Analisis Perbandingan Material Slab Beton Pada Perkerasan Apron Dengan Menggunakan Program Bantu Elemen Hingga

Directory of Open Access Journals (Sweden)

Hendrawan Setyo Warsito

2016-04-01

Full Text Available Kekuatan slab beton sangat dipengaruhi oleh jenis material yang dipakai. Jenis material yang dimaksud adalah material beton dengan menggunakan PC (Portland Cement dan penggunaan geopolimer dalam komposisi campuran slab beton. Beton geopolimer merupakan beton yang ramah lingkungan. Permasalahan lain yang timbul adalah letak roda pesawat tidak selalu berada pada titik yang sama disuatu permukaan slab beton apron. Pada tugas akhir ini dimaksudkan untuk menganalisis suatu slab beton yang dibebani roda pesawat dengan campuran variasi material beton dan variasi letak roda pesawat pada slab beton dengan program bantu metode elemen hingga. Dengan data pergerakan pesawat, spesifikasi apron bandara Juanda kondisi eksisting. Dilakukan perhitungan tebal slab beton menggunakan software FAARFIELD dan diperoleh tebal slab beton sebesar 442,5 mm. Dari analisis program bantu elemen hingga dapat diperoleh tegangan pada slab beton yang ditimbulkan oleh pembebanan roda pesawat. Hasil validasi dari analisis tegangan menggunakan program bantu elemen hingga dengan analisis Westergaard yaitu memiliki nilai tegangan yang hampir sama pada ketebalan slab beton 450mm. Nilai tegangan tiap-tiap material beton menunjukan nilai tebal slab beton yang diijinkan untuk tipe pesawat tertentu. Dari analisis menggunakan program bantu elemen hingga tebal slab beton yang diijinkan untuk material slab beton PC yaitu sebesar 425mm. Sedangkan untuk material beton geopolimer yaitu sebesar  415 mm.

Insulin Secretion in Bantu with Siderosis or Hepatoma*

African Journals Online (AJOL)

1971-08-14

Aug 14, 1971 ... Department of Physiology, Medical School, University of Pretoria. SUMMARY. The IR and concomitant GTC was evaluated in 10 siderotic. Bantu patients and ... most probably to significant low deposits in the pancreas. A similar relatively low IR in the presence of elevated blood glucose levels was found in ...

Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

Directory of Open Access Journals (Sweden)

Sarit Suissa

2009-05-01

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

mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory.

Science.gov (United States)

Atkinson, Quentin D; Gray, Russell D; Drummond, Alexei J

2008-02-01

The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.

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

Science.gov (United States)

Badro, Danielle A; Douaihy, Bouchra; Haber, Marc; Youhanna, Sonia C; Salloum, Angélique; Ghassibe-Sabbagh, Michella; Johnsrud, Brian; Khazen, Georges; Matisoo-Smith, Elizabeth; Soria-Hernanz, David F; Wells, R Spencer; Tyler-Smith, Chris; Platt, Daniel E; Zalloua, Pierre A

2013-01-01

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.

A Phenotype-Driven Approach to Generate Mouse Models with Pathogenic mtDNA Mutations Causing Mitochondrial Disease

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Johanna H.K. Kauppila

2016-09-01

Full Text Available Mutations of mtDNA are an important cause of human disease, but few animal models exist. Because mammalian mitochondria cannot be transfected, the development of mice with pathogenic mtDNA mutations has been challenging, and the main strategy has therefore been to introduce mutations found in cell lines into mouse embryos. Here, we describe a phenotype-driven strategy that is based on detecting clonal expansion of pathogenic mtDNA mutations in colonic crypts of founder mice derived from heterozygous mtDNA mutator mice. As proof of concept, we report the generation of a mouse line transmitting a heteroplasmic pathogenic mutation in the alanine tRNA gene of mtDNA displaying typical characteristics of classic mitochondrial disease. In summary, we describe a straightforward and technically simple strategy based on mouse breeding and histology to generate animal models of mtDNA-mutation disease, which will be of great importance for studies of disease pathophysiology and preclinical treatment trials.

Pembuatan Kakas Bantu untuk Mendeteksi Ketidaksesuaian Diagram Urutan (Sequence Diagram dengan Diagram Kasus Penggunaan (Use Case Diagram

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Andrias Meisyal Yuwantoko

2017-03-01

Full Text Available Sebuah diagram urutan dibuat  berdasarkan alur yang ada pada deskripsi kasus penggunaan. Alur tersebut dire- presentasikan dalam  bentuk  interaksi antara aktor  dan  sistem. Pemeriksaan rancangan diagram urutan perlu dilakukan untuk mengetahui ketidaksesuaian urutan alur  kasus penggunaan dengan urutan pesan yang dikirimkan oleh objek-objek pada diagram urutan. Rancangan diagram yang sesuai merupakan kunci ketepatan (correctness implementasi  perangkat lunak. Namun, pemeriksaan ketidaksesuaian masih dilakukan secara manual. Hal ini menjadi masalah apabila sebuah proyek perangkat lunak memiliki banyak  rancangan diagram dan sumber daya manusia tidak  mencukupi. Pemeriksaan membutuhkan waktu yang lama dan memiliki dampak pada waktu pengembangan perangkat lunak. Penelitian ini mengusulkan pembuatan kakas bantu  untuk mendeteksi ketidaksesuaian diagram urutan dengan diagram kasus penggunaan. Ketidaksesuaian dilihat dari kemiripan semantik kalimat antara alur pada deskripsi kasus penggunaan dan triplet. Dari hasil pembuatan kakas bantu, kakas bantu yang dibuat dapat mendeteksi ketidaksesuaian diagram urutan dengan diagram kasus penggunaan. Kakas  bantu ini diharapkan tidak hanya membantu pemeriksaan rancangan diagram akan tetapi mempercepat waktu pengembangan perangkat lunak.

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

Science.gov (United States)

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

2010-06-01

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

serum immunoglobulin levels in white, asiatic and bantu blood donors

African Journals Online (AJOL)

all assays were calculated as a percentage of the mean of. TABLE I. RESULTS OF IMMUNOGLOBULIN ASSAYS OF tOO WHITE, tOO ASIATIC AND 100 BANTU DONORS, EXPRESSED AS A. PERCENTAGE OF A CONTROL SERUM. Parameter. Range. Mean. Variance. Standard deviation. CoefI. of variation.

Collecting and evaluating speech recognition corpora for nine Southern Bantu languages

CSIR Research Space (South Africa)

Badenhorst, JAC

2009-03-01

Full Text Available The authors describes the Lwazi corpus for automatic speech recognition (ASR), a new telephone speech corpus which includes data from nine Southern Bantu languages. Because of practical constraints, the amount of speech per language is relatively...

From Bantu Education to the Fight for Socially Just Education

Science.gov (United States)

Ndimande, Bekisizwe S.

2013-01-01

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

Issues in Scientific Terminology in African / Bantu Languages

OpenAIRE

Taljard , Elsabé

2007-01-01

In 2006, the South African Department of Education initiated a pilot project in which the Matric or Senior Certificate papers for Science, Maths, Biology and History were translated into the nine official African/Bantu languages of the country. Grade 12 learners who use these languages as home languages therefore received a question paper containing questions in English, where every question was followed by its translation into the relevant language. Taking into consideration that these learn...

"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…

Keeping mtDNA in shape between generations.

Directory of Open Access Journals (Sweden)

James B Stewart

2014-10-01

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

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,…

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.

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

Directory of Open Access Journals (Sweden)

Sylvester C Chima

1998-09-01

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

Inferring the population expansions in peopling of Japan.

Directory of Open Access Journals (Sweden)

Min-Sheng Peng

Full Text Available Extensive studies in different fields have been performed to reconstruct the prehistory of populations in the Japanese archipelago. Estimates the ancestral population dynamics based on Japanese molecular sequences can extend our understanding about the colonization of Japan and the ethnogenesis of modern Japanese.We applied Bayesian skyline plot (BSP with a dataset based on 952 Japanese mitochondrial DNA (mtDNA genomes to depict the female effective population size (N(ef through time for the total Japanese and each of the major mtDNA haplogroups in Japanese. Our results revealed a rapid N(ef growth since ∼5 thousand years ago had left ∼72% Japanese mtDNA lineages with a salient signature. The BSP for the major mtDNA haplogroups indicated some different demographic history.The results suggested that the rapid population expansion acted as a major force in shaping current maternal pool of Japanese. It supported a model for population dynamics in Japan in which the prehistoric population growth initiated in the Middle Jomon Period experienced a smooth and swift transition from Jomon to Yayoi, and then continued through the Yayoi Period. The confounding demographic backgrounds of different mtDNA haplogroups could also have some implications for some related studies in future.

Mosaic maternal ancestry in the Great Lakes region of East Africa.

Science.gov (United States)

Gomes, Verónica; Pala, Maria; Salas, Antonio; Álvarez-Iglesias, Vanesa; Amorim, António; Gómez-Carballa, Alberto; Carracedo, Ángel; Clarke, Douglas J; Hill, Catherine; Mormina, Maru; Shaw, Marie-Anne; Dunne, David W; Pereira, Rui; Pereira, Vânia; Prata, Maria João; Sánchez-Diz, Paula; Rito, Teresa; Soares, Pedro; Gusmão, Leonor; Richards, Martin B

2015-09-01

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

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.

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

2013-01-01

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. PMID:23814547

Decreased Circulating mtDNA Levels in Professional Male Volleyball Players.

Science.gov (United States)

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

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

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.

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.

Science.gov (United States)

Le Goaster, Jacqueline; Bouree, Patrice; El Sissy, Franck N; Phuong Bui, Florence; Pokossy Epee, Johanna; Rollin, Paul; Tangy, Frédéric; Haenni, Anne-Lise

2016-01-01

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. 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. 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.

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.

Nuclear DNA but not mtDNA controls tumor phenotypes in mouse cells

International Nuclear Information System (INIS)

Akimoto, Miho; Niikura, Mamoru; Ichikawa, Masami; Yonekawa, Hiromichi; Nakada, Kazuto; Honma, Yoshio; Hayashi, Jun-Ichi

2005-01-01

Recent studies showed high frequencies of homoplasmic mtDNA mutations in various human tumor types, suggesting that the mutated mtDNA haplotypes somehow contribute to expression of tumor phenotypes. We directly addressed this issue by isolating mouse mtDNA-less (ρ 0 ) cells for complete mtDNA replacement between normal cells and their carcinogen-induced transformants, and examined the effect of the mtDNA replacement on expression of tumorigenicity, a phenotype forming tumors in nude mice. The results showed that genome chimera cells carrying nuclear DNA from tumor cells and mtDNA from normal cells expressed tumorigenicity, whereas those carrying nuclear DNA from normal cells and mtDNA from tumor cells did not. These observations provided direct evidence that nuclear DNA, but not mtDNA, is responsible for carcinogen-induced malignant transformation, although it remains possible that mtDNA mutations and resultant respiration defects may influence the degree of malignancy, such as invasive or metastatic properties

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

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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.

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.

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

Human mitochondrial DNA (mtDNA) types in Malaysia

International Nuclear Information System (INIS)

Lian, L.H.; Koh, C.L.; Lim, M.E.

2000-01-01

Each human cell contains hundreds of mitochondria and thousands of double-stranded circular mtDNA. The delineation of human mtDNA variation and genetics over the past decade has provided unique and often startling insights into human evolution, degenerative diseases, and aging. Each mtDNA of 16,569 base pairs, encodes 13 polypeptides essential to the enzymes of the mitochondrial energy generating pathway, plus the necessary tRNAs and rRNAs. The highly polymorphic noncoding D-(displacement) loop region, also called the control region, is approximately 1.2 kb long. It contains two well-characterized hypervariable (HV-) regions, HV1 and HV2. MtDNA identification is usually based on these sequence differences. According to the TWTGDAM (Technical Working Group for DNA Analysis Methods), the minimum requirement for a mtDNA database for HV1 is from positions 16024 to 16365 and for HV2, from positions 00073 to 00340. The targeted Malaysian population subgroups for this study were mainly the Malays, Chinese, Indians, and indigenous Ibans, Bidayuhs, Kadazan-Dusuns, and Bajaus. Research methodologies undertaken included DNA extraction of samples from unrelated individuals, amplification of the specific regions via the polymerase chain reaction (PCR), and preparation of template DNA for sequencing by using an automated DNA sequencer. Sufficient nucleotide sequence data were generated from the mtDNA analysis. When the sequences were analyzed, sequence variations were found to be caused by nucleotide substitutions, insertions, and deletions. Of the three causes of the sequence variations, nucleotide substitutions (86.1%) accounted for the vast majority of polymorphism. It is noted that transitions (83.5%) were predominant when compared to the significantly lower frequencies of transversions (2.6%). Insertions (0.9%) and deletions (13.0%) were rather rare and found only in HV2. The data generated will also form the basis of a Malaysian DNA sequence database of mtDNA D

mtDNA, Metastasis, and the Mitochondrial Unfolded Protein Response (UPRmt).

Science.gov (United States)

Kenny, Timothy C; Germain, Doris

2017-01-01

While several studies have confirmed a link between mitochondrial DNA (mtDNA) mutations and cancer cell metastasis, much debate remains regarding the nature of the alternations in mtDNA leading to this effect. Meanwhile, the mitochondrial unfolded protein response (UPR mt ) has gained much attention in recent years, with most studies of this pathway focusing on its role in aging. However, the UPR mt has also been studied in the context of cancer. More recent work suggests that rather than a single mutation or alternation, specific combinatorial mtDNA landscapes able to activate the UPR mt may be those that are selected by metastatic cells, while mtDNA landscapes unable to activate the UPR mt do not. This review aims at offering an overview of the confusing literature on mtDNA mutations and metastasis and the more recent work on the UPR mt in this setting.

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

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Mayra Eduardoff

2017-09-01

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

Evolutionary history of the European whitefish Coregonus lavaretus (L.) species complex as inferred from mtDNA phylogeography and gill-raker numbers.

Science.gov (United States)

Østbye, K; Bernatchez, L; Naesje, T F; Himberg, K-J M; Hindar, K

2005-12-01

We compared mitochondrial DNA and gill-raker number variation in populations of the European whitefish Coregonus lavaretus (L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single-strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidase b (cyt b) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill-raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500-5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill-raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill-raker variation. Whitefish designations based on gill-raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.

The Dawn of Human Matrilineal Diversity

Science.gov (United States)

Behar, Doron M.; Villems, Richard; Soodyall, Himla; Blue-Smith, Jason; Pereira, Luisa; Metspalu, Ene; Scozzari, Rosaria; Makkan, Heeran; Tzur, Shay; Comas, David; Bertranpetit, Jaume; Quintana-Murci, Lluis; Tyler-Smith, Chris; Wells, R. Spencer; Rosset, Saharon

2008-01-01

The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000–150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000–70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations. PMID:18439549

MtDNA and nuclear data reveal patterns of low genetic differentiation for the isopods Stenosoma lancifer and Stenosoma acuminatum, with low dispersal ability along the northeast Atlantic coast

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Raquel Xavier

2011-11-01

Full Text Available Evidence for a general lack of genetic differentiation of intertidal invertebrate assemblages in the North Atlantic, based on mtDNA sequence variation, has been interpreted as resulting from recent colonization following the Last Glacial Maximum. In the present study, the phylogeographic patterns of one nuclear and one mtDNA gene fragments of two isopods, Stenosoma lancifer (Miers, 1881 and Stenosoma acuminatum Leach, 1814, from the northeast Atlantic were investigated. These organisms have direct development, which makes them poor dispersers, and are therefore expected to maintain signatures of past historical events in their genomes. Lack of genetic structure, significant deviations from neutrality and star-like haplotype networks have been observed for both mtDNA and nuclear markers of S. lancifer, as well as for the mtDNA of S. acuminatum. No sequence variation was observed for the nuclear gene fragment of S. acuminatum. These results suggest a scenario of recent colonization and demographic expansion and/or high population connectivity driven by ocean currents and sporadic long-distance dispersal through rafting.

Myopathic mtDNA Depletion Syndrome Due to Mutation in TK2 Gene.

Science.gov (United States)

Martín-Hernández, Elena; García-Silva, María Teresa; Quijada-Fraile, Pilar; Rodríguez-García, María Elena; Rivera, Henry; Hernández-Laín, Aurelio; Coca-Robinot, David; Fernández-Toral, Joaquín; Arenas, Joaquín; Martín, Miguel A; Martínez-Azorín, Francisco

2017-01-01

Whole-exome sequencing was used to identify the disease gene(s) in a Spanish girl with failure to thrive, muscle weakness, mild facial weakness, elevated creatine kinase, deficiency of mitochondrial complex III and depletion of mtDNA. With whole-exome sequencing data, it was possible to get the whole mtDNA sequencing and discard any pathogenic variant in this genome. The analysis of whole exome uncovered a homozygous pathogenic mutation in thymidine kinase 2 gene ( TK2; NM_004614.4:c.323 C>T, p.T108M). TK2 mutations have been identified mainly in patients with the myopathic form of mtDNA depletion syndromes. This patient presents an atypical TK2-related myopathic form of mtDNA depletion syndromes, because despite having a very low content of mtDNA (TK2 gene in mtDNA depletion syndromes and expanded the phenotypic spectrum.

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

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

Mitochondrial DNA copy number threshold in mtDNA depletion myopathy.

Science.gov (United States)

Durham, S E; Bonilla, E; Samuels, D C; DiMauro, S; Chinnery, P F

2005-08-09

The authors measured the absolute amount of mitochondrial DNA (mtDNA) within single muscle fibers from two patients with thymidine kinase 2 (TK2) deficiency and two healthy controls. TK2 deficient fibers containing more than 0.01 mtDNA/microm3 had residual cytochrome c oxidase (COX) activity. This defines the minimum amount of wild-type mtDNA molecules required to maintain COX activity in skeletal muscle and provides an explanation for the mosaic histochemical pattern seen in patients with mtDNA depletion syndrome.

Hypervariable region polymorphism of mtDNA of recurrent oral ulceration in Chinese.

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Mao Sun

Full Text Available BACKGROUND: MtDNA haplogroups could have important implication for understanding of the relationship between the mutations of the mitochondrial genome and diseases. Distribution of a variety of diseases among these haplogroups showed that some of the mitochondrial haplogroups are predisposed to disease. To examine the susceptibility of mtDNA haplogroups to ROU, we sequenced the mtDNA HV1, HV2 and HV3 in Chinese ROU. METHODOLOGY/PRINCIPAL FINDINGS: MtDNA haplogroups were analyzed in the 249 cases of ROU patients and the 237 cases of healthy controls respectively by means of primer extension analysis and DNA sequencing. Haplogroups G1 and H were found significantly more abundant in ROU patients than in healthy persons, while haplogroups D5 and R showed a trend toward a higher frequency in control as compared to those in patients. The distribution of C-stretch sequences polymorphism in mtDNA HV1, HV2 and HV3 regions was found in diversity. CONCLUSIONS/SIGNIFICANCE: For the first time, the relationship of mtDNA haplogroups and ROU in Chinese was investigated. Our results indicated that mtDNA haplogroups G1 and H might constitute a risk factor for ROU, which possibly increasing the susceptibility of ROU. Meanwhile, haplogroups D5 and R were indicated as protective factors for ROU. The polymorphisms of C-stretch sequences might being unstable and influence the mtDNA replication fidelity.

Modelling the Spread of Farming in the Bantu-Speaking Regions of Africa: An Archaeology-Based Phylogeography

OpenAIRE

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 hypothese...

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

Science.gov (United States)

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

2014-01-01

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

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.

Oxidants and not alkylating agents induce rapid mtDNA loss and mitochondrial dysfunction

Science.gov (United States)

Furda, Amy M.; Marrangoni, Adele M.; Lokshin, Anna; Van Houten, Bennett

2013-01-01

Mitochondrial DNA (mtDNA) is essential for proper mitochondrial function and encodes 22 tRNAs, 2 rRNAs and 13 polypeptides that make up subunits of complex I, III, IV, in the electron transport chain and complex V, the ATP synthase. Although mitochondrial dysfunction has been implicated in processes such as premature aging, neurodegeneration, and cancer, it has not been shown whether persistent mtDNA damage causes a loss of oxidative phosphorylation. We addressed this question by treating mouse embryonic fibroblasts with either hydrogen peroxide (H2O2) or the alkylating agent methyl methanesulfonate (MMS) and measuring several endpoints, including mtDNA damage and repair rates using QPCR, levels of mitochondrial- and nuclear-encoded proteins using antibody analysis, and a pharmacologic profile of mitochondria using the Seahorse Extracellular Flux Analyzer. We show that a 60 min treatment with H2O2 causes persistent mtDNA lesions, mtDNA loss, decreased levels of a nuclear-encoded mitochondrial subunit, a loss of ATP-linked oxidative phosphorylation and a loss of total reserve capacity. Conversely, a 60 min treatment with 2 mM MMS causes persistent mtDNA lesions but no mtDNA loss, no decrease in levels of a nuclear-encoded mitochondrial subunit, and no mitochondrial dysfunction. These results suggest that persistent mtDNA damage is not sufficient to cause mitochondrial dysfunction. PMID:22766155

mtDNA sequence diversity of Hazara ethnic group from Pakistan.

Science.gov (United States)

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

2017-09-01

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

Desain Dan Implementasi Augmented Reality Berbasis Web Pada Aplikasi Furniture Shopping Manager Sebagai Alat Bantu Belanja Online

OpenAIRE

Pramono, Basworo Ardi

2012-01-01

Dalam penulisan jurnal ini akan dibahas mengenai pengembangan aplikasi Furniture Shopping Manager (FSM) sebagai suatu alat bantu yang dapat dimanfaatkan oleh para pemilik situs atau toko furniture secara online dalam menjual produknya. FSM dirancang sebagai sebuah aplikasi berbasis web yang terintegrasi ke dalam suatu situs belanja online dengan fitur-fitur yang diharapkan dapat memberikan pengalaman yang baru, unik dan menarik dalam kegiatan belanja furniture online. Aplikasi FSM dikembang...

DESAIN DAN IMPLEMENTASI AUGMENTED REALITY BERBASIS WEB PADA APLIKASI FURNITURE SHOPPING MANAGER SEBAGAI ALAT BANTU BELANJA ONLINE

OpenAIRE

Basworo Ardi Pramono

2012-01-01

Dalam penulisan jurnal ini akan dibahas mengenai pengembangan aplikasi Furniture Shopping Manager (FSM) sebagai suatu alat bantu yang dapat dimanfaatkan oleh para pemilik situs atau toko furniture secara online dalam menjual produknya.  FSM dirancang sebagai sebuah aplikasi berbasis web yang terintegrasi ke dalam suatu situs belanja online dengan fitur-fitur yang diharapkan dapat memberikan pengalaman yang baru, unik dan menarik dalam kegiatan belanja furniture online.   Aplikasi FSM dike...

Random mtDNA mutations modulate proliferation capacity in mouse embryonic fibroblasts

International Nuclear Information System (INIS)

Kukat, Alexandra; Edgar, Daniel; Bratic, Ivana; Maiti, Priyanka; Trifunovic, Aleksandra

2011-01-01

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

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

Science.gov (United States)

Zhang, Yanhong; Pham, Nancy Kim; Zhang, Huixian; Lin, Junda; Lin, Qiang

2014-01-01

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

Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups.

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de Filippo, Cesare; Barbieri, Chiara; Whitten, Mark; Mpoloka, Sununguko Wata; Gunnarsdóttir, Ellen Drofn; Bostoen, Koen; Nyambe, Terry; Beyer, Klaus; Schreiber, Henning; de Knijff, Peter; Luiselli, Donata; Stoneking, Mark; Pakendorf, Brigitte

2011-03-01

Technological and cultural innovations as well as climate changes are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ∼ 10,000 years ago (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ∼ 5,000 ya represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sublineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu-speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 individuals from 26 groups representing all linguistic phyla and covering a large portion of sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggests that their expansion throughout sub-Saharan Africa reflects a rapid spread followed by

Y-chromosomal variation in Sub-Saharan Africa: insights into the history of Niger-Congo groups

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de Filippo, Cesare; Barbieri, Chiara; Whitten, Mark; Mpoloka, Sununguko Wata; Gunnarsdóttir, Ellen Drofn; Bostoen, Koen; Nyambe, Terry; Beyer, Klaus; Schreiber, Henning; de Knijff, Peter; Luiselli, Donata; Stoneking, Mark; Pakendorf, Brigitte

2013-01-01

Technological and cultural innovations, as well as climate changes, are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ~10,000 years ago. The expansion of Bantu languages (a family within the Niger-Congo phylum) ~5,000 years ago represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sub-lineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, D.R.C, and Zambia). With the inclusion of published data, we analyzed 2736 individuals from 26 groups representing all linguistic phyla and covering a large portion of Sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using Linear Discriminant Analysis on STR haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggest that their expansion throughout Sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found

Regional Variation in mtDNA of the Lesser Prairie-Chicken

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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.

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

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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.

The mitochondrial outer membrane protein MDI promotes local protein synthesis and mtDNA replication.

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Zhang, Yi; Chen, Yong; Gucek, Marjan; Xu, Hong

2016-05-17

Early embryonic development features rapid nuclear DNA replication cycles, but lacks mtDNA replication. To meet the high-energy demands of embryogenesis, mature oocytes are furnished with vast amounts of mitochondria and mtDNA However, the cellular machinery driving massive mtDNA replication in ovaries remains unknown. Here, we describe a Drosophila AKAP protein, MDI that recruits a translation stimulator, La-related protein (Larp), to the mitochondrial outer membrane in ovaries. The MDI-Larp complex promotes the synthesis of a subset of nuclear-encoded mitochondrial proteins by cytosolic ribosomes on the mitochondrial surface. MDI-Larp's targets include mtDNA replication factors, mitochondrial ribosomal proteins, and electron-transport chain subunits. Lack of MDI abolishes mtDNA replication in ovaries, which leads to mtDNA deficiency in mature eggs. Targeting Larp to the mitochondrial outer membrane independently of MDI restores local protein synthesis and rescues the phenotypes of mdi mutant flies. Our work suggests that a selective translational boost by the MDI-Larp complex on the outer mitochondrial membrane might be essential for mtDNA replication and mitochondrial biogenesis during oogenesis. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

No evidence of Neandertal mtDNA contribution to early modern humans.

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David Serre

2004-03-01

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

The amount and integrity of mtDNA in maize decline with development.

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Oldenburg, Delene J; Kumar, Rachana A; Bendich, Arnold J

2013-02-01

In maize and other grasses there is a developmental gradient from the meristematic cells at the base of the stalk to the differentiated cells at the leaf tip. This gradient presents an opportunity to investigate changes in mitochondrial DNA (mtDNA) that accompany growth under light and dark conditions, as done previously for plastid DNA. Maize mtDNA was analyzed by DAPI-DNA staining of individual mitochondria, gel electrophoresis/blot hybridization, and real-time qPCR. Both the amount and integrity of the mtDNA were found to decline with development. There was a 20-fold decline in mtDNA copy number per cell from the embryo to the light-grown leaf blade. The amount of DNA per mitochondrial particle was greater in dark-grown leaf blade (24 copies, on average) than in the light (2 copies), with some mitochondria lacking any detectable DNA. Three factors that influence the demise of mtDNA during development are considered: (1) the decision to either repair or degrade mtDNA molecules that are damaged by the reactive oxygen species produced as byproducts of respiration; (2) the generation of ATP by photophosphorylation in chloroplasts, reducing the need for respiratory-competent mitochondria; and (3) the shift in mitochondrial function from energy-generating respiration to photorespiration during the transition from non-green to green tissue.

Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya.

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Khanal, Laxman; Chalise, Mukesh K; He, Kai; Acharya, Bipin K; Kawamoto, Yoshi; Jiang, Xuelong

2018-03-01

Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial-interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121 bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075 ± SD 0.0001) but high haplotype diversity (0.965 ± SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion. © 2018 Wiley Periodicals, Inc.

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

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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

[Whole Genome Sequencing of Human mtDNA Based on Ion Torrent PGM™ Platform].

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Cao, Y; Zou, K N; Huang, J P; Ma, K; Ping, Y

2017-08-01

To analyze and detect the whole genome sequence of human mitochondrial DNA （mtDNA） by Ion Torrent PGM™ platform and to study the differences of mtDNA sequence in different tissues. Samples were collected from 6 unrelated individuals by forensic postmortem examination, including chest blood, hair, costicartilage, nail, skeletal muscle and oral epithelium. Amplification of whole genome sequence of mtDNA was performed by 4 pairs of primer. Libraries were constructed with Ion Shear™ Plus Reagents kit and Ion Plus Fragment Library kit. Whole genome sequencing of mtDNA was performed using Ion Torrent PGM™ platform. Sanger sequencing was used to determine the heteroplasmy positions and the mutation positions on HVⅠ region. The whole genome sequence of mtDNA from all samples were amplified successfully. Six unrelated individuals belonged to 6 different haplotypes. Different tissues in one individual had heteroplasmy difference. The heteroplasmy positions and the mutation positions on HVⅠ region were verified by Sanger sequencing. After a consistency check by the Kappa method, it was found that the results of mtDNA sequence had a high consistency in different tissues. The testing method used in present study for sequencing the whole genome sequence of human mtDNA can detect the heteroplasmy difference in different tissues, which have good consistency. The results provide guidance for the further applications of mtDNA in forensic science. Copyright© by the Editorial Department of Journal of Forensic Medicine

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

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

2015-01-01

The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual’s place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ancestry inferences made by mtDNA-haplogroup membership to those made by autosomal SNPs in ∼940 samples of the Human Genome Diversity Panel and recently admixed populations from the 1000 Genomes Project. Continental-ancestry proportions often varied widely among individuals sharing the same mtDNA haplogroup. For only half of mtDNA haplogroups did the highest average continental-ancestry proportion match the highest continental-ancestry proportion of a majority of individuals with that haplogroup. Prediction of an individual’s mtDNA haplogroup from his or her continental-ancestry proportions was often incorrect. Collectively, these results indicate that for most individuals in the worldwide populations sampled, mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin. PMID:25620206

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

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Hellberg Michael E

2006-03-01

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

Archetyping race, gender and class: advertising in The Bantu World and The World from the 1930s to the 1990s

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Nhlanhla Maake

2006-04-01

Full Text Available This article sets out to interrogate the ideological hegemony of the superstructuring narrative voice in advertisements by studying linguistic, structural devices and encoding that are employed, in order to expose its racial, class and gender undertones embedded in the authorial voice. The sample of advertisements discussed is derived from The Bantu World and its two sequels, The World and The Sowetan. The sample is thinly dispersed over a period of five decades. Most of the advertisements selected were duplicated in the sister newspapers, Mochochono (Sesotho and Imvo (isiXhosa, which were published under the auspices of the Associated Bantu Press. In the latter case the advertisements in the different languages were directly translated from English. The thrust of our argument is that the narrative voice, together with the images, are loaded with a stereotyping preconceived notion of the “other”, which is either conscious or subconscious. We also suggest that the change of the newspaper’s name is accompanied by a perceptible evolution of ideological bias in both the images and the narrative voice.

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

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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.

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

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Yanhong Zhang

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

Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

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Pennarun Erwan

2012-12-01

Full Text Available Abstract Background A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories. Results We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups’ phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000–22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture. Conclusions Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.

PENGEMBANGAN LAMPU BAWAH AIR SEBAGAI ALAT BANTU PADA BAGAN TANCAP DI DESA TAMBAK LEKOK KECAMATAN LEKOK PASURUAN

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F Fuad

2016-03-01

Full Text Available DEVELOPMENT OF UNDER WATER LAMP AS A TOOL TO LIFT NET IN TAMBAK LEKOK VILLAGE PASURUANBagan is one type of fishing gear that uses light to collect fish. The lights are expected to stimulate the fish to come and stay around the light and than arrested with net. The use of light for fishing is growing rapidly, almost all fishing gear to use light as a tool for collecting fish. Application of this technology aims to increase fish catch fishermen in District Lekok through the application of technology underwater lamp with LED. Underwater lamp applied to the bagan tancap with a certain intensity and color to find the intensity of light and color that give the best catches. Best catches in the light of 450 lux is capable of delivering the highest total catch of 254 kg, it is supported by the values of illumination of 1.5 lux at a distance of 5 m. Types of fish that were caught on as much as 23 step chart types where the type of Stolephorus spp, Selaroides spp, Leiognathus spp, Loligo sp, Rastrelliger spp is a type of fish that always caught each fishing operation. Keywords: auxilary, development, lamp, Lekok, lift net  ABSTRAK Bagan merupakan salah satu jenis alat tangkap yang menggunakan lampu sebagai alat bantu pengunpul ikan. Cahaya lampu diharapkan dapat merangsang ikan untuk datang dan berkumpul disekitar sumber cahaya sampai pada suatu catchable area tertentu, lalu penangkapan dilakukan dengan alat jaring maupun pancing. Penggunaan lampu untuk penangkapan ikan saat ini berkembang pesat, hampir semua alat tangkap menggunakan lampu sebagai alat bantu pengumpul ikan. Aplikasi teknologi ini bertujuan untuk meningkatkan hasil tangkapan ikan nelayan bagan tancap di Kecamatan Lekok melalui penerapan teknologi lampu celup bawah air berbasis lampu LED. Lampu celup bawah air diterapkan pada bagan tancap dengan intensitas dan warna tertentu untuk mencari intensitas cahaya dan warna yang memberikan hasil tangkapan yang terbaik. Hasil tangkapan ikan yang

Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota.

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Bagley, Justin C; Sandel, Michael; Travis, Joseph; Lozano-Vilano, María de Lourdes; Johnson, Jerald B

2013-10-09

Climatic and sea-level fluctuations throughout the last Pleistocene glacial cycle (~130-0 ka) profoundly influenced present-day distributions and genetic diversity of Northern Hemisphere biotas by forcing range contractions in many species during the glacial advance and allowing expansion following glacial retreat ('expansion-contraction' model). Evidence for such range dynamics and refugia in the unglaciated Gulf-Atlantic Coastal Plain stems largely from terrestrial species, and aquatic species Pleistocene responses remain relatively uninvestigated. Heterandria formosa, a wide-ranging regional endemic, presents an ideal system to test the expansion-contraction model within this biota. By integrating ecological niche modeling and phylogeography, we infer the Pleistocene history of this livebearing fish (Poeciliidae) and test for several predicted distributional and genetic effects of the last glaciation. Paleoclimatic models predicted range contraction to a single southwest Florida peninsula refugium during the Last Glacial Maximum, followed by northward expansion. We inferred spatial-population subdivision into four groups that reflect genetic barriers outside this refuge. Several other features of the genetic data were consistent with predictions derived from an expansion-contraction model: limited intraspecific divergence (e.g. mean mtDNA p-distance = 0.66%); a pattern of mtDNA diversity (mean Hd = 0.934; mean π = 0.007) consistent with rapid, recent population expansion; a lack of mtDNA isolation-by-distance; and clinal variation in allozyme diversity with higher diversity at lower latitudes near the predicted refugium. Statistical tests of mismatch distributions and coalescent simulations of the gene tree lent greater support to a scenario of post-glacial expansion and diversification from a single refugium than to any other model examined (e.g. multiple-refugia scenarios). Congruent results from diverse data indicate H. formosa fits the classic Pleistocene

Characterization of mtDNA haplogroups in 14 Mexican indigenous populations.

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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.

Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses.

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Morin, Phillip A; Foote, Andrew D; Baker, C Scott; Hancock-Hanser, Brittany L; Kaschner, Kristin; Mate, Bruce R; Mesnick, Sarah L; Pease, Victoria L; Rosel, Patricia E; Alexander, Alana

2018-04-19

Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion versus a selective sweep due to cultural-hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean-specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance, and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

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

mtDNA mutation C1494T, haplogroup A, and hearing loss in Chinese

International Nuclear Information System (INIS)

Wang Chengye; Kong Qingpeng; Yao Yonggang; Zhang Yaping

2006-01-01

Mutation C1494T in mitochondrial 12S rRNA gene was recently reported in two large Chinese families with aminoglycoside-induced and nonsyndromic hearing loss (AINHL) and was claimed to be pathogenic. This mutation, however, was first reported in a sample from central China in our previous study that was aimed to reconstruct East Asian mtDNA phylogeny. All these three mtDNAs formed a subclade defined by mutation C1494T in mtDNA haplogroup A. It thus seems that mutation C1494T is a haplogroup A-associated mutation and this matrilineal background may contribute a high risk for the penetrance of mutation C1494T in Chinese with AINHL. To test this hypothesis, we first genotyped mutation C1494T in 553 unrelated individuals from three regional Chinese populations and performed an extensive search for published complete or near-complete mtDNA data sets (>3000 mtDNAs), we then screened the C1494T mutation in 111 mtDNAs with haplogroup A status that were identified from 1823 subjects across China. The search for published mtDNA data sets revealed no other mtDNA besides the above-mentioned three carrying mutation C1494T. None of the 553 randomly selected individuals and the 111 haplogroup A mtDNAs was found to bear this mutation. Therefore, our results suggest that C1494T is a very rare event. The mtDNA haplogroup A background in general is unlikely to play an active role in the penetrance of mutation C1494T in AINHL

Alterations in mtDNA, gastric carcinogenesis and early diagnosis.

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Rodrigues-Antunes, S; Borges, B N

2018-05-26

Gastric cancer remains one of the most prevalent cancers in the world. Due to this, efforts are being made to improve the diagnosis of this neoplasm and the search for molecular markers that may be involved in its genesis. Within this perspective, the mitochondrial DNA is considered as a potential candidate, since it has several well documented changes and is readily accessible. However, numerous alterations have been reported in mtDNA, not facilitating the visualization of which alterations and molecular markers are truly involved with gastric carcinogenesis. This review presents a compilation of the main known changes relating mtDNA to gastric cancer and their clinical significance.

Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima.

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Kearns, Anna M; Joseph, Leo; Toon, Alicia; Cook, Lyn G

2014-05-30

A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative--the savanna-inhabiting Silver-backed Butcherbird--whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota.

Mitochondrial nucleoid clusters protect newly synthesized mtDNA during Doxorubicin- and Ethidium Bromide-induced mitochondrial stress

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Alán, Lukáš, E-mail: lukas.alan@fgu.cas.cz; Špaček, Tomáš; Pajuelo Reguera, David; Jabůrek, Martin; Ježek, Petr

2016-07-01

Mitochondrial DNA (mtDNA) is compacted in ribonucleoprotein complexes called nucleoids, which can divide or move within the mitochondrial network. Mitochondrial nucleoids are able to aggregate into clusters upon reaction with intercalators such as the mtDNA depletion agent Ethidium Bromide (EB) or anticancer drug Doxorobicin (DXR). However, the exact mechanism of nucleoid clusters formation remains unknown. Resolving these processes may help to elucidate the mechanisms of DXR-induced cardiotoxicity. Therefore, we addressed the role of two key nucleoid proteins; mitochondrial transcription factor A (TFAM) and mitochondrial single-stranded binding protein (mtSSB); in the formation of mitochondrial nucleoid clusters during the action of intercalators. We found that both intercalators cause numerous aberrations due to perturbing their native status. By blocking mtDNA replication, both agents also prevented mtDNA association with TFAM, consequently causing nucleoid aggregation into large nucleoid clusters enriched with TFAM, co-existing with the normal nucleoid population. In the later stages of intercalation (> 48 h), TFAM levels were reduced to 25%. In contrast, mtSSB was released from mtDNA and freely distributed within the mitochondrial network. Nucleoid clusters mostly contained nucleoids with newly replicated mtDNA, however the nucleoid population which was not in replication mode remained outside the clusters. Moreover, the nucleoid clusters were enriched with p53, an anti-oncogenic gatekeeper. We suggest that mitochondrial nucleoid clustering is a mechanism for protecting nucleoids with newly replicated DNA against intercalators mediating genotoxic stress. These results provide new insight into the common mitochondrial response to mtDNA stress and can be implied also on DXR-induced mitochondrial cytotoxicity. - Highlights: • The mechanism for mitochondrial nucleoid clustering is proposed. • DNA intercalators (Doxorubicin or Ethidium Bromide) prevent TFAM

mtDNA point and length heteroplasmy in high- and low radiation areas of Kerala

International Nuclear Information System (INIS)

Forster, L.; Forster, P.; Gurney, S.M.; Spencer, M.; Huang, C.; Röhl, A.; Brinkmann, B.

2010-01-01

A coastal peninsula in Kerala (India) contains the world's highest level of natural radioactivity in a densely populated area, offering an opportunity to characterize radiation-associated DNA mutations. Here, we focus on mitochondrial DNA (mtDNA) mutations, which are passed exclusively from the mother to her children. To analyse point mutations, we sampled 248 pedigrees (988 individuals) in the high-radiation peninsula and in nearby low-radiation islands as a control population. Then, in an extended sample of 1,172 mtDNA sequences (containing some non-Indians for comparison), we also analysed length mutations, which in mtDNA can lead to the phenomenon of length heteroplasmy, i.e. the existence of different DNA types in the same cell. We wished to find out how fast mtDNA mutates between generations, and whether the mutation rate is increased in radioactive conditions compared to the low-irradiation sample

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

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Juan J. Yunis

2013-01-01

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

Pleistocene to holocene expansion of the black-belt cichlid in Central America, Vieja maculicauda (Teleostei: Cichlidae.

