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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

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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

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

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

    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 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.

  3. 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.

  4. mtDNA variability in two Bantu-speaking populations (Shona and Hutu) from Eastern Africa: implications for peopling and migration patterns in sub-Saharan Africa.

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    Castrì, Loredana; Tofanelli, Sergio; Garagnani, Paolo; Bini, Carla; Fosella, Xenia; Pelotti, Susi; Paoli, Giorgio; Pettener, Davide; Luiselli, Donata

    2009-10-01

    In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu-speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu-speaking populations. Moreover, by comparing our data with those from other Niger-Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub-Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu-speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu-speaking populations, but also between Bantu and non-Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu-speakers, with strong interactions between the different lines of Bantu-speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages.

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

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    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)

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    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. Bringing together linguistic and genetic evidence to test the Bantu expansion.

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    de Filippo, Cesare; Bostoen, Koen; Stoneking, Mark; Pakendorf, Brigitte

    2012-08-22

    The expansion of Bantu languages represents one of the most momentous events in the history of Africa. While it is well accepted that Bantu languages spread from their homeland (Cameroon/Nigeria) approximately 5000 years ago (ya), there is no consensus about the timing and geographical routes underlying this expansion. Two main models of Bantu expansion have been suggested: The 'early-split' model claims that the most recent ancestor of Eastern languages expanded north of the rainforest towards the Great Lakes region approximately 4000 ya, while the 'late-split' model proposes that Eastern languages diversified from Western languages south of the rainforest approximately 2000 ya. Furthermore, it is unclear whether the language dispersal was coupled with the movement of people, raising the question of language shift versus demic diffusion. We use a novel approach taking into account both the spatial and temporal predictions of the two models and formally test these predictions with linguistic and genetic data. Our results show evidence for a demic diffusion in the genetic data, which is confirmed by the correlations between genetic and linguistic distances. While there is little support for the early-split model, the late-split model shows a relatively good fit to the data. Our analyses demonstrate that subsequent contact among languages/populations strongly affected the signal of the initial migration via isolation by distance.

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

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    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. Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people.

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    Ansari Pour, Naser; Plaster, Christopher A; Bradman, Neil

    2013-04-01

    The expansion of the Bantu-speaking people (EBSP) during the past 3000-5000 years is an event of great importance in the history of humanity. Anthropology, archaeology, linguistics and, in recent decades, genetics have been used to elucidate some of the events and processes involved. Although it is generally accepted that the EBSP has its origin in the so-called Bantu Homeland situated in the area of the border between Nigeria and the Grassfields of Cameroon, and that it followed both western and eastern routes, much less is known about the number and dates of those expansions, if more than one. Mitochondrial, Y-chromosome and autosomal DNA analyses have been carried out in attempts to understand the demographic events that have taken place. There is an increasing evidence that the expansion was a more complex process than originally thought and that neither a single demographic event nor an early split between western and eastern groups occurred. In this study, we analysed unique event polymorphism and short tandem repeat variation in non-recombining Y-chromosome haplogroups contained within the E1b1a haplogroup, which is exclusive to individuals of recent African ancestry, in a large, geographically widely distributed, set of sub-Saharan Africans (groups=43, n=2757), all of whom, except one Nilo-Saharan-speaking group, spoke a Niger-Congo language and most a Bantu tongue. Analysis of diversity and rough estimates of times to the most recent common ancestors of haplogroups provide evidence of multiple expansions along eastern and western routes and a late, exclusively eastern route, expansion.

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

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

    2011-01-01

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

  12. Genetic homogeneity across Bantu-speaking groups from Mozambique and Angola challenges early split scenarios between East and West Bantu populations.

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    Alves, Isabel; Coelho, Margarida; Gignoux, Christopher; Damasceno, Albertino; Prista, Antonio; Rocha, Jorge

    2011-02-01

    The large scale spread of Bantu-speaking populations remains one of the most debated questions in African population history. In this work we studied the genetic structure of 19 Bantu-speaking groups from Mozambique and Angola using a multilocus approach based on 14 newly developed compound haplotype systems (UEPSTRs), each consisting of a rapidly evolving short tandem repeat (STR) closely linked to a unique event polymorphism (UEP). We compared the ability of UEPs, STRs and UEPSTRs to document genetic variation at the intercontinental level and among the African Bantu populations, and found that UEPSTR systems clearly provided more resolution than UEPs or STRs alone. The observed patterns of genetic variation revealed high levels of genetic homogeneity between major populations from Angola and Mozambique, with two main outliers: the Kuvale from Angola and the Chopi from Mozambique. Within Mozambique, two Kaskazi-speaking populations from the far north (Yao and Mwani) and two Nyasa-speaking groups from the Zambezi River basin (Nyungwe and Sena) could be differentiated from the remaining groups, but no further population structure was observed across the country. The close genetic relationship between most sampled Bantu populations is consistent with high degrees of interaction between peoples living in savanna areas located to the south of the rainforest. Our results highlight the role of gene flow during the Bantu expansions and show that the genetic evidence accumulated so far is becoming increasingly difficult to reconcile with widely accepted models postulating an early split between eastern and western Bantu populations.

  13. The making of the African mtDNA landscape.

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    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. Agreement properties and word order in comparative bantu

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    Morimoto, Yukiko

    2013-01-01

    Agreement is traditionally viewed as a cross-referencing device for core arguments such as subjects and (primary) objects.1 In this paper, I discuss data from Bantu languages that lead to a radical departure from this generally accepted position: agreement in a subset of Bantu languages cross-references a (sentential) topic rather than the subject. The crucial evidence for topic agreement comes from a construction known as subject-object (S-O) reversal, where the fronted patient agrees with w...

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

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    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…

  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. Similar patterns of clonally expanded somatic mtDNA mutations in the colon of heterozygous mtDNA mutator mice and ageing humans

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    Baines, Holly L.; Stewart, James B.; Stamp, Craig; Zupanic, Anze; Kirkwood, Thomas B.L.; Larsson, Nils-Göran; Turnbull, Douglass M.; Greaves, Laura C.

    2014-01-01

    Clonally expanded mitochondrial DNA (mtDNA) mutations resulting in focal respiratory chain deficiency in individual cells are proposed to contribute to the ageing of human tissues that depend on adult stem cells for self-renewal; however, the consequences of these mutations remain unclear. A good animal model is required to investigate this further; but it is unknown whether mechanisms for clonal expansion of mtDNA mutations, and the mutational spectra, are similar between species. Here we show that mice, heterozygous for a mutation disrupting the proof-reading activity of mtDNA polymerase (PolgA+/mut) resulting in an increased mtDNA mutation rate, accumulate clonally expanded mtDNA point mutations in their colonic crypts with age. This results in focal respiratory chain deficiency, and by 81 weeks of age these animals exhibit a similar level and pattern of respiratory chain deficiency to 70-year-old human subjects. Furthermore, like in humans, the mtDNA mutation spectrum appears random and there is an absence of selective constraints. Computer simulations show that a random genetic drift model of mtDNA clonal expansion can accurately model the data from the colonic crypts of wild-type, PolgA+/mut animals, and humans, providing evidence for a similar mechanism for clonal expansion of mtDNA point mutations between these mice and humans. PMID:24915468

  18. 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.

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

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    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.

  20. 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

  1. Demographic expansions in South America: enlightening a complex scenario with genetic and linguistic data.

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    Ramallo, Virginia; Bisso-Machado, Rafael; Bravi, Claudio; Coble, Michael D; Salzano, Francisco M; Hünemeier, Tábita; Bortolini, Maria Cátira

    2013-03-01

    Native Americans are characterized by specific and unique patterns of genetic and cultural/linguistic diversities, and this information has been used to understand patterns of geographic dispersion, and the relationship between these peoples. Particularly interesting are the Tupi and Je speaker dispersions. At present, a large number of individuals speak languages of these two stocks; for instance, Tupi-Guarani is one of the official languages in Paraguay, Bolivia, and the Mercosul economic block. Although the Tupi expansion can be compared in importance to the Bantu migration in Africa, little is known about this event relative to others. Equal and even deeper gaps exist concerning the Je-speakers' expansion. This study aims to elucidate some aspects of these successful expansions. To meet this purpose, we analyzed Native American mtDNA complete control region from nine different populations and included HVS-I sequences available in the literature, resulting in a total of 1,176 samples investigated. Evolutionary relationships were explored through median-joining networks and genetic/geographic/linguistic correlations with Mantel tests and spatial autocorrelation analyses. Both Tupi and Je showed general traces of ancient or more recent fission-fusion processes, but a very different pattern of demographic expansion. Tupi populations displayed a classical isolation-by-distance pattern, while Je groups presented an intricate and nonlinear mode of dispersion. We suggest that the collective memory and other cultural processes could be important factors influencing the fission-fusion events, which likely contributed to the genetic structure, evolution, and dispersion of Native American populations.

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

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    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.

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

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    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.

  4. 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,…

  5. "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…

  6. 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.

  7. 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

  8. The Role of Shift-Induced Interference in the Development of a Typologically Rare Phonological Contrast in Somali Bantu Kizigua

    OpenAIRE

    Tse, Holman

    2016-01-01

    This paper discusses the development of a typologically rare phonological contrast in an under-documented language called Somali Bantu Kizigua. The contrast in question is a contrast between two coronal places of articulation for NC (Nasal + Consonant) clusters, a genetic feature found across Bantu languages. The argument of this paper is that shift-induced interference as a mechanism for contact-induced change (Thomason & Kaufman, 1988) played a crucial role in the development of this contra...

  9. 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.

  10. The origin of HTLV-1 in southern Bahia by phylogenetic, mtDNA and β-globin analysis

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    Milena Magalhães Aleluia

    2015-12-01

    Full Text Available Different hypotheses have been elaborated to explain how the HTLV spread throughout the world. It has been proposed that the virus was introduced in Bahia, during the slave-trade period from the 16th century to 19th century. However, there is no information about the HTLV evolutionary history in southern Bahia. The phylogeny is fundamental in order to clarify its introduction and dispersion. The DNA of 29 samples was extracted, followed by nested-PCR assay for the LTR and DNA sequencing. These sequences were analyzed by phylogenic methods. The mtDNA ancestry markers and βA-globin haplotypes were analyzed by PCR/RFLP. In relation to HTLV subtyping, all samples were classified as cosmopolitan subtype and transcontinental subgroup. Results suggest an ancient post-Columbian introduction of HTLV-1a-A associated with the slave trade between the XVI and late XIX centuries in southern Bahia. As regards the ethnicity of HTLV-infected women, the haplotype characterization of β-globin gene and the mtDNA ethnicity of HTLV-infected women, we have detected a major African contribution, with a predominance of Benin and Bantu types. HTLV-1 infection is spread in Bahia and the point of origin was possibly Salvador.

  11. 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.

  12. 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.

  13. Beta-globin haplotype analysis suggests that a major source of Malagasy ancestry is derived from Bantu-speaking Negroids.

    Science.gov (United States)

    Hewitt, R; Krause, A; Goldman, A; Campbell, G; Jenkins, T

    1996-06-01

    The origins of the inhabitants of Madagascar have not been fully resolved. Anthropological studies and preliminary genetic data point to two main sources of ancestry of the Malagasy, namely, Indonesian and African, with additional contributions from India and Arabia. The sickle-cell (beta s) mutation is found in populations of African and Indian origin. The frequency of the beta s-globin gene, derived from 1,425 Malagasy individuals, varies from 0 in some highland populations to .25 in some coastal populations. The beta s mutation is thought to have arisen at least five times, on the basis of the presence of five distinct beta s-associated haplotypes, each found in a separate geographic area. Twenty-five of the 35 Malagasy beta s haplotypes were of the typical "Bantu" type, 1 "Senegal" haplotype was found, and 2 rare or atypical haplotypes were observed; the remaining 7 haplotypes were consistent with the Bantu haplotype. The Bantu beta s mutation is thought to have been introduced into Madagascar by Bantu-speaking immigrants (colonists or slaves) from central or east Africa. The Senegal beta s mutation may have been introduced to the island via Portuguese naval explorers. This study provides the first definitive biological evidence that a major component of Malagasy ancestry is derived from African populations, in particular, Bantu-speaking Negroids. beta A haplotypes are also consistent with the claim for a significant African contribution to Malagasy ancestry but are also suggestive of Asian/Oceanic and Caucasoid admixture within the Malagasy population.

  14. 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.

  15. 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

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

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    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.

  17. 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.

  18. 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.

  19. 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

  20. mtDNA variation in East Africa unravels the history of Afro-Asiatic groups.

    Science.gov (United States)

    Boattini, Alessio; Castrì, Loredana; Sarno, Stefania; Useli, Antonella; Cioffi, Manuela; Sazzini, Marco; Garagnani, Paolo; De Fanti, Sara; Pettener, Davide; Luiselli, Donata

    2013-03-01

    East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations--explored using spatial Principal Component Analysis and Model-based clustering--turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata.

  1. 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.

  2. 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.

  3. Keeping mtDNA in Shape between Generations

    Science.gov (United States)

    Stewart, James B.; Larsson, Nils-Göran

    2014-01-01

    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. PMID:25299061

  4. KEBIJAKAN PENGOPERASIAN BUBU DENGAN ALAT BANTU TERUMBU KARANG BUATAN DAN RUMPON DI WILAYAH REHABILITASI PERAIRAN KEPULAUAN SERIBU

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    Isa Nagib Edrus

    2014-05-01

    Full Text Available Ujicoba bubu bersama terumbu karang buatan dan rumpon di wilayah rehabilitasi perairan Pulau Pari dan Pramuka adalah untuk menentukan kesesuaian paket teknologi alat tangkap dan alat bantu dalam usaha perikanan yang layak dari sisi teknis, sosial dan ekonomi. Tulisan ini merupakan sintesa kebijakan pola pemanfaatan bubu dengan dua alat bantu pengumpul ikan. Pendekatan yang digunakan adalah analisis kebijakan dengan memformulasikan semua informasi yang relevan dan hasil penelitian terkait. Hasil analisis menunjukkan bahwa penggunaan bubu dalam perikanan multi alat tangkap dengan pemanfaatan alat bantu penangkapan tergolong efektif secara teknis, sosial dan ekonomis. CPUE bubu dari 4 hari perendaman/trip adalah ratarata 1,1 kg/unit/trip untuk nelayan Pulau Pari yang mengoperasikan bubu di dekat terumbu buatan dan 2,4 kg/unit/trip untuk nelayan Pulau Pulau Pramuka yang menaruh bubu di bawah rumpon. Perikanan bubu tergolong layak ekonomi jika terintegrasi dengan perikanan multi alat tangkap. Nilai tambah pendapatan dari penggunaan bubu berkisar pada Rp. 196.000–Rp. 400.000 per trip. Perikanan bubu memiliki prospek yang baik untuk dikembangkan dalam skala besar melalui diversifikasi usaha perikanan di wilayah perairan yang direhabilitasi dan aplikasinya dapat diterima nelayan. Alat bantu rumpon memberikan pengaruh lebih besar pada hasil tangkap bubu dibanding hanya penggunaan karang buatan.   The pot application by using artificial reefs and payaos as rehabilited fishing grounds in the waters of Pari and Pramuka Islands was to determine technological, social and economical feasible fisheries used pots and the both of fish aggregation divices (FAD. This paper is policy making of pot utility design using two kinds of the FAD. Policy analysis is an approach used to formulate any relevant information and related study results. The analysis showed that pot applications in multi gears fisheries using FAD were effective by technical, social and

  5. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations.

    Directory of Open Access Journals (Sweden)

    Danielle A Badro

    Full Text Available The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of F(ST's, R(ST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    Thembi Russell

    Full Text Available 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 (14C 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.

  8. The mutation rate of the human mtDNA deletion mtDNA4977.

    Science.gov (United States)

    Shenkar, R; Navidi, W; Tavaré, S; Dang, M H; Chomyn, A; Attardi, G; Cortopassi, G; Arnheim, N

    1996-10-01

    The human mitochondrial mutation mtDNA4977 is a 4,977-bp deletion that originates between two 13-bp direct repeats. We grew 220 colonies of cells, each from a single human cell. For each colony, we counted the number of cells and amplified the DNA by PCR to test for the presence of a deletion. To estimate the mutation fate, we used a model that describes the relationship between the mutation rate and the probability that a colony of a given size will contain no mutants, taking into account such factors as possible mitochondrial turnover and mistyping due to PCR error. We estimate that the mutation rate for mtDNA4977 in cultured human cells is 5.95 x 10(-8) per mitochondrial genome replication. This method can be applied to specific chromosomal, as well as mitochondrial, mutations.

  9. Toluidine Blue Vital Staining sebagai Alat Bantu Diagnostik pada Karsinoma Sel Skuamosa Lidah

    Directory of Open Access Journals (Sweden)

    Dwi Suhartiningtyas

    2012-12-01

    Full Text Available Latar belakang. Karsinoma sel skuamus oral (KSSO merupakan salah satu kanker mulut yang paling sering terjadi. Deteksi dini kanker mulut menyulitkan oleh karena etiologi yang tidak pasti dan gambaran klinis yang tidak khas. Toluidine blue vital staining (TBVS dilaporkan dapat membantu penegakan diagnosis KSSO. Tujuan. Penulisan ini bertujuan melaporkan kasus KSSO di lidah yang terdiagnosis melalui TBVS. Kasus dan penanganannya. Laki-laki 77 tahun dengan gigi tiruan lengkap mengeluhkan sakit pada lidah sejak 2 minggu lalu, yang tidak sembuh dengan terapi konvensional. Pasien adalah perokok berat selama 60 tahun. Temuan klinis menunujukkan ulkus soliter berdiameter 2,5 cm pada ventral lidah, tepi membulat, indurasi dan tertutup pseudomembran putih. Temuan lain berupa kandidas mulut pada mukosa palatal, kedua sudut mulut dan dorsum lidah. Berdasar anamnesis dan pemeriksaan klinis, dicurigai adanya keganasan pada lesi lidah. Perawatan awal ditujuan untuk pembersihan rongga mulut, terapi anti jamur dan perbaikan status nutrisi. Lima hari kemudian, dilaporkan adanya kaku lidah dan gangguan fungsi mulut. Klinis tampak ulkus pada lidah semakin dalam dan melebar, untuk memastikan kecurigaan keganasan dilaksanakan pemeriksaan TBVS. Hasil pemeriksaan positif sehingga ditegakkan diagnosis kerja KSSO. Pemeriksaan lebih lanjut, pasien dikirim ke Klinik Bedah Mulut Rumah Sakit Dr. Sarjito. Hasil biopsi positif menunjukkan KSSO, selanjutnya pasien dirujuk ke Klinik Onkologi. Kesimpulan. Karsinoma sel skuamus oral memiliki gambaran klinis tidak khas sehingga penyakit ini sulit terdeteksi secara dini. Diagnosis dan perawatan dini KSSO akan meningkatkan survival rate dan kualitas hidup penderitanya. Metode pemeriksaan diagnostic bantu dengan TBVS sangat membantu dalam penegakan diagnosis keganasan di rongga mulut.   Background. Oral squamous cell carcinoma (OSCC is one of the most oral cancers occurred. Early detection of oral cancer is difficult due to uncertain

  10. Studi Perbandingan Perilaku Profil Baja WF dan HSS Sebagai Bresing pada SCBF Akibat Beban Lateral dengan Program Bantu Finite Element Analysis

    Directory of Open Access Journals (Sweden)

    Nuur Aziza Setiyowati

    2012-09-01

    Full Text Available Concentrically Braced Frame (CBF adalah pengembangan dari Moment Resisting Frame (MRF, dimana CBF mempunyai kekakuan yang tinggi sehingga mempunyai simpangan yang lebih kecil dari MRF. Dalam hal ini juga balok, kolom, dan pengaku diatur sehingga membentuk suatu rangka vertikal. Dalam aksi inelastis pengaku diatur mengalami ada dua macam gaya yaitu leleh akibat gaya tarik dan tekuk akibat gaya tekan. Dalam Tugas Akhir ini akan membahas mengenai perbandingan perilaku dari 2 jenis profil baja yang digunakan sebagai bresing, yaitu profil WF dan HSS. Portal yang dianalisa adalah portal baja SCBF dengan tipe inverted-v 1 lantai yang menerima beban lateral. Analisa yang akan dilakukan menggunakan program bantu SAP 2000 v.14 dan kemudian dianalisa lagi dengan program bantu finite element analysis. Dari hasil penelitian menunjukkan bahwa bresing adalah elemen terlemah pada portal SCBF yang ditinjau karena tegangan pada bresing lebih besar daripada elemen pada portal SCBF yang lain.

  11. Coevolution of Drosophila melanogaster mtDNA and Wolbachia genotypes.

    Directory of Open Access Journals (Sweden)

    Yury Ilinsky

    Full Text Available Maternally inherited microorganisms can influence the mtDNA pattern of variation in hosts. This influence is driven by selection among symbionts and can cause the frequency of mitochondrial variants in the population to eventually increase or decrease. Wolbachia infection is common and widespread in Drosophila melanogaster populations. We compared genetic variability of D. melanogaster mitotypes with Wolbachia genotypes among isofemale lines associated with different geographic locations and time intervals to study coevolution of the mtDNA and Wolbachia. Phylogenetic analysis of D. melanogaster mtDNA revealed two clades diverged in Africa, each associated with one of the two Wolbachia genotype groups. No evidence of horizontal transmission of Wolbachia between maternal lineages has been found. All the mtDNA variants that occur in infected isofemale lines are found in uninfected isofemale lines and vice versa, which is indicative of a recent loss of infection from some maternal fly lineages and confirms a significant role of Wolbachia in the D. melanogaster mtDNA pattern of variation. Finally, we present a comparative analysis of biogeographic distribution of D. melanogaster mitotypes all over the world.

  12. MtDNA haplogroups and elite Korean athlete status.

    Science.gov (United States)

    Kim, K C; Cho, H I; Kim, W

    2012-01-01

    Mitochondrial DNA (mtDNA) variation has recently been suggested to have an association with athletic performance or physical endurance. Since mtDNA is haploid and lacks recombination, specific mutations in the mtDNA genome associated with human exercise tolerance or intolerance arise and remain in particular genetic backgrounds referred to as haplogroups. To assess the possible contribution of mtDNA haplogroup-specific variants to differences in elite athletic performance, we performed a population-based study of 152 Korean elite athletes [77 sprint/power athletes (SPA) and 75 endurance/middle-power athletes (EMA)] and 265 non-athletic controls (CON). The overall haplogroup distribution of EMA differed significantly from CON (p<0.01), but that of SPA did not. The EMA have an excess of haplogroups M* (OR 4.38, 95% CI 1.63-11.79, p=0.003) and N9 (OR 2.32, 95% CI 0.92-5.81, p=0.042), but a dearth of haplogroup B (OR 0.26, 95% CI 0.09-0.75, p=0.003) compared with the CON. Thus, our data imply that specific mtDNA lineages may provide a significant effect on elite Korean endurance status, although functional studies with larger sample sizes are necessary to further substantiate these findings.

  13. The hematologic characteristics of sickle cell anemia bearing the Bantu haplotype: the relationship between G gamma and HbF level.

    Science.gov (United States)

    Nagel, R L; Rao, S K; Dunda-Belkhodja, O; Connolly, M M; Fabry, M E; Georges, A; Krishnamoorthy, R; Labie, D

    1987-04-01

    Previous work has demonstrated that the HbS gene has appeared and expanded three times in Africa in three separate geographic locations and that these three distinct mutational events can be identified by linked DNA polymorphic sites (haplotypes) surrounding the abnormal gene. We have reported that the Senegalese and Beninian haplotypes differ in G gamma expression, mean percentage of HbF, and percentage of dense cells. We now report on the third haplotype, the Bantu, and find that it has intermediate features, namely, the high mean percentage of HbF and low percentage of dense cells associated with the Senegalese haplotype, but with a low percentage of G gamma expression similar to the Beninian haplotype. The distribution of percent HbF is quite different from Senegal haplotype-bearing sickle cell anemia patients since it covers a much wider range. The low G gamma expression is also different from the Beninians since it contains a significant and unique cluster of individuals with lower than 38% G gamma. Interestingly, among the Bantu there is a strong correlation between HbF levels and G gamma expression, which is not seen with the other haplotypes. These findings open the possibility that among the Bantu haplotype-bearing individuals two chromosomal types exist that define different levels of G gamma and HbF expression. Further structural exploration of these two potential subhaplotypes is needed.

  14. Schizophrenia: maternal inheritance and heteroplasmy of mtDNA mutations.

    Science.gov (United States)

    Ichikawa, Tomoe; Arai, Makoto; Miyashita, Mitsuhiro; Arai, Mayumi; Obata, Nanako; Nohara, Izumi; Oshima, Kenichi; Niizato, Kazuhiro; Okazaki, Yuji; Doi, Nagafumi; Itokawa, Masanari

    2012-01-01

    Role of mitochondrial pathology in schizophrenia has not been fully clarified. We searched for distinctive variants in mtDNA extracted from the gray matter of postmortem brains and from peripheral blood samples. We screened mtDNA region containing 5 genes encoding subunits of cytochrome c oxidase and ATPases. Polymorphisms not already reported in databases are recorded as unregistered rare variants. Four unregistered, non-synonymous rare variants were detected in 4 schizophrenic samples. Seven registered non-synonymous variants were not previously detected in non-psychotic Japanese samples registered in the mtSNP database. These variants may contribute to disease pathophysiology. In one family, compound mutations showed co-segregation with schizophrenia. MtDNA mutations could confer a risk for schizophrenia in the Japanese population, although further analyses are needed.

  15. Depletion of mtDNA: syndromes and genes.

    Science.gov (United States)

    Alberio, Simona; Mineri, Rossana; Tiranti, Valeria; Zeviani, Massimo

    2007-01-01

    Maintenance of mitochondrial DNA (mtDNA) requires the concerted activity of several nuclear-encoded factors that participate in its replication, being part of the mitochondrial replisome or ensuring the balanced supply of dNTPs to mitochondria. In the past decade, a growing number of syndromes associated with dysfunction due to tissue-specific depletion of mtDNA (MDS) have been reported. This article reviews the current knowledge of the genes responsible for these disorders, the impact of different mutations in the epidemiology of MDS and their role in the pathogenic mechanisms underlying the different clinical presentations.

  16. Pattern Recognition of mtDNA with Associative Models

    Directory of Open Access Journals (Sweden)

    Acevedo María Elena

    2016-01-01

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

  17. The Bantu-Romance-Greek connection revisited: Processing constraints in auxiliary and clitic placement from a cross-linguistic perspective

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    Stergios Chatzikyriakidis

    2017-02-01

    Full Text Available This paper explores a connection between Romance and Greek on the one hand, and Bantu on the other. More specifically, we look at auxiliary placement in Rangi and clitic placement in Tobler Mussafia languages, with a special emphasis on Cypriot Greek, and argue that a common explanation for their distribution can be found once a move into a dynamic framework is made. Rangi exhibits an unusual word order alternation in auxiliary constructions under which the position of the auxiliary appears to be sensitive to an element appearing at the left periphery of the clause. A similar sensitivity to a left-peripheral element can be seen to regulate clitic placement in Cypriot Greek (and generally in the so-called Tobler Mussafia clitic languages. The paper presents a parsing-oriented account of these two phenomena in the Dynamic Syntax framework, arguing that the similarities in syntactic distribution are the result of the encoding in the lexicon of processing strategies that were potentially pragmatic preferences in earlier stages of the respective languages. The account thus leans on the role played by the lexical entries for auxiliary and clitic forms, as well as the assumption that underspecification is inherent in the process of establishing meaning in context. The account is further supplemented by possible pathways of diachronic change that could have given rise to the systems found in present day varieties.

  18. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome.

    Science.gov (United States)

    Pett, Walker; Ryan, Joseph F; Pang, Kevin; Mullikin, James C; Martindale, Mark Q; Baxevanis, Andreas D; Lavrov, Dennis V

    2011-08-01

    Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum--Ctenophora--has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we Polymerase Chain Reaction (PCR) amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10 kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, likely to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies.

  19. Extreme Mitochondrial Evolution in the Ctenophore Mnemiopsis leidyi: Insights from mtDNA and the Nuclear Genome

    Science.gov (United States)

    Pett, Walker; Ryan, Joseph F.; Pang, Kevin; Mullikin, James C.; Martindale, Mark Q.; Baxevanis, Andreas D.; Lavrov, Dennis V.

