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Sample records for haploid genome equivalents

  1. Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents

    International Nuclear Information System (INIS)

    Albertsen, H.M.; Abderrahim, H.; Cann, H.M.; Dausset, J.; Le Paslier, D.; Cohen, D.

    1990-01-01

    Prior to constructing a library of yeast artificial chromosomes (YACs) containing very large human DNA fragments, the authors performed a series of preliminary experiments aimed at developing a suitable protocol. They found an inverse relationship between YAC insert size and transformation efficiency. Evidence of occasional rearrangement within YAC inserts was found resulting in clonally stable internal deletions or clonally unstable size variations. A protocol was developed for preparative electrophoretic enrichment of high molecular mass human DNA fragments from partial restriction digests and ligation with the YAC vector in agarose. A YAC library has been constructed from large fragments of DNA from an Epstein-Barr virus-transformed human lymphoblastoid cell line. The library presently contains 50,000 clones, 95% of which are greater than 250 kilobase pairs in size. The mean YAC size of the library, calculated from 132 randomly isolated clones, is 430 kilobase pairs. The library thus contains the equivalent of approximately seven haploid human genomes

  2. Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

    Science.gov (United States)

    Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudoh, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

    2014-10-27

    Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

  3. A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

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    Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

    2018-01-01

    To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  4. Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

    OpenAIRE

    Daetwyler, Hans D.; Hayden, Matthew J.; Spangenberg, German C.; Hayes, Ben J.

    2015-01-01

    Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selec...

  5. Generation of Mouse Haploid Somatic Cells by Small Molecules for Genome-wide Genetic Screening

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    Zheng-Quan He

    2017-08-01

    Full Text Available The recent success of derivation of mammalian haploid embryonic stem cells (haESCs has provided a powerful tool for large-scale functional analysis of the mammalian genome. However, haESCs rapidly become diploidized after differentiation, posing challenges for genetic analysis. Here, we show that the spontaneous diploidization of haESCs happens in metaphase due to mitotic slippage. Diploidization can be suppressed by small-molecule-mediated inhibition of CDK1 and ROCK. Through ROCK inhibition, we can generate haploid somatic cells of all three germ layers from haESCs, including terminally differentiated neurons. Using piggyBac transposon-based insertional mutagenesis, we generated a haploid neural cell library harboring genome-wide mutations for genetic screening. As a proof of concept, we screened for Mn2+-mediated toxicity and identified the Park2 gene. Our findings expand the applications of mouse haploid cell technology to somatic cell types and may also shed light on the mechanisms of ploidy maintenance.

  6. Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection.

    Science.gov (United States)

    Daetwyler, Hans D; Hayden, Matthew J; Spangenberg, German C; Hayes, Ben J

    2015-08-01

    Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations. Copyright © 2015 by the Genetics Society of America.

  7. Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives

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    Brown, Steven D.; Klingeman, Dawn M.; Johnson, Courtney M.; Clum, Alicia; Aerts, Andrea; Salamov, Asaf; Sharma, Aditi; Zane, Matthew; Barry, Kerrie; Grigoriev, Igor V.; Davison, Brian H.; Lynd, Lee R.; Gilna, Paul; Hau, Heidi; Hogsett, David A.; Froehlich, Allan C.

    2013-04-19

    Saccharomyces cerevisiae strain M3707 was isolated from a sample of commercial distillers yeast, and its genome sequence together with the genome sequences for the four derived haploid strains M3836, M3837, M3838, and M3839 has been determined. Yeasts have potential for consolidated bioprocessing (CBP) for biofuel production, and access to these genome sequences will facilitate their development.

  8. Multiplicity of genome equivalents in the radiation-resistant bacterium Micrococcus radiodurans.

    Science.gov (United States)

    Hansen, M T

    1978-01-01

    The complexity of the genome of Micrococcus radiodurans was determined to be (2.0 +/- 0.3) X 10(9) daltons by DNA renaturation kinetics. The number of genome equivalents of DNA per cell was calculated from the complexity and the content of DNA. A lower limit of four genome equivalents per cell was approached with decreasing growth rate. Thus, no haploid stage appeared to be realized in this organism. The replication time was estimated from the kinetics and amount of residual DNA synthesis after inhibiting initiation of new rounds of replication. From this, the redundancy of terminal genetic markers was calculated to vary with growth rate from four to approximately eight copies per cell. All genetic material, including the least abundant, is thus multiply represented in each cell. The potential significance of the maintenance in each cell of multiple gene copies is discussed in relation to the extreme radiation resistance of M. radiodurans. PMID:649572

  9. A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

    Science.gov (United States)

    Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

    2018-04-01

    We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. Copyright © 2018 by the Genetics Society of America.

  10. Strategies for implementing genomic selection in family-based aquaculture breeding schemes: double haploid sib test populations

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    Nirea Kahsay G

    2012-10-01

    Full Text Available Abstract Background Simulation studies have shown that accuracy and genetic gain are increased in genomic selection schemes compared to traditional aquaculture sib-based schemes. In genomic selection, accuracy of selection can be maximized by increasing the precision of the estimation of SNP effects and by maximizing the relationships between test sibs and candidate sibs. Another means of increasing the accuracy of the estimation of SNP effects is to create individuals in the test population with extreme genotypes. The latter approach was studied here with creation of double haploids and use of non-random mating designs. Methods Six alternative breeding schemes were simulated in which the design of the test population was varied: test sibs inherited maternal (Mat, paternal (Pat or a mixture of maternal and paternal (MatPat double haploid genomes or test sibs were obtained by maximum coancestry mating (MaxC, minimum coancestry mating (MinC, or random (RAND mating. Three thousand test sibs and 3000 candidate sibs were genotyped. The test sibs were recorded for a trait that could not be measured on the candidates and were used to estimate SNP effects. Selection was done by truncation on genome-wide estimated breeding values and 100 individuals were selected as parents each generation, equally divided between both sexes. Results Results showed a 7 to 19% increase in selection accuracy and a 6 to 22% increase in genetic gain in the MatPat scheme compared to the RAND scheme. These increases were greater with lower heritabilities. Among all other scenarios, i.e. Mat, Pat, MaxC, and MinC, no substantial differences in selection accuracy and genetic gain were observed. Conclusions In conclusion, a test population designed with a mixture of paternal and maternal double haploids, i.e. the MatPat scheme, increases substantially the accuracy of selection and genetic gain. This will be particularly interesting for traits that cannot be recorded on the

  11. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

    Science.gov (United States)

    Schneider, Valerie A; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A; Murphy, Terence D; Pruitt, Kim D; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T; Threadgold, Glen; Torrance, James; Wood, Jonathan M; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M; Durbin, Richard; Wilson, Richard K; Flicek, Paul; Eichler, Evan E; Church, Deanna M

    2017-05-01

    The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. © 2017 Schneider et al.; Published by Cold Spring Harbor Laboratory Press.

  12. Technical note: Equivalent genomic models with a residual polygenic effect.

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    Liu, Z; Goddard, M E; Hayes, B J; Reinhardt, F; Reents, R

    2016-03-01

    Routine genomic evaluations in animal breeding are usually based on either a BLUP with genomic relationship matrix (GBLUP) or single nucleotide polymorphism (SNP) BLUP model. For a multi-step genomic evaluation, these 2 alternative genomic models were proven to give equivalent predictions for genomic reference animals. The model equivalence was verified also for young genotyped animals without phenotypes. Due to incomplete linkage disequilibrium of SNP markers to genes or causal mutations responsible for genetic inheritance of quantitative traits, SNP markers cannot explain all the genetic variance. A residual polygenic effect is normally fitted in the genomic model to account for the incomplete linkage disequilibrium. In this study, we start by showing the proof that the multi-step GBLUP and SNP BLUP models are equivalent for the reference animals, when they have a residual polygenic effect included. Second, the equivalence of both multi-step genomic models with a residual polygenic effect was also verified for young genotyped animals without phenotypes. Additionally, we derived formulas to convert genomic estimated breeding values of the GBLUP model to its components, direct genomic values and residual polygenic effect. Third, we made a proof that the equivalence of these 2 genomic models with a residual polygenic effect holds also for single-step genomic evaluation. Both the single-step GBLUP and SNP BLUP models lead to equal prediction for genotyped animals with phenotypes (e.g., reference animals), as well as for (young) genotyped animals without phenotypes. Finally, these 2 single-step genomic models with a residual polygenic effect were proven to be equivalent for estimation of SNP effects, too. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  13. Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

    Science.gov (United States)

    Liu, Changqing; Bai, Chunyu; Guo, Yu; Liu, Dan; Lu, Taofeng; Li, Xiangchen; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

    2014-01-01

    Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger. PMID:24608928

  14. Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

    Directory of Open Access Journals (Sweden)

    Changqing Liu

    2014-03-01

    Full Text Available Bacterial artificial chromosome (BAC libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12, consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger.

  15. Characterization of in vitro haploid and doubled haploid Chrysanthemum morifolium plants via unfertilized ovule culture for phenotypical traits and DNA methylation pattern.

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    Haibin eWang

    2014-12-01

    Full Text Available Chrysanthemum is one of important ornamental species in the world. Its highly heterozygous state complicates molecular analysis, so it is of interest to derive haploid forms. A total of 2,579 non-fertilized chrysanthemum ovules pollinated by Argyranthemum frutescens were cultured in vitro to isolate haploid progeny. One single regenerant emerged from each of three of the 105 calli produced. Chromosome counts and microsatellite fingerprinting showed that only one of the regenerants was a true haploid. Nine doubled haploid derivatives were subsequently generated by colchicine treatment of 80 in vitro cultured haploid nodal segments. Morphological screening showed that the haploid plant was shorter than the doubled haploids, and developed smaller leaves, flowers and stomata. An in vitro pollen germination test showed that few of the haploid's pollen were able to germinate and those which did so were abnormal. Both the haploid and the doubled haploids produced yellow flowers, whereas those of the maternal parental cultivar were mauve. Methylation-sensitive amplification polymorphism (MSAP profiling was further used to detect alterations in cytosine methylation caused by the haploidization and/or the chromosome doubling processes. While 52.2% of the resulting amplified fragments were cytosine methylated in the maternal parent's genome, the corresponding proportions for the haploid's and doubled haploids' genomes were, respectively, 47.0% and 51.7%, demonstrating a reduction in global cytosine methylation caused by haploidization and a partial recovery following chromosome doubling.

  16. Haploid rice plants in mutation studies

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, S [Institute of Radiation Breeding, Ministry of Agriculture and Forestry, Ohmiya, Ibaraki-ken (Japan)

    1970-03-01

    Studies were made on chlorophyll-deficient sectors and diploid-like sectors in haploid rice plants exposed to chronic gamma irradiation, and on germinal mutations in diploid strains derived from the haploid plants. The induction and elimination of somatic mutations in haploid plants and the occurrence of drastic germinal mutations in diploid strains from haploid plants are discussed. (author)

  17. Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

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    Hong-Da Chen

    Full Text Available BACKGROUND: Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed. METHODS/PRINCIPAL FINDINGS: Here, we show that equivalent length, or L(e, a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(es of 865 complete chromosomes and found that they have nearly universal but (k-dependent values. The differences among the L(e of a chromosome and those of its coding and non-coding parts were found to be slight. CONCLUSIONS: We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative "point" mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (1-5 x 10(-3/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

  18. Induction of gynogenetic and androgenetic haploid and doubled haploid development in the brown trout (Salmo trutta Linnaeus 1758).

    Science.gov (United States)

    Michalik, O; Dobosz, S; Zalewski, T; Sapota, M; Ocalewicz, K

    2015-04-01

    Gynogenetic and androgenetic brown trout (Salmo trutta Linnaeus 1758) haploids (Hs) and doubled haploids (DHs) were produced in the present research. Haploid development was induced by radiation-induced genetic inactivation of spermatozoa (gynogenesis) or eggs (androgenesis) before insemination. To provide DHs, gynogenetic and androgenetic haploid zygotes were subjected to the high pressure shock to suppress the first mitotic cleavage. Among haploids, gynogenetic embryos were showing lower mortality when compared to the androgenetic embryos; however, most of them die before the first feeding stage. Gynogenetic doubled haploids provided in the course of the brown trout eggs activation performed by homologous and heterologous sperm (rainbow trout) were developing equally showing hatching rates of 14.76 ± 2.4% and 16.14 ± 2.90% and the survival rates at the first feeding stage of 10.48 ± 3.48% and 12.78 ± 2.18%, respectively. Significantly, lower survival rate was observed among androgenetic progenies from the diploid groups with only few specimens that survived to the first feeding stage. Cytogenetic survey showed that among embryos from the diploid variants of the research, only gynogenetic individuals possessed doubled sets of chromosomes. Thus, it is reasonable to assume that radiation employed for the genetic inactivation of the brown trout eggs misaligned mechanism responsible for the cell divisions and might have delayed or even arrested the first mitotic cleavage in the androgenetic brown trout zygotes. Moreover, protocol for the radiation-induced inactivation of the paternal and maternal genome should be adjusted as some of the cytogenetically surveyed gynogenetic and androgenetic embryos exhibited fragments of the irradiated chromosomes. © 2015 Blackwell Verlag GmbH.

  19. Production of haploids and doubled haploids in oil palm

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    Croxford Adam E

    2010-10-01

    Full Text Available Abstract Background Oil palm is the world's most productive oil-food crop despite yielding well below its theoretical maximum. This maximum could be approached with the introduction of elite F1 varieties. The development of such elite lines has thus far been prevented by difficulties in generating homozygous parental types for F1 generation. Results Here we present the first high-throughput screen to identify spontaneously-formed haploid (H and doubled haploid (DH palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences. Conclusions This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest.

  20. In vitro wheat haploid embryo production by wheat x maize cross system under different environmental conditions

    International Nuclear Information System (INIS)

    Khan, M.A.; Ahmad, J.

    2011-01-01

    Haploids are helpful in studies for inter genomic relationship, identifying molecular markers, reducing time period of varietal development and increasing efficiency of breeding program. In case of bread wheat (Triticum aestivum L.), wheat x maize cross system is the most successful system due to its higher efficiency, more haploid embryo production and low genetic specificity. The haploid embryo production is affected by many factors i.e. light, temperature, relative humidity and tiller culture media. A study was carried out comprising 25 genotypes of bread wheat for haploid embryo production using 100 mgL/sup -1/ 2,4-D, 40Gl/sup -1/ Sucrose and 8mlL/sup -1/ Sulphurous acid. Haploid embryo production was observed at various levels of environmental factors i.e. maize pollen collection temperature, time of pollination after tiller emasculation, light intensity and relative humidity during haploid seed formation. Maximum haploid embryo formation recorded was 9.52%. Best temperature observed for pollination was 21-26 degree C, optimum time duration for pollination was 24 hours after emasculation, light intensity was 10,000 Lux and relative humidity was 60-65% at 20-22 degree C. (author)

  1. Haploids in Conifer Species: Characterization and Chromosomal Integrity of a Maritime Pine Cell Line

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    José Antonio Cabezas

    2016-11-01

    Full Text Available Haploids are a valuable tool for genomic studies in higher plants, especially those with huge genome size and long juvenile periods, such as conifers. In these species, megagametophyte cultures have been widely used to obtain haploid callus and somatic embryogenic lines. One of the main problems associated with tissue culture is the potential genetic instability of the regenerants. Because of this, chromosomal stability of the callus and/or somatic embryos should also be assessed. To this end, chromosome counting, flow cytometry and genotyping using microsatellites have been reported. Here, we present an overview of the work done in conifers, with special emphasis on the production of a haploid cell line in maritime pine (Pinus pinaster L. and the use of a set of molecular markers, which includes Single Nucleotide Polymorphisms (SNPs and microsatellites or Single Sequence Repeats (SSRs, to validate chromosomal integrity confirming the presence of all chromosomic arms.

  2. Construction of a llama bacterial artificial chromosome library with approximately 9-fold genome equivalent coverage.

    Science.gov (United States)

    Airmet, K W; Hinckley, J D; Tree, L T; Moss, M; Blumell, S; Ulicny, K; Gustafson, A K; Weed, M; Theodosis, R; Lehnardt, M; Genho, J; Stevens, M R; Kooyman, D L

    2012-01-01

    The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be 2.4 × 10⁹ bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.

  3. Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens

    DEFF Research Database (Denmark)

    Timms, Richard T.; Menzies, Sam A.; Tchasovnikarova, Iva A.

    2016-01-01

    The application of forward genetic screens to cultured human cells represents a powerful method to study gene function. The repurposing of the bacterial CRISPR/Cas9 system provides an effective method to disrupt gene function in mammalian cells, and has been applied to genome-wide screens. Here, we...... compare the efficacy of genome-wide CRISPR/Cas9-mediated forward genetic screens versus gene-trap mutagenesis screens in haploid human cells, which represent the existing ‘gold standard’ method. This head-to-head comparison aimed to identify genes required for the endoplasmic reticulum....../3-associated disulphide reductase. Genome-wide CRISPR/Cas9-mediated screens together with haploid genetic screens provide a powerful addition to the forward genetic toolbox....

  4. Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia

    KAUST Repository

    Mojib, Nazia; Amad, Maan H.; Thimma, Manjula; Aldanondo, Naroa; Kumaran, Mande; Irigoien, Xabier

    2014-01-01

    The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue-pigmented organisms from the phylum Arthropoda, subclass Copepoda (Acartia fossae) and the phylum Chordata, class Appendicularia (Oikopleura dioica) in the Red Sea. Previous studies have shown that carotenoid–protein complexes are responsible for blue coloration in crustaceans. Therefore, we performed carotenoid metabolic profiling using both targeted and nontargeted (high-resolution mass spectrometry) approaches in four different blue-pigmented genera of copepods and one blue-pigmented species of appendicularia. Astaxanthin was found to be the principal carotenoid in all the species. The pathway analysis showed that all the species can synthesize astaxanthin from β-carotene, ingested from dietary sources, via 3-hydroxyechinenone, canthaxanthin, zeaxanthin, adonirubin or adonixanthin. Further, using de novo assembled transcriptome of blue A. fossae (subclass Copepoda), we identified highly expressed homologous β-carotene hydroxylase enzymes and putative carotenoid-binding proteins responsible for astaxanthin formation and the blue phenotype. In blue O. dioica (class Appendicularia), corresponding putative genes were identified from the reference genome. Collectively, our data provide molecular evidences for the bioconversion and accumulation of blue astaxanthin–protein complexes underpinning the observed ecological functional equivalence and adaptive convergence among neustonic mesozooplankton.

  5. Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia

    KAUST Repository

    Mojib, Nazia

    2014-06-01

    The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue-pigmented organisms from the phylum Arthropoda, subclass Copepoda (Acartia fossae) and the phylum Chordata, class Appendicularia (Oikopleura dioica) in the Red Sea. Previous studies have shown that carotenoid–protein complexes are responsible for blue coloration in crustaceans. Therefore, we performed carotenoid metabolic profiling using both targeted and nontargeted (high-resolution mass spectrometry) approaches in four different blue-pigmented genera of copepods and one blue-pigmented species of appendicularia. Astaxanthin was found to be the principal carotenoid in all the species. The pathway analysis showed that all the species can synthesize astaxanthin from β-carotene, ingested from dietary sources, via 3-hydroxyechinenone, canthaxanthin, zeaxanthin, adonirubin or adonixanthin. Further, using de novo assembled transcriptome of blue A. fossae (subclass Copepoda), we identified highly expressed homologous β-carotene hydroxylase enzymes and putative carotenoid-binding proteins responsible for astaxanthin formation and the blue phenotype. In blue O. dioica (class Appendicularia), corresponding putative genes were identified from the reference genome. Collectively, our data provide molecular evidences for the bioconversion and accumulation of blue astaxanthin–protein complexes underpinning the observed ecological functional equivalence and adaptive convergence among neustonic mesozooplankton.

  6. Genome size variation in the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme as determined by flow cytometry

    Science.gov (United States)

    Claire L Anderson; Thomas L Kubisiak; C Dana Nelson; Jason A Smith; John M Davis

    2010-01-01

    The genome size of the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme (Cqf) was determined by flow cytometric analysis of propidium iodide-stained, intact haploid pycniospores with haploid spores of two genetically well characterized fungal species, Sclerotinia sclerotiorum and Puccinia graminis f.sp. tritici, as size standards. The Cqf haploid genome...

  7. Qtl mapping of wheat doubled haploids for chlorophyll content and chlorophyll fluorescence kinetics under drought stress imposed at anthesis stage

    International Nuclear Information System (INIS)

    Ilyas, M.; Ilyas, N.; Arshad, M.; Kazi, A.G.

    2014-01-01

    Drought stress is one of the major environmental constraints to crop plants including wheat worldwide. Synthetic hexaploid can act as a vehicle for improving crop tolerance against biotic and abiotic stresses. Doubled haploid population consisting of one hundred and forty individuals derived from cross of Opata and SH223 was used in the present study to identify genomic regions associated with various quantitative attributes of physiological nature. Doubled haploid mapping population was phenotyped for chlorophyll content and chlorophyll fluorescence kinetics under control and drought stress imposed at anthesis stage. Genotyping of population was accomplished by utilizing two hundred and sixty one polymorphic Gaterslaben wheat microsatellites and Beltsville agriculture research center simple sequence repeats. Linkage map of doubled haploid population comprising of 19 linkage groups and covering map length of two thousands six hundred and twenty six (2626) cM was constructed using map maker software. Major and minor QTLs associated with quantitative traits were identified using QGene software. Major QTL for chlorophyll content (QTc.wwc-1B-S11) of doubled haploid mapping population under anthesis drought stress was mapped on chromosome 1B and explained 10.09 percent of phenotypic variation at LOD score of 5.5. Seven major and minor QTLs for PCFK of doubled haploids were identified on chromosome 1B, 7A and 7D under control and drought stress at anthesis stage. The identified QTLs are of prime importance for high resolution mapping in synthetic hexaploid wheat. Genomic synteny of doubled haploids was observed with rice chromosome 2, 4, 7 and maize chromosome 7 owing to occurrence of orthologous QTLs for chlorophyll content and chlorophyll fluorescence respectively. (author)

  8. Discrimination of haploid and diploid maize kernels via multispectral imaging

    DEFF Research Database (Denmark)

    De La Fuente, Gerald N.; Carstensen, Jens Michael; Adsetts Edberg Hansen, Michael

    2017-01-01

    sorting of haploids would increase the efficiency of DH line development. In this study, six inbred lines were crossed with the maternal haploid inducer ‘RWS/RWK-76’ and a sample of seed was sorted manually for each line. Using the VideometerLab 3 system, spectral imaging techniques were applied...

  9. Doubled haploid production in Flax (Linum usitatissimum L.).

    Science.gov (United States)

    Obert, Bohus; Zácková, Zuzana; Samaj, Jozef; Pretová, Anna

    2009-01-01

    There is a requirement of haploid and double haploid material and homozygous lines for cell culture studies and breeding in flax. Anther culture is currently the most successful method producing doubled haploid lines in flax. Recently, ovary culture was also described as a good source of doubled haploids. In this review we focus on tissue and plants regeneration using anther culture, and cultivation of ovaries containing unfertilized ovules. The effect of genotype, physiological status of donor plants, donor material pre-treatment and cultivation conditions for flax anthers and ovaries is discussed here. The process of plant regeneration from anther and ovary derived calli is also in the focus of this review. Attention is paid to the ploidy level of regenerated tissue and to the use of molecular markers for determining of gametic origin of flax plants derived from anther and ovary cultures. Finally, some future prospects on the use of doubled haploids in flax biotechnology are outlined here.

  10. Diploidization of cucumber (Cucumis sativus L. haploids by colchicine treatment

    Directory of Open Access Journals (Sweden)

    Vesselina Nikolova

    2014-01-01

    Full Text Available Haploid cucumber plants are totally infertile and do not undergo spontaneous diploidization. The use of haploids depends on the possibility of doubling the chromosome number and the obtaining of stable doubled haploids (DH. Four haploids of different genotypes propagated vegetatively were treated with colchicine in order to obtain DH. The following procedures were used: 1 apical shoot meristem treatment, 2 soaking of shoot explants, 3 placing of shoot explants on medium with colchicine. Plants of the C1 generation were evaluated in respect to morphological and cytological characters and fertility. The best result of 20.9% DH was obtained after repeated treatment of the meristem with colchicine. A large group of chimeras (28.5% was also distinguished as were haploids and tetraploids. DH plants were fertile and gave uniform progeny. Chimeras had a decreased fertility and showed disturbances in meiotic divisions.

  11. Near-haploid and low-hypodiploid acute lymphoblastic leukemia

    DEFF Research Database (Denmark)

    Safavi, Setareh; Paulsson, Kajsa

    2017-01-01

    Hypodiploidy leukemia (ALL) in both children and adults. It has long been clear by cytogenetic analyses, and recently confirmed by mutational profiling, that these cases may be further subdivided into 2 subtypes: near-haploid ALL...

  12. Chromosome length scaling in haploid, asexual reproduction

    International Nuclear Information System (INIS)

    Oliveira, P M C de

    2007-01-01

    We study the genetic behaviour of a population formed by haploid individuals which reproduce asexually. The genetic information for each individual is stored along a bit-string (or chromosome) with L bits, where 0-bits represent the wild allele and 1-bits correspond to harmful mutations. Each newborn inherits this chromosome from its parent with a few random mutations: on average a fixed number m of bits are flipped. Selection is implemented according to the number N of 1-bits counted along the individual's chromosome: the smaller N the higher the probability an individual has to survive a new time step. Such a population evolves, with births and deaths, and its genetic distribution becomes stabilized after sufficiently many generations have passed. The question we pose concerns the procedure of increasing L. The aim is to get the same distribution of genetic loads N/L among the equilibrated population, in spite of a larger L. Should we keep the same mutation rate m/L for different values of L? The answer is yes, which intuitively seems to be plausible. However, this conclusion is not trivial, according to our simulation results: the question also involves the population size

  13. Generation of genetically modified mice using CRISPR/Cas9 and haploid embryonic stem cell systems

    Directory of Open Access Journals (Sweden)

    Li-Fang JIN

    2016-07-01

    Full Text Available With the development of high-throughput sequencing technology in the post-genomic era, researchers have concentrated their efforts on elucidating the relationships between genes and their corresponding functions. Recently, important progress has been achieved in the generation of genetically modified mice based on CRISPR/Cas9 and haploid embryonic stem cell (haESC approaches, which provide new platforms for gene function analysis, human disease modeling, and gene therapy. Here, we review the CRISPR/Cas9 and haESC technology for the generation of genetically modified mice and discuss the key challenges in the application of these approaches.

  14. Verification and characterization of chromosome duplication in haploid maize.

    Science.gov (United States)

    de Oliveira Couto, E G; Resende Von Pinho, E V; Von Pinho, R G; Veiga, A D; de Carvalho, M R; de Oliveira Bustamante, F; Nascimento, M S

    2015-06-26

    Doubled haploid technology has been used by various private companies. However, information regarding chromosome duplication methodologies, particularly those concerning techniques used to identify duplication in cells, is limited. Thus, we analyzed and characterized artificially doubled haploids using microsatellites molecular markers, pollen viability, and flow cytometry techniques. Evaluated material was obtained using two different chromosome duplication protocols in maize seeds considered haploids, resulting from the cross between the haploid inducer line KEMS and 4 hybrids (GNS 3225, GNS 3032, GNS 3264, and DKB 393). Fourteen days after duplication, plant samples were collected and assessed by flow cytometry. Further, the plants were transplanted to a field, and samples were collected for DNA analyses using microsatellite markers. The tassels were collected during anthesis for pollen viability analyses. Haploid, diploid, and mixoploid individuals were detected using flow cytometry, demonstrating that this technique was efficient for identifying doubled haploids. The microsatellites markers were also efficient for confirming the ploidies preselected by flow cytometry and for identifying homozygous individuals. Pollen viability showed a significant difference between the evaluated ploidies when the Alexander and propionic-carmin stains were used. The viability rates between the plodies analyzed show potential for fertilization.

  15. Simple Meets Single: The Application of CRISPR/Cas9 in Haploid Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Zixi Yin

    2017-01-01

    Full Text Available The CRISPR/Cas9 system provides a powerful method for the genetic manipulation of the mammalian genome, allowing knockout of individual genes as well as the generation of genome-wide knockout cell libraries for genetic screening. However, the diploid status of most mammalian cells restricts the application of CRISPR/Cas9 in genetic screening. Mammalian haploid embryonic stem cells (haESCs have only one set of chromosomes per cell, avoiding the issue of heterozygous recessive mutations in diploid cells. Thus, the combination of haESCs and CRISPR/Cas9 facilitates the generation of genome-wide knockout cell libraries for genetic screening. Here, we review recent progress in CRISPR/Cas9 and haPSCs and discuss their applications in genetic screening.