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Caleb D McMahan

Full Text Available The distributions of many Northern Hemisphere organisms have been influenced by fluctuations in sea level and climatic conditions during Pleistocene interglacial periods. These cycles are associated with range contraction and refugia for northern-distributed organisms as a response to glaciers. However, lower sea levels in the tropics and sub-tropics created available habitat for expansion of the ranges of freshwater organisms. The goal of this study was to use ecological niche modeling to test the hypothesis of north to south range expansion of Vieja maculicauda associated with Pleistocene glacial cycles. Understanding the biogeography of this widespread species may help us better understand the geology and interconnectivity of Central American freshwaters. Occurrence data for V. maculicauda was based on georeferencing of all museum records of specimens recovered from FishNet2. General patterns of phylogeographic structure were assessed with mtDNA. Present day niche models were generated and subsequently projected onto paleoclimatic maps of the region during the Last Interglacial, Last Glacial Maximum, and mid-Holocene. Phylogenetic analysis of mtDNA sequence data showed no phylogeographic structure throughout the range of this widespread species. Present day niche models were congruent with the observed distribution of V. maculicauda in Central America. Results showed a lack of suitable freshwater habitat in northern Central America and Mexico during the Last Interglacial, with greatest range expansion during the Last Glacial Maximum and mid-Holocene. Results support the hypothesis of a north to south range expansion of V. maculicauda associated with glacial cycles. The wide distribution of this species compared to other closely related cichlids indicates the latter did not respond to the degree of V. maculicauda in expansion of their distributions. Future work aimed at comparisons with other species and modeling of future climatic scenarios

A defect in the thymidine kinase 2 gene causing isolated mitochondrial myopathy without mtDNA depletion.

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Leshinsky-Silver, E; Michelson, M; Cohen, S; Ginsberg, M; Sadeh, M; Barash, V; Lerman-Sagie, T; Lev, D

2008-07-01

Isolated mitochondrial myopathies (IMM) are either due to primary defects in mtDNA, in nuclear genes that control mtDNA abundance and structure such as thymidine kinase 2 (TK2), or due to CoQ deficiency. Defects in the TK2 gene have been found to be associated with mtDNA depletion attributed to a depleted mitochondrial dNTP pool in non-dividing cells. We report an unusual case of IMM, homozygous for the H90N mutation in the TK2 gene but unlike other cases with the same mutation, does not demonstrate mtDNA depletion. The patient's clinical course is relatively mild and a muscle biopsy showed ragged red muscle fibers with a mild decrease in complexes I and an increase in complexes IV and II activities. This report extends the phenotypic expression of TK2 defects and suggests that all patients who present with an IMM even with normal quantities of mtDNA should be screened for TK2 mutations.

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

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

2018-05-01

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

Infantile presentation of the mtDNA A3243G tRNA(Leu (UUR)) mutation.

NARCIS (Netherlands)

Okhuijsen-Kroes, E.J.; Trijbels, J.M.F.; Sengers, R.C.A.; Mariman, E.C.M.; Heuvel, L.P.W.J. van den; Wendel, U.A.H.; Koch, G.; Smeitink, J.A.M.

2001-01-01

Mitochondrial DNA (mtDNA) disorders are clinically very heterogeneous, ranging from single organ involvement to severe multisystem disease. One of the most frequently observed mtDNA mutations is the A-to-G transition at position 3243 of the tRNA(Leu (UUR)) gene. This mutation is often related to

Thymidine kinase 2 deficiency-induced mtDNA depletion in mouse liver leads to defect β-oxidation.

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Xiaoshan Zhou

Full Text Available Thymidine kinase 2 (TK2 deficiency in humans causes mitochondrial DNA (mtDNA depletion syndrome. To study the molecular mechanisms underlying the disease and search for treatment options, we previously generated and described a TK2 deficient mouse strain (TK2(-/- that progressively loses its mtDNA. The TK2(-/- mouse model displays symptoms similar to humans harboring TK2 deficient infantile fatal encephalomyopathy. Here, we have studied the TK2(-/- mouse model to clarify the pathological role of progressive mtDNA depletion in liver for the severe outcome of TK2 deficiency. We observed that a gradual depletion of mtDNA in the liver of the TK2(-/- mice was accompanied by increasingly hypertrophic mitochondria and accumulation of fat vesicles in the liver cells. The levels of cholesterol and nonesterified fatty acids were elevated and there was accumulation of long chain acylcarnitines in plasma of the TK2(-/- mice. In mice with hepatic mtDNA levels below 20%, the blood sugar and the ketone levels dropped. These mice also exhibited reduced mitochondrial β-oxidation due to decreased transport of long chain acylcarnitines into the mitochondria. The gradual loss of mtDNA in the liver of the TK2(-/- mice causes impaired mitochondrial function that leads to defect β-oxidation and, as a result, insufficient production of ketone bodies and glucose. This study provides insight into the mechanism of encephalomyopathy caused by TK2 deficiency-induced mtDNA depletion that may be used to explore novel therapeutic strategies.

Thymidine kinase 2 deficiency-induced mtDNA depletion in mouse liver leads to defect β-oxidation.

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Zhou, Xiaoshan; Kannisto, Kristina; Curbo, Sophie; von Döbeln, Ulrika; Hultenby, Kjell; Isetun, Sindra; Gåfvels, Mats; Karlsson, Anna

2013-01-01

Thymidine kinase 2 (TK2) deficiency in humans causes mitochondrial DNA (mtDNA) depletion syndrome. To study the molecular mechanisms underlying the disease and search for treatment options, we previously generated and described a TK2 deficient mouse strain (TK2(-/-)) that progressively loses its mtDNA. The TK2(-/-) mouse model displays symptoms similar to humans harboring TK2 deficient infantile fatal encephalomyopathy. Here, we have studied the TK2(-/-) mouse model to clarify the pathological role of progressive mtDNA depletion in liver for the severe outcome of TK2 deficiency. We observed that a gradual depletion of mtDNA in the liver of the TK2(-/-) mice was accompanied by increasingly hypertrophic mitochondria and accumulation of fat vesicles in the liver cells. The levels of cholesterol and nonesterified fatty acids were elevated and there was accumulation of long chain acylcarnitines in plasma of the TK2(-/-) mice. In mice with hepatic mtDNA levels below 20%, the blood sugar and the ketone levels dropped. These mice also exhibited reduced mitochondrial β-oxidation due to decreased transport of long chain acylcarnitines into the mitochondria. The gradual loss of mtDNA in the liver of the TK2(-/-) mice causes impaired mitochondrial function that leads to defect β-oxidation and, as a result, insufficient production of ketone bodies and glucose. This study provides insight into the mechanism of encephalomyopathy caused by TK2 deficiency-induced mtDNA depletion that may be used to explore novel therapeutic strategies.

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

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

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

2011-03-01

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. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Genetic variations of ND5 gene of mtDNA in populations of Anopheles sinensis (Diptera: Culicidae) malaria vector in China

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2013-01-01

Background Anopheles sinensis is a principal vector for Plasmodium vivax malaria in most parts of China. Understanding of genetic structure and genetic differentiation of the mosquito should contribute to the vector control and malaria elimination in China. Methods The present study investigated the genetic structure of An. sinensis populations using a 729 bp fragment of mtDNA ND5 among 10 populations collected from seven provinces in China. Results ND5 was polymorphic by single mutations within three groups of An. sinensis that were collected from 10 different geographic populations in China. Out of 140 specimens collected from 10 representative sites, 84 haplotypes and 71 variable positions were determined. The overall level of genetic differentiation of An. sinensis varied from low to moderate across China and with a FST range of 0.00065 – 0.341. Genealogy analysis clustered the populations of An. sinensis into three main clusters. Each cluster shared one main haplotype. Pairwise variations within populations were higher (68.68%) than among populations (31.32%) and with high fixation index (FST = 0.313). The results of the present study support population growth and expansion in the An. sinensis populations from China. Three clusters of An. sinensis populations were detected in this study with each displaying different proportion patterns over seven Chinese provinces. No correlation between genetic and geographic distance was detected in overall populations of An. sinensis (R2 = 0.058; P = 0.301). Conclusions The results indicate that the ND5 gene of mtDNA is highly polymorphic in An. sinensis and has moderate genetic variability in the populations of this mosquito in China. Demographic and spatial results support evidence of expansion in An. sinensis populations. PMID:24192424

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

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

2017-06-26

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

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

Therapeutic Targeting of the Mitochondria Initiates Excessive Superoxide Production and Mitochondrial Depolarization Causing Decreased mtDNA Integrity.

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Pokrzywinski, Kaytee L; Biel, Thomas G; Kryndushkin, Dmitry; Rao, V Ashutosh

2016-01-01

Mitochondrial dysregulation is closely associated with excessive reactive oxygen species (ROS) production. Altered redox homeostasis has been implicated in the onset of several diseases including cancer. Mitochondrial DNA (mtDNA) and proteins are particularly sensitive to ROS as they are in close proximity to the respiratory chain (RC). Mitoquinone (MitoQ), a mitochondria-targeted redox agent, selectively damages breast cancer cells possibly through damage induced via enhanced ROS production. However, the effects of MitoQ and other triphenylphosphonium (TPP+) conjugated agents on cancer mitochondrial homeostasis remain unknown. The primary objective of this study was to determine the impact of mitochondria-targeted agent [(MTAs) conjugated to TPP+: mitoTEMPOL, mitoquinone and mitochromanol-acetate] on mitochondrial physiology and mtDNA integrity in breast (MDA-MB-231) and lung (H23) cancer cells. The integrity of the mtDNA was assessed by quantifying the degree of mtDNA fragmentation and copy number, as well as by measuring mitochondrial proteins essential to mtDNA stability and maintenance (TFAM, SSBP1, TWINKLE, POLG and POLRMT). Mitochondrial status was evaluated by measuring superoxide production, mitochondrial membrane depolarization, oxygen consumption, extracellular acidification and mRNA or protein levels of the RC complexes along with TCA cycle activity. In this study, we demonstrated that all investigated MTAs impair mitochondrial health and decrease mtDNA integrity in MDA-MB-231 and H23 cells. However, differences in the degree of mitochondrial damage and mtDNA degradation suggest unique properties among each MTA that may be cell line, dose and time dependent. Collectively, our study indicates the potential for TPP+ conjugated molecules to impair breast and lung cancer cells by targeting mitochondrial homeostasis.

Endurance exercise rescues progeroid aging and induces systemic mitochondrial rejuvenation in mtDNA mutator mice

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Safdar, Adeel; Bourgeois, Jacqueline M.; Ogborn, Daniel I.; Little, Jonathan P.; Hettinga, Bart P.; Akhtar, Mahmood; Thompson, James E.; Melov, Simon; Mocellin, Nicholas J.; Kujoth, Gregory C.; Prolla, Tomas A.; Tarnopolsky, Mark A.

2011-01-01

A causal role for mitochondrial DNA (mtDNA) mutagenesis in mammalian aging is supported by recent studies demonstrating that the mtDNA mutator mouse, harboring a defect in the proofreading-exonuclease activity of mitochondrial polymerase gamma, exhibits accelerated aging phenotypes characteristic of human aging, systemic mitochondrial dysfunction, multisystem pathology, and reduced lifespan. Epidemiologic studies in humans have demonstrated that endurance training reduces the risk of chronic diseases and extends life expectancy. Whether endurance exercise can attenuate the cumulative systemic decline observed in aging remains elusive. Here we show that 5 mo of endurance exercise induced systemic mitochondrial biogenesis, prevented mtDNA depletion and mutations, increased mitochondrial oxidative capacity and respiratory chain assembly, restored mitochondrial morphology, and blunted pathological levels of apoptosis in multiple tissues of mtDNA mutator mice. These adaptations conferred complete phenotypic protection, reduced multisystem pathology, and prevented premature mortality in these mice. The systemic mitochondrial rejuvenation through endurance exercise promises to be an effective therapeutic approach to mitigating mitochondrial dysfunction in aging and related comorbidities. PMID:21368114

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

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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

MtDNA T4216C variation in multiple sclerosis

DEFF Research Database (Denmark)

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

2016-01-01

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

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

Science.gov (United States)

Stumpf, Jeffrey D; Copeland, William C

2014-10-01

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 replication but

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

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Alberto Gómez-Carballa

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

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

Science.gov (United States)

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

2011-01-01

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

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

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...... 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...

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

Science.gov (United States)

Rueda, Manuel; Torkamani, Ali

2017-08-18

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

Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders.

Science.gov (United States)

Lorenz, Carmen; Lesimple, Pierre; Bukowiecki, Raul; Zink, Annika; Inak, Gizem; Mlody, Barbara; Singh, Manvendra; Semtner, Marcus; Mah, Nancy; Auré, Karine; Leong, Megan; Zabiegalov, Oleksandr; Lyras, Ekaterini-Maria; Pfiffer, Vanessa; Fauler, Beatrix; Eichhorst, Jenny; Wiesner, Burkhard; Huebner, Norbert; Priller, Josef; Mielke, Thorsten; Meierhofer, David; Izsvák, Zsuzsanna; Meier, Jochen C; Bouillaud, Frédéric; Adjaye, James; Schuelke, Markus; Wanker, Erich E; Lombès, Anne; Prigione, Alessandro

2017-05-04

Mitochondrial DNA (mtDNA) mutations frequently cause neurological diseases. Modeling of these defects has been difficult because of the challenges associated with engineering mtDNA. We show here that neural progenitor cells (NPCs) derived from human induced pluripotent stem cells (iPSCs) retain the parental mtDNA profile and exhibit a metabolic switch toward oxidative phosphorylation. NPCs derived in this way from patients carrying a deleterious homoplasmic mutation in the mitochondrial gene MT-ATP6 (m.9185T>C) showed defective ATP production and abnormally high mitochondrial membrane potential (MMP), plus altered calcium homeostasis, which represents a potential cause of neural impairment. High-content screening of FDA-approved drugs using the MMP phenotype highlighted avanafil, which we found was able to partially rescue the calcium defect in patient NPCs and differentiated neurons. Overall, our results show that iPSC-derived NPCs provide an effective model for drug screening to target mtDNA disorders that affect the nervous system. Copyright © 2016 Elsevier Inc. All rights reserved.

The worldwide expansion of the Argentine ant

DEFF Research Database (Denmark)

Vogel, Valerie; Pedersen, Jes Søe; Giraud, Tatiana

2010-01-01

Aim The aim of this study was to determine the number of successful establishments of the invasive Argentine ant outside native range and to see whether introduced supercolonies have resulted from single or multiple introductions. We also compared the genetic diversity of native versus introduced...... supercolonies to assess the size of the propagules (i.e. the number of founding individuals) at the origin of the introduced supercolonies. Location Global. Methods We used mitochondrial DNA (mtDNA) markers and microsatellite loci to study 39 supercolonies of the Argentine ant Linepithema humile covering both......) 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...

Internucleotide correlations and nucleotide periodicity in Drosophila mtDNA: New evidence for panselective evolution

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Carlos Y Valenzuela

2010-01-01

Full Text Available Analysis for the homogeneity of the distribution of the second base of dinucleotides in relation to the first, whose bases are separated by 0, 1, 2,... 21 nucleotide sites, was performed with the VIH-1 genome (cDNA, the Drosophila mtDNA, the Drosophila Torso gene and the human p-globin gene. These four DNA segments showed highly significant heterogeneities of base distributions that cannot be accounted for by neutral or nearly neutral evolution or by the "neighbor influence" of nucleotides on mutation rates. High correlations are found in the bases of dinucleotides separated by 0, 1 and more number of sites. A periodicity of three consecutive significance values (measured by the x²9 was found only in Drosophila mtDNA. This periodicity may be due to an unknown structure or organization of mtDNA. This non-random distribution of the two bases of dinucleotides widespread throughout these DNA segments is rather compatible with panselective evolution and generalized internucleotide co-adaptation.

Why are tropical mountain passes "low" for some species? Genetic and stable-isotope tests for differentiation, migration and expansion in elevational generalist songbirds.

Science.gov (United States)

Gadek, Chauncey R; Newsome, Seth D; Beckman, Elizabeth J; Chavez, Andrea N; Galen, Spencer C; Bautista, Emil; Witt, Christopher C

2018-05-01

Most tropical bird species have narrow elevational ranges, likely reflecting climatic specialization. This is consistent with Janzen's Rule, the tendency for mountain passes to be effectively "higher" in the tropics. Hence, those few tropical species that occur across broad elevational gradients (elevational generalists) represent a contradiction to Janzen's Rule. Here, we aim to address the following questions. Are elevational generalists being sundered by diversifying selection along the gradient? Does elevational movement cause these species to resist diversification or specialization? Have they recently expanded, suggesting that elevational generalism is short-lived in geological time? To answer these questions, we tested for differentiation, movement and expansion in four elevational generalist songbird species on the Andean west slope. We used morphology and mtDNA to test for genetic differentiation between high- and low-elevation populations. To test for elevational movements, we measured hydrogen isotope (δ 2 H) values of metabolically inert feathers and metabolically active liver. Morphology differed for House Wren (Troglodytes aedon) and Hooded Siskin (Spinus magellanicus), but not for Cinereous Conebill (Conirostrum cinereum) and Rufous-collared Sparrow (Zonotrichia capensis) respectively. mtDNA was structured by elevation only in Z. capensis. δ 2 H data indicated elevational movements by two tree- and shrub-foraging species with moderate-to-high vagility (C. cinereum and S. magellanicus), and sedentary behaviour by two terrestrial-foraging species with low-to-moderate vagility (T. aedon and Z. capensis). In S. magellanicus, elevational movements and lack of mtDNA structure contrast with striking morphological divergence, suggesting strong diversifying selection on body proportions across the c. 50 km gradient. All species except C. cinereum exhibited mtDNA haplotype variation consistent with recent population expansion across the elevational

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

NARCIS (Netherlands)

Jahangir Tafrechi, Roshan Sakineh

2008-01-01

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

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

Science.gov (United States)

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

2016-09-01

To evaluate the pattern of Romanian population from a mitochondrial perspective and to establish an appropriate mtDNA forensic database, we generated a high-quality mtDNA control region dataset from 407 Romanian subjects belonging to four major historical regions: Moldavia, Transylvania, Wallachia and Dobruja. The entire control region (CR) was analyzed by Sanger-type sequencing assays and the resulting 306 different haplotypes were classified into haplogroups according to the most updated mtDNA phylogeny. The Romanian gene pool is mainly composed of West Eurasian lineages H (31.7%), U (12.8%), J (10.8%), R (10.1%), T (9.1%), N (8.1%), HV (5.4%),K (3.7%), HV0 (4.2%), with exceptions of East Asian haplogroup M (3.4%) and African haplogroup L (0.7%). The pattern of mtDNA variation observed in this study indicates that the mitochondrial DNA pool is geographically homogeneous across Romania and that the haplogroup composition reveals signals of admixture of populations of different origin. The PCA scatterplot supported this scenario, with Romania located in southeastern Europe area, close to Bulgaria and Hungary, and as a borderland with respect to east Mediterranean and other eastern European countries. High haplotype diversity (0.993) and nucleotide diversity indices (0.00838±0.00426), together with low random match probability (0.0087) suggest the usefulness of this control region dataset as a forensic database in routine forensic mtDNA analysis and in the investigation of maternal genetic lineages in the Romanian population. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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.

Allozyme and mtDNA variation of white seabream Diplodus sargus ...

African Journals Online (AJOL)

These results can be explained by the chaotic genetic patchiness hypothesis. In contrast, the mtDNA data indicated genetic homogeneity among localities showing the absence of structure in white seabream populations across the Siculo-Tunisian Strait. Historical demography of this species suggests that it has undergone ...

Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru.

Science.gov (United States)

Lewis, Cecil M; Tito, Raúl Y; Lizárraga, Beatriz; Stone, Anne C

2005-07-01

Despite a long history of complex societies and despite extensive present-day linguistic and ethnic diversity, relatively few populations in Peru have been sampled for population genetic investigations. In order to address questions about the relationships between South American populations and about the extent of correlation between genetic distance, language, and geography in the region, mitochondrial DNA (mtDNA) hypervariable region I sequences and mtDNA haplogroup markers were examined in 33 individuals from the state of Ancash, Peru. These sequences were compared to those from 19 American Indian populations using diversity estimates, AMOVA tests, mismatch distributions, a multidimensional scaling plot, and regressions. The results show correlations between genetics, linguistics, and geographical affinities, with stronger correlations between genetics and language. Additionally, the results suggest a pattern of differential gene flow and drift in western vs. eastern South America, supporting previous mtDNA and Y chromosome investigations. (c) 2004 Wiley-Liss, Inc

Primary quantitative analysis of the mtDNA4977bp deletion induced by lonizing radiation in human peripheral blood u-sing real-time PCR

International Nuclear Information System (INIS)

Duan Zhikai; Liu Jiangong; Guo Wanlong; Zhang Shuxian

2011-01-01

Objective: To observe the influence of mtDNA4977bp deletion induced by different dose of γ ray in human peripheral blood in order to explore the feasibility of mtDNA4977bp deletion as biodosimeter. Methods: Human peripheral blood samples were collected from three healthy donors and irradiated by γ ray, MtDNA4977bp deletion was detected by real-time PCR. Results: It indicated that that from the range of 0 ∼ 8 Gy, the relationship between mtDNA4977bp deletion and irradiation dose represents certain curvilinear correlation (Y=1.2693+1.0660X+0.0198X 2 ). Conclusion: We find that γ ray has influence on the mtDNA4977bp deletion, so it may be an important biodosmeter in future. (authors)

Deep sequencing shows that oocytes are not prone to accumulate mtDNA heteroplasmic mutations during ovarian ageing.

Science.gov (United States)

Boucret, L; Bris, C; Seegers, V; Goudenège, D; Desquiret-Dumas, V; Domin-Bernhard, M; Ferré-L'Hotellier, V; Bouet, P E; Descamps, P; Reynier, P; Procaccio, V; May-Panloup, P

2017-10-01

Does ovarian ageing increase the number of heteroplasmic mitochondrial DNA (mtDNA) point mutations in oocytes? Our results suggest that oocytes are not subject to the accumulation of mtDNA point mutations during ovarian ageing. Ageing is associated with the alteration of mtDNA integrity in various tissues. Primary oocytes, present in the ovary since embryonic life, may accumulate mtDNA mutations during the process of ovarian ageing. This was an observational study of 53 immature oocyte-cumulus complexes retrieved from 35 women undergoing IVF at the University Hospital of Angers, France, from March 2013 to March 2014. The women were classified in two groups, one including 19 women showing signs of ovarian ageing objectified by a diminished ovarian reserve (DOR), and the other, including 16 women with a normal ovarian reserve (NOR), which served as a control group. mtDNA was extracted from isolated oocytes, and from their corresponding cumulus cells (CCs) considered as a somatic cell compartment. The average mtDNA content of each sample was assessed by using a quantitative real-time PCR technique. Deep sequencing was performed using the Ion Torrent Proton for Next-Generation Sequencing. Signal processing and base calling were done by the embedded pre-processing pipeline and the variants were analyzed using an in-house workflow. The distribution of the different variants between DOR and NOR patients, on one hand, and oocyte and CCs, on the other, was analyzed with the generalized mixed linear model to take into account the cluster of cells belonging to a given mother. There were no significant differences between the numbers of mtDNA variants between the DOR and the NOR patients, either in the oocytes (P = 0.867) or in the surrounding CCs (P = 0.154). There were also no differences in terms of variants with potential functional consequences. De-novo mtDNA variants were found in 28% of the oocytes and in 66% of the CCs with the mean number of variants being

Perangkat Bantu Pendeteksi Kerusakan Smartphone Android Jaringan 3G menggunakan Metode Forward Chaining

Directory of Open Access Journals (Sweden)

Lisa Kurnia

2017-06-01

Full Text Available Telepon genggam (Handphone yang dahulu hanya berfungsi untuk menelepon dan mengirimkan pesan sekarang berkembang menjadi telepon pintar (Smartphone. Dalam perkembangannya sekarang smartphone bukan hanya sebagai alat komunikasi namun juga berfungsi sebagai alat yang memudahkan untuk mengakses internet ataupun mempermudah dalam transaksi online kebutuhan pengguna. Namun dalam penggunaannya jika terjadi kerusakan pada Smartphone umumnya pengguna tidak bisa mengetahui secara langsung jenis kerusakannya dan lebih memilih menyerahkannya pada teknisi atau tempat reparasi telepon. Dengan latar belakang tersebut, maka pembuatan penelitian ini, penulis membangun sebuah perangkat bantu untuk mendeteksi kerusakan pada smartphone menggunakan metode forward chaining. Desain perancangan sistem pakar  menggunakan UML (Unified Modelling Language untuk visualisasi, merancang dan mendokumentasikan sistem perangkat lunak. Yang dilakukan adalah dengan membuat Use Case Diagram dengan menjelaskan yang dilakukan oleh sistem yang dibangun dan siapa yang berinteraksi dengan sistem. Setelah itu dilanjutkan dengan pembuatan Class Diagram, diagram ini menggambarkan struktur statis dari sebuah sistem yang akan dibangun dan menjelaskan hubungan dari class-class yang ada secara logika.Hasil dari penelitian ini adalah aplikasi berbasis website dengan menggunakan bahasa pemrograman php. Dengan adanya aplikasi ini dapat mempermudah dan membantu pengguna atau teknisi smartphone untuk mendiagosa kerusakan smartphone dalam waktu yang relatif singkat.

Mutations of mtDNA polymerase-γ and hyperlactataemia in the HIV ...

African Journals Online (AJOL)

Mutations of mtDNA polymerase-γ and hyperlactataemia in the HIV-infected Zulu population of South Africa. ... D B A Ojwach, C Aldous, P Kocheleff, B Sartorius ... of their capacity to impede human mitochondrial DNA polymerase-γ (POLG), ...

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.

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

DEFF Research Database (Denmark)

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

2017-01-01

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 ≥ 45 years. The study shows that increased awareness of this symptom should be given to address appropriate...

Thymidine Kinase 2 Deficiency-Induced mtDNA Depletion in Mouse Liver Leads to Defect beta-Oxidation

OpenAIRE

Zhou, Xiaoshan; Kannisto, Kristina; Curbo, Sophie; von Dobeln, Ulrika; Hultenby, Kjell; Isetun, Sindra; Gåfvels, Mats; Karlsson, Anna

2013-01-01

Thymidine kinase 2 (TK2) deficiency in humans causes mitochondrial DNA (mtDNA) depletion syndrome. To study the molecular mechanisms underlying the disease and search for treatment options, we previously generated and described a TK2 deficient mouse strain (TK2(-/-)) that progressively loses its mtDNA. The TK2(-/-) mouse model displays symptoms similar to humans harboring TK2 deficient infantile fatal encephalomyopathy. Here, we have studied the TK2(-/-) mouse model to clarify the pathologica...

mtDNA variation in the Yanomami: evidence for additional New World founding lineages.

Science.gov (United States)

Easton, R D; Merriwether, D A; Crews, D E; Ferrell, R E

1996-07-01

Native Americans have been classified into four founding haplogroups with as many as seven founding lineages based on mtDNA RFLPs and DNA sequence data. mtDNA analysis was completed for 83 Yanomami from eight villages in the Surucucu and Catrimani Plateau regions of Roraima in northwestern Brazil. Samples were typed for 15 polymorphic mtDNA sites (14 RFLP sites and 1 deletion site), and a subset was sequenced for both hypervariable regions of the mitochondrial D-loop. Substantial mitochondrial diversity was detected among the Yanomami, five of seven accepted founding haplotypes and three others were observed. Of the 83 samples, 4 (4.8%) were lineage B1, 1 (1.2%) was lineage B2, 31 (37.4%) were lineage C1, 29 (34.9%) were lineage C2, 2 (2.4%) were lineage D1, 6 (7.2%) were lineage D2, 7 (8.4%) were a haplotype we designated "X6," and 3 (3.6%) were a haplotype we designated "X7." Sequence analysis found 43 haplotypes in 50 samples. B2, X6, and X7 are previously unrecognized mitochondrial founding lineage types of Native Americans. The widespread distribution of these haplotypes in the New World and Asia provides support for declaring these lineages to be New World founding types.

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

DESAIN DAN IMPLEMENTASI AUGMENTED REALITY BERBASIS WEB PADA APLIKASI FURNITURE SHOPPING MANAGER SEBAGAI ALAT BANTU BELANJA ONLINE

Directory of Open Access Journals (Sweden)

Basworo Ardi Pramono

2012-07-01

Full Text Available Dalam penulisan jurnal ini akan dibahas mengenai pengembangan aplikasi Furniture Shopping Manager (FSM sebagai suatu alat bantu yang dapat dimanfaatkan oleh para pemilik situs atau toko furniture secara online dalam menjual produknya.  FSM dirancang sebagai sebuah aplikasi berbasis web yang terintegrasi ke dalam suatu situs belanja online dengan fitur-fitur yang diharapkan dapat memberikan pengalaman yang baru, unik dan menarik dalam kegiatan belanja furniture online.   Aplikasi FSM dikembangkan dengan mengimplementasikan beberapa komponen  teknologi utama yaitu Augmented Reality (AR, engine 3D ke dalam aplikasi.  Keseluruhan komponen tersebut dirancang agar dapat  menghadirkan suasana belanja yang menarik di hadapan user secara digital. Dengan demikian user dapat mencoba apakah furniture yang di beli cocok dengan ruangan. Dengan menggunakan FSM, user dapat mencoba model 3D furniture, memilih model furniture hingga mengambil foto ruangannya dengan hasil visualisasi model furniture 3D yang disukai untuk selanjutnya dapat disimpan.

An economical mtDNA SNP assay detecting different mitochondrial haplogroups in identical HVR 1 samples of Caucasian ancestry.

Science.gov (United States)

Köhnemann, Stephan; Hohoff, Carsten; Pfeiffer, Heidi

2009-09-01

We had sequenced 329 Caucasian samples in Hypervariable Region 1 (HVR 1) and found that they belong to eleven different mitochondrial DNA (mtDNA) haplotypes. The sample set was further analysed by an mtDNA assay examining 32 single nucleotide polymorphisms (SNPs) for haplogroup discrimination. In a validation study on 160 samples of different origin it was shown that these SNPs were able to discriminate between the evolved superhaplogroups worldwide (L, M and N) and between the nine most common Caucasian haplogroups (H, I, J, K, T, U, V, W and X). The 32 mtDNA SNPs comprised 42 different SNP haplotypes instead of only eleven haplotypes after HVR 1 sequencing. The assay provided stable results in a range of 5ng genomic DNA down to virtually no genomic DNA per reaction. It was possible to detect samples of African, Asian and Eurasian ancestry, respectively. The 32 mtDNA SNP assay is a helpful adjunct to further distinguish between identical HVR 1 sequences of Caucasian origin. Our results suggest that haplogroup prediction using HVR 1 sequencing provides instable results. The use of coding region SNPs for haplogroup assignment is more suited than using HVR 1 haplotypes.

The mtDNA haplogroup P of modern Asian cattle: A genetic legacy of Asian aurochs?

Science.gov (United States)

Noda, Aoi; Yonesaka, Riku; Sasazaki, Shinji

2018-01-01

Background Aurochs (Bos primigenius) were distributed throughout large parts of Eurasia and Northern Africa during the late Pleistocene and the early Holocene, and all modern cattle are derived from the aurochs. Although the mtDNA haplogroups of most modern cattle belong to haplogroups T and I, several additional haplogroups (P, Q, R, C and E) have been identified in modern cattle and aurochs. Haplogroup P was the most common haplogroup in European aurochs, but so far, it has been identified in only three of >3,000 submitted haplotypes of modern Asian cattle. Methodology We sequenced the complete mtDNA D-loop region of 181 Japanese Shorthorn cattle and analyzed these together with representative bovine mtDNA sequences. The haplotype P of Japanese Shorthorn cattle was analyzed along with that of 36 previously published European aurochs and three modern Asian cattle sequences using the hypervariable 410 bp of the D-loop region. Conclusions We detected the mtDNA haplogroup P in Japanese Shorthorn cattle with an extremely high frequency (83/181). Phylogenetic networks revealed two main clusters, designated as Pa for haplogroup P in European aurochs and Pc in modern Asian cattle. We also report the genetic diversity of haplogroup P compared with the sequences of extinct aurochs. No shared haplotypes are observed between the European aurochs and the modern Asian cattle. This finding suggests the possibility of local and secondary introgression events of haplogroup P in northeast Asian cattle, and will contribute to a better understanding of its origin and genetic diversity. PMID:29304129

The mtDNA haplogroup P of modern Asian cattle: A genetic legacy of Asian aurochs?

Science.gov (United States)

Noda, Aoi; Yonesaka, Riku; Sasazaki, Shinji; Mannen, Hideyuki

2018-01-01

Aurochs (Bos primigenius) were distributed throughout large parts of Eurasia and Northern Africa during the late Pleistocene and the early Holocene, and all modern cattle are derived from the aurochs. Although the mtDNA haplogroups of most modern cattle belong to haplogroups T and I, several additional haplogroups (P, Q, R, C and E) have been identified in modern cattle and aurochs. Haplogroup P was the most common haplogroup in European aurochs, but so far, it has been identified in only three of >3,000 submitted haplotypes of modern Asian cattle. We sequenced the complete mtDNA D-loop region of 181 Japanese Shorthorn cattle and analyzed these together with representative bovine mtDNA sequences. The haplotype P of Japanese Shorthorn cattle was analyzed along with that of 36 previously published European aurochs and three modern Asian cattle sequences using the hypervariable 410 bp of the D-loop region. We detected the mtDNA haplogroup P in Japanese Shorthorn cattle with an extremely high frequency (83/181). Phylogenetic networks revealed two main clusters, designated as Pa for haplogroup P in European aurochs and Pc in modern Asian cattle. We also report the genetic diversity of haplogroup P compared with the sequences of extinct aurochs. No shared haplotypes are observed between the European aurochs and the modern Asian cattle. This finding suggests the possibility of local and secondary introgression events of haplogroup P in northeast Asian cattle, and will contribute to a better understanding of its origin and genetic diversity.

Defining mtDNA origins and population stratification in Rio de Janeiro.

Science.gov (United States)

Simão, Filipa; Ferreira, Ana Paula; de Carvalho, Elizeu Fagundes; Parson, Walther; Gusmão, Leonor

2018-05-01

The genetic composition of the Brazilian population was shaped by interethnic admixture between autochthonous Native Americans, Europeans settlers and African slaves. This structure, characteristic of most American populations, implies the need for large population forensic databases to capture the high diversity that is usually associated with admixed populations. In the present work, we sequenced the control region of mitochondrial DNA from 205 non-related individuals living in the Rio de Janeiro metropolitan region. Overall high haplotype diversity (0.9994 ± 0.0006) was observed, and pairwise comparisons showed a high proportion of haplotype pairs with more than one-point differences. When ignoring homopolymeric tracts, pairwise comparisons showed no differences 0.18% of the time, and differences in a single position were found with a frequency of 0.32%. A high percentage of African mtDNA was found (42%), with lineages showing a major South West origin. For the West Eurasian and Native American haplogroups (representing 32% and 26%, respectively) it was not possible to evaluate a clear geographic or linguistic affiliation. When grouping the mtDNA lineages according to their continental origin (Native American, European and African), differences were observed for the ancestry proportions estimated with autosomal ancestry-informative markers, suggesting some level of genetic substructure. The results from this study are in accordance with historical data where admixture processes are confirmed with a strong maternal contribution of African maternal ancestry and a relevant contribution of Native American maternal ancestry. Moreover, the evidence for some degree of association between mtDNA and autosomal information should be considered when combining these types of markers in forensic analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

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

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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.

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

Science.gov (United States)

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

2010-03-09

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

Cytoplasmic transfer of heritable elements other than mtDNA from SAMP1 mice into mouse tumor cells suppresses their ability to form tumors in C57BL6 mice.

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Shimizu, Akinori; Tani, Haruna; Takibuchi, Gaku; Ishikawa, Kaori; Sakurazawa, Ryota; Inoue, Takafumi; Hashimoto, Tetsuo; Nakada, Kazuto; Takenaga, Keizo; Hayashi, Jun-Ichi

2017-11-04

In a previous study, we generated transmitochondrial P29mtSAMP1 cybrids, which had nuclear DNA from the C57BL6 (referred to as B6) mouse strain-derived P29 tumor cells and mitochondrial DNA (mtDNA) exogenously-transferred from the allogeneic strain SAMP1. Because P29mtSAMP1 cybrids did not form tumors in syngeneic B6 mice, we proposed that allogeneic SAMP1 mtDNA suppressed tumor formation of P29mtSAMP1 cybrids. To test this hypothesis, current study generated P29mt(sp)B6 cybrids carrying all genomes (nuclear DNA and mtDNA) from syngeneic B6 mice by eliminating SAMP1 mtDNA from P29mtSAMP1 cybrids and reintroducing B6 mtDNA. However, the P29mt(sp)B6 cybrids did not form tumors in B6 mice, even though they had no SAMP1 mtDNA, suggesting that SAMP1 mtDNA is not involved in tumor suppression. Then, we examined another possibility of whether SAMP1 mtDNA fragments potentially integrated into the nuclear DNA of P29mtSAMP1 cybrids are responsible for tumor suppression. We generated P29 H (sp)B6 cybrids by eliminating nuclear DNA from P29mt(sp)B6 cybrids and reintroducing nuclear DNA with no integrated SAMP1 mtDNA fragment from mtDNA-less P29 cells resistant to hygromycin in selection medium containing hygromycin. However, the P29 H (sp)B6 cybrids did not form tumors in B6 mice, even though they carried neither SAMP1 mtDNA nor nuclear DNA with integrated SAMP1 mtDNA fragments. Moreover, overproduction of reactive oxygen species (ROS) and bacterial infection were not involved in tumor suppression. These observations suggest that tumor suppression was caused not by mtDNA with polymorphic mutations or infection of cytozoic bacteria but by hypothetical heritable cytoplasmic elements other than mtDNA from SAMP1 mice. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes.

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Streicher, Jeffrey W; McEntee, Jay P; Drzich, Laura C; Card, Daren C; Schield, Drew R; Smart, Utpal; Parkinson, Christopher L; Jezkova, Tereza; Smith, Eric N; Castoe, Todd A

2016-07-01

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern-local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation-not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male-biased dispersal. © 2016 The Author(s).

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

African Journals Online (AJOL)

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

The Mitochondrial DNA (mtDNA)-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination

KAUST Repository

Blomme, Jonas

2017-04-19

In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared with their animal counterparts, and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana. Gainand loss-of-function mutants provided evidence for a role of SWIB5 in influencing mtDNA architecture and homologous recombination at specific intermediate-sized repeats both under normal and genotoxic conditions. SWIB5 interacts with other mitochondrial SWIB proteins. Gene expression and mutant phenotypic analysis of SWIB5 and SWIB family members suggests a link between organellar genome maintenance and cell proliferation. Taken together, our work presents a protein family that influences mtDNA architecture and homologous recombination in plants and suggests a link between organelle functioning and plant development.

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. © 2014 Wiley Periodicals, Inc.

Anti-replicative recombinant 5S rRNA molecules can modulate the mtDNA heteroplasmy in a glucose-dependent manner.

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Loutre, Romuald; Heckel, Anne-Marie; Jeandard, Damien; Tarassov, Ivan; Entelis, Nina

2018-01-01

Mutations in mitochondrial DNA are an important source of severe and incurable human diseases. The vast majority of these mutations are heteroplasmic, meaning that mutant and wild-type genomes are present simultaneously in the same cell. Only a very high proportion of mutant mitochondrial DNA (heteroplasmy level) leads to pathological consequences. We previously demonstrated that mitochondrial targeting of small RNAs designed to anneal with mutant mtDNA can decrease the heteroplasmy level by specific inhibition of mutant mtDNA replication, thus representing a potential therapy. We have also shown that 5S ribosomal RNA, partially imported into human mitochondria, can be used as a vector to deliver anti-replicative oligoribonucleotides into human mitochondria. So far, the efficiency of cellular expression of recombinant 5S rRNA molecules bearing therapeutic insertions remained very low. In the present study, we designed new versions of anti-replicative recombinant 5S rRNA targeting a large deletion in mitochondrial DNA which causes the KSS syndrome, analyzed their specific annealing to KSS mitochondrial DNA and demonstrated their import into mitochondria of cultured human cells. To obtain an increased level of the recombinant 5S rRNA stable expression, we created transmitochondrial cybrid cell line bearing a site for Flp-recombinase and used this system for the recombinase-mediated integration of genes coding for the anti-replicative recombinant 5S rRNAs into nuclear genome. We demonstrated that stable expression of anti-replicative 5S rRNA versions in human transmitochondrial cybrid cells can induce a shift in heteroplasmy level of KSS mutation in mtDNA. This shift was directly dependent on the level of the recombinant 5S rRNA expression and the sequence of the anti-replicative insertion. Quantification of mtDNA copy number in transfected cells revealed the absence of a non-specific effect on wild type mtDNA replication, indicating that the decreased proportion

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....

Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds.

Science.gov (United States)

Guo, H W; Li, C; Wang, X N; Li, Z J; Sun, G R; Li, G X; Liu, X J; Kang, X T; Han, R L

2017-10-01

1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

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

Science.gov (United States)

Matte, Eunice M.; Castilho, Camila S.; Miotto, Renata A.; Sana, Denis A.; Johnson, Warren E.; O’Brien, Stephen J.; de Freitas, Thales R. O.; Eizirik, Eduardo

2013-01-01

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. PMID:24385863

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.

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

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Anderson Nonato do Rosário Marinho

2011-01-01

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

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.

Quantitation of heteroplasmy of mtDNA sequence variants identified in a population of AD patients and controls by array-based resequencing.

Science.gov (United States)

Coon, Keith D; Valla, Jon; Szelinger, Szabolics; Schneider, Lonnie E; Niedzielko, Tracy L; Brown, Kevin M; Pearson, John V; Halperin, Rebecca; Dunckley, Travis; Papassotiropoulos, Andreas; Caselli, Richard J; Reiman, Eric M; Stephan, Dietrich A

2006-08-01

The role of mitochondrial dysfunction in the pathogenesis of Alzheimer's disease (AD) has been well documented. Though evidence for the role of mitochondria in AD seems incontrovertible, the impact of mitochondrial DNA (mtDNA) mutations in AD etiology remains controversial. Though mutations in mitochondrially encoded genes have repeatedly been implicated in the pathogenesis of AD, many of these studies have been plagued by lack of replication as well as potential contamination of nuclear-encoded mitochondrial pseudogenes. To assess the role of mtDNA mutations in the pathogenesis of AD, while avoiding the pitfalls of nuclear-encoded mitochondrial pseudogenes encountered in previous investigations and showcasing the benefits of a novel resequencing technology, we sequenced the entire coding region (15,452 bp) of mtDNA from 19 extremely well-characterized AD patients and 18 age-matched, unaffected controls utilizing a new, reliable, high-throughput array-based resequencing technique, the Human MitoChip. High-throughput, array-based DNA resequencing of the entire mtDNA coding region from platelets of 37 subjects revealed the presence of 208 loci displaying a total of 917 sequence variants. There were no statistically significant differences in overall mutational burden between cases and controls, however, 265 independent sites of statistically significant change between cases and controls were identified. Changed sites were found in genes associated with complexes I (30.2%), III (3.0%), IV (33.2%), and V (9.1%) as well as tRNA (10.6%) and rRNA (14.0%). Despite their statistical significance, the subtle nature of the observed changes makes it difficult to determine whether they represent true functional variants involved in AD etiology or merely naturally occurring dissimilarity. Regardless, this study demonstrates the tremendous value of this novel mtDNA resequencing platform, which avoids the pitfalls of erroneously amplifying nuclear-encoded mtDNA pseudogenes, and

Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands.