    2012-01-01

    Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum – Ctenophora – has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as an invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we PCR amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologues in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, probably to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies. PMID:21985407

  20. Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences

    Indian Academy of Sciences (India)

    FATAH ZAREI; HASSAN RAJABI-MAHAM

    2016-12-01

    Throughout the history of modern humans, the current Kurdish-inhabited area has served as part of a tricontinental crossroad for major human migrations. Also, a significant body of archaeological evidence points to this area as the site of Neolithic transition. To investigate the phylogeography, origins and demographic history, mtDNA D-loop region of individuals representing four Kurdish groups from Iran were analysed. Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased drift due to small population size; while in the Kurmanji group it indicated a bias towards drift or mass migration events during the 5–18th century AD. The Mantel test showed strong isolation by distance, and AMOVA results for global and regional scales confirmed that the geography had acted as the main driving force in shaping the current pattern of mtDNA diversity, rather than linguistic similarity. The results of demographic analyses, in agreement with archaeological data, revealed a recent expansion of the Kurds (∼9,500 years before present) related to the Neolithic transition from hunting and gathering, to farmingand cattle breeding in the Near East. Further, the high frequencies of typical haplogroups for early farmers (H; 37.1%) and hunter-gatherers (U; 13.8%) in the Kurds may testify the earlier hunter-gatherers in the Kurdish-inhabited area that adopted and admixed the Kurds ancestors following the Neolithic transition.

  1. HSV-1/HSV-2 Infection-Related Cancers in Bantu Populations Driving HIV-1 Prevalence in Africa: Tracking the Origin of AIDS at the Onset of the 20th Century

    Directory of Open Access Journals (Sweden)

    Jacqueline Le Goaster

    2016-11-01

    Full Text Available Introduction: At the onset of the 20th century, ancient clinical observations of cancer epidemics in Bantu populations of Sub-Saharan Africa were discovered. They were reported from 1914 to 1960, but remained unexplained. In 1983, in San Francisco, Calif., USA, cancer epidemics were related to infections by the human immunodeficiency virus type 1 (HIV-1 known as AIDS disease. Yet since 1996, it is known that HIV-1 strains are not the only ones involved. In Sub-Saharan Africa, recurrent orobuccal herpes simplex virus type 1 (HSV-1 and genital recurrent herpes simplex virus type 2 (HSV-2 appeared many times prior to infection by HIV-1. Case Reports: Data on these ancient medical observations regarding African cancer epidemics can today be referred to as the relationship between the unfortunate immune deficiency of herpes in Bantu populations and HIV-1 viral strains. For centuries, the Bantu populations dispersed in forests were living in close proximity to chimpanzees infected by simian immunodeficiency virus (SIV and were exposed to SIV contamination which became HIV-1 in human beings. Presently, these unexplained Bantu cancer epidemics can be linked to the viral partnership of HSV-1/HSV-2 to HIV-1 strains. Conclusion: The key issue is now to prevent HSV-1/HSV-2 diseases related to HIV-1. An anti-herpes treatment administered early during childhood to Bantu populations will offer a mean of preventing herpes diseases related to HIV-1 infection and hence avoid cancer epidemics.

  2. An improved method with a wider applicability to isolate plant mitochondria for mtDNA extraction

    OpenAIRE

    2015-01-01

    Background Mitochondria perform a principal role in eukaryotic cells. Mutations in mtDNA can cause mitochondrial dysfunction and are frequently associated with various abnormalities during plant development. Extraction of plant mitochondria and mtDNA is the basic requirement for the characterization of mtDNA mutations and other molecular studies. However, currently available methods for mitochondria isolation are either tissue specific or species specific. Extracted mtDNA may contain substant...

  3. 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.

  4. Phylogeography of the rice frog, Fejervarya multistriata (Anura: Ranidae), from China based on mtDNA D-loop sequences.

    Science.gov (United States)

    Zhong, Jing; Liu, Zhong-Quan; Wang, Yi-Quan

    2008-08-01

    The rice frog, Fejervarya multistriata, is an amphibian widely distributed in China. In this study, we sampled the species across its distributional area in China and sequenced the mtDNA D-loop to investigate the genetic diversity and geographical pattern of the frog population. The results revealed 38 haplotypes in the population, with K2P values varying from 0.19% to 4.22%. Both a phylogenetic analysis and a nested clade analysis (NCA) detected two geographically isolated lineages respectively distributed around the Yangtze drainage (Yangtze lineage) and the south of China (southern lineage). NCA inferred a contiguous range expansion within the Yangtze lineage and allopatric fragmentation within the southern lineage, which might be partly due to the limited samples from this lineage. Accordingly, Fu's Fs test also indicated a population expansion after glacial movement. Therefore, we assumed that the species history responding to glacial events shaped the present population pattern of F. multistriata on the Chinese mainland.

  5. Expansive Cements

    Science.gov (United States)

    1970-10-01

    sale: is disributici is unlimited = F’)RIWRD Seior Ignacio Soto, Rrecutive President, Instituto Mexicano del Cementc y Concreto , invited Mr. Bryant... Concreto , a.c., Kwidco, D. F., Mexico. Based on info.mation largely obtained from ACT Committee 223, Expansive ’ement. Concretes, ACI Journal, August 1Q70

  6. 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.

  7. mtDNA diversity in Azara's owl monkeys (Aotus azarai azarai) of the Argentinean Chaco.

    Science.gov (United States)

    Babb, Paul L; Fernandez-Duque, Eduardo; Baiduc, Caitlin A; Gagneux, Pascal; Evans, Sian; Schurr, Theodore G

    2011-10-01

    Owl monkeys (Aotus spp.) inhabit much of South America yet represent an enigmatic evolutionary branch among primates. While morphological, cytogenetic, and immunological evidence suggest that owl monkey populations have undergone isolation and diversification since their emergence in the New World, problems with adjacent species ranges, and sample provenance have complicated efforts to characterize genetic variation within the genus. As a result, the phylogeographic history of owl monkey species and subspecies remains unclear, and the extent of genetic diversity at the population level is unknown. To explore these issues, we analyzed mitochondrial DNA (mt DNA) variation in a population of wild Azara's owl monkeys (Aotus azarai azarai) living in the Gran Chaco region of Argentina. We sequenced the complete mitochondrial genome from one individual (16,585 base pairs (bp)) and analyzed 1,099 bp of the hypervariable control region (CR) and 696 bp of the cytochrome oxidase II (COII) gene in 117 others. In addition, we sequenced the mitochondrial genome (16,472 bp) of one Nancy Ma's owl monkey (A. nancymaae). Based on the whole mtDNA and COII data, we observed an ancient phylogeographic discontinuity among Aotus species living north, south, and west of the Amazon River that began more than eight million years ago. Our population analyses identified three major CR lineages and detected a high level of haplotypic diversity within A. a. azarai. These data point to a recent expansion of Azara's owl monkeys into the Argentinean Chaco. Overall, we provide a detailed view of owl monkey mtDNA variation at genus, species, and population levels.

  8. 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.

  9. 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.

  10. Huntington's disease and mitochondrial DNA deletions: event or regular mechanism for mutant huntingtin protein and CAG repeats expansion?!

    Science.gov (United States)

    Banoei, Mohammad Mehdi; Houshmand, Massoud; Panahi, Mehdi Shafa Shariat; Shariati, Parvin; Rostami, Maryam; Manshadi, Masoumeh Dehghan; Majidizadeh, Tayebeh

    2007-11-01

    The mitochondrial DNA (mtDNA) may play an essential role in the pathogenesis of the respiratory chain complex activities in neurodegenerative disorders such as Huntington's disease (HD). Research studies were conducted to determine the possible levels of mitochondrial defect (deletion) in HD patients and consideration of interaction between the expanded Huntingtin gene as a nuclear gene and mitochondria as a cytoplasmic organelle. To determine mtDNA damage, we investigated deletions based in four areas of mitochondrial DNA, in a group of 60 Iranian patients clinically diagnosed with HD and 70 healthy controls. A total of 41 patients out of 60 had CAG expansion (group A). About 19 patients did not show expansion but had the clinical symptoms of HD (group B). MtDNA deletions were classified into four groups according to size; 9 kb, 7.5 kb, 7 kb, and 5 kb. We found one of the four-mtDNA deletions in at least 90% of samples. Multiple deletions have also been observed in 63% of HD patients. None of the normal control (group C) showed mtDNA deletions. The sizes or locations of the deletions did not show a clear correlation with expanded CAG repeat and age in our samples. The study presented evidence that HD patients had higher frequencies of mtDNA deletions in lymphocytes in comparison to the controls. It is thus proposed that CAG repeats instability and mutant Htt are causative factor in mtDNA damage.

  11. No recombination of mtDNA after heteroplasmy for 50 generations in the mouse maternal germline

    Science.gov (United States)

    Hagström, Erik; Freyer, Christoph; Battersby, Brendan J.; Stewart, James B.; Larsson, Nils-Göran

    2014-01-01

    Variants of mitochondrial DNA (mtDNA) are commonly used as markers to track human evolution because of the high sequence divergence and exclusive maternal inheritance. It is assumed that the inheritance is clonal, i.e. that mtDNA is transmitted between generations without germline recombination. In contrast to this assumption, a number of studies have reported the presence of recombinant mtDNA molecules in cell lines and animal tissues, including humans. If germline recombination of mtDNA is frequent, it would strongly impact phylogenetic and population studies by altering estimates of coalescent time and branch lengths in phylogenetic trees. Unfortunately, this whole area is controversial and the experimental approaches have been widely criticized as they often depend on polymerase chain reaction (PCR) amplification of mtDNA and/or involve studies of transformed cell lines. In this study, we used an in vivo mouse model that has had germline heteroplasmy for a defined set of mtDNA mutations for more than 50 generations. To assess recombination, we adapted and validated a method based on cloning of single mtDNA molecules in the λ phage, without prior PCR amplification, followed by subsequent mutation analysis. We screened 2922 mtDNA molecules and found no germline recombination after transmission of mtDNA under genetically and evolutionary relevant conditions in mammals. PMID:24163253

  12. 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.

  13. 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.

  14. Metabolic rescue in pluripotent cells from patients with mtDNA disease.

    Science.gov (United States)

    Ma, Hong; Folmes, Clifford D L; Wu, Jun; Morey, Robert; Mora-Castilla, Sergio; Ocampo, Alejandro; Ma, Li; Poulton, Joanna; Wang, Xinjian; Ahmed, Riffat; Kang, Eunju; Lee, Yeonmi; Hayama, Tomonari; Li, Ying; Van Dyken, Crystal; Gutierrez, Nuria Marti; Tippner-Hedges, Rebecca; Koski, Amy; Mitalipov, Nargiz; Amato, Paula; Wolf, Don P; Huang, Taosheng; Terzic, Andre; Laurent, Louise C; Izpisua Belmonte, Juan Carlos; Mitalipov, Shoukhrat

    2015-08-13

    Mitochondria have a major role in energy production via oxidative phosphorylation, which is dependent on the expression of critical genes encoded by mitochondrial (mt)DNA. Mutations in mtDNA can cause fatal or severely debilitating disorders with limited treatment options. Clinical manifestations vary based on mutation type and heteroplasmy (that is, the relative levels of mutant and wild-type mtDNA within each cell). Here we generated genetically corrected pluripotent stem cells (PSCs) from patients with mtDNA disease. Multiple induced pluripotent stem (iPS) cell lines were derived from patients with common heteroplasmic mutations including 3243A>G, causing mitochondrial encephalomyopathy and stroke-like episodes (MELAS), and 8993T>G and 13513G>A, implicated in Leigh syndrome. Isogenic MELAS and Leigh syndrome iPS cell lines were generated containing exclusively wild-type or mutant mtDNA through spontaneous segregation of heteroplasmic mtDNA in proliferating fibroblasts. Furthermore, somatic cell nuclear transfer (SCNT) enabled replacement of mutant mtDNA from homoplasmic 8993T>G fibroblasts to generate corrected Leigh-NT1 PSCs. Although Leigh-NT1 PSCs contained donor oocyte wild-type mtDNA (human haplotype D4a) that differed from Leigh syndrome patient haplotype (F1a) at a total of 47 nucleotide sites, Leigh-NT1 cells displayed transcriptomic profiles similar to those in embryo-derived PSCs carrying wild-type mtDNA, indicative of normal nuclear-to-mitochondrial interactions. Moreover, genetically rescued patient PSCs displayed normal metabolic function compared to impaired oxygen consumption and ATP production observed in mutant cells. We conclude that both reprogramming approaches offer complementary strategies for derivation of PSCs containing exclusively wild-type mtDNA, through spontaneous segregation of heteroplasmic mtDNA in individual iPS cell lines or mitochondrial replacement by SCNT in homoplasmic mtDNA-based disease.

  15. Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups.

    Science.gov (United States)

    Sharma, Swarkar; Saha, Anjana; Rai, Ekta; Bhat, Audesh; Bamezai, Ramesh

    2005-01-01

    We have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.

  16. Folate deficiency increases mtDNA and D-1 mtDNA deletion in aged brain of mice lacking uracil-DNA glycosylase.

    Science.gov (United States)

    Kronenberg, Golo; Gertz, Karen; Overall, Rupert W; Harms, Christoph; Klein, Jeanette; Page, Melissa M; Stuart, Jeffrey A; Endres, Matthias

    2011-04-01

    Strong epidemiological and experimental evidence links folate deficiency and resultant hyperhomocysteinemia with cognitive decline and neurodegeneration. Here, we tested the hypothesis that uracil misincorporation contributes to mitochondrial pathology in aged brain following folate deprivation. In a 2 × 2 design, 14-month-old mice lacking uracil DNA glycosylase (Ung-/-) versus wild-type controls were subjected to a folate-deficient versus a regular diet for six weeks. Folate-deficient feeding significantly enhanced mtDNA content and overall abundance of the D-1 mtDNA deletion in brain of Ung-/-, but not of wild-type mice. Independent of folate status, the frequency of the D-1 mtDNA deletion in mtDNA was significantly increased in Ung-/- mice. The rate of mitochondrial biogenesis as assessed at six weeks of the experimental diet by mRNA expression levels of transcriptional coactivator peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α and of mitochondrial transcription factor A (Tfam) was not affected by either Ung-/- genotype or short-term folate deficiency. Similarly, citrate synthase (CS) activity in the brain did not differ across experimental groups. By contrast, independent of genotype, lactate dehydrogenase (LDH) activity was significantly reduced in folate-deficient animals. Our results suggest that impaired uracil excision repair causes an increase in mitochondrial mutagenesis in aged brain along with a compensatory increase in mtDNA content in response to low folate status. Folate deficiency may contribute to neurodegeneration via mtDNA damage.

  17. 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.

  18. 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.

  19. 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

  20. 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.

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

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    Candela L Hernández

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

  2. 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.

  3. 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.

  4. 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.

  5. Mutation patterns of mtDNA: Empirical inferences for the coding region

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    Alvarez Luis

    2008-06-01

    Full Text Available Abstract Background Human mitochondrial DNA (mtDNA has been extensively used in population and evolutionary genetics studies. Thus, a valid estimate of human mtDNA evolutionary rate is important in many research fields. The small number of estimations performed for the coding region of the molecule, showed important differences between phylogenetic and empirical approaches. We analyzed a portion of the coding region of mtDNA (tRNALeu, ND1 and tRNAIle genes, using individuals belonging to extended families from the Azores Islands (Portugal with the main aim of providing empirical estimations of the mutation rate of the coding region of mtDNA under different assumptions, and hence to better understand the mtDNA evolutionary process. Results Heteroplasmy was detected in 6.5% (3/46 of the families analyzed. In all of the families the presence of mtDNA heteroplasmy resulted from three new point mutations, and no cases of insertions or deletions were identified. Major differences were found in the proportion and type of heteroplasmy found in the genes studied when compared to those obtained in a previous report for the D-loop. Our empirical estimation of mtDNA coding region mutation rate, calculated taking into account the sex of individuals carrying new mutations, the probability of intra-individual fixation of mutations present in heteroplasmy and, to the possible extent, the effect of selection, is similar to that obtained using phylogenetic approaches. Conclusion Based on our results, the discrepancy previously reported between the human mtDNA coding region mutation rates observed along evolutionary timescales and estimations obtained using family pedigrees can be resolved when correcting for the previously cited factors.

  6. The occurrence of mtDNA heteroplasmy in multiple cetacean species.

    Science.gov (United States)

    Vollmer, Nicole L; Viricel, Amélia; Wilcox, Lynsey; Katherine Moore, M; Rosel, Patricia E

    2011-04-01

    In population genetics and phylogenetic studies, mitochondrial DNA (mtDNA) is commonly used for examining differences both between and within groups of individuals. For these studies, correct interpretation of every nucleotide position is crucial but can be complicated by the presence of ambiguous bases resulting from heteroplasmy. Particularly for non-model taxa, the presence of heteroplasmy in mtDNA is rarely reported, therefore, it is unclear how commonly it occurs and how it can affect phylogenetic relationships among taxa and the overall understanding of evolutionary processes. We examined the occurrence of both site and length heteroplasmy within the mtDNA of ten marine mammal species, for most of which mtDNA heteroplasmy has never been reported. After sequencing a portion of the mtDNA control region for 5,062 individuals, we found heteroplasmy in at least 2% of individuals from seven species, including Stenella frontalis where 58.9% were heteroplasmic. We verified the presence of true heteroplasmy, ruling out artifacts from amplification and sequencing methods and the presence of nuclear copies of mitochondrial genes. We found no evidence that mtDNA heteroplasmy influenced phylogenetic relationships, however, its occurrence does have the potential to increase the genetic diversity for all species in which it is found. This study stresses the importance of both detecting and reporting the occurrence of heteroplasmy in wild populations in order to enhance the knowledge of both the introduction and the persistence of mutant mitochondrial haplotypes in the evolutionary process.

  7. A Statistical Framework for the Interpretation of mtDNA Mixtures: Forensic and Medical Applications

    Science.gov (United States)

    Egeland, Thore; Salas, Antonio

    2011-01-01

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

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    Arzu Tatar

    2014-04-01

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

  10. 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.

  11. Inspecting close maternal relatedness: Towards better mtDNA population samples in forensic databases

    Science.gov (United States)

    Bodner, Martin; Irwin, Jodi A.; Coble, Michael D.; Parson, Walther

    2011-01-01

    Reliable data are crucial for all research fields applying mitochondrial DNA (mtDNA) as a genetic marker. Quality control measures have been introduced to ensure the highest standards in sequence data generation, validation and a posteriori inspection. A phylogenetic alignment strategy has been widely accepted as a prerequisite for data comparability and database searches, for forensic applications, for reconstructions of human migrations and for correct interpretation of mtDNA mutations in medical genetics. There is continuing effort to enhance the number of worldwide population samples in order to contribute to a better understanding of human mtDNA variation. This has often lead to the analysis of convenience samples collected for other purposes, which might not meet the quality requirement of random sampling for mtDNA data sets. Here, we introduce an additional quality control means that deals with one aspect of this limitation: by combining autosomal short tandem repeat (STR) marker with mtDNA information, it helps to avoid the bias introduced by related individuals included in the same (small) sample. By STR analysis of individuals sharing their mitochondrial haplotype, pedigree construction and subsequent software-assisted calculation of likelihood ratios based on the allele frequencies found in the population, closely maternally related individuals can be identified and excluded. We also discuss scenarios that allow related individuals in the same set. An ideal population sample would be representative for its population: this new approach represents another contribution towards this goal. PMID:21067986

  12. 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.

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

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    Riikka H. Hämäläinen

    2015-06-01

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

  14. Presequence-Independent Mitochondrial Import of DNA Ligase Facilitates Establishment of Cell Lines with Reduced mtDNA Copy Number.

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    Domenico Spadafora

    Full Text Available Due to the essential role played by mitochondrial DNA (mtDNA in cellular physiology and bioenergetics, methods for establishing cell lines with altered mtDNA content are of considerable interest. Here, we report evidence for the existence in mammalian cells of a novel, low- efficiency, presequence-independent pathway for mitochondrial protein import, which facilitates mitochondrial uptake of such proteins as Chlorella virus ligase (ChVlig and Escherichia coli LigA. Mouse cells engineered to depend on this pathway for mitochondrial import of the LigA protein for mtDNA maintenance had severely (up to >90% reduced mtDNA content. These observations were used to establish a method for the generation of mouse cell lines with reduced mtDNA copy number by, first, transducing them with a retrovirus encoding LigA, and then inactivating in these transductants endogenous Lig3 with CRISPR-Cas9. Interestingly, mtDNA depletion to an average level of one copy per cell proceeds faster in cells engineered to maintain mtDNA at low copy number. This makes a low-mtDNA copy number phenotype resulting from dependence on mitochondrial import of DNA ligase through presequence-independent pathway potentially useful for rapidly shifting mtDNA heteroplasmy through partial mtDNA depletion.

  15. Presequence-Independent Mitochondrial Import of DNA Ligase Facilitates Establishment of Cell Lines with Reduced mtDNA Copy Number.

    Science.gov (United States)

    Spadafora, Domenico; Kozhukhar, Natalia; Alexeyev, Mikhail F

    2016-01-01

    Due to the essential role played by mitochondrial DNA (mtDNA) in cellular physiology and bioenergetics, methods for establishing cell lines with altered mtDNA content are of considerable interest. Here, we report evidence for the existence in mammalian cells of a novel, low- efficiency, presequence-independent pathway for mitochondrial protein import, which facilitates mitochondrial uptake of such proteins as Chlorella virus ligase (ChVlig) and Escherichia coli LigA. Mouse cells engineered to depend on this pathway for mitochondrial import of the LigA protein for mtDNA maintenance had severely (up to >90%) reduced mtDNA content. These observations were used to establish a method for the generation of mouse cell lines with reduced mtDNA copy number by, first, transducing them with a retrovirus encoding LigA, and then inactivating in these transductants endogenous Lig3 with CRISPR-Cas9. Interestingly, mtDNA depletion to an average level of one copy per cell proceeds faster in cells engineered to maintain mtDNA at low copy number. This makes a low-mtDNA copy number phenotype resulting from dependence on mitochondrial import of DNA ligase through presequence-independent pathway potentially useful for rapidly shifting mtDNA heteroplasmy through partial mtDNA depletion.

  16. On skin expansion.

    Science.gov (United States)

    Pamplona, Djenane C; Velloso, Raquel Q; Radwanski, Henrique N

    2014-01-01

    This article discusses skin expansion without considering cellular growth of the skin. An in vivo analysis was carried out that involved expansion at three different sites on one patient, allowing for the observation of the relaxation process. Those measurements were used to characterize the human skin of the thorax during the surgical process of skin expansion. A comparison between the in vivo results and the numerical finite elements model of the expansion was used to identify the material elastic parameters of the skin of the thorax of that patient. Delfino's constitutive equation was chosen to model the in vivo results. The skin is considered to be an isotropic, homogeneous, hyperelastic, and incompressible membrane. When the skin is extended, such as with expanders, the collagen fibers are also extended and cause stiffening in the skin, which results in increasing resistance to expansion or further stretching. We observed this phenomenon as an increase in the parameters as subsequent expansions continued. The number and shape of the skin expanders used in expansions were also studied, both mathematically and experimentally. The choice of the site where the expansion should be performed is discussed to enlighten problems that can lead to frustrated skin expansions. These results are very encouraging and provide insight into our understanding of the behavior of stretched skin by expansion. To our knowledge, this study has provided results that considerably improve our understanding of the behavior of human skin under expansion.

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

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    Alessandra eMaresca

    2015-03-01

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

  18. Advances in Human Mitochondrial Diseases Molecular Genetic Analysis of Pathogenic mtDNA Mutations.

    Science.gov (United States)

    Davidson, E; King, M P

    1997-01-01

    The mitochondrial diseases are a heterogeneous group of disorders that have been defined by specific morphological alterations in muscle and by deficits of the mitochondrial respiratory chain. The morphological hallmarks of these diseases include ragged-red fibers (an extensive proliferation of mitochondria in muscle fibers) and abnormal paracrystalline inclusions and membrane structures in mitochondria. The identification of pathogenic mutations in mitochondrial DNA (mtDNA) has resulted in a genetic classification of mitochondrial diseases. Investigations are being conducted to understand the molecular basis for the biochemical and morphological alterations of mitochondria associated with mtDNA mutations. © 1997, Elsevier Science Inc. (Trends Cardiovasc Med 1997;7:16-24).

  19. Cytonuclear conflict in interpopulation hybrids: the role of RNA polymerase in mtDNA transcription and replication.

    Science.gov (United States)

    Ellison, C K; Burton, R S

    2010-03-01

    Organismal fitness requires functional integration of nuclear and mitochondrial genomes. Structural and regulatory elements coevolve within lineages and several studies have found that interpopulation hybridization disrupts mitonuclear interactions. Because mitochondrial RNA polymerase (mtRPOL) plays key roles in both mitochondrial DNA (mtDNA) replication and transcription, the interaction between mtRPOL and coevolved regulatory sites in the mtDNA may be central to mitonuclear integration. Here, we generate interpopulation hybrids between divergent populations of the copepod Tigriopus californicus to obtain lines having different combinations of mtRPOL and mtDNA. Lines were scored for mtDNA copy number and ATP6 (mtDNA) gene expression. We find that there is a genotype-dependent negative association between mitochondrial transcriptional response and mtDNA copy number. We argue that an observed increase in mtDNA copy number and reduced mtDNA transcription in hybrids reflects the regulatory role of mtRPOL; depending on the mitonuclear genotype, hybridization may disrupt the normal balance between transcription and replication of the mitochondrial genome.

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

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    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.

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

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    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

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

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    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

  3. Absence of mtDNA mutations in leukocytes of CADASIL patients

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    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.

  4. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing

    DEFF Research Database (Denmark)

    Weiler, NEC; Baca, K; Ballard, D;

    2017-01-01

    ) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment. The samples had a variable...

  5. 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.

  6. 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...

  7. 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...

  8. 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.

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

    Science.gov (United States)

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

    2011-11-01

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

  10. 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

  11. 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

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    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

  12. Negative thermal expansion

    Energy Technology Data Exchange (ETDEWEB)

    Barrera, G D [Departamento de QuImica, Universidad Nacional de la Patagonia SJB, Ciudad Universitaria, 9000 Comodoro Rivadavia (Argentina); Bruno, J A O [Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de QuImica Inorganica, AnalItica y QuImica FIsica, Pabellon 2, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Barron, T H K [School of Chemistry, University of Bristol, Cantock' s Close, Bristol BS8 1TS (United Kingdom); Allan, N L [School of Chemistry, University of Bristol, Cantock' s Close, Bristol BS8 1TS (United Kingdom)

    2005-02-02

    There has been substantial renewed interest in negative thermal expansion following the discovery that cubic ZrW{sub 2}O{sub 8} contracts over a temperature range in excess of 1000 K. Substances of many different kinds show negative thermal expansion, especially at low temperatures. In this article we review the underlying thermodynamics, emphasizing the roles of thermal stress and elasticity. We also discuss vibrational and non-vibrational mechanisms operating on the atomic scale that are responsible for negative expansion, both isotropic and anisotropic, in a wide range of materials. (topical review)

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

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    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

  14. 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

  15. Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae

    Science.gov (United States)

    Wang, Xiujuan; Lavrov, Dennis V.

    2008-01-01

    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, occurred in

  16. Thermal Expansion "Paradox."

    Science.gov (United States)

    Fakhruddin, Hasan

    1993-01-01

    Describes a paradox in the equation for thermal expansion. If the calculations for heating a rod and subsequently cooling a rod are determined, the new length of the cool rod is shorter than expected. (PR)

  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. Role of adenine nucleotide translocator 1 in mtDNA maintenance.

    Science.gov (United States)

    Kaukonen, J; Juselius, J K; Tiranti, V; Kyttälä, A; Zeviani, M; Comi, G P; Keränen, S; Peltonen, L; Suomalainen, A

    2000-08-04

    Autosomal dominant progressive external ophthalmoplegia is a rare human disease that shows a Mendelian inheritance pattern, but is characterized by large-scale mitochondrial DNA (mtDNA) deletions. We have identified two heterozygous missense mutations in the nuclear gene encoding the heart/skeletal muscle isoform of the adenine nucleotide translocator (ANT1) in five families and one sporadic patient. The familial mutation substitutes a proline for a highly conserved alanine at position 114 in the ANT1 protein. The analogous mutation in yeast caused a respiratory defect. These results indicate that ANT has a role in mtDNA maintenance and that a mitochondrial disease can be caused by a dominant mechanism.

  19. 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.

  20. 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

  1. Two Distinct mtDNA Lineages among Captive African Penguins in Japan

    OpenAIRE

    Murata, Michiko; Murakami, Masaru

    2013-01-01

    ABSTRACT 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 b...