  16. Fixation Probability in a Haploid-Diploid Population.

    Science.gov (United States)

    Bessho, Kazuhiro; Otto, Sarah P

    2017-01-01

    Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species. Copyright © 2017 by the Genetics Society of America.

  17. An analysis of radiation-induced damage in the spider mite. Relationship between mortality of haploid and diploid eggs in two successive generations

    International Nuclear Information System (INIS)

    Leenhouts, H.P.; Chadwick, K.H.

    1976-01-01

    Unfertilized females of the spider mite (Tetranychus urticae) produce only haploid eggs which develop into a haploid male. Fertilized females produce both haploid eggs (unfertilized), which develop into males, and diploid eggs (fertilized), which develop into females. Radiobiological experiments performed by A.M. Feldmann (Association Euratom-ITAL) made data available on the radiation-induced mortality of haploid and diploid eggs in the F 1 and F 2 generation following irradiation of either males or females with X rays or fast neutrons. The data have been analysed using the molecular theory of cell survival where it is assumed that DNA double strand breaks, induced randomly in the cell, are the critical radiation-induced lesions, which lead to cell death. Theoretical relationships are derived for the dose dependence of hatchability in haploid and diploid eggs in the first and second generations expressed as a function of the radiation damage in the parental genome. These theoretical relationships can be used to derive the inter-relationship between the different hatchabilities, and the results from the spider mite have been analysed using these considerations. It is concluded that the radiation-induced genetic damage arises from one type of initial lesion. The eventual radiobiological implications of this analysis are discussed, expecially with respect to the transmittance of radiation-induced genetic damage after low-level radiation. (author)

  18. Direct Differentiation of Human Pluripotent Stem Cells into Haploid Spermatogenic Cells

    Directory of Open Access Journals (Sweden)

    Charles A. Easley, IV

    2012-09-01

    Full Text Available Human embryonic stem cells (hESCs and induced pluripotent stem cells (hiPSCs have been shown to differentiate into primordial germ cells (PGCs but not into spermatogonia, haploid spermatocytes, or spermatids. Here, we show that hESCs and hiPSCs differentiate directly into advanced male germ cell lineages, including postmeiotic, spermatid-like cells, in vitro without genetic manipulation. Furthermore, our procedure mirrors spermatogenesis in vivo by differentiating PSCs into UTF1-, PLZF-, and CDH1-positive spermatogonia-like cells; HIWI- and HILI-positive spermatocyte-like cells; and haploid cells expressing acrosin, transition protein 1, and protamine 1 (proteins that are uniquely found in spermatids and/or sperm. These spermatids show uniparental genomic imprints similar to those of human sperm on two loci: H19 and IGF2. These results demonstrate that male PSCs have the ability to differentiate directly into advanced germ cell lineages and may represent a novel strategy for studying spermatogenesis in vitro.

  19. The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

    Science.gov (United States)

    Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

    2014-04-01

    Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

  20. Meiosis and Haploid Gametes in the Pathogen Trypanosoma brucei

    OpenAIRE

    Peacock, Lori; Bailey, Mick; Carrington, Mark; Gibson, Wendy

    2014-01-01

    Summary In eukaryote pathogens, sex is an important driving force in spreading genes for drug resistance, pathogenicity, and virulence [1]. For the parasitic trypanosomes that cause African sleeping sickness, mating occurs during transmission by the tsetse vector [2, 3] and involves meiosis [4], but haploid gametes have not yet been identified. Here, we show that meiosis is a normal part of development in the insect salivary glands for all subspecies of Trypanosoma brucei, including the human...

  1. The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

    Science.gov (United States)

    Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

    2016-06-03

    The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Equivalent Lagrangians

    International Nuclear Information System (INIS)

    Hojman, S.

    1982-01-01

    We present a review of the inverse problem of the Calculus of Variations, emphasizing the ambiguities which appear due to the existence of equivalent Lagrangians for a given classical system. In particular, we analyze the properties of equivalent Lagrangians in the multidimensional case, we study the conditions for the existence of a variational principle for (second as well as first order) equations of motion and their solutions, we consider the inverse problem of the Calculus of Variations for singular systems, we state the ambiguities which emerge in the relationship between symmetries and conserved quantities in the case of equivalent Lagrangians, we discuss the problems which appear in trying to quantize classical systems which have different equivalent Lagrangians, we describe the situation which arises in the study of equivalent Lagrangians in field theory and finally, we present some unsolved problems and discussion topics related to the content of this article. (author)

  3. Evaluasi keseragaaman, keragaman, dan kestabilan karakter agronomi galur-galur padi haploid ganda hasil kultur antera

    Directory of Open Access Journals (Sweden)

    PRIATNA SASMITA

    2011-05-01

    Full Text Available Sasmita P. 2011. Evaluasi keseragaman, keragaman, dan kestabilan karakter agronomi galur-galur padi haploid ganda hasil kultur antera. Bioteknologi 8: 10-17. Pembentukan galur haploid ganda dalam kultur antera bertujuan untuk mempercepat perolehan galur murni. Seleksi karakter yang diinginkan dapat dilakukan langsung terhadap progeni hasil kultur antera pada generasi awal. Percobaan ini bertujuan untuk mengetahui karakteristik agronomi, keseragaman, dan kestabilan galur haploid ganda, serta mendapatkan putatif galur-gallur haploid ganda sebagai bahan evaluasi lebih lanjut untuk mendapatkan galur harapan. Percobaan pertama menggunakan rancangan acak lengkap diulang lima kali. Perlakuannya aadalah 111 galur haploid ganda hasil kultur antera generasi pertama (DH1. Percobaan kedua menggunakan rancangan petak terpisah dengan perlakuan petak utama adalah galur haploid ganda hasil kultur antera dan perlakuan anak petaknya generasi galur haploid ganda kedua (DH2 hingga kelima (DDH5. Hasil percobaan menunjukkan bahwa setiap tanaman dalam galur yang sama memiliki karakter agronnomi seragam, sedangkan tanaman antar galur berbeda memiliki karakter agronomi beragam. Hasil evaluasi lebih lanjut terhadap tiga dari 111 galur haploid ganda yang berasal dari generasi kedua hingga kelima menunjukkan tidak terdapat perbedaan karakter antar generasi untuk setiap p galur yang sama. Hasil penelitian tersebut menunjukkan pula bahwa karakteristik agronomi galur haploid ganda stabil dari generasi ke generasi.

  4. Development of a doubled haploid system for wheat through wheat ...

    African Journals Online (AJOL)

    La variété de maïs Kelvedon glory, avait la meilleure réponse parmi les variétés des maïs. Des considérables différences variétales dans le rendement de production d'haploides étaient évidentes à la fois dans les variétés de blé et de maïs. Mots Clés: Plantes homozygènes, protocole de rendement, Tritium aestivum, Zea ...

  5. Meiosis and haploid gametes in the pathogen Trypanosoma brucei.

    Science.gov (United States)

    Peacock, Lori; Bailey, Mick; Carrington, Mark; Gibson, Wendy

    2014-01-20

    In eukaryote pathogens, sex is an important driving force in spreading genes for drug resistance, pathogenicity, and virulence. For the parasitic trypanosomes that cause African sleeping sickness, mating occurs during transmission by the tsetse vector and involves meiosis, but haploid gametes have not yet been identified. Here, we show that meiosis is a normal part of development in the insect salivary glands for all subspecies of Trypanosoma brucei, including the human pathogens. By observing insect-derived trypanosomes during the window of peak expression of meiosis-specific genes, we identified promastigote-like (PL) cells that interacted with each other via their flagella and underwent fusion, as visualized by the mixing of cytoplasmic red and green fluorescent proteins. PL cells had a short, wide body, a very long anterior flagellum, and either one or two kinetoplasts, but only the anterior kinetoplast was associated with the flagellum. Measurement of nuclear DNA contents showed that PL cells were haploid relative to diploid metacyclics. Trypanosomes are among the earliest diverging eukaryotes, and our results support the hypothesis that meiosis and sexual reproduction are ubiquitous in eukaryotes and likely to have been early innovations. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Genetical Studies On Haploid Production In Some Ornamental Plants

    International Nuclear Information System (INIS)

    MOSTAFA, M.A.M.

    2013-01-01

    Haploid are plants with a gametophytic chromosome number and doubled haploid are dihaploids that have undergone chromosome duplication. The production of haploid and doubled haploid (DHs) through gametic embryogenesis allows a single-step development of complete homozygous lines from heterozygous parents, shortening the time required to produce homozygous plants in comparison with the conventional breeding methods that employ several generations of selfing. The production of haploid and DHs provides a particularly attractive biotechnological tool, and the development of haploidy technology and protocols to produce homozygous plants has had a significant impact on agricultural systems. Nowadays, these bio technologies represent an integral part of the breeding programmes of many agronomically important crops. There are several available methods to obtain haploid and DHs, of which in vitro anther or isolated microspore culture are the most effective and widely used (Germana Maria 2011). Tissue culture techniques, particularly short-term culture procedures such as shoot-tip culture and regeneration from primary explants, have been proposed as methods for obtaining large numbers of plants identical to the plant used as an explant source( Evans et al., 1984). Nicotiana spp. are one of the most important commercial crops in the world ( Liu and Zhang, 2008). Nicotiana alata is member from family solanacea, it is ornamental plant and the diploid cells contains 18 chromosomes. Nitsch (1969) reported the first production of haploid plants through anther culture and regeneration of plants of Nicotiana alata, For these reasons they have been considered to suitable candidates for model species in somatic cell genetics research( Bourgin et al., 1979). Radiobiological studies on plant tissues in culture may provide information on the cell growth behavior, radiosensitivity and the induction of mutations. The radiosensitivity of plants and calli can be manifested mostly in three

  7. Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes.

    Science.gov (United States)

    Ezawa, Kiyoshi; Innan, Hideki

    2013-07-01

    The population genetic behavior of mutations in sperm genes is theoretically investigated. We modeled the processes at two levels. One is the standard population genetic process, in which the population allele frequencies change generation by generation, depending on the difference in selective advantages. The other is the sperm competition during each genetic transmission from one generation to the next generation. For the sperm competition process, we formulate the situation where a huge number of sperm with alleles A and B, produced by a single heterozygous male, compete to fertilize a single egg. This "minimal model" demonstrates that a very slight difference in sperm performance amounts to quite a large difference between the alleles' winning probabilities. By incorporating this effect of paternity-sharing sperm competition into the standard population genetic process, we show that fierce sperm competition can enhance the fixation probability of a mutation with a very small phenotypic effect at the single-sperm level, suggesting a contribution of sperm competition to rapid amino acid substitutions in haploid-expressed sperm genes. Considering recent genome-wide demonstrations that a substantial fraction of the mammalian sperm genes are haploid expressed, our model could provide a potential explanation of rapid evolution of sperm genes with a wide variety of functions (as long as they are expressed in the haploid phase). Another advantage of our model is that it is applicable to a wide range of species, irrespective of whether the species is externally fertilizing, polygamous, or monogamous. The theoretical result was applied to mammalian data to estimate the selection intensity on nonsynonymous mutations in sperm genes.

  8. The role of epistatic interactions underpinning resistance to parasitic Varroa mites in haploid honey bee (Apis mellifera) drones.

    Science.gov (United States)

    Conlon, Benjamin H; Frey, Eva; Rosenkranz, Peter; Locke, Barbara; Moritz, Robin F A; Routtu, Jarkko

    2018-06-01

    The Red Queen hypothesis predicts that host-parasite coevolutionary dynamics can select for host resistance through increased genetic diversity, recombination and evolutionary rates. However, in haplodiploid organisms such as the honeybee (Apis mellifera), models suggest the selective pressure is weaker than in diploids. Haplodiploid sex determination, found in A. mellifera, can allow deleterious recessive alleles to persist in the population through the diploid sex with negative effects predominantly expressed in the haploid sex. To overcome these negative effects in haploid genomes, epistatic interactions have been hypothesized to play an important role. Here, we use the interaction between A. mellifera and the parasitic mite Varroa destructor to test epistasis in the expression of resistance, through the inhibition of parasite reproduction, in haploid drones. We find novel loci on three chromosomes which explain over 45% of the resistance phenotype. Two of these loci interact only additively, suggesting their expression is independent of each other, but both loci interact epistatically with the third locus. With drone offspring inheriting only one copy of the queen's chromosomes, the drones will only possess one of two queen alleles throughout the years-long lifetime of the honeybee colony. Varroa, in comparison, completes its highly inbred reproductive cycle in a matter of weeks, allowing it to rapidly evolve resistance. Faced with the rapidly evolving Varroa, a diversity of pathways and epistatic interactions for the inhibition of Varroa reproduction could therefore provide a selective advantage to the high levels of recombination seen in A. mellifera. This allows for the remixing of phenotypes despite a fixed queen genotype. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

  9. Inter Simple Sequence Repeat DNA (ISSR) Polymorphism Utility in Haploid Nicotiana Alata Irradiated Plants for Finding Markers Associated with Gamma Irradiation and Salinity

    International Nuclear Information System (INIS)

    El-Fiki, A.; Adly, M.; El-Metabteb, G.

    2017-01-01

    Nicotiana alata is an ornamental plant. It is a member of family Solanasea. Tobacco (Nicotiana spp.) is one of the most important commercial crops in the world. Wild Nicotiana species, as a store house of genes for several diseases and pests, in addition to genes for several important phytochemicals and quality traits which are not present in cultivated varieties. Inter simple sequence repeat DNA (ISSR) analysis was used to determine the degree of genetic variation in treated haploid Nicotiana alata plants. Total genomic DNAs from different treated haploid plant lets were amplified using five specific primers. All primers were polymorphic. A total of 209 bands were amplified of which 135 (59.47%) polymorphic across the radiation treatments. Whilst, the level of polymorphism among the salinity treatments were 181 (85.6 %). Whereas, the polymorphism among the combined effects between gamma radiation doses and salinity concentrations were 283 ( 73.95% ). Treatments relationships were estimated through cluster analysis (UPGMA) based on ISSR data

  10. Exact Markov chains versus diffusion theory for haploid random mating.

    Science.gov (United States)

    Tyvand, Peder A; Thorvaldsen, Steinar

    2010-05-01

    Exact discrete Markov chains are applied to the Wright-Fisher model and the Moran model of haploid random mating. Selection and mutations are neglected. At each discrete value of time t there is a given number n of diploid monoecious organisms. The evolution of the population distribution is given in diffusion variables, to compare the two models of random mating with their common diffusion limit. Only the Moran model converges uniformly to the diffusion limit near the boundary. The Wright-Fisher model allows the population size to change with the generations. Diffusion theory tends to under-predict the loss of genetic information when a population enters a bottleneck. 2010 Elsevier Inc. All rights reserved.

  11. Improvement of ethanol-tolerance of haploid Saccharomyces diastaticus

    International Nuclear Information System (INIS)

    Song, S.H.; Kim, K.; Lee, M.W.

    1994-01-01

    Several mutation procedures have been compared to obtain an ethanol-tolerant Saccharomyces diastaticus strain secreting glucoamylase. These procedures include spontaneous mutation, EMS treatment, UV irradiation, and combination of EMS treatment and UV irradiation. All these methods were followed by adaptation of the yeast cells to gradually higher ethanol concentration. Among these procedures, the combined method of EMS treatment and UV irradiation gave the promising result, i.e. the ethanol tolerance of the yeast increased from 11.5%(v/v) to 14.0%(v/v). Respiratory deficient petite mutants of industrial and ethanol-tolerant yeast strains have been isolated and hybridized with haploid S. diastaticus strains. The resulting hybrids showed increased ethanol tolerance and starch-fermentability

  12. Techniques of radiation induced haploid breeding of wheat

    International Nuclear Information System (INIS)

    Xuan Pu; Xu Liyuan; Qu Shihong; Yu Guirong; Yin Chunrong; Yue Chunfang

    2000-01-01

    With the treatment of different doses of 60 Co γ-ray irradiation to F 1 hybrid seeds and donor plants from M 1 F 1 or M 2 F 2 , wheat anther culture was made based on the media of MW 14 and modified MS. A series of studies on the applied doses of radiation induction, low temperature treatment on donor spikes and calli, variable temperature induced incubation and yield of pollen callus and calli giving green plant lets, pollen plant lets control over summertime and pollen plant let transplantation were carried out in order to increase the efficiency of obtaining double haploid-pure diploid plant lets of wheat with stable heredity and propagation. Theses plant lets could be used directly in rapid breeding

  13. Mutagenesis and haploid culture for disease resistance in Brassica napus

    Energy Technology Data Exchange (ETDEWEB)

    MacDonald, M V; Ahmad, I; Ingram, D S [Botany School, University of Cambridge, Cambridge (United Kingdom)

    1990-01-01

    Full text: Most winter oilseed rape cultivars share parentage and therefore show little genetic diversity. There is no known resistance to Alternaria spp. in oilseed rape or in any related Brassica species. Experiments with tissue culture yielded only transient, non-genetic resistance. Therefore, mutagenesis may be used to generate heritable resistance to Alternaria spp. Gamma irradiation was applied to seeds of 'Bienvenue', secondary embryoids of cvs 'Primor' and 'Rapora', and buds of cvs 'Primor' and 'Ariana'. Isolated microspores from cv 'Ariana' and rapid cycling B. napus were also treated. The doses used ranged from 0-100 Gy for isolated microspores and buds, up to 600 Gy for seeds and 960 Gy for secondary embryoids. EMS was used to treat seeds of line WRG-42 (supplied by Nickersons RPB) and microspores of cv 'Bienvenue' and rapid cycling B. napus. Seeds were treated with up to 2.0% EMS for 0.2 h. before plating them on the culture medium. Seed irradiation up to 600 Gy did not reduce germination. M{sub 1} and M{sub 2} progenies were tested both in the laboratory and in field trials, and none of these were found to be resistant to Alternaria. However, considerable variation for other characters was observed. Haploid cultures from these plants were extremely difficult to regenerate, and for this reason no regenerant plants have been tested for resistance. For irradiated secondary embryoids the regeneration capacity decreased with increasing dose. Regenerated plants have been tested for resistance to Alternaria, but stable resistance was not observed. Haploid cultures were obtained from irradiated buds, using both anther and microspore culture. Low irradiation treatment was beneficial to developing embryoids. Some regenerants have been obtained from EMS treated microspores and seeds. Four plants have repeatedly given increased levels of resistance to A. brassicicola, and progenies are being tested to determine the genetic nature of the resistance. (author)

  14. Generation of doubled haploid transgenic wheat lines by microspore transformation.

    Directory of Open Access Journals (Sweden)

    Rhoda A T Brew-Appiah

    Full Text Available Microspores can be induced to develop homozygous doubled haploid plants in a single generation. In the present experiments androgenic microspores of wheat have been genetically transformed and developed into mature homozygous transgenic plants. Two different transformation techniques were investigated, one employing electroporation and the other co-cultivation with Agrobacterium tumefaciens. Different tissue culture and transfection conditions were tested on nine different wheat cultivars using four different constructs. A total of 19 fertile transformants in five genotypes from four market classes of common wheat were recovered by the two procedures. PCR followed by DNA sequencing of the products, Southern blot analyses and bio/histo-chemical and histological assays of the recombinant enzymes confirmed the presence of the transgenes in the T0 transformants and their stable inheritance in homozygous T1∶2 doubled haploid progenies. Several decisive factors determining the transformation and regeneration efficiency with the two procedures were determined: (i pretreatment of immature spikes with CuSO4 solution (500 mg/L at 4°C for 10 days; (ii electroporation of plasmid DNA in enlarged microspores by a single pulse of ∼375 V; (iii induction of microspores after transfection at 28°C in NPB-99 medium and regeneration at 26°C in MMS5 medium; (iv co-cultivation with Agrobacterium AGL-1 cells for transfer of plasmid T-DNA into microspores at day 0 for <24 hours; and (v elimination of AGL-1 cells after co-cultivation with timentin (200-400 mg/L.

  15. Mutagenesis and haploid culture for disease resistance in Brassica napus

    International Nuclear Information System (INIS)

    MacDonald, M.V.; Ahmad, I.; Ingram, D.S.

    1990-01-01

    Full text: Most winter oilseed rape cultivars share parentage and therefore show little genetic diversity. There is no known resistance to Alternaria spp. in oilseed rape or in any related Brassica species. Experiments with tissue culture yielded only transient, non-genetic resistance. Therefore, mutagenesis may be used to generate heritable resistance to Alternaria spp. Gamma irradiation was applied to seeds of 'Bienvenue', secondary embryoids of cvs 'Primor' and 'Rapora', and buds of cvs 'Primor' and 'Ariana'. Isolated microspores from cv 'Ariana' and rapid cycling B. napus were also treated. The doses used ranged from 0-100 Gy for isolated microspores and buds, up to 600 Gy for seeds and 960 Gy for secondary embryoids. EMS was used to treat seeds of line WRG-42 (supplied by Nickersons RPB) and microspores of cv 'Bienvenue' and rapid cycling B. napus. Seeds were treated with up to 2.0% EMS for 0.2 h. before plating them on the culture medium. Seed irradiation up to 600 Gy did not reduce germination. M 1 and M 2 progenies were tested both in the laboratory and in field trials, and none of these were found to be resistant to Alternaria. However, considerable variation for other characters was observed. Haploid cultures from these plants were extremely difficult to regenerate, and for this reason no regenerant plants have been tested for resistance. For irradiated secondary embryoids the regeneration capacity decreased with increasing dose. Regenerated plants have been tested for resistance to Alternaria, but stable resistance was not observed. Haploid cultures were obtained from irradiated buds, using both anther and microspore culture. Low irradiation treatment was beneficial to developing embryoids. Some regenerants have been obtained from EMS treated microspores and seeds. Four plants have repeatedly given increased levels of resistance to A. brassicicola, and progenies are being tested to determine the genetic nature of the resistance. (author)

  16. Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

    Science.gov (United States)

    Kovacevic, Lejla; Tambets, Kristiina; Ilumäe, Anne-Mai; Kushniarevich, Alena; Yunusbayev, Bayazit; Solnik, Anu; Bego, Tamer; Primorac, Dragan; Skaro, Vedrana; Leskovac, Andreja; Jakovski, Zlatko; Drobnic, Katja; Tolk, Helle-Viivi; Kovacevic, Sandra; Rudan, Pavao; Metspalu, Ene; Marjanovic, Damir

    2014-01-01

    Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula. PMID:25148043

  17. Standing at the gateway to Europe--the genetic structure of Western balkan populations based on autosomal and haploid markers.

    Science.gov (United States)

    Kovacevic, Lejla; Tambets, Kristiina; Ilumäe, Anne-Mai; Kushniarevich, Alena; Yunusbayev, Bayazit; Solnik, Anu; Bego, Tamer; Primorac, Dragan; Skaro, Vedrana; Leskovac, Andreja; Jakovski, Zlatko; Drobnic, Katja; Tolk, Helle-Viivi; Kovacevic, Sandra; Rudan, Pavao; Metspalu, Ene; Marjanovic, Damir

    2014-01-01

    Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.

  18. A review of methods for the production of haploids in seed plants

    International Nuclear Information System (INIS)

    Brunkener, L.

    1974-01-01

    This paper is a review of the methods which have been tried to produce haploids in seed plants. Because of their unique genetic constitution the haploids provide useful material for the study of various fundamental cytological and genetic problems. Thus the diploidization of haploids in conifers and subsequent intercrossing might allow the use of the same breeding technique as those which have been used with great success in maize breeding. Induced parthenogenesis in angiosperms has led to the formation of haploids in at least 25 genera but the number of plants obtained is generally too low for a practical utilization. The most promising method in angiosperms is in vitro cultivation of anthers which has hitherto yielded haploids in relatively large numbers in at least l5 genera but certainly can be applied with success in many more. Isolation of protoplasts or whole cells of diploid and haploid tissues and regeneration of entire plants from these protoplasts or cells have been accomplished in a few angiosperm genera. In gymnosperms all attempts to produce complete haploid plants have up to now failed. In this group there is possibly a relationship between polyembryonic seeds and the presence of small, haploid embryos. Therefore, the in vitro cultivation of small embryos of such seeds may result in the formation of independent haploid plants. In vitro cultivation of whole microsporangia or pollen has led to the production of calli in a few gymnosperm genera and in one case roots have even been induced. In some gymnosperms female gametophytes cultured on nutrient medium have yielded calli and in a few genera even root-like organs or small seedlings have arisen. (author)

  19. Gyrokinetic equivalence

    International Nuclear Information System (INIS)

    Parra, Felix I; Catto, Peter J

    2009-01-01

    We compare two different derivations of the gyrokinetic equation: the Hamiltonian approach in Dubin D H E et al (1983 Phys. Fluids 26 3524) and the recursive methodology in Parra F I and Catto P J (2008 Plasma Phys. Control. Fusion 50 065014). We prove that both approaches yield the same result at least to second order in a Larmor radius over macroscopic length expansion. There are subtle differences in the definitions of some of the functions that need to be taken into account to prove the equivalence.

  20. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  1. Haploid Barley from the Intergeneric Cross Hordeum vulgare x Psathyrostachys fragilis

    DEFF Research Database (Denmark)

    Bothmer, Roland; Jacobsen, Niels; Bagger Jørgensen, Rikke

    1984-01-01

    The intergeneric hybrid Hordeum vulgare x Psathyrostachys fragilis was fairly easily obtained. During each growing season the intermediate, perennial hybrid yielded haploid tillers of H. vulgare. Late in one season few, hybrid tillers headed. The morphology, cytology and enzymatic patterns...

  2. High production of wheat double haploids via anther culture

    Directory of Open Access Journals (Sweden)

    Kondić-Šipka Ankica

    2007-01-01

    Full Text Available Androgenous and regeneration abilities of 14 randomly selected F1 hybrids of wheat (Triticum aestivum L. were analyzed. Anthers were grown in vitro on a modified Potato-2 inductive medium. The hybrid NS111-95/Ana had the highest average values for androgenous capacity (33% and callus yield (119%, while the hybrid NS 92-250/Tiha had the lowest values for these traits (9 and 21%, respectively. Seven genotypes (50% had a frequency of green plants relative to the number of isolated anthers of over 10%, with the highest frequency of 21.3% (NS111-95/Sremica. This hybrid produced 12.8 doubled haploid (DH lines per spike used for isolation. In the other genotypes, the number of produced DH lines per spike ranged from 1 (30­Sc.Smoc.88-89/Hays-2 to 11.2 (NS111-95/Ana. As half of the randomly selected genotypes exhibited high green plant regeneration ability and a high production of DH lines per spike, it can be concluded that in vitro anther culture can be successfully used in breeding programs for rapid production of homozygous wheat lines.

  3. Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

    Directory of Open Access Journals (Sweden)

    Annette M. Bartkiewicz

    2018-05-01

    Full Text Available Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL for four phenotypic traits.

  4. Semiconservative quasispecies equations for polysomic genomes: The general case

    Science.gov (United States)

    Itan, Eran; Tannenbaum, Emmanuel

    2010-06-01

    This paper develops a formulation of the quasispecies equations appropriate for polysomic, semiconservatively replicating genomes. This paper is an extension of previous work on the subject, which considered the case of haploid genomes. Here, we develop a more general formulation of the quasispecies equations that is applicable to diploid and even polyploid genomes. Interestingly, with an appropriate classification of population fractions, we obtain a system of equations that is formally identical to the haploid case. As with the work for haploid genomes, we consider both random and immortal DNA strand chromosome segregation mechanisms. However, in contrast to the haploid case, we have found that an analytical solution for the mean fitness is considerably more difficult to obtain for the polyploid case. Accordingly, whereas for the haploid case we obtained expressions for the mean fitness for the case of an analog of the single-fitness-peak landscape for arbitrary lesion repair probabilities (thereby allowing for noncomplementary genomes), here we solve for the mean fitness for the restricted case of perfect lesion repair.

  5. Whole-genome sequencing of spermatocytic tumors provides insights into the mutational processes operating in the male germline

    DEFF Research Database (Denmark)

    Giannoulatou, Eleni; Maher, Geoffrey J; Ding, Zhihao

    2017-01-01

    Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover...

  6. Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells.

