interact to give a spectrum of clinical presentations.

  18. Cigarette toxicity triggers Leber's hereditary optic neuropathy by affecting mtDNA copy number, oxidative phosphorylation and ROS detoxification pathways

    Science.gov (United States)

    Giordano, L; Deceglie, S; d'Adamo, P; Valentino, M L; La Morgia, C; Fracasso, F; Roberti, M; Cappellari, M; Petrosillo, G; Ciaravolo, S; Parente, D; Giordano, C; Maresca, A; Iommarini, L; Del Dotto, V; Ghelli, A M; Salomao, S R; Berezovsky, A; Belfort, R; Sadun, A A; Carelli, V; Loguercio Polosa, P; Cantatore, P

    2015-01-01

    Leber's hereditary optic neuropathy (LHON), the most frequent mitochondrial disease, is associated with mitochondrial DNA (mtDNA) point mutations affecting Complex I subunits, usually homoplasmic. This blinding disorder is characterized by incomplete penetrance, possibly related to several genetic modifying factors. We recently reported that increased mitochondrial biogenesis in unaffected mutation carriers is a compensatory mechanism, which reduces penetrance. Also, environmental factors such as cigarette smoking have been implicated as disease triggers. To investigate this issue further, we first assessed the relationship between cigarette smoke and mtDNA copy number in blood cells from large cohorts of LHON families, finding that smoking was significantly associated with the lowest mtDNA content in affected individuals. To unwrap the mechanism of tobacco toxicity in LHON, we exposed fibroblasts from affected individuals, unaffected mutation carriers and controls to cigarette smoke condensate (CSC). CSC decreased mtDNA copy number in all cells; moreover, it caused significant reduction of ATP level only in mutated cells including carriers. This implies that the bioenergetic compensation in carriers is hampered by exposure to smoke derivatives. We also observed that in untreated cells the level of carbonylated proteins was highest in affected individuals, whereas the level of several detoxifying enzymes was highest in carriers. Thus, carriers are particularly successful in reactive oxygen species (ROS) scavenging capacity. After CSC exposure, the amount of detoxifying enzymes increased in all cells, but carbonylated proteins increased only in LHON mutant cells, mostly from affected individuals. All considered, it appears that exposure to smoke derivatives has a more deleterious effect in affected individuals, whereas carriers are the most efficient in mitigating ROS rather than recovering bioenergetics. Therefore, the identification of genetic modifiers that

  19. Cigarette toxicity triggers Leber's hereditary optic neuropathy by affecting mtDNA copy number, oxidative phosphorylation and ROS detoxification pathways.

    Science.gov (United States)

    Giordano, L; Deceglie, S; d'Adamo, P; Valentino, M L; La Morgia, C; Fracasso, F; Roberti, M; Cappellari, M; Petrosillo, G; Ciaravolo, S; Parente, D; Giordano, C; Maresca, A; Iommarini, L; Del Dotto, V; Ghelli, A M; Salomao, S R; Berezovsky, A; Belfort, R; Sadun, A A; Carelli, V; Loguercio Polosa, P; Cantatore, P

    2015-12-17

    Leber's hereditary optic neuropathy (LHON), the most frequent mitochondrial disease, is associated with mitochondrial DNA (mtDNA) point mutations affecting Complex I subunits, usually homoplasmic. This blinding disorder is characterized by incomplete penetrance, possibly related to several genetic modifying factors. We recently reported that increased mitochondrial biogenesis in unaffected mutation carriers is a compensatory mechanism, which reduces penetrance. Also, environmental factors such as cigarette smoking have been implicated as disease triggers. To investigate this issue further, we first assessed the relationship between cigarette smoke and mtDNA copy number in blood cells from large cohorts of LHON families, finding that smoking was significantly associated with the lowest mtDNA content in affected individuals. To unwrap the mechanism of tobacco toxicity in LHON, we exposed fibroblasts from affected individuals, unaffected mutation carriers and controls to cigarette smoke condensate (CSC). CSC decreased mtDNA copy number in all cells; moreover, it caused significant reduction of ATP level only in mutated cells including carriers. This implies that the bioenergetic compensation in carriers is hampered by exposure to smoke derivatives. We also observed that in untreated cells the level of carbonylated proteins was highest in affected individuals, whereas the level of several detoxifying enzymes was highest in carriers. Thus, carriers are particularly successful in reactive oxygen species (ROS) scavenging capacity. After CSC exposure, the amount of detoxifying enzymes increased in all cells, but carbonylated proteins increased only in LHON mutant cells, mostly from affected individuals. All considered, it appears that exposure to smoke derivatives has a more deleterious effect in affected individuals, whereas carriers are the most efficient in mitigating ROS rather than recovering bioenergetics. Therefore, the identification of genetic modifiers that

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

    OpenAIRE

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

    2008-01-01

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

  1. mtDNA from hair and nail clarifies the genetic relationship of the 15th century Qilakitsoq Inuit mummies

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Djurhuus, Durita; Melchior, Linea;

    2007-01-01

    DNA from hair and nail, we have reanalyzed the mummies. The results allowed the unambiguous assignment of each of the mummies to one of three mtDNA haplogroups: A2b (I/5); A2a (I/2, I/3, II/6, II/8); A2a-311 (I/1, I/4, II/7), excluded some of the previous relations, and pointed to new ones. I/5...

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

    International Nuclear Information System (INIS)

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

  3. A Study on the D-loop Region of Mitochondrial DNA (mtDNA) Mutation in Cervical Carcinomas

    Institute of Scientific and Technical Information of China (English)

    XUE Wen-qun; CHEN Dao-zhen

    2009-01-01

    Objective Background-study on genesis and development of tumor is mainly concentrated on gene mutation in nucleus. In recent years, however, the role of mitochondrial DNA (mtDNA) mutation in tumor genesis has been given more and more attention, which is the only extra-nucleus DNA in cells of higher animals. Carcinoma of the uterine cervix is a common tumor in gynecology, but there are few reports of mtDNA mutation in this area. The focus of this study was to investigate the mtDNA mutation in tumor tissues of cervical carcinomas and their relationship to tumorigenesis and tumor development. Methods The D-loop region of 24 cervical carcinomas together with the adjacent normal tissues were amplified by PCR and sequenced. Results Among the 24 cervical carcinomas, 30 mutations in 9 patients′ specimen were identified with the mutations rate of 37.5%(9/24). There were 8 microsatellite instabilities among the mutations and 13 new polymorphisms which were not reported previously in the Genbank. Conclusions The D-loop region of mitochondrial DNA is a highly polymorphoric and mutable region and the mutation rate is relatively high in patients with cervical carcinomas.

  4. Long-term bezafibrate treatment improves skin and spleen phenotypes of the mtDNA mutator mouse.

    Directory of Open Access Journals (Sweden)

    Lloye M Dillon

    Full Text Available Pharmacological agents, such as bezafibrate, that activate peroxisome proliferator-activated receptors (PPARs and PPAR γ coactivator-1α (PGC-1α pathways have been shown to improve mitochondrial function and energy metabolism. The mitochondrial DNA (mtDNA mutator mouse is a mouse model of aging that harbors a proofreading-deficient mtDNA polymerase γ. These mice develop many features of premature aging including hair loss, anemia, osteoporosis, sarcopenia and decreased lifespan. They also have increased mtDNA mutations and marked mitochondrial dysfunction. We found that mutator mice treated with bezafibrate for 8-months had delayed hair loss and improved skin and spleen aging-like phenotypes. Although we observed an increase in markers of fatty acid oxidation in these tissues, we did not detect a generalized increase in mitochondrial markers. On the other hand, there were no improvements in muscle function or lifespan of the mutator mouse, which we attributed to the rodent-specific hepatomegaly associated with fibrate treatment. These results showed that despite its secondary effects in rodent's liver, bezafibrate was able to improve some of the aging phenotypes in the mutator mouse. Because the associated hepatomegaly is not observed in primates, long-term bezafibrate treatment in humans could have beneficial effects on tissues undergoing chronic bioenergetic-related degeneration.

  5. Functional Characterization of Three Concomitant MtDNA LHON Mutations Shows No Synergistic Effect on Mitochondrial Activity.

    Science.gov (United States)

    Cruz-Bermúdez, Alberto; Vicente-Blanco, Ramiro J; Hernández-Sierra, Rosana; Montero, Mayte; Alvarez, Javier; González Manrique, Mar; Blázquez, Alberto; Martín, Miguel Angel; Ayuso, Carmen; Garesse, Rafael; Fernández-Moreno, Miguel A

    2016-01-01

    The presence of more than one non-severe pathogenic mutation in the same mitochondrial DNA (mtDNA) molecule is very rare. Moreover, it is unclear whether their co-occurrence results in an additive impact on mitochondrial function relative to single mutation effects. Here we describe the first example of a mtDNA molecule harboring three Leber's hereditary optic neuropathy (LHON)-associated mutations (m.11778G>A, m.14484T>C, m.11253T>C) and the analysis of its genetic, biochemical and molecular characterization in transmitochondrial cells (cybrids). Extensive characterization of cybrid cell lines harboring either the 3 mutations or the single classic m.11778G>A and m.14484T>C mutations revealed no differences in mitochondrial function, demonstrating the absence of a synergistic effect in this model system. These molecular results are in agreement with the ophthalmological characteristics found in the triple mutant patient, which were similar to those carrying single mtDNA LHON mutations.

  6. Low penetrance of the 14484 LHON mutation when it arises in a non-haplogroup J mtDNA background.

    Science.gov (United States)

    Howell, Neil; Herrnstadt, Corinna; Shults, Cliff; Mackey, David A

    2003-06-01

    The penetrance in Leber's hereditary optic neuropathy (LHON) pedigrees is determined primarily by a mutation in the mitochondrial genome (mtDNA), but secondary factors are also necessary for manifestation of the disorder. It has been proposed that mtDNA polymorphisms affect penetrance in LHON pedigrees. In particular, it has been postulated that one or more polymorphisms associated with European haplogroup J mtDNAs substantially increase the penetrance of the primary LHON mutation at nucleotide 14484. We report here a haplogroup H matrilineal pedigree (VIC14) in which the single affected member carries the 14484 LHON mutation, but who manifested a milder and atypical optic nerve disorder. In addition, during a population screen, we identified an individual who carried the 14484 mutation but who had normal vision. Finally, the 14484 mutation is under-represented among haplogroup H mtDNAs that carry a LHON mutation. These results, in conjunction with other studies that are reviewed, indicate that 14484 LHON mutations have a low penetrance when they arise in a haplogroup H mtDNA background.

  7. Functional Characterization of Three Concomitant MtDNA LHON Mutations Shows No Synergistic Effect on Mitochondrial Activity.

    Directory of Open Access Journals (Sweden)

    Alberto Cruz-Bermúdez

    Full Text Available The presence of more than one non-severe pathogenic mutation in the same mitochondrial DNA (mtDNA molecule is very rare. Moreover, it is unclear whether their co-occurrence results in an additive impact on mitochondrial function relative to single mutation effects. Here we describe the first example of a mtDNA molecule harboring three Leber's hereditary optic neuropathy (LHON-associated mutations (m.11778G>A, m.14484T>C, m.11253T>C and the analysis of its genetic, biochemical and molecular characterization in transmitochondrial cells (cybrids. Extensive characterization of cybrid cell lines harboring either the 3 mutations or the single classic m.11778G>A and m.14484T>C mutations revealed no differences in mitochondrial function, demonstrating the absence of a synergistic effect in this model system. These molecular results are in agreement with the ophthalmological characteristics found in the triple mutant patient, which were similar to those carrying single mtDNA LHON mutations.

  8. Functional Characterization of Three Concomitant MtDNA LHON Mutations Shows No Synergistic Effect on Mitochondrial Activity

    Science.gov (United States)

    Cruz-Bermúdez, Alberto; Vicente-Blanco, Ramiro J.; Hernández-Sierra, Rosana; Montero, Mayte; Alvarez, Javier; González Manrique, Mar; Blázquez, Alberto; Martín, Miguel Angel; Ayuso, Carmen; Garesse, Rafael; Fernández-Moreno, Miguel A.

    2016-01-01

    The presence of more than one non-severe pathogenic mutation in the same mitochondrial DNA (mtDNA) molecule is very rare. Moreover, it is unclear whether their co-occurrence results in an additive impact on mitochondrial function relative to single mutation effects. Here we describe the first example of a mtDNA molecule harboring three Leber's hereditary optic neuropathy (LHON)-associated mutations (m.11778G>A, m.14484T>C, m.11253T>C) and the analysis of its genetic, biochemical and molecular characterization in transmitochondrial cells (cybrids). Extensive characterization of cybrid cell lines harboring either the 3 mutations or the single classic m.11778G>A and m.14484T>C mutations revealed no differences in mitochondrial function, demonstrating the absence of a synergistic effect in this model system. These molecular results are in agreement with the ophthalmological characteristics found in the triple mutant patient, which were similar to those carrying single mtDNA LHON mutations. PMID:26784702

  9. Phylogenetic Relationship of Duttaphrynus melanostictus From India and China as Revealed from the Study of 12S and 16S mtDNA Genes

    OpenAIRE

    Sanjib Kr. Das; Debojyoti Dutta

    2013-01-01

    In the present study, the phylogenetic relationship of Duttaphrynus melanostictus from West Bengal, India with other members of the Bufonidiae group was undertaken using partial mitochondrial DNA (mtDNA) genes. Mitochondria were isolated from the liver of Duttaphrynus melanostictus by a non-conventional method of membrane filtration. The technique allows trapping of mitochondria on cellulose acetate membrane followed by mtDNA isolation. 12S ribosomal RNA and 16S ribosomal RNA was sequenced wi...

  10. [A case or Leber hereditary optic neuropathy (LHON): differential diagnosis with post inflammatory atrophy of nerve II using the mtDNA analysis].

    Science.gov (United States)

    Lubos, Leszek; Wajgt, Andrzej; Maciejowski, Maciej; Mroczek-Tońska, Katarzyna; Bartnik, Ewa; Dziekanowska, Danuta

    2003-01-01

    The Leber hereditary optic neuropathy (LHON) is a disease due to a mtDNA mutation. The disorder results from enzymatic perturbations in the mitochondrial respiratory chain. Clinically the LHON may present as a progressive axonal atrophy of the optic nerves with or without other neurological symptoms. The process of reaching the diagnosis of the LHON by means of the molecular analysis of mtDNA is discussed.

  11. Genus expansion of HOMFLY polynomials

    CERN Document Server

    Mironov, A; Sleptsov, A

    2013-01-01

    In the planar limit of the 't Hooft expansion, the Wilson-loop average in 3d Chern-Simons theory (i.e. the HOMFLY polynomial) depends in a very simple way on representation (the Young diagram), so that the (knot-dependent) Ooguri-Vafa partition function becomes a trivial KP tau-function. We study higher genus corrections to this formula in the form of expansion in powers of z = q-q^{-1}. Expansion coefficients are expressed through the eigenvalues of the cut-and-join operators, i.e. symmetric group characters. Moreover, the z-expansion is naturally exponentiated. Representation through cut-and-join operators makes contact with Hurwitz theory and its sophisticated integrability properties. Our formulas describe the shape of genus expansion for the HOMFLY polynomials, which for their matrix model counterparts is usually controlled by Virasoro like constraints and AMM/EO topological recursion. The genus expansion differs from the better studied weak coupling expansion at finite number of colors N, which is descr...

  12. Phylogeography of mtDNA haplogroup R7 in the Indian peninsula

    Directory of Open Access Journals (Sweden)

    Shukla Parul

    2008-08-01

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

  13. ANALISA KEANDALAN TERHADAP LIFETIME SYSTEM PENDINGIN KAPAL IKAN KM. RUKUN ARTA SENTOSA 06 MENGGUNAKAN REFRIGERAN CO2 DAN KOMPRESI BANTU DARI ENERGI PANAS

    Directory of Open Access Journals (Sweden)

    Eko Sasmito Hadi

    2012-03-01

    Full Text Available The cooling system using CO2 refrigerant is one of the vital systems to increase the quality of hauled fishing and it is more effective and more efficient and also this system is environmentally harmless than the conventional cooling system. Reliability is one of so many criteria that had to be concerned in the process of taking the decision of invention such as planning/drafting, production, or reparation process. The aim of this research is to evaluate the design of fish hatch cooling system using CO2 refrigerant and auxiliary compression by heat power in KM. RAS (Rukun Arta Sentosa 06 using the approximation based on reliability. Some steps that had been used in this research are collecting the data, design process, and evaluation by qualitative and quantitative approach. The qualitative approach is using the Failure Mode and Effect Analysis (FMEA method and also using Fault Tree Analysis (FTA method. Otherwise, the quantitative approach is using the method of Markov Process. Analytical approach is done by make a design model of the available invention system through the block diagram reliability and decrease the reliability function of the system, and for the next step those system is to be used as the base rule of quantitative evaluation system. The report of the research tells that the severity level and the failure rate are showed in some components, such as compressor, condenser, heat exchanger and expansion valve. The analytical approach will obtain the value of MTTF (Mean Time To Failure system for 250 hours and the availability value is 0,6308 or 63,08% and the unavailability value is 0,3692 or 36,92%.

  14. Binomial expansions modulo prime powers

    Directory of Open Access Journals (Sweden)

    Paul W. Haggard

    1980-01-01

    Full Text Available In this note a result is given and proved concerning binomial expansions modulo prime powers. In the proof congruence modulo prime powers is generalized to the rational numbers via valuations.

  15. Gradient expansion for anisotropic hydrodynamics

    CERN Document Server

    Florkowski, Wojciech; Spaliński, Michał

    2016-01-01

    We compute the gradient expansion for anisotropic hydrodynamics. The results are compared with the corresponding expansion of the underlying kinetic-theory model with the collision term treated in the relaxation time approximation. We find that a recent formulation of anisotropic hydrodynamics based on an anisotropic matching principle yields the first three terms of the gradient expansion in agreement with those obtained for the kinetic theory. This gives further support for this particular hydrodynamic model as a good approximation of the kinetic-theory approach. We further find that the gradient expansion of anisotropic hydrodynamics is an asymptotic series, and the singularities of the analytic continuation of its Borel transform indicate the presence of non-hydrodynamic modes.

  16. Stability ordering of cycle expansions

    CERN Document Server

    Dettmann, C P

    1997-01-01

    We propose that cycle expansions be ordered with respect to stability rather than orbit length for many chaotic systems, particularly those exhibiting crises. This is illustrated with the strong field Lorentz gas, where we obtain significant improvements over traditional approaches.

  17. Warp drive with zero expansion

    CERN Document Server

    Natario, J

    2002-01-01

    It is commonly believed that Alcubierre's warp drive works by contracting space in front of the warp bubble and expanding the space behind it. We show that this contraction/expansion is but a marginal consequence of the choice made by Alcubierre and explicitly construct a similar spacetime where no contraction/expansion occurs. Global and optical properties of warp-drive spacetimes are also discussed.

  18. Warp drive with zero expansion

    International Nuclear Information System (INIS)

    It is commonly believed that Alcubierre's warp drive works by contracting space in front of the warp bubble and expanding the space behind it. We show that this contraction/expansion is but a marginal consequence of the choice made by Alcubierre and explicitly construct a similar spacetime where no contraction/expansion occurs. Global and optical properties of warp-drive spacetimes are also discussed

  19. Strategic Complexity and Global Expansion

    DEFF Research Database (Denmark)

    Oladottir, Asta Dis; Hobdari, Bersant; Papanastassiou, Marina;

    2012-01-01

    The purpose of this paper is to analyse the determinants of global expansion strategies of newcomer Multinational Corporations (MNCs) by focusing on Iceland, Israel and Ireland. We argue that newcomer MNCs from small open economies pursue complex global expansion strategies (CGES). We distinguish....... The empirical evidence suggests that newcomer MNCs move away from simplistic dualities in the formulation of their strategic choices towards more complex options as a means of maintaining and enhancing their global competitiveness....

  20. Estimates of expansion time scales

    International Nuclear Information System (INIS)

    Monte Carlo simulations of the expansion of a spacefaring civilization show that descendants of that civilization should be found near virtually every useful star in the Galaxy in a time much less than the current age of the Galaxy. Only extreme assumptions about local population growth rates, emigration rates, or ship ranges can slow or halt an expansion. The apparent absence of extraterrestrials from the solar system suggests that no such civilization has arisen in the Galaxy. 1 figure

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

    Directory of Open Access Journals (Sweden)

    Specht Günther

    2010-03-01

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

  2. Results of the 2003-2004 GEP-ISFG collaborative study on mitochondrial DNA: focus on the mtDNA profile of a mixed semen-saliva stain.

    Science.gov (United States)

    Crespillo, Manuel; Paredes, Miguel R; Prieto, Lourdes; Montesino, Marta; Salas, Antonio; Albarran, Cristina; Alvarez-Iglesias, V; Amorin, Antonio; Berniell-Lee, Gemma; Brehm, Antonio; Carril, Juan C; Corach, Daniel; Cuevas, Nerea; Di Lonardo, Ana M; Doutremepuich, Christian; Espinheira, Rosa M; Espinoza, Marta; Gómez, Felix; González, Alberto; Hernández, Alexis; Hidalgo, M; Jimenez, Magda; Leite, Fabio P N; López, Ana M; López-Soto, Manuel; Lorente, Jose A; Pagano, Shintia; Palacio, Ana M; Pestano, José J; Pinheiro, Maria F; Raimondi, Eduardo; Ramón, M M; Tovar, Florangel; Vidal-Rioja, Lidia; Vide, Maria C; Whittle, Martín R; Yunis, Juan J; Garcia-Hirschfel, Julia

    2006-07-13

    We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003-2004. Five reference bloodstains from five donors (M1-M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1-M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1-M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.

  3. Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

    Directory of Open Access Journals (Sweden)

    Mastana Sarabjit

    2004-08-01

    Full Text Available Abstract Background Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia. Results Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades. Conclusions Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.

  4. Haplotype affinities resolve a major component of goat (Capra hircus MtDNA D-loop diversity and reveal specific features of the Sardinian stock.

    Directory of Open Access Journals (Sweden)

    Daniela Piras

    Full Text Available Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1 to provide an operational definition of meaningful mtDNA units within haplogroup A, 2 to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3 to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591 which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.

  5. Molecular evidence for a recent demographic expansion in the puma (Puma concolor (Mammalia, Felidae

    Directory of Open Access Journals (Sweden)

    Eunice M. Matte

    2013-01-01

    Full Text Available The puma is an iconic predator that ranges throughout the Americas, occupying diverse habitats. Previous phylogeographic analyses have revealed that it exhibits moderate levels of genetic structure across its range, with few of the classically recognized subspecies being supported as distinct demographic units. Moreover, most of the species' molecular diversity was found to be in South America. To further investigate the phylogeographic structure and demographic history of pumas we analyzed mtDNA sequences from 186 individuals sampled throughout their range, with emphasis on South America. Our objectives were to refine the phylogeographic assessment within South America and to investigate the demographic history of pumas using a coalescent approach. Our results extend previous phylogeographic findings, reassessing the delimitation of historical population units in South America and demonstrating that this species experienced a considerable demographic expansion in the Holocene, ca. 8,000 years ago. Our analyses indicate that this expansion occurred in South America, prior to the hypothesized re-colonization of North America, which was therefore inferred to be even more recent. The estimated demographic history supports the interpretation that pumas suffered a severe demographic decline in the Late Pleistocene throughout their distribution, followed by population expansion and re-colonization of the range, initiating from South America.

  6. A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons

    Directory of Open Access Journals (Sweden)

    Chan Yi-Chiao

    2012-08-01

    Full Text Available Abstract Background The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs. Results To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome. Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1 the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2 the species H. lar and H. pileatus are monophyletic in the mtgenome phylogeny, respectively, but a H. pileatus individual falls into the H. lar Y chromosome clade. Conclusions Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of

  7. Expansion Nets and Expansion Processes of Elementary Net Systems

    Institute of Scientific and Technical Information of China (English)

    曹存根

    1995-01-01

    Occurrence nets are insufficient to precisely describe executions of elementary net systems with contacts.Traditionally,S-complementation is used for removal of contacts from the systems.Although the main behavior and properties of the original elementary net systems are preserved during S-complementation,their topologies may be changed greatly.This paper introduces a new kind of nets-expansion nets-for representing behavior of elementary net systems.As shown in the paper,expansion nets are natural as well as sufficient for describing the precise behavior of elementary net systems with or without contactks.

  8. mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft

    Directory of Open Access Journals (Sweden)

    Ramaswamy Krishna

    2008-11-01

    Full Text Available Abstract Background Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in eukaryotic cellular function. However, the effects mitochondrial DNA (mtDNA levels have on the nuclear transcriptome have not been defined under physiological conditions. In order to address this issue, we characterized the gene expression profiles of A549 lung cancer cells and their mtDNA-depleted ρ0 counterparts grown in culture and as tumor xenografts in immune-deficient mice. Results Cultured A549 ρ0 cells were respiration-deficient and showed enhanced levels of transcripts relevant to metal homeostasis, initiation of the epithelial-mesenchymal transition, and glucuronidation pathways. Several well-established HIF-regulated transcripts showed increased or decreased abundance relative to the parental cell line. Furthermore, growth in culture versus xenograft has a significantly greater influence on expression profiles, including transcripts involved in mitochondrial structure and both aerobic and anaerobic energy metabolism. However, both in vitro and in vivo, mtDNA levels explained the majority of the variance observed in the expression of transcripts in glucuronidation, tRNA synthetase, and immune surveillance related pathways. mtDNA levels in A549 xenografts also affected the expression of genes, such as AMACR and PHYH, involved in peroxisomal lipid metabolic pathways. Conclusion We have identified mtDNA-dependent gene expression profiles that are shared in cultured cells and in xenografts. These profiles indicate that mtDNA-depleted cells could provide informative model systems for the testing the efficacy of select classes of therapeutics, such as anti-angiogenesis agents. Furthermore, mtDNA-depleted cells grown culture and in xenografts provide a powerful means to investigate possible relationships between mitochondrial activity and gene expression profiles in normal and pathological cells.

  9. On genus expansion of superpolynomials

    Energy Technology Data Exchange (ETDEWEB)

    Mironov, Andrei, E-mail: mironov@itep.ru [Lebedev Physics Institute, Moscow 119991 (Russian Federation); ITEP, Moscow 117218 (Russian Federation); National Research Nuclear University MEPhI, Moscow 115409 (Russian Federation); Morozov, Alexei, E-mail: morozov@itep.ru [ITEP, Moscow 117218 (Russian Federation); National Research Nuclear University MEPhI, Moscow 115409 (Russian Federation); Sleptsov, Alexei, E-mail: sleptsov@itep.ru [ITEP, Moscow 117218 (Russian Federation); Laboratory of Quantum Topology, Chelyabinsk State University, Chelyabinsk 454001 (Russian Federation); KdVI, University of Amsterdam (Netherlands); Smirnov, Andrey, E-mail: asmirnov@math.columbia.edu [ITEP, Moscow 117218 (Russian Federation); Columbia University, Department of Mathematics, New York (United States)

    2014-12-15

    Recently it was shown that the (Ooguri–Vafa) generating function of HOMFLY polynomials is the Hurwitz partition function, i.e. that the dependence of the HOMFLY polynomials on representation R is naturally captured by symmetric group characters (cut-and-join eigenvalues). The genus expansion and expansion through Vassiliev invariants explicitly demonstrate this phenomenon. In the present paper we claim that the superpolynomials are not functions of such a type: symmetric group characters do not provide an adequate linear basis for their expansions. Deformation to superpolynomials is, however, straightforward in the multiplicative basis: the Casimir operators are β-deformed to Hamiltonians of the Calogero–Moser–Sutherland system. Applying this trick to the genus and Vassiliev expansions, we observe that the deformation is fully straightforward only for the thin knots. Beyond the family of thin knots additional algebraically independent terms appear in the Vassiliev and genus expansions. This can suggest that the superpolynomials do in fact contain more information about knots than the colored HOMFLY and Kauffman polynomials. However, even for the thin knots the beta-deformation is non-innocent: already in the simplest examples it seems inconsistent with the positivity of colored superpolynomials in non-(anti)symmetric representations, which also happens in I. Cherednik's (DAHA-based) approach to the torus knots.

  10. Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system.

    Science.gov (United States)

    Yen, Hsiu-Chuan; Li, Shiue-Li; Hsu, Wei-Chien; Tang, Petrus

    2014-01-01

    High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detecting human mtDNA variants and found that its performance was slightly better than that of denaturing high-performance liquid chromatography (DHPLC). The potential interference from co-amplified NUMTs on screening mtDNA heteroplasmy when using these 2 highly sensitive techniques was further examined by using 2 published primer sets containing a total of 65 primer pairs, which were originally designed to be used with one of the 2 techniques. We confirmed that 24 primer pairs could amplify NUMTs by conducting bioinformatic analysis and PCR with the DNA from 143B-ρ0 cells. Using mtDNA extracted from the mitochondria of human 143B cells and a cybrid line with the nuclear background of 143B-ρ0 cells, we demonstrated that NUMTs could affect the patterns of chromatograms for cell DNA during SN-WAVE/HS analysis of mtDNA, leading to incorrect judgment of mtDNA homoplasmy or heteroplasmy status. However, we observed such interference only in 2 of 24 primer pairs selected, and did not observe such effects during DHPLC analysis. These results indicate that NUMTs can affect the screening of low-level mtDNA variants, but it might not be predicted by bioinformatic analysis or the amplification of DNA from 143B-ρ0 cells. Therefore, using purified mtDNA from cultured cells with proven purity to evaluate the effects of NUMTs from a primer pair on mtDNA detection by using PCR-based high-sensitivity methods prior to the use of a primer pair in real studies would be a more practical strategy.