  2. Mitochondrial Inverted Repeats Strongly Correlate with Lifespan: mtDNA Inversions and Aging

    Science.gov (United States)

    Yang, Jiang-Nan; Seluanov, Andrei; Gorbunova, Vera

    2013-01-01

    Mitochondrial defects are implicated in aging and in a multitude of age-related diseases, such as cancer, heart failure, Parkinson’s disease, and Huntington’s disease. However, it is still unclear how mitochondrial defects arise under normal physiological conditions. Mitochondrial DNA (mtDNA) deletions caused by direct repeats (DRs) are implicated in the formation of mitochondrial defects, however, mitochondrial DRs show relatively weak (Pearson’s r = −0.22, p<0.002; Spearman’s ρ = −0.12, p = 0.1) correlation with maximum lifespan (MLS). Here we report a stronger correlation (Pearson’s r = −0.55, p<10–16; Spearman’s ρ = −0.52, p<10–14) between mitochondrial inverted repeats (IRs) and lifespan across 202 species of mammals. We show that, in wild type mice under normal conditions, IRs cause inversions, which arise by replication-dependent mechanism. The inversions accumulate with age in the brain and heart. Our data suggest that IR-mediated inversions are more mutagenic than DR-mediated deletions in mtDNA, and impose stronger constraint on lifespan. Our study identifies IR-induced mitochondrial genome instability during mtDNA replication as a potential cause for mitochondrial defects. PMID:24069185

  3. Mitochondrial inverted repeats strongly correlate with lifespan: mtDNA inversions and aging.

    Directory of Open Access Journals (Sweden)

    Jiang-Nan Yang

    Full Text Available Mitochondrial defects are implicated in aging and in a multitude of age-related diseases, such as cancer, heart failure, Parkinson's disease, and Huntington's disease. However, it is still unclear how mitochondrial defects arise under normal physiological conditions. Mitochondrial DNA (mtDNA deletions caused by direct repeats (DRs are implicated in the formation of mitochondrial defects, however, mitochondrial DRs show relatively weak (Pearson's r = -0.22, p<0.002; Spearman's ρ = -0.12, p = 0.1 correlation with maximum lifespan (MLS. Here we report a stronger correlation (Pearson's r = -0.55, p<10(-16; Spearman's ρ = -0.52, p<10(-14 between mitochondrial inverted repeats (IRs and lifespan across 202 species of mammals. We show that, in wild type mice under normal conditions, IRs cause inversions, which arise by replication-dependent mechanism. The inversions accumulate with age in the brain and heart. Our data suggest that IR-mediated inversions are more mutagenic than DR-mediated deletions in mtDNA, and impose stronger constraint on lifespan. Our study identifies IR-induced mitochondrial genome instability during mtDNA replication as a potential cause for mitochondrial defects.

  4. Toward a mtDNA Locus-Specific Mutation Database Using the LOVD Platform

    Science.gov (United States)

    Elson, Joanna L.; Sweeney, Mary G.; Procaccio, Vincent; Yarham, John W.; Salas, Antonio; Kong, Qing-Peng; van der Westhuizen, Francois H.; Pitceathly, Robert D.S.; Thorburn, David R.; Lott, Marie T.; Wallace, Douglas C.; Taylor, Robert W.; McFarland, Robert

    2015-01-01

    The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information. PMID:22581690

  5. 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.

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

    Science.gov (United States)

    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 (ESI-MS) system (PLEX-ID) to an mtDNA population study to compare its performance with respect to throughput and concordance to STS. We found that the loss of information power was relatively low compared to the gain in speed and analytical standardization. The detection of point and length heteroplasmy turned out to be roughly comparable between the technologies with some individual differences related to the processes. We confirm that ESI-MS provides a valuable platform for analyzing mtDNA variation that can also be applied in the forensic context. PMID:24054029

  7. Evaluating sequence-derived mtDNA length heteroplasmy by amplicon size analysis

    Science.gov (United States)

    Berger, C.; Hatzer-Grubwieser, P.; Hohoff, C.; Parson, W.

    2011-01-01

    Length heteroplasmy (LH) in mitochondrial (mt)DNA is usually observed in homopolymeric tracts and manifest as mixture of various length variants. The generally used difference-coded annotation to report mtDNA haplotypes does not express the degree of LH variation present in a sample, even more so, it is sometimes difficult to establish which length variants are present and clearly distinguishable from background noise. It has therefore become routine practice for some researchers to call the dominant type, the “major molecule”, which represents the LH variant that is most abundant in a DNA extract. In the majority of cases a clear single dominant variant can be identified. However, in some samples this interpretation is difficult, i.e. when (almost) equally quantitative LH variants are present or when multiple sequencing primers result in the presentation of different dominant types. To better understand those cases we designed amplicon sizing assays for the five most relevant LH regions in the mtDNA control region (around ntps 16,189, 310, 460, 573, and the AC-repeat between 514 and 524) to determine the ratio of the LH variants by fluorescence based amplicon sizing assays. For difficult LH constellations derived by Sanger sequencing (with Big Dye terminators) these assays mostly gave clear and unambiguous results. In the vast majority of cases we found agreement between the results of the sequence and amplicon analyses and propose this alternative method in difficult cases. PMID:21067985

  8. Detection of age-related duplications in mtDNA from human muscles and bones.

    Science.gov (United States)

    Lacan, Marie; Thèves, Catherine; Keyser, Christine; Farrugia, Audrey; Baraybar, Jose-Pablo; Crubézy, Eric; Ludes, Bertrand

    2011-03-01

    Several studies have demonstrated the age-related accumulation of duplications in the D-loop of mitochondrial DNA (mtDNA) extracted from skeletal muscle. This kind of mutation had not yet been studied in bone. The detection of age-related mutations in bone tissue could help to estimate age at death within the context of legal medicine or/and anthropological identification procedures, when traditional osteological markers studied are absent or inefficient. As we detected an accumulation of a point mutation in mtDNA from an older individual's bones in a previous study, we tried here to identify if three reported duplications (150, 190, 260 bp) accumulate in this type of tissue. We developed a sensitive method which consists in the use of back-to-back primers during amplification followed by an electrophoresis capillary analysis. The aim of this study was to confirm that at least one duplication appears systematically in muscle tissue after the age of 20 and to evaluate the duplication age appearance in bones extracted from the same individuals. We found that the number of duplications increase from 38 years and that at least one duplicated fragment is present in 50% of cases after 70 years in this tissue. These results confirm that several age-related mutations can be detected in the D-loop of mtDNA and open the way for the use of molecular markers for age estimation in forensic and/or anthropological identification.

  9. 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.

  10. Effect of Population Reduction on mtDNA Diversity and Demographic History of Korean Cattle Populations.

    Science.gov (United States)

    Dadi, Hailu; Lee, Seung-Hwan; Jung, Kyoung Sup; Choi, Jae Won; Ko, Moon-Suck; Han, Young-Joon; Kim, Jong-Joo; Kim, Kwan-Suk

    2012-09-01

    The population sizes of three Korean indigenous cattle populations have been drastically reduced over the past decades. In this study, we examined the extent to which reduction in populations influenced genetic diversity, population structure and demographic history using complete mitochondrial DNA (mtDNA) control region sequences. The complete mtDNA control region was sequenced in 56 individuals from Korean Black (KB), Jeju Black (JEB) and Korean Brindle (BRI) cattle populations. We included 27 mtDNA sequences of Korean Brown (BRO) from the GenBank database. Haplotype diversity estimate for the total population was high (0.870) while nucleotide diversity was low (0.004). The KB showed considerably low nucleotide (π = 0.001) and haplotype (h = 0.368) diversities. Analysis of molecular variance revealed a low level of genetic differentiation but this was highly significant (ppopulations. Of the total genetic diversity, 7.6% was attributable to among cattle populations diversity and the rest (92.4%) to differences within populations. The mismatch distribution analysis and neutrality tests revealed that KB population was in genetic equilibrium or decline. Indeed, unless an appropriate breeding management practice is developed, inbreeding and genetic drift will further impoverish genetic diversity of these cattle populations. Rational breed development and conservation strategy is needed to safeguard these cattle population.

  11. Surveyor nuclease detection of mutations and polymorphisms of mtDNA in children.

    Science.gov (United States)

    Pilch, Jacek; Asman, Marek; Jamroz, Ewa; Kajor, Maciej; Kotrys-Puchalska, Elżbieta; Goss, Małgorzata; Krzak, Maria; Witecka, Joanna; Gmiński, Jan; Sieroń, Aleksander L

    2010-11-01

    Mitochondrial encephalomyopathies are complex disorders with wide range of clinical manifestations. Particularly time-consuming is the identification of mutations in mitochondrial DNA. A group of 20 children with clinical manifestations of mitochondrial encephalomyopathies was selected for molecular studies. The aims were (a) to identify mutations in mtDNA isolated from muscle and (b) to verify detected mutations in DNA isolated from blood, in order to assess the utility of a Surveyor nuclease assay kit for patient screening. The most common changes found were polymorphisms, including a few missense mutations altering the amino acid sequence of mitochondrial proteins. In two boys with MELAS (i.e., mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes), a mutation A→G3243 was detected in the tRNALeu gene of mtDNA isolated from muscle and blood. In one boy, the carrier status of his mother was confirmed, based on molecular analysis of DNA isolated from blood. A method using Surveyor nuclease allows systematic screening for small mutations in mtDNA, using as its source blood of the patients and asymptomatic carriers. The method still requires confirmation studying a larger group. In some patients, the use of this method should precede and might limit indications for traumatic muscle and skin biopsy.

  12. 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.

  13. Selection of rodent species appropriate for mtDNA transfer to generate transmitochondrial mito-mice expressing mitochondrial respiration defects.

    Science.gov (United States)

    Enoki, Shunkei; Shimizu, Akinori; Hayashi, Chisato; Imanishi, Hirotake; Hashizume, Osamu; Mekada, Kazuyuki; Suzuki, Hitoshi; Hashimoto, Tetsuo; Nakada, Kazuto; Hayashi, Jun-Ichi

    2014-01-01

    Previous reports have shown that transmitochondrial mito-mice with nuclear DNA from Mus musculus and mtDNA from M. spretus do not express respiration defects, whereas those with mtDNA from Rattus norvegicus cannot be generated from ES cybrids with mtDNA from R. norvegicus due to inducing significant respiration defects and resultant losing multipotency. Here, we isolated transmitochondrial cybrids with mtDNA from various rodent species classified between M. spretus and R. norvegicus, and compared the O2 consumption rates. The results showed a strong negative correlation between phylogenetic distance and reduction of O2 consumption rates, which would be due to the coevolution of nuclear and mitochondrial genomes and the resultant incompatibility between the nuclear genome from M. musculus and the mitochondrial genome from the other rodent species. These observations suggested that M. caroli was an appropriate mtDNA donor to generate transmitochondrial mito-mice with nuclear DNA from M. musculus. Then, we generated ES cybrids with M. caroli mtDNA, and found that these ES cybrids expressed respiration defects without losing multipotency and can be used to generate transmitochondrial mito-mice expressing mitochondrial disorders.

  14. Composite asymptotic expansions

    CERN Document Server

    Fruchard, Augustin

    2013-01-01

    The purpose of these lecture notes is to develop a theory of asymptotic expansions for functions involving two variables, while at the same time using functions involving one variable and functions of the quotient of these two variables. Such composite asymptotic expansions (CAsEs) are particularly well-suited to describing solutions of singularly perturbed ordinary differential equations near turning points. CAsEs imply inner and outer expansions near turning points. Thus our approach is closely related to the method of matched asymptotic expansions. CAsEs offer two unique advantages, however. First, they provide uniform expansions near a turning point and away from it. Second, a Gevrey version of CAsEs is available and detailed in the lecture notes. Three problems are presented in which CAsEs are useful. The first application concerns canard solutions near a multiple turning point. The second application concerns so-called non-smooth or angular canard solutions. Finally an Ackerberg-O’Malley resonance pro...

  15. 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

  16. 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

  17. 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.

  18. Uniform gradient expansions

    Directory of Open Access Journals (Sweden)

    Massimo Giovannini

    2015-06-01

    Full Text Available 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. Association of AluYb8 insertion/deletion polymorphism in the MUTYH gene with mtDNA maintain in the type 2 diabetes mellitus patients.

    Science.gov (United States)

    Guo, Wenwen; Zheng, Bixia; Guo, Dong; Cai, Zhenming; Wang, Yaping

    2015-07-05

    A common AluYb8-element insertion/deletion polymorphism of the MUTYH gene (AluYb8MUTYH) is a novel genetic risk factor for type 2 diabetes mellitus (T2DM). In the present study, mtDNA sequencing analysis indicated that the mtDNA sequence heteroplasmy was not associated with AluYb8MUTYH polymorphism. To better understand the genetic risk for T2DM, we investigated the association of this polymorphism with mtDNA content, mtDNA breakage and mtDNA transcription in the leukocytes of T2DM patients. The mtDNA content and unbroken mtDNA were significantly increased in the mutant patients than in the wild-type patients (P <0.05, respectively). However, no association between mtDNA transcription and AluYb8MUTYH variant was observed. The results suggested that the AluYb8MUTYH variant was associated with an altered mtDNA maintain in T2DM patients. The high level of mtDNA content observed in the mutant patients may have resulted from inefficient base excision repair of mitochondrial MUTYH and a compensatory mechanism that is triggered by elevated oxidative stress.

  20. Sieve in expansion

    CERN Document Server

    Kowalski, Emmanuel

    2010-01-01

    This is a survey report for the Bourbaki Seminar (Exp. no. 1028, November 2010) concerning sieve and expanders, in particular the recent works of Bourgain, Gamburd and Sarnak introducing "sieve in orbits", and the related developments concerning expansion properties of Cayley graphs of finite linear groups.

  1. 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...

  2. The 'Expansion-Contraction' model of Pleistocene biogeography: rocky shores suffer a sea change?

    Science.gov (United States)

    Marko, Peter B; Hoffman, Jessica M; Emme, Sandra A; Mcgovern, Tamara M; Keever, Carson C; Cox, L Nicole

    2010-01-01

    Approximately 20,000 years ago the last glacial maximum (LGM) radically altered the distributions of many Northern Hemisphere terrestrial organisms. Fewer studies describing the biogeographic responses of marine species to the LGM have been conducted, but existing genetic data from coastal marine species indicate that fewer taxa show clear signatures of post-LGM recolonization. We have assembled a mitochondrial DNA (mtDNA) data set for 14 co-distributed northeastern Pacific rocky-shore species from four phyla by combining new sequences from ten species with previously published sequences from eight species. Nuclear sequences from four species were retrieved from GenBank, plus we gathered new elongation factor 1-alpha sequences from the barnacle Balanus glandula. Results from demographic analyses of mtDNA for five (36%) species (Evasterias troschelii, Pisaster ochraceus, Littorina sitkana, L. scutulata, Xiphister mucosus) were consistent with large population expansions occurring near the LGM, a pattern expected if these species recently recolonized the region. However, seven (50%) species (Mytilus trossulus, M. californianus, B. glandula, S. cariosus, Patiria miniata, Katharina tunicata, X. atropurpureus) exhibited histories consistent with long-term stability in effective population size, a pattern indicative of regional persistence during the LGM. Two species of Nucella with significant mtDNA genetic structure showed spatially variable demographic histories. Multilocus analyses for five species were largely consistent with mtDNA: the majority of multilocus interpopulation divergence times significantly exceeded the LGM. Our results indicate that the LGM did not extirpate the majority of species in the northeastern Pacific; instead, regional persistence during the LGM appears a common biogeographic history for rocky-shore organisms in this region.

  3. 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.

  4. 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

  5. Admixture estimates for Caracas, Venezuela, based on autosomal, Y-chromosome, and mtDNA markers.

    Science.gov (United States)

    Martínez, Helios; Rodríguez-Larralde, Alvaro; Izaguirre, Mary Helen; De Guerra, Dinorah Castro

    2007-04-01

    The present Venezuelan population is the product of admixture of Amerindians, Europeans, and Africans, a process that was not homogeneous throughout the country. Blood groups, short tandem repeats (STRs), mtDNA, and Y-chromosome markers have been used successfully in admixture studies, but few such studies have been conducted in Venezuela. In this study we aim to estimate the admixture components of samples from two different socioeconomic levels from Caracas, Venezuela's capital city, compare their differences, and infer sexual asymmetry in the European Amerindian union patterns. Gene frequencies for blood groups ABO and Rh (CDE) and for the STRs VWA, F13A01, and FES/FPS and mtDNA and Y-chromosome haplogroups were studied in a sample of 60 individuals living in Caracas, taken from a private clinic (high socioeconomic level), and 50 individuals, also living in Caracas, drawn from a public maternity clinic (low socioeconomic level). The admixture analysis for the five autosomal markers gives a high European component (0.78) and an almost negligible African sub-Saharan component (0.06) for the high socioeconomic level, whereas for the low socioeconomic level the sub-Saharan, European, and Amerindian components were 0.21, 0.42, and 0.36, respectively. Estimates of admixture based on mtDNA and Y-chromosome markers reveal that the Amerindian contribution to these Caracas samples is almost entirely through females, because the Y-chromosome Amerindian and African sub-Saharan chromosomes found in this study were scarce. Our study reveals that the identification of the grandparents' geographic origin is an important methodological aspect to take into account in genetic studies related to the reconstruction of historical events.

  6. 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.

  7. mtDNA variation in caste populations of Andhra Pradesh, India.

    Science.gov (United States)

    Bamshad, M; Fraley, A E; Crawford, M H; Cann, R L; Busi, B R; Naidu, J M; Jorde, L B

    1996-02-01

    Various anthropological analyses have documented extensive regional variation among populations on the subcontinent of India using morphological, protein, blood group, and nuclear DNA polymorphisms. These patterns are the product of complex population structure (genetic drift, gene flow) and a population history noted for numerous branching events. As a result, the interpretation of relationships among caste populations of South India and between Indians and continental populations remains controversial. The Hindu caste system is a general model of genetic differentiation among endogamous populations stratified by social forces (e.g., religion and occupation). The mitochondrial DNA (mtDNA) molecule has unique properties that facilitate the exploration of population structure. We analyzed 36 Hindu men born in Andhra Pradesh who were unrelated matrilineally through at least 3 generations and who represent 4 caste populations: Brahmin (9), Yadava (10), Kapu (7), and Relli (10). Individuals from Africa (36), Asia (36), and Europe (36) were sampled for comparison. A 200-base-pair segment of hypervariable segment 2 (HVS2) of the mtDNA control region was sequenced in all individuals. In the Indian castes 25 distinct haplotypes are identified. Aside from the Cambridge reference sequence, only two haplotypes are shared between caste populations. Middle castes form a highly supported cluster in a neighbor-joining network. Mean nucleotide diversity within each caste is 0.015, 0.012, 0.011, and 0.012 for the Brahmin, Yadava, Kapu, and Relli, respectively. mtDNA variation is highly structured between castes (GST = 0.17; p caste populations of Andhra Pradesh cluster more often with Africans than with Asians or Europeans. This is suggestive of admixture with African populations.

  8. 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.

  9. 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%.

  10. 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...

  11. 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...

  12. 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

    The intraspecific phylogeography of Grant's gazelles Nanger granti was assessed with mitochondrial DNA control region sequences. Samples of 177 individuals from 17 Kenyan and Tanzanian populations were analysed. Three highly divergent, reciprocally monophyletic lineages were found, with among group...... 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...... (granti) petersii within the Grant's gazelles superspecies....

  13. Transcriptional requirements of the distal heavy-strand promoter of mtDNA

    OpenAIRE

    2012-01-01

    The heavy strand of mtDNA contains two promoters with nonoverlapping functions. The role of the minor heavy-strand promoter (HSP2) is controversial, because the promoter has been difficult to activate in an in vitro system. We have isolated HSP2 by excluding its interaction with the more powerful HSP1 promoter, and we find that it is transcribed efficiently by recombinant mtRNA polymerase and mitochondrial transcription factor B2. The mitochondrial transcription factor A is not required for i...

  14. Mouse mtDNA mutant model of Leber hereditary optic neuropathy.

    Science.gov (United States)

    Lin, Chun Shi; Sharpley, Mark S; Fan, Weiwei; Waymire, Katrina G; Sadun, Alfredo A; Carelli, Valerio; Ross-Cisneros, Fred N; Baciu, Peter; Sung, Eric; McManus, Meagan J; Pan, Billy X; Gil, Daniel W; Macgregor, Grant R; Wallace, Douglas C

    2012-12-04

    An animal model of Leber hereditary optic neuropathy (LHON) was produced by introducing the human optic atrophy mtDNA ND6 P25L mutation into the mouse. Mice with this mutation exhibited reduction in retinal function by elecroretinogram (ERG), age-related decline in central smaller caliber optic nerve fibers with sparing of larger peripheral fibers, neuronal accumulation of abnormal mitochondria, axonal swelling, and demyelination. Mitochondrial analysis revealed partial complex I and respiration defects and increased reactive oxygen species (ROS) production, whereas synaptosome analysis revealed decreased complex I activity and increased ROS but no diminution of ATP production. Thus, LHON pathophysiology may result from oxidative stress.

  15. 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.

  16. MtDNA T4216C variation in multiple sclerosis: a systematic review and meta-analysis.

    Science.gov (United States)

    Andalib, Sasan; Emamhadi, Mohammadreza; Yousefzadeh-Chabok, Shahrokh; Salari, Arsalan; Sigaroudi, Abdolhosein Emami; Vafaee, Manouchehr Seyedi

    2016-12-01

    MtDNA T4216C variation has frequently been investigated in Multiple Sclerosis (MS) patients; nonetheless, controversy has existed about the evidence of association of this variation with susceptibility to MS. The present systematic review and meta-analysis converge the results of the preceding publications, pertaining to association of mtDNA T4216C variation with susceptibility to MS, into a common conclusion. A computerized literature search in English was carried out to retrieve relevant publications from which required data were extracted. Using a fixed effect model, pooled odds ratio (OR), 95 % confidence interval (95 % CI), and P value were calculated for association of mtDNA T4216C variation with susceptibility to MS. The pooled results showed that there was a significant association between mtDNA T4216C variation and MS (OR = 1.38, 95 % CI = 1.13-1.67, P = 0.001). The present systematic review and meta-analysis suggest that mtDNA T4216C variation is a contributory factor in susceptibility to MS.

  17. 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

    Reproduction 131, 233–245). However, the correlation between size and mtDNA copy number in single oocytes has not been determined. This study describes the relation between oocytes of defined diameters from individual pre- and postpubertal pigs and mtDNA copy number. Cumulus-oocyte complexes were aspirated......Oocyte competence has been related to mtDNA copy number, but a large variation in mtDNA copy number between oocytes has been observed, caused by, e.g. oocyte donor and oocyte size (Sato et al. 2014 PLOS ONE 9, e94488; Cotterill et al. 2013 Mol. Hum. Reprod. 19, 444–450; El Shourbagy et al. 2006...... from ovaries of 10 pre- and 10 post-pubertal pigs. Cumulus cells were removed and the oocytes were measured (inside-ZP-diameter). Oocytes were transferred to DNAase-free tubes, snap-frozen, and stored at –80°C. The genes ND1 and COX1 were used to determine the mtDNA copy number. Plasmid preparations...

  18. The GHEP–EMPOP collaboration on mtDNA population data—A new resource for forensic casework

    Science.gov (United States)

    Prieto, L.; Zimmermann, B.; Goios, A.; Rodriguez-Monge, A.; Paneto, G.G.; Alves, C.; Alonso, A.; Fridman, C.; Cardoso, S.; Lima, G.; Anjos, M.J.; Whittle, M.R.; Montesino, M.; Cicarelli, R.M.B.; Rocha, A.M.; Albarrán, C.; de Pancorbo, M.M.; Pinheiro, M.F.; Carvalho, M.; Sumita, D.R.; Parson, W.

    2011-01-01

    Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP–EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). PMID:21075696

  19. Bigravity from gradient expansion

    Energy Technology Data Exchange (ETDEWEB)

    Yamashita, Yasuho [Yukawa Institute for Theoretical Physics, Kyoto University,606-8502, Kyoto (Japan); Tanaka, Takahiro [Yukawa Institute for Theoretical Physics, Kyoto University,606-8502, Kyoto (Japan); Department of Physics, Kyoto University,606-8502, Kyoto (Japan)

    2016-05-04

    We discuss how the ghost-free bigravity coupled with a single scalar field can be derived from a braneworld setup. We consider DGP two-brane model without radion stabilization. The bulk configuration is solved for given boundary metrics, and it is substituted back into the action to obtain the effective four-dimensional action. In order to obtain the ghost-free bigravity, we consider the gradient expansion in which the brane separation is supposed to be sufficiently small so that two boundary metrics are almost identical. The obtained effective theory is shown to be ghost free as expected, however, the interaction between two gravitons takes the Fierz-Pauli form at the leading order of the gradient expansion, even though we do not use the approximation of linear perturbation. We also find that the radion remains as a scalar field in the four-dimensional effective theory, but its coupling to the metrics is non-trivial.

  20. 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.

  1. 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.

  2. 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.

  3. Ensemble learning algorithms for classification of mtDNA into haplogroups.

    Science.gov (United States)

    Wong, Carol; Li, Yuran; Lee, Chih; Huang, Chun-Hsi

    2011-01-01

    Classification of mitochondrial DNA (mtDNA) into their respective haplogroups allows the addressing of various anthropologic and forensic issues. Unique to mtDNA is its abundance and non-recombining uni-parental mode of inheritance; consequently, mutations are the only changes observed in the genetic material. These individual mutations are classified into their cladistic haplogroups allowing the tracing of different genetic branch points in human (and other organisms) evolution. Due to the large number of samples, it becomes necessary to automate the classification process. Using 5-fold cross-validation, we investigated two classification techniques on the consented database of 21 141 samples published by the Genographic project. The support vector machines (SVM) algorithm achieved a macro-accuracy of 88.06% and micro-accuracy of 96.59%, while the random forest (RF) algorithm achieved a macro-accuracy of 87.35% and micro-accuracy of 96.19%. In addition to being faster and more memory-economic in making predictions, SVM and RF are better than or comparable to the nearest-neighbor method employed by the Genographic project in terms of prediction accuracy.

  4. Relationship between seasonal cold acclimatization and mtDNA haplogroup in Japanese

    Directory of Open Access Journals (Sweden)

    Nishimura Takayuki

    2012-08-01

    Full Text Available Abstract Background The purpose of this study was to elucidate the interaction between mtDNA haplogroup and seasonal variation that contributes to cold adaptation. Methods There were 15 subjects (seven haplotype D subjects and eight haplotype non-D subjects. In summer and winter, the subjects were placed in an environment where the ambient temperature dropped from 27 °C to 10 °C in 30 minutes. After that, they were exposed to cold for 60 minutes. Results In summer, the decrease in rectal temperature and increase in oxygen consumption was smaller and cold tolerance was higher in the haplotype non-D group than in the haplotype D group. In winter, no significant differences were seen in rectal temperature or oxygen consumption, but the respiratory exchange ratio decreased in the haplotype D group. Conclusions The results of the present study suggest that haplogroup D subjects are a group that changes energy metabolism more, and there appears to be a relationship between differences in cold adaptability and mtDNA polymorphism within the population. Moreover, group differences in cold adaptability seen in summer may decrease in winter due to supplementation by seasonal cold acclimatization.

  5. 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.

  6. Thermal expansion of glassy polymers.

    Science.gov (United States)

    Davy, K W; Braden, M

    1992-01-01

    The thermal expansion of a number of glassy polymers of interest in dentistry has been studied using a quartz dilatometer. In some cases, the expansion was linear and therefore the coefficient of thermal expansion readily determined. Other polymers exhibited non-linear behaviour and values appropriate to different temperature ranges are quoted. The linear coefficient of thermal expansion was, to a first approximation, a function of both the molar volume and van der Waal's volume of the repeating unit.

  7. Dysphagia is prevalent in patients with CPEO and single, large-scale deletions in mtDNA

    DEFF Research Database (Denmark)

    Hedermann, Gitte; Løkken, Nicoline; Dahlqvist, Julia R

    2016-01-01

    BACKGROUND: The aim of this study was to assess the frequency of subjective and objective dysphagia in patients with chronic progressive external ophthalmoplegia (CPEO) due to single, large-scale deletions (LSDs) of mitochondrial DNA (mtDNA). METHODS: Sixteen patients with CPEO and single LSDs...... and single LSDs of mtDNA had a prolonged cold-water test, including one with a PEG-tube, who was unable to perform the test, and nine patients reported subjective swallowing problems (56.3%). All mitochondrial myopathy patients in the control group had a normal duration of the cold-water test. CONCLUSIONS......: The study shows that dysphagia is a common problem in patients with CPEO and LSDs of mtDNA. Dysphagia seems to be progressive with age as abnormal swallowing occurred preferentially in persons ≥45years. The study shows that increased awareness of this symptom should be given to address appropriate treatment...

  8. Respiratory function in cybrid cell lines carrying European mtDNA haplogroups: implications for Leber's hereditary optic neuropathy.