    Science.gov (United States)

    Tokunaga, Masahiro; Kokubu, Chikara; Maeda, Yusuke; Sese, Jun; Horie, Kyoji; Sugimoto, Nakaba; Kinoshita, Taroh; Yusa, Kosuke; Takeda, Junji

    2014-11-24

    Genome-wide saturation mutagenesis and subsequent phenotype-driven screening has been central to a comprehensive understanding of complex biological processes in classical model organisms such as flies, nematodes, and plants. The degree of "saturation" (i.e., the fraction of possible target genes identified) has been shown to be a critical parameter in determining all relevant genes involved in a biological function, without prior knowledge of their products. In mammalian model systems, however, the relatively large scale and labor intensity of experiments have hampered the achievement of actual saturation mutagenesis, especially for recessive traits that require biallelic mutations to manifest detectable phenotypes. By exploiting the recently established haploid mouse embryonic stem cells (ESCs), we present an implementation of almost complete saturation mutagenesis in a mammalian system. The haploid ESCs were mutagenized with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and processed for the screening of mutants defective in various steps of the glycosylphosphatidylinositol-anchor biosynthetic pathway. The resulting 114 independent mutant clones were characterized by a functional complementation assay, and were shown to be defective in any of 20 genes among all 22 known genes essential for this well-characterized pathway. Ten mutants were further validated by whole-exome sequencing. The predominant generation of single-nucleotide substitutions by ENU resulted in a gene mutation rate proportional to the length of the coding sequence, which facilitated the experimental design of saturation mutagenesis screening with the aid of computational simulation. Our study enables mammalian saturation mutagenesis to become a realistic proposition. Computational simulation, combined with a pilot mutagenesis experiment, could serve as a tool for the estimation of the number of genes essential for biological processes such as drug target pathways when a positive selection of

  7. The evolution of sex chromosomes in organisms with separate haploid sexes.

    Science.gov (United States)

    Immler, Simone; Otto, Sarah Perin

    2015-03-01

    The evolution of dimorphic sex chromosomes is driven largely by the evolution of reduced recombination and the subsequent accumulation of deleterious mutations. Although these processes are increasingly well understood in diploid organisms, the evolution of dimorphic sex chromosomes in haploid organisms (U/V) has been virtually unstudied theoretically. We analyze a model to investigate the evolution of linkage between fitness loci and the sex-determining region in U/V species. In a second step, we test how prone nonrecombining regions are to degeneration due to accumulation of deleterious mutations. Our modeling predicts that the decay of recombination on the sex chromosomes and the addition of strata via fusions will be just as much a part of the evolution of haploid sex chromosomes as in diploid sex chromosome systems. Reduced recombination is broadly favored, as long as there is some fitness difference between haploid males and females. The degeneration of the sex-determining region due to the accumulation of deleterious mutations is expected to be slower in haploid organisms because of the absence of masking. Nevertheless, balancing selection often drives greater differentiation between the U/V sex chromosomes than in X/Y and Z/W systems. We summarize empirical evidence for haploid sex chromosome evolution and discuss our predictions in light of these findings. © 2015 The Author(s).

  8. Use of intergeneric cross for production of doubled haploid wheat (triticum aestivum l.)

    International Nuclear Information System (INIS)

    Khan, M.A.; Shaukat, S.; Kashif, M.; Khan, A.S.

    2012-01-01

    The main purpose of conventional breeding or hybridisation is to bring about homozygosity, for which 6 to 7 years may be required. Wheat and maize crosses have proved to be more efficient in DH lines production than anther culture methods, because of its lower genetic specificity. Doubled haploid technique facilitates the development of homozygous plants within one generation. The system is developed through haploid production, followed by chromosome doubling, to produce homozygous plants in a single generation. For doubled haploid production method wheat and maize crossing system is better than anther culture and ovule culture because maize pollens are highly responsive and produce stable progeny population. Wheat is being used as female parent and maize as a male parent for the production of doubled haploid. Moreover, Silver Nitrate (AgNO/sub 3/) in tiller culture media can improve the frequency of haploid embryo production in this crossing system. Our result showed that DH production through wheat and maize crossing system was proved to be time saving (2 years) as compared to other conventional breeding methods (6 years). (author)

  9. A set of haploid strains available for genetic studies of Saccharomyces cerevisiae flor yeasts.

    Science.gov (United States)

    Coi, Anna Lisa; Legras, Jean-Luc; Zara, Giacomo; Dequin, Sylvie; Budroni, Marilena

    2016-09-01

    Flor yeasts of Saccharomyces cerevisiae have been extensively studied for biofilm formation, however the lack of specific haploid model strains has limited the application of genetic approaches such as gene knockout, allelic replacement and Quantitative Trait Locus mapping for the deciphering of the molecular basis of velum formation under biological ageing. The aim of this work was to construct a set of flor isogenic haploid strains easy to manipulate genetically. The analysis of the allelic variations at 12 minisatellite loci of 174 Saccharomyces cerevisiae strains allowed identifying three flor parental strains with different phylogenic positions. These strains were characterized for sporulation efficiency, growth on galactose, adherence to polystyrene, agar invasion, growth on wine and ability to develop a biofilm. Interestingly, the inability to grow on galactose was found associated with a frameshift in GAL4 gene that seems peculiar of flor strains. From these wild flor strains, isogenic haploid strains were constructed by deleting HO gene with a loxP-KanMX-loxP cassette followed by the removal of the kanamycin cassette. Haploid strains obtained were characterized for their phenotypic and genetic properties and compared with the parental strains. Preliminary results showed that the haploid strains represent new tools for genetic studies and breeding programs on biofilm formation. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes

    Directory of Open Access Journals (Sweden)

    María Arriba

    2017-01-01

    Full Text Available AIM: To investigate whether chromosomal instability (CIN is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability and CIMP (CpG island methylator phenotype in early-onset colorectal cancer (EOCRC. METHODS: Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis were analyzed by array comparative genomic hybridization (aCGH, in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs and the MSI/CIMP condition in EOCRC. RESULTS: Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B and four secondary clusters (A1, A2, B3, B4. The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC, which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected particular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS: Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.

  11. Efficiency of anther culture technique in the production of wheat double haploids

    Directory of Open Access Journals (Sweden)

    Kondić-Špika Ankica Đ.

    2008-01-01

    Full Text Available The objective of the study was to investigate efficiency of anther culture in the production of spontaneous double haploids from randomly selected heterozygous genotypes of wheat (Triticum aestivum L.. Anthers of 20 F1 wheat combinations were grown in vitro on a modified Potato-2 medium. All of the examined genotypes have shown the ability to produce pollen calluses as well as to regenerate green plants. On average for the whole experiment material, 47.2 calluses were produced per 100 cultured anthers. The green plant regeneration ranged from 0.8 to 13.4 green plants per spike, with an overall mean of 5.8. From the total of 582 regenerated green plants, 47.9% (279 were spontaneous double haploids. The final average yield from the study was 2.8 double haploids per spike.

  12. Segregation distortion in F2 and doubled haploid populations of ...

    Indian Academy of Sciences (India)

    2Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane 690-8504, Japan. 3Institute of the Society .... population of 212 DH lines was developed through anther culture of the F1 ... 2001), and 10-base random primers (Operon Technolo- ... tific researches (public data in the Rice Genome Project,.

  13. Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter.

    Science.gov (United States)

    Duewer, David L; Kline, Margaret C; Romsos, Erica L; Toman, Blaza

    2018-05-01

    The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI). Unlike values assigned using conventional relationships between ultraviolet absorbance and DNA mass concentration, entity-based ddPCR measurements are expected to be stable over time. However, the forensic community expects DNA quantity to be stated in terms of mass concentration rather than entity concentration. The transformation can be accomplished given SI-traceable values and uncertainties for the number of nucleotide bases per human haploid genome equivalent (HHGE) and the average molar mass of a nucleotide monomer in the DNA polymer. This report presents the considerations required to establish the metrological traceability of ddPCR-based mass concentration estimates of human nuclear DNA. Graphical abstract The roots of metrological traceability for human nuclear DNA mass concentration results. Values for the factors in blue must be established experimentally. Values for the factors in red have been established from authoritative source materials. HHGE stands for "haploid human genome equivalent"; there are two HHGE per diploid human genome.

  14. Genetic control of the development of the haploid generation in Oenothera

    Directory of Open Access Journals (Sweden)

    Cornelia Harte

    2014-01-01

    Full Text Available The haploid generation of higher plants has to be considered in its own individuality. Special experimental designs are needed to investigate the developmental processes of the male and female gametophytes between meiosis and fertilization. Experiments on Oenothera demonstrate the existence of genes, which action can be described as influencing the competition between meiospores or between gametophytes, or as interaction between different individuals, the gametophytic-gametophytic and gametophytic-sporophytic incompatibility. The development of the haploid generation is regulated by genes. Some of these genes are active only in this phase of the life cycle.

  15. Genetic Diversity in Haploid Nicotiana alata Induced by Gamma Irradiation, Salt Tolerance and Detection of These Differences by RAPD

    Directory of Open Access Journals (Sweden)

    Ayman EL-FIKI

    2016-03-01

    Full Text Available Haploid plants of Nicotiana alata were cultured in vitro on MS medium with IAA + KIN. The resulting plantlets were irradiated using gamma radiation doses of 10, 15, 20 and 25 Gy. Single node pieces were cut and transferred onto fresh MS medium. Gamma radiation doses caused the death of 9% and up to 28% of explants. NaCl concentrations caused the death of 8% up to 36% of explants, while the combined effect between gamma radiation doses and salinity had an impact suffused on the percentage of survival. The combined effect of gamma radiation doses 20 Gy and 25 Gy on NaCl concentrations of 100, 150 and 200 mM were deadly. Even more, the combined effect of gamma radiation doses and salinity had a severe negative impact on both the proline content and total soluble protein. Random amplified polymorphic DNA (RAPD analysis was used to determine the degree of genetic variation in treated haploid Nicotiana alata plants. Total genomic DNAs from different haploid plantlets treated were amplified using five arbitrary primers. Two hundred and seventy bands were detected from plantlets irradiated with doses of 15, 20 and 25 Gy, with polymorphic band number 226 (83.7%. The total number of bands resulted from plant grew on 150 mM and 200 mM NaCl were 260 bands with polymorphic bands 185 (85.6%. However, the total number of bands produced from combined effects between gamma rays and salinity (20 Gy X 50 mM NaCl, 20 Gy X 100 mM NaCl and 25 Gy X 50 mM NaCl were 270, with polymorphic band number 231 (85.5%. High similarity between treatments was revealed. Treatments relationships were estimated through cluster analysis (UPGMA based on RAPD data.

  16. Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones.

    Science.gov (United States)

    Clément, D; Lanaud, C; Sabau, X; Fouet, O; Le Cunff, L; Ruiz, E; Risterucci, A M; Glaszmann, J C; Piffanelli, P

    2004-05-01

    We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

  17. In vitro selection of rape variants resistant to oxalic acid using haploid stem apexes

    International Nuclear Information System (INIS)

    Wang Yifei; Huang Jianhua; Lu Ruiju; Sun Yuefang; Zhou Runmei; Zhou Zhijiang; Xie Zhujie; Liu Chenghong

    2002-01-01

    Mutagenic treatment was made of the haploid stem apexes rape strain '9841' and '9885' with Pingyangmycin. As a result of positive selection with oxalic acid providing selection pressure, variants with significantly higher tolerance to oxalic acid than the original ones were obtained. 3 germplasm with significantly higher resistance to Sclerotinia sclerotiorum than cultivar Hu You 12 were selected from field test

  18. Reduced Self-Diploidization and Improved Survival of Semi-cloned Mice Produced from Androgenetic Haploid Embryonic Stem Cells through Overexpression of Dnmt3b

    Directory of Open Access Journals (Sweden)

    Wenteng He

    2018-02-01

    Full Text Available Summary: Androgenetic haploid embryonic stem cells (AG-haESCs hold great promise for exploring gene functions and generating gene-edited semi-cloned (SC mice. However, the high incidence of self-diploidization and low efficiency of SC mouse production are major obstacles preventing widespread use of these cells. Moreover, although SC mice generation could be greatly improved by knocking out the differentially methylated regions of two imprinted genes, 50% of the SC mice did not survive into adulthood. Here, we found that the genome-wide DNA methylation level in AG-haESCs is extremely low. Subsequently, downregulation of both de novo methyltransferase Dnmt3b and other methylation-related genes was determined to be responsible for DNA hypomethylation. We further demonstrated that ectopic expression of Dnmt3b in AG-haESCs could effectively improve DNA methylation level, and the high incidence of self-diploidization could be markedly rescued. More importantly, the developmental potential of SC embryos was improved, and most SC mice could survive into adulthood. : Ectopic expression of Dnmt3b could rescue DNA methylation level in repetitive sequences of hypomethylated AG-haESCs, suppress high incidence of self-diploidization, and promote developmental potential of SC embryos, and most SC mice could survive into adulthood. Keywords: androgenetic haploid embryonic stem cells, self-diploidization, semi-cloned mice, DNA methylation, Dnmt3b

  19. Survival and DNA repair in ultraviolet-irradiated haploid and diploid cultured frog cells

    International Nuclear Information System (INIS)

    Freed, J.J.; Hoess, R.H.; Angelosanto, F.A.; Massey, H.C. Jr.

    1979-01-01

    Survival and repair of DNA following ultraviolet (254-nm) radiation have been investigated in ICR 2A, a cultured cell line from haploid embryos of the grassfrog, Rana pipiens. Survival curves from cells recovering in the dark gave mean lethal dose value (D 0 ) in the range 1.5-1.7 Jm -2 for both haploid and diploid cell stocks. The only significant difference observed between haploids and diploids was in the extent of the shoulder at low fluence (Dsub(q)), the value for exponentially multiplying diploid cells (3.0 Jm -2 ) being higher than that found for haploids (1.2 Jm -2 ). Irradiation of cultures reversibly blocked in the G1 phase of the cell cycle gave survival-curve coefficients indistinguishable between haploids and diploids. Post-irradiation exposure to visible light restored colony-forming capacity and removed chromatographically estimated pyrimidine dimers from DNA at the same rates. After fluences killing 90% of the cells, complete restoration of survival was obtained after 60-min exposure to 500 foot-candles, indicating that in this range lethality is entirely photoreversible and therefore attributable to pyrimidine dimers in DNA. Dimer removal required illumination following ultraviolet exposure, intact cells and physiological temperature, implying that the photoreversal involved DNA photolyase activity. Excision-repair capacity was slight, since no loss of dimers could be detected chromoatographically during up to 48 h incubation in the dark and since autoradiographically detected 'unscheduled DNA synthesis' was limited to a 2-fold increase saturated at 10 Jm -2 . These properties make ICR 2A frog cells useful to explore how DNA-repair pathways influence mutant yield. (Auth.)

  20. Meiosis Drives Extraordinary Genome Plasticity in the Haploid Fungal Plant Pathogen Mycosphaerella Graminicola

    Science.gov (United States)

    Meiosis in the plant-pathogenic fungus Mycosphaerella graminicola results in eight ascospores due to a mitotic division following the two meiotic divisions. The transient diploid phase allows for recombination among homologous chromosomes. However, some chromosomes of M. graminicola lack homologs an...

  1. Politico-economic equivalence

    DEFF Research Database (Denmark)

    Gonzalez Eiras, Martin; Niepelt, Dirk

    2015-01-01

    Traditional "economic equivalence'' results, like the Ricardian equivalence proposition, define equivalence classes over exogenous policies. We derive "politico-economic equivalence" conditions that apply in environments where policy is endogenous and chosen sequentially. A policy regime and a st......Traditional "economic equivalence'' results, like the Ricardian equivalence proposition, define equivalence classes over exogenous policies. We derive "politico-economic equivalence" conditions that apply in environments where policy is endogenous and chosen sequentially. A policy regime...... their use in the context of several applications, relating to social security reform, tax-smoothing policies and measures to correct externalities....

  2. Global gene transcription patterns in in vitro-cultured fertilized embryos and diploid and haploid murine parthenotes

    International Nuclear Information System (INIS)

    Cui Xiangshun; Li Xingyu; Kim, Nam-Hyung

    2007-01-01

    To gain insights into the roles the paternal genome and chromosome number play in pre-implantation development, we cultured fertilized embryos and diploid and haploid parthenotes (DPs and HPs, respectively), and compared their development and gene expression patterns. The DPs and fertilized embryos did not differ in developmental ability but HPs development was slower and characterized by impaired compaction and blastocoel formation. Microarray analysis revealed that fertilized blastocysts expressed several genes at higher levels than DP blastocysts; these included the Y-chromosome-specific gene eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked (Eif2s3y) and the imprinting gene U2 small nuclear ribonucleoprotein auxiliary factor 1, related sequence 1 (U2af1-rs1). We also found that when DPs and HPs were both harvested at 44 and 58 h of culture, they differed in the expression of 38 and 665 genes, respectively. However, when DPs and HPs were harvested at the midpoints of 4-cell stage (44 and 49 h, respectively), no differences in expression was observed. Similarly, when the DPs and HPs were harvested when they became blastocysts (102 and 138 h, respectively), only 15 genes showed disparate expression. These results suggest that while transcripts needed for early development are delayed in HPs, it does progress sufficiently for the generation of the various developmental stages despite the lack of genetic components

  3. Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

    Science.gov (United States)

    2009-01-01

    Background Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38,000 expressed sequence tags from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism. Results The haploid and diploid transcriptomes showed a dramatic differentiation, with approximately 20% greater transcriptome richness in diploid cells than in haploid cells and only ≤ 50% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog. Conclusions This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined. PMID:19832986

  4. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

    Directory of Open Access Journals (Sweden)

    Kudrna David

    2011-03-01

    Full Text Available Abstract Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1 digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb to 157 Kb (Eg_Ba, very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×, contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae

  5. A haploid genetic screen identifies the G1/S regulatory machinery as a determinant of Wee1 inhibitor sensitivity.

    Science.gov (United States)

    Heijink, Anne Margriet; Blomen, Vincent A; Bisteau, Xavier; Degener, Fabian; Matsushita, Felipe Yu; Kaldis, Philipp; Foijer, Floris; van Vugt, Marcel A T M

    2015-12-08

    The Wee1 cell cycle checkpoint kinase prevents premature mitotic entry by inhibiting cyclin-dependent kinases. Chemical inhibitors of Wee1 are currently being tested clinically as targeted anticancer drugs. Wee1 inhibition is thought to be preferentially cytotoxic in p53-defective cancer cells. However, TP53 mutant cancers do not respond consistently to Wee1 inhibitor treatment, indicating the existence of genetic determinants of Wee1 inhibitor sensitivity other than TP53 status. To optimally facilitate patient selection for Wee1 inhibition and uncover potential resistance mechanisms, identification of these currently unknown genes is necessary. The aim of this study was therefore to identify gene mutations that determine Wee1 inhibitor sensitivity. We performed a genome-wide unbiased functional genetic screen in TP53 mutant near-haploid KBM-7 cells using gene-trap insertional mutagenesis. Insertion site mapping of cells that survived long-term Wee1 inhibition revealed enrichment of G1/S regulatory genes, including SKP2, CUL1, and CDK2. Stable depletion of SKP2, CUL1, or CDK2 or chemical Cdk2 inhibition rescued the γ-H2AX induction and abrogation of G2 phase as induced by Wee1 inhibition in breast and ovarian cancer cell lines. Remarkably, live cell imaging showed that depletion of SKP2, CUL1, or CDK2 did not rescue the Wee1 inhibition-induced karyokinesis and cytokinesis defects. These data indicate that the activity of the DNA replication machinery, beyond TP53 mutation status, determines Wee1 inhibitor sensitivity, and could serve as a selection criterion for Wee1-inhibitor eligible patients. Conversely, loss of the identified S-phase genes could serve as a mechanism of acquired resistance, which goes along with development of severe genomic instability.

  6. On the effect of certain mutations on the radiosensitivity of haploid and diploid yeast cells

    International Nuclear Information System (INIS)

    Sokurova, E.N.; Korogodin, V.I.

    1978-01-01

    Mutation ade 1-6 in haploid cell Saccharomyces cerevisiae increases half as much against radioresistance of cells. Diploid cells lacking in adenine, homozygous by ade 1-6 mutation, are nearly twice as radiosensitive as prototrophic cells. Hence ade 1-6 mutation increases radioresistance of haploid cells and decreases that of diplois. These changes in radioresistance are not connected with variations in the extrapolation number of survival curve, the ability of cells to recover from radiation damages upon cultivation in an innutrient medium, and with the inactivation form ratio. Lack of adenine influences the radioresistance of diploid yeast irrespective of whether it is or it is not affected by homo- or heterozygosity by the locus of mating type

  7. Influence of time of auxin application on wheat haploid embrio formation

    Directory of Open Access Journals (Sweden)

    Prodanović Slaven

    2005-01-01

    Full Text Available A hybrid interspecies zygote appears after crosses between wheat and maize Zygote derived after usual self-fertilization in wheat is dividing by mitotic divisions into embryo. However, interspecies zygote aborts soon. Auxin treatment is widely used to promote its development. Growth hormones auxins have stimulative ortoxic effects on plant tissue sin relation to its concentration and the time of application. In this paper the effect of time of auxin dicamba application on embryo in wheat x maize crosses was investigated. Chromosomes of pollen donor parent are eliminated quickly in cells of such embryos and they become haploid. It was concluded that for the production of haploid embryos the best time for auxin application is one day after pollination with maize.

  8. Cellular heredity in haploid cultures of somatic cells, March 1968-April 1981. Final report

    International Nuclear Information System (INIS)

    Freed, J.J.

    1982-03-01

    An account is given of the development and application to cell-culture genetics of unique haploid cell lines from frog embryo developed in this laboratory. Since 1968, the main aim of this project has been to develop the haploid cell system for studies of mutagenesis in culture, particularly by ultraviolet radiation. In the course of this work we isolated chromosomally stable cell lines, derived and characterized a number of variants, and adapted cell hybridization and other methods to this material. Particular emphasis was placed on ultraviolet photobiology, including studies of cell survival, mutagenesis, and pathways of repair of uv-damaged DNA. Although at present less widely used for genetic experiments than mammalian cell lines, the frog cells offer the advantages of authentic haploidy and a favorable repertory of DNA repair pathways for study of uv mutagenesis

  9. Mutation induction in haploid yeast after split-dose radiation-exposure. Pt. 1

    International Nuclear Information System (INIS)

    Schenk, K.; Zoelzer, F.; Kiefer, J.

    1989-01-01

    Mutation induction was investigated in wild-type haploid yeast Saccharomyces cerevisiae after split-dose UV-irradiation. Cells were exposed to fractionated 254 nm-UV-doses separated by intervals from 0 to 6 h with incubation either on non-nutrient or nutrient agar between. The test parameter was resistance to canavanine. If modifications of sensitivity due to incubation are appropriately taken into account there is no change of mutation frequency. (orig.)

  10. Stimulating effect of gamma radiation on haploid wheat production through microscope over co-culture system

    International Nuclear Information System (INIS)

    Naseri, M.; Rahimi, M.; Faramarz, M.

    2004-01-01

    Haploid production focuses on low plant regeneration in some wheat genotypes. Haploid application gamma ray as an electromagnetic ray has ionizing properties which can produce ions when passing through biological matter. It can produce genetic variation therefore, is applied in crop and ornamental improvement to enhance agronomic traits. The most important changes caused by gamma radiation is in DNA structure existing in the nucleus of cell. The desirable agronomic changes then will be passed on through generations. Another property of gamma ray can be it's stimulating effect which is the aim in this investigation. Microspore-overy co-culture of wheat along with application of low doses of gamma radiation 2,3 and 4 Gy as absorbing doses were implemented with the aim to evaluate wheat haploid production. Modified Morashig and Skoog medium was used as induction medium and 190-2 medium for regeneration. Two winter and two spring wheat cultivars were used as genetic material. Low doses of gamma radiation simulated microspore cell division and produced more calli relative to non-irradiated microspores only in winter type wheats. In microspore overy co-culture, filtered microspores were centrifuged and then plated in Petri dishes containing MMS+500 mg/I glutamine with 25 overies

  11. Effects of gamma irradiation of pollen on parthenogenetic haploid production in muskmelon (Cucumis melo L.)

    International Nuclear Information System (INIS)

    Cuny, F.; Grotte, M.; Dumas de Vaulx, R.; Rieu, A.

    1993-01-01

    The effects of increasing gamma ray exposures on muskmelon pollen of the Védrantais genotype were evaluated after autofertilization and hybridization with the F1.G1 genotype. Regardless of doses of between 0.15 and 1.6 kGy, fruit set and number of seeds per fruit were comparable to those of the control. The pollen tube from pollen irradiated with up to 2.5 kGy grew in styles and reached the ovules. When pollen was cultivated in vitro, relatively high doses of irradiation (1.6 kGy) were needed to reduce the level of germination. Radiation-induced changes in the generative nucleus led to the formation of two chromosomally unbalanced sperm cells (as indicated by the appearance of morphological dimorphism) which induced parthenogenetic development of the egg to form a haploid embryo. Haploid embryo production by gamma-irradiated pollen was genotype dependent. For exposures of between 0.15 and 2.5 kGy, the production of embryos was the same, about 3.4%; a maximum of 70% of these embryos placed in a specific culture medium produced haploid plants. The ploidy of the plantlets in vitro was determined by flow cytometry. No aneuploidy was detected. All resulting plants exhibited normal phenotypes. (author) [fr

  12. Characters that differ between diploid and haploid honey bee (Apis mellifera) drones.

    Science.gov (United States)

    Herrmann, Matthias; Trenzcek, Tina; Fahrenhorst, Hartmut; Engels, Wolf

    2005-12-30

    Diploid males have long been considered a curiosity contradictory to the haplo-diploid mode of sex determination in the Hymenoptera. In Apis mellifera, 'false' diploid male larvae are eliminated by worker cannibalism immediately after hatching. A 'cannibalism substance' produced by diploid drone larvae to induce worker-assisted suicide has been hypothesized, but it has never been detected. Diploid drones are only removed some hours after hatching. Older larvae are evidently not regarded as 'false males' and instead are regularly nursed by the brood-attending worker bees. As the pheromonal cues presumably are located on the surface of newly hatched bee larvae, we extracted the cuticular secretions and analyzed their chemical composition by gas chromatograph-mass spectrometry (GC-MS) analyses. Larvae were sexed and then reared in vitro for up to three days. The GC-MS pattern that was obtained, with alkanes as the major compounds, was compared between diploid and haploid drone larvae. We also examined some physical parameters of adult drones. There was no difference between diploid and haploid males in their weight at the day of emergence. The diploid adult drones had fewer wing hooks and smaller testes. The sperm DNA content was 0.30 and 0.15 pg per nucleus, giving an exact 2:1 ratio for the gametocytes of diploid and haploid drones, respectively. Vitellogenin was found in the hemolymph of both types of imaginal drones at 5 to 6 days, with a significantly lower titer in the diploids.

  13. Study on the in vitro culture of cut plants in wheat haploid embryo induction by a wheat × maize cross

    Institute of Scientific and Technical Information of China (English)

    Jian GU; Kun LIU; Shaoxiang LI; Yuxian TIAN; Hexian YANG; Mujun YANG

    2008-01-01

    The wheat × maize system is one of the most effective ways to produce haploids in wheat. Whether and how it could be successfully applied in practical breeding mostly depends upon the efficiency of haploid embryo pro-duction. To perfect the protocols of haploid embryo induc-tion, the efficiency of haploid embryo production between in vitro culture of cut plant and intact plant growth for hybrid spikes with two F1 wheat hybrids and two maize varieties was compared. Effects of different cutting plant times and formulas of nutrient solutions for cut plant cul-ture on haploid embryo formation were also studied. Results indicated that the embryo rate of in vitro culture was 3.29 times that of intact plant growth, with the figures of 31.6% vs 9.6%, respectively. The optimal time for cut plant culture was 24 h after pollination. Formulas of nutri-ent solutions significantly affected the efficiency of haploid embryo induction. With an embryo rate of 0-35.5%, add-could raise the caryopsis and embryo rates. According to this study, the best medium for cut plant culture was: phate, with which a caryopsis rate of 95% and an embryo rate of about 30% could be obtained.