  11. Low thermal expansion glass ceramics

    CERN Document Server

    1995-01-01

    This book is one of a series reporting on international research and development activities conducted by the Schott group of companies With the series, Schott aims to provide an overview of its activities for scientists, engineers, and managers from all branches of industry worldwide where glasses and glass ceramics are of interest Each volume begins with a chapter providing a general idea of the current problems, results, and trends relating to the subjects treated This volume describes the fundamental principles, the manufacturing process, and applications of low thermal expansion glass ceramics The composition, structure, and stability of polycrystalline materials having a low thermal expansion are described, and it is shown how low thermal expansion glass ceramics can be manufactured from appropriately chosen glass compositions Examples illustrate the formation of this type of glass ceramic by utilizing normal production processes together with controlled crystallization Thus glass ceramics with thermal c...

  12. Thermal Expansion of Hafnium Carbide

    Science.gov (United States)

    Grisaffe, Salvatore J.

    1960-01-01

    Since hafnium carbide (HfC) has a melting point of 7029 deg. F, it may have many high-temperature applications. A literature search uncovered very little information about the properties of HfC, and so a program was initiated at the Lewis Research Center to determine some of the physical properties of this material. This note presents the results of the thermal expansion investigation. The thermal-expansion measurements were made with a Gaertner dilatation interferometer calibrated to an accuracy of +/- 1 deg. F. This device indicates expansion by the movement of fringes produced by the cancellation and reinforcement of fixed wave-length light rays which are reflected from the surfaces of two parallel quartz glass disks. The test specimens which separate these disks are three small cones, each approximately 0.20 in. high.

  13. Low Thermal Expansion Glass Ceramics

    CERN Document Server

    Bach, Hans

    2005-01-01

    This book appears in the authoritative series reporting the international research and development activities conducted by the Schott group of companies. This series provides an overview of Schott's activities for scientists, engineers, and managers from all branches of industry worldwide in which glasses and glass ceramics are of interest. Each volume begins with a chapter providing a general idea of the current problems, results, and trends relating to the subjects treated. This new extended edition describes the fundamental principles, the manufacturing process, and applications of low thermal expansion glass ceramics. The composition, structure, and stability of polycrystalline materials having a low thermal expansion are described, and it is shown how low thermal expansion glass ceramics can be manufactured from appropriately chosen glass compositions. Examples illustrate the formation of this type of glass ceramic by utilizing normal production processes together with controlled crystallization. Thus g...

  14. Shrub expansion in SW Greenland

    DEFF Research Database (Denmark)

    Jørgensen, Rasmus Halfdan

    Arctic regions have experienced higher temperatures in recent decades, and the warming trend is projected to continue in the coming years. Arctic ecosystems are considered to be particularly vulnerable to climate change. Expansion of shrubs has been observed widely in tundra areas across the Arctic......, and has a range of ecosystem effects where it occurs. Shrub expansion has to a large extend been attributed to increasing temperatures over the past century, while grazing and human disturbance have received less attention. Alnus viridis ssp. crispa is a common arctic species that contributes...... information on changes in shrub cover, and a long and complex land use history has to be taken into account. In this thesis a combination of descriptive and experimental approaches are used to investigate: I. Whether landscape scale shrub expansion occurred in SW Greenland, and to what extend it is influenced...

  15. Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, J.V.; Cevario, S.; O`Brien, S.J. [National Cancer Institute, Frederick, MD (United States)

    1996-04-15

    The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motifs at opposite ends of the control region contribute to the relatively large size (1559 bp) of this carnivore mtDNA. Alignment of the feline mtDNA genome to a homologous 7946-bp nuclear mtDNA tandem repeat DNA sequence in the cat, Numt, indicates simple repeat motifs associated with insertion/deletion mutations. Overall DNA sequence divergence between Numt and cytoplasmic mtDNA sequence was only 5.1%. Substitutions predominate at the third codon position of homologous feline protein genes. Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species. 86 refs., 4 figs., 3 tabs.

  16. Congenital encephalomyopathy and adult-onset myopathy and diabetes mellitus: Different phenotypic associations of a new heteroplasmic mtDNA tRNA glutamic acid mutation

    Energy Technology Data Exchange (ETDEWEB)

    Hanna, M.G.; Nelson, I.; Sweeney, M.G.; Cooper, J.M.; Watkins, P.J.; Morgan-Hughes, J.A.; Harding, A.E. [Kings College Hospital, London (United Kingdom)

    1995-05-01

    We report the clinical, biochemical, and molecular genetic findings in a family with an unusual mitochondrial disease phenotype harboring a novel mtDNA tRNA glutamic acid mutation at position 14709. The proband and his sister presented with congenital myopathy and mental retardation and subsequently developed cerebellar ataxia. Other family members had either adult-onset diabetes mellitus with muscle weakness or adult-onset diabetes mellitus alone. Ragged-red and cytochrome c oxidase (COX)-negative fibers were present in muscle biopsies. Biochemical studies of muscle mitochondria showed reduced complex I and IV activities. The mtDNA mutation was heteroplasmic in blood and muscle in all matrilineal relatives analyzed. Primary myoblast, but not fibroblast, cultures containing high proportions of mutant mtDNA exhibited impaired mitochondrial translation. These observations indicate that mtDNA tRNA point mutations should be considered in the differential diagnosis of congenital myopathy. In addition they illustrate the diversity of phenotypes associated with this mutation in the same family and further highlight the association between mtDNA mutations and diabetes mellitus. 43 refs., 4 figs., 1 tab.

  17. Multipole Expansion in Generalized Electrodynamics

    CERN Document Server

    Bonin, C A; Ortega, P H

    2016-01-01

    In this article we study some classical aspects of Podolsky Electrodynamics in the static regime. We develop the multipole expansion for the theory in both the electrostatic and the magnetostatic cases. We also address the problem of consistently truncating the infinite series associated with the several kinds of multipoles, yielding approximations for the static Podolskian electromagnetic field to any degree of precision required. Moreover, we apply the general theory of multipole expansion to some specific physical problems. In those problems we identify the first terms of the series with the monopole, dipole and quadrupole terms in the generalized theory. We also propose a situation in which Podolsky theory can be experimentally tested.

  18. Properties of Ettringite Type Expansive Agent

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    By employing different forms and amounts of materials,many kinds of ettringite type expansive agents had been prepared.The relationship between the compositions and properties of expansive agents was analyzed.The design methods of expansive agent have been put forward according to the property requirement of expansive concrete.

  19. The Thermal Expansion Of Feldspars

    Science.gov (United States)

    Hovis, G. L.; Medford, A.; Conlon, M.

    2009-12-01

    Hovis and others (1) investigated the thermal expansion of natural and synthetic AlSi3 feldspars and demonstrated that the coefficient of thermal expansion (α) decreases significantly, and linearly, with increasing room-temperature volume (VRT). In all such feldspars, therefore, chemical expansion limits thermal expansion. The scope of this work now has been broadened to include plagioclase and Ba-K feldspar crystalline solutions. X-ray powder diffraction data have been collected between room temperature and 925 °C on six plagioclase specimens ranging in composition from anorthite to oligoclase. When combined with thermal expansion data for albite (2,3,4) a steep linear trend of α as a function of VRT emerges, reflecting how small changes in composition dramatically affect expansion behavior. The thermal expansion data for five synthetic Ba-K feldspars ranging in composition from 20 to 100 mole percent celsian, combined with data for pure K-feldspar (3,4), show α-VRT relationships similar in nature to the plagioclase series, but with a slope and intercept different from the latter. Taken as a group all Al2Si2 feldspars, including anorthite and celsian from the present study along with Sr- (5) and Pb-feldspar (6) from other workers, show very limited thermal expansion that, unlike AlSi3 feldspars, has little dependence on the divalent-ion (or M-) site occupant. This apparently is due to the necessitated alternation of Al and Si in the tetrahedral sites of these minerals (7), which in turn locks the tetrahedral framework and makes the M-site occupant nearly irrelevant to expansion behavior. Indeed, in feldspar series with coupled chemical substitution it is the change away from a 1:1 Al:Si ratio that gives feldspars greater freedom to expand. Overall, the relationships among α, chemical composition, and room-temperature volume provide useful predictive tools for estimating feldspar thermal expansion and give insight into the controls of expansion behavior in

  20. Removable Type Expansion Bolt Innovative Design

    Science.gov (United States)

    Wang, Feng-Lan; Zhang, Bo; Gao, Bo; Liu, Yan-Xin; Gao, Bo

    2016-05-01

    Expansion bolt is a kind of the most common things in our daily life. Currently, there are many kinds of expansion bolts in the market. However, they have some shortcomings that mainly contain underuse and unremovement but our innovation of design makes up for these shortcomings very well. Principle of working follows this: expansion tube is fixed outside of bolt, steel balls and expansion covers are fixed inside. Meanwhile, the steel balls have 120° with each other. When using it ,expansion cover is moved in the direction of its internal part. So the front part of expansion bolt cover is increasingly becoming big and steel halls is moved outside. Only in this way can it be fixed that steel balls make expansion tube expand. When removing them, expansion bolt is moved outside. So the front part of expansion bolt cover is gradually becoming small and steel balls moves inside, after expansion tube shrinks, we can detach them.

  1. Coexistence of minicircular and a highly rearranged mtDNA molecule suggests that recombination shapes mitochondrial genome organization.

    Science.gov (United States)

    Mao, Meng; Austin, Andrew D; Johnson, Norman F; Dowton, Mark

    2014-03-01

    Recombination has been proposed as a possible mechanism to explain mitochondrial (mt) gene rearrangements, although the issue of whether mtDNA recombination occurs in animals has been controversial. In this study, we sequenced the entire mt genome of the megaspilid wasp Conostigmus sp., which possessed a highly rearranged mt genome. The sequence of the A+T-rich region contained a number of different types of repeats, similar to those reported previously in the nematode Meloidogyne javanica, in which recombination was discovered. In Conostigmus, we detected the end products of recombination: a range of minicircles. However, using isolated (cloned) fragments of the A+T-rich region, we established that some of these minicircles were found to be polymerase chain reaction (PCR) artifacts. It appears that regions with repeats are prone to PCR template switching or PCR jumping. Nevertheless, there is strong evidence that one minicircle is real, as amplification primers that straddle the putative breakpoint junction produce a single strong amplicon from genomic DNA but not from the cloned A+T-rich region. The results provide support for the direct link between recombination and mt gene rearrangement. Furthermore, we developed a model of recombination which is important for our understanding of mtDNA evolution.

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

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

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

  3. Minding the gap: Frequency of indels in mtDNA control region sequence data and influence on population genetic analyses

    Science.gov (United States)

    Pearce, J.M.

    2006-01-01

    Insertions and deletions (indels) result in sequences of various lengths when homologous gene regions are compared among individuals or species. Although indels are typically phylogenetically informative, occurrence and incorporation of these characters as gaps in intraspecific population genetic data sets are rarely discussed. Moreover, the impact of gaps on estimates of fixation indices, such as FST, has not been reviewed. Here, I summarize the occurrence and population genetic signal of indels among 60 published studies that involved alignments of multiple sequences from the mitochondrial DNA (mtDNA) control region of vertebrate taxa. Among 30 studies observing indels, an average of 12% of both variable and parsimony-informative sites were composed of these sites. There was no consistent trend between levels of population differentiation and the number of gap characters in a data block. Across all studies, the average influence on estimates of ??ST was small, explaining only an additional 1.8% of among population variance (range 0.0-8.0%). Studies most likely to observe an increase in ??ST with the inclusion of gap characters were those with control region DNA appears small, dependent upon total number of variable sites in the data block, and related to species-specific characteristics and the spatial distribution of mtDNA lineages that contain indels. ?? 2006 Blackwell Publishing Ltd.

  4. Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations

    Directory of Open Access Journals (Sweden)

    Speller Camilla F

    2011-07-01

    Full Text Available Abstract Background The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis. Results By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mtDNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo, Canada goose (Branta canadensis, blue heron (Ardea herodias and pygmy owl (Glaucidium californicum. The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique. Conclusions By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.

  5. Mitochondrial DNA (mtDNA haplogroups and serum levels of anti-oxidant enzymes in patients with osteoarthritis

    Directory of Open Access Journals (Sweden)

    Fernandez-Moreno Mercedes

    2011-11-01

    Full Text Available Abstract Background Oxidative stress play a main role in the initiation and progression of the OA disease and leads to the degeneration of mitochondria. To prevent this, the chondrocytes possess a well-coordinated enzymatic antioxidant system. Besides, the mitochondrial DNA (mtDNA haplogroups are associated with the OA disease. Thus, the main goal of this work is to assess the incidence of the mtDNA haplogroups on serum levels of two of the main antioxidant enzymes, Manganese Superoxide Dismutase (Mn-SOD or SOD2 and catalase, and to test the suitability of these two proteins for potential OA-related biomarkers. Methods We analyzed the serum levels of SOD2 and catalase in 73 OA patients and 77 healthy controls carrying the haplogroups J, U and H, by ELISA assay. Knee and hip radiographs were classified according to Kellgren and Lawrence (K/L scoring from Grade 0 to Grade IV. Appropriate statistical analyses were performed to test the effects of clinical variables, including gender, body mass index (BMI, age, smoking status, diagnosis, haplogroups and radiologic K/L grade on serum levels of these enzymes. Results Serum levels of SOD2 appeared statistically increased in OA patients when compared with healthy controls (p Conclusions The increased levels of SOD2 in OA patients indicate an increased oxidative stress OA-related, therefore this antioxidant enzyme could be a suitable candidate biomarker for diagnosis of OA. Mitochondrial haplogroups significantly correlates with serum levels of catalase

  6. mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans

    Energy Technology Data Exchange (ETDEWEB)

    Torroni, A.; Schurr, T.G.; Cabell, M.F.; Wallace, D.C. (Emory Univ., Atlanta, GA (United States)); Sukernik, R.I.; Starikovskaya, Y.B. (Institute of Cytology and Genetics, Novosibirsk (Russian Federation)); Crawford, M.H.; Comuzzie, A.G. (Univ. of Kansas, Lawrence, KS (United States))

    1993-09-01

    The mtDNA variation of 411 individuals from 10 aboriginal Siberian populations was analyzed in an effort to delineate the relationships between Siberian and Native American populations. All mtDNAs were characterized by PCR amplification and restriction analysis, and a subset of them was characterized by control region sequencing. The resulting data were then compiled with previous mtDNA data from Native Americans and Asians and were used for phylogenetic analysis and sequence divergence estimations. Aboriginal Siberian populations exhibited mtDNAs from three (A, C, and D) of the four haplogroups observed in Native Americans. However, none of the Siberian populations showed mtDNAs from the fourth haplogroup, group B. The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas. These findings support the hypothesis that the first humans to move from Siberia to the Americas carried with them a limited number of founding mtDNAs and that the initial migration occurred between 17,000-34,000 years before present. 61 refs., 5 figs., 7 tabs.

  7. Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    To evaluate the gene admixture on the current genetic landscape in Gansu Corridor (GC) in China, the upper part of the ancient Silk Road which connects the Eastern and Central Asia, we examined mitochondrial DNA (mtDNA) polymorphisms of five ethnic populations in this study. Using PCR-RFLP and sequencing, we analyzed mtDNA haplotypes in 242 unrelated samples in three ethnic populations from the GC region and two ethnic populations from the adjacent Xinjiang Uygur Autonomous Region of China. We analyzed the data in comparison with the previously reported data from Eastern, Central and Western Asia and Europe. We found that both European-specific haplogroups and Eastern Asian-specific haplogroups exist in the Gansu Corridor populations, while a modest matrilineal gene flow from Europeans to this region was revealed. The Gansu Corridor populations are genetically located between Eastern Asians and Central Asians, both of who contributed significantly to the maternal lineages of the GC populations. This study made the landscape of the gene flow and admixture along the Silk Road from Europe, through Central Asia, to the upper part of the Silk Road more complete.

  8. Ancient Mtdna Sequences And Radiocarbon Dating Of Human Bones From The Chalcolithic Caves Of Wadi El-Makkukh.

    Science.gov (United States)

    Salamon, M.; Tzur, S.; Arensburg, B.; Zias, J.; Nagar, Y.; Weiner, S.; Boaretto, E.

    DNA from fossil human bones can provide valuable information for understanding intra- and inter-population relationships. Using the DNA preserved inside crystal aggregates from human fossil bones containing relatively large amounts of collagen, we demonstrate the presence of reproducible mtDNA control region sequences. Radiocarbon dates from each bone show that the burial caves were used for up to 600 years during the Chalcolithic period (5th-4th millennium BP). A comparison of the ancient DNA sequences with modern mtDNA databases indicates that all samples can most likely be assigned to the R haplogroup sub-clades, which are common in West-Eurasia. In four cases more precise and confident haplogroup identifications could be achieved (H, U3a and H6). The H haplogroup is present in three out of the four assigned ancient samples. This haplogroup is prevalent today in West - Eurasia. The results reported here tend to genetically link this Chalcolithic group of individuals to the current West Eurasian populations.

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

    Directory of Open Access Journals (Sweden)

    David Caramelli

    Full Text Available BACKGROUND: DNA sequences from ancient specimens may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal and early modern (Cro-Magnoid Europeans. METHODOLOGY/PRINCIPAL FINDINGS: We typed the mitochondrial DNA (mtDNA hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23 and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. CONCLUSIONS/SIGNIFICANCE: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.

  10. Mutation of mtDNA ND1 Gene in 20 Type 2 Diabetes Mellitus Patients of Gorontalonese and Javanese Ethnicity

    Directory of Open Access Journals (Sweden)

    AMIEN RAMADHAN ISHAK

    2014-12-01

    Full Text Available Mitochondrial gene mutation plays a role in the development of type two diabetes mellitus (T2DM. A point mutation in the mitochondrial gene Nicotinamide adenine dinucleotide dehydrogenase 1 (mtDNA ND1 gene mainly reported as the most common mutation related to T2DM. However, several studies have identified another SNP (single-nucleotide polymorphisms in the RNA region of mtDNA from patients from specific ethnic populations in Indonesia. Building on those findings, this study aimed to use PCR and DNA sequencing technology to identify nucleotides in RNA and ND1 fragment from 20 Gorontalonese and 20 Javanese T2DM patients, that may trigger T2DM expression. The results showed successful amplification of RNA along 294 bp for all samples. From these samples, we found two types of point mutation in Javanese patients in the G3316A and T3200C points of the rRNA and ND1 gene. In samples taken from Gorontalonese patients, no mutation were found in the RNA or ND1 region. We conclude that T2DM was triggered differently in our two populations. While genetic mutation is implicated for the 20 Javanese patients, T2DM pathogenesis in the Gorontalonese patients must be traced to other genetic, environmental, or behavioral factors.

  11. Response to immunotherapy in a patient with adult onset Leigh syndrome and T9176C mtDNA mutation.

    Science.gov (United States)

    Chuquilin, Miguel; Govindarajan, Raghav; Peck, Dawn; Font-Montgomery, Esperanza

    2016-09-01

    Leigh syndrome is a mitochondrial disease caused by mutations in different genes, including ATP6A for which no known therapy is available. We report a case of adult-onset Leigh syndrome with response to immunotherapy. A twenty year-old woman with baseline learning difficulties was admitted with progressive behavioral changes, diplopia, headaches, bladder incontinence, and incoordination. Brain MRI and PET scan showed T2 hyperintensity and increased uptake in bilateral basal ganglia, respectively. Autoimmune encephalitis was suspected and she received plasmapheresis with clinical improvement. She was readmitted 4 weeks later with dysphagia and aspiration pneumonia. Plasmapheresis was repeated with resolution of her symptoms. Given the multisystem involvement and suggestive MRI changes, genetic testing was done, revealing a homoplasmic T9176C ATPase 6 gene mtDNA mutation. Monthly IVIG provided clinical improvement with worsening when infusions were delayed. Leigh syndrome secondary to mtDNA T9176C mutations could have an autoimmune mechanism that responds to immunotherapy. PMID:27408822

  12. The bootstrap and edgeworth expansion

    CERN Document Server

    Hall, Peter

    1992-01-01

    This monograph addresses two quite different topics, in the belief that each can shed light on the other. Firstly, it lays the foundation for a particular view of the bootstrap. Secondly, it gives an account of Edgeworth expansion. Chapter 1 is about the bootstrap, witih almost no mention of Edgeworth expansion; Chapter 2 is about Edgeworth expansion, with scarcely a word about the bootstrap; and Chapters 3 and 4 bring these two themes together, using Edgeworth expansion to explore and develop the properites of the bootstrap. The book is aimed a a graduate level audience who has some exposure to the methods of theoretical statistics. However, technical details are delayed until the last chapter (entitled "Details of Mathematical Rogour"), and so a mathematically able reader without knowledge of the rigorous theory of probability will have no trouble understanding the first four-fifths of the book. The book simultaneously fills two gaps in the literature; it provides a very readable graduate level account of t...

  13. On persistently positively expansive maps

    Directory of Open Access Journals (Sweden)

    Alexander Arbieto

    2010-06-01

    Full Text Available In this paper, we prove that any C¹-persistently positively expansive map is expanding. This improves a result due to Sakai (Sakai 2004.Neste artigo, mostramos que todo mapa C¹-persistentemente positivamente expansivo e expansor. Isto melhora um resultado devido a Sakai (Sakai 2004.

  14. Series expansions and sudden singularities

    CERN Document Server

    Barrow, John D; Tsokaros, A

    2013-01-01

    We construct solutions of the Friedmann equations near a sudden singularity using generalized series expansions for the scale factor, the density, and the pressure of the fluid content. In this way, we are able to arrive at a solution with a sudden singularity containing two free constants, as required for a general solution of the cosmological equations.

  15. Phylogeography of the common vampire bat (Desmodus rotundus: Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

    Directory of Open Access Journals (Sweden)

    Morgante João S

    2009-12-01

    Full Text Available Abstract Background The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA marker and two nuclear markers (RAG2 and DRB to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat. Results Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA, Amazon and Cerrado (AMC, Pantanal (PAN, Northern Atlantic Forest (NAF and Southern Atlantic Forest (SAF. The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar. Conclusions We therefore conclude that the pattern exhibited by the common vampire bat, with marked

  16. Phylogenetic Relationship of Duttaphrynus melanostictus From India and China as Revealed from the Study of 12S and 16S mtDNA Genes

    Directory of Open Access Journals (Sweden)

    Sanjib Kr. Das

    2013-01-01

    Full Text Available In the present study, the phylogenetic relationship of Duttaphrynus melanostictus from West Bengal, India with other members of the Bufonidiae group was undertaken using partial mitochondrial DNA (mtDNA genes. Mitochondria were isolated from the liver of Duttaphrynus melanostictus by a non-conventional method of membrane filtration. The technique allows trapping of mitochondria on cellulose acetate membrane followed by mtDNA isolation. 12S ribosomal RNA and 16S ribosomal RNA was sequenced with primers designed in our laboratory. mtDNA sequence from 18 different Bufo sp. found across the world were used for the phylogenetic analysis. Results were interpreted from the transition/transversion of nucleotides, genetic distance and maximum parsimony analysis. The findings indicates that D. melanostictus is very closely related to the Bufo melanostictus of China. The possible reasons of such close similarity between two distantly residing species (D. melanostictus of India and Bufo melanostictus of China have been discussed.

  17. Effective Expansion: Balance between Shrinkage and Hygroscopic Expansion.

    Science.gov (United States)

    Suiter, E A; Watson, L E; Tantbirojn, D; Lou, J S B; Versluis, A

    2016-05-01

    The purpose of this study was to investigate the relationship between hygroscopic expansion and polymerization shrinkage for compensation of polymerization shrinkage stresses in a restored tooth. One resin-modified glass-ionomer (RMGI) (Ketac Nano, 3M ESPE), 2 compomers (Dyract, Dentsply; Compoglass, Ivoclar), and a universal resin-based composite (Esthet•X HD, Dentsply) were tested. Volumetric change after polymerization ("total shrinkage") and during 4 wk of water storage at 37°C was measured using an optical method (n= 10). Post-gel shrinkage was measured during polymerization using a strain gauge method (n= 10). Extracted human molars with large mesio-occluso-distal slot preparations were restored with the tested restorative materials. Tooth surfaces at baseline (preparation), after restoration, and during 4 wk of 37°C water storage were scanned with an optical scanner to determine cuspal flexure (n= 8). Occlusal interface integrity was measured using dye penetration. Data were analyzed using analysis of variance and post hoc tests (significance level 0.05). All tested materials shrunk after polymerization. RMGI had the highest total shrinkage (4.65%) but lowest post-gel shrinkage (0.35%). Shrinkage values dropped significantly during storage in water but had not completely compensated polymerization shrinkage after 4 wk. All restored teeth initially exhibited inward (negative) cuspal flexure due to polymerization shrinkage. Cuspal flexure with the RMGI restoration was significantly less (-6.4 µm) than with the other materials (-12.1 to -14.1 µm). After 1 d, cuspal flexure reversed to +5.0 µm cuspal expansion with the RMGI and increased to +9.3 µm at 4 wk. After 4 wk, hygroscopic expansion compensated cuspal flexure in a compomer (Compoglass) and reduced flexure with Dyract and resin-based composite. Marginal integrity (93.7% intact restoration wall) was best for the Compoglass restorations and lowest (73.1%) for the RMGI restorations. Hygroscopic

  18. Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature.

    Science.gov (United States)

    Arnason, U; Gullberg, A

    1993-10-01

    The sequence of the mitochondrial DNA (mtDNA) molecule of the blue whale (Balaenoptera musculus) was determined. The molecule is 16,402 bp long and its organization conforms with that of other eutherian mammals. The molecule was compared with the mtDNA of the congeneric fin whale (B. physalus). It was recently documented that the two species can hybridize and that male offspring are infertile whereas female offspring may be fertile. The present comparison made it possible to determine the degree of mtDNA difference that occurs between two species that are not completely separated by hybridization incompatibility. The difference between the complete mtDNA sequences was 7.4%. Lengths of peptide coding genes were the same in both species. Except for a small portion of the control region, disruption in alignment was usually limited to insertion/deletion of a single nucleotide. Nucleotide differences between peptide coding genes ranged from 7.1 to 10.5%, and difference at the inferred amino acid level was 0.0-7.9%. In the rRNA genes the mean transition difference was 3.8%. This figure is similar in degree to the difference (3.4%) between the 12S rRNA gene of humans and the chimpanzee. The mtDNA differences between the two whale species, involving both peptide coding and rRNA genes, suggest an evolutionary separation of > or = 5 million years. Although hybridization between more distantly related mammalian species may not be excluded, it is probable that the blue and fin whales are nearly as different in their mtDNA sequences as hybridizing mammal species may be. PMID:8308901

  19. High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation.

    Science.gov (United States)

    Piwczyński, M; Pabijan, M; Grzywacz, A; Glinkowski, W; Bereś, P K; Buszko, J

    2016-08-01

    The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation. PMID:27019346

  20. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

    Science.gov (United States)

    Li, Mingkun; Rothwell, Rebecca; Vermaat, Martijn; Wachsmuth, Manja; Schröder, Roland; Laros, Jeroen F.J.; van Oven, Mannis; de Bakker, Paul I.W.; Bovenberg, Jasper A.; van Duijn, Cornelia M.; van Ommen, Gert-Jan B.; Slagboom, P. Eline; Swertz, Morris A.; Wijmenga, Cisca; Kayser, Manfred; Boomsma, Dorret I.; Zöllner, Sebastian; de Knijff, Peter; Stoneking, Mark

    2016-01-01

    Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies. PMID:26916109

  1. The role of mtDNA background in disease expression: a new primary LHON mutation associated with Western Eurasian haplogroup J.

    Science.gov (United States)

    Brown, Michael D; Starikovskaya, Elena; Derbeneva, Olga; Hosseini, Seyed; Allen, Jon C; Mikhailovskaya, Irina E; Sukernik, Rem I; Wallace, Douglas C

    2002-02-01

    Leber's hereditary optic neuropathy (LHON) is a maternally transmitted form of blindness caused by mitochondrial DNA (mtDNA) mutations. Approximately 90% of LHON cases are caused by 3460A, 11778A, or 14484C mtDNA mutations. These are designated "primary" mutations because they impart a high risk for LHON expression. Although the 11778A and 14484C mutations unequivocally predispose carriers to LHON, they are preferentially associated with mtDNA haplogroup J, one of nine Western Eurasian mtDNA lineages, suggesting a synergistic and deleterious interaction between these LHON mutations and haplogroup J polymorphism(s). We report here the characterization of a new primary LHON mutation in the mtDNA ND4L gene at nucleotide pair 10663. The homoplasmic 10663C mutation has been found in three independent LHON patients who lack a known primary mutation and all of which belong to haplogroup J. This mutation has not been found in a large number of haplotype-matched or non-haplogroup-J control mtDNAs. Phylogenetic analysis with primarily complete mtDNA sequence data demonstrates that the 10663C mutation has arisen at least three independent times in haplogroup J, indicating that it is not a rare lineage-specific polymorphism. Analysis of complex I function in patient lymphoblasts and transmitochondrial cybrids has revealed a partial complex I defect similar in magnitude to the 14484C mutation. Thus, the 10663C mutation appears to be a new primary LHON mutation that is pathogenic when co-occurring with haplogroup J. These results strongly support a role for haplogroup J in the expression of certain LHON mutations.