    Science.gov (United States)

    Carelli, Valerio; Vergani, Lodovica; Bernazzi, Barbara; Zampieron, Claudia; Bucchi, Laura; Valentino, Maria; Rengo, Chiara; Torroni, Antonio; Martinuzzi, Andrea

    2002-10-09

    The possibility that some combinations of mtDNA polymorphisms, previously associated with Leber's hereditary optic neuropathy (LHON), may affect mitochondrial respiratory function was tested in osteosarcoma-derived transmitochondrial cytoplasmic hybrids (cybrids). In this cellular system, in the presence of the same nuclear background, different exogenous mtDNAs are used to repopulate a parental cell line previously devoid of its original mtDNA. No detectable differences in multiple parameters exploring respiratory function were observed when mtDNAs belonging to European haplogroups X, H, T and J were used. Different possible explanations for the previously established association between haplogroup J and LHON 11778/ND4 and 14484/ND6 pathogenic mutations are discussed, including the unconventional proposal that mtDNA haplogroup J may exert a protective rather than detrimental effect.

  9. Phylogenetic analysis of the endangered takin in the confluent zone of the Qinling and Minshan Mountains using mtDNA control region.

    Science.gov (United States)

    Yao, Gang; Li, Yanhong; Li, Dayong; Williams, Peter; Hu, Jie

    2016-07-01

    The takin (Budorcas taxicolor) is an Endangered ungulate. We analyzed the variation within mtDNA control region sequences of takin populations in the Qinling Mountains, the Minshan Mountains and the confluence of these two mountain ranges. We did not find any shared haplotypes among the populations. We observed apparent variation in the control region length among the three populations, and independent population expansions in the late of Pleistocene, which suggests these populations may have independent evolutionary histories. We found only one haplotype, and the lowest measures of genetic diversity (h = 0; π = 0) in the population from the confluent zone, which suggests populations in the confluent zone may have grown from small founder populations and gene flow with other populations has ceased. Based on their phylogenetic relationships, we concluded that the takin population in the confluent zone was in the same clade as the Tangjiahe population, which suggests that these takin populations are Sichuan takin (Budorcas taxicolor tibetana).

  10. Post-glacial recolonization of the Great Lakes region by the common gartersnake (Thamnophis sirtalis) inferred from mtDNA sequences.

    Science.gov (United States)

    Placyk, John S; Burghardt, Gordon M; Small, Randall L; King, Richard B; Casper, Gary S; Robinson, Jace W

    2007-05-01

    Pleistocene events played an important role in the differentiation of North American vertebrate populations. Michigan, in particular, and the Great Lakes region, in general, were greatly influenced by the last glaciation. While several hypotheses regarding the recolonization of this region have been advanced, none have been strongly supported. We generated 148 complete ND2 mitochondrial DNA (mtDNA) sequences from common gartersnake (Thamnophis sirtalis) populations throughout the Great Lakes region to evaluate phylogeographic patterns and population structure and to determine whether the distribution of haplotypic variants is related to the post-Pleistocene retreat of the Wisconsinan glacier. The common gartersnake was utilized, as it is believed to have been one of the primary vertebrate invaders of the Great Lakes region following the most recent period of glacial retreat and because it has been a model species for a variety of evolutionary, ecological, behavioral, and physiological studies. Several genetically distinct evolutionary lineages were supported by both genealogical and molecular population genetic analyses, although to different degrees. The geographic distribution of the majority of these lineages is interpreted as reflecting post-glacial recolonization dynamics during the late Pleistocene. These findings generally support previous hypotheses of range expansion in this region.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques

    Science.gov (United States)

    Cardoso, Sergio; Valverde, Laura; Alfonso-Sánchez, Miguel A.; Palencia-Madrid, Leire; Elcoroaristizabal, Xabier; Algorta, Jaime; Catarino, Susana; Arteta, David; Herrera, Rene J.; Zarrabeitia, María Teresa; Peña, José A.; de Pancorbo, Marian M.

    2013-01-01

    The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ∼10,000 years before present (YBP), with signals of expansions at ∼3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre

  16. 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

  17. phylogeography of the phrynocephalus vlangalii species complex in the upper reaches of the yellow river inferred from mtdna nd4-trnaleu segments

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    the ching hai toad-headed agama (phrynocephalus vlangalii) complex is a small toad-headed viviparous lizard that is endemic to the qinghai-tibetan plateau.a fragment of mtdna nd4-trnaleu from 189 samples in 26 populations was used to infer the phylogeographic history of this species complex in the upper reaches of the yellow river.phylogenetic analyses revealed that p.vlangalii and another proposed species (p.putjatia) do not form a monophyletic mtdna clade,which in contrast with a previous study,includes p.theobaldi and p forsythii.lineage diversification occurred in the middle pleistocene for p.vlangali (ca.0.95 ma) and in the early pleistocene for p.putjatia (ca.1.78 ma).the uplift of the a'nyemaqen mountains and glaciations since the mid-late pleistocene,especially during the kunlun glaciation,are considered to have promoted the allopartric divergence of p vlangalii.the diversification of p.putjatia may be triggered by the tectonic movement in the huangshui river valley during the c phase of qingzang movement.subsequently,the glacial climate throughout the pleistocene may have continuedto impede the gene flow of p.putjatia,eventually resulting in the genetic divergence of p.putjatia in the allopatric regions.demographic estimates revealed weak population expansion in one lineage of p vlangalii (a2,the qaidam basin lineage) and one lineage of p.putjatia (b2,the north qinghai lake lineage) after approximately 42 000 years before present.however,constant population size through time was inferred for two lineages (a1 and b1),the source of yellow river lineage of p.vlangalii and the southeast of qinghai lake lineage of p putjatia,possibly due to stable populations persisting in areas unaffected by glacial advances.our results also suggest:1) at least four differentiated lineages of p.vlangalii complex may have evolved allopatrically in different regions during the pleistocene glaciation events; 2) in support of several recent studies,p.putjatia is a valid species

  18. mtDNA Deletion in an Iranian Infant with Pearson Marrow Syndrome

    Directory of Open Access Journals (Sweden)

    Massoud Houshmand

    2010-03-01

    Full Text Available Background:Pearson syndrome (PS is a rare multisystem mitochondrial disorder of hematopoietic system, characterized by refractory sideroblastic anemia, pancytopenia, exocrine pancreatic insufficiency, and variable neurologic, hepatic, renal, and endocrine failure. Case Presentation:We describe a six-month-old female infant with Pearson marrow syndrome who presented with neurological manifestations. She had several episodes of seizures. Hematopoietic abnormalities were macrocytic anemia and neutropenia. Bone marrow aspiration revealed a cellular marrow with marked vacuolization of erythroid and myeloid precursors. Analysis of mtDNA in peripheral blood showed 8.5 kb deletion that was compatible with the diagnosis of PS. Conclusion:PS should be considered in infants with neurologic diseases, in patients with cytopenias, and also in patients with acidosis or refractory anemia.

  19. 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.

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

    Science.gov (United States)

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

    2013-09-01

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

  1. 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.

  2. Population structure of Haliotis rubra from South Australia inferred from nuclear and mtDNA analyses

    Institute of Scientific and Technical Information of China (English)

    LI Zhongbao; Sharon A Appleyard; Nicholas G Elliott

    2006-01-01

    Microsatellite loci and mtDNA-RFLPs were surveyed in four spatially separated populations of Haliotis rubra and two populations of putative Haliotis conicorpora from South Australia. A high level of microsatellite genetic diversity was observed in all populations although several loci were characterized by homozygote excesses, probably due to null alleles. MtDNA variation was also moderate with an average of 80% haplotype variation across the six populations. Despite the high levels of genetic variation, significant pair-wise spatial differentiation is not detected among the populations. Hierarchical AMOVA analysis revealed very low levels of genetic partitioning on either a spatial or putative species level. Both molecular techniques revealed little genetic differentiation across the six populations, suggesting a panmictic population model for these South Australian abalone populations. Furthermore, no molecular evidence suggests that the putative H. conicorpora individuals sampled from South Australia belong to a separate species.

  3. 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.

  4. Maternal inheritance of mitochondrial DNA (mtDNA) in the Pacific oyster (Crassostrea gigas): a preliminary study using mtDNA sequence analysis with evidence of random distribution of MitoTracker-stained sperm mitochondria in fertilized eggs.

    Science.gov (United States)

    Obata, Mayu; Shimizu, Michiyo; Sano, Natsumi; Komaru, Akira

    2008-03-01

    In many bivalve species, paternal and maternal mitochondrial DNA (mtDNA) from sperm and eggs is transmitted to the offspring. This phenomenon is known as doubly uniparental inheritance (DUI). In these species, sperm mtDNA (M type) is inherited by the male gonad of the offspring. Egg mtDNA (F type) is inherited by both male and female somatic cells and female gonadal cells. In Mytilidae, sperm mitochondria are distributed in the cytoplasm of differentiating male germ cells because they are transmitted to the male gonad. In the present study, we investigated maternal inheritance of mtDNA in the Pacific oyster, Crassostrea gigas. Sequence analysis of two mitochondrial non-coding regions revealed an identical sequence pattern in the gametes and adductor muscle samples taken from six males and five females. To observe whether sperm mitochondria were specifically located in the cytoplasm of differentiating germ cells, their distribution was recorded in C. gigas fertilized eggs by vital staining with MitoTracker Green. Although the 1D blastomere was identified in the cytoplasm of differentiating germ cells, sperm mitochondria were located at the 1D blastomere in only 32% of eggs during the 8-cell stage. Thus, in C. gigas, sperm mitochondria do not specifically locate in the germ cell region at the 1D blastomere. We suggest that the distribution of sperm mitochondria is not associated with germ cell formation in C. gigas. Furthermore, as evidenced by the mtDNA sequences of two non-coding regions, we conclude that mitochondrial DNA is maternally inherited in this species.

  5. 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.

  6. 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.

  7. 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.

  8. MtDNA diversity of Ghana: a forensic and phylogeographic view

    Science.gov (United States)

    Fendt, Liane; Röck, Alexander; Zimmermann, Bettina; Bodner, Martin; Thye, Thorsten; Tschentscher, Frank; Owusu-Dabo, Ellis; Göbel, Tanja M.K.; Schneider, Peter M.; Parson, Walther

    2012-01-01

    West Africa is characterized by a migration history spanning more than 150,000 years. Climate changes but also political circumstances were responsible for several early but also recent population movements that shaped the West African mitochondrial landscape. The aim of the study was to establish a Ghanaian mtDNA dataset for forensic purposes and to investigate the diversity of the Ghanaian population sample with respect to surrounding populations. We sequenced full mitochondrial control regions of 193 Akan people from Ghana and excluded two apparently close maternally related individuals due to preceding kinship testing. The remaining dataset comprising 191 sequences was applied as etalon for quasi-median network analysis and was subsequently combined with 99 additional control region sequences from surrounding West African countries. All sequences were incorporated into the EMPOP database enriching the severely underrepresented African mtDNA pool. For phylogeographic considerations, the Ghanaian haplotypes were compared to those of 19 neighboring populations comprising a total number of 6198 HVS1 haplotypes. We found extensive genetic admixture between the Ghanaian lineages and those from adjacent populations diminishing with geographical distance. The extent of genetic admixture reflects the long but also recent history of migration waves within West Africa mainly caused by changing environmental conditions. Also, evidence for potential socio-economical influences such as trade routes is provided by the occurrence of U6b and U6d sequences found in Dubai but also in Tunisia leading to the African West Coast via Mauritania and Senegal but also via Niger, Nigeria to Cameroon. PMID:21723214

  9. 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.

  10. 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

    2016-06-24

    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.

  11. Optical imaging. Expansion microscopy.

    Science.gov (United States)

    Chen, Fei; Tillberg, Paul W; Boyden, Edward S

    2015-01-30

    In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. We discovered that by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification. By covalently anchoring specific labels located within the specimen directly to the polymer network, labels spaced closer than the optical diffraction limit can be isotropically separated and optically resolved, a process we call expansion microscopy (ExM). Thus, this process can be used to perform scalable superresolution microscopy with diffraction-limited microscopes. We demonstrate ExM with apparent ~70-nanometer lateral resolution in both cultured cells and brain tissue, performing three-color superresolution imaging of ~10(7) cubic micrometers of the mouse hippocampus with a conventional confocal microscope.

  12. Rethinking expansive learning

    DEFF Research Database (Denmark)

    Kolbæk, Ditte; Lundh Snis, Ulrika

    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...... 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...... in their professional organisation and how they developed their identity to become more skilled practitioners. We discuss the effects of the written discussions and reflections on the students’ endeavour to become authors in practice. Our contribution to the research consists of considerations of changing the spoken...

  13. 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.

  14. Mitochondrial DNA Ligase Is Dispensable for the Viability of Cultured Cells but Essential for mtDNA Maintenance*

    Science.gov (United States)

    Shokolenko, Inna N.; Fayzulin, Rafik Z.; Katyal, Sachin; McKinnon, Peter J.; Wilson, Glenn L.; Alexeyev, Mikhail F.

    2013-01-01

    Multiple lines of evidence support the notion that DNA ligase III (LIG3), the only DNA ligase found in mitochondria, is essential for viability in both whole organisms and in cultured cells. Previous attempts to generate cells devoid of mitochondrial DNA ligase failed. Here, we report, for the first time, the derivation of viable LIG3-deficient mouse embryonic fibroblasts. These cells lack mtDNA and are auxotrophic for uridine and pyruvate, which may explain the apparent lethality of the Lig3 knock-out observed in cultured cells in previous studies. Cells with severely reduced expression of LIG3 maintain normal mtDNA copy number and respiration but show reduced viability in the face of alkylating and oxidative damage, increased mtDNA degradation in response to oxidative damage, and slow recovery from mtDNA depletion. Our findings clarify the cellular role of LIG3 and establish that the loss of viability in LIG3-deficient cells is conditional and secondary to the ρ0 phenotype. PMID:23884459

  15. 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.

  16. 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

  17. Rare mtDNA haplogroups and genetic differences in rich and poor Danish Iron-Age villages

    DEFF Research Database (Denmark)

    Melchior, L; Gilbert, M T P; Kivisild, T;

    2008-01-01

    The Roman Iron-Age (0-400 AD) in Southern Scandinavia was a formative period, where the society changed from archaic chiefdoms to a true state formation, and the population composition has likely changed in this period due to immigrants from Middle Scandinavia. We have analyzed mtDNA from 22 indi...

  18. Mitochondrial DNA ligase is dispensable for the viability of cultured cells but essential for mtDNA maintenance.

    Science.gov (United States)

    Shokolenko, Inna N; Fayzulin, Rafik Z; Katyal, Sachin; McKinnon, Peter J; Wilson, Glenn L; Alexeyev, Mikhail F

    2013-09-13

    Multiple lines of evidence support the notion that DNA ligase III (LIG3), the only DNA ligase found in mitochondria, is essential for viability in both whole organisms and in cultured cells. Previous attempts to generate cells devoid of mitochondrial DNA ligase failed. Here, we report, for the first time, the derivation of viable LIG3-deficient mouse embryonic fibroblasts. These cells lack mtDNA and are auxotrophic for uridine and pyruvate, which may explain the apparent lethality of the Lig3 knock-out observed in cultured cells in previous studies. Cells with severely reduced expression of LIG3 maintain normal mtDNA copy number and respiration but show reduced viability in the face of alkylating and oxidative damage, increased mtDNA degradation in response to oxidative damage, and slow recovery from mtDNA depletion. Our findings clarify the cellular role of LIG3 and establish that the loss of viability in LIG3-deficient cells is conditional and secondary to the ρ(0) phenotype.

  19. 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.

  20. 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.

  1. Lattice harmonics expansion revisited

    Science.gov (United States)

    Kontrym-Sznajd, G.; Holas, A.

    2017-04-01

    The main subject of the work is to provide the most effective way of determining the expansion of some quantities into orthogonal polynomials, when these quantities are known only along some limited number of sampling directions. By comparing the commonly used Houston method with the method based on the orthogonality relation, some relationships, which define the applicability and correctness of these methods, are demonstrated. They are verified for various sets of sampling directions applicable for expanding quantities having the full symmetry of the Brillouin zone of cubic and non-cubic lattices. All results clearly show that the Houston method is always better than the orthogonality-relation one. For the cubic symmetry we present a few sets of special directions (SDs) showing how their construction and, next, a proper application depend on the choice of various sets of lattice harmonics. SDs are important mainly for experimentalists who want to reconstruct anisotropic quantities from their measurements, performed at a limited number of sampling directions.

  2. Orthogonal Query Expansion

    CERN Document Server

    Ackerman, Margareta; Lopez-Ortiz, Alejandro

    2011-01-01

    Over the last fifteen years, web searching has seen tremendous improvements. Starting from a nearly random collection of matching pages in 1995, today, search engines tend to satisfy the user's informational need on well-formulated queries. One of the main remaining challenges is to satisfy the users' needs when they provide a poorly formulated query. When the pages matching the user's original keywords are judged to be unsatisfactory, query expansion techniques are used to alter the result set. These techniques find keywords that are similar to the keywords given by the user, which are then appended to the original query leading to a perturbation of the result set. However, when the original query is sufficiently ill-posed, the user's informational need is best met using entirely different keywords, and a small perturbation of the original result set is bound to fail. We propose a novel approach that is not based on the keywords of the original query. We intentionally seek out orthogonal queries, which are r...

  3. 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.

  4. 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%.

  5. 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

  6. 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...

  7. 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).

  8. Transcriptional requirements of the distal heavy-strand promoter of mtDNA.

    Science.gov (United States)

    Zollo, Ornella; Tiranti, Valeria; Sondheimer, Neal

    2012-04-24

    The heavy strand of mtDNA contains two promoters with nonoverlapping functions. The role of the minor heavy-strand promoter (HSP2) is controversial, because the promoter has been difficult to activate in an in vitro system. We have isolated HSP2 by excluding its interaction with the more powerful HSP1 promoter, and we find that it is transcribed efficiently by recombinant mtRNA polymerase and mitochondrial transcription factor B2. The mitochondrial transcription factor A is not required for initiation, but it has the ability to alternatively activate and repress the HSP2 transcriptional unit depending on the ratio between mitochondrial transcription factor A and other transcription factors. The positioning of transcriptional initiation agrees with our current understanding of HSP2 activity in vivo. Serial deletion of HSP2 shows that only proximal sequences are required. Several mutations, including the disruption of a polycytosine track upstream of the HSP2 initiation site, influence transcriptional activity. Transcription from HSP2 is also observed when HeLa cell mitochondrial extract is used as the source of mitochondrial polymerase, and this transcription is maintained when HSP2 is provided in proper spacing and context to the HSP1 promoter. Studies of the linked heavy-strand promoters show that they are differentially regulated by ATP dosage. We conclude that HSP2 is transcribed and has features that allow it to regulate mitochondrial mRNA synthesis.

  9. VARIASI GENETIK IKAN TUNA SIRIP KUNING, Thunnus albacares DENGAN ANALISIS ELEKTROFORESIS ALLOZYME DAN Mt-DNA

    Directory of Open Access Journals (Sweden)

    Gusti Ngurah Permana

    2007-04-01

    Full Text Available Sampel ikan tuna sirip kuning, T. albacares diambil dari tiga lokasi (perairan Bali, Sulawesi Utara, dan Maluku Utara dan dilakukan analisis variasi genetik dengan metode elektroforesis allozyme menggunakan 15 enzim dan mt-DNA dengan 4 enzim restriksi. Hasil penelitian ini diperoleh 4 lokus enzim polimorfik yaitu: Idh-*2 (isocitrate dehydrogenase, Gpi-2* (glucose phoshate dehydrogenase , Mdh-1* (malat e dehydrogenase, dan Est-1* (esterase. Frekuensi alel allozyme terlihat adanya perbedaan yang nyata (Fst = 0,12; P<0,05 antar lokasi yaitu Bali (A, B, C, D, Sulawesi Utara dan Maluku Utara (A, B, C. 15 komposit haplotipe ditemukan pada populasi Bali, Sulawesi Utara, dan Maluku Utara. Haplotype diversity pada populasi Bali 0,886; Sulawesi Utara 0,790; dan Maluku Utara 0,785; dengan rata-rata dari haplotype diversity adalah 0,857. Jarak genetik dari ketiga populasi berkisar antara 0,003--0,023 (rata-rata 0,016. Populasi Maluku Utara dan Sulawesi Utara mempunyai jarak genetik terdekat yaitu 0,003. Hal ini merupakan indikator bahwa Sulawesi Utara dan Maluku Utara sering digunakan sebagai jalur migrasi dengan adanya kesamaan alel yang ditemukan pada kedua populasi tesebut, jika dibandingkan dengan populasi Bali (0,023.

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Hojun Song

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

  12. History of Lipizzan horse maternal lines as revealed by mtDNA analysis

    Directory of Open Access Journals (Sweden)

    Dovč Peter

    2002-09-01

    Full Text Available Abstract Sequencing of the mtDNA control region (385 or 695 bp of 212 Lipizzans from eight studs revealed 37 haplotypes. Distribution of haplotypes among studs was biased, including many private haplotypes but only one haplotype was present in all the studs. According to historical data, numerous Lipizzan maternal lines originating from founder mares of different breeds have been established during the breed's history, so the broad genetic base of the Lipizzan maternal lines was expected. A comparison of Lipizzan sequences with 136 sequences of domestic- and wild-horses from GenBank showed a clustering of Lipizzan haplotypes in the majority of haplotype subgroups present in other domestic horses. We assume that haplotypes identical to haplotypes of early domesticated horses can be found in several Lipizzan maternal lines as well as in other breeds. Therefore, domestic horses could arise either from a single large population or from several populations provided there were strong migrations during the early phase after domestication. A comparison of Lipizzan haplotypes with 56 maternal lines (according to the pedigrees showed a disagreement of biological parentage with pedigree data for at least 11% of the Lipizzans. A distribution of haplotype-frequencies was unequal (0.2%–26%, mainly due to pedigree errors and haplotype sharing among founder mares.

  13. 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.

  14. 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.

  15. Thermal Expansion of Polyurethane Foam

    Science.gov (United States)

    Lerch, Bradley A.; Sullivan, Roy M.

    2006-01-01

    Closed cell foams are often used for thermal insulation. In the case of the Space Shuttle, the External Tank uses several thermal protection systems to maintain the temperature of the cryogenic fuels. A few of these systems are polyurethane, closed cell foams. In an attempt to better understand the foam behavior on the tank, we are in the process of developing and improving thermal-mechanical models for the foams. These models will start at the microstructural level and progress to the overall structural behavior of the foams on the tank. One of the key properties for model characterization and verification is thermal expansion. Since the foam is not a material, but a structure, the modeling of the expansion is complex. It is also exacerbated by the anisoptropy of the material. During the spraying and foaming process, the cells become elongated in the rise direction and this imparts different properties in the rise direction than in the transverse directions. Our approach is to treat the foam as a two part structure consisting of the polymeric cell structure and the gas inside the cells. The polymeric skeleton has a thermal expansion of its own which is derived from the basic polymer chemistry. However, a major contributor to the thermal expansion is the volume change associated with the gas inside of the closed cells. As this gas expands it exerts pressure on the cell walls and changes the shape and size of the cells. The amount that this occurs depends on the elastic and viscoplastic properties of the polymer skeleton. The more compliant the polymeric skeleton, the more influence the gas pressure has on the expansion. An additional influence on the expansion process is that the polymeric skeleton begins to breakdown at elevated temperatures and releases additional gas species into the cell interiors, adding to the gas pressure. The fact that this is such a complex process makes thermal expansion ideal for testing the models. This report focuses on the thermal

  16. Modern humans did not admix with Neanderthals during their range expansion into Europe.

    Directory of Open Access Journals (Sweden)

    Mathias Currat

    2004-12-01

    Full Text Available The process by which the Neanderthals were replaced by modern humans between 42,000 and 30,000 before present is still intriguing. Although no Neanderthal mitochondrial DNA (mtDNA lineage is found to date among several thousands of Europeans and in seven early modern Europeans, interbreeding rates as high as 25% could not be excluded between the two subspecies. In this study, we introduce a realistic model of the range expansion of early modern humans into Europe, and of their competition and potential admixture with local Neanderthals. Under this scenario, which explicitly models the dynamics of Neanderthals' replacement, we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species.

  17. 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.

  18. 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.

  19. 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.

  20. DNA Ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair

    Science.gov (United States)

    Gao, Yankun; Katyal, Sachin; Lee, Youngsoo; Zhao, Jingfeng; Rehg, Jerold E.; Russell, Helen R.; McKinnon, Peter J.

    2011-01-01

    DNA replication and repair in mammalian cells involves three distinct DNA ligases; ligase I (Lig1), ligase III (Lig3) and ligase IV (Lig4)1. Lig3 is considered a key ligase during base excision repair because its stability depends upon its nuclear binding partner Xrcc1, a critical factor for this DNA repair pathway2,3. Lig3 is also present in the mitochondria where its role in mitochondrial DNA (mtDNA) maintenance is independent of Xrcc14. However, the biological role of Lig3 is unclear as inactivation of murine Lig3 results in early embryonic lethality5. Here we report that Lig3 is essential for mtDNA integrity but dispensable for nuclear DNA repair. Inactivation of Lig3 in the mouse nervous system resulted in mtDNA loss leading to profound mitochondrial dysfunction, disruption of cellular homeostasis and incapacitating ataxia. Similarly, inactivation of Lig3 in cardiac muscle resulted in mitochondrial dysfunction and defective heart pump function leading to heart failure. However, Lig3 inactivation did not result in nuclear DNA repair deficiency, indicating essential DNA repair functions of Xrcc1 can occur in the absence of Lig3. Instead, we found that Lig1 was critical for DNA repair, but in a cooperative manner with Lig3. Additionally, Lig3 deficiency did not recapitulate the hallmark features of neural Xrcc1 inactivation such as DNA damage-induced cerebellar interneuron loss6, further underscoring functional separation of these DNA repair factors. Therefore, our data reveal that the critical biological role of Lig3 is to maintain mtDNA integrity and not Xrcc1-dependent DNA repair. PMID:21390131

  1. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

    DEFF Research Database (Denmark)

    Takahashi, Hiroshi; Møller, Peter Rask; Shedko, Sergei V.;

    2016-01-01

    Pungitius is a highly diversified genus of sticklebacks (Gasterosteidae) occurring widely in northern parts of the Northern Hemisphere. Several ecologically and genetically divergent types that are largely isolated reproductively but occasionally hybridize in sympatry have been discovered...... in Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type...

  2. 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...

  3. 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.

  4. 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

  5. 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

  6. 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.

  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.

  9. 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.

  10. 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

  11. Degradation of paternal mitochondria after fertilization: implications for heteroplasmy, assisted reproductive technologies and mtDNA inheritance.

    Science.gov (United States)

    Sutovsky, Peter; Van Leyen, Klaus; McCauley, Tod; Day, Billy N; Sutovsky, Miriam

    2004-01-01

    Maternal inheritance of mitochondrial DNA has long been regarded as a major paradox in developmental biology. While some confusion may still persist in popular science, research data clearly document that the paternal sperm-borne mitochondria of most mammalian species enter the ooplasm at fertilization and are specifically targeted for degradation by the resident ubiquitin system. Ubiquitin is a proteolytic chaperone that forms covalently linked polyubiquitin chains on the targeted proteinaceous substrates. The polyubiquitin tag redirects the substrate proteins to a 26-S proteasome, a multi-subunit proteolytic organelle. Thus, specific proteasomal inhibitors reversibly block sperm mitochondrial degradation in ooplasm. Lysosomal degradation and the activity of membrane-lipoperoxidating enzyme 15-lipoxygenase (15-LOX) may also contribute to sperm mitochondrial degradation in the ooplasm, but probably is not crucial. Prohibitin, the major protein of the inner mitochondrial membrane, appears to be ubiquitinated in the sperm mitochondria. Occasional occurrence of paternal inheritance of mtDNA has been suggested in mammals including humans. While most such evidence has been widely disputed, it warrants further examination. Of particular concern is the documented heteroplasmy, i.e. mixed mtDNA inheritance after ooplasmic transplantation. Intracytoplasmic sperm injection (ICSI) has inherent potential for delaying the degradation of sperm mitochondria. However, paternal mtDNA inheritance after ICSI has not been documented so far.

  12. 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.

  13. 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

    and of mortality risk in the elderly. Our study provides new evidence on the relevance of mtDNA somatic mutations in aging and longevity and confirms that the occurrence of specific point mutations in the mtDNA control region may represent a strategy for the age-related remodelling of organismal functions.......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...