  14. Diploid, but not haploid, human embryonic stem cells can be derived from microsurgically repaired tripronuclear human zygotes

    Science.gov (United States)

    Fan, Yong; Li, Rong; Huang, Jin; Yu, Yang; Qiao, Jie

    2013-01-01

    Human embryonic stem cells have shown tremendous potential in regenerative medicine, and the recent progress in haploid embryonic stem cells provides new insights for future applications of embryonic stem cells. Disruption of normal fertilized embryos remains controversial; thus, the development of a new source for human embryonic stem cells is important for their usefulness. Here, we investigated the feasibility of haploid and diploid embryo reconstruction and embryonic stem cell derivation using microsurgically repaired tripronuclear human zygotes. Diploid and haploid zygotes were successfully reconstructed, but a large proportion of them still had a tripolar spindle assembly. The reconstructed embryos developed to the blastocyst stage, although the loss of chromosomes was observed in these zygotes. Finally, triploid and diploid human embryonic stem cells were derived from tripronuclear and reconstructed zygotes (from which only one pronucleus was removed), but haploid human embryonic stem cells were not successfully derived from the reconstructed zygotes when two pronuclei were removed. Both triploid and diploid human embryonic stem cells showed the general characteristics of human embryonic stem cells. These results indicate that the lower embryo quality resulting from abnormal spindle assembly contributed to the failure of the haploid embryonic stem cell derivation. However, the successful derivation of diploid embryonic stem cells demonstrated that microsurgical tripronuclear zygotes are an alternative source of human embryonic stem cells. In the future, improving spindle assembly will facilitate the application of triploid zygotes to the field of haploid embryonic stem cells. PMID:23255130

  15. Schrödinger’s Cheshire Cat: Are Haploid Emiliania huxleyi Cells Resistant to Viral Infection or Not?

    Directory of Open Access Journals (Sweden)

    Gideon J. Mordecai

    2017-03-01

    Full Text Available Emiliania huxleyi is the main calcite producer on Earth and is routinely infected by a virus (EhV; a double stranded DNA (dsDNA virus belonging to the family Phycodnaviridae. E. huxleyi exhibits a haplodiploid life cycle; the calcified diploid stage is non-motile and forms extensive blooms. The haploid phase is a non-calcified biflagellated cell bearing organic scales. Haploid cells are thought to resist infection, through a process deemed the “Cheshire Cat” escape strategy; however, a recent study detected the presence of viral lipids in the same haploid strain. Here we report on the application of an E. huxleyi CCMP1516 EhV-86 combined tiling array (TA that further confirms an EhV infection in the RCC1217 haploid strain, which grew without any signs of cell lysis. Reverse transcription polymerase chain reaction (RT-PCR and PCR verified the presence of viral RNA in the haploid cells, yet indicated an absence of viral DNA, respectively. These infected cells are an alternative stage of the virus life cycle deemed the haplococcolithovirocell. In this instance, the host is both resistant to and infected by EhV, i.e., the viral transcriptome is present in haploid cells whilst there is no evidence of viral lysis. This superimposed state is reminiscent of Schrödinger’s cat; of being simultaneously both dead and alive.

  16. Schrödinger's Cheshire Cat: Are Haploid Emiliania huxleyi Cells Resistant to Viral Infection or Not?

    Science.gov (United States)

    Mordecai, Gideon J; Verret, Frederic; Highfield, Andrea; Schroeder, Declan C

    2017-03-18

    Emiliania huxleyi is the main calcite producer on Earth and is routinely infected by a virus (EhV); a double stranded DNA (dsDNA) virus belonging to the family Phycodnaviridae . E. huxleyi exhibits a haplodiploid life cycle; the calcified diploid stage is non-motile and forms extensive blooms. The haploid phase is a non-calcified biflagellated cell bearing organic scales. Haploid cells are thought to resist infection, through a process deemed the "Cheshire Cat" escape strategy; however, a recent study detected the presence of viral lipids in the same haploid strain. Here we report on the application of an E. huxleyi CCMP1516 EhV-86 combined tiling array (TA) that further confirms an EhV infection in the RCC1217 haploid strain, which grew without any signs of cell lysis. Reverse transcription polymerase chain reaction (RT-PCR) and PCR verified the presence of viral RNA in the haploid cells, yet indicated an absence of viral DNA, respectively. These infected cells are an alternative stage of the virus life cycle deemed the haplococcolithovirocell. In this instance, the host is both resistant to and infected by EhV, i.e., the viral transcriptome is present in haploid cells whilst there is no evidence of viral lysis. This superimposed state is reminiscent of Schrödinger's cat; of being simultaneously both dead and alive.

  17. Schrödinger’s Cheshire Cat: Are Haploid Emiliania huxleyi Cells Resistant to Viral Infection or Not?

    Science.gov (United States)

    Mordecai, Gideon J.; Verret, Frederic; Highfield, Andrea; Schroeder, Declan C.

    2017-01-01

    Emiliania huxleyi is the main calcite producer on Earth and is routinely infected by a virus (EhV); a double stranded DNA (dsDNA) virus belonging to the family Phycodnaviridae. E. huxleyi exhibits a haplodiploid life cycle; the calcified diploid stage is non-motile and forms extensive blooms. The haploid phase is a non-calcified biflagellated cell bearing organic scales. Haploid cells are thought to resist infection, through a process deemed the “Cheshire Cat” escape strategy; however, a recent study detected the presence of viral lipids in the same haploid strain. Here we report on the application of an E. huxleyi CCMP1516 EhV-86 combined tiling array (TA) that further confirms an EhV infection in the RCC1217 haploid strain, which grew without any signs of cell lysis. Reverse transcription polymerase chain reaction (RT-PCR) and PCR verified the presence of viral RNA in the haploid cells, yet indicated an absence of viral DNA, respectively. These infected cells are an alternative stage of the virus life cycle deemed the haplococcolithovirocell. In this instance, the host is both resistant to and infected by EhV, i.e., the viral transcriptome is present in haploid cells whilst there is no evidence of viral lysis. This superimposed state is reminiscent of Schrödinger’s cat; of being simultaneously both dead and alive. PMID:28335465

  18. Application of Doubled Haploid (DH) Technique in Mutation and Conventional Wheat Breeding in Kenya

    International Nuclear Information System (INIS)

    Njau, P.N.

    2002-01-01

    Wheat is the second most important staple cereal in Kenya after maize.over the last six years wheat improvement for various stresses and agronomic characteristics have been undertaken through various biotechnological approaches which have been used as complements to the traditional breeding methods. The prime objective in any breeding program is the prevention of the debilitating effects of breeding. In self-pollinated crops such as wheat selection is more efficient homozygous lines than in segregating population. During repeated selfing, to develop homozygousity the vigour of the F1 of M1 plats is lost. Application of biotechnology in crop movement has been suggested as the useful tool in a faster variety development. The double haploid (DH) technique does not only shorten the time of developing homozygous lines but also maintains the heterosis of the F 1 , increase the selection of the efficiency of selection in mutants and increase the effectiveness of selection. in this study DHs were developed from F1 and M4 generation developed from drought tolerance.This was accomplished through the following step: (i)F 1 crosses were produced by crossing three drought tolerant varieties namely Kenya Mbweha, Duma and Ngamia with two highly yielding commercial varieties namely Kenya Chiriku and Kwale in 1998 while mutants were developed through gamma ray irradiation in 1995. (ii) The haploids were produced through chromosome elimination by crossing the F 1 s and the M 4 with maize pollen and (iii) the Double Haploid (DH) were produced by treating the haploid with colchicine. Twenty DH lines were produced from F 1 haploid and 5 from M 4 ones. The DH technique tend to increase uniformity, stability and distinctiveness of the mutants and the segregating populations. Most of the DHs showed wide variation indicating high potential of selection for various agronomic characteristics. Heterosis was realized on a number of characteristics in the DH lines. Through this technique the

  19. Hapsembler: An Assembler for Highly Polymorphic Genomes

    Science.gov (United States)

    Donmez, Nilgun; Brudno, Michael

    As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a challenge as most assemblers are unable to handle highly divergent haplotypes in a single individual. In this paper we describe Hapsembler, an assembler for highly polymorphic genomes, which makes use of paired reads. Our experiments show that Hapsembler produces accurate and contiguous assemblies of highly polymorphic genomes, while performing on par with the leading tools on haploid genomes. Hapsembler is available for download at http://compbio.cs.toronto.edu/hapsembler.

  20. Equivalence principles and electromagnetism

    Science.gov (United States)

    Ni, W.-T.

    1977-01-01

    The implications of the weak equivalence principles are investigated in detail for electromagnetic systems in a general framework. In particular, it is shown that the universality of free-fall trajectories (Galileo weak equivalence principle) does not imply the validity of the Einstein equivalence principle. However, the Galileo principle plus the universality of free-fall rotation states does imply the Einstein principle.

  1. Genetic effects of formaldehyde in yeast. Current status and limitations of the radiation equivalence concept

    International Nuclear Information System (INIS)

    Chanet, R.; Magana-Schwencke, N.; Moustacchi, E.

    1980-01-01

    Values of radiation equivalents of chemicals have been calculated for formaldehyde (FA) from detailed data on its genetic effects on yeast, Saccharomyces cerevisiae, and compared with the effects induced by gamma radiation. For the haploid yeast strain, 1 (mmol FA.ltr -1 ).min (i.e. 1 mM FA.min) is equivalent to 9.6 rad, and for diploid yeast it is equivalent to 33 rad. These values are within the range of values calculated for E. coli and mammalian cells. Some major differences in the response to FA and radiation are encountered, depending upon the cellular physiological conditions, the genetic background and the degree of ploidy (haploid versus diploid) and growth phase (exponential versus stationary), among others. Difficulties encountered in the estimation of rad-equivalent values for specific chemicals and for defined biological end-points (e.g. rate of reverse mutation in the specific biochemical loci) are discussed. It is concluded that by exercising appropriate caution relating to the differences in the mechanisms of action of the chemical mutagens and radiations, meaningful rad-equivalent values could be estimated that could help express the comparative biological effects of chemicals in terms of radiation unit. (author)

  2. In vivo evolutionary engineering for ethanol-tolerance of Saccharomyces cerevisiae haploid cells triggers diploidization.

    Science.gov (United States)

    Turanlı-Yıldız, Burcu; Benbadis, Laurent; Alkım, Ceren; Sezgin, Tuğba; Akşit, Arman; Gökçe, Abdülmecit; Öztürk, Yavuz; Baykal, Ahmet Tarık; Çakar, Zeynep Petek; François, Jean M

    2017-09-01

    Microbial ethanol production is an important alternative energy resource to replace fossil fuels, but at high level, this product is highly toxic, which hampers its efficient production. Towards increasing ethanol-tolerance of Saccharomyces cerevisiae, the so far best industrial ethanol-producer, we evaluated an in vivo evolutionary engineering strategy based on batch selection under both constant (5%, v v -1 ) and gradually increasing (5-11.4%, v v -1 ) ethanol concentrations. Selection under increasing ethanol levels yielded evolved clones that could tolerate up to 12% (v v -1 ) ethanol and had cross-resistance to other stresses. Quite surprisingly, diploidization of the yeast population took place already at 7% (v v -1 ) ethanol level during evolutionary engineering, and this event was abolished by the loss of MKT1, a gene previously identified as being implicated in ethanol tolerance (Swinnen et al., Genome Res., 22, 975-984, 2012). Transcriptomic analysis confirmed diploidization of the evolved clones with strong down-regulation in mating process, and in several haploid-specific genes. We selected two clones exhibiting the highest viability on 12% ethanol, and found productivity and titer of ethanol significantly higher than those of the reference strain under aerated fed-batch cultivation conditions. This higher fermentation performance could be related with a higher abundance of glycolytic and ribosomal proteins and with a relatively lower respiratory capacity of the evolved strain, as revealed by a comparative transcriptomic and proteomic analysis between the evolved and the reference strains. Altogether, these results emphasize the efficiency of the in vivo evolutionary engineering strategy for improving ethanol tolerance, and the link between ethanol tolerance and diploidization. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  3. Genetic mapping of centromeres in the nine Citrus clementina chromosomes using half-tetrad analysis and recombination patterns in unreduced and haploid gametes.

    Science.gov (United States)

    Aleza, Pablo; Cuenca, José; Hernández, María; Juárez, José; Navarro, Luis; Ollitrault, Patrick

    2015-03-08

    Mapping centromere locations in plant species provides essential information for the analysis of genetic structures and population dynamics. The centromere's position affects the distribution of crossovers along a chromosome and the parental heterozygosity restitution by 2n gametes is a direct function of the genetic distance to the centromere. Sexual polyploidisation is relatively frequent in Citrus species and is widely used to develop new seedless triploid cultivars. The study's objectives were to (i) map the positions of the centromeres of the nine Citrus clementina chromosomes; (ii) analyse the crossover interference in unreduced gametes; and (iii) establish the pattern of genetic recombination in haploid clementine gametes along each chromosome and its relationship with the centromere location and distribution of genic sequences. Triploid progenies were derived from unreduced megagametophytes produced by second-division restitution. Centromere positions were mapped genetically for all linkage groups using half-tetrad analysis. Inference of the physical locations of centromeres revealed one acrocentric, four metacentric and four submetacentric chromosomes. Crossover interference was observed in unreduced gametes, with variation seen between chromosome arms. For haploid gametes, a strong decrease in the recombination rate occurred in centromeric and pericentromeric regions, which contained a low density of genic sequences. In chromosomes VIII and IX, these low recombination rates extended beyond the pericentromeric regions. The genomic region corresponding to a genetic distance recombination pattern along each chromosome. However, regions with low recombination rates extended beyond the pericentromeric regions of some chromosomes into areas richer in genic sequences. The persistence of strong linkage disequilibrium between large numbers of genes promotes the stability of epistatic interactions and multilocus-controlled traits over successive generations but

  4. Sexagesimal scale for mapping human genome Escala sexagesimal para mapear el genoma humano

    Directory of Open Access Journals (Sweden)

    RICARDO CRUZ-COKE

    2001-03-01

    Full Text Available In a previous work I designed a diagram of the human genome based on a circular ideogram of the haploid set of chromosomes, using a low resolution scale of Megabase units. The purpose of this work is to draft a new scale to measure the physical map of the human genome at the highest resolution level. The entire length of the haploid genome of males is deployed in a circumference, marked with a sexagesimal scale with 360 degrees and 1296000 arc seconds. The radio of this circunference displays a semilogaritmic metric scale from 1 m up to the nanometer level. The base pair level of DNA sequences, 10-9 of this circunsference, is measured in milliarsec unit (mas, equivalent to a thousand of arcsecond. The "mas" unit, correspond to 1.27 nanometers (nm or 0.427 base pair (bp and it is the framework for measure DNA sequences. Thus the three billion base pairs of the human genome may be identified by 1296000000 "mas" units in continous correlation from number 1 to number 1296000000. This sexagesimal scale covers all the levels of the nuclear genetic material, from nucleotides to chromosomes. The locations of every codon and every gene may be numbered in the physical map of chomosome regions according to this new scale, instead of the partial kilobase and Megabase scales used today. The advantage of the new scale is the unification of the set of chromosomes under a continous scale of measurement at the DNA level, facilitating the correlation with the phenotypes of man and other speciesEn un trabajo anterior yo diseñé un diagrama del genoma humano basado en un ideograma circular del conjunto haploide de cromosomas, usando una escala de baja resolución en megabases. El propósito de este trabajo es el de diseñar una nueva escala para medir el mapa físico del genoma humano al más alto nivel de resolución. La longitud completa del genoma haploide del varon es extendido en una circunsferencia, marcada con una escala sexagesimal de 360 grados y 1296000

  5. Dicer is required for haploid male germ cell differentiation in mice.

    Directory of Open Access Journals (Sweden)

    Hanna M Korhonen

    Full Text Available BACKGROUND: The RNase III endonuclease Dicer is an important regulator of gene expression that processes microRNAs (miRNAs and small interfering RNAs (siRNAs. The best-characterized function of miRNAs is gene repression at the post-transcriptional level through the pairing with mRNAs of protein-encoding genes. Small RNAs can also act at the transcriptional level by controlling the epigenetic status of chromatin. Dicer and other mediators of small RNA pathways are present in mouse male germ cells, and several miRNAs and endogenous siRNAs are expressed in the testis, suggesting that Dicer-dependent small RNAs are involved in the control of the precisely timed and highly organised process of spermatogenesis. PRINCIPAL FINDINGS: Being interested in the Dicer-mediated functions during spermatogenesis, we have analysed here a male germ cell-specific Dicer1 knockout mouse model, in which the deletion of Dicer1 takes place during early postnatal development in spermatogonia. We found that Dicer1 knockout testes were reduced in size and spermatogenesis within the seminiferous tubules was disrupted. Dicer1 knockout epididymides contained very low number of mature sperm with pronounced morphological abnormalities. Spermatogonial differentiation appeared unaffected. However, the number of haploid cells was decreased in knockout testes, and an increased number of apoptotic spermatocytes was observed. The most prominent defects were found during late haploid differentiation, and Dicer was demonstrated to be critical for the normal organization of chromatin and nuclear shaping of elongating spermatids. CONCLUSIONS/SIGNIFICANCE: We demonstrate that Dicer and Dicer-dependent small RNAs are imperative regulators of haploid spermatid differentiation and essential for male fertility.

  6. Response of haploid and diploid protoplasts from Datura innoxia Mill. and Petunia hybrida L. to treatment with X-rays and a chemical mutagen

    International Nuclear Information System (INIS)

    Krumbiegel, G.

    1979-01-01

    Haploid and diploid protoplasts of the two Solanaceous species Datura innoxia Mill. and Petunia Hybridia L., were exposed to two different mutagens, increased doses of X-rays and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). With both species the survival rates of haploid protoplasts decreased exponentially with increased doses of X-rays and increased concentrations of MNNG. Diploid protoplasts showed a higher resistance than haploids only at higher mutagen doses or concentrations. After the MNNG-treatment of haploid protoplasts from Datura innoxia, four mutants with altered pigment patterns were isolated. (author)

  7. Polyamine patterns in haploid and diploid tobacco tissues and in vitro cultures

    Directory of Open Access Journals (Sweden)

    Sílvia Bicudo Carone

    2010-04-01

    Full Text Available The aim of this work was to determine PAs levels in pith tissues and callus cultures from haploid and diploid tobacco plants, explanted from the apical and basal regions of the stem. These explants were cultured in an RM-64 medium supplied with IAA and kinetin, under light or in the dark, during successive subcultures. PAs levels followed a basipetal decrease in diploid and an increase in haploid, pith tissues. A similar pattern of total PAs (free + conjugated was observed for the callus of diploid and haploid plants maintained in the light, and for the haploid callus in the dark, whereas the diploid callus in the dark showed a constant increase in total PAs levels until the end of culture. The PA increase in the diploid callus in the dark was related to free Put levels increase. The ploidy status of the plants could express different PA gradients together with the plant pith and in vitro callus cultures.O objetivo deste trabalho foi determinar os níveis de PAs em tecidos de medula e cultura de calos de plantas haplóides e diplóides de tabaco, obtidas da região apical e basal do caule. Estes explantes foram cultivados em meio RM-64 suplementado com AIA e cinetina, na luz e no escuro, durante vários subcultivos. Nos tecidos medulares, os níveis de PAs apresentam um decréscimo basípeto em diplóides e um aumento em haplóides.Um padrão similar nos níveis de PAs totais (livres+ conjugadas foi observado em calos haplóides e diplóides mantidos na luz, e haplóides no escuro, enquanto os diplóides cultivados no escuro mostraram um aumento constante até o final do cultivo. O aumento no conteúdo de PAs nos calos diplóides no escuro, foi devido ao aumento do conteúdo de Put livre. Foi observado que a ploidia da planta pode expressar diferentes gradientes de PA ao longo do tecido medular e nas culturas de calos in vitro.

  8. Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol.

    Science.gov (United States)

    Kim, Soo Rin; Skerker, Jeffrey M; Kong, In Iok; Kim, Heejin; Maurer, Matthew J; Zhang, Guo-Chang; Peng, Dairong; Wei, Na; Arkin, Adam P; Jin, Yong-Su

    2017-03-01

    Many desired phenotypes for producing cellulosic biofuels are often observed in industrial Saccharomyces cerevisiae strains. However, many industrial yeast strains are polyploid and have low spore viability, making it difficult to use these strains for metabolic engineering applications. We selected the polyploid industrial strain S. cerevisiae ATCC 4124 exhibiting rapid glucose fermentation capability, high ethanol productivity, strong heat and inhibitor tolerance in order to construct an optimal yeast strain for producing cellulosic ethanol. Here, we focused on developing a general approach and high-throughput screening method to isolate stable haploid segregants derived from a polyploid parent, such as triploid ATCC 4124 with a poor spore viability. Specifically, we deleted the HO genes, performed random sporulation, and screened the resulting segregants based on growth rate, mating type, and ploidy. Only one stable haploid derivative (4124-S60) was isolated, while 14 other segregants with a stable mating type were aneuploid. The 4124-S60 strain inherited only a subset of desirable traits present in the parent strain, same as other aneuploids, suggesting that glucose fermentation and specific ethanol productivity are likely to be genetically complex traits and/or they might depend on ploidy. Nonetheless, the 4124-60 strain did inherit the ability to tolerate fermentation inhibitors. When additional genetic perturbations known to improve xylose fermentation were introduced into the 4124-60 strain, the resulting engineered strain (IIK1) was able to ferment a Miscanthus hydrolysate better than a previously engineered laboratory strain (SR8), built by making the same genetic changes. However, the IIK1 strain showed higher glycerol and xylitol yields than the SR8 strain. In order to decrease glycerol and xylitol production, an NADH-dependent acetate reduction pathway was introduced into the IIK1 strain. By consuming 2.4g/L of acetate, the resulting strain (IIK1A

  9. Genome engineering in human cells.

    Science.gov (United States)

    Song, Minjung; Kim, Young-Hoon; Kim, Jin-Soo; Kim, Hyongbum

    2014-01-01

    Genome editing in human cells is of great value in research, medicine, and biotechnology. Programmable nucleases including zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases recognize a specific target sequence and make a double-strand break at that site, which can result in gene disruption, gene insertion, gene correction, or chromosomal rearrangements. The target sequence complexities of these programmable nucleases are higher than 3.2 mega base pairs, the size of the haploid human genome. Here, we briefly introduce the structure of the human genome and the characteristics of each programmable nuclease, and review their applications in human cells including pluripotent stem cells. In addition, we discuss various delivery methods for nucleases, programmable nickases, and enrichment of gene-edited human cells, all of which facilitate efficient and precise genome editing in human cells.

  10. Apomixis and the problem of obtaining haploids and homozygote diploids in pear (Pyrus communis L.

    Directory of Open Access Journals (Sweden)

    Є. О. Долматов

    2013-02-01

    Full Text Available The article highlights results of research over simulative apomixes in pear and its utilization for obtaining haploids and homozygote diploids. It has been established that over 50% pear varieties with failed remote hybridization are capable of generating seeds of apomictic origin producing diploid plants. Genotypes displaying maximal inclination to apomixes have been singled out. Apomictic pear seedlings obtained from foreign pollination within the limits of the same combination are inherent in profound morphological diversity. Fruit-bearing apomicts originated from one and the same maternal plant differ to the same extent as hybrid seedlings of the same family. Genetic markers have enabled to establish that these are embryo sacs in which meiosis has completed that give rise to apomictic seeds. In vitro method as used for the purpose of increasing apomictic plants output has been illustrated. The greatest induction of apomictic shoots in vitro has been reached by alternation of BAP cytokinin at concentration of 1mg/l and 2 mg/l on the background of GA3 amounting to 1,5 mg/l. Grafting with shoots in vitro on non-sterile rootstocks of pear (Pyrus communis has increased the output of plants up to 80%. A cytological assessment of 9 apomictic samples is provided. The cytological analysis of samples of apomictic forms has certified the presence of simulative haploid parthenogenesis in pear.

  11. Brewing characteristics of haploid strains isolated from sake yeast Kyokai No. 7.

    Science.gov (United States)

    Katou, Taku; Kitagaki, Hiroshi; Akao, Takeshi; Shimoi, Hitoshi

    2008-11-01

    Sake yeast exhibit various characteristics that make them more suitable for sake brewing compared to other yeast strains. Since sake yeast strains are Saccharomyces cerevisiae heterothallic diploid strains, it is likely that they have heterozygous alleles on homologous chromosomes (heterozygosity) due to spontaneous mutations. If this is the case, segregation of phenotypic traits in haploid strains after sporulation and concomitant meiosis of sake yeast strains would be expected to occur. To examine this hypothesis, we isolated 100 haploid strains from Kyokai No. 7 (K7), a typical sake yeast strain in Japan, and compared their brewing characteristics in small-scale sake-brewing tests. Analyses of the resultant sake samples showed a smooth and continuous distribution of analytical values for brewing characteristics, suggesting that K7 has multiple heterozygosities that affect brewing characteristics and that these heterozygous alleles do segregate after sporulation. Correlation and principal component analyses suggested that the analytical parameters could be classified into two groups, indicating fermentation ability and sake flavour. (c) 2008 John Wiley & Sons, Ltd.

  12. Salix transect of Europe: variation in ploidy and genome size in willow-associated common nettle, Urtica dioica L. sens. lat., from Greece to arctic Norway.

    Science.gov (United States)

    Cronk, Quentin; Hidalgo, Oriane; Pellicer, Jaume; Percy, Diana; Leitch, Ilia J

    2016-01-01

    The common stinging nettle, Urtica dioica L. sensu lato, is an invertebrate "superhost", its clonal patches maintaining large populations of insects and molluscs. It is extremely widespread in Europe and highly variable, and two ploidy levels (diploid and tetraploid) are known. However, geographical patterns in cytotype variation require further study. We assembled a collection of nettles in conjunction with a transect of Europe from the Aegean to Arctic Norway (primarily conducted to examine the diversity of Salix and Salix -associated insects). Using flow cytometry to measure genome size, our sample of 29 plants reveals 5 diploids and 24 tetraploids. Two diploids were found in SE Europe (Bulgaria and Romania) and three diploids in S. Finland. More detailed cytotype surveys in these regions are suggested. The tetraploid genome size (2C value) varied between accessions from 2.36 to 2.59 pg. The diploids varied from 1.31 to 1.35 pg per 2C nucleus, equivalent to a haploid genome size of c. 650 Mbp. Within the tetraploids, we find that the most northerly samples (from N. Finland and arctic Norway) have a generally higher genome size. This is possibly indicative of a distinct population in this region.

  13. Effective dose equivalent

    International Nuclear Information System (INIS)

    Huyskens, C.J.; Passchier, W.F.

    1988-01-01

    The effective dose equivalent is a quantity which is used in the daily practice of radiation protection as well as in the radiation hygienic rules as measure for the health risks. In this contribution it is worked out upon which assumptions this quantity is based and in which cases the effective dose equivalent can be used more or less well. (H.W.)

  14. Characterization of revenue equivalence

    NARCIS (Netherlands)

    Heydenreich, B.; Müller, R.; Uetz, Marc Jochen; Vohra, R.

    2009-01-01

    The property of an allocation rule to be implementable in dominant strategies by a unique payment scheme is called revenue equivalence. We give a characterization of revenue equivalence based on a graph theoretic interpretation of the incentive compatibility constraints. The characterization holds

  15. Characterization of Revenue Equivalence

    NARCIS (Netherlands)

    Heydenreich, Birgit; Müller, Rudolf; Uetz, Marc Jochen; Vohra, Rakesh

    2008-01-01

    The property of an allocation rule to be implementable in dominant strategies by a unique payment scheme is called \\emph{revenue equivalence}. In this paper we give a characterization of revenue equivalence based on a graph theoretic interpretation of the incentive compatibility constraints. The

  16. On the operator equivalents

    International Nuclear Information System (INIS)

    Grenet, G.; Kibler, M.

    1978-06-01

    A closed polynomial formula for the qth component of the diagonal operator equivalent of order k is derived in terms of angular momentum operators. The interest in various fields of molecular and solid state physics of using such a formula in connection with symmetry adapted operator equivalents is outlined

  17. Construction of a Bacterial Artificial Chromosome Library of TM-1, a Standard Line for Genetics and Genomics in Upland Cotton

    Institute of Scientific and Technical Information of China (English)

    Yan Hu; Wang-Zhen Guo; Tian-Zhen Zhang

    2009-01-01

    A bacterial artificial chromosome (BAC) library was constructed for Gossyplum hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384- well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carded out by four-round polymerase chain reactions using 23 simple sequence repeats (SSR) markers, three sequence-related amplified polymorphism markers and one pair of pdmere for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were Identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 (A12) and 26 (D12) according to the genetic map, these BAC clonee are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with Important agronomic traits.

  18. The first insight into the salvia (lamiaceae) genome via bac library construction and high-throughput sequencing of target bac clones

    International Nuclear Information System (INIS)

    Hao, D.C.; Vautrin, S.; Berges, H.; Chen, S.L.

    2015-01-01

    Salvia is a representative genus of Lamiaceae, a eudicot family with significant species diversity and population adaptibility. One of the key goals of Salvia genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of medicinal plants to increase their health and productivity. Large-insert genomic libraries are a fundamental tool for achieving this purpose. We report herein the construction, characterization and screening of a gridded BAC library for Salvia officinalis (sage). The S. officinalis BAC library consists of 17,764 clones and the average insert size is 107 Kb, corresponding to 3 haploid genome equivalents. Seventeen positive clones (average insert size 115 Kb) containing five terpene synthase (TPS) genes were screened out by PCR and 12 of them were subject to Illumina HiSeq 2000 sequencing, which yielded 28,097,480 90-bp raw reads (2.53 Gb). Scaffolds containing sabinene synthase (Sab), a Sab homolog, TPS3 (kaurene synthase-like 2), copalyl diphosphate synthase 2 and one cytochrome P450 gene were retrieved via de novo assembly and annotation, which also have flanking noncoding sequences, including predicted promoters and repeat sequences. Among 2,638 repeat sequences, there are 330 amplifiable microsatellites. This BAC library provides a new resource for Lamiaceae genomic studies, including microsatellite marker development, physical mapping, comparative genomics and genome sequencing. Characterization of positive clones provided insights into the structure of the Salvia genome. These sequences will be used in the assembly of a future genome sequence for S. officinalis. (author)

  19. Equivalent Dynamic Models.

    Science.gov (United States)

    Molenaar, Peter C M

    2017-01-01

    Equivalences of two classes of dynamic models for weakly stationary multivariate time series are discussed: dynamic factor models and autoregressive models. It is shown that exploratory dynamic factor models can be rotated, yielding an infinite set of equivalent solutions for any observed series. It also is shown that dynamic factor models with lagged factor loadings are not equivalent to the currently popular state-space models, and that restriction of attention to the latter type of models may yield invalid results. The known equivalent vector autoregressive model types, standard and structural, are given a new interpretation in which they are conceived of as the extremes of an innovating type of hybrid vector autoregressive models. It is shown that consideration of hybrid models solves many problems, in particular with Granger causality testing.