  2. Transcription from the second heavy-strand promoter of human mtDNA is repressed by transcription factor A in vitro

    OpenAIRE

    Lodeiro, Maria F.; Uchida, Akira; Bestwick, Megan; Moustafa, Ibrahim M.; Arnold, Jamie J.; Shadel, Gerald S.; Cameron, Craig E.

    2012-01-01

    Cell-based studies support the existence of two promoters on the heavy strand of mtDNA: heavy-strand promoter 1 (HSP1) and HSP2. However, transcription from HSP2 has been reported only once in a cell-free system, and never when recombinant proteins have been used. Here, we document transcription from HSP2 using an in vitro system of defined composition. An oligonucleotide template representing positions 596–685 of mtDNA was sufficient to observe transcription by the human mtRNA polymerase (PO...

  3. Exponential Expansion in Evolutionary Economics

    DEFF Research Database (Denmark)

    Frederiksen, Peter; Jagtfelt, Tue

    2013-01-01

    concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light......This article attempts to solve current problems of conceptual fragmentation within the field of evolutionary economics. One of the problems, as noted by a number of observers, is that the field suffers from an assemblage of fragmented and scattered concepts (Boschma and Martin 2010). A solution...... to this problem is proposed in the form of a model of exponential expansion. The model outlines the overall structure and function of the economy as exponential expansion. The pictographic model describes four axiomatic concepts and their exponential nature. The interactive, directional, emerging and expanding...

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

    Directory of Open Access Journals (Sweden)

    Finnilä Saara

    2010-05-01

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

  5. Relationship Development in Greenfield Expansions

    DEFF Research Database (Denmark)

    Drogendijk, Rian; Andersson, Ulf

    2013-01-01

    This paper investigates conceptually how new Greenfield subsidiaries develop relationships over time. We focus our analysis on the earliest start-up stage of new Greenfield subsidiaries, and on the dynamics of relationships development with five different groups of actors within the MNC and the l...... dependency theory and network approaches. In the concluding sections we suggest directions for future work to enhance understanding of the dynamics of relationship management in new Greenfield expansions....

  6. RELIABILITY OF LENTICULAR EXPANSION COMPENSATORS

    Directory of Open Access Journals (Sweden)

    Gabriel BURLACU,

    2011-11-01

    Full Text Available Axial lenticular compensators are made to take over the longitudinal heat expansion, shock , vibration and noise, made elastic connections for piping systems. In order to have a long life for installations it is necessary that all elements, including lenticular compensators, have a good reliability. This desire can be did by technology of manufactoring and assembly of compensators, the material for lenses and by maintenance.of compensator

  7. Topological expansion and boundary conditions

    CERN Document Server

    Eynard, Bertrand

    2008-01-01

    In this article, we compute the topological expansion of all possible mixed-traces in a hermitian two matrix model. In other words we give a recipe to compute the number of discrete surfaces of given genus, carrying an Ising model, and with all possible given boundary conditions. The method is recursive, and amounts to recursively cutting surfaces along interfaces. The result is best represented in a diagrammatic way, and is thus rather simple to use.

  8. Multiscale expansions in discrete world

    Indian Academy of Sciences (India)

    Ömer Ünsal; Filiz Taşcan; Mehmet Naci Özer

    2014-07-01

    In this paper, we show the attainability of KdV equation from some types of nonlinear Schrödinger equation by using multiscale expansions discretely. The power of this manageable method is confirmed by applying it to two selected nonlinear Schrödinger evolution equations. This approach can also be applied to other nonlinear discrete evolution equations. All the computations have been made with Maple computer packet program.

  9. Clinical grade expansion of MSCs.

    Science.gov (United States)

    Capelli, C; Pedrini, O; Valgardsdottir, R; Da Roit, F; Golay, J; Introna, M

    2015-12-01

    Producing advanced therapy medicinal products (ATMP) according to Good Manufacturing Practice (GMP) guidelines represents a global challenge for the expansion of cells intended for human use. Mesenchymal stromal cells (MSCs) from different sources are one of the most actively developed cell type for a variety of clinical applications in cellular therapy. Complying with GMP means defining accurately both the production process and the release criteria required for a final safe product. We have here reported our manufacturing experience on 103 consecutive clinical-grade in vitro expansions of both bone marrow-derived and umbilical cord-derived mesenchymal stromal cells together with description of methods and reagents utilized in our Cell Factory. The same animal- and serum-free medium, additioned with human platelet lysate, has been used for all the expansions performed. This is the largest experience published so far with this alternative and clinical-grade reagent (compared to the traditional fetal bovine serum) and shows the feasibility and the reproducibility of the method. Indeed, we have been able to produce a sufficient number of MSCs to treat 57 patients so far, enrolled in 7 different experimental phase I/II protocols. PMID:26092523

  10. Preparation and Expansion Properties Analysis of C60 Expansive Self-compacting Concrete

    Directory of Open Access Journals (Sweden)

    Jia Li-li

    2016-01-01

    Full Text Available Concrete Design of concrete filled steel tube should not only meet the requirements of self-compacting, but also need suitable expansion properties. On the basis of working performance requirement, study impact of expansive agent on concrete working performance, strength and expansion properties, preparation of C60 concrete filled steel to meet the self-compacting and expansion properties. Expander should not be too much, otherwise working performance and strength will be affected. Meanwhile study the correlation between restrained expansion and free expansion of expansive concrete, and analyze the mechanism of expansive concrete.

  11. 78 FR 36165 - Reorganization/Expansion of Foreign-Trade Zone 104; (Expansion of Service Area and Expansion of...

    Science.gov (United States)

    2013-06-17

    ... Federal Register (77 FR 43047, 07/23/12) and the application has been processed pursuant to the FTZ Act... Foreign-Trade Zones Board Reorganization/Expansion of Foreign-Trade Zone 104; (Expansion of Service Area and Expansion of Zone); Under Alternative Site Framework, Savannah, Georgia Pursuant to its...

  12. High penetrance of sequencing errors and interpretative shortcomings in mtDNA sequence analysis of LHON patients.

    Science.gov (United States)

    Bandelt, Hans-Jürgen; Yao, Yong-Gang; Salas, Antonio; Kivisild, Toomas; Bravi, Claudio M

    2007-01-12

    For identifying mutation(s) that are potentially pathogenic it is essential to determine the entire mitochondrial DNA (mtDNA) sequences from patients suffering from a particular mitochondrial disease, such as Leber hereditary optic neuropathy (LHON). However, such sequencing efforts can, in the worst case, be riddled with errors by imposing phantom mutations or misreporting variant nucleotides, and moreover, by inadvertently regarding some mutations as novel and pathogenic, which are actually known to define minor haplogroups. Under such circumstances it remains unclear whether the disease-associated mutations would have been determined adequately. Here, we re-analyse four problematic LHON studies and propose guidelines by which some of the pitfalls could be avoided.

  13. Previously Unclassified Mutation of mtDNA m.3472T>C: Evidence of Pathogenicity in Leber's Hereditary Optic Neuropathy.

    Science.gov (United States)

    Sheremet, N L; Nevinitsyna, T A; Zhorzholadze, N V; Ronzina, I A; Itkis, Y S; Krylova, T D; Tsygankova, P G; Malakhova, V A; Zakharova, E Y; Tokarchuk, A V; Panteleeva, A A; Karger, E M; Lyamzaev, K G; Avetisov, S E

    2016-07-01

    Leber's hereditary optic neuropathy (LHON) refers to a group of mitochondrial diseases and is characterized by defects of the mitochondrial electron transport chain and decreased level of oxidative phosphorylation. The list of LHON primary mtDNA mutations is regularly updated. In this study, we describe the homoplasmic nucleotide substitution m.3472T>C in the MT-ND1 (NADH-ubiquinone oxidoreductase chain 1) gene and specific changes in cell metabolism in a patient with LHON and his asymptomatic sister. To confirm the presence of mutation-related mitochondrial dysfunction, respiration of skin fibroblasts and platelets from the patient and his sister was studied, as well as the mitochondrial potential and production of reactive oxygen species in the skin fibroblasts. In addition, based on characteristics of the toxic effect of paraquat, a new approach was developed for detecting the functional activity of complex I of the mitochondrial respiratory chain.

  14. Strict sex-specific mtDNA segregation in the germ line of the DUI species Venerupis philippinarum (Bivalvia: Veneridae).

    Science.gov (United States)

    Ghiselli, Fabrizio; Milani, Liliana; Passamonti, Marco

    2011-02-01

    Doubly Uniparental Inheritance (DUI) is one of the most striking exceptions to the common rule of standard maternal inheritance of metazoan mitochondria. In DUI, two mitochondrial genomes are present, showing different transmission routes, one through eggs (F-type) and the other through sperm (M-type). In this paper, we report results from a multiplex real-time quantitative polymerase chain reaction analysis on the Manila clam Venerupis philippinarum (formerly Tapes philippinarum). We quantified M- and F-types in somatic tissues, gonads, and gametes. Nuclear and external reference sequences were used, and the whole experimental process was designed to avoid any possible cross-contamination. In most male somatic tissues, the M-type is largely predominant: This suggests that the processes separating sex-linked mitochondrial DNAs (mtDNAs) in somatic tissues are less precise than in other DUI species. In the germ line, we evidenced a strict sex-specific mtDNA segregation because both sperm and eggs do carry exclusively M- and F-types, respectively, an observation that is in contrast with a previous analysis on Mytilus galloprovincialis. More precisely, whereas two mtDNAs are present in the whole gonad, only the sex-specific one is detected in gametes. Because of this, we propose that the mtDNA transmission is achieved through a three-checkpoint process in V. philippinarum. The cytological mechanisms of male mitochondria segregation in males and degradation in females during the embryo development (here named Checkpoint #1 and Checkpoint #2) are already well known for DUI species; a Checkpoint #3 would act when primordial germ cells (PGCs) are first formed and would work in both males and females. We believe that Checkpoint #3 is a mere variation of the "mitochondrial bottleneck" in species with standard maternal inheritance, established when their PGCs separate during embryo cleavage.

  15. Low mtDNA diversity among widespread Australian diamondback moth Plutella xylostella (L.) suggests isolation and a founder effect

    Institute of Scientific and Technical Information of China (English)

    JESSLYN SAW; NANCY M. ENDERSBY; STEPHEN W. MCKECHNIE

    2006-01-01

    Populations of Australian diamondback moth (DBM) Plutella xylostella (L.), a serious pest of cruciferous crops, display extremely low levels of genetic differentiation across Australia and New Zealand sample locations, as determined previously using microsatellite markers. These data suggest high levels of contemporary gene flow that is consistent with Australian DBM being a vagile species. Here we examine Australian DBM samples for haplotype variation using the mitochondrial DNA sequences of a 257 bp fragment of the CO1 gene. We compare this variation to equivalent mtDNA sequence variation in samples from New Zealand, Kenya and Korea. Using 42 moths collected throughout Australia we show that Australian DBM have both low mtDNA haplotype and nucleotide diversities. The three Australian haplotypes detected are closely related and they cluster with the common haplotype group from Indonesia. In addition the Australian haplotype frequency distribution resembled more that from Indonesia than that from Kenya or Korea. These data are consistent with an original strong Australian/New Zealand founder effect, from a south-eastern Asian source, with subsequent continued isolation. In a single season, the frequency of PXMt01, the most common Australian haplotype, was estimated at 15 locations spread across southern Australia and New Zealand using a polymerase chain reaction BiPASA method. The PXMt01 haplotype frequency variation was heterogenous,suggesting a small degree of population isolation that was not detected using microsatellites.Differentiation was not a function of geographical distance. These data suggest transient and sporadic local colonisation events by small numbers of founding females.

  16. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

    DEFF Research Database (Denmark)

    Li, Shengting; Besenbacher, Søren; Li, Yingrui;

    2014-01-01

    In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise...

  17. Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data

    DEFF Research Database (Denmark)

    Pinto, M Alice; Henriques, Dora; Chávez-Galarza, Julio;

    2014-01-01

    to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data from the tRNAleu-cox2 intergenic mtDNA region and a genome-wide scan, with over 1183 single nucleotide...

  18. Increased genetic diversity in Greek populations of the genus Ligidium (Crustacea: Isopoda: Oniscidea) revealed by RFLP analysis of mtDNA segments

    NARCIS (Netherlands)

    Klossa-Kilia, E.; Kilias, G.; Sfenthourakis, S.

    2005-01-01

    We investigated mtDNA genetic differentiation and the phylogenetic relationships of 11 populations of the oniscidean genus Ligidium. We studied nine populations from Greece, assigned to three nominal species (L. euboicum, L. germanicum and L. beieri), and two from central Europe (L. germanicum and L

  19. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and non-random loss

    Energy Technology Data Exchange (ETDEWEB)

    Lavrov, Dennis V.; Boore, Jeffrey L.; Brown, Wesley M.

    2001-11-08

    We determined the complete mtDNA sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified in both genomes all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from that inferred to be ancestral for arthropods by the location of four genes/gene clusters. This novel gene arrangement is unusual for animal mtDNA, in that genes with opposite transcriptional polarities are clustered in the genome and the two clusters are separated by two non-coding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.

  20. Identification of West Eurasian mitochondrial haplogroups by mtDNA SNP screening: results of the 2006-2007 EDNAP collaborative exercise

    DEFF Research Database (Denmark)

    Parson, Walther; Fendt, Liane; Ballard, David;

    2008-01-01

    The European DNA Profiling (EDNAP) Group performed a collaborative exercise on a mitochondrial (mt) DNA screening assay that targeted 16 nucleotide positions in the coding region and allowed for the discrimination of major west Eurasian mtDNA haplogroups. The purpose of the exercise was to evalua...

  1. Computer Aided Series Expansions for Critical Phenomena

    CERN Document Server

    Meyer-Ortmanns, H; Meyer-Ortmanns, Hildegard; Reisz, Thomas

    1996-01-01

    Under quite general conditions critical phenomena can be described with high order linked cluster expansions. The coefficients of the series admit a graphical expansion that is generated with the aid of computers. Our generalization of linked cluster expansions from an infinite to a finite volume allows to perform a finite size scaling analysis. We also indicate a generalization to Dynamical Linked Cluster Expansions with possible applications to spin glasses and neural networks with coupled spin and interaction dynamics.

  2. An All-Orders Derivative Expansion

    OpenAIRE

    Dunne, Gerald(Department of Physics, University of Connecticut, Storrs, CT, 06269, U.S.A.)

    1996-01-01

    We evaluate the exact $QED_{2+1}$ effective action for fermions in the presence of a family of static but spatially inhomogeneous magnetic field profiles. This exact result yields an all-orders derivative expansion of the effective action, and indicates that the derivative expansion is an asymptotic, rather than a convergent, expansion.

  3. Multiplier theorems for special Hermite expansions on

    Institute of Scientific and Technical Information of China (English)

    张震球; 郑维行

    2000-01-01

    The weak type (1,1) estimate for special Hermite expansions on Cn is proved by using the Calderon-Zygmund decomposition. Then the multiplier theorem in Lp(1 < p < ω ) is obtained. The special Hermite expansions in twisted Hardy space are also considered. As an application, the multipli-ers for a certain kind of Laguerre expansions are given in Lp space.

  4. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Science.gov (United States)

    Milá, Borja; Tavares, Erika S; Muñoz Saldaña, Alberto; Karubian, Jordan; Smith, Thomas B; Baker, Allan J

    2012-01-01

    The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys

  5. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Directory of Open Access Journals (Sweden)

    Borja Milá

    Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

  6. Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecologically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila.

    Directory of Open Access Journals (Sweden)

    Sergei V Drovetski

    Full Text Available Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early-Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris with respect to the Temminck's lark (E. bilopha. In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.

  7. Gravitational entropy of cosmic expansion

    CERN Document Server

    Sussman, Roberto A

    2014-01-01

    We apply a recent proposal to define "gravitational entropy" to the expansion of cosmic voids within the framework of non-perturbative General Relativity. By considering CDM void configurations compatible with basic observational constraints, we show that this entropy grows from post-inflationary conditions towards a final asymptotic value in a late time fully non-linear regime described by the Lemaitre-Tolman-Bondi (LTB) dust models. A qualitatively analogous behavior occurs if we assume a positive cosmological constant consistent with a $\\Lambda$-CDM background model. However, the $\\Lambda$ term introduces a significant suppression of entropy growth with the terminal equilibrium value reached at a much faster rate.

  8. Contribution of thermal expansion and

    Directory of Open Access Journals (Sweden)

    O.I.Pursky

    2007-01-01

    Full Text Available A theoretical model is developed to describe the experimental results obtained for the isobaric thermal conductivity of rare gas solids (RGS. The isobaric thermal conductivity of RGS has been analysed within Debye approximation with regard to the effect of thermal expansion. The suggested model takes into consideration the fact that thermal conductivity is determined by U-processes while above the phonon mobility edge it is determined by "diffusive" modes migrating randomly from site to site. The mobility edge ω0 is determined from the condition that the phonon mean-free path restricted by the U-processes cannot be smaller than half of the phonon wavelength.

  9. Cosmic Growth and Expansion Conjoined

    CERN Document Server

    Linder, Eric V

    2016-01-01

    Cosmological measurements of both the expansion history and growth history have matured, and the two together provide an important test of general relativity. We consider their joint evolutionary track, showing that this has advantages in distinguishing cosmologies relative to considering them individually or at isolated redshifts. In particular, the joint comparison relaxes the shape degeneracy that makes $f\\sigma_8(z)$ curves difficult to separate from the overall growth amplitude. The conjoined method further helps visualization of which combinations of redshift ranges provide the clearest discrimination. We examine standard dark energy cosmologies, modified gravity, and "stuttering" growth, each showing distinct signatures.

  10. Gyrification from constrained cortical expansion

    CERN Document Server

    Tallinen, Tuomas; Biggins, John S; Mahadevan, L

    2015-01-01

    The exterior of the mammalian brain - the cerebral cortex - has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated as a soft solid lead to the formation of cusped sulci and smooth gyri similar to those in the brain. The resulting gyrification patterns are a function of relative cortical expansion and relative thickness (compared with brain size), and are consistent with observations of a wide range of brains, ranging from smooth to highl...

  11. Imagination as expansion of experience.

    Science.gov (United States)

    Zittoun, Tania; Cerchia, Frédéric

    2013-09-01

    This paper proposes a developmental view on imagination: from this perspective, imagination can be seen as triggered by some disrupting event, which generates a disjunction from the person's unfolding experience of the "real" world, and as unfolding as a loop, which eventually comes back to the actual experience. Examining recent and classical theorization of imagination in psychology, the paper opposes a deficitary view of imagination to an expansive notion of imagination. The paper explores Piaget, Vygotsky, Harris and Pelaprat & Cole consider: 1) What does provoke a "rupture" or disjunction? 2) What are the psychological processes involved in the imaginary loop? 3) What nourishes such processes? 4) What are the consequences of such imaginary loop, or what does it enable doing? The paper proposes to adopt an expansive view of imagination, as Vygotsky proposed-a perspective that has been under-explored empirically since his seminal work. To stimulate such sociocultural psychology of imagination, two empirical examples are provided, one showing how children make sense of metaphor in an experimental setting, the other showing a young person using a novel met at school as symbolic resource. PMID:23625542

  12. Evolutionary expansion of the Monogenea.

    Science.gov (United States)

    Kearn, G C

    1994-12-01

    The evolutionary expansion of the monogeneans has taken place in parallel with the diversification of the fish-like vertebrates. In this article the main trends in monogenean evolution are traced from a hypothetical skin-parasitic ancestor on early vertebrates. Special consideration is given to the following topics: early divergence between skin feeders and blood feeders; diversification and specialization of the haptor for attachment to skin; transfer from host to host, viviparity and the success of the gyrodactylids; predation on skin parasites and camouflage; colonization of the buccal and branchial cavities; diversification and specialization of the haptor for attachment to the gills; phoresy in gill parasites; the development of endoparasitism and the origin of the cestodes; the success of dactylogyroidean gill parasites; the uniqueness of the polyopisthocotyleans; ovoviviparity and the colonization of the tetrapods. Host specificity has been the guiding force of coevolution between monogeneans and their vertebrate hosts, but the establishment of monogeneans on unrelated hosts sharing the same environment (host-switching) may have been underestimated. Host-switching has provided significant opportunities for evolutionary change of direction and is probably responsible for the establishment of monogeneans on cephalopod molluscs, on the hippopotamus and possibly on chelonians. There are indications that host-switching may be more common in monogeneans that spread by direct transfer of adults/juveniles from host to host. A limitation on the further expansion of monogeneans is the need for water for the dispersal of the infective larva (oncomiracidium).

  13. Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the near east and neolithic dispersals within Europe.

    Directory of Open Access Journals (Sweden)

    Anna Olivieri

    Full Text Available The current human mitochondrial (mtDNA phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.

  14. ANALYSIS ON mtDNA POLYMORPHISM OF HUMAN ECHINOCOCCOSIS IN SOUTHERN QINGHAI PLATEAU%青南高原人体棘球蚴 mtDNA 基因多态性分析

    Institute of Scientific and Technical Information of China (English)

    赵海龙; 曹得萍; 黄欣; 白海燕; 李伟; 廖博

    2015-01-01

    Objective Detection and analysis of the human Echinococcus mtDNA genotype in southern plateau of Qinghai Province.MethOds The sample were collected fromYushu,Guoluo,Hainan and Huangnan Tibetan Auton-omous Prefecture of Qinghai Province.63 cases of human hydatid isolated strains were amplified by PCR using prim-ers specific for the mitochondrial DNA(mtDNA cox Ⅰ,nad Ⅰ,Atp6 )and the mitochondrial DNA specific fragment sequence was analysed and identificated. Results 1)63 human Echinococcus granulosus isolates were common sheep strain(G1);2)Among nine genotypes there were three specific genetypes in southern Qinghai Plateau.COn-clusiOn The results of this study show that there have the general epidemiological characteristics of Echinococcus granulosus in south Qinghai area.At the same time,Echinococcus granulosus in southern Qinghai Plateau has its u-nique nucleotide variations.%目的:检测分析青南高原人体棘球蚴 mtDNA 基因型。方法对从青海玉树、果洛、海南、黄南藏族自治州收集的63个人体棘球蚴分离株,运用线粒体 DNA 的 cox Ⅰ、nad Ⅰ、atp6基因的特异性引物进行 PCR 扩增,对线粒体 DNA 特异目的片段进行序列分析鉴定。结果1)63个人体细粒棘球蚴分离株均为普通羊株(G1);2)结果所得的9个基因型中有3个为青南高原地区所特有的基因型。结论本研究结果显示青南地区细粒棘球绦虫具有广泛性和普遍性的流行病学特征;同时青南高原又存在细粒棘球绦虫独特的核苷酸变异。

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

    Directory of Open Access Journals (Sweden)

    Miao Miao

    2012-02-01

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

  16. Multiple differences in calling songs and other traits between solitary and gregarious Mormon crickets from allopatric mtDNA clades

    Directory of Open Access Journals (Sweden)

    Bailey William V

    2007-01-01

    Full Text Available Abstract Background In acoustic species, traits such as male calling song are likely to diverge quickly between allopatric populations due to sexual selection, and divergence in parameters such as carrier frequency, chirp structure, and other important song characters can influence sexual isolation. Here we make use of two forms of Mormon crickets to examine differences in a broad suite of traits that have the potential to influence speciation via sexual isolation. Mormon crickets in "gregarious" populations aggregate into dense migratory bands, and females are the sexually competitive sex (sex-role reversal. There is also a non-outbreak "solitary" form. These two forms are largely but not perfectly correlated with a significant mtDNA subdivision within the species that is thought to have arisen in allopatry. Combined information about multiple, independently evolving traits, such as morphology and structural and behavioural differences in calling song, provides greater resolution of the overall differences between these allopatric populations, and allows us to assess their stage of divergence. We test two predictions, first that the forms differ in song and second that gregarious males are more reluctant to sing than solitary males due to sex role reversal. We also tested for a difference in the relationship between the size of the forewing resonator, the mirror, and carrier frequency, as most models of sound production in crickets indicate that mirror size should predict carrier frequency. Results Multivariate analyses showed that solitary and gregarious individuals from different populations representing the two mtDNA clades had almost non-overlapping distributions based on multiple song and morphological measurements. Carrier frequency differed between the two, and gregarious males were more reluctant to sing overall. Mirror size predicted carrier frequency; however, the relationship between mirror size and surface area varied between

  17. Multiple symmetric lipomas with high levels of mtDNA with the tRNA(Lys) A-->G(8344) mutation as the only manifestation of disease in a carrier of myoclonus epilepsy and ragged-red fibers (MERRF) syndrome.

    OpenAIRE

    Holme, E; Larsson, N G; Oldfors, A; Tulinius, M; Sahlin, P; Stenman, G

    1993-01-01

    We have investigated the morphology, cytogenetics, and the fraction of mtDNA with the tRNA(Lys) A-->G(8344) mutation in three lipomas in a carrier of this mutation. The son of the patient had myoclonus epilepsy and ragged-red fibers syndrome. The fraction of mtDNA with the tRNA(Lys) mutation varied between 62% and 80% in cultured skin fibroblasts, lymphocytes, normal adipose tissue, and muscle. In the three lipomas the mean fraction of mutated mtDNA was 90%, 94%, and 94%. Ultrastructural exam...

  18. On the Equisummability of Hermite and Fourier Expansions

    Indian Academy of Sciences (India)

    E K Narayanan; S Thangavelu

    2001-02-01

    We prove an equisummability result for the Fourier expansions and Hermite expansions as well as special Hermite expansions. We also prove the uniform boundedness of the Bochner-Riesz means associated to the Hermite expansions for polyradial functions.

  19. Novel thermal expansion of lead titanate

    Institute of Scientific and Technical Information of China (English)

    XING Xianran; DENG Jinxia; CHEN Jun; LIU Guirong

    2003-01-01

    Lattice parameters of lead titanate were precisely re-determined in the ternperature range of-150-950℃ by high precision XRPD measurements. It was clarified that there was no any evidence for a new phase transition at low temperatures. Tetragonal distortion strain decreases with temperature increasing. A novel thermal expansion was observed, positive thermal expansion from-150℃ to room temperature (RT) and above 490℃, and the negative thermal expansion in the temperature range of RT-490℃. A big jump of thermal expansion coefficient is attributed to the tetragonal-cubic phase transition. A rationalization for the negative thermal expansion of PbTiO3 is due to the decrease of anion-anion repulsion as polyhedra become more regular at heating. The mechanisms of positive and negative thermal expansions were elucidated as the same nature in the homogenous tetragonal phase at present case.

  20. Perturbative quantum damping of cosmological expansion

    CERN Document Server

    Broda, Bogusław

    2013-01-01

    Perturbative quantum gravity in the framework of the Schwinger-Keldysh formalism is applied to compute lowest-order corrections to the actual expansion of the Universe described in terms of the spatially flat Friedman-Lematre-Robertson-Walker solution. The classical metric is approximated by a third order polynomial perturbation around the Minkowski metric. It is shown that the quantum contribution to the classical expansion, although extremely small, has damping properties (quantum friction), i.e. it slows down the expansion.

  1. Effects of subsurface cavity expansion in clays

    OpenAIRE

    Au, SKA; Yeung, AT; Soga, K; Cheng, YM

    2007-01-01

    Subsurface cavity expansion in clay induced by compaction grouting can generate upward displacement of clay and/or increase in effective stress leading to consolidation, resulting in settlement compensation and/or shear strength enhancement respectively. However, the two potential benefits of subsurface cavity expansion may offset each other. Experiments and numerical simulations on the engineering behaviour of E-grade kaolin induced by subsurface pressure-controlled cavity expansion were con...

  2. $\\delta$-Expansion at Finite Temperature

    OpenAIRE

    Ramos, Rudnei O.

    1996-01-01

    We apply the $\\delta$-expansion perturbation scheme to the $\\lambda \\phi^{4}$ self-interacting scalar field theory in 3+1 D at finite temperature. In the $\\delta$-expansion the interaction term is written as $\\lambda (\\phi^{2})^{ 1 + \\delta}$ and $\\delta$ is considered as the perturbation parameter. We compute within this perturbative approach the renormalized mass at finite temperature at a finite order in $\\delta$. The results are compared with the usual loop-expansion at finite temperature.

  3. GAUSSIAN WHITE NOISE CALCULUS OF GENERALIZED EXPANSION

    Institute of Scientific and Technical Information of China (English)

    陈泽乾

    2002-01-01

    A new framework of Gaussian white noise calculus is established, in line with generalized expansion in [3, 4, 7]. A suitable frame of Fock expansion is presented on Gaussian generalized expansion functionals being introduced here, which provides the integral kernel operator decomposition of the second quantization of Koopman operators for chaotic dynamical systems, in terms of annihilation operators (e)t and its dual, creation operators (e)*t.

  4. Structure and thermal expansion of liquid bismuth

    Directory of Open Access Journals (Sweden)

    Mudry S.