Science.gov (United States)

Barik, S S; Sahani, R; Prasad, B V R; Endicott, P; Metspalu, M; Sarkar, B N; Bhattacharya, S; Annapoorna, P C H; Sreenath, J; Sun, D; Sanchez, J J; Ho, S Y W; Chandrasekar, A; Rao, V R

2008-05-01

The population genetics of the Indian subcontinent is central to understanding early human prehistory due to its strategic location on the proposed corridor of human movement from Africa to Australia during the late Pleistocene. Previous genetic research using mtDNA has emphasized the relative isolation of the late Pleistocene colonizers, and the physically isolated Andaman Island populations of Island South-East Asia remain the source of claims supporting an early split between the populations that formed the patchy settlement pattern along the coast of the Indian Ocean. Using whole-genome sequencing, combined with multiplexed SNP typing, this study investigates the deep structure of mtDNA haplogroups M31 and M32 in India and the Andaman Islands. The identification of a so far unnoticed rare polymorphism shared between these two lineages suggests that they are actually sister groups within a single haplogroup, M31'32. The enhanced resolution of M31 allows for the inference of a more recent colonization of the Andaman Islands than previously suggested, but cannot reject the very early peopling scenario. We further demonstrate a widespread overlap of mtDNA and cultural markers between the two major language groups of the Andaman archipelago. Given the "completeness" of the genealogy based on whole genome sequences, and the multiple scenarios for the peopling of the Andaman Islands sustained by this inferred genealogy, our study hints that further mtDNA based phylogeographic studies are unlikely to unequivocally support any one of these possibilities. (c) 2008 Wiley-Liss, Inc.

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

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Angela L Sremba

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

Somatic mtDNA mutation spectra in the aging human putamen.

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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.

Defects of mtDNA Replication Impaired Mitochondrial Biogenesis During Trypanosoma cruzi Infection in Human Cardiomyocytes and Chagasic Patients: The Role of Nrf1/2 and Antioxidant Response

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Wan, Xianxiu; Gupta, Shivali; Zago, Maria P.; Davidson, Mercy M.; Dousset, Pierre; Amoroso, Alejandro; Garg, Nisha Jain

2012-01-01

Background Mitochondrial dysfunction is a key determinant in chagasic cardiomyopathy development in mice; however, its relevance in human Chagas disease is not known. We determined if defects in mitochondrial biogenesis and dysregulation of peroxisome proliferator-activated receptor gamma (PPARγ) coactivator-1 (PGC-1)–regulated transcriptional pathways constitute a mechanism or mechanisms underlying mitochondrial oxidative-phosphorylation (OXPHOS) deficiency in human Chagas disease. Methods and Results We utilized human cardiomyocytes and left-ventricular tissue from chagasic and other cardiomyopathy patients and healthy donors (n>6/group). We noted no change in citrate synthase activity, yet mRNA and/or protein levels of subunits of the respiratory complexes were significantly decreased in Trypanosoma cruzi–infected cardiomyocytes (0 to 24 hours) and chagasic hearts. We observed increased mRNA and decreased nuclear localization of PGC-1-coactivated transcription factors, yet the expression of genes for PPARγ-regulated fatty acid oxidation and nuclear respiratory factor (NRF1/2)–regulated mtDNA replication and transcription machinery was enhanced in infected cardiomyocytes and chagasic hearts. The D-loop formation was normal or higher, but mtDNA replication and mtDNA content were decreased by 83% and 40% to 65%, respectively. Subsequently, we noted that reactive oxygen species (ROS), oxidative stress, and mtDNA oxidation were significantly increased, yet NRF1/2-regulated antioxidant gene expression remained compromised in infected cardiomyocytes and chagasic hearts. Conclusions The replication of mtDNA was severely compromised, resulting in a significant loss of mtDNA and expression of OXPHOS genes in T cruzi–infected cardiomyocytes and chagasic hearts. Our data suggest increased ROS generation and selective functional incapacity of NRF2-mediated antioxidant gene expression played a role in the defects in mtDNA replication and unfitness of mtDNA for

[Sequence polymorphism of mtDNA HVR Iand HVR II of Oroqen ethnic group in Inner Mongolia].

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Yan, Chun-Xia; Chen, Feng; Dang, Yong-Hui; Li, Tao; Zheng, Hai-Bo; Chen, Teng; Li, Sheng-Bin

2008-04-01

Venous blood samples from 50 unrelated Oroqen individuals living in Inner Mongolia were collected and their mtDNA HVR I and HVR II sequences were detected by using ABI PRISM377 sequencers. The number of polymorphic loci, haplotype, haplotype frequence, average nucleotide variability and other polymorphic parameters were calculated. Based on Oroqen mtDNA sequence data obtained in our experiments and published data, genetic distance between Oroqen ethnic group and other populations were computered by Nei's measure. Phylogenetic tree was constructed by Neighbor Joining method. Comparing with Anderson sequence, 52 polymorphic loci in HVR I and 24 loci in HVR II were found in Oroqen mtDNA sequence, 38 and 27 haplotypes were defined herewith. Haplotype diversity and average nucleotide variability were 0.964+/-0.018 and 7.379 in HVR I, 0.929+/-0.019 and 2.408 in HVR II respectively. Fst and dA genetic distance between 12 populations were calculated based on HVR I sequence, and their relative coefficients were 0.993(P HVR I and HVR II in Oroqen ethnic group has some specificities compared with that of other populations. These data provide a useful tool in forensic identification, population genetic study and other research fields.

Comparative mtDNA analyses of three sympatric macropodids from a conservation area on the Huon Peninsula, Papua New Guinea.

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McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2016-07-01

Matschie's tree kangaroo (Dendrolagus matschiei), New Guinea pademelon (Thylogale browni), and small dorcopsis (Dorcopsulus vanheurni) are sympatric macropodid taxa, of conservation concern, that inhabit the Yopno-Urawa-Som (YUS) Conservation Area on the Huon Peninsula, Papua New Guinea. We sequenced three partial mitochondrial DNA (mtDNA) genes from the three taxa to (i) investigate network structure; and (ii) identify conservation units within the YUS Conservation Area. All three taxa displayed a similar pattern in the spatial distribution of their mtDNA haplotypes and the Urawa and Som rivers on the Huon may have acted as a barrier to maternal gene flow. Matschie's tree kangaroo and New Guinea pademelon within the YUS Conservation Area should be managed as single conservation units because mtDNA nucleotides were not fixed for a given geographic area. However, two distinct conservation units were identified for small dorcopsis from the two different mountain ranges within the YUS Conservation Area.

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

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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.

Targeted transgenic overexpression of mitochondrial thymidine kinase (TK2) alters mitochondrial DNA (mtDNA) and mitochondrial polypeptide abundance: transgenic TK2, mtDNA, and antiretrovirals.

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Hosseini, Seyed H; Kohler, James J; Haase, Chad P; Tioleco, Nina; Stuart, Tami; Keebaugh, Erin; Ludaway, Tomika; Russ, Rodney; Green, Elgin; Long, Robert; Wang, Liya; Eriksson, Staffan; Lewis, William

2007-03-01

Mitochondrial toxicity limits nucleoside reverse transcriptase inhibitors (NRTIs) for acquired immune deficiency syndrome. NRTI triphosphates, the active moieties, inhibit human immunodeficiency virus reverse transcriptase and eukaryotic mitochondrial DNA polymerase pol-gamma. NRTI phosphorylation seems to correlate with mitochondrial toxicity, but experimental evidence is lacking. Transgenic mice (TGs) with cardiac overexpression of thymidine kinase isoforms (mitochondrial TK2 and cytoplasmic TK1) were used to study NRTI mitochondrial toxicity. Echocardiography and nuclear magnetic resonance imaging defined cardiac performance and structure. TK gene copy and enzyme activity, mitochondrial (mt) DNA and polypeptide abundance, succinate dehydrogenase and cytochrome oxidase histochemistry, and electron microscopy correlated with transgenesis, mitochondrial structure, and biogenesis. Antiretroviral combinations simulated therapy. Untreated hTK1 or TK2 TGs exhibited normal left ventricle mass. In TK2 TGs, cardiac TK2 gene copy doubled, activity increased 300-fold, and mtDNA abundance doubled. Abundance of the 17-kd subunit of complex I, succinate dehydrogenase histochemical activity, and cristae density increased. NRTIs increased left ventricle mass 20% in TK2 TGs. TK activity increased 3 logs in hTK1 TGs, but no cardiac phenotype resulted. NRTIs abrogated functional effects of transgenically increased TK2 activity but had no effect on TK2 mtDNA abundance. Thus, NRTI mitochondrial phosphorylation by TK2 is integral to clinical NRTI mitochondrial toxicity.

The extremely divergent maternally- and paternally-transmitted mitochondrial genomes are co-expressed in somatic tissues of two freshwater mussel species with doubly uniparental inheritance of mtDNA

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Breton, Sophie; Bouvet, Karim; Auclair, Gabrielle; Ghazal, Stephanie; Sietman, Bernard E.; Johnson, Nathan A.; Bettinazzi, Stefano; Dtewart, Donald T.; Guerra, Davide

2017-01-01

Freshwater mussel species with doubly uniparental inheritance (DUI) of mtDNA are unique because they are naturally heteroplasmic for two extremely divergent mtDNAs with ~50% amino acid differences for protein-coding genes. The paternally-transmitted mtDNA (or M mtDNA) clearly functions in sperm in these species, but it is still unknown whether it is transcribed when present in male or female soma. In the present study, we used PCR and RT-PCR to detect the presence and expression of the M mtDNA in male and female somatic and gonadal tissues of the freshwater mussel species Venustaconcha ellipsiformis and Utterbackia peninsularis (Unionidae). This is the first study demonstrating that the M mtDNA is transcribed not only in male gonads, but also in male and female soma in freshwater mussels with DUI. Because of the potentially deleterious nature of heteroplasmy, we suggest the existence of different mechanisms in DUI species to deal with this possibly harmful situation, such as silencing mechanisms for the M mtDNA at the transcriptional, post-transcriptional and/or post-translational levels. These hypotheses will necessitate additional studies in distantly-related DUI species that could possess different mechanisms of action to deal with heteroplasmy.

Heterozygous SSBP1 start loss mutation co-segregates with hearing loss and the m.1555A>G mtDNA variant in a large multigenerational family.

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Kullar, Peter J; Gomez-Duran, Aurora; Gammage, Payam A; Garone, Caterina; Minczuk, Michal; Golder, Zoe; Wilson, Janet; Montoya, Julio; Häkli, Sanna; Kärppä, Mikko; Horvath, Rita; Majamaa, Kari; Chinnery, Patrick F

2018-01-01

The m.1555A>G mtDNA variant causes maternally inherited deafness, but the reasons for the highly variable clinical penetrance are not known. Exome sequencing identified a heterozygous start loss mutation in SSBP1, encoding the single stranded binding protein 1 (SSBP1), segregating with hearing loss in a multi-generational family transmitting m.1555A>G, associated with mtDNA depletion and multiple deletions in skeletal muscle. The SSBP1 mutation reduced steady state SSBP1 levels leading to a perturbation of mtDNA metabolism, likely compounding the intra-mitochondrial translation defect due to m.1555A>G in a tissue-specific manner. This family demonstrates the importance of rare trans-acting genetic nuclear modifiers in the clinical expression of mtDNA disease. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain.

mtDNA depletion myopathy: elucidation of the tissue specificity in the mitochondrial thymidine kinase (TK2) deficiency.

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Saada, Ann; Shaag, Avraham; Elpeleg, Orly

2003-05-01

Decreased mitochondrial thymidine kinase (TK2) activity is associated with mitochondrial DNA (mtDNA) depletion and respiratory chain dysfunction and is manifested by isolated, fatal skeletal myopathy. Other tissues such as liver, brain, heart, and skin remain unaffected throughout the patients' life. In order to elucidate the mechanism of tissue specificity in the disease we have investigated the expression of the mitochondrial deoxynucleotide carrier, the mtDNA content and the activity of TK2 in mitochondria of various tissues. Our results suggest that low basal TK2 activity combined with a high requirement for mitochondrial encoded proteins in muscle predispose this tissue to the devastating effect of TK2 deficiency.

A novel quantitative assay of mitophagy: Combining high content fluorescence microscopy and mitochondrial DNA load to quantify mitophagy and identify novel pharmacological tools against pathogenic heteroplasmic mtDNA.

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Diot, Alan; Hinks-Roberts, Alex; Lodge, Tiffany; Liao, Chunyan; Dombi, Eszter; Morten, Karl; Brady, Stefen; Fratter, Carl; Carver, Janet; Muir, Rebecca; Davis, Ryan; Green, Charlotte J; Johnston, Iain; Hilton-Jones, David; Sue, Carolyn; Mortiboys, Heather; Poulton, Joanna

2015-10-01

Mitophagy is a cellular mechanism for the recycling of mitochondrial fragments. This process is able to improve mitochondrial DNA (mtDNA) quality in heteroplasmic mtDNA disease, in which mutant mtDNA co-exists with normal mtDNA. In disorders where the load of mutant mtDNA determines disease severity it is likely to be an important determinant of disease progression. Measuring mitophagy is technically demanding. We used pharmacological modulators of autophagy to validate two techniques for quantifying mitophagy. First we used the IN Cell 1000 analyzer to quantify mitochondrial co-localisation with LC3-II positive autophagosomes. Unlike conventional fluorescence and electron microscopy, this high-throughput system is sufficiently sensitive to detect transient low frequency autophagosomes. Secondly, because mitophagy preferentially removes pathogenic heteroplasmic mtDNA mutants, we developed a heteroplasmy assay based on loss of m.3243A>G mtDNA, during culture conditions requiring oxidative metabolism ("energetic stress"). The effects of the pharmacological modulators on these two measures were consistent, confirming that the high throughput imaging output (autophagosomes co-localising with mitochondria) reflects mitochondrial quality control. To further validate these methods, we performed a more detailed study using metformin, the most commonly prescribed antidiabetic drug that is still sometimes used in Maternally Inherited Diabetes and Deafness (MIDD). This confirmed our initial findings and revealed that metformin inhibits mitophagy at clinically relevant concentrations, suggesting that it may have novel therapeutic uses. Copyright © 2015. Published by Elsevier Ltd.

Heterogeneous periodicity of drosophila mtDNA: new refutations of neutral and nearly neutral evolution

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Carlos Y Valenzuela

2011-01-01

Full Text Available We found a consistent 3-site periodicity of the X²9 values for the heterogeneity of the distribution of the second base in relation to the first base of dinucleotides separated by 0 (contiguous, 1, 2, 3 ... 17 (K nucleotide sites in Drosophila mtDNA. Triplets of X²9 values were found where the first was over 300 and the second and third ranged between 37 and 114 (previous studies. In this study, the periodicity was significant until separation of 2011K, and a structure of deviations from randomness among dinucleotides was found. The most deviant dinucleotides were G-G, G-C and C-G for the first, second and third element of the triplet, respectively. In these three cases there were more dinucleotides observed than expected. This inter-bases correlation and periodicity may be related to the tertiary structure of circular DNA, like that of prokaryotes and mitochondria, to protect and preserve it. The mtDNA with 19.517 bp was divided into four equal segments of 4.879 bp. The fourth sub-segment presented a very low proportion of G and C, the internucleotide interaction was weaker in this sub-segment and no periodicity was found. The maintenance of this mtDNA structure and organization for millions of generations, in spite of a high recurrent mutation rate, does not support the notion of neutralism or near neutralism. The high level of internucleotide interaction and periodicity indicate that every nucleotide is co-adapted with the residual genome.

Comprehensive view of the population history of Arabia as inferred by mtDNA variation

Czech Academy of Sciences Publication Activity Database

Černý, Viktor; Čížková, M.; Poloni, E. S.; Al-Meeri, A.; Mulligan, C. J.

2016-01-01

Roč. 159, č. 4 (2016), s. 607-616 ISSN 0002-9483 R&D Projects: GA ČR GA13-37998S Institutional support: RVO:67985912 Keywords : mtDNA variation * Arabian Peninsula * migrations Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 2.552, year: 2016

Recent introgressive hybridization revealed by exclusive mtDNA transfer from Oreochromis leucostictus (Trewavas, 1933) to Oreochromis niloticus (Linnaeus, 1758) in Lake Baringo, Kenya

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Nyingi, Dorothy W.; Agnèse, Jean-François

2007-01-01

Nuclear DNA and mtDNA polymorphisms were surveyed in various species of East African Oreochromis. In Lake Baringo, where only Oreochromis niloticus baringoensis is present, alien mtDNA haplotypes were observed, apparently the result of introgressive hybridization with Oreochromis leucostictus. This introgression is not accompanied by any substantial or recorded transfer of nuclear genes into O. n. baringoensis.

MtDNA genomes reveal a relaxation of selective constraints in low-BMI individuals in a Uyghur population.

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Zheng, Hong-Xiang; Li, Lei; Jiang, Xiao-Yan; Yan, Shi; Qin, Zhendong; Wang, Xiaofeng; Jin, Li

2017-10-01

Considerable attention has been focused on the effect of deleterious mutations caused by the recent relaxation of selective constraints on human health, including the prevalence of obesity, which might represent an adaptive response of energy-conserving metabolism under the conditions of modern society. Mitochondrial DNA (mtDNA) encoding 13 core subunits of oxidative phosphorylation plays an important role in metabolism. Therefore, we hypothesized that a relaxation of selection constraints on mtDNA and an increase in the proportion of deleterious mutations have played a role in obesity prevalence. In this study, we collected and sequenced the mtDNA genomes of 722 Uyghurs, a typical population with a high prevalence of obesity. We identified the variants that occurred in the Uyghur population for each sample and found that the number of nonsynonymous mutations carried by Uyghur individuals declined with elevation of their BMI (P = 0.015). We further calculated the nonsynonymous and synonymous ratio (N/S) of the high-BMI and low-BMI haplogroups, and the results showed that a significantly higher N/S occurred in the whole mtDNA genomes of the low-BMI haplogroups (0.64) than in that of the high-BMI haplogroups (0.35, P = 0.030) and ancestor haplotypes (0.41, P = 0.032); these findings indicated that low-BMI individuals showed a recent relaxation of selective constraints. In addition, we investigated six clinical characteristics and found that fasting plasma glucose might be correlated with the N/S and selective pressures. We hypothesized that a higher proportion of deleterious mutations led to mild mitochondrial dysfunction, which helps to drive glucose consumption and thereby prevents obesity. Our results provide new insights into the relationship between obesity predisposition and mitochondrial genome evolution.

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

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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.

Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation

Czech Academy of Sciences Publication Activity Database

Al-Abri, A.-R.; Podgorná, E.; Rose, J. I.; Pereira, L.; Mulligan, C. J.; Silva, N. M.; Bayoumi, R.; Soares, P.; Černý, Viktor

2012-01-01

Roč. 149, č. 2 (2012), s. 291-298 ISSN 0002-9483 R&D Projects: GA MŠk ME 917 Institutional research plan: CEZ:AV0Z80020508 Keywords : mtDNA variation * Arabian Peninsula * migrations Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 2.481, year: 2012

mtDNA of Fulani Nomads and Their Genetic Relationships to Neighboring Sedentary Populations

Czech Academy of Sciences Publication Activity Database

Černý, Viktor; Hájek, Martin; Bromová, Markéta; Čmejla, R.; Diallo, I.; Brdička, R.

2006-01-01

Roč. 78, č. 1 (2006), s. 9-27 ISSN 0018-7143 R&D Projects: GA ČR(CZ) GA404/03/0318 Institutional research plan: CEZ:AV0Z80020508 Keywords : mtDNA variation * HVS-I * Fulani nomads * sub-Saharan populations * Chad * Cameroon * Burkina Faso Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 1.132, year: 2006

Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity.

Science.gov (United States)

Costa, Marta D; Cherni, Lotfi; Fernandes, Verónica; Freitas, Fernando; Ammar El Gaaied, Amel Ben; Pereira, Luísa

2009-04-01

Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.

Global mtDNA genetic structure and hypothesized invasion history of a major pest of citrus, Diaphorina citri (Hemiptera: Liviidae).

Science.gov (United States)

Luo, Yufa; Agnarsson, Ingi

2018-01-01

The Asian citrus psyllid Diaphorina citri Kuwayama is a key pest of citrus as the vector of the bacterium causing the "huanglongbing" disease (HLB). To assess the global mtDNA population genetic structure, and possible dispersal history of the pest, we investigated genetic variation at the COI gene collating newly collected samples with all previously published data. Our dataset consists of 356 colonies from 106 geographic sites worldwide. High haplotype diversity (H-mean = 0.702 ± 0.017), low nucleotide diversity (π-mean = 0.003), and significant positive selection (Ka/Ks = 32.92) were observed. Forty-four haplotypes (Hap) were identified, clustered into two matrilines: Both occur in southeastern and southern Asia, North and South America, and Africa; lineages A and B also occur in eastern and western Asia, respectively. The most abundant haplotypes were Hap4 in lineage A (35.67%), and Hap9 in lineage B (41.29%). The haplotype network identified them as the ancestral haplotypes within their respective lineages. Analysis of molecular variance showed significant genetic structure ( F ST  = 0.62, p  analysis suggests geographic structuring. We hypothesize a southern and/or southeastern Asia origin, three dispersal routes, and parallel expansions of two lineages. The hypothesized first route involved the expansion of lineage B from southern Asia into North America via West Asia. The second, the expansion of some lineage A individuals from Southeast Asia into East Asia, and the third involved both lineages from Southeast Asia spreading westward into Africa and subsequently into South America. To test these hypotheses and gain a deeper understanding of the global history of D. citri , more data-rich approaches will be necessary from the ample toolkit of next-generation sequencing (NGS). However, this study may serve to guide such sampling and in the development of biological control programs against the global pest D. citri .

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

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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.

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

Science.gov (United States)

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

2006-01-01

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

Neurotoxicity of cytarabine (Ara-C) in dorsal root ganglion neurons originates from impediment of mtDNA synthesis and compromise of mitochondrial function.

Science.gov (United States)

Zhuo, Ming; Gorgun, Murat F; Englander, Ella W

2018-06-01

Peripheral Nervous System (PNS) neurotoxicity caused by cancer drugs hinders attainment of chemotherapy goals. Due to leakiness of the blood nerve barrier, circulating chemotherapeutic drugs reach PNS neurons and adversely affect their function. Chemotherapeutic drugs are designed to target dividing cancer cells and mechanisms underlying their toxicity in postmitotic neurons remain to be fully clarified. The objective of this work was to elucidate progression of events triggered by antimitotic drugs in postmitotic neurons. For proof of mechanism study, we chose cytarabine (ara-C), an antimetabolite used in treatment of hematological cancers. Ara-C is a cytosine analog that terminates DNA synthesis. To investigate how ara-C affects postmitotic neurons, which replicate mitochondrial but not genomic DNA, we adapted a model of Dorsal Root Ganglion (DRG) neurons. We showed that DNA polymerase γ, which is responsible for mtDNA synthesis, is inhibited by ara-C and that sublethal ara-C exposure of DRG neurons leads to reduction in mtDNA content, ROS generation, oxidative mtDNA damage formation, compromised mitochondrial respiration and diminution of NADPH and GSH stores, as well as, activation of the DNA damage response. Hence, it is plausible that in ara-C exposed DRG neurons, ROS amplified by the high mitochondrial content shifts from physiologic to pathologic levels signaling stress to the nucleus. Combined, the findings suggest that ara-C neurotoxicity in DRG neurons originates in mitochondria and that continuous mtDNA synthesis and reliance on oxidative phosphorylation for energy needs sensitize the highly metabolic neurons to injury by mtDNA synthesis terminating cancer drugs. Copyright © 2018 Elsevier Inc. All rights reserved.

Human Retinal Transmitochondrial Cybrids with J or H mtDNA Haplogroups Respond Differently to Ultraviolet Radiation: Implications for Retinal Diseases

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Malik, Deepika; Hsu, Tiffany; Falatoonzadeh, Payam; Cáceres-del-Carpio, Javier; Tarek, Mohamed; Chwa, Marilyn; Atilano, Shari R.; Ramirez, Claudio; Nesburn, Anthony B.; Boyer, David S.; Kuppermann, Baruch D.; Jazwinski, S. Michal; Miceli, Michael V.; Wallace, Douglas C.; Udar, Nitin; Kenney, M. Cristina

2014-01-01

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

MtDNA variation in the Altai-Kizhi population of southern Siberia: a synthesis of genetic variation.

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Phillips-Krawczak, Christine; Devor, Eric; Zlojutro, Mark; Moffat-Wilson, Kristin; Crawford, Michael H

2006-08-01

The native peoples of Gorno Altai in southern Siberia represent a genetically diverse population and have been of great interest to anthropological genetics. In particular, the southern Altaian population is argued to be the best candidate for the New World ancestral population. In this study we sampled Altai-Kizhi from the southern Altaian village of Mendur-Sokkon, analyzed mtDNA RFLP markers and HVS-I sequences, and compared the results to other published mtDNA data from Derenko et al. (2003) and Shields et al. (1993) encompassing the same region. Because each independent study uses different sampling techniques in characterizing gene pools, in this paper we explore the accuracy and reliability of evolutionary studies on human populations. All the major Native American haplogroups (A, B, C, and D) were identified in the Mendur-Sokkon sample, including a single individual belonging to haplogroup X. The most common mtDNA lineages are C (35.7%) and D (13.3%), which is consistent with the haplogroup profiles of neighboring Siberian groups. The Mendur-Sokkon sample exhibits depressed HVS-I diversity values and neutrality test scores, which starkly differs from the Derenko et al. (2003) data set and more closely resembles the results for neighboring south Siberian groups. Furthermore, the multidimensional scaling plot of DA genetic distances does not cluster the Altai samples, showing different genetic affinities with various Asian groups. The findings underscore the importance of sampling strategy in the reconstruction of evolutionary history at the population level.

MtDNA barcode identification of fish larvae in the southern Great Barrier Reef – Australia

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Graham G. Pegg

2006-10-01

Full Text Available Planktonic larvae were captured above a shallow coral reef study site on the Great Barrier Reef (GBR around spring-summer new moon periods (October-February using light trap or net capture devices. Larvae were identified to the genus or species level by comparison with a phylogenetic tree of tropical marine fish species using mtDNA HVR1 sequence data. Further analysis showed that within-species HVR1 sequence variation was typically 1-3%, whereas between-species variation for the same genus ranged up to 50%, supporting the suitability of HVR1 for species identification. Given the current worldwide interest in DNA barcoding and species identification using an alternative mtDNA gene marker (cox1, we also explored the efficacy of different primer sets for amplification of cox1 in reef fish, and its suitability for species identification. Of those tested, the Fish-F1 and -R1 primer set recently reported by Ward et al. (2005 gave the best results.

Data on haplotype diversity in the hypervariable region I, II and III of mtDNA amongst the Brahmin population of Haryana

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Kapil Verma

2018-04-01

Full Text Available Human mitochondrial DNA (mtDNA is routinely analysed for pathogenic mutations, evolutionary studies, estimation of time of divergence within or between species, phylogenetic studies and identification of degraded remains. The data on various regions of human mtDNA has added enormously to the knowledge pool of population genetics as well as forensic genetics. The displacement-loop (D-loop in the control region of mtDNA is rated as the most rapidly evolving part, due to the presence of variations in this region. The control region consists of three hypervariable regions. These hypervariable regions (HVI, HVII and HVIII tend to mutate 5–10 times faster than nuclear DNA. The high mutation rate of these hypervariable regions is used in population genetic studies and human identity testing. In the present data, potentially informative hypervariable regions of mitochondrial DNA (mtDNA i.e. HVI (np 16024–16365, HVII (np 73–340 and HVIII (np 438–576 were estimated to understand the genetic diversity amongst Brahmin population of Haryana. Blood samples had been collected from maternally unrelated individuals from the different districts of Haryana. An array of parameters comprising of polymorphic sites, transitions, transversions, deletions, gene diversity, nucleotide diversity, pairwise differences, Tajima's D test, Fu's Fs test, mismatch observed variance and expected heterozygosity were estimated. The observed polymorphisms with their respective haplogroups in comparison to rCRS were assigned. Keywords: Mitochondrial DNA, D-loop, Hypervariable regions, Forensic genetics

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

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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...

The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies.

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Alessandro Achilli

Full Text Available Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s contributed only six (successful founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.

mtDNA as a Mediator for Expression of Hypoxia-Inducible Factor 1α and ROS in Hypoxic Neuroblastoma Cells.

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Kuo, Chung-Wen; Tsai, Meng-Han; Lin, Tsu-Kung; Tiao, Mao-Meng; Wang, Pei-Wen; Chuang, Jiin-Haur; Chen, Shang-Der; Liou, Chia-Wei

2017-06-07

Mitochondria consume O₂ to produce ATP and are critical for adaption of hypoxia, but the role of mitochondria in HIF-1α pathway is as yet unclear. In this study, mitochondrial DNA (mtDNA) enriched (SK-N-AS) and depleted (ρ⁰) cells of neuroblastoma were cultured in a hypoxic chamber to simulate a hypoxic condition and then the major components involved in mitochondrial related pathways, hypoxia-inducible factor 1α (HIF-1α) and reactive oxygen species (ROS) were measured. The results showed that hypoxia-stimulated exposure elevated expression of HIF-1α, which was additionally influenced by level of generated ROS within the cytosol. Moreover, elevation of HIF-1α also resulted in increases of lactate dehydrogenase A (LDH-A) and pyruvate dehydrogenase kinase 1 (PDK1) in both hypoxic cells. The expression of mitochondrial biogenesis related proteins and metabolic components were noted to increase significantly in hypoxic SK-N-AS cells, indicating that mtDNA was involved in mitochondrial retrograde signaling and metabolic pathways. An analysis of dynamic proteins found elevated levels of HIF-1α causing an increased expression of dynamin-related protein 1 (DRP1) during hypoxia; further, the existence of mtDNA also resulted in higher expression of DRP1 during hypoxia. By using siRNA of HIF-1α or DRP1, expression of DRP1 decreased after suppression of HIF-1α; moreover, the expression of HIF-1α was also affected by the suppression of DRP1. In this study, we demonstrated that mtDNA is a mediator of HIF-1α in eliciting metabolic reprogramming, and mitochondrial biogenesis. Identification of a mutual relationship between HIF-1α and DRP1 may be a critical tool in the future development of clinical applications.

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

OpenAIRE

Barros, Maria Claudene; Sampaio, Iracilda; Schneider, Horacio

2008-01-01

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...

Forensic and phylogeographic characterisation of mtDNA lineages from Somalia

DEFF Research Database (Denmark)

Mikkelsen, Martin; Fendt, Liane; Röck, Alexander W.

2012-01-01

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...

Sex-specific influences of mtDNA mitotype and diet on mitochondrial functions and physiological traits in Drosophila melanogaster.

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Wen C Aw

Full Text Available Here we determine the sex-specific influence of mtDNA type (mitotype and diet on mitochondrial functions and physiology in two Drosophila melanogaster lines. In many species, males and females differ in aspects of their energy production. These sex-specific influences may be caused by differences in evolutionary history and physiological functions. We predicted the influence of mtDNA mutations should be stronger in males than females as a result of the organelle's maternal mode of inheritance in the majority of metazoans. In contrast, we predicted the influence of diet would be greater in females due to higher metabolic flexibility. We included four diets that differed in their protein: carbohydrate (P:C ratios as they are the two-major energy-yielding macronutrients in the fly diet. We assayed four mitochondrial function traits (Complex I oxidative phosphorylation, reactive oxygen species production, superoxide dismutase activity, and mtDNA copy number and four physiological traits (fecundity, longevity, lipid content, and starvation resistance. Traits were assayed at 11 d and 25 d of age. Consistent with predictions we observe that the mitotype influenced males more than females supporting the hypothesis of a sex-specific selective sieve in the mitochondrial genome caused by the maternal inheritance of mitochondria. Also, consistent with predictions, we found that the diet influenced females more than males.

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

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Sell Jerzy

2007-09-01

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

Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors

International Nuclear Information System (INIS)

Pereira, Luísa; Soares, Pedro; Máximo, Valdemar; Samuels, David C

2012-01-01

The presence of somatic mitochondrial DNA (mtDNA) mutations in cancer cells has been interpreted in controversial ways, ranging from random neutral accumulation of mutations, to positive selection for high pathogenicity, or conversely to purifying selection against high pathogenicity variants as occurs at the population level. Here we evaluated the predicted pathogenicity of somatic mtDNA mutations described in cancer and compare these to the distribution of variations observed in the global human population and all possible protein variations that could occur in human mtDNA. We focus on oncocytic tumors, which are clearly associated with mitochondrial dysfunction. The protein variant pathogenicity was predicted using two computational methods, MutPred and SNPs&GO. The pathogenicity score of the somatic mtDNA variants were significantly higher in oncocytic tumors compared to non-oncocytic tumors. Variations in subunits of Complex I of the electron transfer chain were significantly more common in tumors with the oncocytic phenotype, while variations in Complex V subunits were significantly more common in non-oncocytic tumors. Our results show that the somatic mtDNA mutations reported over all tumors are indistinguishable from a random selection from the set of all possible amino acid variations, and have therefore escaped the effects of purifying selection that act strongly at the population level. We show that the pathogenicity of somatic mtDNA mutations is a determining factor for the oncocytic phenotype. The opposite associations of the Complex I and Complex V variants with the oncocytic and non-oncocytic tumors implies that low mitochondrial membrane potential may play an important role in determining the oncocytic phenotype

Phenotypic and mtDNA variation in Philippine Kappaphycus cottonii (Gigartinales, Rhodophyta).

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Dumilag, Richard V; Gallardo, William George M; Garcia, Christian Philip C; You, YeaEun; Chaves, Alyssa Keren G; Agahan, Lance

2017-11-09

Members of the carrageenan-producing seaweeds of the genus Kappapphycus have a complicated taxonomic history particularly with regard to species identification. Many taxonomic challenges in this group have been currently addressed with the use of mtDNA sequences. The phylogenetic status and genetic diversity of one of the lesser known species, Kappaphycus cottonii, have repeatedly come into question. This study explored the genetic variation in Philippine K. cottonii using the mtDNA COI-5P gene and cox2-3 spacer sequences. The six phenotypic forms in K. cottonii did not correspond to the observed genetic variability; hinting at the greater involvement of environmental factors in determining changes to the morphology of this alga. Our results revealed that the Philippine K. cottonii has the richest number of haplotypes that have been detected, so far, for any Kappaphycus species. Our inferred phylogenetic trees suggested two lineages: a lineage, which exclusively includes K. cottonii and another lineage comprising the four known Kappaphycus species: K. alvarezii, K. inermis, K. malesianus, and K. striatus. The dichotomy supports the apparent synamorphy for each of these lineages (the strictly terete thalli, lack of protuberances, and the presence of a hyphal central core in the latter group, while the opposite of these morphologies in K. cottonii). These findings shed new light on understanding the evolutionary history of the genus. Assessing the breadth of the phenotypic and genetic variation in K. cottonii has implications for the conservation and management of the overall Kappaphycus genetic resources, especially in the Philippines.

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

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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

'Mitominis': multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples.

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Eichmann, Cordula; Parson, Walther

2008-09-01

The traditional protocol for forensic mitochondrial DNA (mtDNA) analyses involves the amplification and sequencing of the two hypervariable segments HVS-I and HVS-II of the mtDNA control region. The primers usually span fragment sizes of 300-400 bp each region, which may result in weak or failed amplification in highly degraded samples. Here we introduce an improved and more stable approach using shortened amplicons in the fragment range between 144 and 237 bp. Ten such amplicons were required to produce overlapping fragments that cover the entire human mtDNA control region. These were co-amplified in two multiplex polymerase chain reactions and sequenced with the individual amplification primers. The primers were carefully selected to minimize binding on homoplasic and haplogroup-specific sites that would otherwise result in loss of amplification due to mis-priming. The multiplexes have successfully been applied to ancient and forensic samples such as bones and teeth that showed a high degree of degradation.

Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses.

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Lin, Xiang; Zheng, Hong-Xiang; Davie, Allan; Zhou, Shi; Wen, Li; Meng, Jun; Zhang, Yong; Aladaer, Qimude; Liu, Bin; Liu, Wu-Jun; Yao, Xin-Kui

2018-03-01

Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens.

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Larissa Rosa de Oliveira

Full Text Available The South American sea lion (Otaria flavescens is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil, Argentina and Falkland (Malvinas Islands and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean.

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens)

Science.gov (United States)

Gehara, Marcelo C. M.; Fraga, Lúcia D.; Lopes, Fernando; Túnez, Juan Ignacio; Cassini, Marcelo H.; Majluf, Patricia; Cárdenas-Alayza, Susana; Pavés, Héctor J.; Crespo, Enrique Alberto; García, Nestor; Loizaga de Castro, Rocío; Hoelzel, A. Rus; Sepúlveda, Maritza; Olavarría, Carlos; Valiati, Victor Hugo; Quiñones, Renato; Pérez-Alvarez, Maria Jose; Ott, Paulo Henrique

2017-01-01

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean. PMID:28654647

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

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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

What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

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Alexander, Alana; Steel, Debbie; Hoekzema, Kendra; Mesnick, Sarah L; Engelhaupt, Daniel; Kerr, Iain; Payne, Roger; Baker, C Scott

2016-06-01

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394-bp mtDNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (π = 0.430%) reflecting an expansion event worldwide population expansion followed by rapid assortment due to female social organization. © 2016 John Wiley & Sons Ltd.

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

Science.gov (United States)

Speller, Camilla F; Nicholas, George P; Yang, Dongya Y

2011-07-28

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. By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mt)DNA-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. 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.

A Signal, from Human mtDNA, of Postglacial Recolonization in Europe

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Torroni, Antonio; Bandelt, Hans-Jürgen; Macaulay, Vincent; Richards, Martin; Cruciani, Fulvio; Rengo, Chiara; Martinez-Cabrera, Vicente; Villems, Richard; Kivisild, Toomas; Metspalu, Ene; Parik, Jüri; Tolk, Helle-Viivi; Tambets, Kristiina; Forster, Peter; Karger, Bernd; Francalacci, Paolo; Rudan, Pavao; Janicijevic, Branka; Rickards, Olga; Savontaus, Marja-Liisa; Huoponen, Kirsi; Laitinen, Virpi; Koivumäki, Satu; Sykes, Bryan; Hickey, Eileen; Novelletto, Andrea; Moral, Pedro; Sellitto, Daniele; Coppa, Alfredo; Al-Zaheri, Nadia; Santachiara-Benerecetti, A. Silvana; Semino, Ornella; Scozzari, Rosaria

2001-01-01

Mitochondrial HVS-I sequences from 10,365 subjects belonging to 56 populations/geographical regions of western Eurasia and northern Africa were first surveyed for the presence of the T→C transition at nucleotide position 16298, a mutation which has previously been shown to characterize haplogroup V mtDNAs. All mtDNAs with this mutation were then screened for a number of diagnostic RFLP sites, revealing two major subsets of mtDNAs. One is haplogroup V proper, and the other has been termed “pre*V,” since it predates V phylogenetically. The rather uncommon pre*V tends to be scattered throughout Europe (and northwestern Africa), whereas V attains two peaks of frequency: one situated in southwestern Europe and one in the Saami of northern Scandinavia. Geographical distributions and ages support the scenario that pre*V originated in Europe before the Last Glacial Maximum (LGM), whereas the more recently derived haplogroup V arose in a southwestern European refugium soon after the LGM. The arrival of V in eastern/central Europe, however, occurred much later, possibly with (post-)Neolithic contacts. The distribution of haplogroup V mtDNAs in modern European populations would thus, at least in part, reflect the pattern of postglacial human recolonization from that refugium, affecting even the Saami. Overall, the present study shows that the dissection of mtDNA variation into small and well-defined evolutionary units is an essential step in the identification of spatial frequency patterns. Mass screening of a few markers identified using complete mtDNA sequences promises to be an efficient strategy for inferring features of human prehistory. PMID:11517423

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel.

Science.gov (United States)

Pereira, Luísa; Cerný, Viktor; Cerezo, María; Silva, Nuno M; Hájek, Martin; Vasíková, Alzbeta; Kujanová, Martina; Brdicka, Radim; Salas, Antonio

2010-08-01

The Tuareg presently live in the Sahara and the Sahel. Their ancestors are commonly believed to be the Garamantes of the Libyan Fezzan, ever since it was suggested by authors of antiquity. Biological evidence, based on classical genetic markers, however, indicates kinship with the Beja of Eastern Sudan. Our study of mitochondrial DNA (mtDNA) sequences and Y chromosome SNPs of three different southern Tuareg groups from Mali, Burkina Faso and the Republic of Niger reveals a West Eurasian-North African composition of their gene pool. The data show that certain genetic lineages could not have been introduced into this population earlier than approximately 9000 years ago whereas local expansions establish a minimal date at around 3000 years ago. Some of the mtDNA haplogroups observed in the Tuareg population were involved in the post-Last Glacial Maximum human expansion from Iberian refugia towards both Europe and North Africa. Interestingly, no Near Eastern mtDNA lineages connected with the Neolithic expansion have been observed in our population sample. On the other hand, the Y chromosome SNPs data show that the paternal lineages can very probably be traced to the Near Eastern Neolithic demic expansion towards North Africa, a period that is otherwise concordant with the above-mentioned mtDNA expansion. The time frame for the migration of the Tuareg towards the African Sahel belt overlaps that of early Holocene climatic changes across the Sahara (from the optimal greening approximately 10 000 YBP to the extant aridity beginning at approximately 6000 YBP) and the migrations of other African nomadic peoples in the area.