  20. Cellular heredity in haploid cultures of somatic cells. Annual progress report, March 1, 1975--March 31, 1976. [UV radiation

    Energy Technology Data Exchange (ETDEWEB)

    Freed, J.J.

    1976-01-01

    In experiments with haploid and diploid derivatives from the haploid frog embryo cell line ICR 2A, we have investigated aspects of cell survival, DNA repair and mutant induction after exposure to 254 nm radiation. Survival curves for haploid and diploid cells in random growth or blocked in the Gl phase of the cell cycle were determined; the survival data do not differ sufficiently to permit the use of such comparisons as an index of recessive lethal induction. Studies of the induction of thymine dimers in DNA indicated that the incidence of dimers in DNA from haploid and diploid cells is similar after exposure of the cells to equal doses of ultraviolet. The cells are capable of photoreversing dimers but appear to be deficient in excision repair. In an attempt to examine the effect of the permitted mode of DNA repair on the yield of mutations, we compared the incidence of ouabain-resistant variants among survivors of ultraviolet exposure and of ultraviolet exposure followed by photoreversal. Although the yield of resistant colonies was small, the data suggest that photoreversal lowers the yield of resistant colonies and thus that the induction of this phenotype is related to dimer persistence in DNA. We have also observed by fluorescence microscopy that an acridine mustard mutagen, ICR 191, is preferentially accumulated in cytoplasmic granules having the intracellular distribution pattern of lysosomes. This form of incorporation may be significant in the apparently non-genetic early toxicity of this compound observed in experiments with cultured cells.

  1. Cellular heredity in haploid cultures of somatic cells. Annual progress report, March 1, 1975--March 31, 1976

    International Nuclear Information System (INIS)

    Freed, J.J.

    1976-01-01

    In experiments with haploid and diploid derivatives from the haploid frog embryo cell line ICR 2A, we have investigated aspects of cell survival, DNA repair and mutant induction after exposure to 254 nm radiation. Survival curves for haploid and diploid cells in random growth or blocked in the Gl phase of the cell cycle were determined; the survival data do not differ sufficiently to permit the use of such comparisons as an index of recessive lethal induction. Studies of the induction of thymine dimers in DNA indicated that the incidence of dimers in DNA from haploid and diploid cells is similar after exposure of the cells to equal doses of ultraviolet. The cells are capable of photoreversing dimers but appear to be deficient in excision repair. In an attempt to examine the effect of the permitted mode of DNA repair on the yield of mutations, we compared the incidence of ouabain-resistant variants among survivors of ultraviolet exposure and of ultraviolet exposure followed by photoreversal. Although the yield of resistant colonies was small, the data suggest that photoreversal lowers the yield of resistant colonies and thus that the induction of this phenotype is related to dimer persistence in DNA. We have also observed by fluorescence microscopy that an acridine mustard mutagen, ICR 191, is preferentially accumulated in cytoplasmic granules having the intracellular distribution pattern of lysosomes. This form of incorporation may be significant in the apparently non-genetic early toxicity of this compound observed in experiments with cultured cells

  2. Inheritance patterns of the response to in vitro doubled haploid induction in perennial ryegrass (Lolium perenne L.)

    Czech Academy of Sciences Publication Activity Database

    Begheyn, R. F.; Roulund, N.; Vangsgaard, K.; Kopecký, David; Studer, B.

    2017-01-01

    Roč. 130, č. 3 (2017), s. 667-679 ISSN 0167-6857 Institutional support: RVO:61389030 Keywords : Androgenesis * Androgenic capacity * Anther culture * Doubled haploid (DH) * Perennial ryegrass (Lolium perenne L.) Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 2.002, year: 2016

  3. Quantitative trait loci mapping of heat tolerance in a doubled haploid population of broccoli using genotyping-by-sequencing

    Science.gov (United States)

    Broccoli is a cool weather vegetable crop with a vernalization requirement to initiate and maintain floral development. Breeding for heat tolerance in broccoli has the potential to both expand viable production areas and extend the growing season. A doubled haploid (DH) population of broccoli (Bras...

  4. Cytomorphological studies in X-ray induced glandless haploids in Gossypium hirsutum L. (cotton)

    Energy Technology Data Exchange (ETDEWEB)

    Mehetre, S.S.; Thombre, M.V. (Mahatma Phule Krishi Vidyapeeth, Rahuri (India))

    1981-08-01

    Six haploid plants were obtained in M/sub 2/ generation of the 25 kr. X-ray irradiated Gossypium hirsutum L. cotton variety H.G. 108. The cytomorphological studies on these plants indicated highly irregular meiosis, giving on an average six bivalents, the range being 0-9. Unequal separation of chromosomes and chromatids at anaphase-1 and II respectively led to formation of abnormal tetrads and pollens with high size variations leading to high pollen sterility. These plants were characterized by miniature stature, shorter stem and internodes, smaller leaves, flowers and stomata with fewer chloroplasts, male and female sterility and halving of chromosomes. The reduction in morphological characters was nearly in the proportion of 1:2 as compared to their diploid counterparts. 31 refs.; 5 tables; 12 figures.

  5. Analysis of QTLs Associated with the Rice Quality Related Gene by Double Haploid Populations

    Science.gov (United States)

    Lee, Gyu-Ho; Yun, Byung-Wook

    2014-01-01

    We investigated the growth characteristics and analyzed the physicochemical properties of a doubled haploid population derived from a cross between “Cheongcheong” and “Nagdong” to breed a rice variety that tastes good after cooking and to detect quantitative trait loci (QTLs) associated with the taste of cooked rice. The results showed that these compounds also represent a normal distribution. Correlation analysis of the amylose, protein, and lipid contents indicated that each compound is related to the taste of cooked rice. The QTLs related to amylose content were 4 QTLs, protein content was 2 QTLs, and lipid content was 2 QTLs. Four of the QTLs associated with amylose content were detected on chromosomes 7 and 11. The index of coincidence for the QTLs related to amylose, protein, and lipid content was 70%, respectively. These markers showing high percentage of coincidence can be useful to select desirable lines for rice breeding. PMID:25478566

  6. Analysis of QTLs Associated with the Rice Quality Related Gene by Double Haploid Populations

    Directory of Open Access Journals (Sweden)

    Gyu-Ho Lee

    2014-01-01

    Full Text Available We investigated the growth characteristics and analyzed the physicochemical properties of a doubled haploid population derived from a cross between “Cheongcheong” and “Nagdong” to breed a rice variety that tastes good after cooking and to detect quantitative trait loci (QTLs associated with the taste of cooked rice. The results showed that these compounds also represent a normal distribution. Correlation analysis of the amylose, protein, and lipid contents indicated that each compound is related to the taste of cooked rice. The QTLs related to amylose content were 4 QTLs, protein content was 2 QTLs, and lipid content was 2 QTLs. Four of the QTLs associated with amylose content were detected on chromosomes 7 and 11. The index of coincidence for the QTLs related to amylose, protein, and lipid content was 70%, respectively. These markers showing high percentage of coincidence can be useful to select desirable lines for rice breeding.

  7. Effect of gamma-radiations on haploid cultured cells of Datura innoxia

    International Nuclear Information System (INIS)

    Jain, R.K.; Maherchandani, N.; Sharma, D.R.; Chowdhury, V.K.

    1981-01-01

    The effects of gamma-radiations were studied in haploid cultured cells of Datura innoxia. Growth of callus cultures and shoot differentiation were stimulated at low doses (0.2 and 1.0 kR), while the higher dose (5.0 kR) was inhibitory. Root differentiation was observed only in cultures exposed to 1.0 kR dose. Enzyme activities of alpha-amylase, peroxidase, malate dehydrogenase and phosphatases, and the amounts of buffer extractable proteins were stimulated at 0.2 and 1.0 kR and inhibited at 5.0 kR. Mitotic index too decreased at 5.0 kR. Mean nuclear volume increased with increase in radiation dose, probably due to increased ploidy. (author)

  8. Cellular heredity in haploid cultures of somatic cells. Comprehensive report, April 1975--June 1977

    International Nuclear Information System (INIS)

    Freed, J.J.

    1977-07-01

    This report reviews genetic studies carried out since 1975 on a haploid cultured cell line from frog embryos (ICR 2A). Although a single chromosome set would be expected to facilitate recovery of recessive mutants, experiments suggested that cell culture variants might arise through processes more complex than the selection of simple mutational changes. Therefore, the objectives of the work reported here have been to throw light on just how cell culture variants arise in this system. First, we have continued to characterize the ICR 2A line, with emphasis on stability of karyotype and DNA content. Second, we have studied in detail the origin of two classes of drug-resistant variants. Bromodeoxyuridine resistance of the thymidine deficiency type has been shown to arise through sequential loss of two forms of thymidine-phosphorylating enzyme; loss of the second form of enzyme is complex, suggesting that changes more complex than simple recessive mutations may be involved. Another form of resistance, in which tolerance of high levels of bromodeoxyuridine is found in cells that continue to express thymidine kinase, remains under study. Variants resistant to microtubule inhibitors were isolated. It was found that these haploid strains have properties distinguishing them from analogous resistant strains isolated from diploid mammalian cell cultures in other laboratories. In order to understand better how mutagens are involved in the origin of cell culture variants, we have examined the effect of different forms of DNA repair on the frequency of drug-resistant colonies induced by ultraviolet radiation. Preliminary experiments suggest that the frequency of such colonies is greater when repair takes place through (presumably error-prone) dark repair than when (error-free) photoreversal is allowed to occur. Such experiments can determine whether new phenotypes arise from alterations in DNA, and thus whether, in a broad sense, they are likely to be mutational in nature

  9. Cellular heredity in haploid cultures of somatic cells. Comprehensive report, April 1975--June 1977. [UV radiation

    Energy Technology Data Exchange (ETDEWEB)

    Freed, J.J.

    1977-07-01

    This report reviews genetic studies carried out since 1975 on a haploid cultured cell line from frog embryos (ICR 2A). Although a single chromosome set would be expected to facilitate recovery of recessive mutants, experiments suggested that cell culture variants might arise through processes more complex than the selection of simple mutational changes. Therefore, the objectives of the work reported here have been to throw light on just how cell culture variants arise in this system. First, we have continued to characterize the ICR 2A line, with emphasis on stability of karyotype and DNA content. Second, we have studied in detail the origin of two classes of drug-resistant variants. Bromodeoxyuridine resistance of the thymidine deficiency type has been shown to arise through sequential loss of two forms of thymidine-phosphorylating enzyme; loss of the second form of enzyme is complex, suggesting that changes more complex than simple recessive mutations may be involved. Another form of resistance, in which tolerance of high levels of bromodeoxyuridine is found in cells that continue to express thymidine kinase, remains under study. Variants resistant to microtubule inhibitors were isolated. It was found that these haploid strains have properties distinguishing them from analogous resistant strains isolated from diploid mammalian cell cultures in other laboratories. In order to understand better how mutagens are involved in the origin of cell culture variants, we have examined the effect of different forms of DNA repair on the frequency of drug-resistant colonies induced by ultraviolet radiation. Preliminary experiments suggest that the frequency of such colonies is greater when repair takes place through (presumably error-prone) dark repair than when (error-free) photoreversal is allowed to occur. Such experiments can determine whether new phenotypes arise from alterations in DNA, and thus whether, in a broad sense, they are likely to be mutational in nature.

  10. The genome of the fire ant Solenopsis invicta

    DEFF Research Database (Denmark)

    Wurm, Yannick; Wang, John; Riba-Grognuz, Oksana

    2011-01-01

    Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothe...

  11. Doubled haploid production from Spanish onion (Allium cepa L.) germplasm: embryogenesis induction, plant regeneration and chromosome doubling.

    Science.gov (United States)

    Fayos, Oreto; Vallés, María P; Garcés-Claver, Ana; Mallor, Cristina; Castillo, Ana M

    2015-01-01

    The use of doubled haploids in onion breeding is limited due to the low gynogenesis efficiency of this species. Gynogenesis capacity from Spanish germplasm, including the sweet cultivar Fuentes de Ebro, the highly pungent landrace BGHZ1354 and the two Valenciana type commercial varieties Recas and Rita, was evaluated and optimized in this study. The OH-1 population, characterized by a high gynogenesis induction, was used as control. Growing conditions of the donor plants were tested with a one-step protocol and field plants produced a slightly higher percentage of embryogenesis induction than growth chamber plants. A one-step protocol was compared with a two-step protocol for embryogenesis induction. Spanish germplasm produced a 2-3 times higher percentage of embryogenesis with the two-step protocol, Recas showing the highest percentage (2.09%) and Fuentes de Ebro the lowest (0.53%). These percentages were significantly lower than those from the OH-1 population, with an average of 15% independently of the protocol used. The effect of different containers on plant regeneration was tested using both protocols. The highest percentage of acclimated plants was obtained with the two-step protocol in combination with Eco2box (70%), whereas the lowest percentage was observed with glass tubes in the two protocols (20-23%). Different amiprofos-methyl (APM) treatments were applied to embryos for chromosome doubling. A similar number of doubled haploid plants were recovered with 25 or 50 μM APM in liquid medium. However, the application of 25 μM in solid medium for 24 h produced the highest number of doubled haploid plants. Somatic regeneration from flower buds of haploid and mixoploid plants proved to be a successful approach for chromosome doubling, since diploid plants were obtained from the four regenerated lines. In this study, doubled haploid plants were produced from the four Spanish cultivars, however further improvements are needed to increase their gynogenesis

  12. Doubled haploid production from Spanish onion (Allium cepa L. germplasm: embryogenesis induction, plant regeneration and chromosome doubling

    Directory of Open Access Journals (Sweden)

    Oreto eFayos

    2015-05-01

    Full Text Available The use of doubled haploids in onion breeding is limited due to the low gynogenesis efficiency of this species. Gynogenesis capacity from Spanish germplasm, including the sweet cultivar Fuentes de Ebro, the highly pungent landrace BGHZ1354 and the two Valenciana type commercial varieties Recas and Rita, was evaluated and optimized in this study. The OH-1 population, characterized by a high gynogenesis induction, was used as control. Growing conditions of the donor plants were tested with a one-step protocol and field plants produced a slightly higher percentage of embryogenesis induction than growth chamber plants. A one-step protocol was compared with a two-step protocol for embryogenesis induction. Spanish germplasm produced a 2 to 3 times higher percentage of embryogenesis with the two-step protocol, Recas showing the highest percentage (2.09% and Fuentes de Ebro the lowest (0.53%. These percentages were significantly lower than those from the OH-1 population, with an average of 15% independently of the protocol used. The effect of different containers on plant regeneration was tested using both protocols. The highest percentage of acclimated plants was obtained with the two-step protocol in combination with Eco2box (70%, whereas the lowest percentage was observed with glass tubes in the two protocols (20-23%. Different amiprofos-methyl (APM treatments were applied to embryos for chromosome doubling. A similar number of doubled haploid plants were recovered with 25 or 50 µM APM in liquid medium. However, the application of 25 µM in solid medium for 24 h produced the highest number of doubled haploid plants. Somatic regeneration from flower buds of haploid and mixoploid plants proved to be a successful approach for chromosome doubling, since diploid plants were obtained from the 4 regenerated lines. In this study, doubled haploid plants were produced from the four Spanish cultivars, however further improvements are needed to increase their

  13. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  14. The principle of equivalence

    International Nuclear Information System (INIS)

    Unnikrishnan, C.S.

    1994-01-01

    Principle of equivalence was the fundamental guiding principle in the formulation of the general theory of relativity. What are its key elements? What are the empirical observations which establish it? What is its relevance to some new experiments? These questions are discussed in this article. (author). 11 refs., 5 figs

  15. Radioactive waste equivalence

    International Nuclear Information System (INIS)

    Orlowski, S.; Schaller, K.H.

    1990-01-01

    The report reviews, for the Member States of the European Community, possible situations in which an equivalence concept for radioactive waste may be used, analyses the various factors involved, and suggests guidelines for the implementation of such a concept. Only safety and technical aspects are covered. Other aspects such as commercial ones are excluded. Situations where the need for an equivalence concept has been identified are processes where impurities are added as a consequence of the treatment and conditioning process, the substitution of wastes from similar waste streams due to the treatment process, and exchange of waste belonging to different waste categories. The analysis of factors involved and possible ways for equivalence evaluation, taking into account in particular the chemical, physical and radiological characteristics of the waste package, and the potential risks of the waste form, shows that no simple all-encompassing equivalence formula may be derived. Consequently, a step-by-step approach is suggested, which avoids complex evaluations in the case of simple exchanges

  16. Equivalent Colorings with "Maple"

    Science.gov (United States)

    Cecil, David R.; Wang, Rongdong

    2005-01-01

    Many counting problems can be modeled as "colorings" and solved by considering symmetries and Polya's cycle index polynomial. This paper presents a "Maple 7" program link http://users.tamuk.edu/kfdrc00/ that, given Polya's cycle index polynomial, determines all possible associated colorings and their partitioning into equivalence classes. These…

  17. Correspondences. Equivalence relations

    International Nuclear Information System (INIS)

    Bouligand, G.M.

    1978-03-01

    We comment on sections paragraph 3 'Correspondences' and paragraph 6 'Equivalence Relations' in chapter II of 'Elements de mathematique' by N. Bourbaki in order to simplify their comprehension. Paragraph 3 exposes the ideas of a graph, correspondence and map or of function, and their composition laws. We draw attention to the following points: 1) Adopting the convention of writting from left to right, the composition law for two correspondences (A,F,B), (U,G,V) of graphs F, G is written in full generality (A,F,B)o(U,G,V) = (A,FoG,V). It is not therefore assumed that the co-domain B of the first correspondence is identical to the domain U of the second (EII.13 D.7), (1970). 2) The axiom of choice consists of creating the Hilbert terms from the only relations admitting a graph. 3) The statement of the existence theorem of a function h such that f = goh, where f and g are two given maps having the same domain (of definition), is completed if h is more precisely an injection. Paragraph 6 considers the generalisation of equality: First, by 'the equivalence relation associated with a map f of a set E identical to (x is a member of the set E and y is a member of the set E and x:f = y:f). Consequently, every relation R(x,y) which is equivalent to this is an equivalence relation in E (symmetrical, transitive, reflexive); then R admits a graph included in E x E, etc. Secondly, by means of the Hilbert term of a relation R submitted to the equivalence. In this last case, if R(x,y) is separately collectivizing in x and y, theta(x) is not the class of objects equivalent to x for R (EII.47.9), (1970). The interest of bringing together these two subjects, apart from this logical order, resides also in the fact that the theorem mentioned in 3) can be expressed by means of the equivalence relations associated with the functions f and g. The solutions of the examples proposed reveal their simplicity [fr

  18. The equivalence theorem

    International Nuclear Information System (INIS)

    Veltman, H.

    1990-01-01

    The equivalence theorem states that, at an energy E much larger than the vector-boson mass M, the leading order of the amplitude with longitudinally polarized vector bosons on mass shell is given by the amplitude in which these vector bosons are replaced by the corresponding Higgs ghosts. We prove the equivalence theorem and show its validity in every order in perturbation theory. We first derive the renormalized Ward identities by using the diagrammatic method. Only the Feynman-- 't Hooft gauge is discussed. The last step of the proof includes the power-counting method evaluated in the large-Higgs-boson-mass limit, needed to estimate the leading energy behavior of the amplitudes involved. We derive expressions for the amplitudes involving longitudinally polarized vector bosons for all orders in perturbation theory. The fermion mass has not been neglected and everything is evaluated in the region m f ∼M much-lt E much-lt m Higgs

  19. Parallel or convergent evolution in human population genomic data revealed by genotype networks

    OpenAIRE

    Vahdati, Ali R; Wagner, Andreas

    2016-01-01

    Background Genotype networks are representations of genetic variation data that are complementary to phylogenetic trees. A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. Results We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The struc...

  20. Spontaneous and UV-induced variations in the activity of biomass synthesis in Candida utilis haploid and diploid strains

    International Nuclear Information System (INIS)

    Kondrat'eva, T.F.; Lin'kova, M.A.; Lobacheva, N.A.

    1988-01-01

    Candida utilis diploid strains have greater variations induced by UV irradiation in the activity of biomass synthesis as compared with the parent haploid culture. Clones with an activity of the synthesis greater that the mean population one appear more frequently in the diploid strains. Mathematical analysis has confirmed the significance of the results and the hypothesis according to which the frequency of variants more active in biomass synthesis rises after the action of UV

  1. Mutation induction in haploid yeast after split-dose radiation-exposure. I. Fractionated UV-irradiation.

    Science.gov (United States)

    Schenk, K; Zölzer, F; Kiefer, J

    1989-01-01

    Mutation induction was investigated in wild-type haploid yeast Saccharomyces cerevisiae after split-dose UV-irradiation. Cells were exposed to fractionated 254 nm-UV-doses separated by intervals from 0 to 6 h with incubation either on non-nutrient or nutrient agar between. The test parameter was resistance to canavanine. If modifications of sensitivity due to incubation are appropriately taken into account there is no change of mutation frequency.

  2. Transformation of haploid, microspore-derived cell suspension protoplasts of rice (Oryza sativa L.).

    Science.gov (United States)

    Chaïr, H; Legavre, T; Guiderdoni, E

    1996-06-01

    We compared the transient activity of three cereal gene-derived promoter-gus fusions and the efficiency of selection mediated by three different selectable genes in a polyethylene glycol transformation system with haploid cell suspension protoplasts of rice. The maize ubiquitin promoter was found to be the most active in transformed protoplasts, and selection on ammonium glufosinate mediated by the bar gene was the most efficient for producing resistant calluses. Cotransformation of protoplasts with two separate plasmids carrying the gus and the bar genes, at either a 2∶1 or 1∶1 ratio, led to 0.8 × 10(-5) and 1.6 × 10(-5) resistant callus recovery frequencies and 59.7 and 37.9 cotransformation efficiencies respectively. No escapes were detected in dot blot analyses of 100 resistant calluses with a probe consisting of the bar coding region. Cotransformation efficiency, based on resistance to basta and β-glucuronidase staining of the leaf tissue of 115 regenerated plants, was 47%. Resistance tests and Southern analysis of seed progenies of three diploid transgenic plants demonstrated homozygous integration of multiple copies of the transgene at one locus at least in the first plant, heterozygous integration at one locus in the second plant and heterozygous integration at two loci in the third plant.

  3. Human DAZL, DAZ and BOULE genes modulate primordial germ cell and haploid gamete formation

    Science.gov (United States)

    Kee, Kehkooi; Angeles, Vanessa T; Flores, Martha; Nguyen, Ha Nam; Pera, Renee A Reijo

    2009-01-01

    The leading cause of infertility in men and women is quantitative and qualitative defects in human germ cell (oocyte and sperm) development. Yet, it has not been possible to examine the unique developmental genetics of human germ cell formation and differentiation due to inaccessibility of germ cells during fetal development. Although several studies have shown that germ cells can be differentiated from mouse and human embryonic stem cells, human germ cells differentiated in these studies generally did not develop beyond the earliest stages1-8. Here we used a germ cell reporter to quantitate and isolate primordial germ cells derived from both male and female hESCs. Then, by silencing and overexpressing genes that encode germ cell-specific cytoplasmic RNA-binding proteins (not transcription factors), we modulated human germ cell formation and developmental progression. We observed that human DAZL (Deleted in AZoospermia-Like) functions in primordial germ cell formation, whereas closely-related genes, DAZ and BOULE, promote later stages of meiosis and development of haploid gametes. These results are significant to the generation of gametes for future basic science and potential clinical applications. PMID:19865085

  4. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Gyu-Ho Lee

    2016-01-01

    Full Text Available The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH population of rice (Oryza sativa L.. A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning.

  5. Haploid deletion strains of Saccharomyces cerevisiae that determine survival during space flight

    Science.gov (United States)

    Johanson, Kelly; Allen, Patricia L.; Gonzalez-Villalobos, Romer A.; Nesbit, Jacqueline; Nickerson, Cheryl A.; Höner zu Bentrup, Kerstin; Wilson, James W.; Ramamurthy, Rajee; D'Elia, Riccardo; Muse, Kenneth E.; Hammond, Jeffrey; Freeman, Jake; Stodieck, Louis S.; Hammond, Timothy G.

    2007-02-01

    This study identifies genes that determine survival during a space flight, using the model eukaryotic organism, Saccharomyces cerevisiae. Select strains of a haploid yeast deletion series grew during storage in distilled water in space, but not in ground based static or clinorotation controls. The survival advantages in space in distilled water include a 133-fold advantage for the deletion of PEX19, a chaperone and import receptor for newly- synthesized class I peroxisomal membrane proteins, to 77-40 fold for deletion strains lacking elements of aerobic respiration, isocitrate metabolism, and mitochondrial electron transport. Following automated addition of rich growth media, the space flight was associated with a marked survival advantage of strains with deletions in catalytically active genes including hydrolases, oxidoreductases and transferases. When compared to static controls, space flight was associated with a marked survival disadvantage of deletion strains lacking transporter, antioxidant and catalytic activity. This study identifies yeast deletion strains with a survival advantage during storage in distilled water and space flight, and amplifies our understanding of the genes critical for survival in space.

  6. Exact Markov chain and approximate diffusion solution for haploid genetic drift with one-way mutation.

    Science.gov (United States)

    Hössjer, Ola; Tyvand, Peder A; Miloh, Touvia

    2016-02-01

    The classical Kimura solution of the diffusion equation is investigated for a haploid random mating (Wright-Fisher) model, with one-way mutations and initial-value specified by the founder population. The validity of the transient diffusion solution is checked by exact Markov chain computations, using a Jordan decomposition of the transition matrix. The conclusion is that the one-way diffusion model mostly works well, although the rate of convergence depends on the initial allele frequency and the mutation rate. The diffusion approximation is poor for mutation rates so low that the non-fixation boundary is regular. When this happens we perturb the diffusion solution around the non-fixation boundary and obtain a more accurate approximation that takes quasi-fixation of the mutant allele into account. The main application is to quantify how fast a specific genetic variant of the infinite alleles model is lost. We also discuss extensions of the quasi-fixation approach to other models with small mutation rates. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Assessment of mutagenic damage by monofunctional alkylating agents and gamma radiation in haploid and diploid frogs, Xenopus laevis

    International Nuclear Information System (INIS)

    Hart, D.R.; Armstrong, J.B.

    1984-01-01

    Adult male South African clawed frogs, Xenopus laevis, were mutagenized by 3-day immersion in aqueous solutions of ethyl methanesulfonate (EMS), diethyl nitrosamine (DEN), or ethyl nitrosourea (ENU), or by acute exposure to gamma radiation. They were then spawned repeatedly at 2-week intervals with untreated females, and embryonic survival of the progeny was used to assess genetic damage. Recessive lethal effects were assessed from reduced survival of androgenetic haploid progeny. Neither recessive nor dominant lethal effects were obtained after exposure to 100 mg/liter EMS or 2 g/liter DEN. At 250 mg/liter EMS, peak dominant lethality occurred 3-5 weeks after treatment. Most embryos hatched, but many were abnormal and died shortly after hatching. Haploid survival was significantly reduced over a broader period, from 1 to 13 weeks after mutagenesis. Treatment with 75 mg/liter ENU produced effects similar to the 250-mg/liter EMS mutagenesis. At 400 mg/liter EMS, the frequency and severity of the effects on both diploid and haploid embryos were increased over the lower dose. Gamma irradiation at 1500 R produced effects similar to the 400-mg/liter mutagenesis, except that peak dominant lethality extended from 1 to 7 weeks

  8. Production of haploid plant of 'Banpeiyu' pummelo [Citrus maxima (Burm.) Merr.] by pollination with soft X-ray-irradiated pollen

    International Nuclear Information System (INIS)

    Yahata, Masaki; Yasuda, Kiichi; Kunitake, Hisato; Nagasawa, Kohji; Harusaki, Seiichi; Komatsu, Haruki

    2010-01-01

    To induce haploid plants in Citrus maxima (Burm.) Merr. 'Banpeiyu', we evaluated the effect of pollination with soft X-ray-irradiated pollen on fruit set and seed development, and carried out ovule culture. When 'Banpeiyu' pummelo pistils were pollinated with X-ray-irradiated pollen of 'Fukuhara' sweet orange [C. sinensis (L.) Osbeck], the exposure doses affected the fruit set. The number of seeds per fruit was also affected by the exposure dose, and tended to decrease as the dose increased; however, all developed seeds obtained from these crosses were diploid. In the ovule culture of 'Banpeiyu' pummelo, six embryoids shown haploidy were obtained in all treatments. One haploid plantlet with 9 chromosomes was regenerated from an embryoid in a culture of ovules established 40 days after pollination with 400 Gray (Gy)-irradiated pollen of 'Tosa-buntan' pummelo (C. maxima). This haploid was suggested to be derived from 'Banpeiyu' pummelo by random amplified polymorphic DNA (RAPD) and cleaved amplified polymorphic sequence (CAPS) analysis. (author)

  9. Breeding of a xylose-fermenting hybrid strain by mating genetically engineered haploid strains derived from industrial Saccharomyces cerevisiae.