  14. Mitochondrial DNA Polymorphism in Natural Populations of Drosophila albomicans (Ⅰ)——Remarkable mtDNA Polymorphism in the Population of D.albomicans

    Institute of Scientific and Technical Information of China (English)

    王文; 凌发瑶; 施立明

    1994-01-01

    The technique of mtDNA restriction fragments length polymorphism(RFLP)was used tosurvey the population structure of D.albomicans.Remarkable mtDNA polymorphism has been observed inD.albomicans populations.A total of 34 nucleomorphs were detected from 82 isofemale lines assayed by only8 restriction enzymes.The cause and the effect of this phenomenon were discussed.As a result,it is sug-gested that a mechanism which maintains mtDNA diversity exists in this fly,and that the high intra-popula-tional polymorphism could numerically conceal the extent of differentiation between populations.In addition,on the base of restriction maps,it was found that the mtDNA molecule of D.albomicans might be impactedby the selection pressure during its evolution process both on the nucleotide composition and on the function-al regions.

  15. Gradient expansion for anisotropic hydrodynamics

    Science.gov (United States)

    Florkowski, Wojciech; Ryblewski, Radoslaw; Spaliński, Michał

    2016-12-01

    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 nonhydrodynamic modes.

  16. 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.

  17. [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.

  18. 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....

  19. Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Kivisild, Toomas; Grønnow, Bjarne;

    2008-01-01

    The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures is unknown. We sequenced a ...

  20. 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

  1. mtDNA sequences suggest a recent evolutionary divergence for Beringian and Northern American populations

    Energy Technology Data Exchange (ETDEWEB)

    Shields, G.F.; Schmiechen, A.M.; Reed, J.K. (Univ. of Alaska, Fairbanks, AK (United States)); Frazier, B.L.; Redd, A.; Ward, R.H. (Univ. of Utah, Salt Lake City, UT (United States)); Voevoda, M.I. (Institute of Internal Medicine, Novosibirsk (Russian Federation))

    1993-09-01

    Conventional descriptions of the pattern and process of human entry into the New World from Asia are incomplete and controversial. In order to gain an evolutionary insight into this process, the authors have sequenced the control region of mtDNA in samples of contemporary tribal populations of eastern Siberia, Alaska, and Greenland and have compared them with those of Amerind speakers of the Pacific Northwest and with those of the Altai of central Siberia. Specifically, they have analyzed sequence diversity in 33 mitochondiral lineages identified in 90 individuals belonging to five Circumpolar populations of Beringia, North America, and Greenland: Chukchi from Siberia, Inupiaq Eskimos and Athapaskans from Alaska, Eskimos from West Greenland, and Haida from Canada. Hereafter, these five populations are referred to as Circumarctic peoples'. These data were then compared with the sequence diversity in 47 mitochondrial lineages identified in a sample of 145 individuals from three Amerind-speaking tribes (Bella Coola, Nuu-Chah-Nulth, and Yakima) of the Pacific Northwest, plus 16 mitrochondrial lineages identified in a sample of 17 Altai from central Siberia. Sequence diversity within and among Circumarctic populations is considerably less than the sequence diversity observed within and among the three Amerind tribes. The similarity of sequences found among the geographically dispersed Circumarctic groups, plus the small values of mean pairwise sequence differences within Circumarctic populations, suggest a recent and rapid evolutionary radiation of these populations. In addition, Circumarctic populations lack the 9-bp deletion which has been used to trace various migrations out of Asia, while populations of southeastern Siberia possess this deletion. On the basis of these observations, while the evolutionary affinities of Native Americans extend west to the Circumarctic populations of eastern Siberia, they do not include the Altai of central Siberia.

  2. Association of mtDNA mutation with Autism in Iranian patients

    Directory of Open Access Journals (Sweden)

    Massoud Houshmand

    2013-12-01

    Full Text Available The autism spectrum disorders (ASD are amongst the most heritable complex disorders. Although there have been many efforts to locate the genes associated with ASD risk, many has been remained to be disclosed about the genetics of ASD. Scrutiny's have only disclosed a small number of de novo and inherited variants significantly associated with susceptibility to ASD. These only comprise a small number of total genetic risk factors. Some studies confirm the contribution of mitochondrial genome mutations to the pathophysiology of the autism, but some other studies rejected such a contribution. In the current study we tried to scrutinize the association between mitochondrial tRNA genes mutations and the risk of Autism. DNA was extracted from the blood of 24 patients with ASD and 40 age-matched healthy controls from Special Medical Center in Tehran. 22 tRNA genes of mitochondrial genome were PCR amplified using 12 primer pairs and sequenced. Sequencing results were searched for mutations using clustalW Progran and then the association of mutations with the autism risk was assessed by statistical analysis using SPSS version 15. Many of the observed mutations were sporadic mutations without any significant relationship with the risk of autism, and the other mutations including those of high frequency showed no significant relationship with the risk of disease as well (p-value > 0.05 except mutations 16126T>C (p-value=0.01 , 14569G>A(pvalue=0.02 and 1811A>G(p-value=0.04. These three mutations were in the noncoding regions of the mitochondrial genome near tRNA genes. The mutation 16126T>C was in the mtDNA control region.

  3. 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.

  4. Reed's Conjecture on hole expansions

    CERN Document Server

    Fouquet, Jean-Luc

    2012-01-01

    In 1998, Reed conjectured that for any graph $G$, $\\chi(G) \\leq \\lceil \\frac{\\omega(G) + \\Delta(G)+1}{2}\\rceil$, where $\\chi(G)$, $\\omega(G)$, and $\\Delta(G)$ respectively denote the chromatic number, the clique number and the maximum degree of $G$. In this paper, we study this conjecture for some {\\em expansions} of graphs, that is graphs obtained with the well known operation {\\em composition} of graphs. We prove that Reed's Conjecture holds for expansions of bipartite graphs, for expansions of odd holes where the minimum chromatic number of the components is even, when some component of the expansion has chromatic number 1 or when a component induces a bipartite graph. Moreover, Reed's Conjecture holds if all components have the same chromatic number, if the components have chromatic number at most 4 and when the odd hole has length 5. Finally, when $G$ is an odd hole expansion, we prove $\\chi(G)\\leq\\lceil\\frac{\\omega(G)+\\Delta(G)+1}{2}\\rceil+1$.

  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. Complex patterns of population genetic structure of moose, Alces alces, after recent spatial expansion in Poland revealed by sex-linked markers.

    Science.gov (United States)

    Swisłocka, Magdalena; Czajkowska, Magdalena; Duda, Norbert; Danyłow, Jan; Owadowska-Cornil, Edyta; Ratkiewicz, Mirosław

    2013-01-01

    In recent years, human activity directly and indirectly influenced the demography of moose in Poland. The species was close to extinction, and only a few isolated populations survived after the Second World War; then, unprecedented demographic and spatial expansions had occurred, possibly generating a very complex pattern of population genetic structure at the present-day margins of the species range in Poland. Over 370 moose from seven populations were collected from Poland, and partial sequences of the mitochondrial control region (mtDNA-cr; 607 bp) were obtained. In addition, the entire mtDNA cytochrome b gene (1,140 bp) and Y-chromosome markers (1,982 bp in total) were studied in a chosen set of individuals. Twelve mtDNA haplotypes that all belonged to the European moose phylogroup were recorded. They could be divided into two distinct clades: Central Europe and the Ural Mountains. The first clade consists of three distinct groups/branches: Biebrza, Polesie, and Fennoscandia. The Biebrza group has experienced spatial and demographic expansion in the recent past. Average genetic differentiation among moose populations in Poland at mtDNA-cr was great and significant (ΦST = 0.407, p moose that colonized Poland from the east (Lithuania, Belarus, and Ukraine) and the north (former East Prussia). Among all the sequenced Y-chromosome markers, polymorphisms were found in the DBY14 marker in three populations only; four haplotypes were recorded in total. No significant differentiation was detected for this Y-linked marker among moose populations in Poland. Our mtDNA study revealed that a variety of different factors-bottleneck, the presence of relict, autochthonous populations, translocations, limited female dispersal, and the colonization from the east and north-are responsible for the observed complex pattern of population genetic structure after demographic and spatial expansion of moose in Poland.

  7. 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.

  8. 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...

  9. 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...

  10. Energy efficient perlite expansion process

    Energy Technology Data Exchange (ETDEWEB)

    Jenkins, K.L.

    1982-08-31

    A thermally efficient process for the expansion of perlite ore is described. The inlet port and burner of a perlite expansion chamber (Preferably a vertical expander) are enclosed such that no ambient air can enter the chamber. Air and fuel are metered to the burner with the amount of air being controlled such that the fuel/air premix contains at least enough air to start and maintain minimum combustion, but not enough to provide stoichiometric combustion. At a point immediately above the burner, additional air is metered into an insulated enclosure surrounding the expansion chamber where it is preheated by the heat passing through the chamber walls. This preheated additional air is then circulated back to the burner where it provides the remainder of the air needed for combustion, normally full combustion. Flow of the burner fuel/air premix and the preheated additional air is controlled so as to maintain a long luminous flame throughout a substantial portion of the expansion chamber and also to form a moving laminar layer of air on the inner surface of the expansion chamber. Preferably the burner is a delayed mixing gas burner which materially aids in the generation of the long luminous flame. The long luminous flame and the laminar layer of air at the chamber wall eliminate hot spots in the expansion chamber, result in relatively low and uniform temperature gradients across the chamber, significantly reduce the amount of fuel consumed per unit of perlite expanded, increase the yield of expanded perlite and prevent the formation of a layer of perlite sinter on the walls of the chamber.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

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

    Science.gov (United States)

    Piras, Daniela; Doro, Maria Grazia; Casu, Giuseppina; Melis, Paola Maria; Vaccargiu, Simona; Piras, Ignazio; Parracciani, Debora; Stradoni, Roberta; Frongia, Bruno; Lai, Graziano; Sale, Salvatore; Cattari, Walter; Piras, Roberto; Querci, Ombretta; Demuro, Piergiorgio; Cui, Sandro; Atzori, Franco; Mancosu, Marco; Marchiori, Francesca; Cammelli, Rossana; Spiga, Alessandra; Loddo, Pier Paolo; Pili, Gianfranco; Boi, Roberto; Argiolas, Giuseppe; Mereu, Paolo; Leoni, Giovanni Giuseppe; Naitana, Salvatore; Pirastu, Mario; Novelletto, Andrea

    2012-01-01

    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.

  16. 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.

  17. Thermal Expansion of Irradiated Polytetrafluoroethylene

    OpenAIRE

    Subrahmanyam, HN; Subramanyam, SV

    1987-01-01

    The thermal expansion coefficient of gamma-irradiated Polytetrafluoroethylene (PTFE) has been measured in the temperature range 80-340 K by using a three-terminal capacitance technique. The samples are irradiated in air at room temperature with gamma rays from a $Co^{60}$ source at a dose rate of 0.26 Mrad/h. The change in crystallinity is measured by an x-ray technique. The expansion coefficient is found to increase with radiation dose below 140 K owing to the predominant effect of degradati...

  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. Bearing-Mounting Concept Accommodates Thermal Expansion

    Science.gov (United States)

    Nespodzany, Robert; Davis, Toren S.

    1995-01-01

    Pins or splines allow radial expansion without slippage. Design concept for mounting rotary bearing accommodates differential thermal expansion between bearing and any structure(s) to which bearing connected. Prevents buildup of thermal stresses by allowing thermal expansion to occur freely but accommodating expansion in such way not to introduce looseness. Pin-in-slot configuration also maintains concentricity.

  20. 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

  1. 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.

  2. 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.

  3. mtDNA sequence variants in subtypes of epithelial ovarian cancer stages in relation to ethnic and age difference

    Directory of Open Access Journals (Sweden)

    Yao Xuebiao

    2008-07-01

    Full Text Available Abstract Epithelial ovarian cancer is the fifth leading cause of cancer mortality among women in the United States. For this disease, differences in age-adjusted incidence and survival rates between African American and Caucasian women are substantial. The objective of this study was to examine mtDNA sequence variants in 118 frozen tissues of three subtypes of epithelial ovarian cancer (serous, n = 48 endometrioid, n = 47 and mucinous, n = 23 and matched paracancerous normal tissues (n = 18 in relation to racial/ethnic and age differences. Restriction fragment length polymorphism (RFLP and polymerase chain reaction (PCR-based sequencing were used to evaluate two regions of mtDNA spanning 5317 to 7608 and 8282 to 10110 bp and including ND subunits 2, 3, MT-COI, II, and III, ATPase 8, a part of ATPase 6, and tRNA genes in frozen ovarian tissues obtained from the southern regional Cooperative Human Tissue Network (CHTN and University of Alabama-Birmingham (UAB Ovarian Spore Center. Thirty-nine mtDNA variants were detected of which 28 were previously unreported. One somatic variant of C9500T was observed. A variant, C7028T in the MT-CO1 gene, had an ascending frequency from borderline (8% to stages III/IV (75% among the three ovarian cancer subtypes and stages. It was found in 86% (42/49 of African-American and 43% (37/87 of the Caucasian women. A variant, T8548G in the ATPase 6 gene was detected at a frequency of 72% (18/25 in ovarian serous subtype tissues in stages III/IV. Of the African American patients under age 40, 95% (20/21 harbored the T8548G variant; this was in contrast to only 22% (8/35 of Caucasian patients in same age group. Variants C7256T and G7520A had a frequency of 54% (6/11 in endometrioid stage III; no corresponding variants were observed in mucinous subtype stage III. Furthermore, variants C7256T and G7520A were absent in serous ovarian cancer subtype. Interestingly, the C7520T variant in tRNA gene was present in 74% (36/49 of

  4. Regulation of gas infrastructure expansion

    NARCIS (Netherlands)

    De Joode, J.

    2012-01-01

    The topic of this dissertation is the regulation of gas infrastructure expansion in the European Union (EU). While the gas market has been liberalised, the gas infrastructure has largely remained in the regulated domain. However, not necessarily all gas infrastructure facilities – such as gas storag

  5. 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.

  6. On Fourier re-expansions

    OpenAIRE

    Liflyand, E.

    2012-01-01

    We study an extension to Fourier transforms of the old problem on absolute convergence of the re-expansion in the sine (cosine) Fourier series of an absolutely convergent cosine (sine) Fourier series. The results are obtained by revealing certain relations between the Fourier transforms and their Hilbert transforms.

  7. Large N Expansion. Vector Models

    CERN Document Server

    Nissimov, E; Nissimov, Emil; Pacheva, Svetlana

    2006-01-01

    Preliminary version of a contribution to the "Quantum Field Theory. Non-Perturbative QFT" topical area of "Modern Encyclopedia of Mathematical Physics" (SELECTA), eds. Aref'eva I, and Sternheimer D, Springer (2007). Consists of two parts - "main article" (Large N Expansion. Vector Models) and a "brief article" (BPHZL Renormalization).

  8. Histone deacetylase complexes promote trinucleotide repeat expansions.

    Directory of Open Access Journals (Sweden)

    Kim Debacker

    2012-02-01

    Full Text Available Expansions of DNA trinucleotide repeats cause at least 17 inherited neurodegenerative diseases, such as Huntington's disease. Expansions can occur at frequencies approaching 100% in affected families and in transgenic mice, suggesting that specific cellular proteins actively promote (favor expansions. The inference is that expansions arise due to the presence of these promoting proteins, not their absence, and that interfering with these proteins can suppress expansions. The goal of this study was to identify novel factors that promote expansions. We discovered that specific histone deacetylase complexes (HDACs promote CTG•CAG repeat expansions in budding yeast and human cells. Mutation or inhibition of yeast Rpd3L or Hda1 suppressed up to 90% of expansions. In cultured human astrocytes, expansions were suppressed by 75% upon inhibition or knockdown of HDAC3, whereas siRNA against the histone acetyltransferases CBP/p300 stimulated expansions. Genetic and molecular analysis both indicated that HDACs act at a distance from the triplet repeat to promote expansions. Expansion assays with nuclease mutants indicated that Sae2 is one of the relevant factors regulated by Rpd3L and Hda1. The causal relationship between HDACs and expansions indicates that HDACs can promote mutagenesis at some DNA sequences. This relationship further implies that HDAC3 inhibitors being tested for relief of expansion-associated gene silencing may also suppress somatic expansions that contribute to disease progression.

  9. MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants.

    Directory of Open Access Journals (Sweden)

    Jeffrey D Stumpf

    2014-10-01

    Full Text Available Mitochondrial DNA (mtDNA encodes proteins essential for ATP production. Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging, genetic diseases, and sensitivity to environmental agents. We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mutations affecting conserved regions of the mtDNA polymerase, Mip1, in the presence of the wild type Mip1. Mutant frequency arising from mtDNA base substitutions that confer erythromycin resistance and deletions between 21-nucleotide direct repeats was determined. Previously, increased mutagenesis was observed in strains encoding mutant variants that were insufficient to maintain mtDNA and that were not expected to reduce polymerase fidelity or exonuclease proofreading. Increased mutagenesis could be explained by mutant variants stalling the replication fork, thereby predisposing the template DNA to irreparable damage that is bypassed with poor fidelity. This hypothesis suggests that the exogenous base-alkylating agent, methyl methanesulfonate (MMS, would further increase mtDNA mutagenesis. Mitochondrial mutagenesis associated with MMS exposure was increased up to 30-fold in mip1 mutants containing disease-associated alterations that affect polymerase activity. Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1. A novel subset of C to G transversions was responsible for about half of the mutants arising after MMS exposure implicating error-prone bypass of methylated cytosines as the predominant mutational mechanism. Exposure to MMS does not disrupt exonuclease activity that suppresses deletions between 21-nucleotide direct repeats, suggesting the MMS-induce mutagenesis is not explained by inactivated exonuclease activity. Further, trace amounts of CdCl2 inhibit mtDNA

  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. 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.

    Directory of Open Access Journals (Sweden)

    Hsiu-Chuan Yen

    Full Text Available 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

  12. 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

  13. 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.

  14. 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.

  15. New Paramecium quadecaurelia strains (P. aurelia spp. complex, Ciliophora) identified by molecular markers (rDNA and mtDNA).

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Dusi, Eike

    2013-08-01

    Paramecium quadecaurelia is a rare species (previously known only from two locations) belonging to the P. aurelia species complex. In the present paper, fragments of an rDNA gene (ITS1-5.8S-ITS2-5' rDNA) and mtDNA genes (cytochrome oxidase subunit I and cytochrome b regions) were employed to assist in the identification and characterization of three new strains collected from Ecuador and Thailand. Molecular data were confirmed by mating reactions. In rDNA and mtDNA trees constructed for species of the P. aurelia complex, all P. quadecaurelia strains, including the three new strains discussed in this study and two known previously from Australia and Africa, form a monophyletic but differentiated clade. The present study shows that genetic differentiation among the strains of P. quadecaurelia is equal to or even greater than the distances between some other P. aurelia species, e.g., P. primaurelia and P. pentaurelia. Such great intra-specific differentiation may indicate a future splitting of the P. quadecaurelia species into reproductively isolated lines.

  16. 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.

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

    Institute of Scientific and Technical Information of China (English)

    YANG LiuQi; TAN SiJie; YU HaiJing; ZHENG BingRong; QIAO EnFa; DONG YongLi; ZAN RuiGuang; XIAO ChunJie

    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.

  18. 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.

  19. Monomelic amyotrophy associated with the 7472insC mutation in the mtDNA tRNASer(UCN) gene.

    Science.gov (United States)

    Fetoni, Vincenza; Briem, Egill; Carrara, Franco; Mora, Marina; Zeviani, Massimo

    2004-11-01

    We describe a 49-year-old male patient who experienced progressive amyotrophy with no sensorial abnormality in the left arm since 45 years of age. The neuromuscular syndrome was identical to that known as Hirayama disease, a rare form of focal lower motor neuron disease affecting the C7-C8-T1 metamers of the spinal cord. Asymmetric neurosensorial hearing loss was present since age 35 in the patient, and was also documented in an elder sister and in the mother. A muscle biopsy showed cytochrome c oxidase (COX) negative fibers but no ragged-red fibers, and mild reduction of COX was confirmed biochemically. The patient was found to have high levels of a known pathogenic mutation of mtDNA, the 7472insC in the gene encoding the tRNA(Ser(UCN)). Investigation on several family members showed a correlation between mutation load and clinical severity. This is the second report documenting the association of lower motor neurone involvement with a specific mtDNA.

  20. History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation.

    Science.gov (United States)

    Tishkoff, Sarah A; Gonder, Mary Katherine; Henn, Brenna M; Mortensen, Holly; Knight, Alec; Gignoux, Christopher; Fernandopulle, Neil; Lema, Godfrey; Nyambo, Thomas B; Ramakrishnan, Uma; Reed, Floyd A; Mountain, Joanna L

    2007-10-01

    Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    David Caramelli

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

  3. Eight new mtDNA sequences of glass sponges reveal an extensive usage of +1 frameshifting in mitochondrial translation.

    Science.gov (United States)

    Haen, Karri M; Pett, Walker; Lavrov, Dennis V

    2014-02-10

    Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate the mechanism of frameshifting, we determined eight new complete or nearly complete mtDNA sequences from glass sponges and examined individual mitochondrial genes from three others. We found nine new instances of single nucleotide insertions in these sequences and analyzed them both comparatively and phylogenetically. The base insertions appear to have been gained and lost repeatedly in hexactinellid mt protein genes, suggesting no functional significance for the frameshifting sites. A high degree of sequence conservation, the presence of unusual tRNAs, and a distinct pattern of codon usage suggest the "out-of-frame pairing" model of translational frameshifting. Additionally, we provide evidence that relaxed selection pressure on glass sponge mtDNA - possibly a result of their low growth rates and deep-water lifestyle - has allowed frameshift insertions to be tolerated for hundreds of millions of years. Our study provides the first example of a phylogenetically diverse and extensive usage of translational frameshifting in animal mitochondrial coding sequences.

  4. Rapid proliferation of repetitive palindromic elements in mtDNA of the endemic Baikalian sponge Lubomirskia baicalensis.

    Science.gov (United States)

    Lavrov, Dennis V

    2010-04-01

    Animal mitochondrial DNA (mtDNA) is a remarkably compact molecule largely because of the scarcity of noncoding "selfish" DNA. Recently, however, we found that mitochondrial genomes of several phylogenetically diverse species of demosponges contain small repetitive palindromic sequences, interspersed within intergenic regions and fused in protein and ribosomal RNA genes. Here, I report and analyze the proliferation of such elements in the mitochondrial genome of the endemic sponge of Lake Baikal Lubomirskia baicalensis. Because Baikal sponges are closely related to the circumglobally distributed freshwater sponge Ephydatia muelleri with which they shared a common ancestor approximately 3-10 Ma, both the rate of single nucleotide substitutions and the rate of palindromic repeat insertions can be calculated in this system. I found the rate of nucleotide substitutions in mtDNA of freshwater sponges to be extremely low (0.5-1.6 x 10(-9) per site per year), more similar to that in plants than bilaterian animals. By contrast, the per/nucleotide rate of insertions of repetitive elements is at least four times higher. This rapid rate of proliferation combined with the broad phylogenetic distribution of hairpin elements can make them a defining force in the evolution of mitochondrial genomes of demosponges.

  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. 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.

  7. 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

  8. 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...... of Thomas Kuhn’s notion of scientific paradigms and criteria for a good theory (1977, 1996). The paper thus aims to augment and assimilate the fragmented and scattered body of concepts presently residing within the field of evolutionary economics, by presenting an intuitive framework, applicable within...... 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...

  9. College Expansion and Curriculum Choice

    OpenAIRE

    Kaganovich, Michael; Su, Xuejuan

    2012-01-01

    This paper analyzes the impact of college enrollment expansion on student academic achievements and labor market outcomes in the context of competition among colleges. When public policies promote “access” to college education, colleges adjust their curricula: Less selective public colleges adopt a less demanding curriculum in order to accommodate the influx of less able students. As we argue in the paper, this adjustment benefits low-ability college students at the expense of those of medium...

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Mitochondrial DNA (mtDNA) variants in the European haplogroups HV, JT, and U do not have a major role in schizophrenia.

    Science.gov (United States)

    Torrell, Helena; Salas, Antonio; Abasolo, Nerea; Morén, Constanza; Garrabou, Glòria; Valero, Joaquín; Alonso, Yolanda; Vilella, Elisabet; Costas, Javier; Martorell, Lourdes

    2014-10-01

    It has been reported that certain genetic factors involved in schizophrenia could be located in the mitochondrial DNA (mtDNA). Therefore, we hypothesized that mtDNA mutations and/or variants would be present in schizophrenia patients and may be related to schizophrenia characteristics and mitochondrial function. This study was performed in three steps: (1) identification of pathogenic mutations and variants in 14 schizophrenia patients with an apparent maternal inheritance of the disease by sequencing the entire mtDNA; (2) case-control association study of 23 variants identified in step 1 (16 missense, 3 rRNA, and 4 tRNA variants) in 495 patients and 615 controls, and (3) analyses of the associated variants according to the clinical, psychopathological, and neuropsychological characteristics and according to the oxidative and enzymatic activities of the mitochondrial respiratory chain. We did not identify pathogenic mtDNA mutations in the 14 sequenced patients. Two known variants were nominally associated with schizophrenia and were further studied. The MT-RNR2 1811A > G variant likely does not play a major role in schizophrenia, as it was not associated with clinical, psychopathological, or neuropsychological variables, and the MT-ATP6 9110T > C p.Ile195Thr variant did not result in differences in the oxidative and enzymatic functions of the mitochondrial respiratory chain. The patients with apparent maternal inheritance of schizophrenia did not exhibit any mutations in their mtDNA. The variants nominally associated with schizophrenia in the present study were not related either to phenotypic characteristics or to mitochondrial function. We did not find evidence pointing to a role for mtDNA sequence variation in schizophrenia.

  16. Urban underground network expansion planning

    Energy Technology Data Exchange (ETDEWEB)

    Bozic, Z. [Sinclair Knight Merz Pty Ltd., Perth (Australia); Hobson, E. [HI Consulting Services Pty Ltd., Adelaide (Australia)

    1997-03-01

    The authors describe a three step approach to expansion planning of high voltage (HV) urban underground distribution networks. Although the techniques are specifically oriented to underground systems, they are equally applicable to overhead system design. The fundamental engineering problem is how to connect individual high voltage to low voltage substations (HV/LV SS) and zone HV SS into a future urban underground network. The problem is to rearrange the HV network to minimise the cost of expansion subject to provision of an alternative supply, specified load transfer among the neighbouring zone SS, and other general planning constraints such as feeder capacity, voltage regulation, operational requirements and losses. A review of the current state of the art of distribution expansion planning is provided. The normal manual approach is discussed together with more recent research into computer methods. Three lines of computer research are identified and classified as radially constrained, security constrained and utilisation of travelling salesman/vehicle routing problem algorithms (TSP/VRP). The TSP/VRP line of research has been extended here to produce practical techniques for the assistance of network planners. (Author)

  17. 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...

  18. Haplotype Affinities Resolve a Major Component of Goat (Capra hircus) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock

    OpenAIRE

    Daniela Piras; Maria Grazia Doro; Giuseppina Casu; Paola Maria Melis; Simona Vaccargiu; Ignazio Piras; Debora Parracciani; Roberta Stradoni; Bruno Frongia; Graziano Lai; Salvatore Sale; Walter Cattari; Roberto Piras; Ombretta Querci; Piergiorgio Demuro

    2012-01-01

    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 oper...

  19. Thermal expansion of ceramics around room temperature

    OpenAIRE

    橋本, 忍; 安達, 信泰; 太田, 敏孝; 宮崎, 英敏; ハシモト, シノブ; アダチ, ノブヤス; オオタ, トシタカ; Hashimoto, Shinobu; Adachi, Nobuyasu; Ota, Toshitaka

    2010-01-01

    Thermal expansion of some ceramics, polymers and metals was measured by dilatometer around room temperature (from -140℃to +200℃), and compared with thermal expansion in the high temperature region. The CTE (coefficient of thermal expansion)of almost ceramics changed drastically between room temperature and high temperature region. On the other hand, the CTE ofmetals did not change between room temperature and high temperature region. The difference on thermal expansion betweenceramics and met...

  20. 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

  1. 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.

  2. Quantum fields and "Big Rip" expansion singularities

    CERN Document Server

    Calderon, H; Calderon, Hector; Hiscock, William A.

    2005-01-01

    The effects of quantized conformally invariant massless fields on the evolution of cosmological models containing a ``Big Rip'' future expansion singularity are examined. Quantized scalar, spinor, and vector fields are found to strengthen the accelerating expansion of such models as they approach the expansion singularity.