Rozmanitost projevů heteroplazmické mtDNA mutace 8993 T>G ve dvou rodinách

Czech Academy of Sciences Publication Activity Database

Tesařová, M.; Hansíková, H.; Hlavatá, A.; Klement, P.; Houšťková, H.; Houštěk, Josef; Zeman, J.

2002-01-01

Roč. 141, č. 17 (2002), s. 551-554 ISSN 0008-7335 R&D Projects: GA MZd(CZ) NE6533; GA MZd(CZ) NE6555; GA MŠk(CZ) LN00A079 Institutional research plan: CEZ:AV0Z5011922 Keywords : NARP syndrome * mtDNA mutation 8993 T>G Subject RIV: EB - Genetics ; Molecular Biology

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

are discussed in reference to the four currently recognised subspecies. We suggest Grant's gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite...... their geographic proximity, suggesting reproductive isolation. These constitute evolutionary significant units within the adaptive evolutionary framework. Due to its restricted geographic distribution and genetic and morphological distinctiveness, we suggest the petersii lineage be raised to the species Nanger...

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

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Sergei V Drovetski

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

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.

The Landscape of mtDNA Modifications in Cancer: A Tale of Two Cities.

Science.gov (United States)

Hertweck, Kate L; Dasgupta, Santanu

2017-01-01

Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional implications of mitochondrial mutations in cancer, this article focuses on documenting current knowledge in the abundance and distribution of somatic mitochondrial mutations, followed by elucidation of processes which affect the fate of mutations in cancer cells. The conclusion includes an overview of translational implications for mtDNA mutations, as well as recommendations for future research uniting mitochondrial variants and tumorigenesis.

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

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Charles E. Wani

2014-01-01

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

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

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Miao Miao

2012-02-01

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

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

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Lygia T Budnik

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

Uniparental (mtDNA, Y-chromosome) polymorphisms in French Guiana and two related populations--implications for the region's colonization.

Science.gov (United States)

Mazières, S; Guitard, E; Crubézy, E; Dugoujon, J-M; Bortolini, M C; Bonatto, S L; Hutz, M H; Bois, E; Tiouka, F; Larrouy, G; Salzano, F M

2008-01-01

Blood samples collected in four Amerindian French Guiana populations (Palikur, Emerillon, Wayampi and Kali'na) in the early 1980s were screened for selected mtDNA and Y-chromosome length polymorphisms, and sequenced for the mtDNA hypervariable segment I (HVS-I). In addition, two other Amerindian populations (Apalaí and Matsiguenga) were examined for the same markers to establish the genetic relationships in the area. Strong dissimilarities were observed in the distribution of the founding Amerindian haplogroups, and significant p-values were obtained from F(ST) genetic distances. Interpopulation similarities occurred mainly due to geography. The Palikur did not show obvious genetic similarity to the Matsiguenga, who speak the same language and live in a region from where they could have migrated to French Guiana. The African-origin admixture observed in the Kali'na probably derives from historical contacts they had with the Bushinengue (Noir Marron), a group of escaped slaves who now lead independent lives in a nearby region. This analysis has identified significant clues about the Amerindian peopling of the North-East Amazonian region.

Eurasian otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian Peninsula to Scandinavia.

Science.gov (United States)

Ferrando, Ainhoa; Ponsà, Montserrat; Marmi, Josep; Domingo-Roura, Xavier

2004-01-01

The Eurasian otter, Lutra lutra, has a Palaearctic distribution and has suffered a severe decline throughout Europe during the last century. Previous studies in this and other mustelids have shown reduced levels of variability in mitochondrial DNA, although otter phylogeographic studies were restricted to central-western Europe. In this work we have sequenced 361 bp of the mtDNA control region in 73 individuals from eight countries and added our results to eight sequences available from GenBank and the literature. The range of distribution has been expanded in relation to previous works north towards Scandinavia, east to Russia and Belarus, and south to the Iberian Peninsula. We found a single dominant haplotype in 91.78% of the samples, and six more haplotypes deviating a maximum of two mutations from the dominant haplotype restricted to a single country. Variability was extremely low in western Europe but higher in eastern countries. This, together with the lack of phylogeographical structuring, supports the postglacial recolonization of Europe from a single refugium. The Eurasian otter mtDNA control region has a 220-bp variable minisatellite in Domain III that we sequenced in 29 otters. We found a total of 19 minisatellite haplotypes, but they showed no phylogenetic information.

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

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

2015-05-01

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

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

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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.

Regional Differences in the Distribution of the Sub-Saharan, West Eurasian, and South Asian mtDNA Lineages in Yemen

Czech Academy of Sciences Publication Activity Database

Černý, Viktor; Mulligan, C. J.; Rídl, J.; Žaloudková, M.; Edens, C. M.; Hájek, Martin; Pereira, L.

2008-01-01

Roč. 136, č. 2 (2008), s. 128-137 ISSN 0002-9483 R&D Projects: GA MŠk ME 917 Institutional research plan: CEZ:AV0Z80020508 Keywords : mtDNA diversity * regional sampling * population distances * phylogeography Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 2.353, year: 2008 http://www3.interscience.wiley.com/journal/117899911/abstract

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, Soren; 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...

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

Science.gov (United States)

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

2008-01-01

Background DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. Methodology/Principal Findings We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 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. PMID:18628960

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

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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.

Analysis of mtDNA sequence variants in colorectal adenomatous polyps

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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

Male infertility is significantly associated with multiple deletions in an 8.7-kb segment of sperm mtDNA in Pakistan.

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Mughal, Irfan Afzal; Irfan, Asma; Jahan, Sarwat; Hameed, Abdul

2017-06-12

This study aimed to find a link between sperm mitochondrial DNA mutations and male infertility in Pakistan. DNA from semen samples was extracted and amplified by PCR using 7.8-kb deletion-specific primers. The PCR products were separated on agarose gel, visualized under UV-illumination, and then photographed. The results were genotyped and the data were analyzed using SPSS. Deletion analysis of the 8.7-kb fragment by long PCR revealed multiple deletions. The frequency of deletion was much higher in infertile groups as compared to the control group. Further, on comparison between different subtypes of infertile groups, the deletions were highest in the oligoasthenoteratozoospermia (OAT) group. The statistical analysis of case and control groups showed a significant association of the 8.7-kb deletion with human male infertile groups (P = 0.031), and particularly a very significant association with the OAT subgroup (P = 0.019). A significant association has been found between human male infertility and mtDNA deletions in an 8.7-kb segment of sperm mtDNA in a Pakistani population.

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

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Naumova O, Y u; Rychkov S, Y u

1998-03-01

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

Thermal expansion

International Nuclear Information System (INIS)

Yun, Y.

2015-01-01

Thermal expansion of fuel pellet is an important property which limits the lifetime of the fuels in reactors, because it affects both the pellet and cladding mechanical interaction and the gap conductivity. By fitting a number of available measured data, recommended equations have been presented and successfully used to estimate thermal expansion coefficient of the nuclear fuel pellet. However, due to large scatter of the measured data, non-consensus data have been omitted in formulating the equations. Also, the equation is strongly governed by the lack of appropriate experimental data. For those reasons, it is important to develop theoretical methodologies to better describe thermal expansion behaviour of nuclear fuel. In particular, first-principles and molecular dynamics simulations have been certainly contributed to predict reliable thermal expansion without fitting the measured data. Furthermore, the two theoretical techniques have improved on understanding the change of fuel dimension by describing the atomic-scale processes associated with lattice expansion in the fuels. (author)

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

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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

Low-temperature thermal expansion

International Nuclear Information System (INIS)

Collings, E.W.

1986-01-01

This chapter discusses the thermal expansion of insulators and metals. Harmonicity and anharmonicity in thermal expansion are examined. The electronic, magnetic, an other contributions to low temperature thermal expansion are analyzed. The thermodynamics of the Debye isotropic continuum, the lattice-dynamical approach, and the thermal expansion of metals are discussed. Relative linear expansion at low temperatures is reviewed and further calculations of the electronic thermal expansion coefficient are given. Thermal expansions are given for Cu, Al and Ti. Phenomenologic thermodynamic relationships are also discussed

Doctor Shortage and Health Services*

African Journals Online (AJOL)

1971-08-14

Aug 14, 1971 ... Bantu education was started by missionaries who had to carry the full financial burden, because it was viewed with much suspicion by the public. From 1850 to 1925 the view was held that the State should only control Bantu education by subsidizing missionary and other Bantu educational institutions.

Tracing the phylogeography of human populations in Britain based on 4th-11th century mtDNA genotypes.

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Töpf, A L; Gilbert, M T P; Dumbacher, J P; Hoelzel, A R

2006-01-01

Some of the transitional periods of Britain during the first millennium A.D. are traditionally associated with the movement of people from continental Europe, composed largely of invading armies (e.g., the Roman, Saxon, and Viking invasions). However, the extent to which these were migrations (as opposed to cultural exchange) remains controversial. We investigated the history of migration by women by amplifying mitochondrial DNA (mtDNA) from ancient Britons who lived between approximately A.D. 300-1,000 and compared these with 3,549 modern mtDNA database genotypes from England, Europe, and the Middle East. The objective was to assess the dynamics of the historical population composition by comparing genotypes in a temporal context. Towards this objective we test and calibrate the use of rho statistics to identify relationships between founder and source populations. We find evidence for shared ancestry between the earliest sites (predating Viking invasions) with modern populations across the north of Europe from Norway to Estonia, possibly reflecting common ancestors dating back to the last glacial epoch. This is in contrast with a late Saxon site in Norwich, where the genetic signature is consistent with more recent immigrations from the south, possibly as part of the Saxon invasions.

Population Structure of mtDNA Variation due to Pleistocene Fluctuations in the South American Maned Wolf (Chrysocyon brachyurus, Illiger, 1815): Management Units for Conservation.

Science.gov (United States)

González, Susana; Cosse, Mariana; Franco, María del Rosario; Emmons, Louise; Vynne, Carly; Duarte, José Maurício Barbanti; Beccacesi, Marcelo D; Maldonado, Jesús E

2015-01-01

The maned wolf (Chrysocyon brachyurus) is one of the largest South American canids, and conservation across this charismatic carnivore's large range is presently hampered by a lack of knowledge about possible natural subdivisions which could influence the population's viability. To elucidate the phylogeographic patterns and demographic history of the species, we used 2 mtDNA markers (D-loop and cytochrome b) from 87 individuals collected throughout their range, in Argentina, Bolivia, Brazil, and Uruguay. We found moderate levels of haplotype and nucleotide diversity, and the 14 D-loop haplotypes were closely related. Genetic structure results revealed 4 groups, and when coupled with model inferences from a coalescent analysis, suggested that maned wolves have undergone demographic fluctuations due to changes in climate and habitat during the Pleistocene glaciation period approximately 24000 years before present (YBP). This genetic signature points to an event that occurred within the timing estimated for the start of the contraction of the Cerrado around 50000 YBP. Our results reveal a genetic signature of population size expansion followed by contraction during Pleistocene interglaciations, which had similar impacts on other South American mammals. The 4 groups should for now be considered management units, within which future monitoring efforts should be conducted independently. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

DsbA-L prevents obesity-induced inflammation and insulin resistance by suppressing the mtDNA release-activated cGAS-cGAMP-STING pathway

Science.gov (United States)

Chronic inflammation in adipose tissue plays a key role in obesity-induced insulin resistance. However, the mechanisms underlying obesity-induced inflammation remain elusive. Here we show that obesity promotes mtDNA release into the cytosol, where it triggers inflammatory responses by activating the...

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

Science.gov (United States)

Kemp, Brian M; Lindo, John; Bolnick, Deborah A; Malhi, Ripan S; Chatters, James C

2015-02-20

Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our other observations. Copyright © 2015, American Association for the Advancement of Science.

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.

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge.

Science.gov (United States)

García, O; Fregel, R; Larruga, J M; Álvarez, V; Yurrebaso, I; Cabrera, V M; González, A M

2011-01-01

It has been proposed that the distribution patterns and coalescence ages found in Europeans for mitochondrial DNA (mtDNA) haplogroups V, H1 and H3 are the result of a post-glacial expansion from a Franco-Cantabrian refuge that recolonized central and northern areas. In contrast, in this refined mtDNA study of the Cantabrian Cornice that contributes 413 partial and 9 complete new mtDNA sequences, including a large Basque sample and a sample of Asturians, no experimental evidence was found to support the human refuge-expansion theory. In fact, all measures of gene diversity point to the Cantabrian Cornice in general and the Basques in particular, as less polymorphic for V, H1 and H3 than other southern regions in Iberia or in Central Europe. Genetic distances show the Cantabrian Cornice is a very heterogeneous region with significant local differences. The analysis of several minor subhaplogroups, based on complete sequences, also suggests different focal expansions over a local and peninsular range that did not affect continental Europe. Furthermore, all detected clinal trends show stronger longitudinal than latitudinal profiles. In Northern Iberia, it seems that the highest diversity values for some haplogroups with Mesolithic coalescence ages are centred on the Mediterranean side, including Catalonia and South-eastern France.

Evolutionary history of continental southeast Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data.

Science.gov (United States)

Jinam, Timothy A; Hong, Lih-Chun; Phipps, Maude E; Stoneking, Mark; Ameen, Mahmood; Edo, Juli; Saitou, Naruya

2012-11-01

The population history of the indigenous populations in island Southeast Asia is generally accepted to have been shaped by two major migrations: the ancient "Out of Africa" migration ∼50,000 years before present (YBP) and the relatively recent "Out of Taiwan" expansion of Austronesian agriculturalists approximately 5,000 YBP. The Negritos are believed to have originated from the ancient migration, whereas the majority of island Southeast Asians are associated with the Austronesian expansion. We determined 86 mitochondrial DNA (mtDNA) complete genome sequences in four indigenous Malaysian populations, together with a reanalysis of published autosomal single-nucleotide polymorphism (SNP) data of Southeast Asians to test the plausibility and impact of those migration models. The three Austronesian groups (Bidayuh, Selatar, and Temuan) showed high frequencies of mtDNA haplogroups, which originated from the Asian mainland ∼30,000-10,000 YBP, but low frequencies of "Out of Taiwan" markers. Principal component analysis and phylogenetic analysis using autosomal SNP data indicate a dichotomy between continental and island Austronesian groups. We argue that both the mtDNA and autosomal data suggest an "Early Train" migration originating from Indochina or South China around the late-Pleistocene to early-Holocene period, which predates, but may not necessarily exclude, the Austronesian expansion.

Cells Lacking mtDNA Display Increased dNTP Pools upon DNA Damage

DEFF Research Database (Denmark)

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

Imbalanced dNTP pools are highly mutagenic due to a deleterious effect on DNA polymerase fidelity. Mitochondrial DNA defects, including mutations and deletions, are commonly found in a wide variety of different cancer types. In order to further study the interconnection between dNTP pools...... 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...... shows that normal mitochondrial function is prerequisite for retaining stable dNTP pools upon DNA damage. Therefore it is likely that mitochondrial deficiency defects may cause an increase in DNA mutations by disrupting dNTP pool balance....

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...

Following Surgically Assisted Rapid Palatal Expansion, Do Tooth-Borne or Bone-Borne Appliances Provide More Skeletal Expansion and Dental Expansion?

Science.gov (United States)

Hamedi-Sangsari, Adrien; Chinipardaz, Zahra; Carrasco, Lee

2017-10-01

The aim of this study was to compare outcome measurements of skeletal and dental expansion with bone-borne (BB) versus tooth-borne (TB) appliances after surgically assisted rapid palatal expansion (SARPE). This study was performed to provide quantitative measurements that will help the oral surgeon and orthodontist in selecting the appliance with, on average, the greatest amount of skeletal expansion and the least amount of dental expansion. A computerized database search was performed using PubMed, EBSCO, Cochrane, Scopus, Web of Science, and Google Scholar on publications in reputable oral surgery and orthodontic journals. A systematic review and meta-analysis was completed with the predictor variable of expansion appliance (TB vs BB) and outcome measurement of expansion (in millimeters). Of 487 articles retrieved from the 6 databases, 5 articles were included, 4 with cone-beam computed tomographic (CBCT) data and 1 with non-CBCT 3-dimensional cast data. There was a significant difference in skeletal expansion (standardized mean difference [SMD], 0.92; 95% confidence interval [CI], 0.54-1.30; P appliances. However, there was no significant difference in dental expansion (SMD, 0.05; 95% CI, -0.24 to 0.34; P = .03). According to the literature, to achieve more effective skeletal expansion and minimize dental expansion after SARPE, a BB appliance should be favored. Copyright © 2017 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

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

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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.

The congruence between matrilineal genetic (mtDNA) and geographic diversity of Iranians and the territorial populations

Science.gov (United States)

Bahmanimehr, Ardeshir; Eskandari, Ghafar; Nikmanesh, Fatemeh

2015-01-01

Objective(s): From the ancient era, emergence of Agriculture in the connecting region of Mesopotamia and the Iranian plateau at the foothills of the Zagros Mountains, made Iranian gene pool as an important source of populating the region. It has differentiated the population spread and different language groups. In order to trace the maternal genetic affinity between Iranians and other populations of the area and to establish the place of Iranians in a broad framework of ethnically and linguistically diverse groups of Middle Eastern and South Asian populations, a comparative study of territorial groups was designed and used in the population statistical analysis. Materials and Methods: Mix of 616 samples was sequenced for complete mtDNA or hyper variable regions in this study. A published dataset of neighboring populations was used as a comparison in the Iranian matrilineal lineage study based on mtDNA haplogroups. Results: Statistical analyses data, demonstrate a close genetic structure of all Iranian populations, thus suggesting their origin from a common maternal ancestral gene pool and show that the diverse maternal genetic structure does not reflect population differentiation in the region in their language. Conclusion: In the aggregate of the eastward spreads of proto-Elamo-Dravidian language from the Southwest region of Iran, the Elam province, a reasonable degree of homogeneity has been observed among Iranians in this study. The approach will facilitate our perception of the more detailed relationship of the ethnic groups living in Iran with the other ancient peoples of the area, testing linguistic hypothesis and population movements. PMID:25810873

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

Science.gov (United States)

Pearce, J.M.

2006-01-01

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

Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target.

Science.gov (United States)

Lee, Ping-Shin; Sing, Kong-Wah; Wilson, John-James

2015-01-01

Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii) to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp) DNA mini-barcode could distinguish most mammal species (including separating dark taxa) and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring.

Targeted Transgenic Overexpression of Mitochondrial Thymidine Kinase (TK2) Alters Mitochondrial DNA (mtDNA) and Mitochondrial Polypeptide Abundance

Science.gov (United States)

Hosseini, Seyed H.; Kohler, James J.; Haase, Chad P.; Tioleco, Nina; Stuart, Tami; Keebaugh, Erin; Ludaway, Tomika; Russ, Rodney; Green, Elgin; Long, Robert; Wang, Liya; Eriksson, Staffan; Lewis, William

2007-01-01

Mitochondrial toxicity limits nucleoside reverse transcriptase inhibitors (NRTIs) for acquired immune deficiency syndrome. NRTI triphosphates, the active moieties, inhibit human immunodeficiency virus reverse transcriptase and eukaryotic mitochondrial DNA polymerase pol-γ. NRTI phosphorylation seems to correlate with mitochondrial toxicity, but experimental evidence is lacking. Transgenic mice (TGs) with cardiac overexpression of thymidine kinase isoforms (mitochondrial TK2 and cytoplasmic TK1) were used to study NRTI mitochondrial toxicity. Echocardiography and nuclear magnetic resonance imaging defined cardiac performance and structure. TK gene copy and enzyme activity, mitochondrial (mt) DNA and polypeptide abundance, succinate dehydrogenase and cytochrome oxidase histochemistry, and electron microscopy correlated with transgenesis, mitochondrial structure, and biogenesis. Antiretroviral combinations simulated therapy. Untreated hTK1 or TK2 TGs exhibited normal left ventricle mass. In TK2 TGs, cardiac TK2 gene copy doubled, activity increased 300-fold, and mtDNA abundance doubled. Abundance of the 17-kd subunit of complex I, succinate dehydrogenase histochemical activity, and cristae density increased. NRTIs increased left ventricle mass 20% in TK2 TGs. TK activity increased 3 logs in hTK1 TGs, but no cardiac phenotype resulted. NRTIs abrogated functional effects of transgenically increased TK2 activity but had no effect on TK2 mtDNA abundance. Thus, NRTI mitochondrial phosphorylation by TK2 is integral to clinical NRTI mitochondrial toxicity. PMID:17322372

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

International Nuclear Information System (INIS)

Wang Huawei; Jia Xiaoyun; Ji Yanli; Kong Qingpeng; Zhang Qingjiong; Yao Yonggang; Zhang Yaping

2008-01-01

The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P < 0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate any putatively pathogenic mutation that cosegregated with G11778A in these two pedigrees. Our results suggest that the variable penetrance of LHON in the two Chinese families is independent of both their mtDNA haplotype background and a secondary mutation G13708A. As a result, it is likely that unknown nuclear gene involvement and/or other factors contribute to the strikingly different penetrance of LHON

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...

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...... of hybridization and mtDNA introgression among distinct species. Our results highlight that the marginal seas of Northeast Asia played a key role as barriers to or facilitators of gene flow in the evolution of species diversity of Pungitius concentrated in this region...

MELAS and Kearns–Sayre overlap syndrome due to the mtDNA m. A3243G mutation and large-scale mtDNA deletions

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Nian Yu

2016-09-01

Full Text Available This paper reported an unusual manifestation of a 19-year-old Chinese male patient presented with a complex phenotype of mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS syndrome and Kearns–Sayre syndrome (KSS. He was admitted to our hospital with the chief complaint of “acute fever, headache and slow reaction for 21 days”. He was initially misdiagnosed as “viral encephalitis”. This Chinese man with significant past medical history of intolerating fatigue presented paroxysmal neurobehavioral attacks that started about 10 years ago. During this span, 3 or 4 attack clusters were described during which several attacks occurred over a few days. The further examination found that the hallmark signs of this patient included progressive myoclonus epilepsy, cerebellar ataxia, hearing loss, myopathic weakness, ophthalmoparesis, pigmentary retinopathy and bifascicular heart block (Wolff–Parkinson–White syndrome. By young age the disease progression is characterized by the addition of migraine, vomiting, and stroke-like episodes, symptoms of MELAS expression, which indicated completion of the MELAS/KSS overlap syndrome. The m. A3243G mitochondrial DNA mutation and single large-scale mtDNA deletions were found in this patient. This mutation has been reported with MELAS, KSS, myopathy, deafness and mental disorder with cognitive impairment. This is the first description with a MELAS/KSS syndrome in Chinese.

Negative thermal expansion materials

International Nuclear Information System (INIS)

Evans, J.S.O.

1997-01-01

The recent discovery of negative thermal expansion over an unprecedented temperature range in ZrW 2 O 8 (which contracts continuously on warming from below 2 K to above 1000 K) has stimulated considerable interest in this unusual phenomenon. Negative and low thermal expansion materials have a number of important potential uses in ceramic, optical and electronic applications. We have now found negative thermal expansion in a large new family of materials with the general formula A 2 (MO 4 ) 3 . Chemical substitution dramatically influences the thermal expansion properties of these materials allowing the production of ceramics with negative, positive or zero coefficients of thermal expansion, with the potential to control other important materials properties such as refractive index and dielectric constant. The mechanism of negative thermal expansion and the phase transitions exhibited by this important new class of low-expansion materials will be discussed. (orig.)

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.

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

Directory of Open Access Journals (Sweden)

Koshi Takenaka

2012-01-01

Full Text Available Most materials expand upon heating. However, although rare, some materials contract upon heating. Such negative thermal expansion (NTE materials have enormous industrial merit because they can control the thermal expansion of materials. Recent progress in materials research enables us to obtain materials exhibiting negative coefficients of linear thermal expansion over −30 ppm K−1. Such giant NTE is opening a new phase of control of thermal expansion in composites. Specifically examining practical aspects, this review briefly summarizes materials and mechanisms of NTE as well as composites containing NTE materials, based mainly on activities of the last decade.

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

International Nuclear Information System (INIS)

Takenaka, Koshi

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 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. (topical review)

Thermal expansion of coking coals

Energy Technology Data Exchange (ETDEWEB)

Orlik, M.; Klimek, J. (Vyzkumny a Zkusebni Ustav Nova Hut, Ostrava (Czechoslovakia))

1992-12-01

Analyzes expansion of coal mixtures in coke ovens during coking. Methods for measuring coal expansion on both a laboratory and pilot plant scale are comparatively evaluated. The method, developed, tested and patented in Poland by the Institute for Chemical Coal Processing in Zabrze (Polish standard PN-73/G-04522), is discussed. A laboratory device developed by the Institute for measuring coal expansion is characterized. Expansion of black coal from 10 underground mines in the Ostrava-Karvina coal district and from 9 coal mines in the Upper Silesia basin in Poland is comparatively evaluated. Investigations show that coal expansion reaches a maximum for coal types with a volatile matter ranging from 20 to 25%. With increasing volatile matter in coal, its expansion decreases. Coal expansion increases with increasing swelling index. Coal expansion corresponds with coal dilatation. With increasing coal density its expansion increases. Coal mixtures should be selected in such a way that their expansion does not cause a pressure exceeding 40 MPa. 11 refs.

MtDNA diversity and genetic lineages of four cattle breeds in Malaysia

Directory of Open Access Journals (Sweden)

Somarny, W.W.M.Z.

2015-06-01

Full Text Available There is lack of comprehensive studies on the genetic diversity or phylogenetic analysis of beef cattle breeds in Malaysia. In this study, the partial sequence of mitochondrial DNA cytochrome b gene (cyt b was analysed from blood samples obtained from 25 Chinese Yellow Cattle (CY, 33 Kedah-Kelantan (KK, 32 Brakmas (BM and 30 Bali cattle (BC. Based on these 120 individuals, 19 mtDNA haplotypes (GenBank Accession No. GU67340 - GU67358 were identified by polymorphisms at 31 sites. Hap19 was predominant in BM (78%, KK (82% and CY (100% indicating similar origin or gene flow between breeds whilst Hap11 was exclusively for BC. However, there were only two nucleotide differences between these two major haplotypes. These results can be interpreted that these representative cattle in these haplotypes are admixtures of B. indicus or B. javanicus through maternal ancestry. Conversely, the CY cattle investigated are highly inbred where no variation could be observed in the short segment investigated.

Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target

Science.gov (United States)

Lee, Ping-Shin; Sing, Kong-Wah; Wilson, John-James

2015-01-01

Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii) to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp) DNA mini-barcode could distinguish most mammal species (including separating dark taxa) and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring. PMID:25898278

Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala and a New DNA Mini-Barcode Target.

Directory of Open Access Journals (Sweden)

Ping-Shin Lee

Full Text Available Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp DNA mini-barcode could distinguish most mammal species (including separating dark taxa and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring.

Virial Expansion Bounds

Science.gov (United States)

Tate, Stephen James

2013-10-01

In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.

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

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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.

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

Energy Technology Data Exchange (ETDEWEB)

Wang Huawei [Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223 (China)]|[Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091 (China); Jia Xiaoyun; Ji Yanli [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060 (China); Kong Qingpeng [State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China); Zhang Qingjiong [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060 (China)], E-mail: qingjiongzhang@yahoo.com; Yao Yonggang [Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223 (China)]|[State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China)], E-mail: ygyaozh@yahoo.com; Zhang Yaping [Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091 (China)]|[State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China)

2008-08-25

The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P < 0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate any putatively pathogenic mutation that cosegregated with G11778A in these two pedigrees. Our results suggest that the variable penetrance of LHON in the two Chinese families is independent of both their mtDNA haplotype background and a secondary mutation G13708A. As a result, it is likely that unknown nuclear gene involvement and/or other factors contribute to the strikingly different penetrance of LHON.

Ultra-low thermal expansion realized in giant negative thermal expansion materials through self-compensation

Science.gov (United States)

Shen, Fei-Ran; Kuang, Hao; Hu, Feng-Xia; Wu, Hui; Huang, Qing-Zhen; Liang, Fei-Xiang; Qiao, Kai-Ming; Li, Jia; Wang, Jing; Liu, Yao; Zhang, Lei; He, Min; Zhang, Ying; Zuo, Wen-Liang; Sun, Ji-Rong; Shen, Bao-Gen

2017-10-01

Materials with zero thermal expansion (ZTE) or precisely tailored thermal expansion are in urgent demand of modern industries. However, the overwhelming majority of materials show positive thermal expansion. To develop ZTE or negative thermal expansion (NTE) materials as compensators has become an important challenge. Here, we present the evidence for the realization of ultra-low thermal expansion in Mn-Co-Ge-In particles. The bulk with the Ni2In-type hexagonal structure undergoes giant NTE owing to a martensitic magnetostructural transition. The major finding is that the thermal expansion behavior can be totally controlled by modulating the crystallinity degree and phase transition from atomic scale. Self-compensation effect leads to ultra-low thermal expansion with a linear expansion coefficient as small as +0.68 × 10-6/K over a wide temperature range around room temperature. The present study opens an avenue to reach ZTE particularly from the large class of giant NTE materials based on phase transition.

Ultra-low thermal expansion realized in giant negative thermal expansion materials through self-compensation

Directory of Open Access Journals (Sweden)

Fei-Ran Shen

2017-10-01

Full Text Available Materials with zero thermal expansion (ZTE or precisely tailored thermal expansion are in urgent demand of modern industries. However, the overwhelming majority of materials show positive thermal expansion. To develop ZTE or negative thermal expansion (NTE materials as compensators has become an important challenge. Here, we present the evidence for the realization of ultra-low thermal expansion in Mn–Co–Ge–In particles. The bulk with the Ni2In-type hexagonal structure undergoes giant NTE owing to a martensitic magnetostructural transition. The major finding is that the thermal expansion behavior can be totally controlled by modulating the crystallinity degree and phase transition from atomic scale. Self-compensation effect leads to ultra-low thermal expansion with a linear expansion coefficient as small as +0.68 × 10−6/K over a wide temperature range around room temperature. The present study opens an avenue to reach ZTE particularly from the large class of giant NTE materials based on phase transition.

Ultra-low thermal expansion realized in giant negative thermal expansion materials through self-compensation

OpenAIRE

Fei-Ran Shen; Hao Kuang; Feng-Xia Hu; Hui Wu; Qing-Zhen Huang; Fei-Xiang Liang; Kai-Ming Qiao; Jia Li; Jing Wang; Yao Liu; Lei Zhang; Min He; Ying Zhang; Wen-Liang Zuo; Ji-Rong Sun

2017-01-01

Materials with zero thermal expansion (ZTE) or precisely tailored thermal expansion are in urgent demand of modern industries. However, the overwhelming majority of materials show positive thermal expansion. To develop ZTE or negative thermal expansion (NTE) materials as compensators has become an important challenge. Here, we present the evidence for the realization of ultra-low thermal expansion in Mn–Co–Ge–In particles. The bulk with the Ni2In-type hexagonal structure undergoes giant NTE o...

Population Genetic Structure of Rock Bream (Oplegnathus fasciatus Temminck & Schlegel, 1884) Revealed by mtDNA COI Sequence in Korea and China

Science.gov (United States)

Park, Hyun Suk; Kim, Choong-Gon; Kim, Sung; Park, Yong-Joo; Choi, Hee-Jung; Xiao, Zhizhong; Li, Jun; Xiao, Yongshuang; Lee, Youn-Ho

2018-04-01

The rock bream, Oplegnathus fasciatus, is a common rocky reef game fish in East Asia and recently has become an aquaculture species. Despite its commercial importance, the population genetic structure of this fish species remains poorly understood. In this study, 163 specimens were collected from 6 localities along the coastal waters of Korea and China and their genetic variation was analyzed with mtDNA COI sequences. A total of 34 polymorphic sites were detected which determined 30 haplotypes. The genetic pattern reveals a low level of nucleotide diversity (0.04 ± 0.003) but a high level of haplotype diversity (0.83 ± 0.02). The 30 haplotypes are divided into two major genealogical clades: one that consists of only Zhoushan (ZS, East China Sea) specific haplotypes from the southern East China Sea and the other that consists of the remaining haplotypes from the northern East China Sea, Yellow Sea, Korea Strait, and East Sea/Sea of Japan. The two clades are separated by approximately 330 435 kyBP. Analyses of AMOVA and F st show a significant population differentiation between the ZS sample and the other ones, corroborating separation of the two genealogical clades. Larval dispersal and the fresh Yangtze River plume are invoked as the main determining factors for this population genetic structure of O. fasciatus. Neutrality tests and mismatch distribution analyses indicate late Pleistocene population expansion along the coastal waters of Korea and China approximately 133-183 kyBP during which there were periodic cycles of glaciations and deglaciations. Such population information needs to be taken into account when stock enhancement and conservation measures are implemented for this fisheries species.

Thermal expansion of granite rocks

International Nuclear Information System (INIS)

Stephansson, O.

1978-04-01

The thermal expansion of rocks is strongly controlled by the thermal expansion of the minerals. The theoretical thermal expansion of the Stripa Granite is gound to be 21 . 10 -6 [deg C] -1 at 25 deg C and 38 . 10 -6 [deg C] -1 at 400 deg C. The difference in expansion for the rock forming minerals causes micro cracking at heating. The expansion due to micro cracks is found to be of the same order as the mineral expansion. Most of the micro cracks will close at pressures of the order of 10 - 20 MPa. The thermal expansion of a rock mass including the effect of joints is determined in the pilot heater test in the Stripa Mine

Population Genetic Structure and Isolation by Distance of Helicobacter pylori in Senegal and Madagascar

Science.gov (United States)

Linz, Bodo; Vololonantenainab, Clairette Romaine Raharisolo; Seck, Abdoulaye; Carod, Jean-François; Dia, Daouda; Garin, Benoit; Ramanampamonjy, Rado Manitrala; Thiberge, Jean-Michel; Raymond, Josette; Breurec, Sebastien

2014-01-01

Helicobacter pylori has probably infected the human stomach since our origins and subsequently diversified in parallel with their human hosts. The genetic population history of H. pylori can therefore be used as a marker for human migration. We analysed seven housekeeping gene sequences of H. pylori strains isolated from 78 Senegalese and 24 Malagasy patients and compared them with the sequences of strains from other geographical locations. H. pylori from Senegal and Madagascar can be placed in the previously described HpAfrica1 genetic population, subpopulations hspWAfrica and hspSAfrica, respectively. These 2 subpopulations correspond to the distribution of Niger-Congo speakers in West and most of subequatorial Africa (due to Bantu migrations), respectively. H. pylori appears as a single population in Senegal, indicating a long common history between ethnicities as well as frequent local admixtures. The lack of differentiation between these isolates and an increasing genetic differentiation with geographical distance between sampling locations in Africa was evidence for genetic isolation by distance. The Austronesian expansion that started from Taiwan 5000 years ago dispersed one of the 10 subgroups of the Austronesian language family via insular Southeast Asia into the Pacific and Madagascar, and hspMaori is a marker for the entire Austronesian expansion. Strain competition and replacement of hspMaori by hpAfrica1 strains from Bantu migrants are the probable reasons for the presence of hspSAfrica strains in Malagasy of Southeast Asian descent. hpAfrica1 strains appear to be generalist strains that have the necessary genetic diversity to efficiently colonise a wide host spectrum. PMID:24498084

Chronic inflammatory state in sickle cell anemia patients is associated with HBB(*)S haplotype.

Science.gov (United States)

Bandeira, Izabel C J; Rocha, Lillianne B S; Barbosa, Maritza C; Elias, Darcielle B D; Querioz, José A N; Freitas, Max Vitor Carioca; Gonçalves, Romélia P

2014-02-01

The chronic inflammatory state in sickle cell anemia (SCA) is associated with several factors such as the following: endothelial damage; increased production of reactive oxygen species; hemolysis; increased expression of adhesion molecules by leukocytes, erythrocytes, and platelets; and increased production of proinflammatory cytokines. Genetic characteristics affecting the clinical severity of SCA include variations in the hemoglobin F (HbF) level, coexistence of alpha-thalassemia, and the haplotype associated with the HbS gene. The different haplotypes of SCA are Bantu, Benin, Senegal, Cameroon, and Arab-Indian. These haplotypes are associated with ethnic groups and also based on the geographical origin. Studies have shown that the Bantu haplotype is associated with higher incidence of clinical complications than the other haplotypes and is therefore considered to have the worst prognosis. This study aimed to evaluate the profile of the proinflammatory cytokines interleukin-6, tumor necrosis factor-α, and interleukin-17 in patients with SCA and also to assess the haplotypes associated with beta globin cluster S (HBB(*)S). We analyzed a total of 62 patients who had SCA and had been treated with hydroxyurea; they had received a dose ranging between 15 and 25 (20.0±0.6)mg/kg/day for 6-60 (18±3.4)months; their data were compared with those for 30 normal individuals. The presence of HbS was detected and the haplotypes of the beta S gene cluster were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Our study demonstrated that SCA patients have increased inflammatory profile when compared to the healthy individuals. Further, analysis of the association between the haplotypes and inflammatory profile showed that the levels of IL-6 and TNF-α were greater in subjects with the Bantu/Bantu haplotype than in subjects with the Benin/Benin haplotype. The Bantu/Benin haplotype individuals had lower levels of cytokines than those with

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).

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest

Science.gov (United States)

Menezes, Lucas; Canedo, Clarissa; Batalha-Filho, Henrique; Garda, Adrian Antonio; Gehara, Marcelo; Napoli, Marcelo Felgueiras

2016-01-01

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population’s distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow. PMID:27248688

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest.

Science.gov (United States)

Menezes, Lucas; Canedo, Clarissa; Batalha-Filho, Henrique; Garda, Adrian Antonio; Gehara, Marcelo; Napoli, Marcelo Felgueiras

2016-01-01

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.

Resonant state expansions

International Nuclear Information System (INIS)

Lind, P.

1993-02-01

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

The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula.

Science.gov (United States)

Melo-Ferreira, J; Boursot, P; Randi, E; Kryukov, A; Suchentrunk, F; Ferrand, N; Alves, P C

2007-02-01

The climatic fluctuations during glaciations have affected differently arctic and temperate species. In the northern hemisphere, cooling periods induced the expansion of many arctic species to the south, while temperate species were forced to retract in southern refugia. Consequently, in some areas the alternation of these species set the conditions for competition and eventually hybridization. Hares in the Iberian Peninsula appear to illustrate this phenomenon. Populations of Iberian hare (Lepus granatensis), brown hare (Lepus europaeus) and broom hare (Lepus castroviejoi) in Northern Iberia harbour mitochondrial haplotypes from the mountain hare (Lepus timidus), a mainly boreal and arctic species presently absent from the peninsula. To understand the history of this past introgression we analysed sequence variation and geographical distribution of mitochondrial control region and cytochrome b haplotypes of L. timidus origin found in 378 specimens of these four species. Among 124 L. timidus from the Northern Palaearctic and the Alps we found substantial nucleotide diversity (2.3%) but little differentiation between populations. Based on the mismatch distribution of the L. timidus sequences, this could result from an expansion at a time of temperature decrease favourable to this arctic species. The nucleotide diversity of L. timidus mtDNA found in Iberian L. granatensis, L. europaeus and L. castroviejoi (183, 70 and 1 specimens, respectively) was of the same order as that in L. timidus over its range (1.9%), suggesting repeated introgression of multiple lineages. The structure of the coalescent of L. granatensis sequences indicates that hybridization with L. timidus was followed by expansion of the introgressed haplotypes, as expected during a replacement with competition, and occurred when temperatures started to rise, favouring the temperate species. Whether a similar scenario explains the introgression into Iberian L. europaeus remains unclear but it is possible

Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis.

Science.gov (United States)

Gunbin, Konstantin; Peshkin, Leonid; Popadin, Konstantin; Annis, Sofia; Ackermann, Rebecca R; Khrapko, Konstantin

2017-05-01

Fragments of mitochondrial DNA are known to get inserted into nuclear DNA to form NUMTs, i.e. nuclear pseudogenes of the mtDNA. The insertion of a NUMT is a rare event. Hundreds of pseudogenes have been cataloged in the human genome. NUMTs are, in essence, a special type of mutation with their own internal timer, which is synchronized with an established molecular clock, the mtDNA. Thus insertion of NUMTs can be timed with respect to evolution milestones such as the emergence of new species. We asked whether NUMTs were inserted uniformly over time or preferentially during certain periods of evolution, as implied by the "punctuated evolution" model. To our surprise, the NUMT insertion times do appear nonrandom with at least one cluster positioned at around 2.8 million years ago (Ma). Interestingly, 2.8Ma closely corresponds to the time of emergence of the genus Homo, and to a well-documented period of major climate change ca. 2.9-2.5Ma. It is tempting to hypothesize that the insertion of NUMTs is related to the speciation process. NUMTs could be either "riders", i.e., their insertion could be facilitated by the overall higher genome rearrangement activity during speciation, or "drivers", i.e. they may more readily get fixed in the population due to positive selection associated with speciation. If correct, the hypothesis would support the idea that evolution of our genus may have happened in a rapid, punctuated manner. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Genetic structure in contemporary south Tyrolean isolated populations revealed by analysis of Y-chromosome, mtDNA, and Alu polymorphisms.