    2015-12-01

    Full Text Available Experimental structural data for liquid Bi were used for estimation of the main structure parameters as well as the thermal expansion coefficient both in supercooled and superheated temperature ranges. It was shown that the equilibrium melt had a positive thermal expansion coefficient within a temperature range upon melting and a negative one at higher temperatures. The former was related to structure changes upon melting, whereas the latter with topologic disordering upon further heating. It was found that the superheated melt had a negative thermal expansion coefficient. The results obtained from structural data were compared with the thermal expansion coefficient calculated from the data of density for liquid Bi.

  5. TAYLOR EXPANSION METHOD FOR NONLINEAR EVOLUTION EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    HE Yin-nian

    2005-01-01

    A new numerical method of integrating the nonlinear evolution equations, namely the Taylor expansion method, was presented. The standard Galerkin method can be viewed as the 0-th order Taylor expansion method; while the nonlinear Galerkin method can be viewed as the 1-st order modified Taylor expansion method. Moreover, the existence of the numerical solution and its convergence rate were proven. Finally, a concrete example,namely, the two-dimensional Navier-Stokes equations with a non slip boundary condition,was provided. The result is that the higher order Taylor expansion method is of the higher convergence rate under some assumptions about the regularity of the solution.

  6. Comparison between Mt-DNA D-Loop and Cyt B primers for porcine DNA detection in meat products

    Science.gov (United States)

    Hamzah, Azhana; Mutalib, Sahilah Abd.; Babji, Abdul Salam

    2013-11-01

    This study was conducted to detect the presence of porcine DNA in meat products in the market using conventional polymerase chain reaction (PCR) and commercial PCR-southern hybridization analysis. Porcine DNA detection in meat products was tested due to some issues associated with the adulteration of food products in Malaysia. This is an important issue especially for Halal authentication which is required for some religious practices such as in Islam and Hinduisms. Many techniques have been developed for determining the Halal status of food products. In this paper, mt-DNA D-loop primer and cytochrome (cyt) b were used to detect the presence of porcine DNA in meat products. Positive and negative controls were always present for each batch of extraction. DNA of raw pork meat was used as a positive control while nucleus free water is used as negative control. A pair of oligonucleotide primer was used namely Pork1 and Pork2 which produced amplicon of 531 base pair (bp) in size. While, PCR-southern hybridization was conducted using primers readily supplied by commercial PCR-Southern hybridization and produced amplicon with 276 bp in size. In the present study, demonstrated that none of the samples were contaminated with porcine residuals but selected samples with pork meat were positive. The species-specific PCR amplification yielded excellent results for identification of pork derivatives in food products and it is a potentially reliable and suitable technique in routine food analysis for Halal certification.

  7. [Development of a DNA biochip for detection of known mtDNA mutations associated with MELAS and MERRF syndromes.].

    Science.gov (United States)

    Chen, Gang; Li, Wei; DU, Wei-Dong; Cao, Hui-Min; Tang, Hua-Yang; Tang, Xian-Fa; Sun, Zhong-Wu; Zhao, Hui; Jin, Qing-Hui; Zhao, Jian-Long; Zhang, Xue-Jun

    2008-10-01

    We developed an oligonucleotide biochip for synchronous multiplex detection of 31 known mitochondrial DNA mutations associated with MELAS (Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes) and MERRF (Myoclonic epilepsy with ragged red fibers). Allele-specific oligonucleotide probes were covalently immobilized on aldehyde modified glass slides, and then hybridized with Cy5-labled DNA fragments amplified from sample DNAs by a multiplex asymmetric PCR (MAP) method. Five patients with MELAS, 5 patients with MERRF and 20 healthy controls were investigated using the oligonucleotide biochip. The results showed that all the cases with MELAS had an A3243G mutation in the MT-TL1 gene. In the MERRF group, 4 cases were found to be an A8344G mutation and 1 case was a T8356C mutation, and both mutations were in the MT-TK gene. In the healthy controls, none of the 31 related mutations was found. The results of the DNA biochip were consistent with those by DNA sequencing. Clearly, the DNA biochip combined with MAP method would become a valuable tool in multiplex detecting of the point mutations in mtDNA leading to MELAS and/or MERRF syndrome. Moreover, this biochip format could be modified to extend to the screening scope of SNPs for any other human mitochondrial diseases.

  8. Molecular phylogenetic systematics of twelve species of Acipenseriformes based on mtDNA ND4L -ND4 gene sequence analysis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

  9. Molecular phylogenetic systematics of twelve species of Acipenseriformes based on mtDNA ND4L -ND4 gene sequence analysis

    Institute of Scientific and Technical Information of China (English)

    张四明; 张亚平; 郑向忠; 陈永久; 邓怀; 汪登强; 危起伟; 张云武; 聂龙; 吴清江

    2000-01-01

    Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DMA (mtDNA) ND4L and partial A7D4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

  10. Somatic point mutations in mtDNA control region are influenced by genetic background and associated with healthy aging: a GEHA study

    DEFF Research Database (Denmark)

    Rose, Giuseppina; Romeo, Giuseppe; Dato, Serena;

    2010-01-01

    Tissue specific somatic mutations occurring in the mtDNA control region have been proposed to provide a survival advantage. Data on twins and on relatives of long-lived subjects suggested that the occurrence/accumulation of these mutations may be genetically influenced. To further investigate....... We found a significant correlation of the mtDNA control region heteroplasmy between sibs, confirming a genetic influence on this phenomenon. Furthermore, many subjects showed heteroplasmy due to mutations different from the C150T transition. In these cases heteroplasmy was correlated within sibpairs...... in Finnish and northern Italian samples, but not in southern Italians. This suggested that the genetic contribution to control region mutations may be population specific. Finally, we observed a possible correlation between heteroplasmy and Hand Grip strength, one of the best markers of physical performance...

  11. Novel 12S mtDNA findings in sloths (Pilosa, Folivora and anteaters (Pilosa, Vermilingua suggest a true case of long branch attraction

    Directory of Open Access Journals (Sweden)

    Maria Claudene Barros

    2008-01-01

    Full Text Available We sequenced 12S RNA mtDNA for the majority of the extant species of sloths and anteaters and compared our results with previous data obtained by our group using 16S RNA mtDNA in the same specimens and to GenBank sequences of the extinct giant sloth Mylodon. Our results suggest that pigmy-anteaters may be a case of the long-branch attraction phenomenon and also show the large genetic difference between the Amazonian and Atlantic forest three-toed sloths, contrasting with the small differences observed between the two non-Atlantic forest forms of sloths. These results have important implications for the taxonomy of sloths and anteaters and strongly suggest the placement of pigmy anteaters in their own family (Cyclopidae and raising the taxonomic status of Bradypus torquatus to a genus.

  12. Detection of the mtDNA 14484 mutation on an African-specific haplotype: Implications about its role in causing Leber hereditary optic neuropathy

    Energy Technology Data Exchange (ETDEWEB)

    Torroni, A.; Petrozzi, M.; Terracina, M. [Universita` di Roma (Italy)] [and others

    1996-07-01

    Leber hereditary optic neuropathy (LHON) is a maternally transmitted disease whose primary clinical manifestation is acute or subacute bilateral loss of central vision leading to central scotoma and blindness. To date, LHON has been associated with 18 mtDNA missense mutations, even though, for many of these mutations, it remains unclear whether they cause the disease, contribute to the pathology, or are nonpathogenic mtDNA polymorphisms. On the basis of numerous criteria, which include the specificity for LHON, the frequency in the general population, and the penetrance within affected pedigrees, the detection of associated defects in the respiratory chain, mutations at three nucleotide positions (nps), 11778 (G{r_arrow}A), 3460 (G{r_arrow}A), and 14484 (T{r_arrow}C) have been classified as high-risk and primary LHON mutations. Overall, these three mutations encompass {ge}90% of the LHON cases. 29 refs., 1 fig.

  13. mtDNA G10398A variation provides risk to type 2 diabetes in population group from the Jammu region of India

    Directory of Open Access Journals (Sweden)

    Varun Sharma

    2014-12-01

    Full Text Available Mitochondrion plays an integral role in glucose metabolism and insulin secretion. Mitochondrial electron-transport chain (ETC is involved in adenosine triphosphate (ATP generation and ATP mediated insulin secretion in pancreatic β-cells. β-cell dysfunction is a critical component in the pathogenesis of type 2 diabetes (T2D. The mtDNA G10398A variation (amino acid change: Alanine → Threonine within the NADH dehydrogenase (ND3 subunit of complex I of mtDNA ETC, has emerged as a variation of clinical significance in various disorders including T2D. This variation is supposed to result in altered complex I function, leading to an increased rate of electron leakage and reactive oxygen species (ROS production, which might cause β-cell damage and impaired insulin secretion. The aim of the study was to explore the association of mtDNA G10398A variation with T2D in a total of 439 samples (196 T2D cases and 243 healthy controls belonging to the Jammu region of Jammu and Kashmir (J&K. The candidate gene association analyses showed significant association of mtDNA G10398A variant with T2D and the estimated odds ratio (OR was 2.83 (1.64–4.90 at 95% CI in the studied population group. The extent of genetic heterogeneity in T2D and diversity of the Indian population groups, make such replication studies pertinent to understand the etiology of T2D in these population groups.

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

    Science.gov (United States)

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

    2011-06-01

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

  15. MGB probe assay for rapid detection of mtDNA11778 mutation in the Chinese LHON patients by real-time PCR

    Institute of Scientific and Technical Information of China (English)

    Jian-yong WANG; Yang-shun GU; Jing WANG; Yi TONG; Ying WANG; Jun-bing SHAO; Ming QI

    2008-01-01

    Objective:Leber's hereditary optic neuropathY (LHON)is a maternally inherited degeneration of the optic nerve caused by point mutations of mitochondrial DNA(mtDNA).Many unsolved questions regarding the penetrance and pathophysiological mechanism of LHON demand efficient and reliable mutation testing.This study aims to develop a minor groove binder(MGB) probe assay for rapid detection of mtDNA11778 mutation and heteroplasmy in Chinese LHON patients by real-time polymerase chain reaction(PCR).Methods:Forty-eight patients suspected of having LHON and their maternal relatives underwent a molecular genetic evaluation,with 20 normal individuals as a control group at the same time.A real-time PCR involving two MGB probes was used to detect the mtDNA 11778 mutation and heteroplasmy.A linear standard curve was obtained by pUCmLHONG and pUCmLHONA clones.Results:All 48 LHON patients and their matemal relatives were positive for mtDNA 11778 mutation in our assay,27 heteroplasmic and 21 homoplasmic.Eighteen cases did not show an occurrence of the disease,while 9 developed the disease among the 27 heteroplasmic mutation cases.Eleven did not show an occurrence of the disease,while 10 cases developed the disease among 21 homoplasmic mutation cases.There was a significant difierence in the incidence between the heteroplasmic and the homoplasmic mutation types.The time needed for running a real-time PCR assay was only 80 min.Conclusion:This real-time PCR assay is a rapid,reliable method for mtDNA mutation detection as well as heteroplasmy quantification.Detecting this ratio is very important for predicting phenotypic expression of unaffected carriers.

  16. Simultaneous detection of human mitochondrial DNA and nuclear-inserted mitochondrial-origin sequences (NumtS) using forensic mtDNA amplification strategies and pyrosequencing technology.

    Science.gov (United States)

    Bintz, Brittania J; Dixon, Groves B; Wilson, Mark R

    2014-07-01

    Next-generation sequencing technologies enable the identification of minor mitochondrial DNA variants with higher sensitivity than Sanger methods, allowing for enhanced identification of minor variants. In this study, mixtures of human mtDNA control region amplicons were subjected to pyrosequencing to determine the detection threshold of the Roche GS Junior(®) instrument (Roche Applied Science, Indianapolis, IN). In addition to expected variants, a set of reproducible variants was consistently found in reads from one particular amplicon. A BLASTn search of the variant sequence revealed identity to a segment of a 611-bp nuclear insertion of the mitochondrial control region (NumtS) spanning the primer-binding sites of this amplicon (Nature 1995;378:489). Primers (Hum Genet 2012;131:757; Hum Biol 1996;68:847) flanking the insertion were used to confirm the presence or absence of the NumtS in buccal DNA extracts from twenty donors. These results further our understanding of human mtDNA variation and are expected to have a positive impact on the interpretation of mtDNA profiles using deep-sequencing methods in casework.

  17. Genetic differences between Chibcha and Non-Chibcha speaking tribes based on mitochondrial DNA (mtDNA haplogroups from 21 Amerindian tribes from Colombia

    Directory of Open Access Journals (Sweden)

    Solangy Usme-Romero

    2013-01-01

    Full Text Available We analyzed the frequency of four mitochondrial DNA haplogroups in 424 individuals from 21 Colombian Amerindian tribes. Our results showed a high degree of mtDNA diversity and genetic heterogeneity. Frequencies of mtDNA haplogroups A and C were high in the majority of populations studied. The distribution of these four mtDNA haplogroups from Amerindian populations was different in the northern region of the country compared to those in the south. Haplogroup A was more frequently found among Amerindian tribes in northern Colombia, while haplogroup D was more frequent among tribes in the south. Haplogroups A, C and D have clinal tendencies in Colombia and South America in general. Populations belonging to the Chibcha linguistic family of Colombia and other countries nearby showed a strong genetic differentiation from the other populations tested, thus corroborating previous findings. Genetically, the Ingano, Paez and Guambiano populations are more closely related to other groups of south eastern Colombia, as also inferred from other genetic markers and from archeological data. Strong evidence for a correspondence between geographical and linguistic classification was found, and this is consistent with evidence that gene flow and the exchange of customs and knowledge and language elements between groups is facilitated by close proximity.

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

    Science.gov (United States)

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

    2015-05-01

    Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of nonlocal subspecies of bees which has had an adverse impact on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. To restore the original diversity of this local honeybee subspecies, different conservation centres were set up in Europe. In this study, we established a black honeybee conservation centre Conservatoire de l'Abeille Noire d'Ile de France (CANIF) in the region of Ile-de-France, France. CANIF's honeybee colonies were intensively studied over a 3-year period. This study included a drone congregation area (DCA) located in the conservation centre. MtDNA COI-COII marker was used to evaluate the genetic diversity of CANIF's honeybee populations and the drones found and collected from the DCA. The same marker (mtDNA) was used to estimate the interactions and the haplotype frequency between CANIF's honeybee populations and 10 surrounding honeybee apiaries located outside of the CANIF. Our results indicate that the colonies of the conservation centre and the drones of the DCA show similar stable profiles compared to the surrounding populations with lower level of introgression. The mtDNA marker used on both DCA and colonies of the conservation centre seems to be an efficient approach to monitor and maintain the genetic diversity of the protected honeybee populations. PMID:25335970

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

    Science.gov (United States)

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

    2006-01-01

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

  20. Negative thermal expansion materials: technological key for control of thermal expansion

    OpenAIRE

    Koshi Takenaka

    2012-01-01

    Most materials expand upon heating. However, although rare, some materials contract upon heating. Such negative thermal expansion (NTE) materials have enormous industrial merit because they can control the thermal expansion of materials. Recent progress in materials research enables us to obtain materials exhibiting negative coefficients of linear thermal expansion over −30 ppm K−1. Such giant NTE is opening a new phase of control of thermal expansion in composites. Specifically examining pra...

  1. The heavy quark expansion of QCD

    Energy Technology Data Exchange (ETDEWEB)

    Falk, A.F. [Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Physics and Astronomy

    1997-06-01

    These lectures contain an elementary introduction to heavy quark symmetry and the heavy quark expansion. Applications such as the expansion of heavy meson decay constants and the treatment of inclusive and exclusive semileptonic B decays are included. Heavy hadron production via nonperturbative fragmentation processes is also discussed. 54 refs., 7 figs.

  2. A combinatorial construction of symplectic expansions

    CERN Document Server

    Kuno, Yusuke

    2010-01-01

    The notion of a symplectic expansion directly relates the topology of a surface to formal symplectic geometry. We give a method to construct a symplectic expansion by solving a recurrence formula given in terms of the Baker-Campbell-Hausdorff series.

  3. A reduced volumetric expansion factor plot

    Science.gov (United States)

    Hendricks, R. C.

    1979-01-01

    A reduced volumetric expansion factor plot has been constructed for simple fluids which is suitable for engineering computations in heat transfer. Volumetric expansion factors have been found useful in correlating heat transfer data over a wide range of operating conditions including liquids, gases and the near critical region.

  4. Multipole expansion method for supernova neutrino oscillations

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Huaiyu; Shalgar, Shashank, E-mail: duan@unm.edu, E-mail: shashankshalgar@unm.edu [Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131 (United States)

    2014-10-01

    We demonstrate a multipole expansion method to calculate collective neutrino oscillations in supernovae using the neutrino bulb model. We show that it is much more efficient to solve multi-angle neutrino oscillations in multipole basis than in angle basis. The multipole expansion method also provides interesting insights into multi-angle calculations that were accomplished previously in angle basis.

  5. Earnings Returns to the British Education Expansion

    Science.gov (United States)

    Devereux, Paul J.; Fan, Wen

    2011-01-01

    We study the effects of the large expansion in British educational attainment that took place for cohorts born between 1970 and 1975. Using the Quarterly Labour Force Survey, we find that the expansion caused men to increase education by about a year on average and gain about 8% higher wages; women obtained a slightly greater increase in education…

  6. Virial expansion coefficients in the harmonic approximation

    DEFF Research Database (Denmark)

    R. Armstrong, J.; Zinner, Nikolaj Thomas; V. Fedorov, D.;

    2012-01-01

    The virial expansion method is applied within a harmonic approximation to an interacting N-body system of identical fermions. We compute the canonical partition functions for two and three particles to get the two lowest orders in the expansion. The energy spectrum is carefully interpolated...

  7. The Expansion Postponement in Pure Type Systems

    Institute of Scientific and Technical Information of China (English)

    宋方敏

    1997-01-01

    The expansion postponement problem in Pure Type Systems is an open problem raised by R.Pollack in 1992.In this paper,the author presents a set of necessary and sufficient conditions for this problem and a set of sufficient conditions for it.The author also gives some properties for pure typ systems without the expansion rule.

  8. Development of Soda Residue Concrete Expansion Agent

    Institute of Scientific and Technical Information of China (English)

    WANG Bao-min; WANG Li-jiu; M F Mohd Zain; F C Lai

    2003-01-01

    A new type of concrete expansion agent has been successfully developed for the first time in the world by utilizing an industrial waste residue-soda residue and an industrial wasteliquor.Adding 3%-6% of the agent into Portland cement enables a shrinkage-compensating concrete to be prepared.Mortar and concrete containing this expansion agent have better shrinkage-compensating and mechanical properties.The raw materials component,production process,technical properties,micro-analysis of mortar made with this expansion agent,mechanism of expansion and research results are described in this article.The experimental results show that the new type of concrete expansion agent accords with the standard and its main mineral component is xCaO-ySO3-zAl2O3.

  9. Maxwell superalgebras and Abelian semigroup expansion

    Directory of Open Access Journals (Sweden)

    P.K. Concha

    2014-09-01

    Full Text Available The Abelian semigroup expansion is a powerful and simple method to derive new Lie algebras from a given one. Recently it was shown that the S-expansion of so(3,2 leads us to the Maxwell algebra M. In this paper we extend this result to superalgebras, by proving that different choices of abelian semigroups S lead to interesting D=4 Maxwell Superalgebras. In particular, the minimal Maxwell superalgebra sM and the N-extended Maxwell superalgebra sM(N recently found by the Maurer–Cartan expansion procedure, are derived alternatively as an S-expansion of osp(4|N. Moreover, we show that new minimal Maxwell superalgebras type sMm+2 and their N-extended generalization can be obtained using the S-expansion procedure.

  10. Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China.

    Science.gov (United States)

    Ren, G-P; Abbott, R J; Zhou, Y-F; Zhang, L-R; Peng, Y-L; Liu, J-Q

    2012-05-01

    Although homoploid hybrid speciation in plants is probably more common than previously realized, there are few well-documented cases of homoploid hybrid origin in conifers. We examined genetic divergence between two currently widespread pines in Northeast China, Pinus sylvestris var. mongolica and Pinus densiflora, and also whether two narrowly distributed pines in the same region, Pinus funebris and Pinus takahasii, might have originated from the two widespread species by homoploid hybrid speciation. Our results, based on population genetic analysis of chloroplast (cp), mitochondrial (mt) DNA, and nuclear gene sequence variation, showed that the two widespread species were divergent for both cp- and mtDNA variation, and also for haplotype variation at two of eight nuclear gene loci surveyed. Our analysis further indicated that P. sylvestris var. mongolica and P. densiflora remained allopatric during the most severe Quaternary glacial period that occurred in Northeast China, but subsequently exhibited rapid range expansions. P. funebris and P. takahasii, were found to contain a mixture of chlorotypes and nuclear haplotypes that distinguish P. sylvestris var. mongolica and P. densiflora, in support of the hypothesis that they possibly originated via homoploid hybrid speciation following secondary contact and hybridization between P. sylvestris var. mongolica and P. densiflora. PMID:22187083

  11. Worldwide structure of mtDNA diversity among Cuvier's beaked whales (Ziphius cavirostris): implications for threatened populations.

    Science.gov (United States)

    Dalebout, Merel L; Robertson, Kelly M; Frantzis, Alexandros; Engelhaupt, Dan; Mignucci-Giannoni, Antonio A; Rosario-Delestre, Raul J; Baker, C Scott

    2005-10-01

    We present the first description of phylogeographic structure among Cuvier's beaked whales (Ziphius cavirostris) worldwide using mitochondrial DNA (mtDNA) control region sequences obtained from strandings (n = 70), incidental fisheries takes (n = 11), biopsy (n = 1), and whale-meat markets (n = 5). Over a 290-base pair fragment, 23 variable sites defined 33 unique haplotypes among the total of 87 samples. Nucleotide diversity at the control region was relatively low (pi = 1.27%+/- 0.723%) compared to wide-ranging baleen whales, but higher than strongly matrifocal sperm, pilot and killer whales. Phylogenetic reconstruction using maximum likelihood revealed four distinct haplotype groups, each of which displayed strong frequency differences among ocean basins, but no reciprocal monophyly or fixed character differences. Consistent with this phylogeographic pattern, an analysis of molecular variance showed high levels of differentiation among ocean basins (F(ST) = 0.14, Phi ST = 0.42; P < 0.001). Estimated rates of female migration among ocean basins were low (generally < or = 2 individuals per generation). Regional sample sizes were too small to detect subdivisions within oceans except in the North Atlantic, where the Mediterranean Sea (n = 12) was highly differentiated due to the presence of two private haplotypes. One market product purchased in South Korea grouped with other haplotypes found only in the North Atlantic, suggesting a violation of current agreements banning international trade in cetacean species. Together, these results demonstrate a high degree of isolation and low maternal gene flow among oceanic, and in some cases, regional populations of Cuvier's beaked whales. This has important implications for understanding the threats of human impact, including fisheries by-catch, direct hunting, and disturbance or mortality from anthropogenic sound.

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

    Directory of Open Access Journals (Sweden)

    M. Houshmand

    2006-06-01

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

  13. Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes.

    Directory of Open Access Journals (Sweden)

    Maria Grazia Doro

    Full Text Available We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.

  14. Shrinkage and Expansive Strain of Concrete with Fly Ash and Expansive Agent

    Institute of Scientific and Technical Information of China (English)

    GAO Peiwei; LU Xiaolin; TANG Mingshu

    2009-01-01

    The effects of fly ash and MgO-type expansive agent on the shrinkage and expan-sive strain of concrete with high magnesia cement were investigated. The results show that high volumes of fly ash may reduce the shrinkage strain of concrete and inhibit the expansive strain of concrete with MgO-type expansive agent, but can not eliminate the shrinkage of concrete. MgO-type expansive agent may produce expansive strain and compensate the shrinkage strain of concrete, re-lieve the cracking risk, but the hydration product of magnesia tends to get together in paste and pro-duce expansive cracking of concrete with high magnesia content according to SEM observation.

  15. Concentric ring flywheel without expansion separators

    Science.gov (United States)

    Kuklo, Thomas C.

    1999-01-01

    A concentric ring flywheel wherein the adjacent rings are configured to eliminate the need for differential expansion separators between the adjacent rings. This is accomplished by forming a circumferential step on an outer surface of an inner concentric ring and forming a matching circumferential step on the inner surface of an adjacent outer concentric ring. During operation the circumferential steps allow the rings to differentially expand due to the difference in the radius of the rings without the formation of gaps therebetween, thereby eliminating the need for expansion separators to take up the gaps formed by differential expansion.

  16. Critical exponents from large mass expansion

    CERN Document Server

    Yamada, Hirofumi

    2014-01-01

    We perform estimation of critical exponents via large mass expansion under crucial help of delta-expansion. We address to the three dimensional Ising model at high temperature and estimate omega, the correction-to-scaling exponent, nu, eta and gamma in unbiased and self-contained manner. The results read at the highest 25th order expansion omega=0.8002, nu=0.6295, eta=0.0369 and gamma=1.2357. Estimation biased by omega=0.84(4) is also performed and proved to be in agreement with the summary of recent literatures.

  17. Hubble expansion is not a velocity

    Science.gov (United States)

    Ma, Yin-Zhe; Zhang, Shuang-Nan

    2016-11-01

    In this paper, we clarify the difference between the Hubble expansion and the Doppler shift pedagogically and illustrate both physically and mathematically why the Hubble expansion cannot be regarded as a velocity. Therefore, we suggest to replace the misleading word ‘recession velocity’ to be ‘Hubble recession’ to describe the cosmic expansion. We further derive how the peculiar velocity of a galaxy is related to its observed redshift and proper distance, which has practical use in the galaxy redshift and distance surveys.

  18. Born expansions for charged particle scattering

    International Nuclear Information System (INIS)

    High-order terms in Born expansions of scattering amplitudes in powers of charge are frequently divergent when long-range Coulomb interactions are present asymptotically. Expansions which are free from these logarithmic divergences have been constructed recently. This paper illustrates these expansions with the simplest example, namely the non-relativistic Rutherford scattering of two charged particles. This approach represents an adequate framework for the calculation of transition amplitudes and a comprehensive starting point for the development of consistent perturbation approximations in multi-channel descriptions of strongly interacting atomic systems

  19. ON CONVERGENCE OF WAVELET PACKET EXPANSIONS

    Institute of Scientific and Technical Information of China (English)

    Morten Nielsen

    2002-01-01

    It is well known that the-Walsh-Fourier expansion of a function from the block space ([0, 1 ) ), 1 <q≤∞, converges pointwise a.e. We prove that the same result is true for the expansion of a function from in certain periodixed smooth periodic non-stationary wavelet packets bases based on the Haar filters. We also consider wavelet packets based on the Shannon filters and show that the expansion of Lp-functions, 1<p<∞, converges in norm and pointwise almost everywhere.

  20. Extrudate Expansion Modelling through Dimensional Analysis Method

    DEFF Research Database (Denmark)

    A new model framework is proposed to correlate extrudate expansion and extrusion operation parameters for a food extrusion cooking process through dimensional analysis principle, i.e. Buckingham pi theorem. Three dimensionless groups, i.e. energy, water content and temperature, are suggested...... to describe the extrudates expansion. From the three dimensionless groups, an equation with three experimentally determined parameters is derived to express the extrudate expansion. The model is evaluated with whole wheat flour and aquatic feed extrusion experimental data. The average deviations...

  1. Surgically assisted rapid maxillary expansion in adults.

    Science.gov (United States)

    Pogrel, M A; Kaban, L B; Vargervik, K; Baumrind, S

    1992-01-01

    Twelve adults with maxillary width discrepancy of greater than 5 mm were treated by surgically assisted rapid maxillary expansion. The procedure consisted of bilateral zygomatic buttress and midpalatal osteotomies combined with the use of a tooth-borne orthopedic device postoperatively. Mean palatal expansion of 7.5 mm (range of 6 to 13 mm), measured in the first molar region, was achieved within 3 weeks in all patients. Expansion remained stable during the 12-month study period, with a mean relapse for the entire group of 0.88 +/- 0.48 mm. Morbidity was limited to mild postoperative discomfort. The results of this preliminary study indicated that surgically assisted rapid maxillary expansion is a safe, simple, and reliable procedure for achieving a permanent increase in skeletal maxillary width in adults. Further study is necessary to document the three-dimensional movements of the maxillary segments and long-term stability of the skeletal and dental changes.

  2. Testing the isotropy of the Hubble expansion

    CERN Document Server

    Migkas, K

    2016-01-01

    We have used the Union2.1 SNIa compilation to search for possible Hubble expansion anisotropies, dividing the sky in 9 solid angles containing roughly the same number of SNIa, as well as in the two Galactic hemispheres. We identified only one sky region, containing 82 SNIa (~15% of total sample with $z>0.02$), that indeed appears to share a significantly different Hubble expansion than the rest of the sample. However, this behavior appears to be attributed to the joint "erratic" behavior of only three SNIa and not to an anisotropic expansion. We also find that the northern and southern galactic hemispheres have different cosmological parameter solutions but still not significant enough to assert the detection of a Hubble expansion anisotropy. We conclude that even a few outliers can have such an effect as to induce artificial indications of anisotropies, when the number of analysed SNIa is relatively small.