    Science.gov (United States)

    Inoue, Hiroyuki; Hashimoto, Seitaro; Matsushika, Akinori; Watanabe, Seiya; Sawayama, Shigeki

    2014-12-01

    The industrial Saccharomyces cerevisiae IR-2 is a promising host strain to genetically engineer xylose-utilizing yeasts for ethanol fermentation from lignocellulosic hydrolysates. Two IR-2-based haploid strains were selected based upon the rate of xylulose fermentation, and hybrids were obtained by mating recombinant haploid strains harboring heterogeneous xylose dehydrogenase (XDH) (wild-type NAD(+)-dependent XDH or engineered NADP(+)-dependent XDH, ARSdR), xylose reductase (XR) and xylulose kinase (XK) genes. ARSdR in the hybrids selected for growth rates on yeast extract-peptone-dextrose (YPD) agar and YP-xylose agar plates typically had a higher activity than NAD(+)-dependent XDH. Furthermore, the xylose-fermenting performance of the hybrid strain SE12 with the same level of heterogeneous XDH activity was similar to that of a recombinant strain of IR-2 harboring a single set of genes, XR/ARSdR/XK. These results suggest not only that the recombinant haploid strains retain the appropriate genetic background of IR-2 for ethanol production from xylose but also that ARSdR is preferable for xylose fermentation.

  10. Fully-Automated High-Throughput NMR System for Screening of Haploid Kernels of Maize (Corn by Measurement of Oil Content.

    Directory of Open Access Journals (Sweden)

    Hongzhi Wang

    Full Text Available One of the modern crop breeding techniques uses doubled haploid plants that contain an identical pair of chromosomes in order to accelerate the breeding process. Rapid haploid identification method is critical for large-scale selections of double haploids. The conventional methods based on the color of the endosperm and embryo seeds are slow, manual and prone to error. On the other hand, there exists a significant difference between diploid and haploid seeds generated by high oil inducer, which makes it possible to use oil content to identify the haploid. This paper describes a fully-automated high-throughput NMR screening system for maize haploid kernel identification. The system is comprised of a sampler unit to select a single kernel to feed for measurement of NMR and weight, and a kernel sorter to distribute the kernel according to the measurement result. Tests of the system show a consistent accuracy of 94% with an average screening time of 4 seconds per kernel. Field test result is described and the directions for future improvement are discussed.

  11. Fully-Automated High-Throughput NMR System for Screening of Haploid Kernels of Maize (Corn) by Measurement of Oil Content

    Science.gov (United States)

    Xu, Xiaoping; Huang, Qingming; Chen, Shanshan; Yang, Peiqiang; Chen, Shaojiang; Song, Yiqiao

    2016-01-01

    One of the modern crop breeding techniques uses doubled haploid plants that contain an identical pair of chromosomes in order to accelerate the breeding process. Rapid haploid identification method is critical for large-scale selections of double haploids. The conventional methods based on the color of the endosperm and embryo seeds are slow, manual and prone to error. On the other hand, there exists a significant difference between diploid and haploid seeds generated by high oil inducer, which makes it possible to use oil content to identify the haploid. This paper describes a fully-automated high-throughput NMR screening system for maize haploid kernel identification. The system is comprised of a sampler unit to select a single kernel to feed for measurement of NMR and weight, and a kernel sorter to distribute the kernel according to the measurement result. Tests of the system show a consistent accuracy of 94% with an average screening time of 4 seconds per kernel. Field test result is described and the directions for future improvement are discussed. PMID:27454427

  12. Equivalence, commensurability, value

    DEFF Research Database (Denmark)

    Albertsen, Niels

    2017-01-01

    Deriving value in Capital Marx uses three commensurability arguments (CA1-3). CA1 establishes equivalence in exchange as exchangeability with the same third commodity. CA2 establishes value as common denominator in commodities: embodied abstract labour. CA3 establishes value substance...... as commonality of labour: physiological labour. Tensions between these logics have permeated Marxist interpretations of value. Some have supported value as embodied labour (CA2, 3), others a monetary theory of value and value as ‘pure’ societal abstraction (ultimately CA1). They all are grounded in Marx....

  13. Human Genome Sequencing in Health and Disease

    Science.gov (United States)

    Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

    2013-01-01

    Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

  14. Waste Determination Equivalency - 12172

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, Rebecca D. [Savannah River Remediation (United States)

    2012-07-01

    by the Secretary of Energy in January of 2006 based on proposed processing techniques with the expectation that it could be revised as new processing capabilities became viable. Once signed, however, it became evident that any changes would require lengthy review and another determination signed by the Secretary of Energy. With the maturation of additional salt removal technologies and the extension of the SWPF start-up date, it becomes necessary to define 'equivalency' to the processes laid out in the original determination. For the purposes of SRS, any waste not processed through Interim Salt Processing must be processed through SWPF or an equivalent process, and therefore a clear statement of the requirements for a process to be equivalent to SWPF becomes necessary. (authors)

  15. Critical mutation rate has an exponential dependence on population size in haploid and diploid populations.

    Directory of Open Access Journals (Sweden)

    Elizabeth Aston

    Full Text Available Understanding the effect of population size on the key parameters of evolution is particularly important for populations nearing extinction. There are evolutionary pressures to evolve sequences that are both fit and robust. At high mutation rates, individuals with greater mutational robustness can outcompete those with higher fitness. This is survival-of-the-flattest, and has been observed in digital organisms, theoretically, in simulated RNA evolution, and in RNA viruses. We introduce an algorithmic method capable of determining the relationship between population size, the critical mutation rate at which individuals with greater robustness to mutation are favoured over individuals with greater fitness, and the error threshold. Verification for this method is provided against analytical models for the error threshold. We show that the critical mutation rate for increasing haploid population sizes can be approximated by an exponential function, with much lower mutation rates tolerated by small populations. This is in contrast to previous studies which identified that critical mutation rate was independent of population size. The algorithm is extended to diploid populations in a system modelled on the biological process of meiosis. The results confirm that the relationship remains exponential, but show that both the critical mutation rate and error threshold are lower for diploids, rather than higher as might have been expected. Analyzing the transition from critical mutation rate to error threshold provides an improved definition of critical mutation rate. Natural populations with their numbers in decline can be expected to lose genetic material in line with the exponential model, accelerating and potentially irreversibly advancing their decline, and this could potentially affect extinction, recovery and population management strategy. The effect of population size is particularly strong in small populations with 100 individuals or less; the

  16. Quantifying rooting at depth in a wheat doubled haploid population with introgression from wild emmer.

    Science.gov (United States)

    Clarke, Christina K; Gregory, Peter J; Lukac, Martin; Burridge, Amanda J; Allen, Alexandra M; Edwards, Keith J; Gooding, Mike J

    2017-09-01

    The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine whether genetic effects found in the field could have been predicted by other assessment methods. Roots of doubled haploid (DH) lines from a winter wheat ('Shamrock' × 'Shango') population were assessed using a seedling screen in moist paper rolls, in rhizotrons to the end of tillering, and in the field post-anthesis. A linkage map was produced using single nucleotide polymorphism markers to identify quantitative trait loci (QTLs) for rooting traits. Shamrock had greater root length density (RLD) at depth than Shango, in the field and within the rhizotrons. The DH population exhibited diversity for rooting traits within the three environments studied. QTLs were identified on chromosomes 5D, 6B and 7B, explaining variation in RLD post-anthesis in the field. Effects associated with the non-glaucous trait on RLD interacted significantly with depth in the field, and some of this interaction mapped to 2BS. The effect of genotype was strongly influenced by the method of root assessment, e.g. glaucousness expressed in the field was negatively associated with root length in the rhizotrons, but positively associated with length in the seedling screen. To our knowledge, this is the first study to identify QTLs for rooting at depth in field-grown wheat at mature growth stages. Within the population studied here, our results are consistent with the hypothesis that some of the variation in rooting is associated with recent introgression from wild emmer. The expression of genetic effects differed between the methods of root assessment. © The Author 2017. Published by Oxford University Press on behalf of the

  17. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  18. Quantification of the equivalence principle

    International Nuclear Information System (INIS)

    Epstein, K.J.

    1978-01-01

    Quantitative relationships illustrate Einstein's equivalence principle, relating it to Newton's ''fictitious'' forces arising from the use of noninertial frames, and to the form of the relativistic time dilatation in local Lorentz frames. The equivalence principle can be interpreted as the equivalence of general covariance to local Lorentz covariance, in a manner which is characteristic of Riemannian and pseudo-Riemannian geometries

  19. Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.).

    Science.gov (United States)

    Bohn, Martin O; Marroquin, Juan J; Flint-Garcia, Sherry; Dashiell, Kenton; Willmot, David B; Hibbard, Bruce E

    2018-02-09

    Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. New recommendations for dose equivalent

    International Nuclear Information System (INIS)

    Bengtsson, G.

    1985-01-01

    In its report 39, the International Commission on Radiation Units and Measurements (ICRU), has defined four new quantities for the determination of dose equivalents from external sources: the ambient dose equivalent, the directional dose equivalent, the individual dose equivalent, penetrating and the individual dose equivalent, superficial. The rationale behind these concepts and their practical application are discussed. Reference is made to numerical values of these quantities which will be the subject of a coming publication from the International Commission on Radiological Protection, ICRP. (Author)

  1. System equivalent model mixing

    Science.gov (United States)

    Klaassen, Steven W. B.; van der Seijs, Maarten V.; de Klerk, Dennis

    2018-05-01

    This paper introduces SEMM: a method based on Frequency Based Substructuring (FBS) techniques that enables the construction of hybrid dynamic models. With System Equivalent Model Mixing (SEMM) frequency based models, either of numerical or experimental nature, can be mixed to form a hybrid model. This model follows the dynamic behaviour of a predefined weighted master model. A large variety of applications can be thought of, such as the DoF-space expansion of relatively small experimental models using numerical models, or the blending of different models in the frequency spectrum. SEMM is outlined, both mathematically and conceptually, based on a notation commonly used in FBS. A critical physical interpretation of the theory is provided next, along with a comparison to similar techniques; namely DoF expansion techniques. SEMM's concept is further illustrated by means of a numerical example. It will become apparent that the basic method of SEMM has some shortcomings which warrant a few extensions to the method. One of the main applications is tested in a practical case, performed on a validated benchmark structure; it will emphasize the practicality of the method.

  2. The equivalence principle

    International Nuclear Information System (INIS)

    Smorodinskij, Ya.A.

    1980-01-01

    The prerelativistic history of the equivalence principle (EP) is presented briefly. Its role in history of the general relativity theory (G.R.T.) discovery is elucidated. A modern idea states that the ratio of inert and gravitational masses does not differ from 1 at least up to the 12 sign after comma. Attention is paid to the difference of the gravitational field from electromagnetic one. The difference is as follows, the energy of the gravitational field distributed in space is the source of the field. These fields always interact at superposition. Electromagnetic fields from different sources are put together. On the basis of EP it is established the Sun field interact with the Earth gravitational energy in the same way as with any other one. The latter proves the existence of gravitation of the very gravitational field to a heavy body. A problem on gyroscope movement in the Earth gravitational field is presented as a paradox. The calculation has shown that gyroscope at satellite makes a positive precession, and its axis turns in an angle equal to α during a turn of the satellite round the Earth, but because of the space curvature - into the angle two times larger than α. A resulting turn is equal to 3α. It is shown on the EP basis that the polarization plane in any coordinate system does not turn when the ray of light passes in the gravitational field. Together with the historical value of EP noted is the necessity to take into account the requirements claimed by the EP at description of the physical world

  3. Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.

    Science.gov (United States)

    Santos, Anselmo Azevedo; Penha, Helen Alves; Bellec, Arnaud; Munhoz, Carla de Freitas; Pedrosa-Harand, Andrea; Bergès, Hélène; Vieira, Maria Lucia Carneiro

    2014-09-26

    The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n=9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome

  4. Logically automorphically equivalent knowledge bases

    OpenAIRE

    Aladova, Elena; Plotkin, Tatjana

    2017-01-01

    Knowledge bases theory provide an important example of the field where applications of universal algebra and algebraic logic look very natural, and their interaction with practical problems arising in computer science might be very productive. In this paper we study the equivalence problem for knowledge bases. Our interest is to find out how the informational equivalence is related to the logical description of knowledge. Studying various equivalences of knowledge bases allows us to compare d...

  5. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

    Directory of Open Access Journals (Sweden)

    Marisa E. Miller

    2018-02-01

    Full Text Available Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae.

  6. Testing statistical hypotheses of equivalence

    CERN Document Server

    Wellek, Stefan

    2010-01-01

    Equivalence testing has grown significantly in importance over the last two decades, especially as its relevance to a variety of applications has become understood. Yet published work on the general methodology remains scattered in specialists' journals, and for the most part, it focuses on the relatively narrow topic of bioequivalence assessment.With a far broader perspective, Testing Statistical Hypotheses of Equivalence provides the first comprehensive treatment of statistical equivalence testing. The author addresses a spectrum of specific, two-sided equivalence testing problems, from the

  7. Genomic and karyotypic variation in Drosophila parasitoids (Hymenoptera, Cynipoidea, Figitidae

    Directory of Open Access Journals (Sweden)

    Vladimir Gokhman

    2011-08-01

    Full Text Available Drosophila melanogaster Meigen, 1830 has served as a model insect for over a century. Sequencing of the 11 additional Drosophila Fallen, 1823 species marks substantial progress in comparative genomics of this genus. By comparison, practically nothing is known about the genome size or genome sequences of parasitic wasps of Drosophila. Here, we present the first comparative analysis of genome size and karyotype structures of Drosophila parasitoids of the Leptopilina Förster, 1869 and Ganaspis Förster, 1869 species. The gametic genome size of Ganaspis xanthopoda (Ashmead, 1896 is larger than those of the three Leptopilina species studied. The genome sizes of all parasitic wasps studied here are also larger than those known for all Drosophila species. Surprisingly, genome sizes of these Drosophila parasitoids exceed the average value known for all previously studied Hymenoptera. The haploid chromosome number of both Leptopilina heterotoma (Thomson, 1862 and L. victoriae Nordlander, 1980 is ten. A chromosomal fusion appears to have produced a distinct karyotype for L. boulardi (Barbotin, Carton et Keiner-Pillault, 1979 (n = 9, whose genome size is smaller than that of wasps of the L. heterotoma clade. Like L. boulardi, the haploid chromosome number for G. xanthopoda is also nine. Our studies reveal a positive, but non linear, correlation between the genome size and total chromosome length in Drosophila parasitoids. These Drosophila parasitoids differ widely in their host range, and utilize different infection strategies to overcome host defense. Their comparative genomics, in relation to their exceptionally well-characterized hosts, will prove to be valuable for understanding the molecular basis of the host-parasite arms race and how such mechanisms shape the genetic structures of insect communities.

  8. An in vitro, short-term culture method for mammalian haploid round spermatids amenable for molecular manipulation.

    Science.gov (United States)

    Dehnugara, Tushna; Dhar, Surbhi; Rao, M R Satyanarayana

    2012-01-01

    Extensive chromatin remodeling is a characteristic feature of mammalian spermiogenesis. To date, methods for the molecular manipulation of haploid spermatids are not available as there is a lack of a well-established culture system. Biochemical experiments and knockout studies reveal only the final outcome; studying the incremental details of the intricate mechanisms involved is still a challenge. We have established an in vitro culture system for pure haploid round spermatids isolated from rat testes that can be maintained with good viability for up to 72 hr. Changes in cell morphology and flagellar growth were also studied in the cultured spermatids. Further, we have demonstrated that upon treatment of cells with specific histone deacetylase inhibitors, sodium butyrate and trichostatin A, there is an increase in the hyperacetylation status of histone H4, mimicking an important event characteristic of histone replacement process that occurs during later stages of spermiogenesis. We have also tried various methods for introducing DNA and protein into these round spermatids in culture, and report that while DNA transfection is still a challenging task, protein transfection could be achieved using Chariot™ peptide as a transfection reagent. Thus, the method described here sets a stage to study the molecular roles of spermatid-specific proteins and chromatin remodelers in the cellular context. Copyright © 2011 Wiley Periodicals, Inc.

  9. Evaluating the Production of Doubled Haploid Wheat Lines Using Various Methods of Wheat and Maize Crossing to Develop Heat-Tolerant Wheat Varieties

    Directory of Open Access Journals (Sweden)

    Tayebeh BAKHSHI

    2017-02-01

    Full Text Available Abstract. In this study, chromosome elimination method was used to develop doubled haploid wheat lines via crosses with maize. The plant materials used included 11, F1 wheat genotypes and maize genotype BC572. In these crosses, the maize plant was used as the male parent.Three methods of haploid production in wheat comprising conventional (A, detached-tiller culture (B and intermediate (C techniques were used and compared. The traits such as the number of seeds set, the number of embryos obtained and the number of haploid seedlings produced were studied. Comparisons showed that among various methods of storing wheat spikes, method (C was better than other techniques in terms of the percentage of seed production, embryo formation and haploid seedling production. Also, in all three methods, the percentage of seed production, the percentage of embryo formation and the percentage of haploid seedling production were respectively equal to 76.84, 25.22 and 51.89. Among the wheat genotypes in all three methods, genotype DH-133 with 87.28 percent seed set and genotype DH-132 with 32.71 percent embryo formation and 65.08 percent haploid seedling production were the best genotypes. A total of 92 doubled haploid lines were produced. In the field evaluations of 86 doubled haploid lines, traits such as growing season, plant height, lodging, kernel yield and 1000 kernel weight were examined. Finally, 3 lines were selected for adaptation and stability testing under heat stress conditions.Keywords: Wheat, Doubled haploid, Chromosome elimination, Detached-tiller culture Özet. Bu çalışmada, mısır ile çaprazlarla çift katlı haploid buğday hatlarının geliştirilmesi için kromozom eliminasyon yöntemi kullanılmıştır. Kullanılan bitki materyalleri 11, F1 buğday genotipleri ve BC572 mısır genotipini içermektedir. Bu çaprazlarda, mısır bitkisi erkek ebeveyn olarak kullanılmıştır. Geleneksel (A, ayrık-yeke kültürü (B ve ara (C

  10. SAPONIFICATION EQUIVALENT OF DASAMULA TAILA

    OpenAIRE

    Saxena, R. B.

    1994-01-01

    Saponification equivalent values of Dasamula taila are very useful for the technical and analytical work. It gives the mean molecular weight of the glycerides and acids present in Dasamula Taila. Saponification equivalent values of Dasamula taila are reported in different packings.

  11. Saponification equivalent of dasamula taila.

    Science.gov (United States)

    Saxena, R B

    1994-07-01

    Saponification equivalent values of Dasamula taila are very useful for the technical and analytical work. It gives the mean molecular weight of the glycerides and acids present in Dasamula Taila. Saponification equivalent values of Dasamula taila are reported in different packings.

  12. A study on lead equivalent

    International Nuclear Information System (INIS)

    Lin Guanxin

    1991-01-01

    A study on the rules in which the lead equivalent of lead glass changes with the energy of X rays or γ ray is described. The reason of this change is discussed and a new testing method of lead equivalent is suggested

  13. Determination of dose equivalent with tissue-equivalent proportional counters

    International Nuclear Information System (INIS)

    Dietze, G.; Schuhmacher, H.; Menzel, H.G.

    1989-01-01

    Low pressure tissue-equivalent proportional counters (TEPC) are instruments based on the cavity chamber principle and provide spectral information on the energy loss of single charged particles crossing the cavity. Hence such detectors measure absorbed dose or kerma and are able to provide estimates on radiation quality. During recent years TEPC based instruments have been developed for radiation protection applications in photon and neutron fields. This was mainly based on the expectation that the energy dependence of their dose equivalent response is smaller than that of other instruments in use. Recently, such instruments have been investigated by intercomparison measurements in various neutron and photon fields. Although their principles of measurements are more closely related to the definition of dose equivalent quantities than those of other existing dosemeters, there are distinct differences and limitations with respect to the irradiation geometry and the determination of the quality factor. The application of such instruments for measuring ambient dose equivalent is discussed. (author)

  14. Genome size of 14 species of fireflies (Insecta, Coleoptera, Lampyridae

    Directory of Open Access Journals (Sweden)

    Gui-Chun Liu

    2017-11-01

    Full Text Available Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies (Lampyridae (two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis were estimated by propidium iodide (PI-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0.42 to 1.31 pg, a 3.1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.

  15. What is correct: equivalent dose or dose equivalent

    International Nuclear Information System (INIS)

    Franic, Z.

    1994-01-01

    In Croatian language some physical quantities in radiation protection dosimetry have not precise names. Consequently, in practice either terms in English or mathematical formulas are used. The situation is even worse since the Croatian language only a limited number of textbooks, reference books and other papers are available. This paper compares the concept of ''dose equivalent'' as outlined in International Commission on Radiological Protection (ICRP) recommendations No. 26 and newest, conceptually different concept of ''equivalent dose'' which is introduced in ICRP 60. It was found out that Croatian terminology is both not uniform and unprecise. For the term ''dose equivalent'' was, under influence of Russian and Serbian languages, often used as term ''equivalent dose'' even from the point of view of ICRP 26 recommendations, which was not justified. Unfortunately, even now, in Croatia the legal unit still ''dose equivalent'' defined as in ICRP 26, but the term used for it is ''equivalent dose''. Therefore, in Croatian legislation a modified set of quantities introduced in ICRP 60, should be incorporated as soon as possible

  16. Draft genome sequence of the rubber tree Hevea brasiliensis

    Directory of Open Access Journals (Sweden)

    Rahman Ahmad Yamin Abdul

    2013-02-01

    Full Text Available Abstract Background Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR. NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. Results Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. Conclusions The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.

  17. Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae: a comparison with haploid males, queens and workers

    Directory of Open Access Journals (Sweden)

    Andreia A. Borges

    2011-01-01

    Full Text Available In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

  18. Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae) - A comparison with haploid males, queens and workers.

    Science.gov (United States)

    Borges, Andreia A; Humann, Fernanda C; Oliveira Campos, Lucio A; Tavares, Mara G; Hartfelder, Klaus

    2011-10-01

    In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid) on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i) gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii) in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

  19. The effects of quantitative fecundity in the haploid stage on reproductive success and diploid fitness in the aquatic peat moss Sphagnum macrophyllum.

    Science.gov (United States)

    Johnson, M G; Shaw, A J

    2016-06-01

    A major question in evolutionary biology is how mating patterns affect the fitness of offspring. However, in animals and seed plants it is virtually impossible to investigate the effects of specific gamete genotypes. In bryophytes, haploid gametophytes grow via clonal propagation and produce millions of genetically identical gametes throughout a population. The main goal of this research was to test whether gamete identity has an effect on the fitness of their diploid offspring in a population of the aquatic peat moss Sphagnum macrophyllum. We observed a heavily male-biased sex ratio in gametophyte plants (ramets) and in multilocus microsatellite genotypes (genets). There was a steeper relationship between mating success (number of different haploid mates) and fecundity (number of diploid offspring) for male genets compared with female genets. At the sporophyte level, we observed a weak effect of inbreeding on offspring fitness, but no effect of brood size (number of sporophytes per maternal ramet). Instead, the identities of the haploid male and haploid female parents were significant contributors to variance in fitness of sporophyte offspring in the population. Our results suggest that intrasexual gametophyte/gamete competition may play a role in determining mating success in this population.

  20. Obtaining apple haploid plants (Malus X domestica Borkh.) from in situ parthenogenesis induced by irradiated pollen and in vitro culture of immature seeds

    International Nuclear Information System (INIS)

    Zhang, Y.X.; Lespinasse, Y.; Chevreau, E.

    1988-01-01

    Two apple varieties, ''Erovan'' and ''Lodi'', have been pollinated with pollen carrying the marker gene R irradiated by gamma rays from Cobalt 60 with doses of 500, 1000 and 1500 Gy. By in vitro cultures of the immature seeds removed 7 to 13 weeks after pollination, haploid plants (2n=x=17) have been obtained from ''Erovan'' [fr

  1. Plant regeneration from haploid cell suspension-derived protoplasts of Mediterranean rice (Oryza sativa L. cv. Miara).

    Science.gov (United States)

    Guiderdoni, E; Chaïr, H

    1992-11-01

    More than 750 plants were regenerated from protoplasts isolated from microspore callus-derived cell suspensions of the Mediterranean japonica rice Miara, using a nurse-feeder technique and N6-based culture medium. The mean plating efficiency and the mean regeneration ability of the protocalluses were 0.5% and 49% respectively. Flow cytometric evaluation of the DNA contents of 7 month old-cell and protoplast suspensions showed that they were still haploid. Contrastingly, the DNA contents of leaf cell nuclei of the regenerated protoclones ranged from 1C to 5C including 60% 2C plants. This was consistent with the morphological type and the fertility of the mature plants. These results and the absence of chimeric plants suggest that polyploidization occurred during the early phase of protoplast culture.

  2. Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).

    Science.gov (United States)

    Xu, Yan; Huang, Long; Ji, Dehua; Chen, Changsheng; Zheng, Hongkun; Xie, Chaotian

    2015-09-21

    Pyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis. In total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM. The first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical

  3. Desenvolvimento de populações duplo-haplóides de cevada cervejeira associadas à atividade das enzimas (1-3, 1-4-β-glucanases Development of doubled-haploids populations in malting barley associated to activity of enzymes (1-3, 1-4-β-glucanases

    Directory of Open Access Journals (Sweden)

    Janaína Endres Georg-Kraemer

    2011-05-01

    culture protocol. Two crosses were performed with contrasting cultivars to (1-3, 1-4-β-glucanases activity. Parental cultivars used were 'MN 698' and 'CEV 97047' for the development of 'green malt' population (MV and Embrapa 127 and 'CEV 96025' for the development of "dry malt" population (MS. For the MS and MV populations, 10,734 and 4,139 anthers were cultured, respectively. MV population produced 50% more green seedlings as compared to MS population, which reflects the importance of genotype to the culturing of anthers and to regeneration. Most doubled-haploid adult plants were obtained by in vitro spontaneous duplication of the haploid genome, which occurred in 66% of plants from the MS population and 76% of plants from the MV population. Haploid, triploid and tetraploid individuals were also observed, though at low frequencies. The anther culture protocol afforded to develop 204 double-haploid lineages, of which 72 were generated by the 'dry malt' population and 132 from the "green malt" population. This material should be considered as important germplasm for barley genetic improvement.

  4. Symmetries of dynamically equivalent theories

    Energy Technology Data Exchange (ETDEWEB)

    Gitman, D.M.; Tyutin, I.V. [Sao Paulo Univ., SP (Brazil). Inst. de Fisica; Lebedev Physics Institute, Moscow (Russian Federation)

    2006-03-15

    A natural and very important development of constrained system theory is a detail study of the relation between the constraint structure in the Hamiltonian formulation with specific features of the theory in the Lagrangian formulation, especially the relation between the constraint structure with the symmetries of the Lagrangian action. An important preliminary step in this direction is a strict demonstration, and this is the aim of the present article, that the symmetry structures of the Hamiltonian action and of the Lagrangian action are the same. This proved, it is sufficient to consider the symmetry structure of the Hamiltonian action. The latter problem is, in some sense, simpler because the Hamiltonian action is a first-order action. At the same time, the study of the symmetry of the Hamiltonian action naturally involves Hamiltonian constraints as basic objects. One can see that the Lagrangian and Hamiltonian actions are dynamically equivalent. This is why, in the present article, we consider from the very beginning a more general problem: how the symmetry structures of dynamically equivalent actions are related. First, we present some necessary notions and relations concerning infinitesimal symmetries in general, as well as a strict definition of dynamically equivalent actions. Finally, we demonstrate that there exists an isomorphism between classes of equivalent symmetries of dynamically equivalent actions. (author)

  5. Matching of equivalent field regions

    DEFF Research Database (Denmark)

    Appel-Hansen, Jørgen; Rengarajan, S.B.