Science.gov (United States)

Pichler, Irene; Mueller, Jakob C; Stefanov, Stefan A; De Grandi, Alessandro; Volpato, Claudia Beu; Pinggera, Gerd K; Mayr, Agnes; Ogriseg, Martin; Ploner, Franz; Meitinger, Thomas; Pramstaller, Peter P

2006-08-01

Most of the inhabitants of South Tyrol in the eastern Italian Alps can be considered isolated populations because of their physical separation by mountain barriers and their sociocultural heritage. We analyzed the genetic structure of South Tyrolean populations using three types of genetic markers: Y-chromosome, mitochondrial DNA (mtDNA), and autosomal Alu markers. Using random samples taken from the populations of Val Venosta, Val Pusteria, Val Isarco, Val Badia, and Val Gardena, we calculated genetic diversity within and among the populations. Microsatellite diversity and unique event polymorphism diversity (on the Y chromosome) were substantially lower in the Ladin-speaking population of Val Badia compared to the neighboring German-speaking populations. In contrast, the genetic diversity of mtDNA haplotypes was lowest for the upper Val Venosta and Val Pusteria. These data suggest a low effective population size, or little admixture, for the gene pool of the Ladin-speaking population from Val Badia. Interestingly, this is more pronounced for Ladin males than for Ladin females. For the pattern of genetic Alu variation, both Ladin samples (Val Gardena and Val Badia) are among the samples with the lowest diversity. An admixture analysis of one German-speaking valley (Val Venosta) indicates a relatively high genetic contribution of Ladin origin. The reduced genetic diversity and a high genetic differentiation in the Rhaetoroman- and German-speaking South Tyrolean populations may constitute an important basis for future medical genetic research and gene mapping studies in South Tyrol.

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.

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.

PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia.

Science.gov (United States)

Rahim, Mohamamd Hafiz Abdul; Ismail, Patimah; Alias, Rozila; Muhammad, Norwati; Mat Jais, Abdul Manan

2012-02-15

Haruan (Channa striatus) is in great demand in the Malaysian domestic fish market. In the present study, mtDNA cyt b was used to investigate genetic variation of C. striatus among populations in Peninsular Malaysia. The overall population of C. striatus demonstrated a high level of haplotype diversity (h) and a low-to-moderate level of nucleotide diversity (π). Analysis of molecular variance (AMOVA) results showed a significantly different genetic differentiation among 6 populations (F(ST)=0.37566, P=0.01). Gene flow (Nm) was high and ranged from 0.32469 to infinity (∞). No significant relationship between genetic distance and geographic distance was detected. A UPGMA tree based on the distance matrix of net interpopulation nucleotide divergence (d(A)) and haplotype network of mtDNA cyt b revealed that C. striatus is divided into 2 major clades. The neutrality and mismatch distribution tests for all populations suggested that C. striatus in the study areas had undergone population expansion. The estimated time of population expansion in the mtDNA cyt b of C. striatus populations occurred 0.72-6.19 million years ago. Genetic diversity of mtDNA cyt b and population structure among Haruan populations in Peninsular Malaysia will be useful in fisheries management for standardization for Good Agriculture Practices (GAP) in fish-farming technology, as well as providing the basis for Good Manufacturing Practices (GMP). Copyright © 2011 Elsevier B.V. All rights reserved.

Does query expansion limit our learning? A comparison of social-based expansion to content-based expansion for medical queries on the internet.

Science.gov (United States)

Pentoney, Christopher; Harwell, Jeff; Leroy, Gondy

2014-01-01

Searching for medical information online is a common activity. While it has been shown that forming good queries is difficult, Google's query suggestion tool, a type of query expansion, aims to facilitate query formation. However, it is unknown how this expansion, which is based on what others searched for, affects the information gathering of the online community. To measure the impact of social-based query expansion, this study compared it with content-based expansion, i.e., what is really in the text. We used 138,906 medical queries from the AOL User Session Collection and expanded them using Google's Autocomplete method (social-based) and the content of the Google Web Corpus (content-based). We evaluated the specificity and ambiguity of the expansion terms for trigram queries. We also looked at the impact on the actual results using domain diversity and expansion edit distance. Results showed that the social-based method provided more precise expansion terms as well as terms that were less ambiguous. Expanded queries do not differ significantly in diversity when expanded using the social-based method (6.72 different domains returned in the first ten results, on average) vs. content-based method (6.73 different domains, on average).

Screening of respiration deficiency mutants of yeasts (Saccharomyces cerevisiae) induced by ion irradiation and the mtDNA restriction analysis

International Nuclear Information System (INIS)

Mao Shuhong; Chinese Academy of Sciences, Beijing; Jin Genming; Wei Zengquan; Xie Hongmei; Ma Qiufeng; Gu Ying

2005-01-01

Screening of the respiration deficiency mutants of Saccharomyces cerevisiae induced by 5.19 MeV/u 22 Ne 5+ ion irradiation is reported in this paper. Some respiration deficiency mutants of white colony phenotype, in a condition of selective culture of TTC medium, were obtained. A new and simplified method based on mtDNA restriction analysis is described. The authors found that there are many obvious differences in mtDNAs between wild yeasts and the respiration deficiency mutants. The mechanism of obtaining the respiration deficiency mutants induced by heavy ion irradiation is briefly discussed. (authors)

DsbA-L prevents obesity-induced inflammation and insulin resistance by suppressing the mtDNA release-activated cGAS-cGAMP-STING pathway.

Science.gov (United States)

Bai, Juli; Cervantes, Christopher; Liu, Juan; He, Sijia; Zhou, Haiyan; Zhang, Bilin; Cai, Huan; Yin, Dongqing; Hu, Derong; Li, Zhi; Chen, Hongzhi; Gao, Xiaoli; Wang, Fang; O'Connor, Jason C; Xu, Yong; Liu, Meilian; Dong, Lily Q; Liu, Feng

2017-11-14

Chronic inflammation in adipose tissue plays a key role in obesity-induced insulin resistance. However, the mechanisms underlying obesity-induced inflammation remain elusive. Here we show that obesity promotes mtDNA release into the cytosol, where it triggers inflammatory responses by activating the DNA-sensing cGAS-cGAMP-STING pathway. Fat-specific knockout of disulfide-bond A oxidoreductase-like protein (DsbA-L), a chaperone-like protein originally identified in the mitochondrial matrix, impaired mitochondrial function and promoted mtDNA release, leading to activation of the cGAS-cGAMP-STING pathway and inflammatory responses. Conversely, fat-specific overexpression of DsbA-L protected mice against high-fat diet-induced activation of the cGAS-cGAMP-STING pathway and inflammation. Taken together, we identify DsbA-L as a key molecule that maintains mitochondrial integrity. DsbA-L deficiency promotes inflammation and insulin resistance by activating the cGAS-cGAMP-STING pathway. Our study also reveals that, in addition to its well-characterized roles in innate immune surveillance, the cGAS-cGAMP-STING pathway plays an important role in mediating obesity-induced metabolic dysfunction.

Phylogeographic patterns of Lygus pratensis (Hemiptera: Miridae): Evidence for weak genetic structure and recent expansion in northwest China.

Science.gov (United States)

Zhang, Li-Juan; Cai, Wan-Zhi; Luo, Jun-Yu; Zhang, Shuai; Wang, Chun-Yi; Lv, Li-Min; Zhu, Xiang-Zhen; Wang, Li; Cui, Jin-Jie

2017-01-01

Lygus pratensis (L.) is an important cotton pest in China, especially in the northwest region. Nymphs and adults cause serious quality and yield losses. However, the genetic structure and geographic distribution of L. pratensis is not well known. We analyzed genetic diversity, geographical structure, gene flow, and population dynamics of L. pratensis in northwest China using mitochondrial and nuclear sequence datasets to study phylogeographical patterns and demographic history. L. pratensis (n = 286) were collected at sites across an area spanning 2,180,000 km2, including the Xinjiang and Gansu-Ningxia regions. Populations in the two regions could be distinguished based on mitochondrial criteria but the overall genetic structure was weak. The nuclear dataset revealed a lack of diagnostic genetic structure across sample areas. Phylogenetic analysis indicated a lack of population level monophyly that may have been caused by incomplete lineage sorting. The Mantel test showed a significant correlation between genetic and geographic distances among the populations based on the mtDNA data. However the nuclear dataset did not show significant correlation. A high level of gene flow among populations was indicated by migration analysis; human activities may have also facilitated insect movement. The availability of irrigation water and ample cotton hosts makes the Xinjiang region well suited for L. pratensis reproduction. Bayesian skyline plot analysis, star-shaped network, and neutrality tests all indicated that L. pratensis has experienced recent population expansion. Climatic changes and extensive areas occupied by host plants have led to population expansion of L. pratensis. In conclusion, the present distribution and phylogeographic pattern of L. pratensis was influenced by climate, human activities, and availability of plant hosts.

Sequence polymorphism data of the hypervariable regions of mitochondrial DNA in the Yadav population of Haryana.

Science.gov (United States)

Verma, Kapil; Sharma, Sapna; Sharma, Arun; Dalal, Jyoti; Bhardwaj, Tapeshwar

2018-06-01

Genetic variations among humans occur both within and among populations and range from single nucleotide changes to multiple-nucleotide variants. These multiple-nucleotide variants are useful for studying the relationships among individuals or various population groups. The study of human genetic variations can help scientists understand how different population groups are biologically related to one another. Sequence analysis of hypervariable regions of human mitochondrial DNA (mtDNA) has been successfully used for the genetic characterization of different population groups for forensic purposes. It is well established that different ethnic or population groups differ significantly in their mtDNA distributions. In the last decade, very little research has been conducted on mtDNA variations in the Indian population, although such data would be useful for elucidating the history of human population expansion across the world. Moreover, forensic studies on mtDNA variations in the Indian subcontinent are also scarce, particularly in the northern part of India. In this report, variations in the hypervariable regions of mtDNA were analyzed in the Yadav population of Haryana. Different molecular diversity indices were computed. Further, the obtained haplotypes were classified into different haplogroups and the phylogenetic relationship between different haplogroups was inferred.

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, Ppopulations. 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.

A new phylogeographic pattern of endemic Bufo bankorensis in Taiwan Island is attributed to the genetic variation of populations.

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Teng-Lang Yu

Full Text Available To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1 the existence of various geological barriers (Central Mountain Ranges, CMRs; and (2 the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China.Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA D-loop gene (348 bp recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp amplified (279 individuals, 27 localities from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S, corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades.The multiple origins (different clades of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B

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

Czech Academy of Sciences Publication Activity Database

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

2017-01-01

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

Energy expansion planning by considering electrical and thermal expansion simultaneously

International Nuclear Information System (INIS)

Abbasi, Ali Reza; Seifi, Ali Reza

2014-01-01

Highlights: • This paper focused on the expansion planning optimization of energy systems. • Employing two form of energy: the expansion of electrical and thermal energies. • The main objective is to minimize the costs. • A new Modified Honey Bee Mating Optimization (MHBMO) algorithm is applied. - Abstract: This study focused on the expansion planning optimization of energy systems employing two forms of energy: the expansion of electrical and thermal energies simultaneously. The main objective of this investigation is confirming network adequacy by adding new equipment to the network, over a given planning horizon. The main objective of the energy expansion planning (EEP) is to minimize the real energy loss, voltage deviation and the total cost of installation equipments. Since the objectives are different and incommensurable, it is difficult to solve the problem by the conventional approaches that may optimize a single objective. So, the meta-heuristic algorithm is applied to this problem. Here, Honey Bee Mating Optimization algorithm (HBMO) as a new evolutionary optimization algorithm is utilized. In order to improve the total ability of HBMO for the global search and exploration, a new modification process is suggested such a way that the algorithm will search the total search space globally. Also, regarding the uncertainties of the new complicated energy systems, in this paper for the first time, the EEP problem is investigated in a stochastic environment by the use of probabilistic load flow technique based on Point Estimate Method (PEM). In order to evaluate the feasibility and effectiveness of the proposed algorithm, two modified test systems are used as case studies

MtDNA and Y-chromosomal diversity in the Chachapoya, a population from the northeast Peruvian Andes-Amazon divide.

Science.gov (United States)

Guevara, Evelyn K; Palo, Jukka U; Guillén, Sonia; Sajantila, Antti

2016-11-01

The ancient Chachapoya were an aggregate of several ethnic groups that shared a common language, religion, and material culture. They inhabited a territory at the juncture of the Andes and the Amazon basin. Their position between those ecozones most likely influenced their genetic composition. We attempted to better understand their population history by assessing the contemporary genetic diversity in the Chachapoya and three of their immediate neighbors (Huancas, Jivaro, and Cajamarca). We inferred signatures of demographic history and genetic affinities, and contrasted the findings with data from other populations on local and continental scales. We studied mitochondrial DNA (mtDNA; hypervariable segment [HVSI and HVSII]) and Y chromosome (23 short tandem repeats (STRs)) marker data in 382 modern individuals. We used Sanger sequencing for mtDNA and a commercially available kit for Y-chromosomal STR typing. The Chachapoya had affinities with various populations of Andean and Amazonian origin. When examining the Native American component, the Chachapoya displayed high levels of genetic diversity. Together with other parameters, for example, large Tajima's D and Fu's Fs, the data indicated no drastic reduction of the population size in the past. The high level of diversity in the Chachapoya, the lack of evidence of drift in the past, and genetic affinities with a broad range of populations in the Americas reflects an intricate population history in the region. The new genetic data from the Chachapoya indeed seems to point to a genetic complexity that is not yet resolved but beginning to be elucidated. Am. J. Hum. Biol. 28:857-867, 2016. © 2016Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Expansion joints for LMFBR

International Nuclear Information System (INIS)

Dzenus, M.; Hundhausen, W.; Jansing, W.

1980-01-01

This discourse recounts efforts put into the SNR-2 project; specifically the development of compensation devices. The various prototypes of these compensation devices are described and the state of the development reviewed. Large Na (sodium)-heat transfer systems require a lot of valuable space if the component lay-out does not include compensation devices. So, in order to condense the spatial requirement as much as possible, expansion joints must be integrated into the pipe system. There are two basic types to suit the purpose: axial expansion joints and angular expansion joints. The expansion joints were developed on the basis of specific design criteria whereby differentiation is made between expansion joints of small and large nominal diameter. Expansion joints for installation in the sodium-filled primary piping are equipped with safety bellows in addition to the actual working bellows. Expansion joints must be designed and mounted in a manner to completely withstand seismic forces. The design must exclude any damage to the bellows during intermittent operations, that is, when sodium is drained the bellows' folds must be completely empty; otherwise residual solidified sodium could destroy the bellows when restarting. The expansion joints must be engineered on the basis of the following design data for the secondary system of the SNR project: working pressure: 16 bar; failure mode pressure: 5 events; failure mode: 5 sec., 28.5 bar, 520 deg. C; working temperature: 520 deg. C; temperature transients: 30 deg. C/sec.; service life: 200,000 h; number of load cycles: 10 4 ; material: 1.4948 or 1.4919; layer thickness of folds: 0.5 mm; angular deflection (DN 800): +3 deg. C or; axial expansion absorption (DN 600): ±80 mm; calculation: ASME class. The bellows' development work is not handled within this scope. The bellows are supplied by leading manufacturers, and warrant highest quality. Multiple bellows were selected on the basis of maximum elasticity - a property

Expansion joints for LMFBR

Energy Technology Data Exchange (ETDEWEB)

Dzenus, M.; Hundhausen, W.; Jansing, W.

1979-10-15

This discourse recounts efforts put into the SNR-2 project; specifically the development of compensation devices. The various prototypes of these compensation devices are described and the state of development reviewed. The expansion joints were developed on the basis of specific design criteria whereby differentiation is made between expansion joints of small and large nominal diameter. Expansion joints for installation in the sodium-filled primary piping are equipped with safety bellows in addition to the actual working bellows.

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

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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.

Expansions for Coulomb wave functions

NARCIS (Netherlands)

Boersma, J.

1969-01-01

In this paper we derive a number of expansions for Whittaker functions, regular and irregular Coulomb wave functions. The main result consists of a new expansion for the irregular Coulomb wave functions of orders zero and one in terms of regular Coulomb wave functions. The latter expansions are

Características fenotípicas dos pacientes com anemia falciforme de acordo com os haplótipos do gene da βS-globina em Fortaleza, Ceará

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Lilianne B. Silva

2010-02-01

Full Text Available Foram analisados 47 pacientes com diagnóstico clínico, laboratorial e molecular de anemia falciforme, residentes em Fortaleza, Ceará, com a finalidade de fornecer informações sobre a influência dos haplótipos do gene da βS- globina nas características fenotípicas desta doença. A determinação dos valores hematológicos foi realizada em contador automático de células sanguíneas, e os níveis de HbF foram determinados pela técnica da desnaturação alcalina. O DNA foi isolado de leucócitos, a partir de amostras de sangue total. A análise dos haplótipos da mutação βS foi realizada por PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Lenght Polymorphism, sendo analisados seis sítios polimórficos de restrição. Os pacientes foram divididos em cinco grupos, de acordo com o tipo de haplótipo: Bantu/Bantu, Benin/Benin, Bantu/Benin, Bantu/Atípico e Benin/Atípico. O nível de significância considerado nas análises foi p<0,05. Na comparação entre os haplótipos e as características hematológicas estudadas, apenas os valores de HbF e Ht apresentaram diferença estatisticamente significativa. Os níveis de HbF foram maiores no haplótipo Benin, seguido do haplótipo Bantu, o que está em conformidade com os dados da literatura. Foram demonstrados maior presença de crises vaso-oclusivas e episódios de pneumonia no haplótipo Benin/Atípico do que no haplótipo Bantu/Atípico; e maior presença de crises de infecção urinária no haplótipo Benin/Atípico do que no haplótipo Benin/Benin. Não houve diferença estatisticamente significativa entre os haplótipos Bantu/Bantu e Benin/Benin em relação às complicações clínicas; entretanto, foi observado que o haplótipo Bantu/Bantu tem uma maior frequência em todos os eventos clínicos estudados quando comparado ao Benin/Benin. Os resultados demonstram que o tipo de haplótipo do gene da βS-globina influencia as características fenotípicas dos pacientes com

Phylogeography of mtDNA haplogroup R7 in the Indian peninsula

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Shukla Parul

2008-08-01

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

Conformal expansions and renormalons

Energy Technology Data Exchange (ETDEWEB)

Rathsman, J.

2000-02-07

The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

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.

δ expansion applied to quantum electrodynamics

International Nuclear Information System (INIS)

Bender, C.M.; Boettcher, S.; Milton, K.A.

1992-01-01

A recently proposed technique known as the δ expansion provides a nonperturbative treatment of a quantum field theory. The δ-expansion approach can be applied to electrodynamics in such a way that local gauge invariance is preserved. In this paper it is shown that for electrodynamic processes involving only external photon lines and no external electron lines the δ expansion is equivalent to a fermion loop expansion. That is, the coefficient of δ n in the δ expansion is precisely the sum of all n-electron-loop Feynman diagrams in a conventional weak-coupling approximation. This equivalence does not extend to processes having external electron lines. When external electron lines are present, the δ expansion is truly nonperturbative and does not have a simple interpretation as a resummation of conventional Feynman diagrams. To illustrate the nonperturbative character of the δ expansion we perform a speculative calculation of the fermion condensate in the massive Schwinger model in the limit of large coupling constant

Understanding influences of culture and history on mtDNA variation and population structure in three populations from Assam, Northeast India.

Science.gov (United States)

Rej, Peter H; Deka, Ranjan; Norton, Heather L

2017-05-06

Positioned at the nexus of India, China, and Southeast Asia, Northeast India is presumed to have served as a channel for land-based human migration since the Upper Pleistocene. Assam is the largest state in the Northeast. We characterized the genetic background of three populations and examined the ways in which their population histories and cultural practices have influenced levels of intrasample and intersample variation. We examined sequence data from the mtDNA hypervariable control region and selected diagnostic mutations from the coding region in 128 individuals from three ethnic groups currently living in Assam: two Scheduled tribes (Sonowal Kachari and Rabha), and the non-Scheduled Tai Ahom. The populations of Assam sampled here express mtDNA lineages indicative of South Asian, Southeast Asian, and East Asian ancestry. We discovered two completely novel haplogroups in Assam that accounted for 6.2% of the lineages in our sample. We also identified a new subhaplogroup of M9a that is prevalent in the Sonowal Kachari of Assam (19.1%), but not present in neighboring Arunachal Pradesh, indicating substantial regional population structuring. Employing a large comparative dataset into a series of multidimensional scaling (MDS) analyses, we saw the Rabha cluster with populations sampled from Yunnan Province, indicating that the historical matrilineality of the Rabha has maintained lineages from Southern China. Assam has undergone multiple colonization events in the time since the initial peopling event, with populations from Southern China and Southeast Asia having the greatest influence on maternal lineages in the region. © 2017 Wiley Periodicals, Inc.

Deciphering the link between doubly uniparental inheritance of mtDNA and sex determination in bivalves: Clues from comparative transcriptomics

Science.gov (United States)

Capt, Charlotte; Renaut, Sébastien; Ghiselli, Fabrizio; Milani, Liliana; Johnson, Nathan A.; Sietman, Bernard E.; Stewart, Donald; Breton, Sophie

2018-01-01

Bivalves exhibit an astonishing diversity of sexual systems and sex-determining mechanisms. They can be gonochoric, hermaphroditic or androgenetic, with both genetic and environmental factors known to determine or influence sex. One unique sex-determining system involving the mitochondrial genome has also been hypothesized to exist in bivalves with doubly uniparental inheritance (DUI) of mtDNA. However, the link between DUI and sex determination remains obscure. In this study, we performed a comparative gonad transcriptomics analysis for two DUI-possessing freshwater mussel species to better understand the mechanisms underlying sex determination and DUI in these bivalves. We used a BLAST reciprocal analysis to identify orthologs between Venustaconcha ellipsiformis and Utterbackia peninsularis and compared our results with previously published sex-specific bivalve transcriptomes to identify conserved sex-determining genes. We also compared our data with other DUI species to identify candidate genes possibly involved in the regulation of DUI. A total of ∼12,000 orthologous relationships were found, with 2,583 genes differentially expressed in both species. Among these genes, key sex-determining factors previously reported in vertebrates and in bivalves (e.g., Sry, Dmrt1, Foxl2) were identified, suggesting that some steps of the sex-determination pathway may be deeply conserved in metazoans. Our results also support the hypothesis that a modified ubiquitination mechanism could be responsible for the retention of the paternal mtDNA in male bivalves, and revealed that DNA methylation could also be involved in the regulation of DUI. Globally, our results suggest that sets of genes associated with sex determination and DUI are similar in distantly-related DUI species.

Accelerating the loop expansion

International Nuclear Information System (INIS)

Ingermanson, R.

1986-01-01

This thesis introduces a new non-perturbative technique into quantum field theory. To illustrate the method, I analyze the much-studied phi 4 theory in two dimensions. As a prelude, I first show that the Hartree approximation is easy to obtain from the calculation of the one-loop effective potential by a simple modification of the propagator that does not affect the perturbative renormalization procedure. A further modification then susggests itself, which has the same nice property, and which automatically yields a convex effective potential. I then show that both of these modifications extend naturally to higher orders in the derivative expansion of the effective action and to higher orders in the loop-expansion. The net effect is to re-sum the perturbation series for the effective action as a systematic ''accelerated'' non-perturbative expansion. Each term in the accelerated expansion corresponds to an infinite number of terms in the original series. Each term can be computed explicitly, albeit numerically. Many numerical graphs of the various approximations to the first two terms in the derivative expansion are given. I discuss the reliability of the results and the problem of spontaneous symmetry-breaking, as well as some potential applications to more interesting field theories. 40 refs

Thermal expansion data

International Nuclear Information System (INIS)

Taylor, D.

1984-01-01

This paper gives regression data for a modified second order polynomial fitted to the expansion data of, and percentage expansions for dioxides with (a) the fluorite and antifluorite structure: AmO 2 , BkO 2 , CeO 2 , CmO 2 , HfO 2 , Li 2 O, NpO 2 , PrO 2 , PuO 2 , ThO 2 , UO 2 , ZrO 2 , and (b) the rutile structure: CrO 2 , GeO 2 , IrO 2 , MnO 2 , NbO 2 , PbO 2 , SiO 2 , SnO 2 , TeO 2 , TiO 2 and VO 2 . Reduced expansion curves for the dioxides showed only partial grouping into iso-electronic series for the fluorite structures and showed that the 'law of corresponding states' did not apply to the rutile structures. (author)

Thermal expansion of beryllium oxide

International Nuclear Information System (INIS)

Solodukhin, A.V.; Kruzhalov, A.V.; Mazurenko, V.G.; Maslov, V.A.; Medvedev, V.A.; Polupanova, T.I.

1987-01-01

Precise measurements of temperature dependence of the coefficient of linear expansion in the 22-320 K temperature range on beryllium oxide monocrystals are conducted. A model of thermal expansion is suggested; the range of temperature dependence minimum of the coefficient of thermal expansion is well described within the frames of this model. The results of the experiment may be used for investigation of thermal stresses in crystals

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

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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

Convergence of mayer expansions

International Nuclear Information System (INIS)

Brydges, D.C.

1986-01-01

The tree graph bound of Battle and Federbush is extended and used to provide a simple criterion for the convergence of (iterated) Mayer expansions. As an application estimates on the radius of convergence of the Mayer expansion for the two-dimensional Yukawa gas (nonstable interaction) are obtained

Molecular ecology of the big brown bat (Eptesicus fuscus): Genetic and natural history variation in a hybrid zone

Science.gov (United States)

Neubaum, M.A.; Douglas, M.R.; Douglas, M.E.; O'Shea, T.J.

2007-01-01

Several geographically distinct mitochondrial DNA (mtDNA) lineages of the big brown bat (Eptesicus fuscus) have been documented in North America. Individuals from 2 of these lineages, an eastern and a western form, co-occur within maternity colonies in Colorado. The discovery of 2 divergent mtDNA lineages in sympatry prompted a set of questions regarding possible biological differences between haplotypes. We captured big brown bats at maternity roosts in Colorado and recorded data on body size, pelage color, litter size, roosting and overwintering behaviors, and local distributions. Wing biopsies were collected for genetic analysis. The ND2 region of the mtDNA molecule was used to determine lineage of the bats. In addition, nuclear DNA (nDNA) intron 1 of the ??-globin gene was used to determine if mtDNA lineages are hybridizing. Eastern and western mtDNA lineages differed by 10.3% sequence divergence and examination of genetic data suggests recent population expansion for both lineages. Differences in distribution occur along the Colorado Front Range, with an increasing proportion of western haplotypes farther south. Results from nDNA analyses demonstrated hybridization between the 2 lineages. Additionally, no outstanding distinctiveness was found between the mtDNA lineages in natural history characters examined. We speculate that historical climate changes separated this species into isolated eastern and western populations, and that secondary contact with subsequent interbreeding was facilitated by European settlement. ?? 2007 American Society of Mammalogists.

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.

Abundant mtDNA diversity and ancestral admixture in Colombian criollo cattle (Bos taurus).

Science.gov (United States)

Carvajal-Carmona, Luis G; Bermudez, Nelson; Olivera-Angel, Martha; Estrada, Luzardo; Ossa, Jorge; Bedoya, Gabriel; Ruiz-Linares, Andrés

2003-11-01

Various cattle populations in the Americas (known as criollo breeds) have an origin in some of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). These cattle constitute a potentially important genetic reserve as they are well adapted to local environments and show considerable variation in phenotype. To examine the genetic ancestry and diversity of Colombian criollo we obtained mitochondrial DNA control region sequence information for 110 individuals from seven breeds. Old World haplogroup T3 is the most commonly observed CR lineage in criollo (0.65), in agreement with a mostly European ancestry for these cattle. However, criollo also shows considerable frequencies of haplogroups T2 (0.9) and T1 (0.26), with T1 lineages in criollo being more diverse than those reported for West Africa. The distribution and diversity of Old World lineages suggest some North African ancestry for criollo, probably as a result of the Arab occupation of Iberia prior to the European migration to the New World. The mtDNA diversity of criollo is higher than that reported for European and African cattle and is consistent with a differentiated ancestry for some criollo breeds.

$\\delta$-Expansion at Finite Temperature

OpenAIRE

Ramos, Rudnei O.

1996-01-01

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

Electrical Resistance Alloys and Low-Expansion Alloys

DEFF Research Database (Denmark)

Kjer, Torben

1996-01-01

The article gives an overview of electrical resistance alloys and alloys with low thermal expansion. The electrical resistance alloys comprise resistance alloys, heating alloys and thermostat alloys. The low expansion alloys comprise alloys with very low expansion coefficients, alloys with very low...... thermoelastic coefficients and age hardenable low expansion alloys....

Disjoint sum expansion method in FTA

International Nuclear Information System (INIS)

Ruan Keqiang

1987-01-01

An expansion formula for transforming boolean algebraic expressions into disjoint form was proved. Based on this expansion formula, a method for transforming system failure function into disjoint form was devised. The fact that the expansion can be done for several elements simulatneously makes the method flexible and fast. Some examples from fault tree analysis (FTA) and network analysis were examined by the new method to show its algorithm and its merit. Besides, by means of the proved expansion formula some boolean algebraic relations can proved very easily

Maxwell superalgebras and Abelian semigroup expansion

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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.

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.

Fascioliasis transmission by Lymnaea neotropica confirmed by nuclear rDNA and mtDNA sequencing in Argentina.

Science.gov (United States)

Mera y Sierra, Roberto; Artigas, Patricio; Cuervo, Pablo; Deis, Erika; Sidoti, Laura; Mas-Coma, Santiago; Bargues, Maria Dolores

2009-12-03

Fascioliasis is widespread in livestock in Argentina. Among activities included in a long-term initiative to ascertain which are the fascioliasis areas of most concern, studies were performed in a recreational farm, including liver fluke infection in different domestic animal species, classification of the lymnaeid vector and verification of natural transmission of fascioliasis by identification of the intramolluscan trematode larval stages found in naturally infected snails. The high prevalences in the domestic animals appeared related to only one lymnaeid species present. Lymnaeid and trematode classification was verified by means of nuclear ribosomal DNA and mitochondrial DNA marker sequencing. Complete sequences of 18S rRNA gene and rDNA ITS-2 and ITS-1, and a fragment of the mtDNA cox1 gene demonstrate that the Argentinian lymnaeid belongs to the species Lymnaea neotropica. Redial larval stages found in a L. neotropica specimen were ascribed to Fasciola hepatica after analysis of the complete ITS-1 sequence. The finding of L. neotropica is the first of this lymnaeid species not only in Argentina but also in Southern Cone countries. The total absence of nucleotide differences between the sequences of specimens from Argentina and the specimens from the Peruvian type locality at the levels of rDNA 18S, ITS-2 and ITS-1, and the only one mutation at the mtDNA cox1 gene suggest a very recent spread. The ecological characteristics of this lymnaeid, living in small, superficial water collections frequented by livestock, suggest that it may be carried from one place to another by remaining in dried mud stuck to the feet of transported animals. The presence of L. neotropica adds pronounced complexity to the transmission and epidemiology of fascioliasis in Argentina, due to the great difficulties in distinguishing, by traditional malacological methods, between the three similar lymnaeid species of the controversial Galba/Fossaria group present in this country: L. viatrix

Uniform gradient expansions

CERN Document Server

Giovannini, Massimo

2015-01-01

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.

Thin foil expansion into a vacuum

International Nuclear Information System (INIS)

Mora, P.

2005-01-01

Plasma expansion into a vacuum is an old problem which has been renewed recently in various contexts: expansion of ultra-cold plasmas, cluster expansion, of dust grains, expansion of thin foils. In this presentation I will first discuss the physics of the expansion of a thin foil irradiated by an ultra-short ultra-intense laser pulse. The expansion results in the formation of high energy ions. For an infinitely steep plasma-vacuum interface the fastest ions are located in the outer part of the expansion and their velocity is given by ν m ax∼ 2 C s (In ω p it) where c s (Zk B T e /m i )''1/2 is the ion-acoustic velocity ω p i=(n e 0Ze''2/m i e 0 )''1/2 is the ion plasma frequency, n e 0 is the electron density in the unperturbed plasma, Z is the ion charge number. In the above expression, t is either the pulse duration or the effective acceleration time (in particular t∼L/2c s , where L is the width of the foil, when the electron cooling is taken into account). A salient characteristic of the expansion is the occurrence of a double layer structure and a peak of the accelerating electric field at the ion front. I will explain the origin of the peak and predict its temporal behavior. This peak has been diagnosed in recent experiments. I will also discuss the effect of a 2-temperatures electron distribution function on the expansion, showing the dominant role of the hot electron component. Finally I will discuss the occurrence of ion spikes in the expansion when the initial density profile is smooth. The ion spike is due to a wave breaking which cannot be handled in a satisfactory way by a fluid code and requires a kinetic description. A. simple collisionless particle code has been used to treat the evolution of the spike after the wave breaking and the results will be shown. (Author)

Compiling the First Monolingual Lusoga Dictionary

Directory of Open Access Journals (Sweden)

Minah Nabirye

2011-10-01

Full Text Available

Abstract: In this research article a study is made of the approach followed to compile the first-ever monolingual dictionary for Lusoga. Lusoga is a Bantu language spoken in Uganda by slightly over two mil-lion people. Being an under-resourced language, the Lusoga orthography had to be designed, a grammar written, and a corpus built, before embarking on the compilation of the dictionary. This compilation was aimed at attaining an academic degree, hence requiring a rigorous research methodology. Firstly, the prevail-ing methods for compiling dictionaries were mainly practical and insufficient in explaining the theoretical linguistic basis for dictionary compilation. Since dictionaries are based on meaning, the theory of meaning was used to account for all linguistic data considered in dictionaries. However, meaning is considered at a very abstract level, far removed from the process of compiling dictionaries. Another theory, the theory of modularity, was used to bridge the gap between the theory of meaning and the compilation process. The modular theory explains how the different modules of a language contribute information to the different parts of the dictionary article or dictionary information in general. Secondly, the research also had to contend with the different approaches for analysing Bantu languages for Bantu and European audiences. A descrip-tion of the Bantu- and European-centred approaches to Bantu studies was undertaken in respect of (a the classification of Lusoga words, and (b the specification of their citations. As a result, Lusoga lexicography deviates from the prevailing Bantu classification and citation of nouns, adjectives and verbs in particular. The dictionary was tested on two separate occasions and all the feedback was considered in the compilation pro-cess. This article, then, gives an overall summary of all the steps involved in the compilation of the Eiwanika ly'Olusoga, i.e. the Monolingual Lusoga Dictionary

Genetic models reveal historical patterns of sea lamprey population fluctuations within Lake Champlain

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Cassidy C. D’Aloia

2015-10-01

Full Text Available The origin of sea lamprey (Petromyzon marinus in Lake Champlain has been heavily debated over the past decade. Given the lack of historical documentation, two competing hypotheses have emerged in the literature. First, it has been argued that the relatively recent population size increase and concomitant rise in wounding rates on prey populations are indicative of an invasive population that entered the lake through the Champlain Canal. Second, recent genetic evidence suggests a post-glacial colonization at the end of the Pleistocene, approximately 11,000 years ago. One limitation to resolving the origin of sea lamprey in Lake Champlain is a lack of historical and current measures of population size. In this study, the issue of population size was explicitly addressed using nuclear (nDNA and mitochondrial DNA (mtDNA markers to estimate historical demography with genetic models. Haplotype network analysis, mismatch analysis, and summary statistics based on mtDNA noncoding sequences for NCI (479 bp and NCII (173 bp all indicate a recent population expansion. Coalescent models based on mtDNA and nDNA identified two potential demographic events: a population decline followed by a very recent population expansion. The decline in effective population size may correlate with land-use and fishing pressure changes post-European settlement, while the recent expansion may be associated with the implementation of the salmonid stocking program in the 1970s. These results are most consistent with the hypothesis that sea lamprey are native to Lake Champlain; however, the credibility intervals around parameter estimates demonstrate that there is uncertainty regarding the magnitude and timing of past demographic events.

Influence of βS-Globin Haplotypes and Hydroxyurea on Arginase I Levels in Sickle Cell Disease

Directory of Open Access Journals (Sweden)

J. A. Moreira

2016-01-01

Full Text Available Introduction. Sickle cell disease (SCD is characterized by hemoglobin S homozygosity, leading to hemolysis and vasoocclusion. The hemolysis releases arginase I, an enzyme that decreases the bioavailability of nitric oxide, worsening the symptoms. The different SCD haplotypes are related to clinical symptoms and varied hemoglobin F (HbF concentration. The aim of this study was to evaluate the impact of the βS gene haplotypes and HbF concentration on arginase I levels in SCD patients. Methods. Fifty SCD adult patients were enrolled in the study and 20 blood donors composed the control group. Arginase I was measured by ELISA. The βS haplotypes were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP. Statistical analyses were performed with GraphPad Prism program and the significance level was p<0.05. Results. Significant increase was observed in the arginase I levels in SCD patients compared to the control group (p<0.0001. The comparison between the levels of arginase I in three haplotypes groups showed a difference between the Bantu/Bantu × Bantu/Benin groups; Bantu/Bantu × Benin/Benin, independent of HU dosage. An inverse correlation with the arginase I levels and HbF concentration was observed. Conclusion. The results support the hypothesis that arginase I is associated with HbF concentration, also measured indirectly by the association with haplotypes.

Effects of mtDNA in SHR-mtF344 versus SHR conplastic strains on reduced OXPHOS enzyme levels, insulin resistance, cardiac hypertrophy, and systolic dysfunction

Czech Academy of Sciences Publication Activity Database

Houštěk, Josef; Vrbacký, Marek; Hejzlarová, Kateřina; Zídek, Václav; Landa, Vladimír; Šilhavý, Jan; Šimáková, Miroslava; Mlejnek, Petr; Kazdová, L.; Mikšík, Ivan; Neckář, Jan; Papoušek, František; Kolář, František; Kurtz, T. W.; Pravenec, Michal

2014-01-01

Roč. 46, č. 18 (2014), s. 671-678 ISSN 1094-8341 R&D Projects: GA MŠk(CZ) LL1204; GA ČR(CZ) GB14-36804G; GA ČR(CZ) GA13-10267S; GA MŠk(CZ) 7E10067 Institutional support: RVO:67985823 Keywords : SHR conplastic strain with F344 mtDNA * impaired glucose tolerance * systolic dysfunction Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition Impact factor: 2.374, year: 2014

A genetic atlas of human admixture history.

Science.gov (United States)

Hellenthal, Garrett; Busby, George B J; Band, Gavin; Wilson, James F; Capelli, Cristian; Falush, Daniel; Myers, Simon

2014-02-14

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

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

Thermal expansion of L-ascorbic acid

Science.gov (United States)

Nicolaï, B.; Barrio, M.; Tamarit, J.-Ll.; Céolin, R.; Rietveld, I. B.

2017-04-01

The specific volume of vitamin C has been investigated by X-ray powder diffraction as a function of temperature from 110 K up to complete degradation around 440 K. Its thermal expansion is relatively small in comparison with other organic compounds with an expansivity α v of 1.2(3) × 10-4 K-1. The structure consists of strongly bound molecules in the ac plane through a dense network of hydrogen bonds. The thermal expansion is anisotropic. Along the b axis, the expansion has most leeway and is about 10 times larger than in the other directions.

Chemical graph-theoretic cluster expansions

International Nuclear Information System (INIS)

Klein, D.J.

1986-01-01

A general computationally amenable chemico-graph-theoretic cluster expansion method is suggested as a paradigm for incorporation of chemical structure concepts in a systematic manner. The cluster expansion approach is presented in a formalism general enough to cover a variety of empirical, semiempirical, and even ab initio applications. Formally such approaches for the utilization of chemical structure-related concepts may be viewed as discrete analogues of Taylor series expansions. The efficacy of the chemical structure concepts then is simply bound up in the rate of convergence of the cluster expansions. In many empirical applications, e.g., boiling points, chromatographic separation coefficients, and biological activities, this rate of convergence has been observed to be quite rapid. More note will be made here of quantum chemical applications. Relations to questions concerning size extensivity of energies and size consistency of wave functions are addressed

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....

Edgeworth expansion for functionals of continuous diffusion processes

DEFF Research Database (Denmark)

Podolskij, Mark; Yoshida, Nakahiro

This paper presents new results on the Edgeworth expansion for high frequency functionals of continuous diffusion processes. We derive asymptotic expansions for weighted functionals of the Brownian motion and apply them to provide the Edgeworth expansion for power variation of diffusion processes....... Our methodology relies on martingale embedding, Malliavin calculus and stable central limit theorems for semimartingales. Finally, we demonstrate the density expansion for studentized statistics of power variations.......This paper presents new results on the Edgeworth expansion for high frequency functionals of continuous diffusion processes. We derive asymptotic expansions for weighted functionals of the Brownian motion and apply them to provide the Edgeworth expansion for power variation of diffusion processes...

Expansion lyre-shaped tube

International Nuclear Information System (INIS)

Andro, Jean.

1973-01-01

The invention relates the expansion lyre-shaped tube portions formed in dudgeoned tubular bundles between two bottom plates. An expansion lyre comprises at least two sets of tubes of unequal lengths coplanar and symmetrical with respect to the main tube axis, with connecting portions between the tubes forming said sets. The invention applies to apparatus such as heat exchangers, heaters, superheaters or breeders [fr

Investigating the prehistory of Tungusic peoples of Siberia and the Amur-Ussuri region with complete mtDNA genome sequences and Y-chromosomal markers.

Science.gov (United States)

Duggan, Ana T; Whitten, Mark; Wiebe, Victor; Crawford, Michael; Butthof, Anne; Spitsyn, Victor; Makarov, Sergey; Novgorodov, Innokentiy; Osakovsky, Vladimir; Pakendorf, Brigitte

2013-01-01

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.

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.

On the Equisummability of Hermite and Fourier Expansions

Indian Academy of Sciences (India)

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.