  3. Transmission Expansion Planning in Deregulated Power Systems

    OpenAIRE

    Oloomi Buygi, Majid

    2004-01-01

    The main goal of this thesis is to present a centralized static approach for transmission expansion planning in deregulated power systems. Restructuring and deregulation have unbundled the roles of network stakeholders. They exposed transmission planner to the new objectives and uncertainties. Unbundling the roles has brought new challenges for stakeholders. In these environments, stakeholders have different desires and expectations from the performance and expansion of the system. Therefore,...

  4. Thermal Expansion Coefficients of Thin Crystal Films

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The formulas for atomic displacements and Hamiltonian of a thin crystal film in phonon occupation number representation are obtained with the aid of Green's function theory. On the basis of these results, the formulas for thermal expansion coefficients of the thin crystal film are derived with the perturbation theory, and the numerical calculations are carried out. The results show that the thinner films have larger thermal expansion coefficients.

  5. Market Knowledge, Diversification and Export Expansion

    OpenAIRE

    Jean-Emile Denis; Daniel Depelteau

    1985-01-01

    The research focuses on the export expansion process of small and middle-sized manufacturing firms and some of its correlates: diversification and geographical market distribution, means of acquiring information and modes of international distribution. The study reveals the overwhelming influence on export expansion of information acquired from business transactions as opposed to reliance on private or public information services. The impact of market diversification and its nature is confirm...

  6. Fuel Thermal Expansion (FTHEXP). [BWR; PWR

    Energy Technology Data Exchange (ETDEWEB)

    Reymann, G. A.

    1978-07-01

    A model is presented which deals with dimensional changes in LWR fuel pellets caused by changes in temperature. It is capable of dealing with any combination of UO/sub 2/ and PuO/sub 2/ in solid, liquid or mixed phase states, and includes expansion due to the solid-liquid phase change. The function FTHEXP models fuel thermal expansion as a function of temperature, fraction of PuO/sub 2/, and the fraction of fuel which is molten.

  7. A Semigroup Expansion for Pricing Barrier Options

    Directory of Open Access Journals (Sweden)

    Takashi Kato

    2014-01-01

    Full Text Available This paper presents a new asymptotic expansion method for pricing continuously monitoring barrier options. In particular, we develop a semigroup expansion scheme for the Cauchy-Dirichlet problem in the second-order parabolic partial differential equations (PDEs arising in barrier option pricing. As an application, we propose a concrete approximation formula under a stochastic volatility model and demonstrate its validity by some numerical experiments.

  8. Ultracold neutral plasma expansion in two dimensions

    CERN Document Server

    Cummings, E A; Durfee, D S; Bergeson, S D

    2005-01-01

    We extend an isothermal thermal model of ultracold neutral plasma expansion to systems without spherical symmetry, and use this model to interpret new fluorescence measurements on these plasmas. By assuming a self-similar expansion, it is possible to solve the fluid equations analytically and to include velocity effects to predict the fluorescence signals. In spite of the simplicity of this approach, the model reproduces the major features of the experimental data.

  9. Thermal expansion coefficient of binary semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, V.; Sastry, B.S.R. [Indian School of Mines, Dhanbad (India). Dept. of Electronics and Instrumentation

    2001-07-01

    The linear thermal expansion coefficient of tetrahedrally coordinated A{sup II}B{sup VI} and A{sup III}B{sup V} semiconductors has been calculated using plasmon energy data. A simple relation between the bond length and plasmon energy has been derived. The calculated values of thermal expansion coefficient and bond length have been compared with the experimental values and the values reported by different workers. An excellent experiment has been obtained between them. (orig.)

  10. On storm weakening during substorm expansion phase

    Directory of Open Access Journals (Sweden)

    G. L. Siscoe

    Full Text Available Iyemori and Rao recently presented evidence that the strength of a magnetic storm, as measured by -Dst, weakens, or its rate of growth slows, during the substorm expansion phase. Yet the expansion phase is known to inject energetic particles into the ring current, which should strengthen the storm. We propose to reconcile these apparently contradictory results by combining the virial theorem and a principle of energy partitioning between energy storage elements in a system with dissipation. As applied to the unloading description of the substorm expansion phase, the virial theorem states that -Dst is proportional to the sum of the total magnetic energy and twice the total kinetic energy in the magnetosphere including the tail. Thus if expansion phase involves converting magnetic energy stored in the tail into kinetic energy stored in the ring current, a drop in -Dst during expansion phase requires that less than half the drop in magnetic energy goes into the ring current, the rest going into the ionosphere. Indeed Weiss et al., have estimated that the energy dissipated in the ionosphere during expansion phase is twice that injected into the ring current. This conclusion is also consistent with the mentioned energy partitioning principle, which requires that more energy be dissipated than transferred between storage elements. While Iyemori and Rao's observations seem to contradict the hypothesis that storms consist at least in part of a sum of substorms, this mode of description might nonetheless be preserved by including the substorm's growth-phase contribution. Then the change in storm strength measured from before the growth phase to after the expansion phase is positive, even though the expansion phase alone makes a negative contribution.

  11. Screened cluster expansions for partially ionized gases

    OpenAIRE

    Alastuey, A.; Ballenegger, V.; Cornu, F.; Martin, Ph. A.

    2003-01-01

    We consider a partially ionized gas at thermal equilibrium, in the Saha regime. The system is described in terms of a quantum plasma of nuclei and electrons. In this framework, the Coulomb interaction is the source of a large variety of phenomena occuring at different scales: recombination, screening, diffraction, etc. In this paper, we derive a cluster expansion adequate for a coherent treatment of those phenomena. The expansion is obtained by combining the path integral representation of th...

  12. Asymptotic and Exact Expansions of Heat Traces

    Energy Technology Data Exchange (ETDEWEB)

    Eckstein, Michał, E-mail: michal@eckstein.pl [Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science (Poland); Zając, Artur, E-mail: artur.zajac@uj.edu.pl [Jagiellonian University, Faculty of Mathematics and Computer Science (Poland)

    2015-12-15

    We study heat traces associated with positive unbounded operators with compact inverses. With the help of the inverse Mellin transform we derive necessary conditions for the existence of a short time asymptotic expansion. The conditions are formulated in terms of the meromorphic extension of the associated spectral zeta-functions and proven to be verified for a large class of operators. We also address the problem of convergence of the obtained asymptotic expansions. General results are illustrated with a number of explicit examples.

  13. The Dynamics of Regional and Global Expansion

    DEFF Research Database (Denmark)

    Geisler Asmussen, Christian; Nielsen, Bo Bernhard; Osegowitsch, Tom;

    2015-01-01

    domain. Findings – The authors demonstrate that MNEs do penetrate both home-regional and global markets, often simultaneously, and that penetration levels often oscillate within an MNE over time. The authors show firms’ rates of regional and global expansion to be affected by their existing regional...... demarcations. Originality/value – The authors identify complex interdependencies between home-regional and global penetration and growth, paving the way for further studies of the impact of regions on MNE expansion....

  14. Vibrational relaxation in pyridine upon supersonic expansion

    Science.gov (United States)

    Maris, Assimo; Favero, Laura B.; Danieli, Roberto; Favero, Paolo G.; Caminati, Walther

    2000-11-01

    The rotational spectra of five vibrational states of pyridine have been assigned and measured by millimeter wave absorption spectroscopy in a supersonic expansion. The intensities of the lines of the vibrational satellites with respect to the ground state after the supersonic expansion depend on the kind of carrier gas, backing pressure, pyridine concentration, and symmetry of the rotational and vibrational states. Several rotational transitions of the vibrational satellites have also been measured in a conventional cell to complete the spectral assignment.

  15. Magnetization of concentrated polydisperse ferrofluids: Cluster expansion

    OpenAIRE

    Huke, B.; Luecke, M.

    2006-01-01

    The equilibrium magnetization of concentrated ferrofluids described by a system of polydisperse dipolar hard spheres is calculated as a function of the internal magnetic field using the Born--Mayer or cluster expansion technique. This paper extends the results of Phys. Rev. E 62, 6875 (2000) obtained for monodisperse ferrofluids. The magnetization is given as a power series expansion in two parameters related to the volume fraction and the coupling strength of the dipolar interaction, respect...

  16. Agriculture driving male expansion in Neolithic Time

    OpenAIRE

    Wang, Chuan-Chao; Huang, Yunzhi; Wen, Shao-Qing; Chen, Chun; Jin, Li; Li, Hui

    2013-01-01

    The emergence of agriculture is suggested to have driven extensive human population growths. However, genetic evidence from maternal mitochondrial genomes suggests major population expansions began before the emergence of agriculture. Therefore, role of agriculture that played in initial population expansions still remains controversial. Here, we analyzed a set of globally distributed whole Y chromosome and mitochondrial genomes of 526 male samples from 1000 Genome Project. We found that most...

  17. REGENERATIVE GAS TURBINES WITH DIVIDED EXPANSION

    DEFF Research Database (Denmark)

    Elmegaard, Brian; Qvale, Einar Bjørn

    2004-01-01

    divided expansion can be advantageous under certain circumstances. But, in order for todays micro gas turbines to be competitive, the thermodynamic efficiencies will have to be rather high. This requires that all component efficiencies including the recuperator effectiveness will have to be high....... The advantages of the divided expansion manifest themselves over a rather limited range of the operating parameters, that lies outside the range required to make modern micro turbines economically competitive....

  18. Diffusion tensor image registration using polynomial expansion

    International Nuclear Information System (INIS)

    In this paper, we present a deformable registration framework for the diffusion tensor image (DTI) using polynomial expansion. The use of polynomial expansion in image registration has previously been shown to be beneficial due to fast convergence and high accuracy. However, earlier work was developed only for 3D scalar medical image registration. In this work, it is shown how polynomial expansion can be applied to DTI registration. A new measurement is proposed for DTI registration evaluation, which seems to be robust and sensitive in evaluating the result of DTI registration. We present the algorithms for DTI registration using polynomial expansion by the fractional anisotropy image, and an explicit tensor reorientation strategy is inherent to the registration process. Analytic transforms with high accuracy are derived from polynomial expansion and used for transforming the tensor's orientation. Three measurements for DTI registration evaluation are presented and compared in experimental results. The experiments for algorithm validation are designed from simple affine deformation to nonlinear deformation cases, and the algorithms using polynomial expansion give a good performance in both cases. Inter-subject DTI registration results are presented showing the utility of the proposed method. (paper)

  19. Thermal expansion of doped lanthanum gallates

    Indian Academy of Sciences (India)

    K T Jacob; S Jain; V S Saji; P V K Srikanth

    2010-08-01

    Thermal expansion of several compositions of Sr and Mg-doped LaGaO3 including an -site deficient composition (La0.9Sr0.1)0.98(Ga0.8Mg0.2)O2.821 were measured in the temperature range from 298 to 1273 K. The effect of doping on thermal expansion was studied by varying the composition at one site of the perovskite structure (either or ), while keeping the composition at the other site invariant. Thermal expansion varied nonlinearly with temperature and exhibited an inflexion between 550 and 620 K, probably related to the change in crystal structure from orthorhombic to rhombohedral. The dependence of average thermal expansion coefficient (av) on the dopant concentration on either or site of the perovskite structure was found to be linear, when the composition at the other site was kept constant. Mg doping on the -site had a greater effect on the average thermal expansion coefficient than Sr doping on the -site. Cation deficiency at the -site decreases thermal expansion when compositions at both sites are held constant.

  20. Expansive Soil Crack Depth under Cumulative Damage

    Directory of Open Access Journals (Sweden)

    Bei-xiao Shi

    2014-01-01

    Full Text Available The crack developing depth is a key problem to slope stability of the expansive soil and its project governance and the crack appears under the roles of dry-wet cycle and gradually develops. It is believed from the analysis that, because of its own cohesion, the expansive soil will have a certain amount of deformation under pulling stress but without cracks. The soil body will crack only when the deformation exceeds the ultimate tensile strain that causes cracks. And it is also believed that, due to the combined effect of various environmental factors, particularly changes of the internal water content, the inherent basic physical properties of expansive soil are weakened, and irreversible cumulative damages are eventually formed, resulting in the development of expansive soil cracks in depth. Starting from the perspective of volumetric strain that is caused by water loss, considering the influences of water loss rate and dry-wet cycle on crack developing depth, the crack developing depth calculation model which considers the water loss rate and the cumulative damages is established. Both the proposal of water loss rate and the application of cumulative damage theory to the expansive soil crack development problems try to avoid difficulties in matrix suction measurement, which will surely play a good role in promoting and improving the research of unsaturated expansive soil.

  1. Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity

    Directory of Open Access Journals (Sweden)

    Feng Gui

    2011-04-01

    Full Text Available Abstract Background Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps. Results We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes. Conclusions Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA.

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

    Directory of Open Access Journals (Sweden)

    Egarter-Vigl Eduard

    2009-06-01

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

  3. Increased expression of ApoE and protection from amyloid-beta toxicity in transmitochondrial cybrids with haplogroup K mtDNA.

    Science.gov (United States)

    Thaker, Kunal; Chwa, Marilyn; Atilano, Shari R; Coskun, Pinar; Cáceres-Del-Carpio, Javier; Udar, Nitin; Boyer, David S; Jazwinski, S Michal; Miceli, Michael V; Nesburn, Anthony B; Kuppermann, Baruch D; Kenney, M Cristina

    2016-09-01

    Mitochondrial (mt) DNA haplogroups, defined by specific single nucleotide polymorphism (SNP) patterns, represent populations of diverse geographic origins and have been associated with increased risk or protection of many diseases. The H haplogroup is the most common European haplogroup while the K haplogroup is highly associated with the Ashkenazi Jewish population. Transmitochondrial cybrids (cell lines with identical nuclei, but mtDNA from either H (n=8) or K (n=8) subjects) were analyzed by the Seahorse flux analyzer, quantitative polymerase chain reaction (Q-PCR) and immunohistochemistry (IHC). Cybrids were treated with amyloid-β peptides and cell viabilities were measured. Other cybrids were demethylated with 5-aza-2'-deoxycytidine (5-aza-dC) and expression levels for APOE and NFkB2 were measured. Results show K cybrids have (a) significantly lower mtDNA copy numbers, (b) higher expression levels for MT-DNA encoded genes critical for oxidative phosphorylation, (c) lower Spare Respiratory Capacity, (d) increased expression of inhibitors of the complement pathway and important inflammasome-related genes; and (e) significantly higher levels of APOE transcription that were independent of methylation status. After exposure to amyloid-β1-42 peptides (active form), H haplogroup cybrids demonstrated decreased cell viability compared to those treated with amyloid-β42-1 (inactive form) (p<0.0001), while this was not observed in the K cybrids (p=0.2). K cybrids had significantly higher total global methylation levels and differences in expression levels for two acetylation genes and four methylation genes. Demethylation with 5-aza-dC altered expression levels for NFkB2, while APOE transcription patterns were unchanged. Our findings support the hypothesis that mtDNA-nuclear retrograde signaling may mediate expression levels of APOE, a key factor in many age-related diseases. Future studies will focus on identification of the mitochondrial-nuclear retrograde signaling

  4. Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method.

    Science.gov (United States)

    Lee, Eun Young; Lee, Hwan Young; Oh, Se Yoon; Jung, Sang-Eun; Yang, In Seok; Lee, Yang-Han; Yang, Woo Ick; Shin, Kyoung-Jin

    2016-05-01

    The application of next-generation sequencing (NGS) to forensic genetics is being explored by an increasing number of laboratories because of the potential of high-throughput sequencing for recovering genetic information from multiple markers and multiple individuals in a single run. A cumbersome and technically challenging library construction process is required for NGS. In this study, we propose a simplified library preparation method for mitochondrial DNA (mtDNA) analysis that involves two rounds of PCR amplification. In the first-round of multiplex PCR, six fragments covering the entire mtDNA control region and 22 fragments covering interspersed single nucleotide polymorphisms (SNPs) in the coding region that can be used to determine global haplogroups and East Asian haplogroups were amplified using template-specific primers with read sequences. In the following step, indices and platform-specific sequences for the MiSeq(®) system (Illumina) were added by PCR. The barcoded library produced using this simplified workflow was successfully sequenced on the MiSeq system using the MiSeq Reagent Nano Kit v2. A total of 0.4 GB of sequences, 80.6% with base quality of >Q30, were obtained from 12 degraded DNA samples and mapped to the revised Cambridge Reference Sequence (rCRS). A relatively even read count was obtained for all amplicons, with an average coverage of 5200 × and a less than three-fold read count difference between amplicons per sample. Control region sequences were successfully determined, and all samples were assigned to the relevant haplogroups. In addition, enhanced discrimination was observed by adding coding region SNPs to the control region in in silico analysis. Because the developed multiplex PCR system amplifies small-sized amplicons (<250 bp), NGS analysis using the library preparation method described here allows mtDNA analysis using highly degraded DNA samples. PMID:26844917

  5. Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

    Science.gov (United States)

    Weiler, Natalie E C; de Vries, Gerda; Sijen, Titia

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous. PMID:26976467

  6. Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

    Science.gov (United States)

    Weiler, Natalie E C; de Vries, Gerda; Sijen, Titia

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous.

  7. Review of mtDNA in molecular evolution studies%线粒体DNA在分子进化研究中的应用

    Institute of Scientific and Technical Information of China (English)

    陈星; 沈永义; 张亚平

    2012-01-01

    线粒体作为古老的细胞器广泛存在于真核生物中,由于线粒体DNA的高进化速率,已被作为DNA标记广泛应用于现代分子生物学研究.长期以来,线粒体DNA一直被认为是中性进化或者受到纯净化选择.线粒体通过氧化呼吸链提供>95%的动物运动所需的自由能,并提供保持体温的热能.据此,近期已有研究推测并验证了线粒体与动物运动能力及气候适应性的相关性.该文简述线粒体基因组成及其进化,通过列举线粒体DNA在分子进化研究中的应用(如利用线粒体DNA重建物种的系统发育关系、从线粒体DNA角度分析生物能量代谢的适应性进化以及线粒体DNA密码子重定义对生物适应性的作用等),概述了线粒体DNA的分子进化研究.%Mitochondria are old organelles found in most eukaryotic cells. Due to its rapid mutation ratio, mitochondrial DNA (mtDNA) has been widely used as a DNA marker in molecular studies and has long been suggested to undergo neutral evolution or purifying selection. Mitochondria produces 95% of the adenosine triphosphate (ATP) needed for locomotion, and heat for thermoregulation. Recent studies had found that mitochondria play critical roles in energy metabolism, and proved that functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mtDNA. This review summarizes mitochondrial genome composition, evolution, and its applications in molecular evolution studies (reconstruction of species phylogenesis, the relationship between biological energy metabolism and mtDNA evolution, and the mtDNA codon reassignment influences the adaptation in different creatures).

  8. Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework.

    Science.gov (United States)

    Chemale, Gustavo; Paneto, Greiciane Gaburro; Menezes, Meiga Aurea Mendes; de Freitas, Jorge Marcelo; Jacques, Guilherme Silveira; Cicarelli, Regina Maria Barretto; Fagundes, Paulo Roberto

    2013-05-01

    Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) to be typed using SNaPShot(TM) (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons

  9. Negative thermal expansion materials: technological key for control of thermal expansion

    Directory of Open Access Journals (Sweden)

    Koshi Takenaka

    2012-01-01

    Full Text Available Most materials expand upon heating. However, although rare, some materials contract upon heating. Such negative thermal expansion (NTE materials have enormous industrial merit because they can control the thermal expansion of materials. Recent progress in materials research enables us to obtain materials exhibiting negative coefficients of linear thermal expansion over −30 ppm K−1. Such giant NTE is opening a new phase of control of thermal expansion in composites. Specifically examining practical aspects, this review briefly summarizes materials and mechanisms of NTE as well as composites containing NTE materials, based mainly on activities of the last decade.

  10. Preliminary thermal expansion screening data for tuffs

    Energy Technology Data Exchange (ETDEWEB)

    Lappin, A.R.

    1980-03-01

    A major variable in evaluating the potential of silicic tuffs for use in geologic disposal of heat-producing nuclear wastes is thermal expansion. Results of ambient-pressure linear expansion measurements on a group of tuffs that vary treatly in porosity and mineralogy are presente here. Thermal expansion of devitrified welded tuffs is generally linear with increasing temperature and independent of both porosity and heating rate. Mineralogic factors affecting behavior of these tuffs are limited to the presence or absence of cristobalite and altered biotite. The presence of cristobalite results in markedly nonlinear expansion above 200{sup 0}C. If biotite in biotite-hearing rocks alters even slightly to expandable clays, the behavior of these tuffs near the boiling point of water can be dominated by contraction of the expandable phase. Expansion of both high- and low-porosity tuffs containing hydrated silicic glass and/or expandable clays is complex. The behavior of these rocks appears to be completely dominated by dehydration of hydrous phases and, hence, should be critically dependent on fluid pressure. Valid extrapolation of the ambient-pressure results presented here to depths of interest for construction of a nuclear-waste repository will depend on a good understanding of the interaction of dehydration rates and fluid pressures, and of the effects of both micro- and macrofractures on the response of tuff masss.

  11. An entropy-driven cosmic expansion

    CERN Document Server

    Hammad, Fayçal

    2013-01-01

    We examine the evolution of the Friedman Universe within our recent model of space-time identified with an elastic continuous medium whose deformations are described by a vector field constrained to obey a generalized four-dimensional version of the equilibrium equations of standard elasticity. It is found that the demand that the entropy associated with such elastic deformations be always extremal during the expansion of such a Universe turns these equilibrium equations into a single differential equation governing the evolution of the Hubble parameter H. The solution to the resulting dynamics admits both a power-law expansion, analogous to the one induced by an inflaton field, as well as a power-law expansion analogous to the one induced by a phantom field. Analyzing both types of expansions via the induced elastic energy and pressure permits to assign the former to the early Universe and the latter to its late-time expansion. We discuss the possible way for the dynamics to avoid the Big Rip singularity tha...

  12. Irreducible Cartesian tensor expansions of scalar fields

    International Nuclear Information System (INIS)

    It is shown how a scalar function V(parallel R + Σ/sub i equals 1/sup n/ a/sub i/parallel) of a sum of n + 1 vectors can be expanded as a multiple Cartesian tensor series in the vectors a/ sub i/. This expansion is a rearrangement of the multiple Taylor series expansion of such a function. In order to prove the fundamental theorem, generalized Cartesian Legendre polynomials are defined. The theorem is applied to the eigenfunctions of the Laplace operator and to inverse powers. The expansion of the latter type of function leads to forms involving generalized hypergeometric functions in several variables. As a special case, the Cartesian form of the multipole expansion of the electrostatic potential between two linear molecules is derived. A number of sum rules for hypergeometric functions and addition formulas for (standard and modified) spherical Bessel functions are proved by using a reduction property of the generalized Legendre polynomials. The case of the expansion of a tensorial function is also briefly discussed

  13. Control control control: a reassessment and comparison of GenBank and chromatogram mtDNA sequence variation in Baltic grey seals (Halichoerus grypus.

    Directory of Open Access Journals (Sweden)

    Katharina Fietz

    Full Text Available Genetic data can provide a powerful tool for those interested in the biology, management and conservation of wildlife, but also lead to erroneous conclusions if appropriate controls are not taken at all steps of the analytical process. This particularly applies to data deposited in public repositories such as GenBank, whose utility relies heavily on the assumption of high data quality. Here we report on an in-depth reassessment and comparison of GenBank and chromatogram mtDNA sequence data generated in a previous study of Baltic grey seals. By re-editing the original chromatogram data we found that approximately 40% of the grey seal mtDNA haplotype sequences posted in GenBank contained errors. The re-analysis of the edited chromatogram data yielded overall similar results and conclusions as the original study. However, a significantly different outcome was observed when using the uncorrected dataset based on the GenBank haplotypes. We therefore suggest disregarding the existing GenBank data and instead using the correct haplotypes reported here. Our study serves as an illustrative example reiterating the importance of quality control through every step of a research project, from data generation to interpretation and submission to an online repository. Errors conducted in any step may lead to biased results and conclusions, and could impact management decisions.

  14. Investigating the prehistory of Tungusic peoples of Siberia and the Amur-Ussuri region with complete mtDNA genome sequences and Y-chromosomal markers.

    Directory of Open Access Journals (Sweden)

    Ana T Duggan

    Full Text Available Evenks and Evens, Tungusic-speaking reindeer herders and hunter-gatherers, are spread over a wide area of northern Asia, whereas their linguistic relatives the Udegey, sedentary fishermen and hunter-gatherers, are settled to the south of the lower Amur River. The prehistory and relationships of these Tungusic peoples are as yet poorly investigated, especially with respect to their interactions with neighbouring populations. In this study, we analyse over 500 complete mtDNA genome sequences from nine different Evenk and even subgroups as well as their geographic neighbours from Siberia and their linguistic relatives the Udegey from the Amur-Ussuri region in order to investigate the prehistory of the Tungusic populations. These data are supplemented with analyses of Y-chromosomal haplogroups and STR haplotypes in the Evenks, Evens, and neighbouring Siberian populations. We demonstrate that whereas the North Tungusic Evenks and Evens show evidence of shared ancestry both in the maternal and in the paternal line, this signal has been attenuated by genetic drift and differential gene flow with neighbouring populations, with isolation by distance further shaping the maternal genepool of the Evens. The Udegey, in contrast, appear quite divergent from their linguistic relatives in the maternal line, with a mtDNA haplogroup composition characteristic of populations of the Amur-Ussuri region. Nevertheless, they show affinities with the Evenks, indicating that they might be the result of admixture between local Amur-Ussuri populations and Tungusic populations from the north.

  15. Molecular characterization and phylogeny of whipworm nematodes inferred from DNA sequences of cox1 mtDNA and 18S rDNA.

    Science.gov (United States)

    Callejón, Rocío; Nadler, Steven; De Rojas, Manuel; Zurita, Antonio; Petrášová, Jana; Cutillas, Cristina

    2013-11-01

    A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from the mitochondrial cytochrome c oxidase 1 (cox1) and ribosomal 18S genes. The taxa consisted of different described species and several host-associated isolates (undescribed taxa) of Trichuris collected from hosts from Spain. Sequence data from mitochondrial cox1 (partial gene) and nuclear 18S near-complete gene were analyzed by maximum likelihood and Bayesian inference methods, as separate and combined datasets, to evaluate phylogenetic relationships among taxa. Phylogenetic results based on 18S ribosomal DNA (rDNA) were robust for relationships among species; cox1 sequences delimited species and revealed phylogeographic variation, but most relationships among Trichuris species were poorly resolved by mitochondrial sequences. The phylogenetic hypotheses for both genes strongly supported monophyly of Trichuris, and distinct genetic lineages corresponding to described species or nematodes associated with certain hosts were recognized based on cox1 sequences. Phylogenetic reconstructions based on concatenated sequences of the two loci, cox1 (mitochondrial DNA (mtDNA)) and 18S rDNA, were congruent with the overall topology inferred from 18S and previously published results based on internal transcribed spacer sequences. Our results demonstrate that the 18S rDNA and cox1 mtDNA genes provide resolution at different levels, but together resolve relationships among geographic populations and species in the genus Trichuris.

  16. Simultaneous occurrence of the 11778 (ND4) and the 9438 (COX III) mtDNA mutations in Leber hereditary optic neuropathy: Molecular, biochemical, and clinical findings

    Energy Technology Data Exchange (ETDEWEB)

    Oostra, R.J.; Bleeker-Wagemakers, E.M.; Zwart, R. [Ophthalmic Research Institute, Amsterdam (Netherlands)] [and others

    1995-10-01

    Three mtDNA point mutations at nucleotide position (np) 3460, at np 11778 and at np 14484, are thought to be of primary importance in the pathogenesis of Leber hereditary optic neuropathy (LHON), a maternally inherited disease characterized by subacute central vision loss. These mutations are present in genes coding for subunits of complex I (NADH dehydrogenase) of the respiratory chain, occur exclusively in LHON maternal pedigrees, and have never been reported to occur together. Johns and Neufeld postulated that an mtDNA mutation at np 9438, in the gene coding for one of the subunits (COX III) of complex IV (cytochrome c oxidase), was also of primary importance. Johns and Neufeld (1993) found this mutation, which changed a conserved glycine to a serine, in 5 unrelated LHON probands who did not carry one of the presently known primary mutations, but they did not find it in 400 controls. However, the role of this sequence variant has been questioned in the Journal when it has been found to occur in apparently healthy African and Cuban individuals. Subsequently, Johns et al. described this mutation in two Cuban individuals presenting with optic and peripheral neuropathy. 22 refs., 1 fig., 1 tab.

  17. Severe manifestation of Leber's hereditary optic neuropathy due to 11778G>A mtDNA mutation in a female with hypoestrogenism due to Perrault syndrome.

    Science.gov (United States)

    Badura-Stronka, Magdalena; Wawrocka, Anna; Zawieja, Krzysztof; Silska, Sylwia; Krawczyński, Maciej Robert

    2013-11-01

    Perrault syndrome (PS) is a rare autosomal recessive condition with ovarian dysgenesis, hearing deficit and neurological abnormalities in female patients. The molecular basis of the syndrome is heterogeneous, mutations in the HSD17B4 gene have been identified in one family and mutations in the HARS2 gene have been found in another one. We have excluded pathogenic changes in the HSD17B4 gene and in the HARS2 gene by a direct sequencing of all coding exons in a female with clinical hallmarks of PS, ataxia and mild mental retardation. In addition, the patient suffers from severe Leber's hereditary optic neuropathy (LHON) due to 11778G>A mtDNA mutation. This case is the first reported patient with PS and LHON. Possible influence of hypoestrogenism on the manifestation of optic neuropathy in this patient is discussed in the context of recent findings concerning the crucial role of estrogens in supporting the vision capacity in LHON-related mtDNA mutation carriers.