  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. Thermal Expansion in YbGaGe

    OpenAIRE

    Bobev, Svilen; Williams, Darrick J.; Thompson, J.D.; Sarrao, J L

    2004-01-01

    Thermal expansion and magnetic susceptibility measurements as a function of temperature are reported for YbGaGe. Despite the fact that this material has been claimed to show zero thermal expansion over a wide temperature range, we observe thermal expansion typical of metals and Pauli paramagnetic behavior, which perhaps indicates strong sample dependence in this system.

  5. 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.

  6. 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.

  7. 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.

  8. Molecular phylogeny of grey mullets (Teleostei: Mugilidae) in Greece: evidence from sequence analysis of mtDNA segments.

    Science.gov (United States)

    Papasotiropoulos, Vasilis; Klossa-Kilia, Elena; Alahiotis, Stamatis N; Kilias, George

    2007-08-01

    Mitochondrial DNA sequence analysis has been used to explore genetic differentiation and phylogenetic relationships among five species of the Mugilidae family, Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens. DNA was isolated from samples originating from the Messolongi Lagoon in Greece. Three mtDNA segments (12s rRNA, 16s rRNA, and CO I) were PCR amplified and sequenced. Sequencing analysis revealed that the greatest genetic differentiation was observed between M. cephalus and all the other species studied, while C. labrosus and L. aurata were the closest taxa. Dendrograms obtained by the neighbor-joining method and Bayesian inference analysis exhibited the same topology. According to this topology, M. cephalus is the most distinct species and the remaining taxa are clustered together, with C. labrosus and L. aurata forming a single group. The latter result brings into question the monophyletic origin of the genus Liza.

  9. Multiple origins of the mtDNA 7472insC mutation associated with hearing loss and neurological dysfunction.

    Science.gov (United States)

    Hutchin, T P; Navarro-Coy, N C; Van Camp, G; Tiranti, V; Zeviani, M; Schuelke, M; Jaksch, M; Newton, V; Mueller, R F

    2001-05-01

    Several mtDNA mutations have been reported in families with both syndromic and non-syndromic hearing loss. One such mutation is the heteroplasmic 7472insC in the tRNA(Ser(UCN)) gene which has been found in six families, all from Western Europe. However, it was not clear if this distribution was due to a common founder effect or chance sampling of several unrelated families, the 7472insC mutation having occurred multiple times. Haplotype analysis of all six families supports the latter notion. This confirms the pathogenicity of the 7472insC mutation and suggests it may exist in other populations where it may prove to be a small but significant cause of hearing loss, particularly when neurological symptoms are also present.

  10. 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.

  11. 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.

  12. Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA

    Directory of Open Access Journals (Sweden)

    Arthur Gusman

    2016-12-01

    Full Text Available There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA in the animal kingdom: a system named doubly uniparental inheritance (DUI, which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841and the veneroid Scrobicularia plana(Da Costa,1778, increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.

  13. Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA

    Science.gov (United States)

    Gusman, Arthur; Lecomte, Sophia; Stewart, Donald T.; Passamonti, Marco

    2016-01-01

    There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841)and the veneroid Scrobicularia plana(Da Costa,1778), increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented. PMID:27994972

  14. Mixed-stock analysis in green turtles Chelonia mydas: mtDNA decipher current connections among west Atlantic populations.

    Science.gov (United States)

    Costa Jordao, Juliana; Bondioli, Ana Cristina Vigliar; Almeida-Toledo, Lurdes Foresti de; Bilo, Karin; Berzins, Rachel; Le Maho, Yvon; Chevallier, Damien; de Thoisy, Benoit

    2017-03-01

    The green turtle Chelonia mydas undertakes wide-ranging migrations between feeding and nesting sites, resulting in mixing and isolation of genetic stocks. We used mtDNA control region to characterize the genetic composition, population structure, and natal origins of C. mydas in the West Atlantic Ocean, at one feeding ground (State of Rio de Janeiro, Brazil), and three Caribbean nesting grounds (French Guiana, Guadeloupe, and Suriname). The feeding ground presented considerable frequency of common haplotypes from the South Atlantic, whereas the nesting sites presented a major contribution of the most common haplotype from the Caribbean. MSA revealed multiple origins of individuals at the feeding ground, notably from Ascension Island, Guinea Bissau, and French Guiana. This study enables a better understanding of the dispersion patterns and highlights the importance of connecting both nesting and feeding areas. Effective conservation initiatives need to encompass these ecologically and geographically distinct sites as well as those corridors connecting them.

  15. 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.

  16. 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.

  17. Abnormally activated one-carbon metabolic pathway is associated with mtDNA hypermethylation and mitochondrial malfunction in the oocytes of polycystic gilt ovaries.

    Science.gov (United States)

    Jia, Longfei; Li, Juan; He, Bin; Jia, Yimin; Niu, Yingjie; Wang, Chenfei; Zhao, Ruqian

    2016-01-13

    Polycystic ovarian syndrome (PCOS) is associated with hyperhomocysteinemia and polycystic ovaries (PCO) usually produce oocytes of poor quality. However, the intracellular mechanism linking hyperhomocysteinemia and oocyte quality remains elusive. In this study, the quality of the oocytes isolated from healthy and polycystic gilt ovaries was evaluated in vitro in association with one-carbon metabolism, mitochondrial DNA (mtDNA) methylation, and mitochondrial function. PCO oocytes demonstrated impaired polar body extrusion, and significantly decreased cleavage and blastocyst rates. The mitochondrial distribution was disrupted in PCO oocytes, together with decreased mitochondrial membrane potential and deformed mitochondrial structure. The mtDNA copy number and the expression of mtDNA-encoded genes were significantly lower in PCO oocytes. Homocysteine concentration in follicular fluid was significantly higher in PCO group, which was associated with significantly up-regulated one-carbon metabolic enzymes betaine homocysteine methyltransferase (BHMT), glycine N-methyltransferase (GNMT) and the DNA methyltransferase DNMT1. Moreover, mtDNA sequences coding for 12S, 16S rRNA and ND4, as well as the D-loop region were significantly hypermethylated in PCO oocytes. These results indicate that an abnormal activation of one-carbon metabolism and hypermethylation of mtDNA may contribute, largely, to the mitochondrial malfunction and decreased quality of PCO-derived oocytes in gilts.

  18. 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...

  19. 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...

  20. 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...

  1. 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

  2. The co-occurrence of mtDNA mutations on different oxidative phosphorylation subunits, not detected by haplogroup analysis, affects human longevity and is population specific

    DEFF Research Database (Denmark)

    Raule, Nicola; Sevini, Federica; Li, Shengting;

    2014-01-01

    To re-examine the correlation between mtDNA variability and longevity, we examined mtDNAs from samples obtained from over 2200 ultranonagenarians (and an equal number of controls) collected within the framework of the GEHA EU project. The samples were categorized by high-resolution classification...

  3. Identification of interacting partners of Human Mpv17-like protein with a mitigating effect of mitochondrial dysfunction through mtDNA damage.

    Science.gov (United States)

    Iida, Reiko; Ueki, Misuzu; Yasuda, Toshihiro

    2015-10-01

    Human Mpv17-like protein (M-LPH) has been suggested to participate in mitochondrial function. In this study, we investigated the proteins that interact with M-LPH, and identified four: H2A histone family, member X (H2AX), ribosomal protein S14 (RPS14), ribosomal protein S3 (RPS3) and B-cell receptor-associated protein 31 (Bap31). Immunofluorescence and subcellular fractionation studies revealed that M-LPH is localized predominantly in the nucleus, to some extent in a subset of mitochondria, and marginally in the cytosol. Mitochondrial M-LPH appeared as punctate foci, and these were co-localized with a subset of mitochondrial transcription factor A (TFAM) and mtDNA, indicating that M-LPH is localized in or in close proximity to mitochondrial nucleoids. RNAi-mediated knockdown of M-LPH resulted in an increase of mtDNA damage and reduced the expression of mtDNA-encoded genes. A ROS inducer, antimycin A, caused an increase in both the number and size of the mitochondrial M-LPH foci, and these foci were co-localized with two enzymes, DNA polymerase γ (POLG) and DNA ligase III (LIG3), both involved in mtDNA repair. Furthermore, knockdown of M-LPH hampered mitochondrial localization of these enzymes. Taken together, these observations suggest that M-LPH is involved in the maintenance of mtDNA and protects cells from mitochondrial dysfunction.

  4. 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.

  5. 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).

  6. Primordial vorticity and gradient expansion

    Science.gov (United States)

    Giovannini, Massimo; Rezaei, Zahra

    2012-02-01

    The evolution equations of the vorticities of the electrons, ions and photons in a pre-decoupling plasma are derived, in a fully inhomogeneous geometry, by combining the general relativistic gradient expansion and the drift approximation within the Adler-Misner-Deser decomposition. The vorticity transfer between the different species is discussed in this novel framework and a set of general conservation laws, connecting the vorticities of the three-component plasma with the magnetic field intensity, is derived. After demonstrating that a source of large-scale vorticity resides in the spatial gradients of the geometry and of the electromagnetic sources, the total vorticity is estimated to lowest order in the spatial gradients and by enforcing the validity of the momentum constraint. By acknowledging the current bounds on the tensor to scalar ratio in the (minimal) tensor extension of the ΛCDM paradigm, the maximal comoving magnetic field induced by the total vorticity turns out to be, at most, of the order of 10-37 G over the typical comoving scales ranging between 1 and 10 Mpc. While the obtained results seem to be irrelevant for seeding a reasonable galactic dynamo action, they demonstrate how the proposed fully inhomogeneous treatment can be used for the systematic scrutiny of pre-decoupling plasmas beyond the conventional perturbative expansions.

  7. 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...

  8. 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.

  9. 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.

  10. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans.

    Science.gov (United States)

    Wonnapinij, Passorn; Chinnery, Patrick F; Samuels, David C

    2010-04-09

    In cases of inherited pathogenic mitochondrial DNA (mtDNA) mutations, a mother and her offspring generally have large and seemingly random differences in the amount of mutated mtDNA that they carry. Comparisons of measured mtDNA mutation level variance values have become an important issue in determining the mechanisms that cause these large random shifts in mutation level. These variance measurements have been made with samples of quite modest size, which should be a source of concern because higher-order statistics, such as variance, are poorly estimated from small sample sizes. We have developed an analysis of the standard error of variance from a sample of size n, and we have defined error bars for variance measurements based on this standard error. We calculate variance error bars for several published sets of measurements of mtDNA mutation level variance and show how the addition of the error bars alters the interpretation of these experimental results. We compare variance measurements from human clinical data and from mouse models and show that the mutation level variance is clearly higher in the human data than it is in the mouse models at both the primary oocyte and offspring stages of inheritance. We discuss how the standard error of variance can be used in the design of experiments measuring mtDNA mutation level variance. Our results show that variance measurements based on fewer than 20 measurements are generally unreliable and ideally more than 50 measurements are required to reliably compare variances with less than a 2-fold difference.

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

    Directory of Open Access Journals (Sweden)

    Anja Brinckmann

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

  12. 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

  13. The Amerindian mtDNA haplogroup B2 enhances the risk of HPV for cervical cancer: de-regulation of mitochondrial genes may be involved.

    Science.gov (United States)

    Guardado-Estrada, Mariano; Medina-Martínez, Ingrid; Juárez-Torres, Eligia; Roman-Bassaure, Edgar; Macías, Luis; Alfaro, Ana; Alcántara-Vázquez, Avissai; Alonso, Patricia; Gomez, Guillermo; Cruz-Talonia, Fernando; Serna, Luis; Muñoz-Cortez, Sergio; Borges-Ibañez, Manuel; Espinosa, Ana; Kofman, Susana; Berumen, Jaime

    2012-04-01

    Although human papillomavirus (HPV) infection is the main causal factor for cervical cancer (CC), there are data suggesting that genetic factors could modulate the risk for CC. Sibling studies suggest that maternally inherited factors could be involved in CC. To assess whether mitochondrial DNA (mtDNA) polymorphisms are associated to CC, HPV infection and HPV types, a case-control study was performed in the Mexican population. Polymorphism of mtDNA D-loop was investigated in 187 CC patients and 270 healthy controls. HPV was detected and typed in cervical scrapes. The expression of 29 mitochondrial genes was analyzed in a subset of 45 tumor biopsies using the expression microarray ST1.0. The Amerindian haplogroup B2 increased the risk for CC (odds ratio (OR)=1.6; 95% confidence interval (CI): 1.05-2.58) and enhanced 36% (OR=208; 95% CI: 25.2-1735.5) the risk conferred by the HPV alone (OR=152.9; 95% CI: 65.4-357.5). In cases, the distribution of HPV types was similar in all haplogroups but one (D1), in which is remarkable the absence of HPV18, a very low frequency of HPV16 and high frequencies of HPV45, HPV31 and other HPV types. Two mtDNA genes (mitochondrial aspartic acid tRNA (MT-TD), mitochondrial lysine tRNA (MT-TK)) could be involved in the increased risk conferred by the haplogroup B2, as they were upregulated exclusively in B2 tumors (P<0.01, t-test). Although the association of mtDNA with CC and HPV infection is clear, other studies with higher sample size will be needed to elucidate the role of mtDNA in cervical carcinogenesis.

  14. Accelerating Expansion of the Universe

    CERN Document Server

    Chakraborty, Writambhara

    2011-01-01

    This thesis concentrates on the accelerated expansion of the Universe recently explored by measurements of redshift and luminosity-distance relations of type Ia Supernovae. We have considered a model of the universe filled with modified Chaplygin gas and barotropic fluid. The role of dynamical cosmological constant has been explored with Modified Chaplygin Gas as the background fluid. Various phenomenological models for \\Lambda have been studied in presence of the gravitational constant G to be constant or time dependent. A new form of the well known Chaplygin gas model has been presented by introducing inhomogeneity in the EOS. This model explains w=-1 crossing. An interaction of this model with the scalar field has also been investigated through a phenomenological coupling function. Tachyonic field has been depicted as dark energy model to represent the present acceleration of the Universe. A mixture of the tachyonic fluid has been considered with Generalized Chaplygin Gas to show the role of the later as a...

  15. Bilinear Expansion For Redistribution Functions

    Science.gov (United States)

    Harutyunian, Haik; Alecian, Georges; Khachatryan, Knarik; Vardanyan, Ani

    2016-11-01

    We suggest here a method for construction of a bilinear expansion for an angle-averaged redistribution function. This function describes the elementary act of a photon scattering by a model two-level atom with the upper level broadened due to radiation damping. An eigenvalue and eigenvector determination problem is formulated and the relevant matrices are found analytically. Numerical procedures for their computations are elaborated as well. A simple method for the numerical calculations accuracy evaluation is suggested. It is shown that a family of redistribution functions describing the light scattering process within the spectral line frequencies can be constructed if the eigenvalue problem for the considered function is solved. It becomes possible if the eigenvalues and eigenvectors with the appropriate basic functions are used. The Voigt function and its derivatives used as basic functions are studied in detail as well.

  16. Asymptotic expansions in nonlinear rotordynamics

    Science.gov (United States)

    Day, William B.

    1987-01-01

    This paper is an examination of special nonlinearities of the Jeffcott equations in rotordynamics. The immediate application of this analysis is directed toward understanding the excessive vibrations recorded in the LOX pump of the SSME during hot-firing ground testing. Deadband, side force, and rubbing are three possible sources of inducing nonlinearity in the Jeffcott equations. The present analysis initially reduces these problems to the same mathematical description. A special frequency, named the nonlinear natural frequency, is defined and used to develop the solutions of the nonlinear Jeffcott equations as singular asymptotic expansions. This nonlinear natural frequency, which is the ratio of the cross-stiffness and the damping, plays a major role in determining response frequencies.

  17. 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.

  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. Pressurized electrolysis stack with thermal expansion capability

    Science.gov (United States)

    Bourgeois, Richard Scott

    2015-07-14

    The present techniques provide systems and methods for mounting an electrolyzer stack in an outer shell so as to allow for differential thermal expansion of the electrolyzer stack and shell. Generally, an electrolyzer stack may be formed from a material with a high coefficient of thermal expansion, while the shell may be formed from a material having a lower coefficient of thermal expansion. The differences between the coefficients of thermal expansion may lead to damage to the electrolyzer stack as the shell may restrain the thermal expansion of the electrolyzer stack. To allow for the differences in thermal expansion, the electrolyzer stack may be mounted within the shell leaving a space between the electrolyzer stack and shell. The space between the electrolyzer stack and the shell may be filled with a non-conductive fluid to further equalize pressure inside and outside of the electrolyzer stack.

  20. 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.

  1. 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。

  2. 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.

  3. Anomalous thermal expansion in $\\alpha$-titanium

    OpenAIRE

    Souvatzis, P.; O. Eriksson; M. I. Katsnelson

    2007-01-01

    We provide a complete quantitative explanation for the anisotropic thermal expansion of hcp Ti at low temperature. The observed negative thermal expansion along the c-axis is reproduced theoretically by means of a parameter free theory which involves both the electron and phonon contributions to the free energy. The thermal expansion of titanium is calculated and found to be negative along the c-axis for temperatures below $\\sim$ 170 K, in good agreement with observations. We have identified ...

  4. Hydration and Thermal Expansion in Anatase Nanoparticles.

    Science.gov (United States)

    Zhu, He; Li, Qiang; Ren, Yang; Fan, Longlong; Chen, Jun; Deng, Jinxia; Xing, Xianran

    2016-08-01

    A tunable thermal expansion is reported in nanosized anatase by taking advantage of surface hydration. The coefficient of thermal expansion of 4 nm TiO2 along a-axis is negative with a hydrated surface and is positive without a hydrated surface. High-energy synchrotron X-ray pair distribution function analysis combined with ab initio calculations on the specific hydrated surface are carried out to reveal the local structure distortion that is responsible for the unusual negative thermal expansion.

  5. Hydration and Thermal Expansion in Anatase Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, He [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing 100083 China; Li, Qiang [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing 100083 China; Ren, Yang [Argonne National Laboratory, X-Ray Science Division, Argonne IL 60439 USA; Fan, Longlong [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing 100083 China; Chen, Jun [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing 100083 China; Deng, Jinxia [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing 100083 China; Xing, Xianran [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing 100083 China

    2016-06-06

    A tunable thermal expansion is reported in nanosized anatase by taking advantage of surface hydration. The coefficient of thermal expansion of 4 nm TiO2 along a-axis is negative with a hydrated surface and is positive without a hydrated surface. High-energy synchrotron X-ray pair distribution function analysis combined with ab initio calculations on the specific hydrated surface are carried out to reveal the local structure distortion that is responsible for the unusual negative thermal expansion.

  6. 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.

  7. 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.

  8. 亨廷顿舞蹈病患者 mtDNA D环突变及编码区大片段缺失分析%Analysis of D loop mutation and large-scale deletion in coding region of mtDNA from Huntington ’ s disease patients

    Institute of Scientific and Technical Information of China (English)

    姜楠; 周璐; 肖海; 李晓文

    2013-01-01

    Aim:To study the relationship between mtDNA D loop mutation ,large-scale deletions in mtDNA coding re-gion and Huntington ’ s disease ( HD) .Methods:PCR-agarose gel electrophoresis was used to detect mtDNA D loop muta-tion and large-scale deletion in mtDNA coding region of 8 HD patients,20 normal individuals from HD pedigrees , and 20 unrelated normal individuals .Results:None of the HD patients was found insert/deletion mutation in mtDNA D loop .And HVRⅠrs16061-rs16171 was the mutation cluster region .Large-scale deletion in mtDNA coding region was detected in 3 HD patients and 16 normal individuals from HD pedigrees .Conclusion: The insert/deletion mutation in mtDNA D loop and large-scale deletion of mtDNA coding region may not be the main reasons of HD .%目的:探讨人类mtDNA D环突变及编码区大片段缺失与亨廷顿舞蹈病的关系。方法:采用PCR-DNA测序技术对2个亨廷顿舞蹈病家系的8名患者、20名家系内正常人及20名无关健康个体的mtDNA D环高变区突变及编码区大片段缺失进行检测。结果:患者D环高变区未发现片段缺失/插入突变,高变区Ⅰ的rs16061~rs16171是核苷酸歧变的集中区域。3名患者和16名家系内正常人存在mtDNA编码区大片段缺失。结论:mtDNA D环调控序列的大片段缺失/插入突变及编码区大片段缺失可能不是亨廷顿舞蹈病发病机制中的主要因素。

  9. Magnetic Clouds: Global and local expansion

    Science.gov (United States)

    Gulisano, Adriana; Demoulin, Pascal; Soledad Nakwacki, Ms Maria; Dasso, Sergio; Emilia Ruiz, Maria

    Magnetic clouds (MCs) are magnetized objects forming flux ropes, which are expelled from the Sun and travel through the heliosphere, transporting important amounts of energy, mass, magnetic flux, and magnetic helicity from the Sun to the interplanetary medium. To know the detailed dynamical evolution of MCs is very useful to improve the knowledge of solar processes, for instance from linking a transient solar source with its interplanetary manifestation. During its travel, and mainly due to the decrease of the total (magnetic plus thermal) pressure in the surrounding solar wind, MCs are objects in expansion. However, the detailed magnetic structure and the dynamical evolution of MCs is still not fully known. Even the identification of their boundaries is an open question in some cases. In a previous work we have shown that from onepoint observations of the bulk velocity profile, it is possible to infer the 'local' expansion rate for a given MC, i.e., the expansion rate while the MC is observed by the spacecraft. By the another hand, and from the comparison of sizes for different MCs observed at different heliodistances, it is possible to quantify an 'average' expansion law (i.e., a global expansion). In this work, in order to study the variability of the 'local' expansion with respect to the 'average' expansion of MCs during their travel, we present results and a comparison between both approaches. We make a detailed study of one-point observations (magnetic and bulk velocity) using a set of MCs and we get the 'local' expansion rate for each studied event. We compare the obtained 'local' expansion rates with the 'average' expansion law, and also with the expansion rates for the stationary solar wind.

  10. Primordial vorticity and gradient expansion

    CERN Document Server

    Giovannini, Massimo

    2012-01-01

    The evolution equations of the vorticities of the electrons, ions and photons in a pre-decoupling plasma are derived, in a fully inhomogeneous geometry, by combining the general relativistic gradient expansion and the drift approximation within the Adler-Misner-Deser decomposition. The vorticity transfer between the different species is discussed in this novel framework and a set of general conservation laws, connecting the vorticities of the three-component plasma with the magnetic field intensity, is derived. After demonstrating that a source of large-scale vorticity resides in the spatial gradients of the geometry and of the electromagnetic sources, the total vorticity is estimated to lowest order in the spatial gradients and by enforcing the validity of the momentum constraint. By acknowledging the current bounds on the tensor to scalar ratio in the (minimal) tensor extension of the $\\Lambda$CDM paradigm the maximal comoving magnetic field induced by the total vorticity turns out to be, at most, of the or...

  11. 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...

  12. 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…

  13. Expansion techniques for collisionless stellar dynamical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Meiron, Yohai [Kavli Institute for Astronomy and Astrophysics at Peking University, Beijing 100871 (China); Li, Baile; Holley-Bockelmann, Kelly [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Spurzem, Rainer, E-mail: ymeiron@pku.edu.cn [National Astronomical Observatories of China, Chinese Academy of Sciences, Beijing 100012 (China)

    2014-09-10

    We present graphics processing unit (GPU) implementations of two fast force calculation methods based on series expansions of the Poisson equation. One method is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other method is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a 'pure' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took ∼0.1 s (depending on expansion cutoff), making simulations with as many as 10{sup 8} particles fast for a comparatively small number of nodes.

  14. CONCEPT OF TISSUE EXPANSION IN RECONSTRUCTIVE SURGERY

    Directory of Open Access Journals (Sweden)

    Sheeja Rajan

    2015-01-01

    Full Text Available BACKGROUND: Tissue expansion is a unique reconstructive option in the armamentarium of a reconstructive surgeon whereby skin and soft tissues of our body can be stretched to large dimensions for wound coverage. The basis for such stretch ability lies in the inherent viscoelastic properties of skin. AIMS: This paper explores the prospects of using tissue expanders to reconstruct defects arising due to a kaleidoscope of pathological conditions including burns scars, post traumatic scars, congenital anomalies like hairy nevus, involutional scars in haemangioma as well as in post mastectomy breast reconstruction . MATERIALS AND METHODS: Our experience with tissue expansion in 14 patients over 24 months is presented. Tissue expanders made of silicone in sizes from 100 - 250ml, of round, rectangular or croissant (crescent shapes have been used. Areas expanded include scalp, forehead, neck, abdomen and forearm. Multiple expanders have been used when possible. Average expansion time was 8 - 12 weeks and the expanded tissue was transferred as advancement flaps. RESULTS AND CONCLUSIONS: Tissue expansion was successfully completed in 13 patients. Expansion had to be aborted in 1 paediatric patient undergoing neck expansion due to infection. Implant failure occurred in 1 patient during serial expansion. Nevertheless, in our experience tissue expan sion is an invaluable reconstructive tool to give excellent donor tissue with colour and texture match in countless situations demanding aesthetic and functional reconstruction. KEYWORDS: Burns scars, Reconstruction, Tissue expansion .

  15. 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.

  16. 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.

  17. Flash Expansion Threshold in Whirligig Swarms.

    Directory of Open Access Journals (Sweden)

    William L Romey

    Full Text Available In the selfish herd hypothesis, prey animals move toward each other to avoid the likelihood of being selected by a predator. However, many grouped animals move away from each other the moment before a predator attacks. Very little is known about this phenomenon, called flash expansion, such as whether it is triggered by one individual or a threshold and how information is transferred between group members. We performed a controlled experiment with whirligig beetles in which the ratio of sighted to unsighted individuals was systematically varied and emergent flash expansion was measured. Specifically, we examined: the percentage of individuals in a group that startled, the resulting group area, and the longevity of the flash expansion. We found that one or two sighted beetles in a group of 24 was not enough to cause a flash expansion after a predator stimulus, but four sighted beetles usually initiated a flash expansion. Also, the more beetles that were sighted the larger the resulting group area and the longer duration of the flash expansion. We conclude that flash expansion is best described as a threshold event whose adaptive value is to prevent energetically costly false alarms while quickly mobilizing an emergent predator avoidance response. This is one of the first controlled experiments of flash expansion, an important emergent property that has applications to understanding collective motion in swarms, schools, flocks, and human crowds. Also, our study is a convincing demonstration of social contagion, how the actions of one individual can pass through a group.

  18. 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.

  19. 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.

  20. Perturbative expansion of Chern-Simons theory

    OpenAIRE

    SAWON, Justin

    2005-01-01

    An overview of the perturbative expansion of the Chern--Simons path integral is given. The main goal is to describe how trivalent graphs appear: as they already occur in the perturbative expansion of an analogous finite-dimensional integral, we discuss this case in detail.

  1. [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.

  2. Sequence-length variation of mtDNA HVS-I C-stretch in Chinese ethnic groups.

    Science.gov (United States)

    Chen, Feng; Dang, Yong-hui; Yan, Chun-xia; Liu, Yan-ling; Deng, Ya-jun; Fulton, David J R; Chen, Teng

    2009-10-01

    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 approaches. 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, Pexpansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of upstream 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.

  3. 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.

  4. 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.

  5. 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.

  6. Comparison of mtDNA haplogroups in Hungarians with four other European populations: a small incidence of descents with Asian origin.

    Science.gov (United States)

    Nadasi, Edit; Gyurus, P; Czakó, Márta; Bene, Judit; Kosztolányi, Sz; Fazekas, Sz; Dömösi, P; Melegh, B

    2007-06-01

    Hungarians are unique among the other European populations because according to history, the ancient Magyars had come from the eastern side of the Ural Mountains and settled down in the Carpathian basin in the 9th century AD. Since variations in the human mitochondrial genome (mtDNA) are routinely used to infer the histories of different populations, we examined the distribution of restriction fragment length polymorphism (RFLP) sites of the mtDNA in apparently healthy, unrelated Hungarian subjects in order to collect data on the genetic origin of the Hungarian population. Among the 55 samples analyzed, the large majority belonged to haplogroups common in other European populations, however, three samples fulfilled the requirements of haplogroup M. Since haplogroup M is classified as a haplogroup characteristic mainly for Asian populations, the presence of haplogroup M found in approximately 5% of the total suggests that an Asian matrilineal ancestry, even if in a small incidence, can be detected among modern Hungarians.

  7. Sideroblastic anaemia and primary adrenal insufficiency due to a mitochondrial respiratory chain disorder in the absence of mtDNA deletion.