PENGGUNAAN LEAFLET DALAM PENDIDIKAN GIZI DAN PENGARUHNYA TERHADAP TINGKAT PENGETAHUAN IBU

Directory of Open Access Journals (Sweden)

Susilowati Herman

2012-11-01

Full Text Available Selama ini pendidikan gizi umumnya belum memanfaatkan alat bantu pendidikan gizi secara optimal. Selain itu pesan-pesan pendidikan gizi terkadang belum dirancang dengan seksama, sesuai dengan kebutuhan sasaran. Tidak jarang dijumpai pesan yang terlalu banyak, umum atau tidak terarah. Penyampaian pesan-pesan pendidikan gizi yang dilakukan secara berulang dan disertai penggunaan alat bantu pendidikan yang dirancang dengan baik, dapat mempermudah sasaran pendidikan menangkap dan mengerti isi pesan pendidikan. Penelitian ini bertujuan menilai perubahan tingkat pengetahuan gizi sebagai hasil dari paket pendidikan gizi yang terarah dengan menggunakan alat bantu pendidikan berupa leaflet yana dibawa pulang oleh sasaran pendidikan. Sasaran pendidikan adalah ibu-ibu dari anak Balita penderita gizi buruk (KKP berat pengunjung Klinik Gizi, Puslitbang Gizi, Bogor. Kelompok pembanding adalah juga ibu-ibu dari anak Balita penderita gizi buruk pengunjung Klinik Gizi yang sama dan kepadanya juga diberikan pendidikan gizi dengan isi pesan sama, tetapi tidak diberi alat bantu pendidikan berupa leaflet. Hasil penelitian menunjukkan babwa perubahan tingkat pengetahuan gizi ibu-ibu yang diberi leaflet, lebih baik daripada pengetahuan gizi ibu-ibu kelompok pembanding.

Craniodental continuity and change between Iron Age peoples and their descendants

Directory of Open Access Journals (Sweden)

Kerryn A. Warren

2014-07-01

Full Text Available The appearance of the Iron Age of southern Africa early in the first millennium AD is associated with the migration of Bantu speakers who were broadly ancestral to present-day Bantu speakers. While there is sufficient genetic, physical anthropological and cultural evidence to support general continuity into contemporary populations, the extent to which events since colonialism have affected morphological variation is poorly understood. We used dental anthropological techniques and three-dimensional craniomandibular metrics to examine biological relationships among Iron Age farmers, a historical 19th-century Ndebele sample and 20th-century Bantu speakers. We show that, although Iron Age and modern morphologies are generally similar, there are differences. Moreover, the historical sample falls between the precolonial and modern samples, suggesting increased genetic exchange from the 19th century onwards. These results suggest that recent historical events altered the genetic make-up of Bantu speakers and that, as a result, extrapolations from modern groups to the past should be done with caution as morphological variability is relative to historical context.

Plasma expansion: fundamentals and applications

International Nuclear Information System (INIS)

Engeln, R; Mazouffre, S; Vankan, P; Bakker, I; Schram, D C

2002-01-01

The study of plasma expansion is interesting from a fundamental point of view as well as from a more applied point of view. We here give a short overview of the way properties like density, velocity and temperature behave in an expanding thermal plasma. Experimental data show that the basic phenomena of plasma expansion are to some extent similar to those of the expansion of a hot neutral gas. From the application point of view, we present first results on the use of an expanding thermal plasma in the plasma-activated catalysis of ammonia, from N 2 -H 2 mixtures

On genus expansion of superpolynomials

Energy Technology Data Exchange (ETDEWEB)

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

2014-12-15

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

A molecular phylogeny of the Cephinae (Hymenoptera, Cephidae based on mtDNA COI gene: a test of traditional classification

Directory of Open Access Journals (Sweden)

Mahir Budak

2011-09-01

Full Text Available Cephinae is traditionally divided into three tribes and about 24 genera based on morphology and host utilization. There has been no study testing the monophyly of taxa under a strict phylogenetic criterion. A molecular phylogeny of Cephinae based on a total of 68 sequences of mtDNA COI gene, representing seven genera of Cephinae, is reconstructed to test the traditional limits and relationships of taxa. Monophyly of the traditional tribes is not supported. Monophyly of the genera are largely supported except for Pachycephus. A few host shift events are suggested based on phylogenetic relationships among taxa. These results indicate that a more robust phylogeny is required for a more plausible conclusion. We also report two species of Cephus for the first time from Turkey.

On summation of perturbation expansions

International Nuclear Information System (INIS)

Horzela, A.

1985-04-01

The problem of the restoration of physical quantities defined by divergent perturbation expansions is analysed. The Pad'e and Borel summability is proved for alternating perturbation expansions with factorially growing coefficients. The proof is based on the methods of the classical moments theory. 17 refs. (author)

OPEC future capacity expansions

International Nuclear Information System (INIS)

Sandrea, I.

2005-01-01

This conference presentation examined OPEC future capacity expansions including highlights from 2000-2004 from the supply perspective and actions by OPEC; OPEC spare capacity in 2005/2006; medium-term capacity expansion and investments; long-term scenarios, challenges and opportunities; and upstream policies in member countries. Highlights from the supply perspective included worst than expected non-OPEC supply response; non-OPEC supply affected by a number of accidents and strikes; geopolitical tensions; and higher than expected demand for OPEC crude. OPEC's actions included closer relationship with other producers and consumers; capacity expansions in 2004 and 2005/2006; and OPEC kept the market well supplied with crude in 2004. The presentation also provided data using graphical charts on OPEC net capacity additions until 2005/2006; OPEC production versus spare capacity from 2003 to 2005; OPEC production and capacity to 2010; and change in required OPEC production from 2005-2020. Medium term expansion to 2010 includes over 60 projects. Medium-term risks such as project execution, financing, costs, demand, reserves, depletion, integration of Iraq, and geopolitical tensions were also discussed. The presentation concluded that in the long term, large uncertainties remain; the peak of world supply is not imminent; and continued and enhanced cooperation is essential to market stability. tabs., figs

Comparing vowel hiatus resolution in ciNsenga and chiShona: An ...

African Journals Online (AJOL)

Will Bennett

Note also that positing an empty C may not be universal across Bantu. In Zezuru, for example (see Fortune 1984: 10, Mudzingwa 2014: 66), it is ... in loanwords in chiShona and many other Bantu languages that have the CV syllable structure. In this case, vowel epenthesis is used instead of deletion (e.g. „school‟ or ...

Object marking in Swahili: Definiteness, specificity, or both ...

African Journals Online (AJOL)

This article examines the role of object marking in relation to definiteness and specificity in Swahili. Object marking in general has attracted the attention of many scholars in the field of Bantu linguistics due to the complex nature of object markers (OMs) and varying functions they fulfil in Bantu. Opinions differ on the role of ...

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...

The bootstrap and edgeworth expansion

CERN Document Server

Hall, Peter

1992-01-01

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

Fuel Thermal Expansion (FTHEXP)

International Nuclear Information System (INIS)

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 2 and PuO 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 2 , and the fraction of fuel which is molten

Node-Expansion Operators for the UCT Algorithm

Science.gov (United States)

Yajima, Takayuki; Hashimoto, Tsuyoshi; Matsui, Toshiki; Hashimoto, Junichi; Spoerer, Kristian

Recent works on the MCTS and UCT framework in the domain of Go focused on introducing knowledge to the playout and on pruning variations from the tree, but so far node expansion has not been investigated. In this paper we show that delaying expansion according to the number of the siblings delivers a gain of more than 92% when compared to normal expansion. We propose three improvements; one that uses domain knowledge and two that are domain-independent methods. Experimental results show that all advanced operators significantly improve the UCT performance when compared to the basic delaying expansion. From the results we may conclude that the new expansion operators are an appropriate means to improve the UCT algorithm.

Thermal expansion in small metallic particles

International Nuclear Information System (INIS)

Ivanov, A.S.

1985-01-01

An anomalously low thermal expansion observable in small particles is attributed to extending effect of the shell. It is shown that the coefficient of thermal expansion of the oxide-film-coated aluminium particles calculated using elastic constants and coefficients of thermal expansion of massive materials agres well with those measured experimentally. The linear dilatation of the shell, its stress to rupture and the values of the structural tension are estimated vs the temperature

Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history

Science.gov (United States)

da Silva Santos, Anelisie; Trigo, Tatiane Campos; de Oliveira, Tadeu Gomes; Silveira, Leandro

2018-01-01

Abstract The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species’ history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America. PMID:29668017

Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia.

Science.gov (United States)

Rannamäe, E; Lõugas, L; Niemi, M; Kantanen, J; Maldre, L; Kadõrova, N; Saarma, U

2016-04-01

Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations. © 2016 Stichting International Foundation for Animal Genetics.

[Tissular expansion in giant congenital nevi treatment].

Science.gov (United States)

Nguyen Van Nuoi, V; Francois-Fiquet, C; Diner, P; Sergent, B; Zazurca, F; Franchi, G; Buis, J; Vazquez, M-P; Picard, A; Kadlub, N

2014-08-01

Surgical management of giant melanotic naevi remains a surgical challenge. Tissue expansion provides tissue of the same quality for the repair of defects. The aim of this study is to review tissular expansion for giant melanotic naevi. We conducted a retrospective study from 2000 to 2012. All children patients who underwent a tissular expansion for giant congenital naevi had been included. Epidemiological data, surgical procedure, complication rate and results had been analysed. Thirty-tree patients had been included; they underwent 61 procedures with 79 tissular-expansion prosthesis. Previous surgery, mostly simple excision had been performed before tissular expansion. Complete naevus excision had been performed in 63.3% of the cases. Complications occurred in 45% of the cases, however in 50% of them were minor. Iterative surgery increased the complication rate. Tissular expansion is a valuable option for giant congenital naevus. However, complication rate remained high, especially when iterative surgery is needed. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

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.

Negative thermal expansion in functional materials: controllable thermal expansion by chemical modifications.

Science.gov (United States)

Chen, Jun; Hu, Lei; Deng, Jinxia; Xing, Xianran

2015-06-07

Negative thermal expansion (NTE) is an intriguing physical property of solids, which is a consequence of a complex interplay among the lattice, phonons, and electrons. Interestingly, a large number of NTE materials have been found in various types of functional materials. In the last two decades good progress has been achieved to discover new phenomena and mechanisms of NTE. In the present review article, NTE is reviewed in functional materials of ferroelectrics, magnetics, multiferroics, superconductors, temperature-induced electron configuration change and so on. Zero thermal expansion (ZTE) of functional materials is emphasized due to the importance for practical applications. The NTE functional materials present a general physical picture to reveal a strong coupling role between physical properties and NTE. There is a general nature of NTE for both ferroelectrics and magnetics, in which NTE is determined by either ferroelectric order or magnetic one. In NTE functional materials, a multi-way to control thermal expansion can be established through the coupling roles of ferroelectricity-NTE, magnetism-NTE, change of electron configuration-NTE, open-framework-NTE, and so on. Chemical modification has been proved to be an effective method to control thermal expansion. Finally, challenges and questions are discussed for the development of NTE materials. There remains a challenge to discover a "perfect" NTE material for each specific application for chemists. The future studies on NTE functional materials will definitely promote the development of NTE materials.

Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers

Science.gov (United States)

Duggan, Ana T.; Whitten, Mark; Wiebe, Victor; Crawford, Michael; Butthof, Anne; Spitsyn, Victor; Makarov, Sergey; Novgorodov, Innokentiy; Osakovsky, Vladimir; Pakendorf, Brigitte

2013-01-01

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. PMID:24349531

Applications of the large mass expansion

International Nuclear Information System (INIS)

Fleischer, J.; Kotikov, A.V.; ); Veretin, O.L.

1998-01-01

The method of the large mass expansion (LME) is investigated for selfenergy and vertex functions in two-loop order. It has the technical advantage that in many cases the expansion coefficients can be expressed analytically. As long as only one non-zero external momentum squared, q 2 , is involved also the Taylor expansion (TE) w.r.t. small q 2 yields high precision results in a domain sufficient for most applications. In the case of only one non-zero mass M and only one external momentum squared, the expansion w.r.t. q 2 /M 2 is identical for the TE and the LME. In this case the combined techniques yield analytic expressions for many diagrams, which are quite easy to handle numerically. (author)

Hematoma Expansion Following Acute Intracerebral Hemorrhage

Science.gov (United States)

Brouwers, H. Bart; Greenberg, Steven M.

2013-01-01

Intracerebral hemorrhage, the most devastating form of stroke, has no specific therapy proven to improve outcome by randomized controlled trial. Location and baseline hematoma volume are strong predictors of mortality, but are non-modifiable by the time of diagnosis. Expansion of the initial hematoma is a further marker of poor prognosis that may be at least partly preventable. Several risk factors for hematoma expansion have been identified, including baseline ICH volume, early presentation after symptom onset, anticoagulation, and the CT angiography spot sign. Although the biological mechanisms of hematoma expansion remain unclear, accumulating evidence supports a model of ongoing secondary bleeding from ruptured adjacent vessels surrounding the initial bleeding site. Several large clinical trials testing therapies aimed at preventing hematoma expansion are in progress, including aggressive blood pressure reduction, treatment with recombinant factor VIIa guided by CT angiography findings, and surgical intervention for superficial hematomas without intraventricular extension. Hematoma expansion is so far the only marker of outcome that is amenable to treatment and thus a potentially important therapeutic target. PMID:23466430

Renormalization group and mayer expansions

International Nuclear Information System (INIS)

Mack, G.

1984-01-01

Mayer expansions promise to become a powerful tool in exact renormalization group calculations. Iterated Mayer expansions were sucessfully used in the rigorous analysis of 3-dimensional U (1) lattice gauge theory by Gopfert and the author, and it is hoped that they will also be useful in the 2-dimensional nonlinear σ-model, and elsewhere

Asymptotic expansions for high-contrast elliptic equations

KAUST Repository

Calo, Victor M.; Efendiev, Yalchin R.; Galvis, Juan

2014-01-01

In this paper, we present a high-order expansion for elliptic equations in high-contrast media. The background conductivity is taken to be one and we assume the medium contains high (or low) conductivity inclusions. We derive an asymptotic expansion with respect to the contrast and provide a procedure to compute the terms in the expansion. The computation of the expansion does not depend on the contrast which is important for simulations. The latter allows avoiding increased mesh resolution around high conductivity features. This work is partly motivated by our earlier work in [Domain decomposition preconditioners for multiscale flows in high-contrast media, Multiscale Model Simul. 8 (2010) 1461-1483] where we design efficient numerical procedures for solving high-contrast problems. These multiscale approaches require local solutions and our proposed high-order expansion can be used to approximate these local solutions inexpensively. In the case of a large-number of inclusions, the proposed analysis can help to design localization techniques for computing the terms in the expansion. In the paper, we present a rigorous analysis of the proposed high-order expansion and estimate the remainder of it. We consider both high-and low-conductivity inclusions. © 2014 World Scientific Publishing Company.

Asymptotic expansions for high-contrast elliptic equations

KAUST Repository

Calo, Victor M.

2014-03-01

In this paper, we present a high-order expansion for elliptic equations in high-contrast media. The background conductivity is taken to be one and we assume the medium contains high (or low) conductivity inclusions. We derive an asymptotic expansion with respect to the contrast and provide a procedure to compute the terms in the expansion. The computation of the expansion does not depend on the contrast which is important for simulations. The latter allows avoiding increased mesh resolution around high conductivity features. This work is partly motivated by our earlier work in [Domain decomposition preconditioners for multiscale flows in high-contrast media, Multiscale Model Simul. 8 (2010) 1461-1483] where we design efficient numerical procedures for solving high-contrast problems. These multiscale approaches require local solutions and our proposed high-order expansion can be used to approximate these local solutions inexpensively. In the case of a large-number of inclusions, the proposed analysis can help to design localization techniques for computing the terms in the expansion. In the paper, we present a rigorous analysis of the proposed high-order expansion and estimate the remainder of it. We consider both high-and low-conductivity inclusions. © 2014 World Scientific Publishing Company.

Crude oil pipeline expansion summary

International Nuclear Information System (INIS)

2005-02-01

The Canadian Association of Petroleum Producers has been working with producers to address issues associated with the development of new pipeline capacity from western Canada. This document presents an assessment of the need for additional oil pipeline capacity given the changing mix of crude oil types and forecasted supply growth. It is of particular interest to crude oil producers and contributes to current available information for market participants. While detailed, the underlying analysis does not account for all the factors that may come into play when individual market participants make choices about which expansions they may support. The key focus is on the importance of timely expansion. It was emphasized that if pipeline expansions lags the crude supply growth, then the consequences would be both significant and unacceptable. Obstacles to timely expansion are also discussed. The report reviews the production and supply forecasts, the existing crude oil pipeline infrastructure, opportunities for new market development, requirements for new pipeline capacity and tolling options for pipeline development. tabs., figs., 1 appendix

Expansion dynamics

International Nuclear Information System (INIS)

Knoll, J.

1985-10-01

A quantum dynamical model is suggested which describes the expansion and disassembly phase of highly excited compounds formed in energetic heavy-ion collisions. First applications in two space and one time dimensional model world are discussed and qualitatively compared to standard freeze-out concepts. (orig.)

Spatial Linkage and Urban Expansion: AN Urban Agglomeration View

Science.gov (United States)

Jiao, L. M.; Tang, X.; Liu, X. P.

2017-09-01

Urban expansion displays different characteristics in each period. From the perspective of the urban agglomeration, studying the spatial and temporal characteristics of urban expansion plays an important role in understanding the complex relationship between urban expansion and network structure of urban agglomeration. We analyze urban expansion in the Yangtze River Delta Urban Agglomeration (YRD) through accessibility to and spatial interaction intensity from core cities as well as accessibility of road network. Results show that: (1) Correlation between urban expansion intensity and spatial indicators such as location and space syntax variables is remarkable and positive, while it decreases after rapid expansion. (2) Urban expansion velocity displays a positive correlation with spatial indicators mentioned above in the first (1980-1990) and second (1990-2000) period. However, it exhibits a negative relationship in the third period (2000-2010), i.e., cities located in the periphery of urban agglomeration developing more quickly. Consequently, the hypothesis of convergence of urban expansion in rapid expansion stage is put forward. (3) Results of Zipf's law and Gibrat's law show urban expansion in YRD displays a convergent trend in rapid expansion stage, small and medium-sized cities growing faster. This study shows that spatial linkage plays an important but evolving role in urban expansion within the urban agglomeration. In addition, it serves as a reference to the planning of Yangtze River Delta Urban Agglomeration and regulation of urban expansion of other urban agglomerations.

Magnetized relativistic electron-ion plasma expansion

Science.gov (United States)

Benkhelifa, El-Amine; Djebli, Mourad

2016-03-01

The dynamics of relativistic laser-produced plasma expansion across a transverse magnetic field is investigated. Based on a one dimensional two-fluid model that includes pressure, enthalpy, and rest mass energy, the expansion is studied in the limit of λD (Debye length) ≤RL (Larmor radius) for magnetized electrons and ions. Numerical investigation conducted for a quasi-neutral plasma showed that the σ parameter describing the initial plasma magnetization, and the plasma β parameter, which is the ratio of kinetic to magnetic pressure are the key parameters governing the expansion dynamics. For σ ≪ 1, ion's front shows oscillations associated to the break-down of quasi-neutrality. This is due to the strong constraining effect and confinement of the magnetic field, which acts as a retarding medium slowing the plasma expansion.

Renormalization group and Mayer expansions

International Nuclear Information System (INIS)

Mack, G.

1984-02-01

Mayer expansions promise to become a powerful tool in exact renormalization group calculations. Iterated Mayer expansions were sucessfully used in the rigorous analysis of 3-dimensional U(1) lattice gauge theory by Goepfert and the author, and it is hoped that they will also be useful in the 2-dimensional nonlinear sigma-model, and elsewhere. (orig.)

expansion method

Indian Academy of Sciences (India)

of a system under investigation is to model the system in terms of some ... The organization of the paper is as follows: In §2, a brief account of the (G /G)- expansion ...... It is interesting to note that from the general results, one can easily recover.

Expansion of Tubular with Elastomers in Multilateral Wells

Directory of Open Access Journals (Sweden)

Md Velden

2013-06-01

Full Text Available The use of solid expandable tubular technology during the last decade has focused on solving many challenges in well drilling and delivery including zonal isolation, deep drilling, conservation of hole sizes, etc. not only as pioneered solution but also providing cost effective and long lasting solutions. Concurrently, the technology was extended for construction of multilateral in typical wells. The process of horizontal tubular expansion is similar to the vertical expansion of expandable tubular in down-hole environment with the addition of uniformly distributed force due to its weight. The expansion is targeted to increase its diameter such that post expansion characteristics remain within allowable limits. In this study a typical expandable tubular of 57.15 mm outer diameter and 6.35 mm wall thickness was used with two different elastomer seals of 5 and 7 mm thickness placed at equal spacing of 200 mm. The developed stress contours during expansion process clearly showed the high stress areas in the vicinity of expansion region which lies around the mandrel. These high stresses may result in excessive wear of the mandrel. It was also found out that the drawing force increases as the mandrel angle, expansion ratio, and friction coefficient increases. A mandrel angle of 20o  requires minimum expansion force and can be considered as an optimum geometrical parameter to lower the power required for expansion.

Adiabatic supernova expansion into the circumstellar medium

International Nuclear Information System (INIS)

Band, D.L.; Liang, E.P.

1987-01-01

We perform one dimensional numerical simulations with a Lagrangian hydrodynamics code of the adiabatic expansion of a supernova into the surrounding medium. The early expansion follows Chevalier's analytic self-similar solution until the reverse shock reaches the ejecta core. We follow the expansion as it evolves towards the adiabatic blast wave phase. Some memory of the earlier phases of expansion is retained in the interior even when the outer regions expand as a blast wave. We find the results are sensitive to the initial configuration of the ejecta and to the placement of gridpoints. 6 refs., 2 figs

Capillary electrophoresis of Big-Dye terminator sequencing reactions for human mtDNA Control Region haplotyping in the identification of human remains.

Science.gov (United States)

Montesino, Marta; Prieto, Lourdes

2012-01-01

Cycle sequencing reaction with Big-Dye terminators provides the methodology to analyze mtDNA Control Region amplicons by means of capillary electrophoresis. DNA sequencing with ddNTPs or terminators was developed by (1). The progressive automation of the method by combining the use of fluorescent-dye terminators with cycle sequencing has made it possible to increase the sensibility and efficiency of the method and hence has allowed its introduction into the forensic field. PCR-generated mitochondrial DNA products are the templates for sequencing reactions. Different set of primers can be used to generate amplicons with different sizes according to the quality and quantity of the DNA extract providing sequence data for different ranges inside the Control Region.

A genetic atlas of human admixture history

Science.gov (United States)

Hellenthal, Garrett; Busby, George B.J.; Band, Gavin; Wilson, James F.; Capelli, Cristian

2014-01-01

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed using genetic data alone and encompassing over 100 events occurring over the past 4,000 years. We identify events whose dates and participants suggest they describe genetic impacts of the Mongol Empire, Arab slave trade, Bantu expansion, first millennium CE migrations in eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations. PMID:24531965

Decennial plan of expansion 1994-2003

International Nuclear Information System (INIS)

1993-12-01

The Decennial Plan of Expansion 1994-2003 of Electric sector reproduces the results of the studies occurred during the planning cycle of 1992/93 from the Coordinator Groups of the Electric System Planning. Based in the market forecasting, economic-financier and time for finishing the the works, the Decennial Plan of Expansion presents the schedule of the main generation and transmission works for the next ten years, the annual spend in generation, transmission and distribution, the costs of expansion and the evaluation of attending conditions in electric system in Brazil. (C.G.C.)

Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

Science.gov (United States)

Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

2014-01-01

Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

In vitro evaluation of force-expansion characteristics in a newly designed orthodontic expansion screw compared to conventional screws

Directory of Open Access Journals (Sweden)

Oshagh Morteza

2009-01-01

Full Text Available Objective : Expansion screws like Hyrax, Haas and other types, produce heavy interrupted forces which are unfavorable for dental movement and could be harmful to the tooth and periodontium. The other disadvantage of these screws is the need for patient cooperation for their regular activation. The purpose of this study was to design a screw and compare its force- expansion curve with other types. Materials and Methods : A new screw was designed and fabricated in the same dimension, with conventional types, with the ability of 8 mm expansion (Free wire length: 12 mm, initial compression: 4.5 mm, spring wire diameter: 0.4 mm, spring diameter: 3 mm, number of the coils: n0 ine, material: s0 tainless steel. In this in vitro study, the new screw was placed in an acrylic orthodontic appliance, and after mounting on a stone cast, the force-expansion curve was evaluated by a compression test machine and compared to other screws. Results : Force-expansion curve of designed screw had a flatter inclination compared to other screws. Generally it produced a light continuous force (two to 3.5 pounds for every 4 mm of expansion. Conclusion : In comparison with heavy and interrupted forces of other screws, the newly designed screw created light and continuous forces.

Migratory patterns and population structure among breeding and wintering red-breasted mergansers (Mergus serrator) and common mergansers (M. merganser)

Science.gov (United States)

Pearce, J.M.; McCracken, K.G.; Christensen, Thomas K.; Zhuravlev, Y.N.

2009-01-01

Philopatry has long been assumed to structure populations of waterfowl and other species of birds genetically, especially via maternally transmitted mitochondrial DNA (mtDNA), yet other migratory behaviors and nesting ecology (use of ground vs. cavity sites) may also contribute to population genetic structure. We investigated the effects of migration and nesting ecology on the population genetic structure of two Holarctic waterfowl, the Red-breasted Merganser (Mergus serrator) and Common Merganser (M. merganser), using mtDNA control-region sequence data. Red-breasted Mergansers (a ground-nesting species) exhibited lower levels of population differentiation across their North American range, possibly as a result of post-Pleistocene range expansion and population growth. By contrast, Common Mergansers (a cavity-nesting species) breeding in western and eastern North America were strongly differentiated, as were continental groups in North America and Europe. Our hypothesis that population differentiation of breeding female Common Mergansers results from limited migration during non-breeding periods was not supported, in that equally heterogeneous mtDNA lineages were observed in males and females on several wintering areas. The interspecific differences in mtDNA patterns for these two closely related species may have resulted from factors related to nesting ecology (ground vs. cavity nesting) and responses to historical climate change.

Financing electricity expansion

International Nuclear Information System (INIS)

Hyman, L.S.

1994-01-01

Expansion of electricity supply is associated with economic development. The installation and enlargement of power systems in developing countries entails a huge financial burden, however. Energy consumers in such countries must pay not only for supplies but for the cost of raising the capital for expansion on the international markets. Estimates are presented for the capital expenditure for electricity supply over the period 1990 to 2020 for the major world regions, using approximations for the cost of plant and capital and for the returns earned. These data lead to the conclusion that the five regions with the lowest per capita incomes are those which will need the major part of the capital expenditure and the highest percentage of external finance. (6 tables) (UK)

Preparation of Shrinkage Compensating Concrete with HCSA Expansive Agent

Science.gov (United States)

Li, Changcheng; Jia, Fujia

2017-10-01

Shrinkage compensating concrete (SCC) has become one of the best effective methods of preventing and reducing concrete cracking. SCC is prepared by HCSA high performance expansive agent for concrete which restrained expansion rate is optimized by 0.057%. Slump, compressive strength, restrained expansion rate and cracking resistance test were carried out on SCC. The results show that the initial slump of fresh SCC was about 220mm-230mm, while slump after 2 hours was 180mm-200mm. The restrained expansion rate of SCC increased with the mixing amount of expansive agent. After cured in water for 14 days, the restrained expansion rate of C35 and C40 SCC were 0.020%-0.032%. With the dosage of expansive agent increasing, restrained expansion rate of SCC increased, maximum compressive stress and cracking stress improved, cracking temperature fell, thus cracking resistance got effectively improvement.

Use of expansion joints in power stations

International Nuclear Information System (INIS)

Birker; Rommerswinkel.

1976-01-01

The paper discusses the mode of action of different systems of expansion joints. Special regard is given to the problems of expansion of pipelines of high rated diameter as employed in today's large power plant turbines. Due to the limited space available, the important role of the spring rate of the bellows for the reaction forces and moments acting on the connection points is pointed out. Apart from this details are given on the fabrication and materials selection of expansion joint bellows, and problems are discussed which arise in connection with the mechanical or hydraulic deformation of bellows with one or more walls. The non-destructive methods now in use for the testing of expansion pipe joints are mentioned along with experiments to test their behaviour under changing loads. The paper concludes on some remarks concerning proper transport, storage and installation of expansion pipe joints. (orig./AK) [de

Chromatic Derivatives, Chromatic Expansions and Associated Spaces

OpenAIRE

Ignjatovic, Aleksandar

2009-01-01

This paper presents the basic properties of chromatic derivatives and chromatic expansions and provides an appropriate motivation for introducing these notions. Chromatic derivatives are special, numerically robust linear differential operators which correspond to certain families of orthogonal polynomials. Chromatic expansions are series of the corresponding special functions, which possess the best features of both the Taylor and the Shannon expansions. This makes chromatic derivatives and ...

Warp drive with zero expansion

Energy Technology Data Exchange (ETDEWEB)

Natario, Jose [Department of Mathematics, Instituto Superior Tecnico (Portugal)

2002-03-21

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

HUBUNGAN KEKERABATAN BEBERAPA POPULASI KERANG HIJAU (Perna viridis DI INDONESIA BERDASARKAN SEKUEN CYTROCROME B mtDNA

Directory of Open Access Journals (Sweden)

Achmad Sudradjat

2016-11-01

Full Text Available Penelitian ini dilakukan untuk mengetahui hubungan kekerabatan stok kerang hijau (Perna viridis di beberapa perairan Indonesia sebagai informasi dasar bagi program pemuliaan. Sampel kerang hijau yang berasal dari populasi alam perairan Tanjung Kait, Kamal, Panimbang, Cirebon, Pasuruan, Kenjeran, dan Pangkep diambil secara acak. Amplifikasi PCR dan sekuensing mitokondria daerah cytochrome B adalah HCO (F: 5’-TAA ACT TCA GGG TGA CCA AAA AAT CA-3’ (26 bp dan LCO (R: 5’-GGT CAA CAA ATC ATA AAG ATA TTG G-3’ (25 bp. Sekuen DNA yang diperoleh digunakan untuk analisis homologi, analisis genetic distance dan analisis kekerabatan. Hasil analisis homologi susunan nukleotida berdasarkan BLAST-N terhadap sekuen mtDNA Perna viridis yang tersimpan di Genebank menunjukkan similaritas 97%. Hasil analisis didapatkan jarak genetik yang terdekat adalah populasi Tanjung Kait dengan Kenjeran sedangkan jarak genetik terjauh adalah populasi Cirebon dengan Kamal. Hubungan kekerabatan yang ditunjukkan dengan dendrogram diperoleh 2 kelompok yaitu 6 populasi membentuk satu kelompok dan populasi Cirebon membentuk kluster tersendiri. Sekuens tersebut mungkin dapat digunakan sebagai penanda dalam program breeding kerang hijau di Indonesia

The δ expansion for stochastic quantization

International Nuclear Information System (INIS)

Bender, C.M.; Cooper, F.; Milton, K.A.; Department of Physics, Brown University, Providence, Rhode Island 02912; Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexic o 87545; Department of Physics, The Ohio State University, Columbus, Ohio 43210; Department of Physics and Astronomy, University of Oklahoma, Norman, Oklaho ma 73019)

1989-01-01

Using a recently proposed perturbation expansion called the δ expansion, we show how to solve the Langevin equation associated with a gphi 4 field theory. We illustrate the technique in zero- and one-dimensional space-time, and then generalize this approach to d dimensions

Cytochrome b phylogeography of chamois (Rupicapra spp.). Population contractions, expansions and hybridizations governed the diversification of the genus

Czech Academy of Sciences Publication Activity Database

Rodríguez, F.; Hammer, S.; Pérez, T.; Suchentrunk, F.; Lorenzini, R.; Michallet, J.; Martínková, Natália; Albornoz, J.; Domínguez, A.

2009-01-01

Roč. 100, č. 1 (2009), s. 47-55 ISSN 0022-1503 R&D Projects: GA AV ČR IAA600930609 Institutional research plan: CEZ:AV0Z60930519 Keywords : chamois * ice ages * mtDNA * phylogeography * taxonomy Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.052, year: 2009

A meta-analysis of global urban land expansion.

Science.gov (United States)

Seto, Karen C; Fragkias, Michail; Güneralp, Burak; Reilly, Michael K

2011-01-01

The conversion of Earth's land surface to urban uses is one of the most irreversible human impacts on the global biosphere. It drives the loss of farmland, affects local climate, fragments habitats, and threatens biodiversity. Here we present a meta-analysis of 326 studies that have used remotely sensed images to map urban land conversion. We report a worldwide observed increase in urban land area of 58,000 km(2) from 1970 to 2000. India, China, and Africa have experienced the highest rates of urban land expansion, and the largest change in total urban extent has occurred in North America. Across all regions and for all three decades, urban land expansion rates are higher than or equal to urban population growth rates, suggesting that urban growth is becoming more expansive than compact. Annual growth in GDP per capita drives approximately half of the observed urban land expansion in China but only moderately affects urban expansion in India and Africa, where urban land expansion is driven more by urban population growth. In high income countries, rates of urban land expansion are slower and increasingly related to GDP growth. However, in North America, population growth contributes more to urban expansion than it does in Europe. Much of the observed variation in urban expansion was not captured by either population, GDP, or other variables in the model. This suggests that contemporary urban expansion is related to a variety of factors difficult to observe comprehensively at the global level, including international capital flows, the informal economy, land use policy, and generalized transport costs. Using the results from the global model, we develop forecasts for new urban land cover using SRES Scenarios. Our results show that by 2030, global urban land cover will increase between 430,000 km(2) and 12,568,000 km(2), with an estimate of 1,527,000 km(2) more likely.

Considering FACTS in Optimal Transmission Expansion Planning

Directory of Open Access Journals (Sweden)

K. Soleimani

2017-10-01

Full Text Available The expansion of power transmission systems is an important part of the expansion of power systems that requires enormous investment costs. Since the construction of new transmission lines is very expensive, it is necessary to choose the most efficient expansion plan that ensures system security with a minimal number of new lines. In this paper, the role of Flexible AC Transmission System (FACTS devices in the effective operation and expansion planning of transmission systems is examined. Effort was taken to implement a method based on sensitivity analysis to select the optimal number and location of FACTS devices, lines and other elements of the transmission system. Using this method, the transmission expansion plan for a 9 and a 39 bus power system was performed with and without the presence of FACTS with the use of DPL environment in Digsilent software 15.1. Results show that the use of these devices reduces the need for new transmission lines and minimizes the investment cost.

Simulation program for multiple expansion Stirling machines

International Nuclear Information System (INIS)

Walker, G.; Weiss, M.; Fauvel, R.; Reader, G.; Bingham, E.R.

1992-01-01

Multiple expansion Stirling machines have been a topic of interest at the University of Calgary for some years. Recently a second-order computer simulation program with integral graphics package for Stirling cryocoolers with up to four stages of expansion were developed and made available to the Stirling community. Adaptation of the program to multiple expansion Stirling power systems is anticipated. This paper briefly introduces the program and presents a specimen result

Controlling Thermal Expansion: A Metal-Organic Frameworks Route.

Science.gov (United States)

Balestra, Salvador R G; Bueno-Perez, Rocio; Hamad, Said; Dubbeldam, David; Ruiz-Salvador, A Rabdel; Calero, Sofia

2016-11-22

Controlling thermal expansion is an important, not yet resolved, and challenging problem in materials research. A conceptual design is introduced here, for the first time, for the use of metal-organic frameworks (MOFs) as platforms for controlling thermal expansion devices that can operate in the negative, zero, and positive expansion regimes. A detailed computer simulation study, based on molecular dynamics, is presented to support the targeted application. MOF-5 has been selected as model material, along with three molecules of similar size and known differences in terms of the nature of host-guest interactions. It has been shown that adsorbate molecules can control, in a colligative way, the thermal expansion of the solid, so that changing the adsorbate molecules induces the solid to display positive, zero, or negative thermal expansion. We analyze in depth the distortion mechanisms, beyond the ligand metal junction, to cover the ligand distortions, and the energetic and entropic effect on the thermo-structural behavior. We provide an unprecedented atomistic insight on the effect of adsorbates on the thermal expansion of MOFs as a basic tool toward controlling the thermal expansion.

The Economic Impact of Medicaid Expansion on Pennsylvania.

Science.gov (United States)

Price, Carter C; Donohue, Julie M; Saltzman, Evan; Woods, Dulani; Eibner, Christine

2013-01-01

The Affordable Care Act is a substantial reform of the U.S. health care insurance system. Using the RAND COMPARE model, researchers assessed the act's potential economic effects on Pennsylvania, factoring in an optional expansion of Medicaid, and found the state would enjoy significant net benefits. With or without the expansion of Medicaid, the act will increase insurance coverage to hundreds of thousands of Pennsylvanians, but the COMPARE model estimates that the expansion of Medicaid eligibility would cover an additional 350,000 people and bring more than $2 billion in federal spending into the state annually than if the state did not expand. Should the state expand Medicaid, the additional spending will add more than $3 billion a year to the state's GDP and support 35,000 jobs. But Medicaid expansion is not without cost for the state; the estimated cumulative effect on Pennsylvania's Medicaid spending will be $180 million higher with the expansion than without between 2014 and 2020. Substantial reductions in uncompensated care costs for hospitals are possible even without expansion, but savings to hospitals for uncompensated care funding are even larger with the Medicaid expansion, amounting to $550 million or more each year.

Controlling Thermal Expansion: A Metal–Organic Frameworks Route

Science.gov (United States)

2016-01-01

Controlling thermal expansion is an important, not yet resolved, and challenging problem in materials research. A conceptual design is introduced here, for the first time, for the use of metal–organic frameworks (MOFs) as platforms for controlling thermal expansion devices that can operate in the negative, zero, and positive expansion regimes. A detailed computer simulation study, based on molecular dynamics, is presented to support the targeted application. MOF-5 has been selected as model material, along with three molecules of similar size and known differences in terms of the nature of host–guest interactions. It has been shown that adsorbate molecules can control, in a colligative way, the thermal expansion of the solid, so that changing the adsorbate molecules induces the solid to display positive, zero, or negative thermal expansion. We analyze in depth the distortion mechanisms, beyond the ligand metal junction, to cover the ligand distortions, and the energetic and entropic effect on the thermo-structural behavior. We provide an unprecedented atomistic insight on the effect of adsorbates on the thermal expansion of MOFs as a basic tool toward controlling the thermal expansion. PMID:28190918

Platform Expansion Design as Strategic Choice

DEFF Research Database (Denmark)

Staykova, Kalina S.; Damsgaard, Jan

2016-01-01

In this paper, we address how the strategic choice of platform expansion design impacts the subse-quent platform strategy. We identify two distinct approaches to platform expansion – platform bun-dling and platform constellations, which currently co-exist. The purpose of this paper is to outline...

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.

Thermal expansion behavior in fabricated cellular structures

International Nuclear Information System (INIS)

Oruganti, R.K.; Ghosh, A.K.; Mazumder, J.

2004-01-01

Thermal expansion behavior of cellular structures is of interest in applications where undesirable deformation and failure are caused by thermal expansion mismatch. This report describes the role of processing-induced effects and metallurgical aspects of melt-processed cellular structures, such as a bi-material structure designed to contract on heating, as well as uni-material structures of regular and stochastic topology. This bi-material structure utilized the principle of internal geometric constraints to alter the expansion behavior of the internal ligaments to create overall contraction of the structure. Homogenization design method was used to design the structure, and fabrication was by direct metal deposition by laser melting of powder in another part of a joint effort. The degree of porosity and grain size in the fabricated structure are characterized and related to the laser deposition parameters. The structure was found to contract upon heating over a short range of temperature subsequent to which normal expansion ensued. Also examined in this report are uni-material cellular structures, in which internal constraints arise from residual stress variations caused by the fabrication process, and thereby alter their expansion characteristics. A simple analysis of thermal strain of this material supports the observed thermal expansion behavior

Secret-key expansion from covert communication

Science.gov (United States)

Arrazola, Juan Miguel; Amiri, Ryan

2018-02-01

Covert communication allows the transmission of messages in such a way that it is not possible for adversaries to detect that the communication is occurring. This provides protection in situations where knowledge that two parties are talking to each other may be incriminating to them. In this work, we study how covert communication can be used for a different purpose: secret key expansion. First, we show that any message transmitted in a secure covert protocol is also secret and therefore unknown to an adversary. We then propose a covert communication protocol where the amount of key consumed in the protocol is smaller than the transmitted key, thus leading to secure secret key expansion. We derive precise conditions for secret key expansion to occur, showing that it is possible when there are sufficiently low levels of noise for a given security level. We conclude by examining how secret key expansion from covert communication can be performed in a computational security model.

From greedy to lazy expansions and their driving dynamics

NARCIS (Netherlands)

Dajani, K.; Kraaikamp, C.

2001-01-01

In this paper we study the ergodic properties of non-greedy series expansions to non-integer bases β > 1. It is shown that the so-called 'lazy' expansion is isomorphic to the 'greedy' expansion. Furthermore, a class of expansions to base β > 1, β =2 Z, 'in between' the lazy and the greedy

RTEL1 Inhibits Trinucleotide Repeat Expansions and Fragility

Directory of Open Access Journals (Sweden)

Aisling Frizzell

2014-03-01

Full Text Available Human RTEL1 is an essential, multifunctional helicase that maintains telomeres, regulates homologous recombination, and helps prevent bone marrow failure. Here, we show that RTEL1 also blocks trinucleotide repeat expansions, the causal mutation for 17 neurological diseases. Increased expansion frequencies of (CTG⋅CAG repeats occurred in human cells following knockdown of RTEL1, but not the alternative helicase Fbh1, and purified RTEL1 efficiently unwound triplet repeat hairpins in vitro. The expansion-blocking activity of RTEL1 also required Rad18 and HLTF, homologs of yeast Rad18 and Rad5. These findings are reminiscent of budding yeast Srs2, which inhibits expansions, unwinds hairpins, and prevents triplet-repeat-induced chromosome fragility. Accordingly, we found expansions and fragility were suppressed in yeast srs2 mutants expressing RTEL1, but not Fbh1. We propose that RTEL1 serves as a human analog of Srs2 to inhibit (CTG⋅CAG repeat expansions and fragility, likely by unwinding problematic hairpins.