    2005-01-01

    In aperture problems, integral equations for equivalent currents are often found by enforcing matching of equivalent fields. The enforcement is made in the aperture surface region adjoining the two volumes on each side of the aperture. In the case of an aperture in a planar perfectly conducting...... screen, having the same homogeneous medium on both sides and an impressed current on one aide, an alternative procedure is relevant. We make use of the fact that in the aperture the tangential component of the magnetic field due to the induced currents in the screen is zero. The use of such a procedure...... shows that equivalent currents can be found by a consideration of only one of the two volumes into which the aperture plane divides the space. Furthermore, from a consideration of an automatic matching at the aperture, additional information about tangential as well as normal field components...

  6. Transposition of a Ds element from a plasmid into the plant genome in Nicotiana plumbaginifolia protoplast-derived cells.

    Science.gov (United States)

    Houba-Hérin, N; Domin, M; Pédron, J

    1994-07-01

    Nicotiana plumbaginifolia haploid protoplasts were co-transformed with two plasmids, one with a NPT-II/Ds element and one with a gene encoding an amino-terminal truncated Ac transposase. It is shown that Ds can efficiently transpose from extrachromosomal DNA to N. plumbaginifolia chromosomes when the Ac transposase gene is present in trans. Ds has been shown to have transposed into the plant genome in a limited number of copies (1.9 copies per genome), for 21/32 transgenic lines tested. The flanking sequences present in the original plasmid are missing in these 21 plants. In only two of 21 plants was part of the transposase construct integrated. By segregation analysis of transgenic progeny, Ds was shown to be present in the heterozygous state in 10 lines even though haploid protoplasts had been originally transformed. This observation could indicate that integration occurred after or during DNA replication that leads to protoplast diploidization.

  7. Teleparallel equivalent of Lovelock gravity

    Science.gov (United States)

    González, P. A.; Vásquez, Yerko

    2015-12-01

    There is a growing interest in modified gravity theories based on torsion, as these theories exhibit interesting cosmological implications. In this work inspired by the teleparallel formulation of general relativity, we present its extension to Lovelock gravity known as the most natural extension of general relativity in higher-dimensional space-times. First, we review the teleparallel equivalent of general relativity and Gauss-Bonnet gravity, and then we construct the teleparallel equivalent of Lovelock gravity. In order to achieve this goal, we use the vielbein and the connection without imposing the Weitzenböck connection. Then, we extract the teleparallel formulation of the theory by setting the curvature to null.

  8. Attainment of radiation equivalency principle

    International Nuclear Information System (INIS)

    Shmelev, A.N.; Apseh, V.A.

    2004-01-01

    Problems connected with the prospects for long-term development of the nuclear energetics are discussed. Basic principles of the future large-scale nuclear energetics are listed, primary attention is the safety of radioactive waste management of nuclear energetics. The radiation equivalence principle means close of fuel cycle and management of nuclear materials transportation with low losses on spent fuel and waste processing. Two aspects are considered: radiation equivalence in global and local aspects. The necessity of looking for other strategies of fuel cycle management in full-scale nuclear energy on radioactive waste management is supported [ru

  9. Comments on field equivalence principles

    DEFF Research Database (Denmark)

    Appel-Hansen, Jørgen

    1987-01-01

    It is pointed Out that often-used arguments based on a short-circuit concept in presentations of field equivalence principles are not correct. An alternative presentation based on the uniqueness theorem is given. It does not contradict the results obtained by using the short-circuit concept...

  10. Study of variation of tocochromanol and phytosterol contents in black and yellow seeds of Brassica napus L. doubled haploid populations.

    Science.gov (United States)

    Cegielska-Taras, Teresa; Nogala-Kałucka, Małgorzata; Szala, Laurencja; Siger, Aleksander

    2016-01-01

    In the study, an analysis of tocopherols, plastochomanol-8 and phytosterols was conducted using DH lines obtained from F1 hybrids of reciprocal crosses between yellow- and black-seeded lines. The biological material for the study consisted of two DH populations of winter oilseed rape obtained from F1 hybrids of reciprocal crosses between two DH lines: yellow- and black-seeded. Seed color was determined using a ColorFlex spectrophotometer. Fat content was determined via pulsed NMR. The levels of tocopherols, and plastochromanol-8 are analyzed using HPLC. Phytosterol contents and composition were determined by the GC method. The fat content of the black-seeded parental line was 49% and this was higher than that of the yellow-seeded parental line (44%). The fat content of DH line populations ranged from 44 to 51%. Total tocopherol content ranged from 460 to 602 mg/kg and the α-T/γ-T ratio was from 0.66 to 1.09. In parental lines H2-26 and Z-114 the total tocopherol content was 534 and 525 mg/kg, but the α-T/γ-T ratios were 0.81 and 1.21, respectively. The yellow-seeded parental line (Z-114) was characterized by a higher PC-8 content (81 mg/kg) than the H2-26 black-seeded parental line (58 mg/kg). The largest part of the total phytosterol content in seeds of both populations was β-sitosterol from 976 to 2148 mg/kg, followed by campasterol, from 636 to 1364 mg/kg, and brassicasterol from 375 to 678 mg/kg. The total tocopherol content ranged from 462 to 595 mg/kg (population HxZ) and from 460 to 602 mg/kg (population ZxH). Significantly positive correlations were observed between the seed color with α-T (r = 0.38, p phytosterol content were not noted. Considering the range of genetic variation among doubled haploids of two populations, selected DH lines may be good parents for further breeding programs focused on increasing the amount and improving the quality of oilseed rapeseed oil. However, further studies will also be made to determine the influence of the

  11. Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita.

    Science.gov (United States)

    Yamazaki, Tomokazu; Ichihara, Kensuke; Suzuki, Ryogo; Oshima, Kenshiro; Miyamura, Shinichi; Kuwano, Kazuyoshi; Toyoda, Atsushi; Suzuki, Yutaka; Sugano, Sumio; Hattori, Masahira; Kawano, Shigeyuki

    2017-09-15

    The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt - and mt + strains identified highly rearranged MT loci of 1.0 and 1.5 Mb in size and containing 46 and 67 genes, respectively, including 23 gametologs. Molecular evolutionary analyses suggested that the MT loci diverged over a prolonged period in the individual mating types after their establishment in an ancestor. A gene encoding an RWP-RK domain-containing protein was found in the mt - MT locus but was not an ortholog of the chlorophycean mating type determination gene MID. Taken together, our results suggest that the genomic structure and its evolutionary history in the U. partita MT locus are similar to those on other UV chromosomes and that the MT locus genes are quite different from those of Chlorophyceae.

  12. Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy

    DEFF Research Database (Denmark)

    Kaas, Christian Schrøder; Kristensen, Claus; Betenbaugh, Michael J.

    2015-01-01

    Background: The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins.  Results: Here we present the genomic sequence...... of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC -> AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing...... in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find similar to 2...

  13. Generation of meiomaps of genome-wide recombination and chromosome segregation in human oocytes

    DEFF Research Database (Denmark)

    Ottolini, Christian S; Capalbo, Antonio; Newnham, Louise

    2016-01-01

    We have developed a protocol for the generation of genome-wide maps (meiomaps) of recombination and chromosome segregation for the three products of human female meiosis: the first and second polar bodies (PB1 and PB2) and the corresponding oocyte. PB1 is biopsied and the oocyte is artificially......-nucleotide polymorphisms (SNPs) genome-wide by microarray. Informative maternal heterozygous SNPs are phased using a haploid PB2 or oocyte as a reference. A simple algorithm is then used to identify the maternal haplotypes for each chromosome, in all of the products of meiosis for each oocyte. This allows mapping...

  14. EQUIVALENCE VERSUS NON-EQUIVALENCE IN ECONOMIC TRANSLATION

    Directory of Open Access Journals (Sweden)

    Cristina, Chifane

    2012-01-01

    Full Text Available This paper aims at highlighting the fact that “equivalence” represents a concept worth revisiting and detailing upon when tackling the translation process of economic texts both from English into Romanian and from Romanian into English. Far from being exhaustive, our analysis will focus upon the problems arising from the lack of equivalence at the word level. Consequently, relevant examples from the economic field will be provided to account for the following types of non-equivalence at word level: culturespecific concepts; the source language concept is not lexicalised in the target language; the source language word is semantically complex; differences in physical and interpersonal perspective; differences in expressive meaning; differences in form; differences in frequency and purpose of using specific forms and the use of loan words in the source text. Likewise, we shall illustrate a number of translation strategies necessary to deal with the afore-mentioned cases of non-equivalence: translation by a more general word (superordinate; translation by a more neutral/less expressive word; translation by cultural substitution; translation using a loan word or loan word plus explanation; translation by paraphrase using a related word; translation by paraphrase using unrelated words; translation by omission and translation by illustration.

  15. In vitro haploid zygotic embryogenesis due to pollination with maize pollen and induced in vitro androgenesis in Czech wheat breeding genotypes

    Czech Academy of Sciences Publication Activity Database

    Vagera, Jiří; Nesvadba, Z.; Martinek, P.; Ohnoutková, Ludmila

    2001-01-01

    Roč. 47, č. 5 (2001), s. 193-200 ISSN 0370-663X R&D Projects: GA ČR GA521/01/1383; GA ČR GV521/96/K117 Institutional research plan: CEZ:AV0Z5038910 Keywords : haploid zygote * embryogenesis * maize pollen Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.237, year: 2001

  16. Expression Patterns of ERF Genes Underlying Abiotic Stresses in Di-Haploid Populus simonii × P. nigra

    Directory of Open Access Journals (Sweden)

    Shengji Wang

    2014-01-01

    Full Text Available 176 ERF genes from Populus were identified by bioinformatics analysis, 13 of these in di-haploid Populus simonii × P. nigra were investigate by real-time RT-PCR, the results demonstrated that 13 ERF genes were highly responsive to salt stress, drought stress and ABA treatment, and all were expressed in root, stem, and leaf tissues, whereas their expression levels were markedly different in the various tissues. In roots, PthERF99, 110, 119, and 168 were primarily downregulated under drought and ABA treatment but were specifically upregulated under high salt condition. Interestingly, in poplar stems, all ERF genes showed the similar trends in expression in response to NaCl stress, drought stress, and ABA treatment, indicating that they may not play either specific or unique roles in stems in abiotic stress responses. In poplar leaves, PthERF168 was highly induced by ABA treatment, but was suppressed by high salinity and drought stresses, implying that PthERF168 participated in the ABA signaling pathway. The results of this study indicated that ERF genes could play essential but distinct roles in various plant tissues in response to different environment cues and hormonal treatment.

  17. Response of Barley Double Haploid Lines to the Grain Yield and Morphological Traits under Water Deficit Stress Conditions

    Directory of Open Access Journals (Sweden)

    Maroof Khalily

    2017-04-01

    Full Text Available To study the relationships of grain yield and some of agro-morphological traits in 40 doubled haploid (DH lines along with parental and three check genotypes in a randomized complete block design with two replications under two water regimes (normal and stress were evaluated during 2011-2012 and 2012-2013 growing seasons. Combined analysis of variance showed significant difference for all the traits in terms of the year, water regimes, lines, and and line × year. Comparison of group means, between non-stress and stress conditions, showed that DH lines had the lowest reduction percentage for the number of grains per spike, thousand grain weight, grain yield and biological yield as opposed to check genotypes. The correlation between grain yield with biological yield, harvest index, thousand grain weight, and hectoliter of kernel weight in both conditions, were highly significant and positive. Based on stepwise regression the peduncle length, number of seeds per spike, thousand seed weight, and hectoliter of kernel weight had important effect on increasing seed yield. The result of path analysis showed that these traits had the highest direct effect on grain yield. Based on mean comparisons of morphological characters as well as STI and GMP indices it can be concluded that lines No.11, 13, 14, 24, 29, 30, 35 and 39 were distinguished to be desirable lines for grain yield and their related traits and also tolerant lines in terms of response to drought stress conditions.

  18. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust.

    Science.gov (United States)

    Miller, Marisa E; Zhang, Ying; Omidvar, Vahid; Sperschneider, Jana; Schwessinger, Benjamin; Raley, Castle; Palmer, Jonathan M; Garnica, Diana; Upadhyaya, Narayana; Rathjen, John; Taylor, Jennifer M; Park, Robert F; Dodds, Peter N; Hirsch, Cory D; Kianian, Shahryar F; Figueroa, Melania

    2018-02-20

    Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae , is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenae IMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae , which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae , resources to study the

  19. The Source Equivalence Acceleration Method

    International Nuclear Information System (INIS)

    Everson, Matthew S.; Forget, Benoit

    2015-01-01

    Highlights: • We present a new acceleration method, the Source Equivalence Acceleration Method. • SEAM forms an equivalent coarse group problem for any spatial method. • Equivalence is also formed across different spatial methods and angular quadratures. • Testing is conducted using OpenMOC and performance is compared with CMFD. • Results show that SEAM is preferable for very expensive transport calculations. - Abstract: Fine-group whole-core reactor analysis remains one of the long sought goals of the reactor physics community. Such a detailed analysis is typically too computationally expensive to be realized on anything except the largest of supercomputers. Recondensation using the Discrete Generalized Multigroup (DGM) method, though, offers a relatively cheap alternative to solving the fine group transport problem. DGM, however, suffered from inconsistencies when applied to high-order spatial methods. While an exact spatial recondensation method was developed and provided full spatial consistency with the fine group problem, this approach substantially increased memory requirements for realistic problems. The method described in this paper, called the Source Equivalence Acceleration Method (SEAM), forms a coarse-group problem which preserves the fine-group problem even when using higher order spatial methods. SEAM allows recondensation to converge to the fine-group solution with minimal memory requirements and little additional overhead. This method also provides for consistency when using different spatial methods and angular quadratures between the coarse group and fine group problems. SEAM was implemented in OpenMOC, a 2D MOC code developed at MIT, and its performance tested against Coarse Mesh Finite Difference (CMFD) acceleration on the C5G7 benchmark problem and on a 361 group version of the problem. For extremely expensive transport calculations, SEAM was able to outperform CMFD, resulting in speed-ups of 20–45 relative to the normal power

  20. Equivalent statistics and data interpretation.

    Science.gov (United States)

    Francis, Gregory

    2017-08-01

    Recent reform efforts in psychological science have led to a plethora of choices for scientists to analyze their data. A scientist making an inference about their data must now decide whether to report a p value, summarize the data with a standardized effect size and its confidence interval, report a Bayes Factor, or use other model comparison methods. To make good choices among these options, it is necessary for researchers to understand the characteristics of the various statistics used by the different analysis frameworks. Toward that end, this paper makes two contributions. First, it shows that for the case of a two-sample t test with known sample sizes, many different summary statistics are mathematically equivalent in the sense that they are based on the very same information in the data set. When the sample sizes are known, the p value provides as much information about a data set as the confidence interval of Cohen's d or a JZS Bayes factor. Second, this equivalence means that different analysis methods differ only in their interpretation of the empirical data. At first glance, it might seem that mathematical equivalence of the statistics suggests that it does not matter much which statistic is reported, but the opposite is true because the appropriateness of a reported statistic is relative to the inference it promotes. Accordingly, scientists should choose an analysis method appropriate for their scientific investigation. A direct comparison of the different inferential frameworks provides some guidance for scientists to make good choices and improve scientific practice.

  1. Production of haploid plants from ten hybrids of bread wheat (Triticum aestivum L. through wide hybridization with maize (Zea mays L. Producción de plantas haploides a partir de 10 híbridos de trigo para pan (Triticum aestivum L. mediante hibridación interespecífica con maíz (Zea mays L.

    Directory of Open Access Journals (Sweden)

    L.E. Torres

    2010-12-01

    Full Text Available The aim of this work was to obtain haploid plants of bread wheat through wide hybridization with maize. The experimental material included ten bread wheat hybrids (female parent and one population of maize (pollen donor. Two assays were carried out in two different seasons (summer and winter. Wheat spikes were manually emasculated, each spike was pollinated twice with fresh pollen of maize and a solution of 2,4-D (100 mg l-1 was sprayed on pollinated florets and injected in the upper internode. Fifteen and 21 days after pollination caryopses were removed and surface sterilized. Embryos were cultured in tubes containing B5 medium. The ten hybrid combinations produced caryopses, but only eight of these hybrids produced embryos and, in six of them, the recovered embryos developed into haploid plantlets. The results showed that there is genotypic influence of the wheat parents on the percentage of haploid embryo formation, in accordance with the results obtained by other authors. Regardless of the genotype, the sowing season and the harvest date, 69.4% of the pollinated flowers gave place to the formation of caryopses, 5.5% of these caryopses developed into presumably haploid embryos (for their morphological phenotypes and 26.1 % of the recovered embryos developed into haploid plantlets.El objetivo del presente trabajo fue obtener plantas haploides de trigo para pan mediante hibridación interespecífica con maíz. Se utilizaron 10 híbridos de trigo para pan (madre y una población de maíz (donante de polen; se llevaron a cabo dos ensayos en distintas estaciones de cultivo. Cada espiga de trigo fue emasculada manualmente y polinizada dos veces con polen fresco de maíz; las flores polinizadas se pulverizaron con una solución de 2,4-D (100 mg l-1, la que también se inyectó en la base de la espiga. Las semillas se cosecharon a los 15 y 21 días posteriores a la polinización. Los embriones recuperados se colocaron en tubos conteniendo medio de

  2. Equivalent nozzle in thermomechanical problems

    International Nuclear Information System (INIS)

    Cesari, F.

    1977-01-01

    When analyzing nuclear vessels, it is most important to study the behavior of the nozzle cylinder-cylinder intersection. For the elastic field, this analysis in three dimensions is quite easy using the method of finite elements. The same analysis in the non-linear field becomes difficult for designs in 3-D. It is therefore necessary to resolve a nozzle in two dimensions equivalent to a 3-D nozzle. The purpose of the present work is to find an equivalent nozzle both with a mechanical and thermal load. This has been achieved by the analysis in three dimensions of a nozzle and a nozzle cylinder-sphere intersection, of a different radius. The equivalent nozzle will be a nozzle with a sphere radius in a given ratio to the radius of a cylinder; thus, the maximum equivalent stress is the same in both 2-D and 3-D. The nozzle examined derived from the intersection of a cylindrical vessel of radius R=191.4 mm and thickness T=6.7 mm with a cylindrical nozzle of radius r=24.675 mm and thickness t=1.350 mm, for which the experimental results for an internal pressure load are known. The structure was subdivided into 96 finite, three-dimensional and isoparametric elements with 60 degrees of freedom and 661 total nodes. Both the analysis with a mechanical load as well as the analysis with a thermal load were carried out on this structure according to the Bersafe system. The thermal load consisted of a transient typical of an accident occurring in a sodium-cooled fast reactor, with a peak of the temperature (540 0 C) for the sodium inside the vessel with an insulating argon temperature constant at 525 0 C. The maximum value of the equivalent tension was found in the internal area at the union towards the vessel side. The analysis of the nozzle in 2-D consists in schematizing the structure as a cylinder-sphere intersection, where the sphere has a given relation to the

  3. 21 CFR 26.9 - Equivalence determination.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Equivalence determination. 26.9 Section 26.9 Food... Specific Sector Provisions for Pharmaceutical Good Manufacturing Practices § 26.9 Equivalence determination... document insufficient evidence of equivalence, lack of opportunity to assess equivalence or a determination...

  4. Information Leakage from Logically Equivalent Frames

    Science.gov (United States)

    Sher, Shlomi; McKenzie, Craig R. M.

    2006-01-01

    Framing effects are said to occur when equivalent frames lead to different choices. However, the equivalence in question has been incompletely conceptualized. In a new normative analysis of framing effects, we complete the conceptualization by introducing the notion of information equivalence. Information equivalence obtains when no…

  5. Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2013-01-01

    in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

  6. Equivalence relations of AF-algebra extensions

    Indian Academy of Sciences (India)

    In this paper, we consider equivalence relations of *-algebra extensions and describe the relationship between the isomorphism equivalence and the unitary equivalence. We also show that a certain group homomorphism is the obstruction for these equivalence relations to be the same.

  7. Mixed field dose equivalent measuring instruments

    International Nuclear Information System (INIS)

    Brackenbush, L.W.; McDonald, J.C.; Endres, G.W.R.; Quam, W.

    1985-01-01

    In the past, separate instruments have been used to monitor dose equivalent from neutrons and gamma rays. It has been demonstrated that it is now possible to measure simultaneously neutron and gamma dose with a single instrument, the tissue equivalent proportional counter (TEPC). With appropriate algorithms dose equivalent can also be determined from the TEPC. A simple ''pocket rem meter'' for measuring neutron dose equivalent has already been developed. Improved algorithms for determining dose equivalent for mixed fields are presented. (author)

  8. Derived equivalences for group rings

    CERN Document Server

    König, Steffen

    1998-01-01

    A self-contained introduction is given to J. Rickard's Morita theory for derived module categories and its recent applications in representation theory of finite groups. In particular, Broué's conjecture is discussed, giving a structural explanation for relations between the p-modular character table of a finite group and that of its "p-local structure". The book is addressed to researchers or graduate students and can serve as material for a seminar. It surveys the current state of the field, and it also provides a "user's guide" to derived equivalences and tilting complexes. Results and proofs are presented in the generality needed for group theoretic applications.

  9. Phenotypic diversity of diploid and haploid Emiliania huxleyi cells and of cells in different growth phases revealed by comparative metabolomics.

    Science.gov (United States)

    Mausz, Michaela A; Pohnert, Georg

    2015-01-01

    In phytoplankton a high species diversity of microalgae co-exists at a given time. But diversity is not only reflected by the species composition. Within these species different life phases as well as different metabolic states can cause additional diversity. One important example is the coccolithophore Emiliania huxleyi. Diploid cells play an important role in marine ecosystems since they can form massively abundant algal blooms but in addition the less abundant haploid life phase of E. huxleyi occurs in lower quantities. Both life phases may fulfill different functions in the plankton. We hypothesize that in addition to the functional diversity caused by this life phase transition the growth stage of cells can also influence the metabolic composition and thus the ecological impact of E. huxleyi. Here we introduce a metabolomic survey in dependence of life phases as well as different growth phases to reveal such changes. The comparative metabolomic approach is based on the extraction of intracellular metabolites from intact microalgae, derivatization and analysis by gas chromatography coupled to mass spectrometry (GC-MS). Automated data processing and statistical analysis using canonical analysis of principal coordinates (CAP) revealed unique metabolic profiles for each life phase. Concerning the correlations of metabolites to growth phases, complex patterns were observed. As for example the saccharide mannitol showed its highest concentration in the exponential phase, whereas fatty acids were correlated to stationary and sterols to declining phase. These results are indicative for specific ecological roles of these stages of E. huxleyi and are discussed in the context of previous physiological and ecological studies. Copyright © 2014 Elsevier GmbH. All rights reserved.

  10. Calculation methods for determining dose equivalent

    International Nuclear Information System (INIS)

    Endres, G.W.R.; Tanner, J.E.; Scherpelz, R.I.; Hadlock, D.E.

    1987-11-01

    A series of calculations of neutron fluence as a function of energy in an anthropomorphic phantom was performed to develop a system for determining effective dose equivalent for external radiation sources. Critical organ dose equivalents are calculated and effective dose equivalents are determined using ICRP-26 [1] methods. Quality factors based on both present definitions and ICRP-40 definitions are used in the analysis. The results of these calculations are presented and discussed. The effective dose equivalent determined using ICRP-26 methods is significantly smaller than the dose equivalent determined by traditional methods. No existing personnel dosimeter or health physics instrument can determine effective dose equivalent. At the present time, the conversion of dosimeter response to dose equivalent is based on calculations for maximal or ''cap'' values using homogeneous spherical or cylindrical phantoms. The evaluated dose equivalent is, therefore, a poor approximation of the effective dose equivalent as defined by ICRP Publication 26. 3 refs., 2 figs., 1 tab

  11. Proteomic strategy for the identification of critical actors in reorganization of the post-meiotic male genome.

    Science.gov (United States)

    Govin, Jerome; Gaucher, Jonathan; Ferro, Myriam; Debernardi, Alexandra; Garin, Jerome; Khochbin, Saadi; Rousseaux, Sophie

    2012-01-01

    After meiosis, during the final stages of spermatogenesis, the haploid male genome undergoes major structural changes, resulting in a shift from a nucleosome-based genome organization to the sperm-specific, highly compacted nucleoprotamine structure. Recent data support the idea that region-specific programming of the haploid male genome is of high importance for the post-fertilization events and for successful embryo development. Although these events constitute a unique and essential step in reproduction, the mechanisms by which they occur have remained completely obscure and the factors involved have mostly remained uncharacterized. Here, we sought a strategy to significantly increase our understanding of proteins controlling the haploid male genome reprogramming, based on the identification of proteins in two specific pools: those with the potential to bind nucleic acids (basic proteins) and proteins capable of binding basic proteins (acidic proteins). For the identification of acidic proteins, we developed an approach involving a transition-protein (TP)-based chromatography, which has the advantage of retaining not only acidic proteins due to the charge interactions, but also potential TP-interacting factors. A second strategy, based on an in-depth bioinformatic analysis of the identified proteins, was then applied to pinpoint within the lists obtained, male germ cells expressed factors relevant to the post-meiotic genome organization. This approach reveals a functional network of DNA-packaging proteins and their putative chaperones and sheds a new light on the way the critical transitions in genome organizations could take place. This work also points to a new area of research in male infertility and sperm quality assessments.

  12. Editorial: New operational dose equivalent quantities

    International Nuclear Information System (INIS)

    Harvey, J.R.

    1985-01-01

    The ICRU Report 39 entitled ''Determination of Dose Equivalents Resulting from External Radiation Sources'' is briefly discussed. Four new operational dose equivalent quantities have been recommended in ICRU 39. The 'ambient dose equivalent' and the 'directional dose equivalent' are applicable to environmental monitoring and the 'individual dose equivalent, penetrating' and the 'individual dose equivalent, superficial' are applicable to individual monitoring. The quantities should meet the needs of day-to-day operational practice, while being acceptable to those concerned with metrological precision, and at the same time be used to give effective control consistent with current perceptions of the risks associated with exposure to ionizing radiations. (U.K.)

  13. Foreword: Biomonitoring Equivalents special issue.

    Science.gov (United States)

    Meek, M E; Sonawane, B; Becker, R A

    2008-08-01

    The challenge of interpreting results of biomonitoring for environmental chemicals in humans is highlighted in this Foreword to the Biomonitoring Equivalents (BEs) special issue of Regulatory Toxicology and Pharmacology. There is a pressing need to develop risk-based tools in order to empower scientists and health professionals to interpret and communicate the significance of human biomonitoring data. The BE approach, which integrates dosimetry and risk assessment methods, represents an important advancement on the path toward achieving this objective. The articles in this issue, developed as a result of an expert panel meeting, present guidelines for derivation of BEs, guidelines for communication using BEs and several case studies illustrating application of the BE approach for specific substances.

  14. Radiological equivalent of chemical pollutants

    International Nuclear Information System (INIS)

    Medina, V.O.

    1982-01-01

    The development of the peaceful uses of nuclear energy has caused continued effort toward public safety through radiation health protection measures and nuclear management practices. However, concern has not been focused on the development specifically in the operation of chemical pestrochemical industries as well as other industrial processes brought about by technological advancements. This article presents the comparison of the risk of radiation and chemicals. The methods used for comparing the risks of late effects of radiation and chemicals are considered at three levels. (a) as a frame of reference to give an impression of resolving power of biological tests; (b) as methods to quantify risks; (c) as instruments for an epidemiological survey of human populations. There are marked dissimilarities between chemicals and radiation and efforts to interpret chemical activity may not be achieved. Applicability of the concept of rad equivalence has many restrictions and as pointed out this approach is not an established one. (RTD)

  15. Tissue equivalence in neutron dosimetry

    International Nuclear Information System (INIS)

    Nutton, D.H.; Harris, S.J.

    1980-01-01

    A brief review is presented of the essential features of neutron tissue equivalence for radiotherapy and gives the results of a computation of relative absorbed dose for 14 MeV neutrons, using various tissue models. It is concluded that for the Bragg-Gray equation for ionometric dosimetry it is not sufficient to define the value of W to high accuracy and that it is essential that, for dosimetric measurements to be applicable to real body tissue to an accuracy of better than several per cent, a correction to the total absorbed dose must be made according to the test and tissue atomic composition, although variations in patient anatomy and other radiotherapy parameters will often limit the benefits of such detailed dosimetry. (U.K.)