    Science.gov (United States)

    O'Grady, Michael J; Monavari, Ahmad A; Cotter, Melanie; Murphy, Nuala P

    2015-02-26

    A fatigued 8-year-old boy was found to have sideroblastic anaemia (haemoglobin 7.8 g/dL) which over time became transfusion dependent. Subtle neurological dysfunction, initially manifesting as mild spastic diplegia, was slowly progressive and ultimately led to wheelchair dependence. Elevated plasma lactate and urinary 3-methylglutaconate led to a muscle biopsy which confirmed partial complex IV deficiency. PCR in leucocytes and muscle was negative for mitochondrial DNA (mtDNA) deletions. Faltering growth prompted an insulin tolerance test which confirmed growth hormone sufficiency and adrenal insufficiency. Plasma renin was elevated and adrenal androgens were low, suggesting primary adrenal insufficiency. Glucocorticoid and mineralocorticoid replacement therapy was initiated. A renal tubular Fanconi syndrome and diabetes mellitus developed subsequently. Sideroblastic anaemia and primary adrenal insufficiency, both individually and collectively, are associated with mtDNA deletion; however, absence of the same does not exclude the possibility that sideroblastic anaemia and primary adrenal insufficiency are of mitochondrial origin.

  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)

    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.

  9. Identification of a group of cryptic marine limpet species, Cellana karachiensis (Mollusca: Patellogastropoda) off Veraval coast, India, using mtDNA COI sequencing.

    Science.gov (United States)

    Joseph, Sneha; Poriya, Paresh; Vakani, Bhavik; Singh, S P; Kundu, Rahul

    2016-01-01

    Present communication reports the phylogenetic relationship between three groups of a marine limpet having different color banding patterns using COI sequencing. Samples were sequenced for mtDNA COI gene using universal primer. Comparative BLAST revealed that all three types were around 99.59% identical with Cellana karachiensis, first record of this species from Indian coasts. Apart from the morphological variations, the mtDNA COI gene analysis revealed around 1% nucleotide variations between these three types. The observed dissimilarity in COI sequences was possibly too little to consider these types as three different species. The derivation of amino acid positions indicated that these types could possibly be a complex of three cryptic species of C. karachiensis. The study proposes that the Oman and Indian populations of C. karachiensis might have derived by allopatric speciation due to geographical isolation. The group of these three cryptic species, sharing same habitat between themselves, possibly showed sympatric speciation.

  10. 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.

  11. Maxwell superalgebras and Abelian semigroup expansion

    Energy Technology Data Exchange (ETDEWEB)

    Concha, P.K.; Rodríguez, E.K. [Departamento de Física, Universidad de Concepción, Casilla 160-C, Concepción (Chile); Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Torino, Via Pietro Giuria, 1, 10125 Torino (Italy)

    2014-09-15

    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{sup (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 sM{sub m+2} and their N-extended generalization can be obtained using the S-expansion procedure.

  12. 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.

  13. 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.

  14. Abnormally activated one-carbon metabolic pathway is associated with mtDNA hypermethylation and mitochondrial malfunction in the oocytes of polycystic gilt ovaries

    OpenAIRE

    Longfei Jia; Juan Li; Bin He; Yimin Jia; Yingjie Niu; Chenfei Wang; Ruqian Zhao

    2016-01-01

    Polycystic ovarian syndrome (PCOS) is associated with hyperhomocysteinemia and polycystic ovaries (PCO) usually produce oocytes of poor quality. However, the intracellular mechanism linking hyperhomocysteinemia and oocyte quality remains elusive. In this study, the quality of the oocytes isolated from healthy and polycystic gilt ovaries was evaluated in vitro in association with one-carbon metabolism, mitochondrial DNA (mtDNA) methylation, and mitochondrial function. PCO oocytes demonstrated ...

  15. 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.

  16. 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.

  17. A novel frameshift mutation of the mtDNA COIII gene leads to impaired assembly of cytochrome c oxidase in a patient affected by Leigh-like syndrome.

    Science.gov (United States)

    Tiranti, V; Corona, P; Greco, M; Taanman, J W; Carrara, F; Lamantea, E; Nijtmans, L; Uziel, G; Zeviani, M

    2000-11-01

    We report on a novel frameshift mutation in the mtDNA gene encoding cytochrome c oxidase (COX) subunit III. The proband is an 11-year-old girl with a negative family history and an apparently healthy younger brother. Since 4 years of age, she has developed a progressive spastic paraparesis associated with ophthalmoparesis and moderate mental retardation. The presence of severe lactic acidosis and Leigh-like lesions of putamina prompted us to perform muscle and skin biopsies. In both, a profound, isolated defect of COX was found by histochemical and biochemical assays. Sequence analysis of muscle mtDNA resulted in the identification of a virtually homoplasmic frameshift mutation in the COIII gene, due to the insertion of an extra C at nucleotide position 9537 of mtDNA. Although the 9537C(ins) does not impair transcription of COIII, no full-length COX III protein was detected in mtDNA translation assays in vivo. Western blot analysis of two-dimensional blue-native electrophoresis showed a reduction of specific crossreacting material and the accumulation of early-assembly intermediates of COX, whereas the fully assembled complex was absent. One of these intermediates had an electrophoretic mobility different from those seen in controls, suggesting the presence of a qualitative abnormality of COX assembly. Immunostaining with specific antibodies failed to detect the presence of several smaller subunits in the complex lacking COX III, in spite of the demonstration that these subunits were present in the crude mitochondrial fraction of patient's cultured fibroblasts. Taken together, the data indicate a role for COX III in the incorporation and maintenance of smaller COX subunits within the complex.

  18. CANCERIZATION OF CUTANEOUS FLAP RECONSTRUCTION FOR ORAL SQUAMOUS CELL CARCINOMA: REPORT OF THREE CASES STUDIED WITH THE mtDNA D-LOOP SEQUENCE ANALYSIS

    OpenAIRE

    Foschini, Maria Pia; Morandi, Luca; Marchetti, Claudio; Cocchi, Roberto; Eusebi, Leonardo Henry; Farnedi, Anna; Badiali, Giovanni; Gissi, Davide Bartolomeo; Pennesi, Maria Gabriella; Montebugnoli, Lucio

    2011-01-01

    Abstract Aims: tissue defects, resulting from surgical resection of oral squamous cell carcinoma (OSCC), are routinely reconstructed with skin graft. OSCC arising from the grafted skin have been described, however, it is still unclear whether primary and second tumours have a common clonal origin. By screening mitochondrial DNA D-loop region (mtDNA), we evaluated the clonal relationship between the primary OSCC and the second neoplastic features appearing in the skin graft in three...

  19. 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.

  20. 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

    OpenAIRE

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

    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 detectin...

  1. Mesenchymal stem cells transfer mitochondria to the cells with virtually no mitochondrial function but not with pathogenic mtDNA mutations.

    Science.gov (United States)

    Cho, Young Min; Kim, Ju Han; Kim, Mingoo; Park, Su Jin; Koh, Sang Hyeok; Ahn, Hyo Seop; Kang, Gyeong Hoon; Lee, Jung-Bin; Park, Kyong Soo; Lee, Hong Kyu

    2012-01-01

    It has been reported that human mesenchymal stem cells (MSCs) can transfer mitochondria to the cells with severely compromised mitochondrial function. We tested whether the reported intercellular mitochondrial transfer could be replicated in different types of cells or under different experimental conditions, and tried to elucidate possible mechanism. Using biochemical selection methods, we found exponentially growing cells in restrictive media (uridine(-) and bromodeoxyuridine [BrdU](+)) during the coculture of MSCs (uridine-independent and BrdU-sensitive) and 143B-derived cells with severe mitochondrial dysfunction induced by either long-term ethidium bromide treatment or short-term rhodamine 6G (R6G) treatment (uridine-dependent but BrdU-resistant). The exponentially growing cells had nuclear DNA fingerprint patterns identical to 143B, and a sequence of mitochondrial DNA (mtDNA) identical to the MSCs. Since R6G causes rapid and irreversible damage to mitochondria without the removal of mtDNA, the mitochondrial function appears to be restored through a direct transfer of mitochondria rather than mtDNA alone. Conditioned media, which were prepared by treating mtDNA-less 143B ρ(0) cells under uridine-free condition, induced increased chemotaxis in MSC, which was also supported by transcriptome analysis. Cytochalasin B, an inhibitor of chemotaxis and cytoskeletal assembly, blocked mitochondrial transfer phenomenon in the above condition. However, we could not find any evidence of mitochondrial transfer to the cells harboring human pathogenic mtDNA mutations (A3243G mutation or 4,977 bp deletion). Thus, the mitochondrial transfer is limited to the condition of a near total absence of mitochondrial function. Elucidation of the mechanism of mitochondrial transfer will help us create a potential cell therapy-based mitochondrial restoration or mitochondrial gene therapy for human diseases caused by mitochondrial dysfunction.

  2. Mesenchymal stem cells transfer mitochondria to the cells with virtually no mitochondrial function but not with pathogenic mtDNA mutations.

    Directory of Open Access Journals (Sweden)

    Young Min Cho

    Full Text Available It has been reported that human mesenchymal stem cells (MSCs can transfer mitochondria to the cells with severely compromised mitochondrial function. We tested whether the reported intercellular mitochondrial transfer could be replicated in different types of cells or under different experimental conditions, and tried to elucidate possible mechanism. Using biochemical selection methods, we found exponentially growing cells in restrictive media (uridine(- and bromodeoxyuridine [BrdU](+ during the coculture of MSCs (uridine-independent and BrdU-sensitive and 143B-derived cells with severe mitochondrial dysfunction induced by either long-term ethidium bromide treatment or short-term rhodamine 6G (R6G treatment (uridine-dependent but BrdU-resistant. The exponentially growing cells had nuclear DNA fingerprint patterns identical to 143B, and a sequence of mitochondrial DNA (mtDNA identical to the MSCs. Since R6G causes rapid and irreversible damage to mitochondria without the removal of mtDNA, the mitochondrial function appears to be restored through a direct transfer of mitochondria rather than mtDNA alone. Conditioned media, which were prepared by treating mtDNA-less 143B ρ(0 cells under uridine-free condition, induced increased chemotaxis in MSC, which was also supported by transcriptome analysis. Cytochalasin B, an inhibitor of chemotaxis and cytoskeletal assembly, blocked mitochondrial transfer phenomenon in the above condition. However, we could not find any evidence of mitochondrial transfer to the cells harboring human pathogenic mtDNA mutations (A3243G mutation or 4,977 bp deletion. Thus, the mitochondrial transfer is limited to the condition of a near total absence of mitochondrial function. Elucidation of the mechanism of mitochondrial transfer will help us create a potential cell therapy-based mitochondrial restoration or mitochondrial gene therapy for human diseases caused by mitochondrial dysfunction.

  3. 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.

  4. Application of a west Eurasian-specific filter for quasi-median network analysis: Sharpening the blade for mtDNA error detection

    Science.gov (United States)

    Zimmermann, Bettina; Röck, Alexander; Huber, Gabriela; Krämer, Tanja; Schneider, Peter M.; Parson, Walther

    2011-01-01

    The application of quasi-median networks provides an effective tool to check the quality of mtDNA data. Filtering of highly recurrent mutations prior to network analysis is required to simplify the data set and reduce the complexity of the network. The phylogenetic background determines those mutations that need to be filtered. While the traditional EMPOPspeedy filter was based on the worldwide mtDNA phylogeny, haplogroup-specific filters can more effectively highlight potential errors in data of the respective (sub)-continental region. In this study we demonstrate the performance of a new, west Eurasian filter EMPOPspeedyWE for the fine-tuned examination of data sets belonging to macrohaplogroup N that constitutes the main portion of mtDNA lineages in Europe. The effects on the resulting network of different database sizes, high-quality and flawed data, as well as the examination of a phylogenetically distant data set, are presented by examples. The analyses are based on a west Eurasian etalon data set that was carefully compiled from more than 3500 control region sequences for network purposes. Both, etalon data and the new filter file, are provided through the EMPOP database (www.empop.org). PMID:21067984

  5. 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.

  6. 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.

  7. mtDNA COI和ND5基因用于鉴别常见嗜尸性蝇类%Application of mtDNA COI and ND5 genes in the identification of common necrophagous flies

    Institute of Scientific and Technical Information of China (English)

    杨静波; 姜建军; 王江峰

    2012-01-01

    目的 对蝇类mtDNA 523bp COI和347bp ND5基因片段进行序列分析,评价其在以嗜尸性蝇类种属鉴定中应用的可行性.方法 从广州(广东省)、湛江(广东省)、韶关(广东省)、沈丘(河南省)及蜂蛹寨(四川省)采集7种嗜尸性蝇类标本,进行形态学种属鉴定,取其腹部肌肉提取DNA,利用基因特异性引物对线粒体COI、ND5基因进行PCR扩增,产物经纯化后进行测序,MEGA 3.0软件对DNA序列进行碱基组成、进化分歧率和系统发育分析.结果 进化分歧率ND5基因种内小于1.83%,种间大于2.62%;种间与种内进化分歧率范围间没有交叉;COI基因种间在0.48%~14.8%之间,种内在0.24% ~8.3%之间,种内进化分歧范围与种间进化分歧范围存在交叉.结论 ND5基因片段可在种水平有效鉴别常见嗜尸性蝇类,也可鉴别近缘种.而单独运用COI基因不能有效进行种属鉴定.%Objective In order to estimate their feasibility in the identification of necrophagous flies, the mitochondrial DNA (mtDNA) sequences of 523bp of the COI gene and 347bp of the ND5 gene were analyzed. Methods By use of entomological morphology we collected seven types of necrophagous flies from Guangzhou, Zhanjiang, Shaoguan, Guangdong province, Shenqiu, Henan province and Fengyongzhai, Sichuan province. After the DNA was extracted from the abdominal muscles of the flies, mtDNA COI and ND5 genes were amplified using sequence specific primers by PCR, and then the PCR products were purified and sequenced. The DNA sequence, genetic distance and systemic development were analyzed with MEGA3. 0 software. Results The evolutionary difference rate of ND5 gene is less than 1. 83% intraspeciesly, and is more than 2. 62% interspeciesly, which indicates no cross of the two ranges, whereas the evolutionary difference rate of COI gene is between 0.48% and 14.8% intraspeciesly, and is between 0.24% and 8.3% interspeciesly, which shows that the ranges cross

  8. 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.

  9. 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.

  10. Expansion Techniques for Collisionless Stellar Dynamical Simulations

    CERN Document Server

    Meiron, Yohai; Holley-Bockelmann, Kelly; Spurzem, Rainer

    2014-01-01

    We present GPU implementations of two fast force calculation methods, based on series expansions of the Poisson equation. One is the Self-Consistent Field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other is the Multipole Expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field method and optimized for collisionless galactic dynamics, but while SCF is a "pure" expansion, MEX is an expansion in just the angular part; it is thus capable of capturing radial structure easily, where SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took...

  11. Giant negative thermal expansion in magnetic nanocrystals.

    Science.gov (United States)

    Zheng, X G; Kubozono, H; Yamada, H; Kato, K; Ishiwata, Y; Xu, C N

    2008-12-01

    Most solids expand when they are heated, but a property known as negative thermal expansion has been observed in a number of materials, including the oxide ZrW2O8 (ref. 1) and the framework material ZnxCd1-x(CN)2 (refs 2,3). This unusual behaviour can be understood in terms of low-energy phonons, while the colossal values of both positive and negative thermal expansion recently observed in another framework material, Ag3[Co(CN)6], have been explained in terms of the geometric flexibility of its metal-cyanide-metal linkages. Thermal expansion can also be stopped in some magnetic transition metal alloys below their magnetic ordering temperature, a phenomenon known as the Invar effect, and the possibility of exploiting materials with tuneable positive or negative thermal expansion in industrial applications has led to intense interest in both the Invar effect and negative thermal expansion. Here we report the results of thermal expansion experiments on three magnetic nanocrystals-CuO, MnF2 and NiO-and find evidence for negative thermal expansion in both CuO and MnF2 below their magnetic ordering temperatures, but not in NiO. Larger particles of CuO and MnF2 also show prominent magnetostriction (that is, they change shape in response to an applied magnetic field), which results in significantly reduced thermal expansion below their magnetic ordering temperatures; this behaviour is not observed in NiO. We propose that the negative thermal expansion effect in CuO (which is four times larger than that observed in ZrW2O8) and MnF2 is a general property of nanoparticles in which there is strong coupling between magnetism and the crystal lattice.

  12. 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.

  13. 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.

  14. 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...

  15. Does cosmological expansion affect local physics?

    CERN Document Server

    Giulini, Domenico

    2013-01-01

    In this contribution I wish to address the question whether, and how, the global cosmological expansion influences local physics. I argue that a pseudo Newtonian picture can be quite accurate if ``expansion'' is taken to be an attribute of the inertial structure rather than of ``space'' in some substantivalist sense. This contradicts the often-heard suggestion to imagine cosmological expansion as that of ``space itself''. Regarding General Relativity, I emphasise the need for proper geometric characterisations in order to meaningfully compare localised systems in different spacetimes, like black holes in static and expanding environments. Examples of this sort are discussed in some detail to clearly map out the problems.

  16. 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.

  17. 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.

  18. mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Brantacanadensis).

    Science.gov (United States)

    Paxinos, Ellen E; James, Helen F; Olson, Storrs L; Sorenson, Michael D; Jackson, Jennifer; Fleischer, Robert C

    2002-02-05

    Phylogenetic analysis of 1.35 kb of mtDNA sequence from fossils revealed a previously unknown radiation of Hawaiian geese, of which only one representative remains alive (the endangered Hawaiian goose or nene, Branta sandvicensis). This radiation is nested phylogenetically within a living species, the Canada goose (Branta canadensis) and is related most closely to the large-bodied lineage within that species. The barnacle goose (Branta leucopsis) is also nested within the Canada goose species and is related most closely to the small-bodied lineage of Canada geese. The peripheral isolation of the barnacle goose in the Palearctic apparently allowed the evolution of its distinctive plumage pattern, whereas the two Nearctic lineages of Canada geese share a primitive plumage pattern. The Hawaiian lineage of Canada geese diverged more dramatically, splitting into at least three species that differ in body size, body proportions, and flight ability. One fossil species, limited to the island of Hawaii, was related closely to the nene but was over four times larger, flightless, heavy-bodied and had a much more robust cranium. Application of a rate calibration to levels of DNA divergence suggests that this species evolved on the island of Hawaii in less than 500,000 years. This date is consistent with the potassium/argon-based age of the island of Hawaii of 430,000-500,000 years. The giant Hawaii goose resembles the moa-nalos, a group of massive, extinct, flightless ducks that lived on older Hawaiian Islands and thus is an example of convergent evolution of similar morphologies in island ecosystems.

  19. 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.

  20. Dynamics and phylogenetic implications of MtDNA control region sequences in New World Jays (Aves: Corvidae).

    Science.gov (United States)

    Saunders, M A; Edwards, S V

    2000-08-01

    To study the evolution of mtDNA and the intergeneric relationships of New World Jays (Aves: Corvidae), we sequenced the entire mitochondrial DNA control region (CR) from 21 species representing all genera of New World jays, an Old World jay, crows, and a magpie. Using maximum likelihood methods, we found that both the transition/transversion ratio (kappa) and among site rate variation (alpha) were higher in flanking domains I and II than in the conserved central domain and that the frequency of indels was highest in domain II. Estimates of kappa and alpha were much more influenced by the density of taxon sampling than by alternative optimal tree topologies. We implemented a successive approximation method incorporating these parameters into phylogenetic analysis. In addition we compared our study in detail to a previous study using cytochrome b and morphology to examine the effect of taxon sampling, evolutionary rates of genes, and combined data on tree resolution. We found that the particular weighting scheme used had no effect on tree topology and little effect on tree robustness. Taxon sampling had a significant effect on tree robustness but little effect on the topology of the best tree. The CR data set differed nonsignificantly from the tree derived from the cytochrome b/morphological data set primarily in the placement of the genus Gymnorhinus, which is near the base of the CR tree. However, contrary to conventional taxonomy, the CR data set suggested that blue and black jays (Cyanocorax sensu lato) might be paraphyletic and that the brown jay Psilorhinus (=Cyanocorax) morio is the sister group to magpie jays (Calocitta), a phylogenetic hypothesis that is likely as parsimonious with regard to nonmolecular characters as monophyly of Cyanocorax. The CR tree also suggests that the common ancestor of NWJs was likely a cooperative breeder. Consistent with recent systematic theory, our data suggest that DNA sequences with high substitution rates such as the CR may

  1. The earliest settlers' antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage

    Directory of Open Access Journals (Sweden)

    Kotal M

    2008-08-01

    Full Text Available Abstract Background The "out of Africa" model postulating single "southern route" dispersal posits arrival of "Anatomically Modern Human" to Indian subcontinent around 66–70 thousand years before present (kyBP. However the contributions and legacy of these earliest settlers in contemporary Indian populations, owing to the complex past population dynamics and later migrations has been an issue of controversy. The high frequency of mitochondrial lineage "M2" consistent with its greater age and distribution suggests that it may represent the phylogenetic signature of earliest settlers. Accordingly, we attempted to re-evaluate the impact and contribution of earliest settlers in shaping the genetic diversity and structure of contemporary Indian populations; using our newly sequenced 72 and 4 published complete mitochondrial genomes of this lineage. Results The M2 lineage, harbouring two deep rooting subclades M2a and M2b encompasses approximately one tenth of the mtDNA pool of studied tribes. The phylogeographic spread and diversity indices of M2 and its subclades among the tribes of different geographic regions and linguistic phyla were investigated in detail. Further the reconstructed demographic history of M2 lineage as a surrogate of earliest settlers' component revealed that the demographic events with pronounced regional variations had played pivotal role in shaping the complex net of populations phylogenetic relationship in Indian subcontinent. Conclusion Our results suggest that tribes of southern and eastern region along with Dravidian and Austro-Asiatic speakers of central India are the modern representatives of earliest settlers of subcontinent. The Last Glacial Maximum aridity and post LGM population growth mechanised some sort of homogeneity and redistribution of earliest settlers' component in India. The demic diffusion of agriculture and associated technologies around 3 kyBP, which might have marginalized hunter-gatherer, is

  2. High Falls generation station expansion approvals process

    Energy Technology Data Exchange (ETDEWEB)

    Litschko, C. [Lakeland Holding, Bracebridge, ON (Canada)

    2005-07-01

    Lakeland Holding Ltd. is the parent company for Lakeland Power Distribution Ltd., Bracebridge Generation Ltd., and Lakeland Energy Ltd. This PowerPoint presentation highlighted the High Falls generation expansion process. During construction of the High Falls plant, a concrete foundation was built beside the plant for future expansion. The expansion process involves building a 1,500 kilowatt generator to supply electricity to as many as 1600 households. The presentation described the context and background for the expansion and presented information on the water power generation plants. It presented site specifications as well as the approvals process by which final approval was granted in 2004. Observations and lessons learned from the approval process were identified. figs.

  3. Collisional and collisionless expansion of Yukawa balls.

    Science.gov (United States)

    Piel, Alexander; Goree, John A

    2013-12-01

    The expansion of Yukawa balls is studied by means of molecular dynamics simulations of collisionless and collisional situations. High computation speed was achieved by using the parallel computing power of graphics processing units. When the radius of the Yukawa ball is large compared to the shielding length, the expansion process starts with the blow-off of the outermost layer. A rarefactive wave subsequently propagates radially inward at the speed of longitudinal phonons. This mechanism is fundamentally different from Coulomb explosions, which employ a self-similar expansion of the entire system. In the collisionless limit, the outer layers carry away most of the available energy. The simulations are compared with analytical estimates. In the collisional case, the expansion process can be described by a nonlinear diffusion equation that is a special case of the porous medium equation.

  4. 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.

  5. An effective theory of accelerated expansion

    CERN Document Server

    Jimenez, Raul; Verde, Licia

    2011-01-01

    We work out an effective theory of accelerated expansion to describe general phenomena of inflation and acceleration (dark energy) in the Universe. Our aim is to determine from theoretical grounds, in a physically-motivated and model independent way, which and how many (free) parameters are needed to broadly capture the physics of a theory describing cosmic acceleration. Our goal is to make as much as possible transparent the physical interpretation of the parameters describing the expansion. We show that, at leading order, there are five independent parameters, of which one can be constrained via general relativity tests. The other four parameters need to be determined by observing and measuring the cosmic expansion rate only, H(z). Therefore we suggest that future cosmology surveys focus on obtaining an accurate as possible measurement of $H(z)$ to constrain the nature of accelerated expansion (dark energy and/or inflation).

  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. Cluster expansion in the canonical ensemble

    CERN Document Server

    Pulvirenti, Elena

    2011-01-01

    We consider a system of particles confined in a box $\\La\\subset\\R^d$ interacting via a tempered and stable pair potential. We prove the validity of the cluster expansion for the canonical partition function in the high temperature - low density regime. The convergence is uniform in the volume and in the thermodynamic limit it reproduces Mayer's virial expansion providing an alternative and more direct derivation which avoids the deep combinatorial issues present in the original proof.

  8. Index calculation by means of harmonic expansion

    CERN Document Server

    Imamura, Yosuke

    2015-01-01

    We review derivation of superconformal indices by means of supersymmetric localization and spherical harmonic expansion for 3d N=2, 4d N=1, and 6d N=(1,0) supersymmetric gauge theories. We demonstrate calculation of indices for vector multiplets in each dimensions by analysing energy eigenmodes in S^pxR. For the 6d index we consider the perturbative contribution only. We put focus on technical details of harmonic expansion rather than physical applications.

  9. 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.

  10. 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.

  11. Optimized $\\delta$ expansion for relativistic nuclear models

    CERN Document Server

    Krein, G I; Peres-Menezes, D; Nielsen, M; Pinto, M B

    1998-01-01

    The optimized $\\delta$-expansion is a nonperturbative approach for field theoretic models which combines the techniques of perturbation theory and the variational principle. This technique is discussed in the $\\lambda \\phi^4$ model and then implemented in the Walecka model for the equation of state of nuclear matter. The results obtained with the $\\delta$ expansion are compared with those obtained with the traditional mean field, relativistic Hartree and Hartree-Fock approximations.

  12. 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.)

  13. 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.

  14. 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.

  15. 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.

  16. Fixed Point Theorems for Times Reasonable Expansive Mapping

    Directory of Open Access Journals (Sweden)

    Chen Chunfang

    2008-01-01

    Full Text Available Abstract Based on previous notions of expansive mapping, times reasonable expansive mapping is defined. The existence of fixed point for times reasonable expansive mapping is discussed and some new results are obtained.

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

    Science.gov (United States)

    Takenaka, Koshi

    2012-02-01

    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 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.

  18. 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.

  19. The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers.

    Science.gov (United States)

    Andrews, Kimberly R; Perrin, William F; Oremus, Marc; Karczmarski, Leszek; Bowen, Brian W; Puritz, Jonathan B; Toonen, Robert J

    2013-05-01

    The susceptibility of the Y chromosome to sexual selection may make this chromosome an important player in the formation of reproductive isolating barriers, and ultimately speciation. Here, we investigate the role of the Y chromosome in phenotypic divergence and reproductive isolation of spinner dolphin (Stenella longirostris) ecotypes. This species contains six known ecotypes (grouped into four subspecies) that exhibit striking differences in morphology, habitat and mating system, despite having adjacent or overlapping ranges and little genetic divergence at previously studied mtDNA and autosomal markers. We examined the phylogeographic structure for all six ecotypes across the species range (n = 261, 17 geographic locations) using DNA sequences from three Y chromosome markers, two maternally inherited mitochondrial (mtDNA) markers, and a biparentally inherited autosomal intron. mtDNA and autosomal analyses revealed low divergence (most Φ(ST) values <0.1) between ecotypes and geographic regions, concordant with previous studies. In contrast, Y intron analyses revealed fixed differences amongst the three most phenotypically divergent groups: S. l. longirostris vs. S. l. roseiventris vs. combined S. l. orientalis/S. l. centroamericana/Tres Marias ecotypes). Another ecotype (whitebelly), previously postulated to be a hybrid between the two phenotypically most divergent ecotypes, had Y haplotypes from both putative parent ecotypes, supporting a hybrid designation. Reduced introgression of the Y chromosome has previously been observed in other organisms ranging from insects to terrestrial mammals, and here we demonstrate this phenomenon in a marine mammal with high dispersal capabilities. These results indicate that reduced introgression of the Y chromosome occurs in a wide taxonomic range of organisms and support the growing body of evidence that rapid evolution of the Y chromosome is important in evolutionary diversification.

  20. Base composition at mtDNA boundaries suggests a DNA triple helix model for human mitochondrial DNA large-scale rearrangements.