Thermal expansion studies on Hafnium titanate (HfTiO4)

International Nuclear Information System (INIS)

Panneerselvam, G.; Subramanian, G.G.S.; Antony, M.P.

2006-01-01

The lattice thermal expansion characteristics of hafnium titanate (HfTiO 4 ) have been studied by measuring the lattice parameter as a function of temperature by high temperature X-ray diffraction technique (HT-XRD) in the temperature range 298-1973K. Percentage linear thermal expansion and mean linear thermal expansion coefficients were computed from the lattice parameter data. The thermal expansion of HfTiO 4 is highly anisotropic. The expansivity along 'a' axis is large; as compared to the expansivity along 'b' axis which is negative below 1073 K. The percentage linear thermal expansion in the temperature range 298-1973 K along a, b and c axis are 2.74, 0.901 and 1.49 respectively. Thermal expansion values obtained in the present study are in reasonable agreement with the existing thermal expansion data. (author)

Hypersonic expansion of the Fokker--Planck equation

International Nuclear Information System (INIS)

Fernandez-Feria, R.

1989-01-01

A systematic study of the hypersonic limit of a heavy species diluted in a much lighter gas is made via the Fokker--Planck equation governing its velocity distribution function. In particular, two different hypersonic expansions of the Fokker--Planck equation are considered, differing from each other in the momentum equation of the heavy gas used as the basis of the expansion: in the first of them, the pressure tensor is neglected in that equation while, in the second expansion, the pressure tensor term is retained. The expansions are valid when the light gas Mach number is O(1) or larger and the difference between the mean velocities of light and heavy components is small compared to the light gas thermal speed. They can be applied away from regions where the spatial gradient of the distribution function is very large, but it is not restricted with respect to the temporal derivative of the distribution function. The hydrodynamic equations corresponding to the lowest order of both expansions constitute two different hypersonic closures of the moment equations. For the subsequent orders in the expansions, closed sets of moment equations (hydrodynamic equations) are given. Special emphasis is made on the order of magnitude of the errors of the lowest-order hydrodynamic quantities. It is shown that if the heat flux vanishes initially, these errors are smaller than one might have expected from the ordinary scaling of the hypersonic closure. Also it is found that the normal solution of both expansions is a Gaussian distribution at the lowest order

14 CFR 23.969 - Fuel tank expansion space.

Science.gov (United States)

2010-01-01

... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Fuel tank expansion space. 23.969 Section 23.969 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION AIRCRAFT....969 Fuel tank expansion space. Each fuel tank must have an expansion space of not less than two...

Research progress on expansive soil cracks under changing environment.

Science.gov (United States)

Shi, Bei-xiao; Zheng, Cheng-feng; Wu, Jin-kun

2014-01-01

Engineering problems shunned previously rise to the surface gradually with the activities of reforming the natural world in depth, the problem of expansive soil crack under the changing environment becoming a control factor of expansive soil slope stability. The problem of expansive soil crack has gradually become a research hotspot, elaborates the occurrence and development of cracks from the basic properties of expansive soil, and points out the role of controlling the crack of expansive soil strength. We summarize the existing research methods and results of expansive soil crack characteristics. Improving crack measurement and calculation method and researching the crack depth measurement, statistical analysis method, crack depth and surface feature relationship will be the future direction.

MtDNA genetic diversity and structure of Eurasian Collared Dove (Streptopelia decaocto).

Science.gov (United States)

Bagi, Zoltán; Dimopoulos, Evangelos Antonis; Loukovitis, Dimitrios; Eraud, Cyril; Kusza, Szilvia

2018-01-01

The Eurasian Collared Dove (Streptopelia decaocto) is one of the most successful biological invaders among terrestrial vertebrates. However, little information is available on the genetic diversity of the species. A total of 134 Eurasian Collared Doves from Europe, Asia and the Caribbean (n = 20) were studied by sequencing a 658-bp length of mitochondrial DNA (mtDNA) cytochrome oxidase I (COI). Fifty-two different haplotypes and relatively high haplotype and nucleotide diversities (Hd±SD = 0.843±0.037 and π±SD = 0.026±0.013) were detected. Haplotype Ht1 was particularly dominant: it included 44.03% of the studied individuals, and contained sequences from 75% of the studied countries. Various analyses (FST, AMOVA, STRUCTURE) distinguished 2 groups on the genetic level, designated 'A' and 'B'. Two groups were also separated in the median-joining network and the maximum likelihood tree. The results of the neutrality tests were negative (Fu FS = -25.914; Tajima D = -2.606) and significantly different from zero (P≤0.001) for group A, whereas both values for group B were positive (Fu FS = 1.811; Tajima D = 0.674) and not significant (P>0.05). Statistically significant positive autocorrelation was revealed among individuals located up to 2000 km apart (r = 0.124; P = 0.001). The present results provide the first information on the genetic diversity and structure of the Eurasian Collared Dove, and can thereby serve as a factual and comparative basis for similar studies in the future.

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

Craniodental continuity and change between Iron Age peoples and their descendants

OpenAIRE

Kerryn A. Warren; Simon Hall; Rebecca R. Ackermann

2014-01-01

The appearance of the Iron Age of southern Africa early in the first millennium AD is associated with the migration of Bantu speakers who were broadly ancestral to present-day Bantu speakers. While there is sufficient genetic, physical anthropological and cultural evidence to support general continuity into contemporary populations, the extent to which events since colonialism have affected morphological variation is poorly understood. We used dental anthropological techniques and three-dimen...

Zirconium titanate: stability and thermal expansion; Titanato de circonio: estabilidad termodinamica y expansion termica

Energy Technology Data Exchange (ETDEWEB)

Lopez-Lopez, E.; Moreno, R.; Baudin, C.

2011-07-01

Zirconium titanate is a well known compound in the field of electro ceramics, although it has also been used in catalyst and sensors applications. The crystallographic thermal expansion anisotropy of this compound makes it a potential candidate as constituent of structural components. In general, to assure the structural integrity and microstructural homogeneity of a ceramic piece, relatively low cooling rates from the fabrication temperature are required. This requirement is essential for zirconium titanate because thermal expansion as well as phase distribution is affected by small variations in the composition and cooling rate. This work reviews the available data on the phase equilibrium relationships in the systems ZrO{sub 2}-TiO{sub 2} and ZrO{sub 2}-TiO{sub 2}-Y{sub 2}O{sub 3}. The main discrepancies as well as the possible origins of them are discussed. Additionally, the crystallographic thermal expansion data in the current literature are reviewed. (Author) 56 refs.

Semiclassical expansions on and near caustics

International Nuclear Information System (INIS)

Meetz, K.

1984-09-01

We show that the standard WKB expansion can be generalized so that it reproduces the behavior of the wave function on and near a caustic in two-dimensional space time. The expansion is related to the unfolding polynomials of the elementary catastrophes occurring in two dimensions: the fold and the cusp catastrophe. The method determines control parameters and transport coefficients in a self-consistent way from differential equations and does not refer to the asymptotic expansion of Feynman path integrals. The lowest order equations are solved explicitly in terms of the multivalued classical action. The result is a generalized semiclassical approximation on and beyond a caustic. (orig.)

Interbasis expansions for isotropic harmonic oscillator

Energy Technology Data Exchange (ETDEWEB)

Dong, Shi-Hai, E-mail: dongsh2@yahoo.com [Departamento de Física, Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, Unidad Profesional Adolfo López Mateos, Mexico D.F. 07738 (Mexico)

2012-03-12

The exact solutions of the isotropic harmonic oscillator are reviewed in Cartesian, cylindrical polar and spherical coordinates. The problem of interbasis expansions of the eigenfunctions is solved completely. The explicit expansion coefficients of the basis for given coordinates in terms of other two coordinates are presented for lower excited states. Such a property is occurred only for those degenerated states for given principal quantum number n. -- Highlights: ► Exact solutions of harmonic oscillator are reviewed in three coordinates. ► Interbasis expansions of the eigenfunctions is solved completely. ► This is occurred only for those degenerated states for given quantum number n.

Cosmic growth history and expansion history

International Nuclear Information System (INIS)

Linder, Eric V.

2005-01-01

The cosmic expansion history tests the dynamics of the global evolution of the universe and its energy density contents, while the cosmic growth history tests the evolution of the inhomogeneous part of the energy density. Precision comparison of the two histories can distinguish the nature of the physics responsible for the accelerating cosmic expansion: an additional smooth component--dark energy--or a modification of the gravitational field equations. With the aid of a new fitting formula for linear perturbation growth accurate to 0.05%-0.2%, we separate out the growth dependence on the expansion history and introduce a new growth index parameter γ that quantifies the gravitational modification

Correlation expansion: a powerful alternative multiple scattering calculation method

International Nuclear Information System (INIS)

Zhao Haifeng; Wu Ziyu; Sebilleau, Didier

2008-01-01

We introduce a powerful alternative expansion method to perform multiple scattering calculations. In contrast to standard MS series expansion, where the scattering contributions are grouped in terms of scattering order and may diverge in the low energy region, this expansion, called correlation expansion, partitions the scattering process into contributions from different small atom groups and converges at all energies. It converges faster than MS series expansion when the latter is convergent. Furthermore, it takes less memory than the full MS method so it can be used in the near edge region without any divergence problem, even for large clusters. The correlation expansion framework we derive here is very general and can serve to calculate all the elements of the scattering path operator matrix. Photoelectron diffraction calculations in a cluster containing 23 atoms are presented to test the method and compare it to full MS and standard MS series expansion

Treatment of divergent expansions in scattering theory

International Nuclear Information System (INIS)

Gersten, A.; Malin, S.

1978-01-01

One of the biggest obstacles in applying quantum field theory to realistic scattering problems are the divergencies of pertubation expansions for large coupling constants and the divergencies of partial wave expansions for massless particles exchanges. There exist, however, methods of summation of the divergent expansions which can lead to significant application in physics. In this paper we treat the problem of summing such expansions using three methods: (i) a generalization of the Pade approximation to the multivariable case. The suggested definition is unique and preserves unitarity. (ii) The summation of divergent partial waves for arbitrary spins. (iii) A successful application of a series inversion to the 3 P 1 nucleon-nucleon phase shift up to 200 MeV. (orig./WL) [de

The loop expansion as a divergent-power-series expansion

International Nuclear Information System (INIS)

Murai, N.

1981-01-01

The loop expansion should be divergent, possibly an asymptotic one, in the Euclidean path integral formulation. This consideration is important in applications of the symmetric and mass-independent renormalization. The [1,1] Pade approximant is calculated in a PHI 4 model. Its classical vacua may be not truely stable for nonzero coupling constant. (author)

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.

The heavy quark expansion of QCD

International Nuclear Information System (INIS)

Falk, A.F.

1997-01-01

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

Thermal expansion of doped lanthanum gallates

Indian Academy of Sciences (India)

Administrator

Since the components are in intimate mechanical contact, any stress generated due to their thermal expansion mis- match during thermal cycling could lead to catastrophic failure of the cell. The functional materials must have similar thermal expansions to avoid mechanical stresses. Hence it is useful to study the thermal ...

Paleo-eskimo mtDNA genome reveals matrilineal discontinuity in Greenland

DEFF Research Database (Denmark)

Gilbert, Marcus Thomas Pius; Kivisild, Toomas; Grønnow, Bjarne

2008-01-01

a mitochondrial genome from a Paleo-Eskimo human by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian......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 are unknown. We sequenced...

Thermal and hygroscopic expansion characteristics of bamboo

OpenAIRE

Huang, Puxi; Chang, Wen-shao; Ansell, Martin P.; Bowen, Chris R.; Chew, John Y. M.; Adamak, Vana i

2017-01-01

The expansion and contraction of bamboo caused by temperature and moisture variations must be evaluated\\ud if bamboo is to be utilised as a building material. However, detailed expansion data, especially data in the ascent and\\ud descent processes of temperature and moisture are unexplored. The aim of this study is to investigate the expansion\\ud characteristics of Phyllostachys edulis (Moso bamboo) in ascent and descent processes of temperature and moisture.\\ud The measurement of linear ther...

Semiclassical expansions for confined N fermion systems

International Nuclear Information System (INIS)

Krivine, H.; Martorell, J.; Casas, M.

1989-01-01

A new derivation of the Wigner Kirkwood expansion for N-fermion systems is presented, showing explicitly the connection to the WKB approximation for a single level. This allows to study separately the two ansatz required to obtain the semiclassical expansions: the asymptotic expansions in powers of ℎ and the smoothing of quantal effects. We discuss the one dimensional and three dimensional, with spherical symmetry, cases. Applications for standard potentials used in nuclear physics are described in detail

Breaking the Link between Environmental Degradation and Oil Palm Expansion: A Method for Enabling Sustainable Oil Palm Expansion

Science.gov (United States)

Smit, Hans Harmen; Meijaard, Erik; van der Laan, Carina; Mantel, Stephan; Budiman, Arif; Verweij, Pita

2013-01-01

Land degradation is a global concern. In tropical areas it primarily concerns the conversion of forest into non-forest lands and the associated losses of environmental services. Defining such degradation is not straightforward hampering effective reduction in degradation and use of already degraded lands for more productive purposes. To facilitate the processes of avoided degradation and land rehabilitation, we have developed a methodology in which we have used international environmental and social sustainability standards to determine the suitability of lands for sustainable agricultural expansion. The method was developed and tested in one of the frontiers of agricultural expansion, West Kalimantan province in Indonesia. The focus was on oil palm expansion, which is considered as a major driver for deforestation in tropical regions globally. The results suggest that substantial changes in current land-use planning are necessary for most new plantations to comply with international sustainability standards. Through visualizing options for sustainable expansion with our methodology, we demonstrate that the link between oil palm expansion and degradation can be broken. Application of the methodology with criteria and thresholds similar to ours could help the Indonesian government and the industry to achieve its pro-growth, pro-job, pro-poor and pro-environment development goals. For sustainable agricultural production, context specific guidance has to be developed in areas suitable for expansion. Our methodology can serve as a template for designing such commodity and country specific tools and deliver such guidance. PMID:24039700

Mechanism of actuation in conducting polymers: Osmotic expansion

DEFF Research Database (Denmark)

Bay, Lasse; Jacobsen, Torben; West, Keld

2001-01-01

Conducting polymers expand or contract when their redox state is changed. This expansion/contraction effect can be separated in an intrinsic part because of changes of the polymer backbone on reduction/oxidation and a part depending on the surrounding electrolyte phase, because of osmotic expansion...... is compared with measurements on PPy(DBS) films. The experiments show that the expansion decreases as the electrolyte concentration is increased. This means that a considerable part of the total expansion is due to the osmotic effect. The osmotic effect should be taken into account when interpreting...

Mapping Brazilian Cropland Expansion, 2000-2013

Science.gov (United States)

Zalles, V.; Hansen, M.; Potapov, P.

2016-12-01

Brazil is one of the world's leading producers and exporters of agricultural goods. Despite undergoing significant increases in its cropland area in the last decades, it remains one of the countries with the most potential for further agricultural expansion. Most notably, the expansion in production areas of commodity crops such as soybean, corn, and sugarcane has become the leading cause of land cover conversion in Brazil. Natural land covers, such as the Amazon and Cerrado forests, have been negatively affected by this agricultural expansion, causing carbon emissions, biodiversity loss, altered water cycles, and many other disturbances to ecosystem services. Monitoring of change in cropland area extent can provide relevant information to decision makers seeking to understand and manage land cover change drivers and their impacts. In this study, the freely-available Landsat archive was leveraged to produce a large-scale, methodologically consistent map of cropland cover at 30 m. resolution for the entire Brazilian territory in the year 2000. Additionally, we mapped cropland expansion from 2000 to 2013, and used statistical sampling techniques to accurately estimate cropland area per Brazilian state. Using the Global Forest Change product produced by Hansen et al. (2013), we can disaggregate forest cover loss due to cropland expansion by year, revealing spatiotemporal trends that could advance our understanding of the drivers of forest loss.

Thermal expansion of fibre-reinforced composites

International Nuclear Information System (INIS)

Schneider, B.

1991-07-01

The integral thermal expansion and the coefficient of thermal expansion (CTE) of carbon and Kevlar fibre-reinforced composites were measured with high accuracy from 5 K to room temperature. For this, a laser dilatometer and a sophisticated measuring procedure were used. CTE dependence on the orientation angle ω of angle-ply laminates was determined for samples with 5 different fibre alignments (UD 0deg, +/-30deg, +/-45deg, +/-60deg and UD 90deg). A high variability of the CTE with the orientation angle was shown. At angles of approximately +/-30deg even negative CTEs were found. With suitable reinforcing fibres being selected, their absolute values rose up to 30-100% of the positive CTEs of metals. Hence, composites of this type would be suitable as compensating materials in metal constructions where little thermal expansion is desired. To check the lamination theory, theoretical computations of the CTE- ω -dependence were compared with the measured values. An excellent agreement was found. Using the lamination theory, predictions about the expansion behaviour of angle-ply laminates can be made now, if the thermal and mechanical properties of the unidirectional (UD) laminate are known. Furthermore, it is possible to carry out simulation computations aimed at investigating the influence of a single parameter of the UD-laminate (e.g. shear modulus) on the expansion of the angle-ply laminate. (orig.) [de

On equivalence of high temperature series expansion and coupling parameter series expansion in thermodynamic perturbation theory of fluids

International Nuclear Information System (INIS)

Sai Venkata Ramana, A.

2014-01-01

The coupling parameter series expansion and the high temperature series expansion in the thermodynamic perturbation theory of fluids are shown to be equivalent if the interaction potential is pairwise additive. As a consequence, for the class of fluids with the potential having a hardcore repulsion, if the hard-sphere fluid is chosen as reference system, the terms of coupling parameter series expansion for radial distribution function, direct correlation function, and Helmholtz free energy follow a scaling law with temperature. The scaling law is confirmed by application to square-well fluids

Estimates of expansion time scales

International Nuclear Information System (INIS)

Jones, E.M.

1979-01-01

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

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....

Range expansion of heterogeneous populations.

Science.gov (United States)

Reiter, Matthias; Rulands, Steffen; Frey, Erwin

2014-04-11

Risk spreading in bacterial populations is generally regarded as a strategy to maximize survival. Here, we study its role during range expansion of a genetically diverse population where growth and motility are two alternative traits. We find that during the initial expansion phase fast-growing cells do have a selective advantage. By contrast, asymptotically, generalists balancing motility and reproduction are evolutionarily most successful. These findings are rationalized by a set of coupled Fisher equations complemented by stochastic simulations.

Geographic structure and demographic history of Iranian brown bear (Ursus arctos based on mtDNA control region sequences

Directory of Open Access Journals (Sweden)

Mohammad Reza Ashrafzadeh

2015-12-01

Full Text Available In recent years, the brown bear's range has declined and its populations in some areas have faced extinction. Therefore, to have a comprehensive picture of genetic diversity and geographic structure of populations is essential for effective conservation strategies. In this research, we sequenced a 271bp segment of mtDNA control region of seven Iranian brown bears, where a total dataset of 467 sequences (brown and polar bears were used in analyses. Overall, 113 different haplotypes and 77 polymorphic sites were identified within the segment. Based on phylogenetic analyses, Iranian brown bears were not nested in any other clades. The low values of Nm (range=0.014-0.187 and high values of Fst (range=0.728-0.972 among Iranian bears and others revealed a genetically significant differentiation. We aren't found any significant signal of demographic reduction in Iranian bears. The time to the most recent common ancestor of Iranian brown bears (Northern Iran was found to be around 19000 BP.

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...

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...

Regulation of gas infrastructure expansion

International Nuclear Information System (INIS)

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 storage facilities, LNG import terminals and certain gas transmission pipelines - need to be regulated, as there may be scope for competition. In practice, the choice of regulation of gas infrastructure expansion varies among different types of gas infrastructure facilities and across EU Member States. Based on a review of economic literature and on a series of in-depth case studies, this study explains these differences in choices of regulation from differences in policy objectives, differences in local circumstances and differences in the intrinsic characteristics of the infrastructure projects. An important conclusion is that there is potential for a larger role for competition in gas infrastructure expansion.

RTEL1 inhibits trinucleotide repeat expansions and fragility.

Science.gov (United States)

Frizzell, Aisling; Nguyen, Jennifer H G; Petalcorin, Mark I R; Turner, Katherine D; Boulton, Simon J; Freudenreich, Catherine H; Lahue, Robert S

2014-03-13

Human RTEL1 is an essential, multifunctional helicase that maintains telomeres, regulates homologous recombination, and helps prevent bone marrow failure. Here, we show that RTEL1 also blocks trinucleotide repeat expansions, the causal mutation for 17 neurological diseases. Increased expansion frequencies of (CTG⋅CAG) repeats occurred in human cells following knockdown of RTEL1, but not the alternative helicase Fbh1, and purified RTEL1 efficiently unwound triplet repeat hairpins in vitro. The expansion-blocking activity of RTEL1 also required Rad18 and HLTF, homologs of yeast Rad18 and Rad5. These findings are reminiscent of budding yeast Srs2, which inhibits expansions, unwinds hairpins, and prevents triplet-repeat-induced chromosome fragility. Accordingly, we found expansions and fragility were suppressed in yeast srs2 mutants expressing RTEL1, but not Fbh1. We propose that RTEL1 serves as a human analog of Srs2 to inhibit (CTG⋅CAG) repeat expansions and fragility, likely by unwinding problematic hairpins. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Longitudinal expansion of field line dipolarization

Science.gov (United States)

Saka, O.; Hayashi, K.

2017-11-01

We examine the substorm expansions that started at 1155 UT 10 August 1994 in the midnight sector focusing on the longitudinal (eastward) expansion of field line dipolarization in the auroral zone. Eastward expansion of the dipolarization region was observed in all of the H, D, and Z components. The dipolarization that started at 1155 UT (0027 MLT) from 260° of geomagnetic longitude (CMO) expanded to 351°(PBQ) in about 48 min. The expansion velocity was 0.03-0.04°/s, or 1.9 km/s at 62°N of geomagnetic latitude. The dipolarization region expanding to the east was accompanied by a bipolar event at the leading edge of the expansion in latitudes equatorward of the westward electrojet (WEJ). In the midnight sector at the onset meridian, the Magnetospheric Plasma Analyzer (MAP) on board geosynchronous satellite L9 measured electrons and ions between 10 eV and 40 keV. We conclude from the satellite observations that this dipolarization was characterized by the evolution of temperature anisotropies, an increase of the electron and ion temperatures, and a rapid change in the symmetry axis of the temperature tensor. The field line dipolarization and its longitudinal expansion were interpreted in terms of the slow MHD mode triggered by the current disruption. We propose a new magnetosphere-ionosphere coupling (MI-coupling) mechanism based on the scenario that transmitted westward electric fields from the magnetosphere in association with expanding dipolarization produced electrostatic potential (negative) in the ionosphere through differences in the mobility of collisional ions and collisionless electrons. The field-aligned currents that emerged from the negative potential region are arranged in a concentric pattern around the negative potential region, upward toward the center and downward on the peripheral.

Wilson expansion in the minimal subtraction scheme

International Nuclear Information System (INIS)

Smirnov, V.A.

1989-01-01

The small distance expansion of the product of composite fields is constructed for an arbitrary renormalization procedure of the type of minimal subtraction scheme. Coefficient functions of the expansion are expressed explicitly through the Green functions of composite fields. The expansion has the explicity finite form: the ultraviolet (UV) divergences of the coefficient functions and composite fields are removed by the initial renormalization procedure while the infrared (IR) divergences in massless diagrams with nonvanishing contribution into the coefficient functions are removed by the R-operation which is the IR part of the R-operation. The latter is the generalization of the dimensional renormalization in the case when both UV and IR divergences are present. To derive the expansion, a ''pre-subtracting operator'' is introduced and formulas of the counter-term technique are exploited

Thermal Expansion Anomaly Regulated by Entropy

Science.gov (United States)

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

2014-11-01

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.

Territorial expansion and primary state formation.

Science.gov (United States)

Spencer, Charles S

2010-04-20

A major research problem in anthropology is the origin of the state and its bureaucratic form of governance. Of particular importance for evaluating theories of state origins are cases of primary state formation, whereby a first-generation state evolves without contact with any preexisting states. A general model of this process, the territorial-expansion model, is presented and assessed with archaeological data from six areas where primary states emerged in antiquity: Mesoamerica, Peru, Egypt, Mesopotamia, the Indus Valley, and China. In each case, the evidence shows a close correspondence in time between the first appearance of state institutions and the earliest expansion of the state's political-economic control to regions lying more than a day's round-trip from the capital. Although additional research will add detail and clarity to the empirical record, the results to date are consistent with the territorial-expansion model, which argues that the success of such long-distance expansion not only demanded the bureaucratization of central authority but also helped provide the resources necessary to underwrite this administrative transformation.

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

Directory of Open Access Journals (Sweden)

Bailey William V

2007-01-01

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

Thermal expansion of quaternary nitride coatings

Science.gov (United States)

Tasnádi, Ferenc; Wang, Fei; Odén, Magnus; Abrikosov, Igor A.

2018-04-01

The thermal expansion coefficient of technologically relevant multicomponent cubic nitride alloys are predicted using the Debye model with ab initio elastic constants calculated at 0 K and an isotropic approximation for the Grüneisen parameter. Our method is benchmarked against measured thermal expansion of TiN and Ti(1-x)Al x N as well as against results of molecular dynamics simulations. We show that the thermal expansion coefficients of Ti(1-x-y)X y Al x N (X  =  Zr, Hf, Nb, V, Ta) solid solutions monotonously increase with the amount of alloying element X at all temperatures except for Zr and Hf, for which they instead decrease for y≳ 0.5 .

Thermal and Hygric Expansion of High Performance Concrete

Directory of Open Access Journals (Sweden)

J. Toman

2001-01-01

Full Text Available The linear thermal expansion coefficient of two types of high performance concrete was measured in the temperature range from 20 °C to 1000 °C, and the linear hygric expansion coefficient was determined in the moisture range from dry material to saturation water content. Comparative methods were applied for measurements of both coefficients. The experimental results show that both the effect of temperature on the values of linear thermal expansion coefficients and the effect of moisture on the values of linear hygric expansion coefficients are very significant and cannot be neglected in practical applications.

Parabolic cyclinder functions : examples of error bounds for asymptotic expansions

NARCIS (Netherlands)

R. Vidunas; N.M. Temme (Nico)

2002-01-01

textabstractSeveral asymptotic expansions of parabolic cylinder functions are discussedand error bounds for remainders in the expansions are presented. Inparticular Poincaré-type expansions for large values of the argument$z$ and uniform expansions for large values of the parameter areconsidered.

Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan.

Science.gov (United States)

Bhatti, Shahzad; Abbas, Sana; Aslamkhan, Muhammad; Attimonelli, Marcella; Trinidad, Magali Segundo; Aydin, Hikmet Hakan; de Souza, Erica Martinha Silva; Gonzalez, Gerardo Rodriguez

2017-07-26

To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.

A unification of boson expansion theories. (III) Applications

International Nuclear Information System (INIS)

Dobaczewski, J.

1981-10-01

A general scheme of constructing boson expansions that was proposed in earlier work is applied to a number or examples. The Fukutome expansion is obtained by considering the spinor representation of the SO(2N+1) group. Its hermitian, Holstein-Primakofr-type version is also derived. The generalized Dyson expansions for even and odd fermion systems are given in terms of two spinor representations of the SO(2N) group. For fixed fermion number systems the relevant boson expansions are obtained by considering the fundamental representations of SU(N) while for fixed seniority those of Sp(N) are concerned. The collective boson expansions corresponding to the Ginocchio model, the interacting boson model of Arima and Iachello and the Elliot model are given for the symmetric representations of SO(8) and SU(1+1) and any representation of SU(3)

Discrete expansions of continuum functions. General concepts

International Nuclear Information System (INIS)

Bang, J.; Ershov, S.N.; Gareev, F.A.; Kazacha, G.S.

1979-01-01

Different discrete expansions of the continuum wave functions are considered: pole expansion (according to the Mittag-Lefler theorem), Weinberg states. The general property of these groups of states is their completeness in the finite region of space. They satisfy the Schroedinger type equations and are matched with free solutions of the Schroedinger equation at the boundary. Convergence of expansions for the S matrix, the Green functions and the continuous-spectrum wave functions is studied. A new group of states possessing the best convergence is introduced

Edgeworth expansion for the pre-averaging estimator

DEFF Research Database (Denmark)

Podolskij, Mark; Veliyev, Bezirgen; Yoshida, Nakahiro

In this paper, we study the Edgeworth expansion for a pre-averaging estimator of quadratic variation in the framework of continuous diffusion models observed with noise. More specifically, we obtain a second order expansion for the joint density of the estimators of quadratic variation and its...... asymptotic variance. Our approach is based on martingale embedding, Malliavin calculus and stable central limit theorems for continuous diffusions. Moreover, we derive the density expansion for the studentized statistic, which might be applied to construct asymptotic confidence regions....

Oblique photon expansion of QED structure functions

International Nuclear Information System (INIS)

Chahine, C.

1986-01-01

In the oblique photon expansion, the collinear part of photon emission is summed up to all orders in perturbation theory. The number of oblique or non-collinear photons is the expansion order. Unlike in perturbation theory, every term of the expansion is both infrared finite and gauge invariant. The zero oblique photon contribution to the electromagnetic structure tensor in QED is computed in detail. The behaviors of the structure functions F1 and F2 are discussed in the soft and ultra-soft limits

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

AUTO-EXPANSIVE FLOW

Science.gov (United States)

Physics suggests that the interplay of momentum, continuity, and geometry in outward radial flow must produce density and concomitant pressure reductions. In other words, this flow is intrinsically auto-expansive. It has been proposed that this process is the key to understanding...

Studies of Expansive Learning: Foundations, Findings and Future Challenges

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Yrjö Engeström

2013-07-01

Full Text Available The paper examines studies based on the theory of expansive learning, formulated in 1987. In recent years the theory has been used in a wide variety of studies and interventions. The theory builds on foundational ideas put forward by Vygotsky, Leont’ev, Il’enkov, and Davydov, key figures in the Russian school of cultural-historical activity theory. Studies based on the theory are reviewed in six sections: expansive learning as transformation of the object, expansive learning as movement in the zone of proximal development, expansive learning as cycles of learning actions, expansive learning as boundary crossing and network building, expansive learning as distributed and discontinuous movement, and formative interventions.A separate section is devoted to critiques of expansive learning. It is concluded that the ultimate test of learning theories is how they help practitioners to generate learning that grasps pressing issues the humankind is facing. The theory of expansive learning currently expands its analyses both up and down, outward and inward. Moving up and outward, it tackles learning in fields or networks of interconnected activity systems with their partially shared and often contested objects. Moving down and inward, it tackles issues of subjectivity, experiencing, personal sense, emotion, embodiment, identity, and moral commitment.

A Power Series Expansion and Its Applications

Science.gov (United States)

Chen, Hongwei

2006-01-01

Using the power series solution of a differential equation and the computation of a parametric integral, two elementary proofs are given for the power series expansion of (arcsin x)[squared], as well as some applications of this expansion.

Expansion Under Climate Change: The Genetic Consequences.

Science.gov (United States)

Garnier, Jimmy; Lewis, Mark A

2016-11-01

Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-diffusion model coupled to a heterogeneous environment that develops in time due to climate change. We decompose the resulting travelling wave solution into neutral genetic components to analyse the spatio-temporal dynamics of its genetic structure. Our analysis shows that range expansions and range shifts under slow climate change preserve genetic diversity. This is because slow climate change creates range boundaries that promote spatial mixing of genetic components. Mathematically, the mixing leads to so-called pushed travelling wave solutions. This mixing phenomenon is not seen in spatially homogeneous environments, where range expansion reduces genetic diversity through gene surfing arising from pulled travelling wave solutions. However, the preservation of diversity is diminished when climate change occurs too quickly. Using diversity indices, we show that fast expansions and range shifts erode genetic diversity more than slow range expansions and range shifts. Our study provides analytical insight into the dynamics of travelling wave solutions in heterogeneous environments.

Improvement of Expansive Soils Using Chemical Stabilizers

Science.gov (United States)

Ikizler, S. B.; Senol, A.; Khosrowshahi, S. K.; Hatipoğlu, M.

2014-12-01

The aim of this study is to investigate the effect of two chemical stabilizers on the swelling potential of expansive soil. A high plasticity sodium bentonite was used as the expansive soil. The additive materials including fly ash (FA) and lime (L) were evaluated as potential stabilizers to decrease the swelling pressure of bentonite. Depending on the type of additive materials, they were blended with bentonite in different percentages to assess the optimum state and approch the maximum swell pressure reduction. According to the results of swell pressure test, both fly ash and lime reduce the swelling potential of bentonite but the maximum improvement occurs using bentonite-lime mixture while the swelling pressure reduction approaches to 49%. The results reveal a significant reduction of swelling potential of expansive soil using chemical stabilizers. Keywords: Expansive soil; swell pressure; chemical stabilization; fly ash; lime

Thermal expansion: Metallic elements and alloys. [Handbook

Science.gov (United States)

Touloukian, Y. S.; Kirby, R. K.; Taylor, R. E.; Desai, P. D.

1975-01-01

The introductory sections of the work are devoted to the theory of thermal expansion of solids and to methods for the measurement of the linear thermal expansion of solids (X-ray methods, high speed methods, interferometry, push-rod dilatometry, etc.). The bulk of the work is devoted to numerical data on the thermal linear expansion of all the metallic elements, a large number of intermetallics, and a large number of binary alloy systems and multiple alloy systems. A comprehensive bibliography is provided along with an index to the materials examined.

Some Improved Nonperturbative Bounds for Fermionic Expansions

Energy Technology Data Exchange (ETDEWEB)

Lohmann, Martin, E-mail: marlohmann@gmail.com [Universita di Roma Tre, Dipartimento di Matematica (Italy)

2016-06-15

We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.

A non-uniform expansion mechanical safety model of the stent.

Science.gov (United States)

Yang, J; Huang, N; Du, Q

2009-01-01

Stents have a serial unstable structure that readily leads to non-uniform expansion. Non-uniform expansion in turn creates a stent safety problem. We explain how a stent may be simplified to a serial unstable structure, and present a method to calculate the non-uniform expansion of the stent on the basis of the serial unstable structure. We propose a safety criterion based on the expansion displacement instead of the strain, and explain that the parameter Rd, the ratio of the maximum displacement of the elements to normal displacement, is meaningful to assess the safety level of the stent. We also examine how laser cutting influences non-uniform expansion. The examples illustrate how to calculate the parameter Rd to assess non-uniform expansion of the stent, and demonstrate how the laser cutting offset and strengthening coefficient of the material influence the stent expansion behaviour. The methods are valuable for assessing stent safety due to non-uniform expansion.

Synthesis, microstructure and thermal expansion studies

Indian Academy of Sciences (India)

Abstract. We report on the synthesis, microstructure and thermal expansion studies on Ca0.5+/2Sr0.5+/2Zr4P6−2Si2O24 ( = 0.00 to 1.00) system which belongs to NZP family of low thermal expansion ceramics. The ceramics synthesized by co-precipitation method at lower calcination and the sintering temperatures ...

Operator expansion in quantum chromodynamics beyond perturbation theory

International Nuclear Information System (INIS)

Novikov, V.A.; Shifman, M.A.; Vainshtejn, A.I.; Zakharov, V.I.

1980-01-01

The status of operator expansion at short distances is descussed within the frameworks of nonperturbatue QCD. The question of instanton effects is investigated in various aspects. Two-point functions induced by the gluonic currents are considered. It is shown that certain gluonic correlations vanish in the field of definite duality. It is proved that there does exist a very special relation between the expansion coefficients required by consistancy between instanton calculations and the general operator expansion. At last a certain modification of the naive version of operator expansion is proposed, which allows one to go beyond the critical power and construct, if necessary, an infinite series

Studying medium effects with the optimized δ expansion

International Nuclear Information System (INIS)

Krein, G.; Menezes, D.P.; Nielsen, M.; Pinto, M.B.

1995-04-01

The possibility of using the optimized δ expansion for studying medium effects on hadronic properties in quark or nuclear matter is investigated. The δ expansion is employed to study density effects with two commonly used models in hadron and nuclear physics, the Nambu-Jona-Lasinio model for the dynamical chiral symmetry breaking and the Walecka model for the equation of state of nuclear matter. The results obtained with the δ expansion are compared to those obtained with the traditional Hartree-Fock approximation. Perspectives for using the δ expansion in other field theoretic models in hadron and nuclear physics are discussed. (author). 17 refs, 9 figs

Studying medium effects with the optimized {delta} expansion

Energy Technology Data Exchange (ETDEWEB)

Krein, G [Instituto de Fisica Teorica (IFT), Sao Paulo, SP (Brazil); Menezes, D P [Santa Catarina Univ., Florianopolis, SC (Brazil). Dept. de Fisica; Nielsen, M [Sao Paulo Univ., SP (Brazil). Inst. de Fisica; Pinto, M B [Montpellier-2 Univ., 34 (France). Lab. de Physique Mathematique

1995-04-01

The possibility of using the optimized {delta} expansion for studying medium effects on hadronic properties in quark or nuclear matter is investigated. The {delta} expansion is employed to study density effects with two commonly used models in hadron and nuclear physics, the Nambu-Jona-Lasinio model for the dynamical chiral symmetry breaking and the Walecka model for the equation of state of nuclear matter. The results obtained with the {delta} expansion are compared to those obtained with the traditional Hartree-Fock approximation. Perspectives for using the {delta} expansion in other field theoretic models in hadron and nuclear physics are discussed. (author). 17 refs, 9 figs.

Origami structures for tunable thermal expansion

Science.gov (United States)

Boatti, Elisa; Bertoldi, Katia

Materials with engineered thermal expansion, capable of achieving targeted and extreme area/volume changes in response to variations in temperature, are important for a number of aerospace, optical, energy, and microelectronic applications. While most of the proposed structures with tunable coefficient of thermal expansion consist of bi-material 2D or 3D lattices, here we propose a periodic metastructure based on a bilayer Miura-Ori origami fold. We combine experiments and simulations to demonstrate that by tuning the geometrical and mechanical parameters an extremely broad range of thermal expansion coefficients can be obtained, spanning both negative and positive values. Additionally, the thermal properties along different directions can be adjusted independently. Differently from all previously reported systems, the proposed structure is non-porous.

Anisotropic thermal expansion in flexible materials

Science.gov (United States)

Romao, Carl P.

2017-10-01

A definition of the Grüneisen parameters for anisotropic materials is derived based on the response of phonon frequencies to uniaxial stress perturbations. This Grüneisen model relates the thermal expansion in a given direction (αi i) to one element of the elastic compliance tensor, which corresponds to the Young's modulus in that direction (Yi i). The model is tested through ab initio prediction of thermal expansion in zinc, graphite, and calcite using density functional perturbation theory, indicating that it could lead to increased accuracy for structurally complex systems. The direct dependence of αi i on Yi i suggests that materials which are flexible along their principal axes but rigid in other directions will generally display both positive and negative thermal expansion.

Myopathic involvement and mitochondrial pathology in Kennedy disease and in other motor neuron diseases.

Science.gov (United States)

Orsucci, D; Rocchi, A; Caldarazzo Ienco, E; Alì, G; LoGerfo, A; Petrozzi, L; Scarpelli, M; Filosto, M; Carlesi, C; Siciliano, G; Bonuccelli, U; Mancuso, M

2014-01-01

Kennedy disease (spinal and bulbar muscular atrophy, or SBMA) is a motor neuron disease caused by a CAG expansion in the androgen-receptor (AR) gene. Increasing evidence shows that SBMA may have a primary myopathic component and that mitochondrial dysfunction may have some role in the pathogenesis of this disease. In this article, we review the role of mitochondrial dysfunction and of the mitochondrial genome (mtDNA) in SBMA, and we present the illustrative case of a patient who presented with increased CK levels and exercise intolerance. Molecular analysis led to definitive diagnosis of SBMA, whereas muscle biopsy showed a mixed myopathic and neurogenic process with "mitochondrial features" and multiple mtDNA deletions, supporting some role of mitochondria in the pathogenesis of the myopathic component of Kennedy disease. Furthermore, we briefly review the role of mitochondrial dysfunction in two other motor neuron diseases (namely spinal muscular atrophy and amyotrophic lateral sclerosis). Most likely, in most cases mtDNA does not play a primary role and it is involved subsequently. MtDNA deletions may contribute to the neurodegenerative process, but the exact mechanisms are still unclear. It will be important to develop a better understanding of the role of mitochondrial dysfunction in motoneuron diseases, since it may lead to the development of more effective strategies for the treatment of this devastating disorder.

Green turtles (Chelonia mydas foraging at Arvoredo Island in Southern Brazil: genetic characterization and mixed stock analysis through mtDNA control region haplotypes

Directory of Open Access Journals (Sweden)

Maíra Carneiro Proietti

2009-01-01

Full Text Available We analyzed mtDNA control region sequences of green turtles (Chelonia mydas from Arvoredo Island, a foraging ground in southern Brazil, and identified eight haplotypes. Of these, CM-A8 (64% and CM-A5 (22% were dominant, the remainder presenting low frequencies ( 0.05. Mixed Stock Analysis, incorporating eleven Atlantic and one Mediterranean rookery as possible sources of individuals, indicated Ascension and Aves islands as the main contributing stocks to the Arvoredo aggregation (68.01% and 22.96%, respectively. These results demonstrate the extensive relationships between Arvoredo Island and other Atlantic foraging and breeding areas. Such an understanding provides a framework for establishing adequate management and conservation strategies for this endangered species.

Population genetic structure of Diaphorina citri Kuwayama (Hemiptera: Liviidae): host-driven genetic differentiation in China.