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

    Directory of Open Access Journals (Sweden)

    Martyn A. Sharpe

    2012-01-01

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

  19. Occurrence of Deformed wing virus, Chronic bee paralysis virus and mtDNA variants in haplotype K of Varroa destructor mites in Syrian apiaries.

    Science.gov (United States)

    Elbeaino, Toufic; Daher-Hjaij, Nouraldin; Ismaeil, Faiz; Mando, Jamal; Khaled, Bassem Solaiman; Kubaa, Raied Abou

    2016-05-01

    A small-scale survey was conducted on 64 beehives located in four governorates of Syria in order to assess for the first time the presence of honeybee-infecting viruses and of Varroa destructor mites in the country. RT-PCR assays conducted on 192 honeybees (Apis mellifera L.) using virus-specific primers showed that Deformed wing virus (DWV) was present in 49 (25.5%) of the tested samples and Chronic bee paralysis virus (CBPV) in 2 (1.04%), whereas Acute bee paralysis virus, Sacbrood virus, Black queen cell virus and Kashmir bee virus were absent. Nucleotide sequences of PCR amplicons obtained from DWV and CBPV genomes shared 95-97 and 100% identity with isolates reported in the GenBank, respectively. The phylogenetic tree grouped the Syrian DWV isolates in one cluster, distinct from all those of different origins reported in the database. Furthermore, 19 adult V. destructor females were genetically analyzed by amplifying and sequencing four fragments in cytochrome oxidase subunit 1 (cox1), ATP synthase 6 (atp6), cox3 and cytochrome b (cytb) mitochondrial DNA (mtDNA) genes. Sequences of concatenated V. destructor mtDNA genes (2696 bp) from Syria were similar to the Korean (K) haplotype and were found recurrently in all governorates. In addition, two genetic lineages of haplotype K with slight variations (0.2-0.3%) were present only in Tartous and Al-Qunaitra governorates. PMID:26914360

  20. Expansions and Extensions : Ergodic, combinatorial and geometric properties of β-expansions with arbitrary digits

    NARCIS (Netherlands)

    Kalle, C.C.C.J.

    2009-01-01

    Let beta be a real number bigger than 1 and A a finite set of arbitrary real numbers. A beta-expansion with digits in A of a real number x is an expression for x by an infinite sum of fractions with powers of beta in the denominators and elements from A in the numerators. Such expansions can be obta

  1. Influence of MgO-type Expansive Agent Hydration Behaviors on Expansive Properties of Concrete

    Institute of Scientific and Technical Information of China (English)

    LU Xiaolin; GENG Fei; ZHANG Hongbo; CHEN Xiong

    2011-01-01

    The hydration behaviors and expansive properties of MgO-type expansive agent curing at different temperatures and environment were investigated. When the curing temperatures changed from 25℃ to 50 ℃, the conductivities of MgO samples increased from 40 to 80 μ s/cm,and the hydrations of MgO were quickened up obviously. Through SEM observation, the hydration product of MgO cured at 50 ℃ for 28 day was about 2-3 μ m in length. The expansion of pastes with 5% of the MgO-type expansive agent was from 0.36% to 1.01% when the curing temperature changed from 25℃ to 50 ℃. When 8% of the MgO-type expansive agent was added, the early shrinkage of concrete was reduced. The expansion ratio increased with the curing temperature, and the expansive cracking of concrete with MgO-type expansive agent might be decreased by blending fly ash.

  2. [Forum on tissue expansion. Expansion of the scalp. Surgical techniques and clinical applications].

    Science.gov (United States)

    Foyatier, J L; Delay, E; Comparin, J P; Latarjet, J; Masson, C L

    1993-02-01

    Repair of all forms of alopecia is one of the principal applications of scalp expansion. The authors have inserted 400 expansion prostheses, including 20 in the scalp. The surgical technique, choice of material and various types of flaps are described and illustrated by clinical cases of extensive alopecia.

  3. Bond return predictability in expansions and recessions

    DEFF Research Database (Denmark)

    Engsted, Tom; Møller, Stig Vinther; Jensen, Magnus David Sander

    We document that over the period 1953-2011 US bond returns are predictable in expansionary periods but unpredictable during recessions. This result holds in both in-sample and out-of-sample analyses and using both univariate regressions and combination forecasting techniques. A simulation study...... shows that our tests have power to reject unpredictability in both expansions and recessions. To judge the economic significance of the results we compute utility gains for a meanvariance investor who takes the predictability patterns into account and show that utility gains are positive in expansions...... but negative in recessions. The results are also consistent with tests showing that the expectations hypothesis of the term structure holds in recessions but not in expansions. However, the results for bonds are in sharp contrast to results for stocks showing that stock returns are predictable in recessions...

  4. A meaningful expansion around detailed balance

    CERN Document Server

    Colangeli, Matteo; Wynants, Bram

    2011-01-01

    We consider Markovian dynamics modeling open mesoscopic systems which are driven away from detailed balance by a nonconservative force. A systematic expansion is obtained of the stationary distribution around an equilibrium reference, in orders of the nonequilibrium forcing. The first order around equilibrium has been known since the work of McLennan (1959), and involves the transient irreversible entropy flux. The expansion generalizes the McLennan formula to higher orders, complementing the entropy flux with the dynamical activity. The latter is more kinetic than thermodynamic and is a possible realization of Landauer's insight (1975) that, for nonequilibrium, the relative occupation of states also depends on the noise along possible escape routes. In that way nonlinear response around equilibrium can be meaningfully discussed in terms of two main quantities only, the entropy flux and the dynamical activity. The expansion makes mathematical sense as shown in the simplest cases from exponential ergodicity.

  5. Thermal expansion in lead zirconate titanate

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The volume anomalies with temperature variations in tin-modified lead zirconate titanate ceramics are investigated. Experimental results show that the volume changes are related to the phase transitions induced with temperature. The magnitude and orientation of crystal volume changes are dependent on the particular phase transition. When antiferroelectrics is transformed to ferroelectrics or paraelectrics the volume expands. Oppositely when ferroelectrics is transformed to antiferroelectrics or paraelectrics the volume contracts. In the transition of antiferroelectric orthorhombic structure to tetragonal structure or ferroelectric low-temperature rhombohedral structure to high-tem- perature rhombohedral structure, there are also revealed apparent anomalies in the curves of thermal expansion. Among them, the volume strain caused by the transition between antiferroelectrics and ferroelectrics is the biggest in magnitude, and the linear expansion dL/L0 and the expansion coefficient (dL/L0)/dT can reach 2.810?3 and 7.5 × 10?4 K?1 respectively.

  6. On Learning Ring-Sum-Expansions

    DEFF Research Database (Denmark)

    Fischer, Paul; Simon, H. -U.

    1992-01-01

    The problem of learning ring-sum-expansions from examples is studied. Ring-sum-expansions (RSE) are representations of Boolean functions over the base {#123;small infinum, (+), 1}#125;, which reflect arithmetic operations in GF(2). k-RSE is the class of ring-sum-expansions containing only monomials...... be learned from positive (negative) examples alone. However, if the restriction that the hypothesis which is output by the learning algorithm is also a k-RSE is suspended, then k-RSE is learnable from positive (negative) examples only. Moreover, it is proved that 2-term-RSE is learnable by a conjunction...... of a 2-CNF and a 1-DNF. Finally the paper presents learning (on-line prediction) algorithms for k-RSE that are optimal with respect to the sample size (worst case mistake bound)...

  7. Radial expansion for spinning conformal blocks

    CERN Document Server

    Costa, Miguel$uPorto U.; Hansen, Tobias; Penedones, João; Trevisani, Emilio

    2016-01-01

    This paper develops a method to compute any bosonic conformal block as a series expansion in the optimal radial coordinate introduced by Hogervorst and Rychkov. The method reduces to the known result when the external operators are all the same scalar operator, but it allows to compute conformal blocks for external operators with spin. Moreover, we explain how to write closed form recursion relations for the coefficients of the expansions. We study three examples of four point functions in detail: one vector and three scalars; two vectors and two scalars; two spin 2 tensors and two scalars. Finally, for the case of two external vectors, we also provide a more efficient way to generate the series expansion using the analytic structure of the blocks as a function of the scaling dimension of the exchanged operator.

  8. Radial expansion for spinning conformal blocks

    Science.gov (United States)

    Costa, Miguel S.; Hansen, Tobias; Penedones, João; Trevisani, Emilio

    2016-07-01

    This paper develops a method to compute any bosonic conformal block as a series expansion in the optimal radial coordinate introduced by Hogervorst and Rychkov. The method reduces to the known result when the external operators are all the same scalar operator, but it allows to compute conformal blocks for external operators with spin. Moreover, we explain how to write closed form recursion relations for the coefficients of the expansions. We study three examples of four point functions in detail: one vector and three scalars; two vectors and two scalars; two spin 2 tensors and two scalars. Finally, for the case of two external vectors, we also provide a more efficient way to generate the series expansion using the analytic structure of the blocks as a function of the scaling dimension of the exchanged operator.

  9. Query Expansion Based on Clustered Results

    CERN Document Server

    Liu, Ziyang; Chen, Yi

    2011-01-01

    Query expansion is a functionality of search engines that suggests a set of related queries for a user-issued keyword query. Typical corpus-driven keyword query expansion approaches return popular words in the results as expanded queries. Using these approaches, the expanded queries may correspond to a subset of possible query semantics, and thus miss relevant results. To handle ambiguous queries and exploratory queries, whose result relevance is difficult to judge, we propose a new framework for keyword query expansion: we start with clustering the results according to user specified granularity, and then generate expanded queries, such that one expanded query is generated for each cluster whose result set should ideally be the corresponding cluster. We formalize this problem and show its APX-hardness. Then we propose two efficient algorithms named iterative single-keyword refinement and partial elimination based convergence, respectively, which effectively generate a set of expanded queries from clustered r...

  10. Graphite thermal expansion reference for high temperature

    Science.gov (United States)

    Gaal, P. S.

    1974-01-01

    The design requirements of the aerospace and high-temperature nuclear reactor industries necessitate reliable thermal expansion data for graphite and other carbonaceous materials. The feasibility of an acceptable reference for calibration of expansion measuring systems that operate in carbon-rich atmospheres at temperatures ranging to 2500 C is the prime subject of this work. Present-day graphite technology provides acceptable materials for stable, reproducible references, as reflected by some of the candidate materials. The repeatability for a single specimen in a given expansion measuring system was found to be plus or minus 1%, while the combined results of several tests made on a number of samples fell within a plus or minus 2.5% band.

  11. Fluctuation spatial expansion and observational redshifts

    CERN Document Server

    Koehler, D R

    2003-01-01

    Classical determinations of galaxy distances and galaxy recessional velocities have been generated from luminosity and emission spectrometric data. The analyses of these galactic spectrometric electromagnetic frequency shifts have resulted in the Hubble law and are understood as a Doppler effect stemming from an expansion of space. In the present work, a galaxy-core expansion model with a time evolving matter and radiation distribution is put forth, leading to a supplementary treatment of the optical redshift measurements. Einstein's gravitational equations are assumed to apply within a galaxy-core spatial domain and, with utilization of a generalized Robertson-Walker-Schwarzschild metric, are used in order to calculate the evolutionary expansion characteristics. The galaxy-core model is described as a flat metric, matter plus radiation, sigma = 1/3, energy distribution. It predicts an early time density fluctuation collapse, understood to be the formation of a galaxy hole, and provides an interpretational ba...

  12. High flux expansion divertor studies in NSTX

    CERN Document Server

    Soukhanovskii, V A; Bell, R E; Gates, D A; Kaita, R; Kugel, H W; LeBlanc, B P; Maqueda, R; Menard, J E; Mueller, D; Paul, S F; Raman, R; Roquemore, A L

    2009-01-01

    High flux expansion divertor studies have been carried out in the National Spherical Torus Experiment using steady-state X-point height variations from 22 to 5-6 cm. Small-ELM H-mode confinement was maintained at all X-point heights. Divertor flux expansions from 6 to 26-28 were obtained, with associated reduction in X-point connection length from 5-6 m to 2 m. Peak divertor heat flux was reduced from 7-8 MW/m$^2$ to 1-2 MW/m$^2$. In low X-point configuration, outer strike point became nearly detached. Among factors affecting deposition of parallel heat flux in the divertor, the flux expansion factor appeared to be dominant

  13. Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis

    Directory of Open Access Journals (Sweden)

    Marwa A. Eltanany

    2016-09-01

    Full Text Available This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC using representative breeds: Sinai (North, Fayoumi (Middle and Dandarawi (South of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (FST = 0.003. The unimodal mismatch distribution and negative values of Tajima’s D (−0.659 and Fu’s Fs (−0.157 indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.

  14. Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis.

    Science.gov (United States)

    Eltanany, Marwa A; Hemeda, Shabaan A

    2016-09-01

    This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC) using representative breeds: Sinai (North), Fayoumi (Middle) and Dandarawi (South) of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (F ST  = 0.003). The unimodal mismatch distribution and negative values of Tajima's D (-0.659) and Fu's Fs (-0.157) indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program. PMID:27489728

  15. Rotational beta expansion: Ergodicity and Soficness

    OpenAIRE

    Akiyama, Shigeki; Caalim, Jonathan

    2015-01-01

    We study a family of piecewise expanding maps on the plane, generated by composition of a rotation and an expansive similitude of expansion constant $\\beta$. We give two constants $B_1$ and $B_2$ depending only on the fundamental domain that if $\\beta>B_1$ then the expanding map has a unique absolutely continuous invariant probability measure, and if $\\beta>B_2$ then it is equivalent to $2$-dimensional Lebesgue measure. Restricting to a rotation generated by $q$-th root of unity $\\zeta$ with ...

  16. Expansive mortar-induced ocular injury.

    Science.gov (United States)

    Balasubramanya, Ramamurthy; Rani, Alka; Sangwan, Virender S

    2006-12-01

    We describe here a case of bilateral chemical injury (with an expansive mortar which is being used in recent times to cut the rocks). On examination limbal ischemia was more in the left eye (9 clock hours) than the right eye (2 clock hours). The case was managed by bilateral removal of foreign bodies, along with conjunctival resection and amniotic membrane transplantation in the left eye. At six-month follow-up, patient had best corrected visual acuity of 20/30 and 20/60 in the right and left eyes respectively. Since this being an occupational hazard, proper eye protection gear should be used by persons using this expansive mortar.

  17. Strategic Expansion Models in Academic Radiology.

    Science.gov (United States)

    Natesan, Rajni; Yang, Wei T; Tannir, Habib; Parikh, Jay

    2016-03-01

    In response to economic pressures, academic institutions in the United States and their radiology practices, are expanding into the community to build a larger network, thereby driving growth and achieving economies of scale. These economies of scale are being achieved variously via brick-and-mortar construction, community practice acquisition, and partnership-based network expansion. We describe and compare these three expansion models within a 4-part framework of: (1) upfront investment; (2) profitability impact; (3) brand impact; and (4) risk of execution. PMID:26786029

  18. An Edgeworth expansion for symmetric statistics

    OpenAIRE

    Bentkus, V.; Götze, F.; van Zwet, W. R.

    1997-01-01

    We consider asymptotically normal statistics which are symmetric functions of N i.i.d. random variables. For these statistics we prove the validity of an Edgeworth expansion with remainder $O(N^{-1})$ under Cramér's condition on the linear part of the statistic and moment assumptions for all parts of the statistic. By means of a counterexample we show that it is generally not possible to obtain an Edgeworth expansion with remainder $o(N^{-1})$ without imposing additional assumptions on the...

  19. Strategic Expansion Models in Academic Radiology.

    Science.gov (United States)

    Natesan, Rajni; Yang, Wei T; Tannir, Habib; Parikh, Jay

    2016-03-01

    In response to economic pressures, academic institutions in the United States and their radiology practices, are expanding into the community to build a larger network, thereby driving growth and achieving economies of scale. These economies of scale are being achieved variously via brick-and-mortar construction, community practice acquisition, and partnership-based network expansion. We describe and compare these three expansion models within a 4-part framework of: (1) upfront investment; (2) profitability impact; (3) brand impact; and (4) risk of execution.

  20. Expansion of the whole wheat flour extrusion

    DEFF Research Database (Denmark)

    Cheng, Hongyuan; Friis, Alan

    2008-01-01

    A new model framework is proposed to describe the expansion of extrudates with extruder operating conditions based on dimensional analysis principle. The Buckingham pi dimensional analysis method is applied to form the basic structure of the model from extrusion process operational parameters....... Using the Central Composite Design (CCD) method, whole wheat flour was processed in a twin-screw extruder with 16 trials. The proposed model can well correlate the expansion of the 16 trials using 3 regression parameters. The average deviation of the correlation is 5.9%....

  1. The Monetary Policy – Restrictive or Expansive?

    Directory of Open Access Journals (Sweden)

    Adam Szafarczyk

    2007-10-01

    Full Text Available The monetary policy plays an important role in macroeconomic policy of government. There is a question concerning type of this policy expansive or restrictive (easy or tidy monetary policy. Unfortunately, we have a lot of criteria. Each of them gives us other answer. So due to equitation of Irving Fisher we have dominantly expansive monetary policy. This same situation exists when we use nominal value of rediscount interest rate of central bank. Opposite result appears when we use real value of this interest rate or level of obligatory reserve. Taking under consideration liquidity on money market we know, that level of interest rate is too high.

  2. Necessary and Sufficient Conditions for Expansions of Wilson Type

    Institute of Scientific and Technical Information of China (English)

    Kun Chuan WANG

    2008-01-01

    We consider expansions of the type arising from Wilson bases.We characterize such expansions for L2(R).As an application,we see that such an expansion must be orthonormal,in contrast to the case of wavelet expansions generated by translations and dilation.

  3. Principles of Thermal Expansion in Feldspars

    Science.gov (United States)

    Hovis, Guy; Medford, Aaron; Conlon, Maricate; Tether, Allison; Romanoski, Anthony

    2010-05-01

    Following the recent thermal expansion work of Hovis et al. (1) on AlSi3 feldspars, we have investigated the thermal expansion of plagioclase, Ba-K, and Ca-K feldspar crystalline solutions. X-ray powder diffraction data were collected between room temperature and 925 °C on six natural plagioclase specimens ranging in composition from anorthite to oligoclase, the K-exchanged equivalents of these plagioclase specimens, and five synthetic Ba-K feldspars with compositions ranging from 25 to 99 mol % BaAl2Si2O8. The resulting thermal expansion coefficients (α) for volume have been combined with earlier results for end-member Na- and K-feldspars (2,3). Unlike AlSi3 feldspars, Al2Si2 feldspars, including anorthite and celsian from the present study plus Sr- and Pb-feldspar from other workers (4,5), show essentially constant and very limited thermal expansion, regardless of divalent cation size. In the context of structures where the Lowenstein rule (6) requires Al and Si to alternate among tetrahedra, the proximity of bridging Al-O-Si oxygen ions to divalent neighbors (ranging from 0 to 2) produces short Ca-O (or Ba-O) bonds (7,8) that apparently are the result of local charge-balance requirements (9). Gibbs et al. (10) suggest that short bonds such as these have a partially covalent character. This in turn stiffens the structure. Thus, for feldspar series with coupled substitution the change away from a purely divalent M-site occupant gives the substituting (less strongly bonded) monovalent cations increasingly greater influence on thermal expansion. Overall, then, thermal expansion in the feldspar system is well represented on a plot of α against room-temperature volume, where one sees a quadrilateral bounded by data for (A) AlSi3 feldspars whose expansion behavior is controlled largely by the size of the monovalent alkali-site occupant, (B) Al2Si2 feldspars whose expansion is uniformly limited by partially-covalent bonds between divalent M-site occupants and

  4. Thermal expansion of Neapolitan Yellow Tuff

    Science.gov (United States)

    Aversa, S.; Evangelista, A.

    1993-10-01

    In saturated rocks and soils it is possible to define different coefficients of thermal expansion depending on the drainage conditions. This topic is first examined from the theoretical point of view with regard to an ideal isotropic thermo-elastic porous medium. Some special features of the behaviour of natural soils and rocks during thermal expansion tests are subsequently discussed. An experimental evaluation of some of these coefficients is presented in the second part of the paper. The material investigated is a pyroclastic rock, the so-called Neapolitan Yellow Tuff. Thermal expansion coefficient in drairend conditions has been evaluated, when this material is saturated with water. The e pressure increase induced by heating has been measured in undrained tes temperatures investigated range between room temperature up to 225°C. Different types of apparatus have been used and, when possible, a comparison between the results has been proposed. The results obtained in undrained thermal expansion tests are in agreement with theoretical predictions. This research is part of an on-going study of the complex phenomena known as Bradyseism, which is occurring in a volcanic area a few kilometers from Naples (Italy). Some considerations on this phenomenon are drawn in the last paragraph of the paper.

  5. Eta-expansion does The Trick

    DEFF Research Database (Denmark)

    Danvy, Olivier; Malmkjær, Karoline; Palsberg, Jens

    1996-01-01

    across dynamic case expressions. This requirement precisely accounts for the nonstandard use of continuation-passing style encountered in partial evaluation. Eta-expansion thus acts as a uniform binding-time coercion between values and contexts, be they of function type, product type, or disjoint...

  6. Eta-Expansion Does The Trick

    DEFF Research Database (Denmark)

    Danvy, Olivier; Malmkjær, Karoline; Palsberg, Jens

    1995-01-01

    across dynamic case expressions. This requirement precisely accounts for the nonstandard use of continuation-passing style encountered in partial evaluation. Eta-expansion thus acts as a uniform binding-time coercion between values and contexts, be they of function type, product type, or disjoint...

  7. Eta-Expansion Does The Trick

    DEFF Research Database (Denmark)

    Danvy, Olivier; Malmkjær, Karoline; Palsberg, Jens

    1996-01-01

    across dynamic case expressions. This requirement precisely accounts for the nonstandard use of continuation-passing style encountered in partial evaluation. Eta-expansion thus acts as a uniform binding-time coercion between values and contexts, be they of function type, product type, or disjoint...

  8. Multipole expansion approach to Ostwald ripening

    International Nuclear Information System (INIS)

    A multipole expansion theory is used to derive a kinetic equation for a collection of droplets undergoing the Ostwald ripening or coarsening in two dimensions. The theory allows the morphological change of coarsening droplets as well as the migration behavior. Numerical computations are performed to give a good estimate to the solution of Laplace equation even in a few mode truncation

  9. Climate Science: Tropical Expansion by Ocean Swing

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jian

    2014-04-01

    The tropical belt has become wider over the past decades, but climate models fall short of capturing the full rate of the expansion. The latest analysis of the climate simulations suggests that a long-term swing of the Pacific Decadal Oscillation is the main missing cause.

  10. Further Notes on the Gaussian Beam Expansion

    Institute of Scientific and Technical Information of China (English)

    DAI Yu-Rong; DING De-Sheng

    2012-01-01

    We provide alternatively a simple way of computing the Fresnel field integral, a further extension to the Gaussian-beam expansion. With a known result that the circ function is approximately decomposed into a sum of Gaussian functions, the zero-order Bessel function of the first kind is similarly expanded by the Bessel-Fourior transform. Two expansions are together inserted in this integral, which is then expressible in terms of the simple algebraic functions. The approach is useful in treatment of the field radiation problem for a large and important group of piston sources in acoustics. As examples, the calculation results for the uniform and the simply supported piston sources are presented, in a good agreement with those evaluated by numerical integration.%We provide alternatively a simple way of computing the Fresnel field integral,a further extension to the Gaussianbeam expansion.With a known result that the circ function is approximately decomposed into a sum of Gaussian functions,the zero-order Bessel function of the first kind is similarly expanded by the Bessel-Fourior transform.Two expansions are together inserted in this integral,which is then expressible in terms of the simple algebraic functions.The approach is useful in treatment of the field radiation problem for a large and important group of piston sources in acoustics.As examples,the calculation results for the uniform and the simply supported piston sources are presented,in a good agreement with those evaluated by numerical integration.

  11. THE COMPLETE ASYMPTOTIC EXPANSION FOR BASKAKOV OPERATORS

    Institute of Scientific and Technical Information of China (English)

    Chungou Zhang; Quane Wang

    2007-01-01

    In this paper, we derive the complete asymptotic expansion of classical Baskakov itly in terms of Stirling number of the first and second kind and another number G(I, p). As a corollary, we also get the Voronovskaja-type result for the operators.

  12. Stakeholder Support for School Food Policy Expansions

    Science.gov (United States)

    Pettigrew, Simone; Pescud, Melanie; Donovan, Robert J.

    2012-01-01

    The aim of this study was to assess the extent to which parents and school-based stakeholders (principals, teachers, canteen managers and Parents & Citizen Committee presidents) are supportive of potential expansions to a new school food policy. Eight additional policy components elicited in preliminary focus groups with parents and 19 additional…

  13. Polytope expansion of Lie characters and applications

    Energy Technology Data Exchange (ETDEWEB)

    Walton, Mark A., E-mail: walton@uleth.ca [Department of Physics and Astronomy, University of Lethbridge, Lethbridge, Alberta T1K 3M4 (Canada)

    2013-12-15

    The weight systems of finite-dimensional representations of complex, simple Lie algebras exhibit patterns beyond Weyl-group symmetry. These patterns occur because weight systems can be decomposed into lattice polytopes in a natural way. Since lattice polytopes are relatively simple, this decomposition is useful, in addition to being more economical than the decomposition into single weights. An expansion of characters into polytope sums follows from the polytope decomposition of weight systems. We study this polytope expansion here. A new, general formula is given for the polytope sums involved. The combinatorics of the polytope expansion are analyzed; we point out that they are reduced from those of the Weyl character formula (described by the Kostant partition function) in an optimal way. We also show that the weight multiplicities can be found easily from the polytope multiplicities, indicating explicitly the equivalence of the two descriptions. Finally, we demonstrate the utility of the polytope expansion by showing how polytope multiplicities can be used in the calculation of tensor product decompositions, and subalgebra branching rules.

  14. Accelerated dryland expansion under climate change

    Science.gov (United States)

    Huang, Jianping; Yu, Haipeng; Guan, Xiaodan; Wang, Guoyin; Guo, Ruixia

    2016-02-01

    Drylands are home to more than 38% of the total global population and are one of the most sensitive areas to climate change and human activities. Projecting the areal change in drylands is essential for taking early action to prevent the aggravation of global desertification. However, dryland expansion has been underestimated in the Fifth Coupled Model Intercomparison Project (CMIP5) simulations considering the past 58 years (1948-2005). Here, using historical data to bias-correct CMIP5 projections, we show an increase in dryland expansion rate resulting in the drylands covering half of the global land surface by the end of this century. Dryland area, projected under representative concentration pathways (RCPs) RCP8.5 and RCP4.5, will increase by 23% and 11%, respectively, relative to 1961-1990 baseline, equalling 56% and 50%, respectively, of total land surface. Such an expansion of drylands would lead to reduced carbon sequestration and enhanced regional warming, resulting in warming trends over the present drylands that are double those over humid regions. The increasing aridity, enhanced warming and rapidly growing human population will exacerbate the risk of land degradation and desertification in the near future in the drylands of developing countries, where 78% of dryland expansion and 50% of the population growth will occur under RCP8.5.

  15. Constraints on anisotropic cosmic expansion from supernovae

    Science.gov (United States)

    Kalus, B.; Schwarz, D. J.; Seikel, M.; Wiegand, A.

    2013-05-01

    Aims: We test the isotropy of the expansion of the Universe by estimating the hemispherical anisotropy of supernova type Ia (SN Ia) Hubble diagrams at low redshifts (z < 0.2). Methods: We compare the best fit Hubble diagrams in pairs of hemispheres and search for the maximal asymmetric orientation. For an isotropic Universe, we expect only a small asymmetry due to noise and the presence of nearby structures. This test does not depend on the assumed content of the Universe, the assumed model of gravity, or the spatial curvature of the Universe. The expectation for possible fluctuations due to large scale structure is evaluated for the Λ cold dark matter (ΛCDM) model and is compared to the supernova data from the Constitution set for four different light curve fitters, thus allowing a study of the systematic effects. Results: The expected order of magnitude of the hemispherical asymmetry of the Hubble expansion agrees with the observed one. The direction of the Hubble asymmetry is established at 95% confidence level (C.L.) using both, the MLCS2k2 and the SALT II light curve fitter. The highest expansion rate is found towards (ℓ,b) ≈ (-35°, -19°), which agrees with directions reported by other studies. Its amplitude is not in contradiction to expectations from the ΛCDM model. The measured Hubble anisotropy is ΔH/H ~ 0.026. With 95% C.L. the expansion asymmetry is ΔH/H < 0.038.

  16. Integrating transcriptional controls for plant cell expansion

    OpenAIRE

    Mockaitis, Keithanne; Estelle, Mark

    2004-01-01

    The plant hormones auxin and brassinosteroid promote cell expansion by regulating gene expression. In addition to independent transcriptional responses generated by the two signals, recent microarray analyses indicate that auxin and brassinosteroid also coordinate the expression of a set of shared target genes.