    Science.gov (United States)

    Rocher, Christophe; Letellier, Thierry; Copeland, William C; Lestienne, Patrick

    2002-06-01

    Different mechanisms have been proposed to account for mitochondrial DNA (mtDNA) instability based on the presence of short homologous sequences (direct repeats, DR) at the potential boundaries of mtDNA rearrangements. Among them, slippage-mispairing of the replication complex during the asymmetric replication cycle of the mammalian mitochondrial DNA has been proposed to account for the preferential localization of deletions. This mechanism involves a transfer of the replication complex from the first neo-synthesized heavy (H) strand of the DR1, to the DR2, thus bypassing the intervening sequence and producing a deleted molecule. Nevertheless, the nature of the bonds between the DNA strands remains unknown as the forward sequence of DR2, beyond the replication complex, stays double-stranded. Here, we have analyzed the base composition of the DR at the boundaries of mtDNA deletions and duplications and found a skewed pyrimidine content of about 75% in the light-strand DNA template. This suggests the possible building of a DNA triple helix between the G-rich neo-synthesized DR1 and the base-paired homologous G.C-rich DR2. In vitro experiments with the purified human DNA polymerase gamma subunits enabled us to show that the third DNA strand may be used as a primer for DNA replication, using a template with the direct repeat forming a hairpin, with which the primer could initiate DNA replication. These data suggest a novel molecular basis for mitochondrial DNA rearrangements through the distributive nature of the DNA polymerase gamma, at the level of the direct repeats. A general model accounting for large-scale mitochondrial DNA deletion and duplication is proposed. These experiments extend to a DNA polymerase from an eucaryote source the use of a DNA triple helix strand as a primer, like other DNA polymerases from phage and bacterial origins.

  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. 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.

  3. 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).

  4. GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

    Directory of Open Access Journals (Sweden)

    Sudarto Sudarto

    2008-12-01

    Full Text Available Research on genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra, based on sequencing gene of mtDNA Cytochrome b and nucleus DNA RAG2 has been done. The objectives of the study were to obtain the representation of genetic differentiation among population of clown loach fishes or botia (Chromobotia macracanthus from Sumatra and Kalimantan and to estimate the time divergence of both population group of botia. Samples of botia population were taken from 3 rivers in Sumatra namely Batanghari, Musi, and Tulang Bawang and one river from Kalimantan namely Kapuas. The genetic analysis was based on the sequencing of mtDNA Cytochrome b and nucleus DNA RAG2. The statistical analysis was done by using APE package on R language. The parameters observed were: nucleotide diversity, genetic distance, and neighbor-joining tree. The result showed that the highest nucleotide diversity was fish population of Musi, while the other two populations, Tulang Bawang (Sumatra and Kapuas (Kalimantan, were considered as the lowest genetic diversity especially based on nucleus DNA RAG2 sequencing. Based on mtDNA Cytochrome-b sequencing, the most distinct population among those populations based on genetic distance were fish populations of Musi and Kapuas. According to the result of neighbor-joining tree analysis, the populations of botia were classified into two groups namely group of Sumatra and group of Kalimantan. The estimation of time divergence among group of population of Sumatra and Kalimantan based on mtDNA Cytochrome b was about 9.25—9.46 million years (Miocene era. The high genetic differences between groups of Sumatra and Kalimantan suggested that the effort of restocking botia from Sumatra into Kalimantan has to be done carefully, because it may disturb the gene originality of both botia populations.

  5. 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

  6. 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.

  7. [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.

  8. MODIFIED PERIODONTAL EXPLORER FOR EXPANSION SCREW ACTIVATION

    Directory of Open Access Journals (Sweden)

    Srinivasan

    2012-08-01

    Full Text Available INTRODUCTION: Accidents with expansion screw activation keys are r eported in the literature 1,2 . A simple method to prevent such accident is to use a modified periodontal explorer as a key for expansion screw activation. A no.17 per iodontal explorer (fig 1 is cut at its first terminal bend (fig 2. The second section is bent m ore vertically to the long axis of the shaft (fig 3. This part which is tapered and stiff enough to ac tivate the screw is tried extra orally into the screw. It is further trimmed in such a way that onl y a mm of instrument can project through the screw hole (fig 4. Now a safe key for activating t he maxillary expansion screw is ready to use (fig 5. Once the patient’s parent or guardian succes sfully repeat the activation procedure in office, the instrument can be given to them for hom e use

  9. Cosmological Constant, Quintessence and Expansive Nondecelerative Universe

    CERN Document Server

    Sima, J; Sima, Jozef; Sukenik, Miroslav

    2001-01-01

    Recent observations of the Universe have led to a conclusion suppressing an up-to-now supposed deceleration of the Universe caused by attractive gravitational forces. Contrary, there is a renaissance of the cosmological member lambda and introduction of enigmatic repulsive dark energy in attempts to rationalize a would-be acceleration of the Universe expansion. It is documented that the model of Expansive Nondecelerative Universe is capable to offer acceptable answers to the questions on the Universe expansion, state equations of the Universe, the parameter omega, the cosmological member lambda without any necessity to introduce new strange kinds of matter or energy being in accord with the fundamental conservation laws and generally accepted parameters of the Universe.

  10. 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...

  11. Does cosmological expansion affect local physics?

    Science.gov (United States)

    Giulini, Domenico

    2014-05-01

    In this contribution I wish to address the question whether, and how, the global cosmological expansion influences local physics, like particle orbits and black hole geometries. Regarding the former I argue that a pseudo Newtonian picture can be quite accurate if "expansion" is taken to be an attribute of the inertial structure rather than of "space" in some substantivalist sense. This contradicts the often-heard suggestion to imagine cosmological expansion as that of "space itself". Regarding isolated objects in full General Relativity, like black holes, I emphasise the need for proper geometric characterisations in order to meaningfully compare them in different spacetimes, like static and expanding ones. Examples are discussed in some detail to clearly map out the problems. A slightly extended version of this contribution may be found at philsci-archive.pitt.edu/10033.

  12. 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.

  13. 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.

  14. Towards finite density QCD with Taylor expansions

    CERN Document Server

    Karsch, Frithjof; Wagner, Mathias; Wambach, Jochen

    2011-01-01

    We analyze general convergence properties of the Taylor expansion of observables to finite chemical potential in the framework of an effective 2+1 flavor Polyakov-quark-meson model. To compute the required higher order coefficients a novel technique based on algorithmic differentiation has been developed. Results for thermodynamic observables as well as the phase structure obtained through the series expansion up to 24th order are compared to the full model solution at finite chemical potential. The available higher order coefficients also allow for resummations, e.g. Pade series, which improve the convergence behavior. In view of our results we discuss the prospects for locating the QCD phase boundary and a possible critical endpoint with the Taylor expansion method.

  15. 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.

  16. Radial expansion for spinning conformal blocks

    CERN Document Server

    Costa, Miguel; 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.

  17. 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.

  18. Geometrization of spin systems using cycle expansions

    CERN Document Server

    Mainieri, R

    1995-01-01

    It is shown that a spin system with long range interactions can be converted into a chaotic dynamical system that is differentiable and low-dimensional. The thermodynamic limit of the spin system is then equivalent to studying the long term behavior of the dynamical system. Cycle expansions of chaotic systems (expansion of the Fredholm determinant) are then used to study the thermodynamic limit. By considering the smooth dynamical system, it is possible to converge to the thermodynamic limit faster than with transfer matrices.

  19. Air expansion in the water rocket

    CERN Document Server

    Romanelli, Alejandro; Madina, Federico González

    2012-01-01

    We study the thermodynamics of the water rocket in the thrust phase, taking into account the expansion of the air with water vapor, vapor condensation and the energy taken from the environment. We set up a simple experimental device with a stationary bottle and verified that the gas expansion in the bottle is well approximated by a polytropic process $PV^\\beta$= constant, where the parameter $\\beta$ depends on the initial conditions. We find an analytical expression for $\\beta $ that only depends on the thermodynamic initial conditions and is in good agreement with the experimental results.

  20. 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.

  1. 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%....

  2. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Yang, Cheng; Madsen, Erik Skov

    2012-01-01

    . Design/methodology/approach – Two case studies are introduced. Empirical data were collected over a period of two years based on interviews and participating observations. Findings – The findings show that (1) knowledge transfer within the replication of a production line is a stepwise expansive process......Purpose – With the aim to support offshore production line replication, this paper specifically aims to explore the use of templates and principles to transfer expansive productive knowledge embedded in a production line and understand the contingencies that influence the mix of these approaches...... and principles to transfer productive knowledge in a specific context, which, in this paper, is a production line....

  3. 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.

  4. Expansion Coefficient on Oxides and Oxide Ceramics.

    Science.gov (United States)

    1986-05-01

    Ferroelectrics )," Ph.D. thesis submitted to the Indian Institute of Science, Bangalore- 12, (1969). 29. B. Alefeld. "The Change of Lattice Parameters of...Kamenetskii. "Anomalous Thermal Expansion of ZrO2 and HfO2 Over the Range 20-1200 0 C," Soy. Phy.-Cryst., 14 (1970) pp. 696-99. 89. A. K. Sreedhar. "Thermal...D. Gac. "Axial and Linear Thermal Expansion of ZrO 2 and HfO2 ," Am. Ceram. Soc. RuZl. 60(4) (1981), pp. 504-506. 167. R. Ruh, G. W. Hollenberg, E

  5. 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...... to reproduce ground state properties at low temperature and the non-interacting large temperature limit of constant virial coefficients. This resembles the smearing of shell effects in finite systems with increasing temperature. Numerical results are discussed for the second and third virial coefficients...

  6. On the Expansions in Spin Foam Cosmology

    CERN Document Server

    Hellmann, Frank

    2011-01-01

    We discuss the expansions used in spin foam cosmology. We point out that already at the one vertex level arbitrarily complicated amplitudes contribute, and discuss the geometric asymptotics of the five simplest ones. We discuss what type of consistency conditions would be required to control the expan- sion. We show that the factorisation of the amplitude originally considered is best interpreted in topological terms. We then consider the next higher term in the graph expansion. We demonstrate the tension between the truncation to small graphs and going to the homogeneous sector, and conclude that it is necessary to truncate the dynamics as well.

  7. Experimental Tests of Local Cosmological Expansion Rates

    CERN Document Server

    Widom, A; Srivastava, Y

    2015-01-01

    Cosmological expansion on a local scale is usually neglected in part due to its smallness, and in part due to components of bound systems (especially those bound by non-gravitational forces such as atoms and nuclei) not following the geodesics of the cosmological metric. However, it is interesting to ask whether or not experimental tests of cosmological expansion on a local scale (well within our own galaxy) might be experimentally accessible in some manner. We point out, using the Pioneer satellites as an example, that current satellite technology allows for this possibility within time scales of less than one human lifetime.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization.

    Science.gov (United States)

    García-Bour, Jaume; Pérez-Pérez, Alejandro; Alvarez, Sara; Fernández, Eva; López-Parra, Ana María; Arroyo-Pardo, Eduardo; Turbón, Daniel

    2004-04-01

    Ancient mtDNA was successfully recovered from 24 skeletal samples of a total of 60 ancient individuals from Patagonia-Tierra del Fuego, dated to 100-400 years BP, for which consistent amplifications and two-strand sequences were obtained. Y-chromosome STRs (DYS434, DYS437, DYS439, DYS393, DYS391, DYS390, DYS19, DYS389I, DYS389II, and DYS388) and the biallelic system DYS199 were also amplified, Y-STR alleles could be characterized in nine cases, with an average of 4.1 loci per sample correctly typed. In two samples of the same ethnic group (Aonikenk), an identical and complete eight-loci haplotype was recovered. The DYS199 biallelic system was used as a control of contamination by modern DNA and, along with DYS19, as a marker of American origin. The analysis of both mtDNA and Y-STRs revealed DNA from Amerindian ancestry. The observed polymorphisms are consistent with the hypothesis that the ancient Fuegians are close to populations from south-central Chile and Argentina, but their high nucleotide diversity and the frequency of single lineages strongly support early genetic differentiation of the Fuegians through combined processes of population bottleneck, isolation, and/or migration, followed by strong genetic drift. This suggests an early genetic diversification of the Fuegians right after their arrival at the southernmost extreme of South America.

  13. Genetic divergence and phylogenetic relationships in grey mullets (Teleostei: Mugilidae) based on PCR-RFLP analysis of mtDNA segments.

    Science.gov (United States)

    Papasotiropoulos, V; Klossa-Kilia, E; Kilias, G; Alahiotis, S

    2002-04-01

    The genetic differentiation and phylogenetic relationships among five species of the Mugilidae family (Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens) were investigated at the mtDNA level, on samples taken from Messolongi lagoon-Greece. RFLP analysis of three PCR-amplified mtDNA gene segments (12s rRNA, 16s rRNA, and CO I) was used. Ten, eight, and nine restriction enzymes were found to have at least one recognition site at 12s rRNA, 16s rRNA, and CO I genes, respectively. Several fragment patterns were revealed to be species-specific, and thus they could be useful in species taxonomy as diagnostic markers, as well as for further evolutionary studies. Seven different haplotypes were detected. The greatest amount of genetic differentiation was observed at the interspecific level, while little variation was revealed at the intraspecific level. The highest values of nucleotide sequence divergence were observed between M. cephalus and all the other species, while the lowest was found between C. labrosus and L. saliens. Dendrograms obtained by the three different methods (UPGMA, Neighbor-Joining, and Dollo parsimony), were found to exhibit in all cases the same topology. According to this, the most distinct species is M. cephalus, while the other species are clustered in two separate groups, thefirst one containing L. aurata and L. ramada, the other L. saliens and C. labrosus. This last clustering makes the monophyletic origin of the genus Liza questionable.

  14. 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.

  15. 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.

  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. Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

    Science.gov (United States)

    Sultana, H.; Seo, D. W.; Bhuiyan, M. S. A.; Choi, N. R.; Hoque, M. R.; Heo, K. N.; Lee, J. H.

    2016-01-01

    The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins. PMID:27004808

  18. 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.

  19. 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.

  20. 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.

  1. 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…

  2. 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.

  3. 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…

  4. 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.

  5. Toeplitz Quantization and Asymptotic Expansions: Geometric Construction

    Directory of Open Access Journals (Sweden)

    Miroslav Englis

    2009-02-01

    Full Text Available For a real symmetric domain G_R/K_R, with complexification G_C/K_C, we introduce the concept of ''star-restriction'' (a real analogue of the ''star-products'' for quantization of Kähler manifolds and give a geometric construction of the G_R-invariant differential operators yielding its asymptotic expansion.

  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. ENTRAINMENT AND EXPANSION CONTROLLED FIREBALL RISE

    Science.gov (United States)

    This paper reports on a detailed analysis of the buoyant rise of fireballs in the earth’s atmosphere. Formulae for the rise velocity and height, and...the density, mass, radius and expansion velocity of the fireball are given. The computation of fireball temperature is discussed in detail; no

  8. Platform Expansion Design as Strategic Choice

    DEFF Research Database (Denmark)

    Staykova, Kalina S.; Damsgaard, Jan

    2016-01-01

    the main characteristics of the two approaches and to identify the potential trade-offs associated with the selection of particular expansion mode. To this end, we construct the Platform Strategy Framework and apply it to two exemplary cases – WeChat, which functions as a feature bundling platform...

  9. 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.

  10. Thermal expansion anomaly regulated by entropy.

    Science.gov (United States)

    Liu, Zi-Kui; Wang, Yi; Shang, ShunLi

    2014-11-13

    Thermal expansion, defined as the temperature dependence of volume under constant pressure, is a common phenomenon in nature and originates from anharmonic lattice dynamics. However, it has been poorly understood how thermal expansion can show anomalies such as colossal positive, zero, or negative thermal expansion (CPTE, ZTE, or NTE), especially in quantitative terms. Here we show that changes in configurational entropy due to metastable micro(scopic)states can lead to quantitative prediction of these anomalies. We integrate the Maxwell relation, statistic mechanics, and first-principles calculations to demonstrate that when the entropy is increased by pressure, NTE occurs such as in Invar alloy (Fe3Pt, for example), silicon, ice, and water, and when the entropy is decreased dramatically by pressure, CPTE is expected such as in anti-Invar cerium, ice and water. Our findings provide a theoretic framework to understand and predict a broad range of anomalies in nature in addition to thermal expansion, which may include gigantic electrocaloric and electromechanical responses, anomalously reduced thermal conductivity, and spin distributions.

  11. 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.

  12. 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.

  13. Transmission network expansion planning under deliberate outages

    Energy Technology Data Exchange (ETDEWEB)

    Alguacil, Natalia; Carrion, Miguel; Arroyo, Jose Manuel [E.T.S. de Ingenieros Industriales, Universidad de Castilla - La Mancha, Campus Universitario s/n, 13071 Ciudad Real (Spain)

    2009-10-15

    The reasons why the transmission network is a potentially attractive target for deliberate outages are twofold: (i) its crucial importance as a critical infrastructure for the society welfare, and (ii) its high level of vulnerability due to the current operation close to its static and dynamic limits. This new context where destructive agents come into play has been recognized by several agencies in Europe and North America, and various initiatives have been launched worldwide in order to assess and mitigate the vulnerability of transmission. Within this framework, this paper proposes the reinforcement and expansion of the transmission network as a way of mitigating the impact of increasingly plausible deliberate outages. The network planner selects the new lines to be built accounting not only for economic issues, as traditionally done, but also for the vulnerability of the transmission network against a set of credible intentional outages. The resulting vulnerability- and economic-constrained transmission expansion planning problem is formulated as a mixed-integer linear program. A number of case studies numerically illustrate the tradeoff between economic- and vulnerability-related issues and its impact on the expansion plans. In addition, we compare the results with those achieved by a traditional expansion planning model based on cost minimization. (author)

  14. 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.

  15. 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...

  16. 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...... of length at most k:. term-RSE is the class of ring-sum-expansions having at most I: monomials. It is shown that k-RSE, k>or=1, is learnable while k-term-RSE, k>2, is not learnable if RPnot=NP. Without using a complexity-theoretical hypothesis, it is proven that k-RSE, k>or=1, and k-term-RSE, k>or=2 cannot...... 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...

  17. Causes and consequences of magnetic cloud expansion

    Science.gov (United States)

    Démoulin, P.; Dasso, S.

    2009-05-01

    Context: A magnetic cloud (MC) is a magnetic flux rope in the solar wind (SW), which, at 1 AU, is observed ~2-5 days after its expulsion from the Sun. The associated solar eruption is observed as a coronal mass ejection (CME). Aims: Both the in situ observations of plasma velocity distribution and the increase in their size with solar distance demonstrate that MCs are strongly expanding structures. The aim of this work is to find the main causes of this expansion and to derive a model to explain the plasma velocity profiles typically observed inside MCs. Methods: We model the flux rope evolution as a series of force-free field states with two extreme limits: (a) ideal magneto-hydrodynamics (MHD) and (b) minimization of the magnetic energy with conserved magnetic helicity. We consider cylindrical flux ropes to reduce the problem to the integration of ordinary differential equations. This allows us to explore a wide variety of magnetic fields at a broad range of distances to the Sun. Results: We demonstrate that the rapid decrease in the total SW pressure with solar distance is the main driver of the flux-rope radial expansion. Other effects, such as the internal over-pressure, the radial distribution, and the amount of twist within the flux rope have a much weaker influence on the expansion. We demonstrate that any force-free flux rope will have a self-similar expansion if its total boundary pressure evolves as the inverse of its length to the fourth power. With the total pressure gradient observed in the SW, the radial expansion of flux ropes is close to self-similar with a nearly linear radial velocity profile across the flux rope, as observed. Moreover, we show that the expansion rate is proportional to the radius and to the global velocity away from the Sun. Conclusions: The simple and universal law found for the radial expansion of flux ropes in the SW predicts the typical size, magnetic structure, and radial velocity of MCs at various solar distances.

  18. 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.

  19. 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.

  20. Thermal Expansion of Vacuum Plasma Sprayed Coatings

    Science.gov (United States)

    Raj, S V.; Palczer, A. R.

    2010-01-01

    Metallic Cu-8%Cr, Cu-26%Cr, Cu-8%Cr-1%Al, NiAl and NiCrAlY monolithic coatings were fabricated by vacuum plasma spray deposition processes for thermal expansion property measurements between 293 and 1223 K. The corrected thermal expansion, (DL/L(sub 0) varies with the absolute temperature, T, as (DL/L(sub 0) = A(T - 293)(sup 3) + BIT - 293)(sup 2) + C(T - 293) + D, where, A, B, C and D are thermal, regression constants. Excellent reproducibility was observed for all of the coatings except for data obtained on the Cu-8%Cr and Cu-26%Cr coatings in the first heat-up cycle, which deviated from those determined in the subsequent cycles. This deviation is attributed to the presence of residual stresses developed during the spraying of the coatings, which are relieved after the first heat-up cycle. In the cases of Cu-8%Cr and NiAl, the thermal expansion data were observed to be reproducible for three specimens. The linear expansion data for Cu-8% Cr and Cu-26%Cr agree extremely well with rule of mixture (ROM) predictions. Comparison of the data for the Cu-8%Cr coating with literature data for Cr and Cu revealed that the thermal expansion behavior of this alloy is determined by the Cu-rich matrix. The data for NiAl and NiCrAlY are in excellent agreement with published results irrespective of composition and the methods used for processing the materials. The implications of these results on coating GRCop-84 copper alloy combustor liners for reusable launch vehicles are discussed.

  1. Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America.

    Directory of Open Access Journals (Sweden)

    Benjamin Cinget

    Full Text Available The phylogeographic structure and postglacial history of balsam fir (Abies balsamea, a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA and chloroplast DNA (cpDNA markers. Genetic structure among 107 populations (mtDNA data and 75 populations (cpDNA data was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only, but also for cpDNA (dispersed by seeds and pollen, indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.

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

    OpenAIRE

    Piras, Daniela; Doro, Maria Grazia; Casu, Giuseppina; Melis, Paola Maria; Vaccargiu, Simona; Piras, Ignazio; Parracciani, Debora; Stradoni, Roberta; Frongia, Bruno; Lai, Graziano; Sale, Salvatore; Cattari, Walter; Piras, Roberto; Querci, Ombretta; Demuro, Piergiorgio

    2012-01-01

    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 oper...

  3. Tunable thermal expansion in framework materials through redox intercalation.

    Science.gov (United States)

    Chen, Jun; Gao, Qilong; Sanson, Andrea; Jiang, Xingxing; Huang, Qingzhen; Carnera, Alberto; Rodriguez, Clara Guglieri; Olivi, Luca; Wang, Lei; Hu, Lei; Lin, Kun; Ren, Yang; Lin, Zheshuai; Wang, Cong; Gu, Lin; Deng, Jinxia; Attfield, J Paul; Xing, Xianran

    2017-02-09

    Thermal expansion properties of solids are of fundamental interest and control of thermal expansion is important for practical applications but can be difficult to achieve. Many framework-type materials show negative thermal expansion when internal cages are empty but positive thermal expansion when additional atoms or molecules fill internal voids present. Here we show that redox intercalation offers an effective method to control thermal expansion from positive to zero to negative by insertion of Li ions into the simple negative thermal expansion framework material ScF3, doped with 10% Fe to enable reduction. The small concentration of intercalated Li ions has a strong influence through steric hindrance of transverse fluoride ion vibrations, which directly controls the thermal expansion. Redox intercalation of guest ions is thus likely to be a general and effective method for controlling thermal expansion in the many known framework materials with phonon-driven negative thermal expansion.

  4. Re-expansion method for circular waveguide discontinuities: Application to concentric expansion chambers

    Science.gov (United States)

    Homentcovschi, Dorel; Miles, Ronald N.

    2012-01-01

    The paper applies the re-expansion method for analyzing planar discontinuities at the junction of two axi-symmetrical circular waveguides. The normal modes in the two waveguides are expanded at the junction plane into a system of functions accounting for velocity singularities at the corner points. As the new expansion has a high convergence order, only a few terms have to be considered for obtaining the solution of most practical problems. This paper gives the equivalent impedance accounting for nonplanar waves into a plane-wave analysis and also the scattering matrix describing the coupling of arbitrary modes at each side of the discontinuity valid in the case of many propagating modes in both sides of the duct. The last section applies the re-expansion technique to some concentric expansion chambers providing an explicit formula for the transmission loss coefficient. PMID:22352491

  5. 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

  6. 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....

  7. 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 .

  8. 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.

  9. Development of new hole expansion testing method

    Science.gov (United States)

    Kim, Hyunok; Shang, Jianhui; Beam, Kevin; Samant, Anoop; Hoschouer, Cliff; Dykeman, Jim

    2016-08-01

    This paper introduces a new hole expansion (HE) testing method that could be more relevant to the edge cracking problem observed in stamping advanced high strength steel (AHSS). The new testing method adopted a large hole diameter of 75 mm compared to the standard hole diameter of 10 mm. An inline monitoring system was developed to visually monitor the hole edge cracking during the test and synchronize the load-displacement data with the recorded video for capturing the initial crack. A new hole expansion testing method was found to be effective in evaluating the edge cracking by considering the effects of material properties and trimming methods. It showed a much larger difference, up to 11%, of the HE ratio between DP980 and TRIP780 compared to the standard HE testing method giving less than a 2% difference.

  10. 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 ...

  11. 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.

  12. 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.

  13. Cosmic expansion in extended quasidilaton massive gravity

    Science.gov (United States)

    Kahniashvili, Tina; Kar, Arjun; Lavrelashvili, George; Agarwal, Nishant; Heisenberg, Lavinia; Kosowsky, Arthur

    2015-02-01

    Quasidilaton massive gravity offers a physically well-defined gravitational theory with nonzero graviton mass. We present the full set of dynamical equations governing the expansion history of the Universe, valid during radiation domination, matter domination, and a late-time self-accelerating epoch related to the graviton mass. The existence of self-consistent solutions constrains the amplitude of the quasidilaton field and the graviton mass, as well as other model parameters. We point out that the effective mass of gravitational waves can be significantly larger than the graviton mass, opening the possibility that a single theory can explain both the late-time acceleration of cosmic expansion and modifications of structure growth leading to the suppression of large-angle correlations observed in the cosmic microwave background.

  14. Cosmic Expansion in Extended Quasidilaton Massive Gravity

    CERN Document Server

    Kahniashvili, Tina; Lavrelashvili, George; Agarwal, Nishant; Heisenberg, Lavinia; Kosowsky, Arthur

    2014-01-01

    Quasidilaton massive gravity offers a physically well-defined gravitational theory with non-zero graviton mass. We present the full set of dynamical equations governing the expansion history of the universe, valid during radiation domination, matter domination, and a late-time self-accelerating epoch related to the graviton mass. The existence of self-consistent solutions constrains the amplitude of the quasi-dilaton field and the graviton mass, as well as other model parameters. We point out that the effective mass of gravitational waves can be significantly larger than the graviton mass, opening the possibility that a single theory can explain both the late-time acceleration of the cosmic expansion and modifications of structure growth leading to the suppression of large-angle correlations observed in the cosmic microwave background.

  15. 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.

  16. 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......Recuperated gas turbines are currently drawing an increased attention due to the recent commercialization of micro gas turbines with recuperation. This system may reach a high efficiency even for the small units of less than 100 kW. In order to improve the economics of the plants, ways to improve....... 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....

  17. 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.

  18. 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.

  19. Fourier series expansion for nonlinear Hamiltonian oscillators.

    Science.gov (United States)

    Méndez, Vicenç; Sans, Cristina; Campos, Daniel; Llopis, Isaac

    2010-06-01

    The problem of nonlinear Hamiltonian oscillators is one of the classical questions in physics. When an analytic solution is not possible, one can resort to obtaining a numerical solution or using perturbation theory around the linear problem. We apply the Fourier series expansion to find approximate solutions to the oscillator position as a function of time as well as the period-amplitude relationship. We compare our results with other recent approaches such as variational methods or heuristic approximations, in particular the Ren-He's method. Based on its application to the Duffing oscillator, the nonlinear pendulum and the eardrum equation, it is shown that the Fourier series expansion method is the most accurate.

  20. Nanoscale imaging of RNA with expansion microscopy.

    Science.gov (United States)

    Chen, Fei; Wassie, Asmamaw T; Cote, Allison J; Sinha, Anubhav; Alon, Shahar; Asano, Shoh; Daugharthy, Evan R; Chang, Jae-Byum; Marblestone, Adam; Church, George M; Raj, Arjun; Boyden, Edward S

    2016-08-01

    The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be covalently attached to a swellable polyelectrolyte gel synthesized throughout a biological specimen. Then, postexpansion, fluorescent in situ hybridization (FISH) imaging of RNA can be performed with high yield and specificity as well as single-molecule precision in both cultured cells and intact brain tissue. Expansion FISH (ExFISH) separates RNAs and supports amplification of single-molecule signals (i.e., via hybridization chain reaction) as well as multiplexed RNA FISH readout. ExFISH thus enables super-resolution imaging of RNA structure and location with diffraction-limited microscopes in thick specimens, such as intact brain tissue and other tissues of importance to biology and medicine.