Science.gov (United States)

Meng, Lixue; Wang, Yongmo; Wei, Wen-Hua; Zhang, Hongyu

2018-01-24

The Asian citrus psyllid Diaphorina citri Kuwayama is a major pest in citrus production, transmitting Candidatus Liberibacter asiaticus. It has spread widely across eastern and southern China. Unfortunately, little is known about the genetic diversity and population structure of D. citri, making pest control difficult. In this study, nine specifically developed SSR markers and three known mitochondrial DNA were used for population genetics study of D. citri using 225 samples collected from all 7 distribution regions in China. Based on the SSR data, D. citri was found highly diverse with a mean observed heterozygosity of 0.50, and three subgroups were structured by host plant: (i) Shatangju, NF mandarin and Ponkan; (ii) Murraya paniculata and Lemon; (iii) Citrus unshiu, Bingtangcheng, Summer orange and Navel. No significant genetic differences were found with mtDNA data. We suggested the host-associated divergence is likely to have occurred very recently. A unimodal distribution of paired differences, the negative and significant Tajima's D and Fu's F S parameters among mtDNA suggested a recent demographic expansion. The extensive citrus cultivation and increased suitable living habitat was recommended as a key for this expansion event.

Cluster expansion of the wavefunction. Symmetry-adapted-cluster expansion, its variational determination, and extension of open-shell orbital theory

International Nuclear Information System (INIS)

Nakatsuji, H.; Hirao, K.

1978-01-01

The symmetry-adapted-cluster (SAC) expansion of an exact wavefunction is given. It is constructed from the generators of the symmetry-adapted excited configurations having the symmetry under consideration, and includes their higher-order effect and self-consistency effect. It is different from the conventional cluster expansions in several important points, and is suitable for applications to open-shell systems as well as closed-shell systems. The variational equation for the SAC wavefunction has a form similar to the generalized Brillouin theorem in accordance with the inclusion of the higher-order effect and the self-consistency effect. We have expressed some existing open-shell orbital theories equivalently in the conventional cluster expansion formulas, and on this basis, we have given the pseudo-orbital theory which is an extension of open-shell orbital theory in the SAC expansion formula

Elastic-plastic analysis of tube expansion in tubesheets

International Nuclear Information System (INIS)

Kasraie, B.; O'Donnell, W.J.; Porowski, J.S.; Selz, A.

1983-01-01

Conditions for expansion of tubes in tubesheets are often determined by the test. The tightness of the joint and pull out force are used as criteria for evaluation of the results. For closely spaced tubes, it is also necessary to control development of the plastic regions in the ligaments surrounding the tube being expanded. High local strains may occur and excessive distortion may result if the expansion of the tube is continued beyond the admissible limits. Elastic-plastic finite element analyses are performed herein in order to establish conditions for rolling of the tubes in tubesheets of low ligament efficiency. Such penetration patterns are often required in the design of tubular reactors for catalytic processes. The model considered includes individual tube expansion in tubesheets with triangular penetration patterns. The effect of prior expansion of the neighboring tubes is also evaluated. Gap elements are used to model the initial clearance of the tube in the hole. Development of the plastic zones and distortion of the ligaments is monitored during radial expansion of the tube diameter. The residual stresses between the tube and the hole surface and the history of gap closing after removal of the expansion tool are determined. The effect of axial extension of the tube on the tube thinning is determined. Tube thinning is often used as a measure of tube expansion in manufacturing processes. For the analyzed ligament efficiency, reliable joints are obtained for a thinning range within 2% to 3%

Instability of a planar expansion wave.

Science.gov (United States)

Velikovich, A L; Zalesak, S T; Metzler, N; Wouchuk, J G

2005-10-01

An expansion wave is produced when an incident shock wave interacts with a surface separating a fluid from a vacuum. Such an interaction starts the feedout process that transfers perturbations from the rippled inner (rear) to the outer (front) surface of a target in inertial confinement fusion. Being essentially a standing sonic wave superimposed on a centered expansion wave, a rippled expansion wave in an ideal gas, like a rippled shock wave, typically produces decaying oscillations of all fluid variables. Its behavior, however, is different at large and small values of the adiabatic exponent gamma. At gamma > 3, the mass modulation amplitude delta(m) in a rippled expansion wave exhibits a power-law growth with time alpha(t)beta, where beta = (gamma - 3)/(gamma - 1). This is the only example of a hydrodynamic instability whose law of growth, dependent on the equation of state, is expressed in a closed analytical form. The growth is shown to be driven by a physical mechanism similar to that of a classical Richtmyer-Meshkov instability. In the opposite extreme gamma - 1 gas with low . Exact analytical expressions for the growth rates are derived for both cases and favorably compared to hydrodynamic simulation results.

Thermal expansion absorbing structure for pipeline

International Nuclear Information System (INIS)

Nagata, Takashi; Yamashita, Takuya.

1995-01-01

A thermal expansion absorbing structure for a pipeline is disposed to the end of pipelines to form a U-shaped cross section connecting a semi-circular torus shell and a short double-walled cylindrical tube. The U-shaped longitudinal cross-section is deformed in accordance with the shrinking deformation of the pipeline and absorbs thermal expansion. Namely, since the central lines of the outer and inner tubes of the double-walled cylindrical tube deform so as to incline, when the pipeline is deformed by thermal expansion, thermal expansion can be absorbed by a simple configuration thereby enabling to contribute to ensure the safety. Then, the entire length of the pipeline can greatly be shortened by applying it to the pipeline disposed in a high temperature state compared with a method of laying around a pipeline using only elbows, which has been conducted so far. Especially, when it is applied to a pipeline for an FBR-type reactor, the cost for the construction of a facility of a primary systems can greater be reduced. In addition, it can be applied to a pipeline for usual chemical plants and any other structures requiring absorption of deformation. (N.H.)

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

Directory of Open Access Journals (Sweden)

Lippold Sebastian

2011-11-01

Full Text Available Abstract Background DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region were investigated for larger sample sets. Results In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73% already existed before the beginning of domestication about 5,000 years ago. Conclusions Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the

The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country

Directory of Open Access Journals (Sweden)

Larruga José M

2006-05-01

Full Text Available Abstract Background It is customary, in population genetics studies, to consider Basques as the direct descendants of the Paleolithic Europeans. However, until now there has been no irrefutable genetic proof to support this supposition. Even studies based on mitochondrial DNA (mtDNA, an ideal molecule for constructing datable maternal genealogies, have failed to achieve this. It could be that incoming gene flow has replaced the Basque ancient lineages but it could also be that these lineages have not been detected due to a lack of resolution of the Basque mtDNA genealogies. To assess this possibility we analyzed here the mtDNA of a large sample of autochthonous Basques using mtDNA genomic sequencing for those lineages that could not be unequivocally classified by diagnostic RFLP analysis and control region (HVSI and HVSII sequencing. Results We show that Basques have the most ancestral phylogeny in Europe for the rare mitochondrial subhaplogroup U8a. Divergence times situate the Basque origin of this lineage in the Upper Palaeolithic. Most probably, their primitive founders came from West Asia. The lack of U8a lineages in Africa points to an European and not a North African route of entrance. Phylogeographic analysis suggest that U8a had two expansion periods in Europe, the first, from a south-western area including the Iberian peninsula and Mediterranean France before 30,000 years ago, and the second, from Central Europe around 15,000–10,000 years ago. Conclusion It has been demonstrated, for the first time, that Basques show the oldest lineages in Europe for subhaplogroup U8a. Coalescence times for these lineages suggest their presence in the Basque country since the Upper Paleolithic. The European U8 phylogeography is congruent with the supposition that Basques could have participated in demographic re-expansions to repopulate central Europe in the last interglacial periods.

The {β}-expansion formalism in perturbative QCD and its extension

Energy Technology Data Exchange (ETDEWEB)

Kataev, A.L. [Institute for Nuclear Research of the Academy of Sciences of Russia,60th October Anniversary Prospect 7a, 117312, Moscow (Russian Federation); Moscow Institute of Physics and Technology,Institutskii per. 9, 141700, Dolgoprudny, Moscow Region (Russian Federation); Mikhailov, S.V. [Bogoliubov Laboratory of Theoretical Physics, JINR,Joliot-Curie 6, 141980 Dubna (Russian Federation)

2016-11-11

We discuss the {β}-expansion for renormalization group invariant quantities tracing this expansion to the different contractions of the corresponding incomplete BPHZ R-operation. All of the coupling renormalizations, which follow from these contractions, should be taken into account for the {β}-expansion. We illustrate this feature considering the nonsinglet Adler function D{sup NS} in the third order of perturbation. We propose a generalization of the {β}-expansion for the renormalization group covariant quantities — the {β,γ}-expansion.

Temperature expansions for magnetic systems

International Nuclear Information System (INIS)

Cangemi, D.; Dunne, G.

1996-01-01

We derive finite temperature expansions for relativistic fermion systems in the presence of background magnetic fields, and with nonzero chemical potential. We use the imaginary-time formalism for the finite temperature effects, the proper-time method for the background field effects, and zeta function regularization for developing the expansions. We emphasize the essential difference between even and odd dimensions, focusing on 2+1 and 3+1 dimensions. We concentrate on the high temperature limit, but we also discuss the T=0 limit with nonzero chemical potential. Copyright copyright 1996 Academic Press, Inc

Thermal expansion data of (Th,U)O2 fuels

International Nuclear Information System (INIS)

Sengupta, A.K.; Banerjee, J.; Bhagat, R.K.; Ramachandran, R.; Majumdar, S.; Purushotham, D.S.C.

2000-04-01

Thermal expansion data for sintered ThO 2 and ThO 2 containing 2, 4, 6, 10 and 20% UO 2 pellets were measured using a high temperature dilatometer in the temperature range from ambient to 1773 K. The dilatometer was first calibrated using a standard graphite sample as reference material. The reproducibility of the dilatometer was tested by measuring the coefficient of expansion of tungsten (NBS SRM 737) and comparing the data with that recommended by National Bureau of Standard. It was observed that there is close agreement between the experimental and reported data. The coefficient of expansion data of (Th,U)O 2 fuel indicate that out of all the six compositions, ThO 2 +2%UO 2 showed the maximum expansion of around 1.75% at 1773 K. However, the expansion data for all the compositions were very close to each other. Empirical equation correlating thermal expansion and temperature for all six compositions have been generated and reported. (author)

Ring-Expansion/Contraction Radical Crossover Reactions of Cyclic Alkoxyamines: A Mechanism for Ring Expansion-Controlled Radical Polymerization

Directory of Open Access Journals (Sweden)

Atsushi Narumi

2018-06-01

Full Text Available Macrocyclic polymers present an important class of macromolecules, displaying the reduced radius of gyration or impossibility to entangle. A rare approach for their synthesis is the ring expansion-controlled radical “vinyl” polymerization, starting from a cyclic alkoxyamine. We here describe ring-expansion radical crossover reactions of cyclic alkoxyamines which run in parallel to chain-propagation reactions in the polymerization system. The radical crossover reactions extensively occurred at 105–125 °C, eventually producing high molecular weight polymers with multiple inherent dynamic covalent bonds (NOC bonds. A subsequent ring-contraction radical crossover reaction and the second ring-expansion radical crossover reaction are also described. The major products for the respective three stages were shown to possess cyclic morphologies by the molecular weight profiles and the residual ratios for the NOC bonds (φ in %. In particular, the high φ values ranging from ca. 80% to 98% were achieved for this cyclic alkoxyamine system. This result verifies the high availability of this system as a tool demonstrating the ring-expansion “vinyl” polymerization that allows them to produce macrocyclic polymers via a one-step vinyl polymerization.

Supersonic expansion of argon into vacuum

Energy Technology Data Exchange (ETDEWEB)

Habets, A H.M.

1977-01-21

A theoretical description of a free supersonic expansion process is given. Three distinct regions in the expansion are discussed, namely the continuum region, the gradual transition to the collisionless regime, and the free-molecular-flow stage. Important topics are the peaking-factor formalism, the thermal-conduction model, and the virtual-source formalism. The formation of the molecular beam from the expansion and condensation phenomena occurring in the expanding gas are discussed. The molecular beam machine used in the measurements is described and special attention is given to the cryopumps used in the supersonic sources as well as to the time-of-flight analysis of the molecular beam velocity distributions. Finally, the processing of experimental data is discussed, particularly the least-squares determination of best-fit representations of the measurements.

Radial expansion for spinning conformal blocks

CERN Document Server

Costa, Miguel S.; Penedones, João; Trevisani, Emilio

2016-07-12

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.

Supersonic expansion of argon into vacuum

International Nuclear Information System (INIS)

Habets, A.H.M.

1977-01-01

A theoretical description of a free supersonic expansion process is given. Three distinct regions in the expansion are discussed, namely the continuum region, the gradual transition to the collisionless regime, and the free-molecular-flow stage. Important topics are the peaking-factor formalism, the thermal-conduction model, and the virtual-source formalism. The formation of the molecular beam from the expansion and condensation phenomena occurring in the expanding gas are discussed. The molecular beam machine used in the measurements is described and special attention is given to the cryopumps used in the supersonic sources as well as to the time-of-flight analysis of the molecular beam velocity distributions. Finally, the processing of experimental data is discussed, particularly the least-squares determination of best-fit representations of the measurements

The relevance of grid expansion under zonal markets

Energy Technology Data Exchange (ETDEWEB)

Bertsch, Joachim; Hagspiel, Simeon; Just, Lisa [ewi Energy Research and Scenarios gGmbH, Cologne (Germany); Cologne Univ. (Germany). Dept. of Economics; Brown, Tom [Frankfurt Institute of Advanced Studies (Germany)

2015-12-15

The European electricity market design is based on zonal markets with uniform prices. Locational price signals within these zones - necessary to ensure long-term efficiency - are not provided. Specifically, if intra-zonal congestion occurs due to missing grid expansion, the market design is revealed as inherently incomplete. This might lead to severe, unwanted distortions of the electricity market, both in the short- and in the long-term. In this paper, we study these distortions with a specific focus on the impact of restricted grid expansion under zonal markets. For this, we use a long term fundamental dispatch and investment model of the European electricity system and gradually restrict the allowed expansion of the transmission grid per decade. We find that the combination of an incomplete market design and restricted grid expansion leads to a misallocation of generation capacities and the inability to transport electricity to where it is needed. Consequences are severe and lead to load curtailment of up to 2-3 %. Moreover, missing grid expansion makes it difficult and costly to reach envisaged energy targets in the power sector. Hence, we argue that in the likely event of restricted grid expansion, either administrative measures or - presumably more efficient - an adaptation of the current market design to include locational signals will become necessary.

The relevance of grid expansion under zonal markets

International Nuclear Information System (INIS)

Bertsch, Joachim; Hagspiel, Simeon; Just, Lisa

2015-01-01

The European electricity market design is based on zonal markets with uniform prices. Locational price signals within these zones - necessary to ensure long-term efficiency - are not provided. Specifically, if intra-zonal congestion occurs due to missing grid expansion, the market design is revealed as inherently incomplete. This might lead to severe, unwanted distortions of the electricity market, both in the short- and in the long-term. In this paper, we study these distortions with a specific focus on the impact of restricted grid expansion under zonal markets. For this, we use a long term fundamental dispatch and investment model of the European electricity system and gradually restrict the allowed expansion of the transmission grid per decade. We find that the combination of an incomplete market design and restricted grid expansion leads to a misallocation of generation capacities and the inability to transport electricity to where it is needed. Consequences are severe and lead to load curtailment of up to 2-3 %. Moreover, missing grid expansion makes it difficult and costly to reach envisaged energy targets in the power sector. Hence, we argue that in the likely event of restricted grid expansion, either administrative measures or - presumably more efficient - an adaptation of the current market design to include locational signals will become necessary.

Controlled Thermal Expansion Alloys

Data.gov (United States)

National Aeronautics and Space Administration — There has always been a need for controlled thermal expansion alloys suitable for mounting optics and detectors in spacecraft applications.  These alloys help...

Controlling Thermal Expansion: A Metal?Organic Frameworks Route

OpenAIRE

Balestra, Salvador R. G.; Bueno-Perez, Rocio; Hamad, Said; Dubbeldam, David; Ruiz-Salvador, A. Rabdel; Calero, Sofia

2016-01-01

Controlling thermal expansion is an important, not yet resolved, and challenging problem in materials research. A conceptual design is introduced here, for the first time, for the use of metal?organic frameworks (MOFs) as platforms for controlling thermal expansion devices that can operate in the negative, zero, and positive expansion regimes. A detailed computer simulation study, based on molecular dynamics, is presented to support the targeted application. MOF-5 has been selected as model m...

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.

Perturbation Expansion in Dynamical Nuclear Field Theory and Its Relation with Boson Expansion Theory : Nuclear Physics

OpenAIRE

Teruo, KISHIMOTO; Tetsuo, KAMMURI; Institute of Physics, University of Tsukuba; Department of Physics, Osaka University

1990-01-01

With the Dynamical Nuclear Field Theory (DNFT) in the Tamm-Dancoff representation we examine higher order corrections in the vibrational mode of a spherical nuclear system. Due to the effects of bubble diagrams, the perturbation expansion in terms of the unrenormalized coupling strength and boson energy fails at full self-consistency. On the other hand, it becomes applicable in the form of linked-cluster expansion when we use thses constants renormalized by the effect of bubble diagrams, in t...

Eta-Expansion Does The Trick

DEFF Research Database (Denmark)

Danvy, Olivier; Malmkjær, Karoline; Palsberg, Jens

1995-01-01

Partial-evaluation folklore has it that massaging one's source programs can make them specialize better. In Jones, Gomard, and Sestoft's recent textbook, a whole chapter is dedicated to listing such “binding-time improvements”: nonstandard use of continuation-passing style, eta-expansion, and a p......Partial-evaluation folklore has it that massaging one's source programs can make them specialize better. In Jones, Gomard, and Sestoft's recent textbook, a whole chapter is dedicated to listing such “binding-time improvements”: nonstandard use of continuation-passing style, eta...... across dynamic case expressions. This requirement precisely accounts for the nonstandard use of continuation-passing style encountered in partial evaluation. Eta-expansion thus acts as a uniform binding-time coercion between values and contexts, be they of function type, product type, or disjoint......-expansion, and a popular transformation called “The Trick.” We provide a unified view of these binding-time improvements, from a typing perspective. Just as a proper treatment of product values in partial evaluation requires partially static values, a proper treatment of disjoint sums requires moving static contexts...

Cluster expansion for vacuum confining fields

International Nuclear Information System (INIS)

Simonov, Yu.A.

1987-01-01

Colored particle Green functions in vacuum background random fields are written as path integrals. Averaging over random fields is done using the cluster (cumulant) expansion. The existence of a finite correlation length for vacuum background fields is shown to produce the linear confinement, in agreement with the results, obtained with the help of averaged Hamiltonians. A modified form of cluster expansion for nonabelian fields is introduced using the path-ordered cumulants

Stochastic quantization and 1/N expansion

International Nuclear Information System (INIS)

Brunelli, J.C.; Mendes, R.S.

1992-10-01

We study the 1/N expansion of field theories in the stochastic quantization method of Parisi and Wu using the supersymmetric functional approach. This formulation provides a systematic procedure to implement the 1/N expansion which resembles the ones used in the equilibrium. The 1/N perturbation theory for the non linear sigma model in two dimensions is worked out as an example. (author). 19 refs., 5 figs

Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

Science.gov (United States)

Takegoshi, K.; Miyazawa, Norihiro; Sharma, Kshama; Madhu, P. K.

2015-04-01

We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order.

Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

International Nuclear Information System (INIS)

Takegoshi, K.; Miyazawa, Norihiro; Sharma, Kshama; Madhu, P. K.

2015-01-01

We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order

Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

Energy Technology Data Exchange (ETDEWEB)

Takegoshi, K., E-mail: takeyan@kuchem.kyoto-u.ac.jp; Miyazawa, Norihiro [Division of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto (Japan); Sharma, Kshama [TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500 075 (India); Madhu, P. K. [TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500 075 (India); Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

2015-04-07

We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order.

A summation procedure for expansions in orthogonal polynomials

International Nuclear Information System (INIS)

Garibotti, C.R.; Grinstein, F.F.

1977-01-01

Approximants to functions defined by formal series expansions in orthogonal polynomials are introduced. They are shown to be convergent even out of the elliptical domain where the original expansion converges

Future urban land expansion and implications for global croplands.

Science.gov (United States)

Bren d'Amour, Christopher; Reitsma, Femke; Baiocchi, Giovanni; Barthel, Stephan; Güneralp, Burak; Erb, Karl-Heinz; Haberl, Helmut; Creutzig, Felix; Seto, Karen C

2017-08-22

Urban expansion often occurs on croplands. However, there is little scientific understanding of how global patterns of future urban expansion will affect the world's cultivated areas. Here, we combine spatially explicit projections of urban expansion with datasets on global croplands and crop yields. Our results show that urban expansion will result in a 1.8-2.4% loss of global croplands by 2030, with substantial regional disparities. About 80% of global cropland loss from urban expansion will take place in Asia and Africa. In both Asia and Africa, much of the cropland that will be lost is more than twice as productive as national averages. Asia will experience the highest absolute loss in cropland, whereas African countries will experience the highest percentage loss of cropland. Globally, the croplands that are likely to be lost were responsible for 3-4% of worldwide crop production in 2000. Urban expansion is expected to take place on cropland that is 1.77 times more productive than the global average. The loss of cropland is likely to be accompanied by other sustainability risks and threatens livelihoods, with diverging characteristics for different megaurban regions. Governance of urban area expansion thus emerges as a key area for securing livelihoods in the agrarian economies of the Global South.

Evolution of density-dependent movement during experimental range expansions.

Science.gov (United States)

Fronhofer, E A; Gut, S; Altermatt, F

2017-12-01

Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Edgeworth Expansion Based Model for the Convolutional Noise pdf

Directory of Open Access Journals (Sweden)

Yonatan Rivlin

2014-01-01

Full Text Available Recently, the Edgeworth expansion up to order 4 was used to represent the convolutional noise probability density function (pdf in the conditional expectation calculations where the source pdf was modeled with the maximum entropy density approximation technique. However, the applied Lagrange multipliers were not the appropriate ones for the chosen model for the convolutional noise pdf. In this paper we use the Edgeworth expansion up to order 4 and up to order 6 to model the convolutional noise pdf. We derive the appropriate Lagrange multipliers, thus obtaining new closed-form approximated expressions for the conditional expectation and mean square error (MSE as a byproduct. Simulation results indicate hardly any equalization improvement with Edgeworth expansion up to order 4 when using optimal Lagrange multipliers over a nonoptimal set. In addition, there is no justification for using the Edgeworth expansion up to order 6 over the Edgeworth expansion up to order 4 for the 16QAM and easy channel case. However, Edgeworth expansion up to order 6 leads to improved equalization performance compared to the Edgeworth expansion up to order 4 for the 16QAM and hard channel case as well as for the case where the 64QAM is sent via an easy channel.

Thermal and Hygric Expansion of High Performance Concrete

OpenAIRE

J. Toman; R. Černý

2001-01-01

The linear thermal expansion coefficient of two types of high performance concrete was measured in the temperature range from 20 °C to 1000 °C, and the linear hygric expansion coefficient was determined in the moisture range from dry material to saturation water content. Comparative methods were applied for measurements of both coefficients. The experimental results show that both the effect of temperature on the values of linear thermal expansion coefficients and the effect of moisture on th...

Cycle expansions: From maps to turbulence

Science.gov (United States)

Lan, Y.

2010-03-01

We present a derivation, a physical explanation and applications of cycle expansions in different dynamical systems, ranging from simple one-dimensional maps to turbulence in fluids. Cycle expansion is a newly devised powerful tool for computing averages of physical observables in nonlinear chaotic systems which combines many innovative ideas developed in dynamical systems, such as hyperbolicity, invariant manifolds, symbolic dynamics, measure theory and thermodynamic formalism. The concept of cycle expansion has a deep root in theoretical physics, bearing a close analogy to cumulant expansion in statistical physics and effective action functional in quantum field theory, the essence of which is to represent a physical system in a hierarchical way by utilizing certain multiplicative structures such that the dominant parts of physical observables are captured by compact, maneuverable objects while minor detailed variations are described by objects with a larger space and time scale. The technique has been successfully applied to many low-dimensional dynamical systems and much effort has recently been made to extend its use to spatially extended systems. For one-dimensional systems such as the Kuramoto-Sivashinsky equation, the method turns out to be very effective while for more complex real-world systems including the Navier-Stokes equation, the method is only starting to yield its first fruits and much more work is needed to enable practical computations. However, the experience and knowledge accumulated so far is already very useful to a large set of research problems. Several such applications are briefly described in what follows. As more research effort is devoted to the study of complex dynamics of nonlinear systems, cycle expansion will undergo a fast development and find wide applications.

Lessons from Early Medicaid Expansions Under Health Reform..

Data.gov (United States)

U.S. Department of Health & Human Services — Lessons from Early Medicaid Expansions Under Health Reform, Interviews with Medicaid Officials In a new study entitled Lessons from Early Medicaid Expansions Under...

Thermal expansion accompanying the glass-liquid transition and crystallization

Directory of Open Access Journals (Sweden)

M. Q. Jiang

2015-12-01

Full Text Available We report the linear thermal expansion behaviors of a Zr-based (Vitreloy 1 bulk metallic glass in its as-cast, annealed and crystallized states. Accompanying the glass-liquid transition, the as-cast Vitreloy 1 shows a continuous decrease in the thermal expansivity, whereas the annealed glass shows a sudden increase. The crystallized Vitreloy 1 exhibits an almost unchanged thermal expansivity prior to its melting. Furthermore, it is demonstrated that the nucleation of crystalline phases can induce a significant thermal shrinkage of the supercooled liquid, but with the growth of these nuclei, the thermal expansion again dominates. These results are explained in the framework of the potential energy landscape, advocating that the configurational and vibrational contributions to the thermal expansion of the glass depend on both, structure and temperature.

Probing the phylogenetic relationships of a few newly recorded intertidal zoanthids of Gujarat coast (India) with mtDNA COI sequences.

Science.gov (United States)

Joseph, Sneha; Poriya, Paresh; Kundu, Rahul

2016-11-01

The present study reports the phylogenetic relationship of six zoanthid species belonging to three genera, Isaurus, Palythoa, and Zoanthus identified using systematic computational analysis of mtDNA gene sequences. All six species are first recorded from the coasts of Kathiawar Peninsula, India. Genus: Isaurus is represented by Isaurus tuberculatus, genus Zoanthus is represented by Zoanthus kuroshio and Zoanthus sansibaricus, while genus Palythoa is represented by Palythoa tuberculosa, P. sp. JVK-2006 and Palythoa heliodiscus. Results of the present study revealed that among the various species observed along the coastline, a minimum of 99% sequence divergence and a maximum of 96% sequence divergence were seen. An interspecific divergence of 1-4% and negligible intraspecific divergence was observed. These results not only highlighted the efficiency of the COI gene region in species identification but also demonstrated the genetic variability of zoanthids along the Saurashtra coastline of the west coast of India.

Thermal expansion model for multiphase electronic packaging materials

International Nuclear Information System (INIS)

Allred, B.E.; Warren, W.E.

1991-01-01

Control of thermal expansion is often necessary in the design and selection of electronic packages. In some instances, it is desirable to have a coefficient of thermal expansion intermediate between values readily attainable with single or two phase materials. The addition of a third phase in the form of fillers, whiskers, or fibers can be used to attain intermediate expansions. To help design the thermal expansion of multiphase materials for specific applications, a closed form model has been developed that accurately predicts the effective elastic properties of isotropic filled materials and transversely isotropic lamina. Properties of filled matrix materials are used as inputs to the lamina model to obtain the composite elastic properties as a function of the volume fraction of each phase. Hybrid composites with two or more fiber types are easily handled with this model. This paper reports that results for glass, quartz, and Kevlar fibers with beta-eucryptite filled polymer matrices show good agreement with experimental results for X, Y, and Z thermal expansion coefficients

Asymptotic expansions for high-contrast linear elasticity

KAUST Repository

Poveda, Leonardo A.; Huepo, Sebastian; Calo, Victor M.; Galvis, Juan

2015-01-01

We study linear elasticity problems with high contrast in the coefficients using asymptotic limits recently introduced. We derive an asymptotic expansion to solve heterogeneous elasticity problems in terms of the contrast in the coefficients. We study the convergence of the expansion in the H1 norm. © 2015 Elsevier B.V.

Asymptotic expansions for high-contrast linear elasticity

KAUST Repository

Poveda, Leonardo A.

2015-03-01

We study linear elasticity problems with high contrast in the coefficients using asymptotic limits recently introduced. We derive an asymptotic expansion to solve heterogeneous elasticity problems in terms of the contrast in the coefficients. We study the convergence of the expansion in the H1 norm. © 2015 Elsevier B.V.

Application of oligonucleotide array CGH to the simultaneous detection of a deletion in the nuclear TK2 gene and mtDNA depletion.

Science.gov (United States)

Zhang, Shulin; Li, Fang-Yuan; Bass, Harold N; Pursley, Amber; Schmitt, Eric S; Brown, Blaire L; Brundage, Ellen K; Mardach, Rebecca; Wong, Lee-Jun

2010-01-01

Thymidine kinase 2 (TK2), encoded by the TK2 gene on chromosome 16q22, is one of the deoxyribonucleoside kinases responsible for the maintenance of mitochondrial deoxyribonucleotide pools. Defects in TK2 mainly cause a myopathic form of the mitochondrial DNA depletion syndrome (MDDS). Currently, only point mutations and small insertions and deletions have been reported in TK2 gene; gross rearrangements of TK2 gene and possible hepatic involvement in patients with TK2 mutations have not been described. We report a non-consanguineous Jordanian family with three deceased siblings due to mtDNA depletion. Sequence analysis of the father detected a heterozygous c.761T>A (p.I254N) mutation in his TK2 gene; however, point mutations in the mother were not detected. Subsequent gene dosage analysis using oligonucleotide array CGH identified an intragenic approximately 5.8-kb deletion encompassing the 5'UTR to intron 2 of her TK2 gene. Sequence analysis confirmed that the deletion spans c.1-495 to c.283-2899 of the TK2 gene (nucleotide 65,136,256-65,142,086 of chromosome 16). Analysis of liver and muscle specimens from one of the deceased infants in this family revealed compound heterozygosity for the paternal point mutation and maternal intragenic deletion. In addition, a significant reduction of the mtDNA content in liver and muscle was detected (10% and 20% of age- and tissue-matched controls, respectively). Prenatal diagnosis was performed in the third pregnancy. The fetus was found to carry both the point mutation and the deletion. This child died 6months after birth due to myopathy. A serum specimen demonstrated elevated liver transaminases in two of the infants from whom results were available. This report expands the mutation spectrum associated with TK2 deficiency. While the myopathic form of MDDS appears to be the main phenotype of TK2 mutations, liver dysfunction may also be a part of the mitochondrial depletion syndrome caused by TK2 gene defects.

The critical thermal expansion of gadolinium

International Nuclear Information System (INIS)

Robinson, K.; Lanchester, P.C.

1978-01-01

Measurements have been made of the critical thermal expansion of single crystals of gadolinium, prepared by solid state electrotransport processing. Although the expansion data can be fitted to a simple power law with exponents lambda + =-0.25, lambda - =-0.33, these values are not predicted by theory and a discontinuity remains at Tsub(c)=293.620 K. It is suggested that the results relate to a region of crossover to uniaxial dipolar behaviour. (Auth.)

Foundations on Expansive Soils; A Review

OpenAIRE

Behzad Kalantari

2012-01-01

This study describes various types of foundation designs to be considered for structural engineering projects when the subsoil foundation consists of expansive or swelling soils. Among civil and architectural engineers expansive soils are known to be difficult foundation materials and problematic. These type of soils swell when they are subjected to moistures and shrink due to moisture loss. Because of this different behaviour upon wetting and drying, they cause minor to major structural dama...

Preliminary thermal expansion screening data for tuffs

International Nuclear Information System (INIS)

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 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

Electric Grid Expansion Planning with High Levels of Variable Generation

Energy Technology Data Exchange (ETDEWEB)

Hadley, Stanton W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); You, Shutang [Univ. of Tennessee, Knoxville, TN (United States); Shankar, Mallikarjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Yilu [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2016-02-01

Renewables are taking a large proportion of generation capacity in U.S. power grids. As their randomness has increasing influence on power system operation, it is necessary to consider their impact on system expansion planning. To this end, this project studies the generation and transmission expansion co-optimization problem of the US Eastern Interconnection (EI) power grid with a high wind power penetration rate. In this project, the generation and transmission expansion problem for the EI system is modeled as a mixed-integer programming (MIP) problem. This study analyzed a time series creation method to capture the diversity of load and wind power across balancing regions in the EI system. The obtained time series can be easily introduced into the MIP co-optimization problem and then solved robustly through available MIP solvers. Simulation results show that the proposed time series generation method and the expansion co-optimization model and can improve the expansion result significantly after considering the diversity of wind and load across EI regions. The improved expansion plan that combines generation and transmission will aid system planners and policy makers to maximize the social welfare. This study shows that modelling load and wind variations and diversities across balancing regions will produce significantly different expansion result compared with former studies. For example, if wind is modeled in more details (by increasing the number of wind output levels) so that more wind blocks are considered in expansion planning, transmission expansion will be larger and the expansion timing will be earlier. Regarding generation expansion, more wind scenarios will slightly reduce wind generation expansion in the EI system and increase the expansion of other generation such as gas. Also, adopting detailed wind scenarios will reveal that it may be uneconomic to expand transmission networks for transmitting a large amount of wind power through a long distance

Dynamical effects in the Colomb expansion following nuclear fragmentation

International Nuclear Information System (INIS)

Chung, K.C.; Donangelo, R.J.; Schechter, H.

1987-01-01

The effects of the Colomb expansion on the fragment Kinetic energy spectrum for a fragmentating hot nuclear system is investigated. In particular, 12 C fragment spectra are calculated and compared with those predicted by the uniform expansion approximation. The results indicate that energy spectra of fragments are quite sensitive to the details of the Coulomb expansion treatment. (Author) [pt

Hadronic mass-relations from topological expansion and string model

International Nuclear Information System (INIS)

Kaidalov, A.B.

1980-01-01

Hadronic mass-relations from topological expansion and string model are derived. For this purpose the space- time picture of hadron interactions at high energies corresponding to planar diagrams of topological expansion is considered. Simple relations between intercepts and slopes of Regge trajectories based on the topological expansion and q anti q-string picture of hadrons are obtained [ru

Thermal expansion of Ti-substituted barium hexaferrite

NARCIS (Netherlands)

Hernandez-Gomez, P.; Francisco, de C.; Brabers, V.A.M.; Dalderop, J.H.J.

2000-01-01

Thermal expansion measurements in the range of 20–500 °C were carried out on both poly- and single crystalline samples of the hexagonal magnetoplumbite ferrite with composition BaTiFe11O19. The continuous scanning of the thermal expansion reveals the existence of a -type anomaly near the Curie

Finnish Higher Education Expansion and Regional Policy

Science.gov (United States)

Saarivirta, Toni

2010-01-01

This paper concentrates on the expansion of Finnish higher education between the 1960s and 1970s, exposes its background in the light of the policy decisions that were made, compares the unique features of this expansion with those of certain other countries, discusses the impact of the controlled "top down" governance of higher…

Spherical-wave expansions of piston-radiator fields.

Science.gov (United States)

Wittmann, R C; Yaghjian, A D

1991-09-01

Simple spherical-wave expansions of the continuous-wave fields of a circular piston radiator in a rigid baffle are derived. These expansions are valid throughout the illuminated half-space and are useful for efficient numerical computation in the near-field region. Multipole coefficients are given by closed-form expressions which can be evaluated recursively.

Series expansion of the modified Einstein Procedure

Science.gov (United States)

Seema Chandrakant Shah-Fairbank

2009-01-01

This study examines calculating total sediment discharge based on the Modified Einstein Procedure (MEP). A new procedure based on the Series Expansion of the Modified Einstein Procedure (SEMEP) has been developed. This procedure contains four main modifications to MEP. First, SEMEP solves the Einstein integrals quickly and accurately based on a series expansion. Next,...

Monitoring Saccharomyces cerevisiae populations by mtDNA restriction analysis and other molecular typing methods during spontaneous fermentation for production of the artisanal cachaça Monitoramento das populações de Saccharomyces cerevisiae pela análise de restrição do mtDNA e outros métodos de tipagem molecular durante a fermentação espontânea para a produção da cachaça artesanal

Directory of Open Access Journals (Sweden)

Roberta A.C. Araújo

2007-06-01

Full Text Available An ecological study on Saccharomyces cerevisiae populations in spontaneous fermentation has been conducted in three vats of a cachaça distillery in Minas Gerais, Brazil. Ninety-seven yeast isolates were collected at the beginning, the middle and at the end of the production period, and were identified by standard methods. Differentiation between the indigenous S. cerevisiae strains isolated was performed by mitochondrial DNA (mtDNA restriction analysis, RAPD-PCR, and PCR fingerprint using an intron splice primer. Analysis of the mtDNA restriction profiles revealed 12 different patterns, 11 corresponding to indigenous yeasts (I to XI and one (XII to a commercial strain of the bakery yeast. Pattern II (53.6% of the population and pattern IV strains were present in all the vats. Pattern IV strain raised from the middle to the end of the period reaching proportions near those of pattern II strain. PCR methods allowed the differentiation of 41 molecular profiles. Both methods showed population fluctuation of S. cerevisiae strains along the period of cachaça production and among different vats of the distillery.Um estudo ecológico das populações de Saccharomyces cerevisiae em fermentações espontâneas foi conduzido em três dornas de uma destilaria de cachaça em Minas Gerais, Brasil. Noventa e sete isolados foram coletados no início, meio e final do período de produção, e identificados por métodos padrões. A diferenciação entre as linhagens isoladas de S. cerevisiae indígenas foi feita pela analise de restrição do DNA mitocondrial (mtDNA, RAPD-PCR, e PCR por impressão digital do DNA utilizando um iniciador complementar a sítios de processamento de íntron. As análises dos perfis de restrição do mtDNA mostraram a ocorrência de 12 perfis diferentes, sendo 11 correspondentes as leveduras indígenas (I ao XI e um (XII a uma linhagem comercial de levedura de panificação. Linhagens com o perfil II (53,6% da população e o perfil

Rapid replacement of bridge deck expansion joints study - phase I.

Science.gov (United States)

2014-12-01

Bridge deck expansion joints are used to allow for movement of the bridge deck due to thermal expansion, dynamics loading, and : other factors. More recently, expansion joints have also been utilized to prevent the passage of winter de-icing chemical...

Global operator expansions in conformally invariant relativistic quantum field theory

International Nuclear Information System (INIS)

Schoer, B.; Swieca, J.A.; Voelkel, A.H.

1974-01-01

A global conformal operator expansions in the Minkowski region in several models and their formulation in the general theory is presented. Whereas the vacuum expansions are termwise manisfestly conformal invariant, the expansions away from the vacuum do not share this property

Expansion reduction of clayey soils through Surcharge application and Lime Treatment

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T. López-Lara

2017-12-01

Full Text Available Expansive clayey soils produce heaving and cracking of floor slabs and walls. Expansive soils owe their characteristics to the presence of swelling clay minerals. This soil expands and contracts due to changes in the moisture content of the soil. In this study the surcharge required to counteract soil expansion was measured in natural expansive soils (untreated soils and lime treated soils starting at 19.61 kPa (2 Ton/m2 and continuing with increments of 19.61 kPa. Additionaly in lime treated soils the amount of lime was determined under different surcharges in order to reduce the expansion. The test results indicated that the surcharges applied to untreated soils were not proportional to the decrease of expansion which is probably due to the increase of soil density. In fact, only the initial surcharge of 19.61 kPa significantly decreased the expansion. According to the results, the soil expansion was considerably reduced (1.54% with the surcharge of 78.45 kPa, therefore this surcharge can be considered as the Swelling pressure. On the other hand the soil tested (high compressibility clay was stabilized with 6% of lime (without surcharges which was determined with the lowest value of liquid limit and plastic index as well as expansion test. After the application of surcharges and lime treatment to expansive soil, the surcharges of 39.22 kPa and 58.84 kPa decreased expansion and increased their resistance. This was concluded by similar low values of expansion (without settlements under both surcharges of each treated soil tested (2, 4 and 6% of lime. It can be concluded that the surcharge contributed to the decrease of soil expansion due to the decrease of the amount of lime required (6% without surcharge. So, 4% of lime was enough for the surcharge of 19.61 kPa and 2% of lime required the surcharge minimum of 39.22 kPa. This shows that the surcharge of a house on expansive soil reduces soil expansion and therefore reduces costs of any

Expansion patterns and parallaxes for planetary nebulae

Science.gov (United States)

Schönberner, D.; Balick, B.; Jacob, R.

2018-02-01

Aims: We aim to determine individual distances to a small number of rather round, quite regularly shaped planetary nebulae by combining their angular expansion in the plane of the sky with a spectroscopically measured expansion along the line of sight. Methods: We combined up to three epochs of Hubble Space Telescope imaging data and determined the angular proper motions of rim and shell edges and of other features. These results are combined with measured expansion speeds to determine individual distances by assuming that line of sight and sky-plane expansions are equal. We employed 1D radiation-hydrodynamics simulations of nebular evolution to correct for the difference between the spectroscopically measured expansion velocities of rim and shell and of their respective shock fronts. Results: Rim and shell are two independently expanding entities, driven by different physical mechanisms, although their model-based expansion timescales are quite similar. We derive good individual distances for 15 objects, and the main results are as follows: (i) distances derived from rim and shell agree well; (ii) comparison with the statistical distances in the literature gives reasonable agreement; (iii) our distances disagree with those derived by spectroscopic methods; (iv) central-star "plateau" luminosities range from about 2000 L⊙ to well below 10 000 L⊙, with a mean value at about 5000 L⊙, in excellent agreement with other samples of known distance (Galactic bulge, Magellanic Clouds, and K648 in the globular cluster M 15); (v) the central-star mass range is rather restricted: from about 0.53 to about 0.56 M⊙, with a mean value of 0.55 M⊙. Conclusions: The expansion measurements of nebular rim and shell edges confirm the predictions of radiation-hydrodynamics simulations and offer a reliable method for the evaluation of distances to suited objects. Results of this paper are based on observations made with the NASA/ESA Hubble Space Telescope in Cycle 16 (GO11122