  17. Global Expansion and English Language Learning

    Science.gov (United States)

    Andrade, Maureen Snow

    2016-01-01

    Demand for higher education is global. As institutions extend opportunities beyond their borders, English language proficiency must be considered. This chapter focuses on considerations related to global expansion, with an emphasis on the role of distance English language courses and the distinct considerations in their development.

  18. Territorial expansion and primary state formation.

    Science.gov (United States)

    Spencer, Charles S

    2010-04-20

    A major research problem in anthropology is the origin of the state and its bureaucratic form of governance. Of particular importance for evaluating theories of state origins are cases of primary state formation, whereby a first-generation state evolves without contact with any preexisting states. A general model of this process, the territorial-expansion model, is presented and assessed with archaeological data from six areas where primary states emerged in antiquity: Mesoamerica, Peru, Egypt, Mesopotamia, the Indus Valley, and China. In each case, the evidence shows a close correspondence in time between the first appearance of state institutions and the earliest expansion of the state's political-economic control to regions lying more than a day's round-trip from the capital. Although additional research will add detail and clarity to the empirical record, the results to date are consistent with the territorial-expansion model, which argues that the success of such long-distance expansion not only demanded the bureaucratization of central authority but also helped provide the resources necessary to underwrite this administrative transformation. PMID:20385804

  19. Religiosity and the expansion of caregiver stress.

    Science.gov (United States)

    Leblanc, A J; Driscoll, A K; Pearlin, L I

    2004-09-01

    We present a stress process framework as a model for understanding how religiosity may influence the expansion of stress. Survey data from informal caregivers to a spouse with Alzheimer's disease or a related dementia (n = 200) were analyzed to observe the relationships among three variables: (1) care-related stress, (2) religiosity, and (3) depression. This sample, which has a mean age of 73 years, demonstrates high rates of self-described religiosity, church attendance and frequency of prayer. Using these criteria, women and racial/ethnic minority caregivers are the most religious. In a series of multivariate analyses, we found strong evidence to suggest that there is an expansion of care-related stressors leading to depression in this sample. Religiosity, as measured here, appears to be largely unrelated to stress and stress expansion. We found no evidence to suggest that it moderates stress expansion. However, these data do suggest that one stressor--feelings of role overload--is correlated with greater levels of self-perceived religiosity, which among caregivers who have health problems of their own is associated with greater depressive symptomatology. Thus, for a sub-sample of these caregivers, we find weak evidence of a mediation effect wherein one subjective, non-organizational dimension of religiosity is a conduit of the harmful effects of stress (rather than a suppressor). Results and data limitations are discussed in relation to better assessing the role of religiosity and spirituality in the experience of the stress process.

  20. Zero bias transformation and asymptotic expansions

    OpenAIRE

    Jiao, Ying

    2012-01-01

    Let W be a sum of independent random variables. We apply the zero bias transformation to deduce recursive asymptotic expansions for $\\mathbb {E}[h(W)]$ in terms of normal expectations, or of Poisson expectations for integer-valued random variables. We also discuss the estimates of remaining errors.

  1. Isentropic expansion of shock-compressed substances.

    Science.gov (United States)

    Zhernokletov, M. V.

    2001-06-01

    The below parts of the paper are devoted to experimental results = obtained by the barrier method when researching metals, explosion = products, and polymers. Metals. The method of isentropic expansion was used to research = trancritical states of copper, lead, bismuth, molybdenum, uranium, = tungsten, nickel, tin, chrome, and zinc. To increase entropy under shock = compression and realize trancritical states during expansion, porous = samples were used. The highest degrees of expansion are reached on = isentropes obtained with use of hemispherical generators of shock waves. = The performed tests showed absence of significant jumps of thermodynamic = function or any hydrodynamic anomalies which could be interpeted as = specific plasma phase transformations. The tests data testify to = continuous change of metals properties at expansion from the condensed = state up to the gas state. Isentropes of explosion products (EP). In tests the shock wave = parameters were determined in inert materials-obstacles directly = contacting HE under research. TNT and two TNT-RDX alloys (50/50 and = 25/75) were used as this HE. The experimental data were compared with = data obtained by calculations using various EOS, including the cubic EOS = (P=3DAρ^3). It is shown that the cubic EOS has significant = disagreement with test in the area below 1 GPa. Polymeric materials. Teflon, polystyrene, plexiglas, phenylone, and = stilbene are studied. Analysis of experimental data testifies that = polystyrene, phenylone, and stilbene undergo a series of = physical-chemical transformations with pressure growth in the front of = shock-waves.

  2. Aspects of the Flavour Expansion Theorem

    CERN Document Server

    Paraskevas, M

    2015-01-01

    The Flavour Expansion Theorem, which has been recently proposed as a more general and elegant algebraic method, for the derivation of the commonly used Mass Insertion Approximation, is revisited. The theorem is reviewed, with respect to its straightforward applications in Flavour physics, and compared against the standard diagrammatic flavour basis techniques, in cases where the latter become inadequate.

  3. Symbiosis catalyses niche expansion and diversification.

    Science.gov (United States)

    Joy, Jeffrey B

    2013-04-01

    Interactions between species are important catalysts of the evolutionary processes that generate the remarkable diversity of life. Symbioses, conspicuous and inherently interesting forms of species interaction, are pervasive throughout the tree of life. However, nearly all studies of the impact of species interactions on diversification have concentrated on competition and predation leaving unclear the importance of symbiotic interaction. Here, I show that, as predicted by evolutionary theories of symbiosis and diversification, multiple origins of a key innovation, symbiosis between gall-inducing insects and fungi, catalysed both expansion in resource use (niche expansion) and diversification. Symbiotic lineages have undergone a more than sevenfold expansion in the range of host-plant taxa they use relative to lineages without such fungal symbionts, as defined by the genetic distance between host plants. Furthermore, symbiotic gall-inducing insects are more than 17 times as diverse as their non-symbiotic relatives. These results demonstrate that the evolution of symbiotic interaction leads to niche expansion, which in turn catalyses diversification. PMID:23390106

  4. A Pedagogical Approach to the Magnus Expansion

    Science.gov (United States)

    Blanes, S.; Casas, F.; Oteo, J. A.; Ros, J.

    2010-01-01

    Time-dependent perturbation theory as a tool to compute approximate solutions of the Schrodinger equation does not preserve unitarity. Here we present, in a simple way, how the "Magnus expansion" (also known as "exponential perturbation theory") provides such unitary approximate solutions. The purpose is to illustrate the importance and…

  5. Effects of forest expansion on mountain grassland

    DEFF Research Database (Denmark)

    Guidi, Claudia; Magid, Jakob; Rodeghiero, Mirco;

    2014-01-01

    Background and aims. Grassland abandonment followed by forest succession is the dominant land-use change in the European Alps. We studied the impact of current forest expansion on mountain grassland on changes in physical soil organic carbon (SOC) fractions along a land-use and management gradient...

  6. The worldwide expansion of the Argentine ant

    DEFF Research Database (Denmark)

    Vogel, Valerie; Pedersen, Jes Søe; Giraud, Tatiana;

    2010-01-01

    ) and secondary introductions (from sites with established invasive supercolonies) were important in the global expansion of the Argentine ant. In combination with the similar social organization of colonies in the native and introduced range, this indicates that invasiveness did not evolve recently as a unique...

  7. Series Expansions for three-dimensional QED

    CERN Document Server

    Hamer, C J; Weihong, Z; Weihong, Zheng

    1998-01-01

    Strong-coupling series expansions are calculated for the Hamiltonian version of compact lattice electrodynamics in (2+1) dimensions, with 4-component fermions. Series are calculated for the ground-state energy per site, the chiral condensate, and the masses of `glueball' and positronium states. Comparisons are made with results obtained by other techniques.

  8. MAP-based infrared image expansion

    Institute of Scientific and Technical Information of China (English)

    Nan Zhang; Weiqi Jin; Binghua Su; Yangyang Liu; Hua Chen

    2005-01-01

    @@ Image expansion plays a very important role in image analysis. Common methods of image expansion, such as the zero-order hold method, may generate a visual mosaic to the expanded image, linear and cubic spline interpolation may blur the image data at peripheral regions. Since infrared images have the characteristics of low contrast and low signal-to-noise ratio (SNR), the expanded images derived from common methods are not satisfactory. As shown in the analysis of the course from images with low resolution to those with high resolution, the expansion of image is found to be an ill-posed inverse problem. An image interpolation algorithm based on MAP estimation under Bayesian framework is proposed in this paper,which can effectively preserve the discontinuities in the original image. Experimental results demonstrate that the expanded images by this method are visually and quantitatively (analyzed by using the criteria of mean squared error (MSE) and mean absolute error (MAE)) superior to the images expanded by common methods of linear interpolation. Even in expansion of infrared images, this method can also give good results. An analysis about choosing regularization parameter α in this algorithm is given.

  9. Research on the different content of weathered sand influence on expansive characteristic of a highway expansive soil in Yichang

    Institute of Scientific and Technical Information of China (English)

    Yang Jun; Li Xinchun; Zhang Guodong; Tang Yunwei; Xie Zhigang

    2013-01-01

    This paper aims at widespread presence of expansive soil which can be obtained in the project from Xiaoxita to Yaqueling first-class highway rebuilding engineering in Yichang City of Hubei Province and weathered sand which can be made full use locally,many experiments have been made. Compaction experiments and expan-sibility index indoor experiments of undisturbed expansive soil and expansive soil mixed with sand ranging from 10%to 50%have been made. Through the test mixing undisturbed expansive soil with different content of weath-ered sand,it can change the expansive soil water characteristics and compaction characteristics. It can influence the expansibility of the expansive soil index and significantly inhibit the expansibility of the expansive soil and reach the standard of roadbed filler.

  10. 216-B-3 expansion ponds closure plan

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

    This document describes the activities for clean closure under the Resource Conservation and Recovery Act of 1976 (RCRA) of the 216-B-3 Expansion Ponds. The 216-B-3 Expansion Ponds are operated by the US Department of Energy, Richland Operations Office (DOE-RL) and co-operated by Westinghouse Hanford Company (Westinghouse Hanford). The 216-B-3 Expansion Ponds consists of a series of three earthen, unlined, interconnected ponds that receive waste water from various 200 East Area operating facilities. The 3A, 3B, and 3C ponds are referred to as Expansion Ponds because they expanded the capability of the B Pond System. Waste water (primarily cooling water, steam condensate, and sanitary water) from various 200 East Area facilities is discharged to the Bypass pipe (Project X-009). Water discharged to the Bypass pipe flows directly into the 216-B-3C Pond. The ponds were operated in a cascade mode, where the Main Pond overflowed into the 3A Pond and the 3A Pond overflowed into the 3C Pond. The 3B Pond has not received waste water since May 1985; however, when in operation, the 3B Pond received overflow from the 3A Pond. In the past, waste water discharges to the Expansion Ponds had the potential to have contained mixed waste (radioactive waste and dangerous waste). The radioactive portion of mixed waste has been interpreted by the US Department of Energy (DOE) to be regulated under the Atomic Energy Act of 1954; the dangerous waste portion of mixed waste is regulated under RCRA.

  11. 216-B-3 expansion ponds closure plan

    International Nuclear Information System (INIS)

    This document describes the activities for clean closure under the Resource Conservation and Recovery Act of 1976 (RCRA) of the 216-B-3 Expansion Ponds. The 216-B-3 Expansion Ponds are operated by the US Department of Energy, Richland Operations Office (DOE-RL) and co-operated by Westinghouse Hanford Company (Westinghouse Hanford). The 216-B-3 Expansion Ponds consists of a series of three earthen, unlined, interconnected ponds that receive waste water from various 200 East Area operating facilities. The 3A, 3B, and 3C ponds are referred to as Expansion Ponds because they expanded the capability of the B Pond System. Waste water (primarily cooling water, steam condensate, and sanitary water) from various 200 East Area facilities is discharged to the Bypass pipe (Project X-009). Water discharged to the Bypass pipe flows directly into the 216-B-3C Pond. The ponds were operated in a cascade mode, where the Main Pond overflowed into the 3A Pond and the 3A Pond overflowed into the 3C Pond. The 3B Pond has not received waste water since May 1985; however, when in operation, the 3B Pond received overflow from the 3A Pond. In the past, waste water discharges to the Expansion Ponds had the potential to have contained mixed waste (radioactive waste and dangerous waste). The radioactive portion of mixed waste has been interpreted by the US Department of Energy (DOE) to be regulated under the Atomic Energy Act of 1954; the dangerous waste portion of mixed waste is regulated under RCRA

  12. Novel expansion techniques for skin grafts

    Science.gov (United States)

    Kadam, Dinesh

    2016-01-01

    The quest for skin expansion is not restricted to cover a large area alone, but to produce acceptable uniform surfaces, robust engraftment to withstand mechanical shear and infection, with a minimal donor morbidity. Ease of the technique, shorter healing period and reproducible results are essential parameters to adopt novel techniques. Significant advances seen in four fronts of autologous grafting are: (1) Dermal–epidermal graft expansion techniques, (2) epidermal graft harvests technique, (3) melanocyte-rich basal cell therapy for vitiligo and (4) robust and faster autologous cell cultures. Meek's original concept that the sum of perimeter of smaller grafts is larger than the harvested graft, and smaller the graft size, the greater is the potential for regeneration is witnessed in newer modification. Further, as graft size becomes smaller or minced, these micrografts can survive on the wound bed exudate irrespective of their dermal orientation. Expansion produced by 4 mm × 4 mm sized Meek micrografts is 10-folds, similarly 0.8 mm × 0.8 mm size micrografts produce 100-fold expansion, which becomes 700-fold with pixel grafts of 0.3 mm × 0.3 mm size. Fractional skin harvest is another new technique with 700 μ size full thickness graft. These provide instant autologous non-cultured graft to cover extensive areas with similar quality of engraftment surface as split skin grafts. Newer tools for epidermal blister graft harvest quickly, with uniform size to produce 7-fold expansions with reproducible results. In addition, donor area heals faster with minimal scar. Melanocyte-rich cell suspension is utilised in vitiligo surgery tapping the potential of hair root melanocytes. Further advances in the cell culture to reduce the cultivation time and provide stronger epidermal sheets with dermal carrier are seen in trials. PMID:27274117

  13. Expansion of World Drylands Under Global Warming

    Science.gov (United States)

    Feng, S.; Fu, Q.; Hu, Q. S.

    2012-12-01

    The world drylands including both semi-arid and arid regions comprise of one-third of the global land surfaces, which support 14% of the world's inhabitants and a significant share of the world agriculture. Because of meager annual precipitation and large potential evaporative water loss, the ecosystems over drylands are fragile and sensitive to the global change. By analyzing the observations during 1948-2008 and 20 fully coupled climate model simulations from CMIP5 for the period 1900-2100, this study evaluated the changes of the world drylands that are defined with a modified form of the Thornthwaite's moisture index. The results based on observational data showed that the world drylands are steadily expanding during the past 60 years. The areas occupied by drylands in 1994-2008 is about 2.0×10^6km^2 (or 4%) larger than the average during the 1950s. Such an expansion is also a robust feature in the simulations of the 20 global climate models, though the rate is much smaller in the models. A stronger expanding rate is projected during the first half of this century than the simulations in the last century, followed by accelerating expansion after 2050s under the high greenhouse gas emission scenario (RCP8.5). By the end of this century, the world drylands are projected to be over 58×10^6km^2 (or 11% increase compared to the 1961-1990 climatology). The projected expansion of drylands, however, is not homogeneous over the world drylands, with major expansion of arid regions over the southwest North America, the northern fringe of Africa, southern Africa and Australia. Major expansions of semi-arid regions are projected over the north side of the Mediterranean, southern Africa, North and South America. The global warming is the main factor causing the increase of potential evapotranspiration estimated by Penman-Monteith algorithm, which in turn dominants the expansion of drylands. The widening of Hadley cell, which has impact on both temperature and precipitation

  14. Defining chemical expansion: the choice of units for the stoichiometric expansion coefficient

    DEFF Research Database (Denmark)

    Marrocchelli, Dario; Chatzichristodoulou, Christodoulos; Bishop, Sean R.

    2014-01-01

    Chemical expansion refers to the spatial dilation of a material that occurs upon changes in its composition. When this dilation is caused by a gradual, iso-structural increase in the lattice parameter with composition, it is related to the composition change by the stoichiometric expansion coeffi...... are provided for changes in oxygen content in fluorite, perovskite, and Ruddlesden-Popper (K2NiF4) phase materials used in solid oxide fuel cells....

  15. Green turtles (Chelonia mydas) foraging at Arvoredo Island in Southern Brazil: Genetic characterization and mixed stock analysis through mtDNA control region haplotypes.

    Science.gov (United States)

    Proietti, Maíra Carneiro; Lara-Ruiz, Paula; Reisser, Júlia Wiener; da Silva Pinto, Luciano; Dellagostin, Odir Antonio; Marins, Luis Fernando

    2009-07-01

    We analyzed mtDNA control region sequences of green turtles (Chelonia mydas) from Arvoredo Island, a foraging ground in southern Brazil, and identified eight haplotypes. Of these, CM-A8 (64%) and CM-A5 (22%) were dominant, the remainder presenting low frequencies (Rocas/Noronha, in Brazil (p > 0.05). Mixed Stock Analysis, incorporating eleven Atlantic and one Mediterranean rookery as possible sources of individuals, indicated Ascension and Aves islands as the main contributing stocks to the Arvoredo aggregation (68.01% and 22.96%, respectively). These results demonstrate the extensive relationships between Arvoredo Island and other Atlantic foraging and breeding areas. Such an understanding provides a framework for establishing adequate management and conservation strategies for this endangered species. PMID:21637527

  16. Green turtles (Chelonia mydas foraging at Arvoredo Island in Southern Brazil: genetic characterization and mixed stock analysis through mtDNA control region haplotypes

    Directory of Open Access Journals (Sweden)

    Maíra Carneiro Proietti

    2009-01-01

    Full Text Available We analyzed mtDNA control region sequences of green turtles (Chelonia mydas from Arvoredo Island, a foraging ground in southern Brazil, and identified eight haplotypes. Of these, CM-A8 (64% and CM-A5 (22% were dominant, the remainder presenting low frequencies ( 0.05. Mixed Stock Analysis, incorporating eleven Atlantic and one Mediterranean rookery as possible sources of individuals, indicated Ascension and Aves islands as the main contributing stocks to the Arvoredo aggregation (68.01% and 22.96%, respectively. These results demonstrate the extensive relationships between Arvoredo Island and other Atlantic foraging and breeding areas. Such an understanding provides a framework for establishing adequate management and conservation strategies for this endangered species.

  17. The Hydration Characteristics and Expansion Machanism of Expansive Cement at Low W/B Ratio

    Institute of Scientific and Technical Information of China (English)

    LU Lin-nu; HE Yong-jia; LI Yue; DING Qing-jun; HU Shu-guang

    2003-01-01

    The hydration characteristics and expansion impetus of three kinds of cement paste under freeand confined-curing conditions were investigated, which were respectively mixed with three different kinds of expansive agent at low W/ B ratio. The results show that the hydration products of pure cement paste and paste mixed with expansive agent are same, but the amount of hydration products , un-hydrated C3 S and C2 S are obviously different at the same hydration age. At 3 d age, the amount of CH in pure cement paste is less than that of paste mixed with expaasive agent, but it is reverse when at 28d age. The amount of AFt at 3d and 28d age in pure cement paste is less than those of paste mixed with expansive agent. Regardless of under free- or confined-curing condition, the amount of ettringite produced varies little since 3 d age. The joint effect of the tumefaction of gel-ettringite due to water absorption and the expansive pressure on the pore caased by the crystalloid ettringite is the cause of the volume expansion of cement paste, and the former effect is much greater than the latter .

  18. Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae.

    Science.gov (United States)

    Kornilios, P; Thanou, E; Kapli, P; Parmakelis, A; Chatzaki, M

    2016-05-01

    The Aegean region, located in the Eastern Mediterranean, is an area of rich biodiversity and endemism. Its position, geographical configuration and complex geological history have shaped the diversification history of many animal taxa. Mygalomorph spiders have drawn the attention of researchers, as excellent model systems for phylogeographical investigations. However, phylogeographic studies of spiders in the Aegean region are scarce. In this study, we focused on the phylogeography of the endemic ctenizid trap-door spider Cyrtocarenum Ausserer, 1871. The genus includes two morphologically described species: C. grajum (C.L. Koch, 1836) and C. cunicularium (Olivier, 1811). We sampled 60 specimens from the distributions of both species and analyzed four mitochondrial and two nuclear markers. Cyrtocarenum served as an example to demonstrate the importance of natural history traits in the inference of phylogeographic scenarios. The mtDNA substitution rates inferred for the genus are profoundly higher compared to araneomorph spiders and other arthropods, which seems tightly associated with their biology. We evaluate published mtDNA substitution rates followed in the literature for mygalomorph spiders and discuss potential pitfalls. Following gene tree (maximum likelihood, Bayesian inference) and species tree approaches ((*)BEAST), we reconstructed a time-calibrated phylogeny of the genus. These results, combined with a biogeographical ancestral-area analysis, helped build a biogeographic scenario that describes how the major palaeogeographic and palaeoclimatic events of the Aegean may have affected the distribution of Cyrtocarenum lineages. The diversification of the genus seems to have begun in the Middle Miocene in the present west Aegean area, while major phylogenetic events occurred at the Miocene-Pliocene boundary for C. cunicularium, probably related to the Messinian Salinity Crisis. Our results also demonstrate the clear molecular distinction of the two

  19. Evolution of opercle bone shape along a macrohabitat gradient: species identification using mtDNA and geometric morphometric analyses in neotropical sea catfishes (Ariidae).

    Science.gov (United States)

    Stange, Madlen; Aguirre-Fernández, Gabriel; Cooke, Richard G; Barros, Tito; Salzburger, Walter; Sánchez-Villagra, Marcelo R

    2016-08-01

    Transitions between the marine and freshwater macrohabitat have occurred repeatedly in the evolution of teleost fishes. For example, ariid catfishes have moved from freshwater to marine environments, and vice versa. Opercles, a skeletal feature that has been shown to change during such transitions, were subjected to 2D geometric morphometric analyses in order to investigate evolutionary shape changes during habitat transition in ariid catfishes and to test the influence of habitat on shape changes. A mtDNA marker, which proved useful in previous studies, was used to verify species identities. It greatly improved the assignment of specimens to a species, which are difficult to assign by morphology alone. The application of a mtDNA marker confirmed the occurrence of Notarius biffi in Central America, South of El Salvador. Molecular identification together with principal component analysis (PCA) and further morphological inspection of neurocrania indicated the existence of a cryptic species within Bagre pinnimaculatus. Principal component (PC) scores of individual specimens clustered in morphospace by genus rather than by habitat. Strong phylogenetic structure was detected using a permutation test of PC scores of species means on a phylogenetic tree. Calculation of Pagel's λ suggested that opercle shape evolved according to a Brownian model of evolution. Yet canonical variate analysis (CVA) conducted on the habitat groups showed significant differences in opercle shapes among freshwater and marine species. Overall, opercle shape in tropical American Ariidae appears to be phylogenetically constrained. This verifies the application of opercle shape as a taxonomic tool for species identification in fossil ariid catfishes. At the same time, adaptation to freshwater habitats shows characteristic opercle shape trajectories in ariid catfishes, which might be used to detect habitat preferences in fossils. PMID:27547357

  20. Female gene pools of Berber and Arab neighboring communities in central Tunisia: microstructure of mtDNA variation in North Africa.

    Science.gov (United States)

    Cherni, Lotfi; Loueslati, Besma Yaacoubi; Pereira, Luísa; Ennafaâ, Hajer; Amorim, António; El Gaaied, Amel Ben Ammar

    2005-02-01

    North African populations are considered genetically closer to Eurasians than to sub-Saharans. However, they display a considerably high mtDNA heterogeneity among them, namely in the frequencies of the U6, East African, and sub-Saharan haplogroups. In this study, we describe and compare the female gene pools of two neighboring Tunisian populations, Kesra (Berber) and Zriba (non-Berber), which have contrasting historical backgrounds. Both populations presented lower diversity values than those observed for other North African populations, and they were the only populations not showing significant negative Fu's F(S) values. Kesra displayed a much higher proportion of typical sub-Saharan haplotypes (49%, including 4.2% of M1 haplogroup) than Zriba (8%). With respect to U6 sequences, frequencies were low (2% in Kesra and 8% in Zriba), and all belonged to the subhaplogroup U6a. An analysis of these data in the context of North Africa reveals that the emerging picture is complex, because Zriba would match the profile of a Berber Moroccan population, whereas Kesra, which shows twice the frequency of sub-Saharan lineages normally observed in northern coastal populations, would match a western Saharan population except for the low U6 frequency. The North African patchy mtDNA landscape has no parallel in other regions of the world and increasing the number of sampled populations has not been accompanied by any substantial increase in our understanding of its phylogeography. Available data up to now rely on sampling small, scattered populations, although they are carefully characterized in terms of their ethnic, linguistic, and historical backgrounds. It is therefore doubtful that this picture truly represents the complex historical demography of the region rather than being just the result of the type of samplings performed so far.

  1. The Nonexistence of Expansive Zd Actions on Graphs

    Institute of Scientific and Technical Information of China (English)

    En Hui SHI; Li Zhen ZHOU

    2005-01-01

    It is well known that if X is an arc or a circle, then there is no expansive homeomorphism on X. In this paper we prove that there is no expansive Zd action on X, which answers the two questions raised by us before. In 1979, Man?proved that there is no expansive homeomorphism on infinite dimensional spaces. Contrary to this result, we construct an expansive Z2 action on an infinite dimensional space. We also construct an expansive Z2 action on a zero dimensional space but no element in Z2 is expansive.

  2. Gradient expansion, curvature perturbations and magnetized plasmas

    CERN Document Server

    Giovannini, Massimo

    2011-01-01

    The properties of magnetized plasmas are always investigated under the hypothesis that the relativistic inhomogeneities stemming from the fluid sources and from the geometry itself are sufficiently small to allow for a perturbative description prior to photon decoupling. The latter assumption is hereby relaxed and pre-decoupling plasmas are described within a suitable expansion where the inhomogeneities are treated to a given order in the spatial gradients. It is argued that the (general relativistic) gradient expansion shares the same features of the drift approximation, customarily employed in the description of cold plasmas, so that the two schemes are physically complementary in the large-scale limit and for the low-frequency branch of the spectrum of plasma modes. The two-fluid description, as well as the magnetohydrodynamical reduction, are derived and studied in the presence of the spatial gradients of the geometry. Various solutions of the coupled system of evolution equations in the anti-Newtonian re...

  3. Locally-smeared operator product expansions

    CERN Document Server

    Monahan, Christopher

    2014-01-01

    We propose a "locally-smeared Operator Product Expansion" (sOPE) to decompose non-local operators in terms of a basis of locally-smeared operators. The sOPE formally connects nonperturbative matrix elements of smeared degrees of freedom, determined numerically using the gradient flow, to non-local operators in the continuum. The nonperturbative matrix elements do not suffer from power-divergent mixing on the lattice, provided the smearing scale is kept fixed in the continuum limit. The presence of this smearing scale prevents a simple connection to the standard operator product expansion and therefore requires the construction of a two-scale formalism. We demonstrate the feasibility of our approach using the example of real scalar field theory.

  4. Locally-smeared operator product expansions

    Energy Technology Data Exchange (ETDEWEB)

    Monahan, Christopher; Orginos, Kostantinos

    2014-12-01

    We propose a "locally-smeared Operator Product Expansion" (sOPE) to decompose non-local operators in terms of a basis of locally-smeared operators. The sOPE formally connects nonperturbative matrix elements of smeared degrees of freedom, determined numerically using the gradient flow, to non-local operators in the continuum. The nonperturbative matrix elements do not suffer from power-divergent mixing on the lattice, provided the smearing scale is kept fixed in the continuum limit. The presence of this smearing scale prevents a simple connection to the standard operator product expansion and therefore requires the construction of a two-scale formalism. We demonstrate the feasibility of our approach using the example of real scalar field theory.

  5. Design of airport pavements for expansive soils

    Science.gov (United States)

    McKeen, R. G.

    1981-01-01

    Expansive soil subgrades exhibit volume changes with variation in moisture condition. These changes result in differential movement of airport pavements resting on these soils. Special design procedures must be used to account for the expansive soil activity during equilibration. In addition, special precautions are required to protect the subgrade from moisture variation with climate. Measurement of soil suction is a key step in quantifying moisture-induced soil behavior. Procedures are outlined for suction characterization of the soil and for estimating the in situ differential movement likely to occur under the pavement. Once the wavelength and amplitude characteristics of the differential movement are obtained, design calculations to select the thickness and materials for the pavement may proceed.

  6. Working fluids and expansion machines for ORC

    Science.gov (United States)

    Richter, Lukáš; Linhart, Jiří

    2016-06-01

    This paper discusses the key technical aspects of the Organic Rankin - Clausius cycle (ORC), unconventional technology with great potential for the use of low-potential heat and the use of geothermal and solar energy, and in connection with the burning of biomass. The principle of ORC has been known since the late 19th century. The development of new organic substances and improvements to the expansion device now allows full commercial exploitation of ORC. The right choice of organic working substances has the most important role in the design of ORC, depending on the specific application. The chosen working substance and achieved operating parameters will affect the selection and construction of the expansion device. For this purpose the screw engine, inversion of the screw compressor, can be used.

  7. 6th International Symposium on Thermal Expansion

    CERN Document Server

    1978-01-01

    This 6th International Symposium on Thermal Expansion, the first outside the USA, was held on August 29-31, 1977 at the Gull Harbour Resort on Hecla Island, Manitoba, Canada. Symposium Chairman was Ian D. Peggs, Atomic Energy of Canada Limited, and our continuing sponsor was CINDAS/Purdue University. We made considerable efforts to broaden the base this year to include more users of expansion data but with little success. We were successful, however, in establishing a session on liquids, an area which is receiving more attention as a logical extension to the high-speed thermophysical property measurements on materials at temperatures close to their melting points. The Symposium had good international representation but the overall attendance was, disappointingly, relatively low. Neverthe­ less, this enhanced the informal atmosphere throughout the meeting with a resultant frank exchange of information and ideas which all attendees appreciated. A totally new item this year was the presentation of a bursary to ...

  8. Anisotropic matching principle for the hydrodynamics expansion

    CERN Document Server

    Tinti, Leonardo

    2015-01-01

    Following the recent success of anisotropic hydrodynamics we propose a new, general prescription for the hydrodynamics expansion around an anisotropic background. The anisotropic distribution is fixing exactly the complete energy-momentum tensor, just like the effective temperature is fixing the proper energy density in the ordinary expansion around local equilibrium. This means that momen- tum anisotropies are already included at the leading order, allowing for large pressure anisotropies without the need of a next to leading order treatment. The first moment of the Boltzmann equation (local four-momentum conservation) provides the time evolution of the proper energy density and the four velocity. Differently from previous prescriptions, the dynamic equations for the pressure corrections are not derived from the zeroth or second moment of the Boltzmann equation, but they are taken directly from the exact evolution given by the Boltzmann equation. We check the effec- tiveness of this new approach by matching ...

  9. Passage with Sudden Expansion or Contraction

    Directory of Open Access Journals (Sweden)

    Shuichi Torii

    1999-01-01

    Full Text Available This paper investigates rotational effects on secondary flow in rotating flow passages with sudden expansion or contraction. Consideration is given to laminar flow. The governing boundary-layer equations are discretized by means of a finite-difference technique and numerically solved to determine the distributions of velocity vector under the appropriate boundary conditions. The Reynolds number (Re and rotation rate are varied to determine their effects on the formation ofsecondary flows. It is disclosed from the study that: (i when laminar flow is introduced into an axially rotating pipe with expansion, the stretch ofthe secondary flow zone is amplified with an increase in the rotation rate and Re, and (ii in contrast, for axially rotating pipe flows with contraction, the secondary flow region is somewhat suppressed due to pipe rotation, and the change is slightly affected by the rotation rate and Re. Results may find applications in automotive and rotating hydraulic transmission lines.

  10. Negative thermal expansion in framework compounds

    Indian Academy of Sciences (India)

    R Mittal

    2008-10-01

    We have studied negative thermal expansion (NTE) compounds with chemi- cal compositions of NX2O8 and NX2O7 (N=Zr, Hf and X=W, Mo, V) and M2O (M=Cu, Ag) using the techniques of inelastic neutron scattering and lattice dynamics. There is a large variation in the negative thermal expansion coefficients of these compounds. The inelastic neutron scattering experiments have been carried out using polycrystalline and single crystal samples at ambient pressure as well as at high pressures. Experimental data are useful to confirm the predictions made from our lattice dynamical calculations as well as to check the quality of the interatomic potentials developed by us. We have been able to successfully model the NTE behaviour of these compounds. Our studies show that unusual phonon softening of low energy modes is able to account for NTE in these compounds.

  11. Tests for the Expansion of the Universe

    CERN Document Server

    Lopez-Corredoira, Martin

    2015-01-01

    Almost all cosmologists accept nowadays that the redshift of the galaxies is due to the expansion of the Universe (cosmological redshift), plus some Doppler effect of peculiar motions, but can we be sure of this fact by means of some other independent cosmological test? Here I will review some recent tests: CMBR temperature versus redshift, time dilation, the Hubble diagram, the Tolman or surface brightness test, the angular size test, the UV surface brightness limit and the Alcock--Paczy\\'nski test. Some tests favour expansion and others favour a static Universe. Almost all the cosmological tests are susceptible to the evolution of galaxies and/or other effects. Tolman or angular size tests need to assume very strong evolution of galaxy sizes to fit the data with the standard cosmology, whereas the Alcock--Paczynski test, an evaluation of the ratio of observed angular size to radial/redshift size, is independent of it.

  12. Fock expansion of multimode pure Gaussian states

    Energy Technology Data Exchange (ETDEWEB)

    Cariolaro, Gianfranco; Pierobon, Gianfranco, E-mail: gianfranco.pierobon@unipd.it [Università di Padova, Padova (Italy)

    2015-12-15

    The Fock expansion of multimode pure Gaussian states is derived starting from their representation as displaced and squeezed multimode vacuum states. The approach is new and appears to be simpler and more general than previous ones starting from the phase-space representation given by the characteristic or Wigner function. Fock expansion is performed in terms of easily evaluable two-variable Hermite–Kampé de Fériet polynomials. A relatively simple and compact expression for the joint statistical distribution of the photon numbers in the different modes is obtained. In particular, this result enables one to give a simple characterization of separable and entangled states, as shown for two-mode and three-mode Gaussian states.

  13. Harmonic function expansion of nearly oblate systems

    CERN Document Server

    Syer, D

    1995-01-01

    We show how to develop an expansion of nearly oblate systems in terms of a set of potential-density pairs. A harmonic (multipole) structure is imposed on the potential set at infinity, and the density can be made everywhere regular. We concentrate on a set whose zeroth order functions describe the perfect oblate spheroid of de Zeeuw (1985). This set is not bi-orthogonal, but it can be shown to be complete in a weak sense. Poisson's equation can be solved approximately by truncating the expansion of the potential in such a set. A simple example of a potential which is not one of the basis functions is expanded using the symmetric members of the basis set up to fourth order. The basis functions up to first order are reconstructed approximately using 10,000 particles to show that this set could be used as part of an N-body code.

  14. Geographic expansion of the cabbage butterfly (Pieris rapae)and the evolution of highly UV-reflecting females

    Institute of Scientific and Technical Information of China (English)

    Yuya Fukano; Toshiyuki Satoh; Tadao Hirota; Yudai Nishide; Yoshiaki Obara

    2012-01-01

    Reflection ofultraviolet (UV) light by the wings of the female Eurasian cabbage butterfly,Pieris rapae,shows a large geographic variation.The wings of the female of the European subspecies,P rapae rapae,reflect little UV light,while butterflies of the Asian subspecies,P.rapae crucivora,may reflect it strongly or at only intermediate levels.The geographic region where P.rapae originated remains to be determined.Moreover,it is not clear if females with wings that reflect little UV light are ancestral to females with wings that reflect UV strongly or vice versa.In the present study,we aimed to determine the geographic origin and ancestral UV pattern of cabbage butterflies through mitochondrial DNA (mtDNA) sequence analysis and amplified fragment length polymorphism (AFLP) analysis.The results of these investigations suggest that P rapae is of European origin and that it has expanded its distribution eastward to Asia.It follows that the ancestral subspecies is the type with UV-absorbing wings.Lower nucleotide diversities and haplotype network patterns ofmtDNA derived from East Asian populations suggest that population expansion from Europe to East Asia probably occurred fairly recently and at a rapid rate.

  15. Market Expansion Opportunity Analysis for Adigy Canada

    OpenAIRE

    Salimi, Mitra

    2008-01-01

    This project develops business and marketing strategies for the expansion of Adigy Canada, a medical heart telemetry device developer, into the golfing market. It researches the needs of this market, analyzes industry forces and recommends target market segments, a business model, distribution channels, and marketing strategies. The design and marketing of a training aid product is recommended as this segment of the golf industry seems to have a medium to high level of attractiveness. The rec...

  16. Multipole expansion in the quantum hall effect

    Science.gov (United States)

    Cappelli, Andrea; Randellini, Enrico

    2016-03-01

    The effective action for low-energy excitations of Laughlin's states is obtained by systematic expansion in inverse powers of the magnetic field. It is based on the W- infinity symmetry of quantum incompressible fluids and the associated higher-spin fields. Besides reproducing the Wen and Wen-Zee actions and the Hall viscosity, this approach further indicates that the low-energy excitations are extended objects with dipolar and multipolar moments.

  17. An Anatomy Of The Export Expansion Process

    OpenAIRE

    Reid, S

    1986-01-01

    This paper examines the export market strategies and export modes used by small and medium sized Italian manufacturing firms. The firms vary extensively in their extent and type of export dependence on different channel arrangements and export markets. Moreover, the exporting modes used do show some peculiar links with export objectives specifically higher dependence on direct sales is associated with planned export expansion and higher dependence on agent/representatives and distributors is ...

  18. Expansion-free Cylindrically Symmetric Models

    CERN Document Server

    Sharif, M

    2013-01-01

    This paper investigates cylindrically symmetric distribution of an-isotropic fluid under the expansion-free condition, which requires the existence of vacuum cavity within the fluid distribution. We have discussed two family of solutions which further provide two exact models in each family. Some of these solutions satisfy Darmois junction condition while some show the presence of thin shell on both boundary surfaces. We also formulate a relation between the Weyl tensor and energy density.

  19. The Lorentz anomaly via operator product expansion

    Energy Technology Data Exchange (ETDEWEB)

    Fredenhagen, Stefan, E-mail: stefan.fredenhagen@aei.mpg.de [Max-Planck-Institut für Gravitationsphysik, Albert-Einstein-Institut Am Mühlenberg 1, 14476 Golm (Germany); Hoppe, Jens, E-mail: hoppe@kth.se; Hynek, Mariusz, E-mail: mkhynek@kth.se [Department of Mathematics, Royal Institute of Technology, KTH 100 44 Stockholm (Sweden)

    2015-10-15

    The emergence of a critical dimension is one of the most striking features of string theory. One way to obtain it is by demanding closure of the Lorentz algebra in the light-cone gauge quantisation, as discovered for bosonic strings more than forty years ago. We give a detailed derivation of this classical result based on the operator product expansion on the Lorentzian world-sheet.

  20. Contradictions of TNCs’ Foreign Economic Expansion

    OpenAIRE

    Melnikov Aleksandr Borisovich; Snimshchikova Irina Viktorovna; Lazgiev Mikhail Maisovich

    2014-01-01

    Some directions of the external economic expansion of multinational corporations in modern conditions of globalization, the contradictions generated by these conditions and the conflicts in the system of world economy are presented in the article. The global strategy of functioning of multinational corporation professes the principle of “double standards”. Multinational corporations, on the one hand, support liberalization and internationalization in scales of world reproduction, on the other...

  1. Multipolar expansion of orbital angular momentum modes

    OpenAIRE

    Molina-Terriza, Gabriel

    2008-01-01

    In this letter a general method for expanding paraxial beams into multipolar electromagnetic fields is presented. This method is applied to the expansion of paraxial modes with orbital angular momentum (OAM), showing how the paraxial OAM is related to the general angular momentum of an electromagnetic wave. This method can be extended to quasi-paraxial beams, i.e. highly focused laser beams. Some applications to the control of electronic transitions in atoms are discussed.

  2. Rapid maxillary expansion in contemporary orthodontic literature

    OpenAIRE

    Sabrina Mutinelli; Mauro Cozzani

    2016-01-01

    We have reviewed our retrospective research about rapid maxillary expansion performed in the early mixed dentition to summarize the results of different studies regarding maxillary dental arch width variation and crowding improvement in light of contemporary literature. The aim is to define the effects of treatments followed until the end of dental arch growth. In all studies, a Haas expander anchored to the deciduous dentition was used. The samples consisted of treated patients with and with...

  3. Eigenvalues and expansion of bipartite graphs

    DEFF Research Database (Denmark)

    Høholdt, Tom; Janwa, Heeralal

    2012-01-01

    We prove lower bounds on the largest and second largest eigenvalue of the adjacency matrix of bipartite graphs and give necessary and sufficient conditions for equality. We give several examples of classes that are optimal with respect to the bouns. We prove that BIBD-graphs are characterized by ...... by their eigenvalues. Finally we present a new bound on the expansion coefficient of (c,d)-regular bipartite graphs and compare that with aclassical bound....

  4. Expansion jet system for gas dynamic lasers

    Energy Technology Data Exchange (ETDEWEB)

    Born, G.; Grosch, G.

    1977-06-02

    The invention deals with an expansion jet system for gas dynamic lasers of parallel arranged two or three-dimensional Laval nozzles in which the nozzle lamellae between the combustion chamber and resonator are put together in a grid or honeycomb fashion and have an inlet section which, seen in flow direction, ends in Laval nozzles for the higher subsonic region and the supersonic region.

  5. Gaussian expansion approach to Coulomb breakup

    CERN Document Server

    Egami, T; Matsumoto, T; Iseri, Y; Kamimura, M; Yahiro, M

    2004-01-01

    An accurate treatment of Coulomb breakup reactions is presented by using both the Gaussian expansion method and the method of continuum discretized coupled channels. As $L^2$-type basis functions for describing Coulomb breakup processes, we take complex-range Gaussian functions, which form in good approximation a complete set in a large configuration space being important for the processes. Accuracy of the method is tested quantitatively for $^{8}{\\rm B}+^{58}$Ni scattering at 25.8 MeV.

  6. 川芎嗪对药物耳毒性线粒体DNA缺失的影响%The effect of tetramethylpyrazine on drug totoxicity with mtDNA deletion

    Institute of Scientific and Technical Information of China (English)

    温丽民; 倪月秋

    2012-01-01

      目的研究川芎嗪(TMP)对庆大霉素(GM)导致药物耳毒性豚鼠的线粒体DNA(mtDNA)缺失影响.方法选择体重200-330g健康豚鼠40只,雌雄不拘,随机平均分成正常对照组、GM组、GM+TMP组和TMP组.四组动物混合饲养,每日测量体重调整药量.采用巢式聚合酶链反应检测血液中mtDNA的缺失情况.结果正常对照组和TMP组无mtDNA的缺失,GM组与GM+TMP组均有mtDNA的缺失,GM组mtDNA的缺失率高于GM+TMP组,两组比较差异具有统计学意义(P<0.05).结论庆大霉素可使豚鼠mtDNA发生缺失而引起听力受损;川芎嗪对可以降低mtDNA的缺失,有效地拮抗庆大霉素的耳毒性损伤,改善听力.%  Objective To investigate the effect of tetramethylpyrazine(TMP) on drug totoxicity of gentamicin(GM) with mtDNA deletion in guinea pigs. Methods Totally 40 healthy guinea pigs, weighing 200-330g, of either gender, were at random divided as normal control group, GM group, TMP+GM group and TMP group, with 10 in each group. Administration was consecutively given for each group, once a day, The body mss was measured every day for regulatingthe dosage. The nested PCR technique was used to test the presence of mtDNA deletion in blood. Results Neither normal control group nor TMP group has mtDNA deletion, both GM group and TMP+GM group have mtDNA deletion. The rate of mtDNA deletion in GM group is higher than that of TMP+GM group, the difference between the two groups is statistically significant(P<0.05). Conclusion GM can induce mtDNA deletion in guinea pigs, resulting in hearing impairment, TMP can reduce mtDNA deletion, effective antagonist of the toxicity of gentamicin ear and improve hearing.

  7. Asymptotic expansions for the Gaussian unitary ensemble

    DEFF Research Database (Denmark)

    Haagerup, Uffe; Thorbjørnsen, Steen

    2012-01-01

    Let g : R ¿ C be a C8-function with all derivatives bounded and let trn denote the normalized trace on the n × n matrices. In Ref. 3 Ercolani and McLaughlin established asymptotic expansions of the mean value ¿{trn(g(Xn))} for a rather general class of random matrices Xn, including the Gaussian...... Unitary Ensemble (GUE). Using an analytical approach, we provide in the present paper an alternative proof of this asymptotic expansion in the GUE case. Specifically we derive for a random matrix Xn that where k is an arbitrary positive integer. Considered as mappings of g, we determine the coefficients...... aj(g), j ¿ N, as distributions (in the sense of L. Schwarts). We derive a similar asymptotic expansion for the covariance Cov{Trn[f(Xn)], Trn[g(Xn)]}, where f is a function of the same kind as g, and Trn = n trn. Special focus is drawn to the case where and for ¿, µ in C\\R. In this case the mean and...

  8. Forecasting Urban Expansion Based on Night Lights

    Science.gov (United States)

    Stathakis, D.

    2016-06-01

    Forecasting urban expansion models are a very powerful tool in the hands of urban planners in order to anticipate and mitigate future urbanization pressures. In this paper, a linear regression forecasting urban expansion model is implemented based on the annual composite night lights time series available from National Oceanic and Atmospheric Administration (NOAA). The product known as 'stable lights' is used in particular, after it has been corrected with a standard intercalibration process to reduce artificial year-to-year fluctuations as much as possible. Forecasting is done for ten years after the end of the time series. Because the method is spatially explicit the predicted expansion trends are relatively accurately mapped. Two metrics are used to validate the process. The first one is the year-to-year Sum of Lights (SoL) variation. The second is the year-to-year image correlation coefficient. Overall it is evident that the method is able to provide an insight on future urbanization pressures in order to be taken into account in planning. The trends are quantified in a clear spatial manner.

  9. Foundations on Expansive Soils; A Review

    Directory of Open Access Journals (Sweden)

    Behzad Kalantari

    2012-09-01

    Full Text Available This study describes various types of foundation designs to be considered for structural engineering projects when the subsoil foundation consists of expansive or swelling soils. Among civil and architectural engineers expansive soils are known to be difficult foundation materials and problematic. These type of soils swell when they are subjected to moistures and shrink due to moisture loss. Because of this different behaviour upon wetting and drying, they cause minor to major structural damages to pavements as well as buildings. Every year millions of dollars spent dealing with the consequences of swelling soils. For design of foundations on swelling soil, it is first essential to recognize and evaluate the soil based on its swelling potential, and then determining the most proper foundation design that can be constructed on this problematic soil. In general, this study presents some of the most common techniques to evaluate the swelling potential of expansive soils. Also, it discusses problems associated with swelling soil, classification of structural damages caused to buildings, and various foundation designs to combat the problems based on the degree of detrimental effects of swelling potential to civil engineering projects.

  10. Expansion Compression Contacts for Thermoelectric Legs

    Science.gov (United States)

    Sakamoto, Jeffrey

    2009-01-01

    In a proposed alternative to previous approaches to making hot-shoe contacts to the legs of thermoelectric devices, one relies on differential thermal expansion to increase contact pressures for the purpose of reducing the electrical resistances of contacts as temperatures increase. The proposed approach is particularly applicable to thermoelectric devices containing p-type (positive-charge-carrier) legs made of a Zintl compound (specifically, Yb14MnSb11) and n-type (negative charge-carrier) legs made of SiGe. This combination of thermoelectric materials has been selected for further development, primarily on the basis of projected thermoelectric performance. However, it is problematic to integrate, into a practical thermoelectric device, legs made of these materials along with a metal or semiconductor hot shoe that is required to be in thermal and electrical contact with the legs. This is partly because of the thermal-expansion mismatch of these materials: The coefficient of thermal expansion (CTE) of SiGe is 4.5 x 10(exp -6) C (exp -1), while the CTE of Yb14MnSb11 is 20 x 10(exp -6) C(exp -1). Simply joining a Yb14MnSb11 and a SiGe leg to a common hot shoe could be expected to result in significant thermal stresses in either or both legs during operation. Heretofore, such thermal stresses have been regarded as disadvantageous. In the proposed approach, stresses resulting from the CTE mismatch would be turned to advantage.

  11. Frequency dependent thermal expansion in binary viscoelasticcomposites

    Energy Technology Data Exchange (ETDEWEB)

    Berryman, James G.

    2007-12-01

    The effective thermal expansion coefficient beta* of abinary viscoelastic composite is shown to be frequency dependent even ifthe thermal expansion coefficients beta A and beta B of both constituentsare themselves frequency independent. Exact calculations for binaryviscoelastic systems show that beta* is related to constituent valuesbeta A, beta B, volume fractions, and bulk moduli KA, KB, as well as tothe overall bulk modulus K* of the composite system. Then, beta* isdetermined for isotropic systems by first bounding (or measuring) K* andtherefore beta*. For anisotropic systems with hexagonal symmetry, theprincipal values of the thermal expansion beta*perp and beta*para can bedetermined exactly when the constituents form a layered system. In allthe examples studied, it is shown explicitly that the eigenvectors of thethermoviscoelastic system possess non-negative dissipation -- despite thecomplicated analytical behavior of the frequency dependent thermalexpansivities themselves. Methods presented have a variety ofapplications from fluid-fluid mixtures to fluid-solid suspensions, andfrom fluid-saturated porous media to viscoelastic solid-solidcomposites.

  12. Expansion of Interstitial Telomeric Sequences in Yeast.

    Science.gov (United States)

    Aksenova, Anna Y; Han, Gil; Shishkin, Alexander A; Volkov, Kirill V; Mirkin, Sergei M

    2015-11-24

    Telomeric repeats located within chromosomes are called interstitial telomeric sequences (ITSs). They are polymorphic in length and are likely hotspots for initiation of chromosomal rearrangements that have been linked to human disease. Using our S. cerevisiae system to study repeat-mediated genome instability, we have previously shown that yeast telomeric (Ytel) repeats induce various gross chromosomal rearrangements (GCR) when their G-rich strands serve as the lagging strand template for replication (G orientation). Here, we show that interstitial Ytel repeats in the opposite C orientation prefer to expand rather than cause GCR. A tract of eight Ytel repeats expands at a rate of 4 × 10(-4) per replication, ranking them among the most expansion-prone DNA microsatellites. A candidate-based genetic analysis implicates both post-replication repair and homologous recombination pathways in the expansion process. We propose a model for Ytel repeat expansions and discuss its applications for genome instability and alternative telomere lengthening (ALT). PMID:26586439

  13. Genetic Algorithm Based Transmission Expansion Planning System

    Directory of Open Access Journals (Sweden)

    Dike, Damian Obioma

    2014-11-01

    Full Text Available This paper presents an application of genetic algorithm (GA to the solution of Static Transmission Expansion Planning (STEP to determine the optimal number of transmission circuits required in each network corridor and their respective network adequacy while satisfying various economic and technical constraints. The uncertainties in generation and distribution networks as a result of power system deregulation cannot be modeled effectively using the conventional mathematical methods. GA, been a probabilistic based approach has the ability to resolve the transmission expansion planning problem in the face of such uncertainties. The model presented in this work will help in the identification of overloaded lines using Gauss Seidel (GS load flow technique. Result from GS is then used as input in the GA simulation to show the extra lines needed to accommodate present load flow in the system. The model was tested on IEEE 14 – bus test network.The model developed and simulation results obtained may be useful in an electric power systems undergoing deregulation. Such is the case in Nigeria presently where the generation and distribution components are increasing significantly without any commensurate boost in the transmission sector. This leads to line overloads necessitating commensurate and immediate expansion of the grid

  14. Anisotropic matching principle for the hydrodynamic expansion

    Science.gov (United States)

    Tinti, Leonardo

    2016-10-01

    Following the recent success of anisotropic hydrodynamics, I propose here a new, general prescription for the hydrodynamic expansion around an anisotropic background. The anisotropic distribution fixes exactly the complete energy-momentum tensor, just like the effective temperature fixes the proper energy density in the ordinary expansion around local equilibrium. This means that momentum anisotropies are already included at the leading order, allowing for large pressure anisotropies without the need of a next-to-leading-order treatment. The first moment of the Boltzmann equation (local four-momentum conservation) provides the time evolution of the proper energy density and the four-velocity. Differently from previous prescriptions, the dynamic equations for the pressure corrections are not derived from the zeroth or second moment of the Boltzmann equation, but they are taken directly from the exact evolution given by the Boltzmann equation. As known in the literature, the exact evolution of the pressure corrections involves higher moments of the Boltzmann distribution, which cannot be fixed by the anisotropic distribution alone. Neglecting the next-to-leading-order contributions corresponds to an approximation, which depends on the chosen form of the anisotropic distribution. I check the the effectiveness of the leading-order expansion around the generalized Romatschke-Stricklad distribution, comparing with the exact solution of the Boltzmann equation in the Bjorken limit with the collisional kernel treated in the relaxation-time approximation, finding an unprecedented agreement.

  15. Genetic signals of demographic expansion in Downy Woodpecker (Picoides pubescens after the last North American glacial maximum.

    Directory of Open Access Journals (Sweden)

    Paulo C Pulgarín-R

    Full Text Available The glacial cycles of the Pleistocene have been recognized as important, large-scale historical processes that strongly influenced the demographic patterns and genetic structure of many species. Here we present evidence of a postglacial expansion for the Downy Woodpecker (Picoides pubescens, a common member of the forest bird communities in North America with a continental distribution. DNA sequences from the mitochondrial tRNA-Lys, and ATPase 6 and 8 genes, and microsatellite data from seven variable loci were combined with a species distribution model (SDM to infer possible historical scenarios for this species after the last glacial maximum. Analyses of Downy Woodpeckers from 23 geographic areas suggested little differentiation, shallow genealogical relationships, and limited population structure across the species' range. Microsatellites, which have higher resolution and are able to detect recent differences, revealed two geographic groups where populations along the eastern edge of the Rocky Mountains (Montana, Utah, Colorado, and southern Alberta were genetically isolated from the rest of the sampled populations. Mitochondrial DNA, an important marker to detect historical patterns, recovered only one group. However, populations in Idaho and southeast BC contained high haplotype diversity and, in general were characterized by the absence of the most common mtDNA haplotype. The SDM suggested several areas in the southern US as containing suitable Downy Woodpecker habitat during the LGM. The lack of considerable geographic structure and the starburst haplotype network, combined with several population genetic tests, suggest a scenario of demographic expansion during the last part of Pleistocene and early Holocene.

  16. The holonomy expansion: Invariants and approximate supersymmetry

    International Nuclear Information System (INIS)

    In this paper we give a new expansion, based on cyclicity of the trace, to study regularity properties of twisted expectations =TrH(γU(θ)X(s)). Here X(s)=X0e-s0Q2X1e-s1Q2...Xke-skQ2 is a product of operators Xj, regularized by heat kernels e-sjQ2 with sj>0. The twist groups γ(set-membership sign)Z2 and U(θ)(set-membership sign)U(1) are commuting symmetries of Q2. The name ''holonomy expansion'' arises from picturing as a circular graph, with vertices in the graph representing the operators Xj, in the order that they appear in the product, and the line-segment following Xj representing the heat kernel e-sjQ2. The trace functional is cyclic, so the graph is circular. We generate our expansion by ''transporting'' a vertex Xk around the circle, ending in its original position. We choose an Xk that transforms under a one-dimensional representation of Z2xU(1). For θ in the complement of the discrete set γsing (where the group Z2xU(1) acts trivially on Xk) we obtain an identity between the original expectation and some new expectations. We study an example from supersymmetric quantum mechanics, with a Dirac operator Q(λ) depending on a parameter λ and with a U(1) group of symmetries U(θ). We apply our expansion to invariants Z(λ;θ)=Z(Q(λ);θ) suggested by non-commutative geometry. These invariants are sums of expectations of the form above. We investigate this example as a first step toward developing an expansion to evaluate related invariants arising in supersymmetric quantum field theory. We establish differentiability of Z(λ; θ) in λ for λ(set-membership sign)(0,1] and show Z(λ; θ) is independent of λ. We wish to evaluate Z(λ; θ) at the endpoint λ=0, but Z(0; θ) is ill-defined. We regularize the endpoint, while preserving the U(θ)-symmetry, by replacing Q(λ)2 with H(ε,λ)=Q(λ)2+ε2|z|2. The regularized function Z(ε, λ; θ) depends on all three variables ε, λ, θ; for fixed θ, it is differentiable in the unit (ε, λ) square, except at

  17. Asymptotic expansion of the wavelet transform with error term

    OpenAIRE

    R. S. Pathak; Pathak, Ashish

    2014-01-01

    UsingWong's technique asymptotic expansion for the wavelet transform is derived and thereby asymptotic expansions for Morlet wavelet transform, Mexican Hat wavelet transform and Haar wavelet transform are obtained.

  18. Lessons from Early Medicaid Expansions Under Health Reform..

    Data.gov (United States)

    U.S. Department of Health & Human Services — Lessons from Early Medicaid Expansions Under Health Reform, Interviews with Medicaid Officials In a new study entitled Lessons from Early Medicaid Expansions Under...

  19. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences

    Science.gov (United States)

    Yue, Yaojing; Guo, Xian; Guo, Tingting; Chu, Min; Wang, Fan; Han, Jilong; Feng, Ruilin; Sun, Xiaoping; Niu, Chune; Yang, Bohui; Guo, Jian; Yuan, Chao

    2016-01-01

    The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species’ genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D) were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau. PMID:27463976

  20. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

    Directory of Open Access Journals (Sweden)

    Jianbin Liu

    Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.