  16. Expanding the Interaction Equivalency Theorem

    Directory of Open Access Journals (Sweden)

    Brenda Cecilia Padilla Rodriguez

    2015-06-01

    Full Text Available Although interaction is recognised as a key element for learning, its incorporation in online courses can be challenging. The interaction equivalency theorem provides guidelines: Meaningful learning can be supported as long as one of three types of interactions (learner-content, learner-teacher and learner-learner is present at a high level. This study sought to apply this theorem to the corporate sector, and to expand it to include other indicators of course effectiveness: satisfaction, knowledge transfer, business results and return on expectations. A large Mexican organisation participated in this research, with 146 learners, 30 teachers and 3 academic assistants. Three versions of an online course were designed, each emphasising a different type of interaction. Data were collected through surveys, exams, observations, activity logs, think aloud protocols and sales records. All course versions yielded high levels of effectiveness, in terms of satisfaction, learning and return on expectations. Yet, course design did not dictate the types of interactions in which students engaged within the courses. Findings suggest that the interaction equivalency theorem can be reformulated as follows: In corporate settings, an online course can be effective in terms of satisfaction, learning, knowledge transfer, business results and return on expectations, as long as (a at least one of three types of interaction (learner-content, learner-teacher or learner-learner features prominently in the design of the course, and (b course delivery is consistent with the chosen type of interaction. Focusing on only one type of interaction carries a high risk of confusion, disengagement or missed learning opportunities, which can be managed by incorporating other forms of interactions.

  17. SNP detection for massively parallel whole-genome resequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Fang, Xiaodong

    2009-01-01

    -genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All...... of this information was integrated into a single quality score for each base under Bayesian theory to measure the accuracy of consensus calling. We tested this methodology using a large-scale human resequencing data set of 36x coverage and assembled a high-quality nonrepetitive consensus sequence for 92.......25% of the diploid autosomes and 88.07% of the haploid X chromosome. Comparison of the consensus sequence with Illumina human 1M BeadChip genotyped alleles from the same DNA sample showed that 98.6% of the 37,933 genotyped alleles on the X chromosome and 98% of 999,981 genotyped alleles on autosomes were covered...

  18. The mobile genetic element Alu in the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Novick, G.E. [Florida International Univ., Miami, FL (United States); Batzer, M.A.; Deininger, P.L. [Louisiana State Univ. Medical Center, New Orleans, LA (United States)] [and others

    1996-01-01

    Genetic material has been traditionally envisioned as relatively static with the exception of occasional, often deleterious mutations. The sequence DNA-to-RNA-to-protein represented for many years the central dogma relating gene structure and function. Recently, the field of molecular genetics has provided revolutionary information on the dynamic role of repetitive elements in the function of the genetic material and the evolution of humans and other organisms. Alu sequences represent the largest family of short interspersed repetitive elements (SINEs) in humans, being present in an excess of 500,000 copies per haploid genome. Alu elements, as well as the other repetitive elements, were once considered to be useless. Today, the biology of Alu transposable elements is being widely examined in order to determine the molecular basis of a growing number of identified diseases and to provide new directions in genome mapping and biomedical research. 66 refs., 5 figs.

  19. Nuclear fusion and genome encounter during yeast zygote formation.

    Science.gov (United States)

    Tartakoff, Alan Michael; Jaiswal, Purnima

    2009-06-01

    When haploid cells of Saccharomyces cerevisiae are crossed, parental nuclei congress and fuse with each other. To investigate underlying mechanisms, we have developed assays that evaluate the impact of drugs and mutations. Nuclear congression is inhibited by drugs that perturb the actin and tubulin cytoskeletons. Nuclear envelope (NE) fusion consists of at least five steps in which preliminary modifications are followed by controlled flux of first outer and then inner membrane proteins, all before visible dilation of the waist of the nucleus or coalescence of the parental spindle pole bodies. Flux of nuclear pore complexes occurs after dilation. Karyogamy requires both the Sec18p/NSF ATPase and ER/NE luminal homeostasis. After fusion, chromosome tethering keeps tagged parental genomes separate from each other. The process of NE fusion and evidence of genome independence in yeast provide a prototype for understanding related events in higher eukaryotes.

  20. Equivalent damage of loads on pavements

    CSIR Research Space (South Africa)

    Prozzi, JA

    2009-05-26

    Full Text Available This report describes a new methodology for the determination of Equivalent Damage Factors (EDFs) of vehicles with multiple axle and wheel configurations on pavements. The basic premise of this new procedure is that "equivalent pavement response...

  1. Investigation of Equivalent Circuit for PEMFC Assessment

    International Nuclear Information System (INIS)

    Myong, Kwang Jae

    2011-01-01

    Chemical reactions occurring in a PEMFC are dominated by the physical conditions and interface properties, and the reactions are expressed in terms of impedance. The performance of a PEMFC can be simply diagnosed by examining the impedance because impedance characteristics can be expressed by an equivalent electrical circuit. In this study, the characteristics of a PEMFC are assessed using the AC impedance and various equivalent circuits such as a simple equivalent circuit, equivalent circuit with a CPE, equivalent circuit with two RCs, and equivalent circuit with two CPEs. It was found in this study that the characteristics of a PEMFC could be assessed using impedance and an equivalent circuit, and the accuracy was highest for an equivalent circuit with two CPEs

  2. 46 CFR 175.540 - Equivalents.

    Science.gov (United States)

    2010-10-01

    ... Safety Management (ISM) Code (IMO Resolution A.741(18)) for the purpose of determining that an equivalent... Organization (IMO) “Code of Safety for High Speed Craft” as an equivalent to compliance with applicable...

  3. Allele coding in genomic evaluation

    DEFF Research Database (Denmark)

    Standen, Ismo; Christensen, Ole Fredslund

    2011-01-01

    Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker...... effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous...... genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call...

  4. Some spectral equivalences between Schroedinger operators

    International Nuclear Information System (INIS)

    Dunning, C; Hibberd, K E; Links, J

    2008-01-01

    Spectral equivalences of the quasi-exactly solvable sectors of two classes of Schroedinger operators are established, using Gaudin-type Bethe ansatz equations. In some instances the results can be extended leading to full isospectrality. In this manner we obtain equivalences between PT-symmetric problems and Hermitian problems. We also find equivalences between some classes of Hermitian operators

  5. The definition of the individual dose equivalent

    International Nuclear Information System (INIS)

    Ehrlich, Margarete

    1986-01-01

    A brief note examines the choice of the present definition of the individual dose equivalent, the new operational dosimetry quantity for external exposure. The consequences of the use of the individual dose equivalent and the danger facing the individual dose equivalent, as currently defined, are briefly discussed. (UK)

  6. Segregation distortion in homozygous lines obtained via anther culture and maize doubled haploid methods in comparison to single seed descent in wheat (Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Tadeusz Adamski

    2014-01-01

    Conclusions: Segregation distortion in DH-AC populations was caused by the development of more than one plant of the same genotype from one callus. This distortion was minimized if only one plant per callus was included in the population. Selection of haploid wheat plants before chromosome doubling based on allele-specific markers allows us to choose genotypes that possess desirable Glu-1 alleles and to reduce the number of plants in the next steps of DH production. The SSD technique appeared to be the most advantageous in terms of Mendelian segregation, thus the occurrence of residual heterozygosity can be minimized by continuous selfing beyond the F6 generation.

  7. The first genetic map of a synthesized allohexaploid Brassica with A, B and C genomes based on simple sequence repeat markers.

    Science.gov (United States)

    Yang, S; Chen, S; Geng, X X; Yan, G; Li, Z Y; Meng, J L; Cowling, W A; Zhou, W J

    2016-04-01

    We present the first genetic map of an allohexaploid Brassica species, based on segregating microsatellite markers in a doubled haploid mapping population generated from a hybrid between two hexaploid parents. This study reports the first genetic map of trigenomic Brassica. A doubled haploid mapping population consisting of 189 lines was obtained via microspore culture from a hybrid H16-1 derived from a cross between two allohexaploid Brassica lines (7H170-1 and Y54-2). Simple sequence repeat primer pairs specific to the A genome (107), B genome (44) and C genome (109) were used to construct a genetic linkage map of the population. Twenty-seven linkage groups were resolved from 274 polymorphic loci on the A genome (109), B genome (49) and C genome (116) covering a total genetic distance of 3178.8 cM with an average distance between markers of 11.60 cM. This is the first genetic framework map for the artificially synthesized Brassica allohexaploids. The linkage groups represent the expected complement of chromosomes in the A, B and C genomes from the original diploid and tetraploid parents. This framework linkage map will be valuable for QTL analysis and future genetic improvement of a new allohexaploid Brassica species, and in improving our understanding of the genetic control of meiosis in new polyploids.

  8. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  9. The X Chromosome Is Necessary for Somatic Development in the Dioecious Silene latifolia: Cytogenetic and Molecular Evidence and Sequencing of a Haploid Genome

    Czech Academy of Sciences Publication Activity Database

    Soukupová, Magda; Nevrtalová, Eva; Čížková, Jana; Vogel, Ivan; Čegan, Radim; Hobza, Roman; Vyskot, Boris

    2014-01-01

    Roč. 143, 1-3 (2014), s. 96-103 ISSN 1424-8581 R&D Projects: GA ČR(CZ) GBP501/12/G090; GA ČR(CZ) GAP501/12/2220; GA ČR(CZ) GAP501/10/0102; GA MŠk(CZ) LM2010005; GA MŠk LO1204 Institutional support: RVO:68081707 Keywords : Anther culture * Cytometry * Dihaploids Subject RIV: BO - Biophysics; EF - Botanics (UEB-Q) Impact factor: 1.561, year: 2014

  10. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  11. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  12. Comparison of Different Methods for Separation of Haploid Embryo Induced through Irradiated Pollen and Their Economic Analysis in Melon (Cucumis melo var. inodorus

    Directory of Open Access Journals (Sweden)

    Gökhan Baktemur

    2013-01-01

    Full Text Available Irradiated pollen technique is the most successful haploidization technique within Cucurbitaceae. After harvesting of fruits pollinated with irradiated pollen, classical method called as “inspecting the seeds one by one” is used to find haploid embryos in the seeds. In this study, different methods were used to extract the embryos more easily, quickly, economically, and effectively. “Inspecting the seeds one by one” was used as control treatment. Other four methods tested were “sowing seeds direct nutrient media,” “inspecting seeds in the light source,” “floating seeds on liquid media,” and “floating seeds on liquid media after surface sterilization.” Y2 and Y3 melon genotypes selected from the third backcross population of Yuva were used as plant material. Results of this study show that there is no statistically significant difference among methods “inspecting the seeds one by one,” “sowing seeds direct CP nutrient media,” and “inspecting seeds in the light source,” although the average number of embryos per fruit is slightly different. No embryo production was obtained from liquid culture because of infection. When considered together with labor costs and time required for embryo rescue, the best methods were “sowing seeds directly in the CP nutrient media“ and ”inspecting seeds in the light source.”

  13. Haploid genetic screens identify an essential role for PLP2 in the downregulation of novel plasma membrane targets by viral E3 ubiquitin ligases.

    Directory of Open Access Journals (Sweden)

    Richard T Timms

    Full Text Available The Kaposi's sarcoma-associated herpesvirus gene products K3 and K5 are viral ubiquitin E3 ligases which downregulate MHC-I and additional cell surface immunoreceptors. To identify novel cellular genes required for K5 function we performed a forward genetic screen in near-haploid human KBM7 cells. The screen identified proteolipid protein 2 (PLP2, a MARVEL domain protein of unknown function, as essential for K5 activity. Genetic loss of PLP2 traps the viral ligase in the endoplasmic reticulum, where it is unable to ubiquitinate and degrade its substrates. Subsequent analysis of the plasma membrane proteome of K5-expressing KBM7 cells in the presence and absence of PLP2 revealed a wide range of novel K5 targets, all of which required PLP2 for their K5-mediated downregulation. This work ascribes a critical function to PLP2 for viral ligase activity and underlines the power of non-lethal haploid genetic screens in human cells to identify the genes involved in pathogen manipulation of the host immune system.

  14. Segregation distortion causes large-scale differences between male and female genomes in hybrid ants.

    Science.gov (United States)

    Kulmuni, Jonna; Seifert, Bernhard; Pamilo, Pekka

    2010-04-20

    Hybridization in isolated populations can lead either to hybrid breakdown and extinction or in some cases to speciation. The basis of hybrid breakdown lies in genetic incompatibilities between diverged genomes. In social Hymenoptera, the consequences of hybridization can differ from those in other animals because of haplodiploidy and sociality. Selection pressures differ between sexes because males are haploid and females are diploid. Furthermore, sociality and group living may allow survival of hybrid genotypes. We show that hybridization in Formica ants has resulted in a stable situation in which the males form two highly divergent gene pools whereas all the females are hybrids. This causes an exceptional situation with large-scale differences between male and female genomes. The genotype differences indicate strong transmission ratio distortion depending on offspring sex, whereby the mother transmits some alleles exclusively to her daughters and other alleles exclusively to her sons. The genetic differences between the sexes and the apparent lack of multilocus hybrid genotypes in males can be explained by recessive incompatibilities which cause the elimination of hybrid males because of their haploid genome. Alternatively, differentiation between sexes could be created by prezygotic segregation into male-forming and female-forming gametes in diploid females. Differentiation between sexes is stable and maintained throughout generations. The present study shows a unique outcome of hybridization and demonstrates that hybridization has the potential of generating evolutionary novelties in animals.

  15. The Complexity of Identifying Large Equivalence Classes

    DEFF Research Database (Denmark)

    Skyum, Sven; Frandsen, Gudmund Skovbjerg; Miltersen, Peter Bro

    1999-01-01

    We prove that at least 3k−4/k(2k−3)(n/2) – O(k)equivalence tests and no more than 2/k (n/2) + O(n) equivalence tests are needed in the worst case to identify the equivalence classes with at least k members in set of n elements. The upper bound is an improvement by a factor 2 compared to known res...

  16. Equivalent Simplification Method of Micro-Grid

    OpenAIRE

    Cai Changchun; Cao Xiangqin

    2013-01-01

    The paper concentrates on the equivalent simplification method for the micro-grid system connection into distributed network. The equivalent simplification method proposed for interaction study between micro-grid and distributed network. Micro-grid network, composite load, gas turbine synchronous generation, wind generation are equivalent simplification and parallel connect into the point of common coupling. A micro-grid system is built and three phase and single phase grounded faults are per...

  17. Calculation methods for determining dose equivalent

    International Nuclear Information System (INIS)

    Endres, G.W.R.; Tanner, J.E.; Scherpelz, R.I.; Hadlock, D.E.

    1988-01-01

    A series of calculations of neutron fluence as a function of energy in an anthropomorphic phantom was performed to develop a system for determining effective dose equivalent for external radiation sources. critical organ dose equivalents are calculated and effective dose equivalents are determined using ICRP-26 methods. Quality factors based on both present definitions and ICRP-40 definitions are used in the analysis. The results of these calculations are presented and discussed

  18. Equivalences of real submanifolds in complex space.

    OpenAIRE

    ZAITSEV, DMITRI

    2001-01-01

    PUBLISHED We show that for any real-analytic submanifold M in CN there is a proper real-analytic subvariety V contained in M such that for any p ? M \\ V , any real-analytic submanifold M? in CN, and any p? ? M?, the germs of the submanifolds M and M? at p and p? respectively are formally equivalent if and only if they are biholomorphically equivalent. More general results for k-equivalences are also stated and proved.

  19. Relations of equivalence of conditioned radioactive waste

    International Nuclear Information System (INIS)

    Kumer, L.; Szeless, A.; Oszuszky, F.

    1982-01-01

    A compensation for the wastes remaining with the operator of a waste management center, to be given by the agent having caused the waste, may be assured by effecting a financial valuation (equivalence) of wastes. Technically and logically, this equivalence between wastes (or specifically between different waste categories) and financial valuation has been established as reasonable. In this paper, the possibility of establishing such equivalences are developed, and their suitability for waste management concepts is quantitatively expressed

  20. Behavioural equivalence for infinite systems - Partially decidable!

    DEFF Research Database (Denmark)

    Sunesen, Kim; Nielsen, Mogens

    1996-01-01

    languages with two generalizations based on traditional approaches capturing non-interleaving behaviour, pomsets representing global causal dependency, and locality representing spatial distribution of events. We first study equivalences on Basic Parallel Processes, BPP, a process calculus equivalent...... of processes between BPP and TCSP, not only are the two equivalences different, but one (locality) is decidable whereas the other (pomsets) is not. The decidability result for locality is proved by a reduction to the reachability problem for Petri nets....

  1. Equivalence in Bilingual Lexicography: Criticism and Suggestions*

    Directory of Open Access Journals (Sweden)

    Herbert Ernst Wiegand

    2011-10-01

    Full Text Available

    Abstract: A reminder of general problems in the formation of terminology, as illustrated by theGerman Äquivalence (Eng. equivalence and äquivalent (Eng. equivalent, is followed by a critical discussionof the concept of equivalence in contrastive lexicology. It is shown that especially the conceptof partial equivalence is contradictory in its different manifestations. Consequently attemptsare made to give a more precise indication of the concept of equivalence in the metalexicography,with regard to the domain of the nominal lexicon. The problems of especially the metalexicographicconcept of partial equivalence as well as that of divergence are fundamentally expounded.In conclusion the direction is indicated to find more appropriate metalexicographic versions of theconcept of equivalence.

    Keywords: EQUIVALENCE, LEXICOGRAPHIC EQUIVALENT, PARTIAL EQUIVALENCE,CONGRUENCE, DIVERGENCE, CONVERGENCE, POLYDIVERGENCE, SYNTAGM-EQUIVALENCE,ZERO EQUIVALENCE, CORRESPONDENCE

    Abstrakt: Äquivalenz in der zweisprachigen Lexikographie: Kritik und Vorschläge.Nachdem an allgemeine Probleme der Begriffsbildung am Beispiel von dt. Äquivalenzund dt. äquivalent erinnert wurde, wird zunächst auf Äquivalenzbegriffe in der kontrastiven Lexikologiekritisch eingegangen. Es wird gezeigt, dass insbesondere der Begriff der partiellen Äquivalenzin seinen verschiedenen Ausprägungen widersprüchlich ist. Sodann werden Präzisierungenzu den Äquivalenzbegriffen in der Metalexikographie versucht, die sich auf den Bereich der Nennlexikbeziehen. Insbesondere der metalexikographische Begriff der partiellen Äquivalenz sowie derder Divergenz werden grundsätzlich problematisiert. In welche Richtung man gehen kann, umangemessenere metalexikographische Fassungen des Äquivalenzbegriffs zu finden, wird abschließendangedeutet.

    Stichwörter: ÄQUIVALENZ, LEXIKOGRAPHISCHES ÄQUIVALENT, PARTIELLE ÄQUIVALENZ,KONGRUENZ, DIVERGENZ, KONVERGENZ, POLYDIVERGENZ

  2. Allele coding in genomic evaluation

    Directory of Open Access Journals (Sweden)

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  3. A Three-Dimensional Model of the Yeast Genome

    Science.gov (United States)

    Noble, William; Duan, Zhi-Jun; Andronescu, Mirela; Schutz, Kevin; McIlwain, Sean; Kim, Yoo Jung; Lee, Choli; Shendure, Jay; Fields, Stanley; Blau, C. Anthony

    Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or factories for transcription and DNA replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

  4. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    Science.gov (United States)

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

  5. Equivalent drawbead performance in deep drawing simulations

    NARCIS (Netherlands)

    Meinders, Vincent T.; Geijselaers, Hubertus J.M.; Huetink, Han

    1999-01-01

    Drawbeads are applied in the deep drawing process to improve the control of the material flow during the forming operation. In simulations of the deep drawing process these drawbeads can be replaced by an equivalent drawbead model. In this paper the usage of an equivalent drawbead model in the

  6. On uncertainties in definition of dose equivalent

    International Nuclear Information System (INIS)

    Oda, Keiji

    1995-01-01

    The author has entertained always the doubt that in a neutron field, if the measured value of the absorbed dose with a tissue equivalent ionization chamber is 1.02±0.01 mGy, may the dose equivalent be taken as 10.2±0.1 mSv. Should it be 10.2 or 11, but the author considers it is 10 or 20. Even if effort is exerted for the precision measurement of absorbed dose, if the coefficient being multiplied to it is not precise, it is meaningless. [Absorbed dose] x [Radiation quality fctor] = [Dose equivalent] seems peculiar. How accurately can dose equivalent be evaluated ? The descriptions related to uncertainties in the publications of ICRU and ICRP are introduced, which are related to radiation quality factor, the accuracy of measuring dose equivalent and so on. Dose equivalent shows the criterion for the degree of risk, or it is considered only as a controlling quantity. The description in the ICRU report 1973 related to dose equivalent and its unit is cited. It was concluded that dose equivalent can be considered only as the absorbed dose being multiplied by a dimensionless factor. The author presented the questions. (K.I.)

  7. Orientifold Planar Equivalence: The Chiral Condensate

    DEFF Research Database (Denmark)

    Armoni, Adi; Lucini, Biagio; Patella, Agostino

    2008-01-01

    The recently introduced orientifold planar equivalence is a promising tool for solving non-perturbative problems in QCD. One of the predictions of orientifold planar equivalence is that the chiral condensates of a theory with $N_f$ flavours of Dirac fermions in the symmetric (or antisymmetric...

  8. 7 CFR 1005.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1005.54 Section 1005.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1005.54 Equivalent price. See § 1000.54. Uniform Prices ...

  9. 7 CFR 1126.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1126.54 Section 1126.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1126.54 Equivalent price. See § 1000.54. Producer Price Differential ...

  10. 7 CFR 1001.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1001.54 Section 1001.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1001.54 Equivalent price. See § 1000.54. Producer Price Differential ...

  11. 7 CFR 1032.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1032.54 Section 1032.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1032.54 Equivalent price. See § 1000.54. Producer Price Differential ...

  12. 7 CFR 1124.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1124.54 Section 1124.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Regulating Handling Class Prices § 1124.54 Equivalent price. See § 1000.54. Producer Price Differential ...

  13. 7 CFR 1030.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1030.54 Section 1030.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1030.54 Equivalent price. See § 1000.54. ...

  14. 7 CFR 1033.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1033.54 Section 1033.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1033.54 Equivalent price. See § 1000.54. Producer Price Differential ...

  15. 7 CFR 1131.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1131.54 Section 1131.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1131.54 Equivalent price. See § 1000.54. Uniform Prices ...

  16. 7 CFR 1006.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1006.54 Section 1006.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1006.54 Equivalent price. See § 1000.54. Uniform Prices ...

  17. 7 CFR 1007.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1007.54 Section 1007.54 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Handling Class Prices § 1007.54 Equivalent price. See § 1000.54. Uniform Prices ...

  18. 7 CFR 1000.54 - Equivalent price.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Equivalent price. 1000.54 Section 1000.54 Agriculture... Prices § 1000.54 Equivalent price. If for any reason a price or pricing constituent required for computing the prices described in § 1000.50 is not available, the market administrator shall use a price or...

  19. Finding small equivalent decision trees is hard

    NARCIS (Netherlands)

    Zantema, H.; Bodlaender, H.L.

    2000-01-01

    Two decision trees are called decision equivalent if they represent the same function, i.e., they yield the same result for every possible input. We prove that given a decision tree and a number, to decide if there is a decision equivalent decision tree of size at most that number is NPcomplete. As

  20. What is Metaphysical Equivalence? | Miller | Philosophical Papers

    African Journals Online (AJOL)

    Theories are metaphysically equivalent just if there is no fact of the matter that could render one theory true and the other false. In this paper I argue that if we are judiciously to resolve disputes about whether theories are equivalent or not, we need to develop testable criteria that will give us epistemic access to the obtaining ...

  1. EQUIVALENT MODELS IN COVARIANCE STRUCTURE-ANALYSIS

    NARCIS (Netherlands)

    LUIJBEN, TCW

    1991-01-01

    Defining equivalent models as those that reproduce the same set of covariance matrices, necessary and sufficient conditions are stated for the local equivalence of two expanded identified models M1 and M2 when fitting the more restricted model M0. Assuming several regularity conditions, the rank

  2. Equivalence in Ventilation and Indoor Air Quality

    Energy Technology Data Exchange (ETDEWEB)

    Sherman, Max; Walker, Iain; Logue, Jennifer

    2011-08-01

    We ventilate buildings to provide acceptable indoor air quality (IAQ). Ventilation standards (such as American Society of Heating, Refrigerating, and Air-Conditioning Enginners [ASHRAE] Standard 62) specify minimum ventilation rates without taking into account the impact of those rates on IAQ. Innovative ventilation management is often a desirable element of reducing energy consumption or improving IAQ or comfort. Variable ventilation is one innovative strategy. To use variable ventilation in a way that meets standards, it is necessary to have a method for determining equivalence in terms of either ventilation or indoor air quality. This study develops methods to calculate either equivalent ventilation or equivalent IAQ. We demonstrate that equivalent ventilation can be used as the basis for dynamic ventilation control, reducing peak load and infiltration of outdoor contaminants. We also show that equivalent IAQ could allow some contaminants to exceed current standards if other contaminants are more stringently controlled.

  3. Beyond Language Equivalence on Visibly Pushdown Automata

    DEFF Research Database (Denmark)

    Srba, Jiri

    2009-01-01

    We study (bi)simulation-like preorder/equivalence checking on the class of visibly pushdown automata and its natural subclasses visibly BPA (Basic Process Algebra) and visibly one-counter automata. We describe generic methods for proving complexity upper and lower bounds for a number of studied...... preorders and equivalences like simulation, completed simulation, ready simulation, 2-nested simulation preorders/equivalences and bisimulation equivalence. Our main results are that all the mentioned equivalences and preorders are EXPTIME-complete on visibly pushdown automata, PSPACE-complete on visibly...... one-counter automata and P-complete on visibly BPA. Our PSPACE lower bound for visibly one-counter automata improves also the previously known DP-hardness results for ordinary one-counter automata and one-counter nets. Finally, we study regularity checking problems for visibly pushdown automata...

  4. Genome size estimation: a new methodology

    Science.gov (United States)

    Álvarez-Borrego, Josué; Gallardo-Escárate, Crisitian; Kober, Vitaly; López-Bonilla, Oscar

    2007-03-01

    Recently, within the cytogenetic analysis, the evolutionary relations implied in the content of nuclear DNA in plants and animals have received a great attention. The first detailed measurements of the nuclear DNA content were made in the early 40's, several years before Watson and Crick proposed the molecular structure of the DNA. In the following years Hewson Swift developed the concept of "C-value" in reference to the haploid phase of DNA in plants. Later Mirsky and Ris carried out the first systematic study of genomic size in animals, including representatives of the five super classes of vertebrates as well as of some invertebrates. From these preliminary results it became evident that the DNA content varies enormously between the species and that this variation does not bear relation to the intuitive notion from the complexity of the organism. Later, this observation was reaffirmed in the following years as the studies increased on genomic size, thus denominating to this characteristic of the organisms like the "Paradox of the C-value". Few years later along with the no-codification discovery of DNA the paradox was solved, nevertheless, numerous questions remain until nowadays unfinished, taking to denominate this type of studies like the "C-value enigma". In this study, we reported a new method for genome size estimation by quantification of fluorescence fading. We measured the fluorescence intensity each 1600 milliseconds in DAPI-stained nuclei. The estimation of the area under the graph (integral fading) during fading period was related with the genome size.

  5. Allelic variations at the haploid TBX1 locus do not influence the cardiac phenotype in cases of 22q11 microdeletion.

    Science.gov (United States)

    Voelckel, Marie-Antoinette; Girardot, Lydie; Giusiano, Bernard; Levy, Nicolas; Philip, Nicole

    2004-01-01

    Microdeletion at the 22q11 locus is characterised by a high clinical variability. Congenital heart defects (CHD) are the most life-threatening manifestations of the syndrome and affect approximately 50% of patients carrying the deleted chromosome 22. The causes of this phenotype variability remain unknown although several hypotheses have been raised. It has been suggested that allelic variations at the haploid locus could modify the phenotypic expression. Regarding this hypothesis, TBX1 was thought to be a major candidate to the cardiac phenotype or its severity in patients carrying the 22q11 microdeletion. A mutational screening was performed in this gene, in a series of 39 deleted patients, with and without CHD. The results indicate that mutations in TBX1 are not likely to be involved in the cardiac phenotype observed in del22q11 patients.

  6. 78 FR 67360 - Ambient Air Monitoring Reference and Equivalent Methods: Designation of Five New Equivalent Methods

    Science.gov (United States)

    2013-11-12

    ... Methods: Designation of Five New Equivalent Methods AGENCY: Office of Research and Development; Environmental Protection Agency (EPA). ACTION: Notice of the designation of five new equivalent methods for...) has designated, in accordance with 40 CFR Part 53, five new equivalent methods, one for measuring...

  7. 77 FR 60985 - Ambient Air Monitoring Reference and Equivalent Methods: Designation of Three New Equivalent Methods

    Science.gov (United States)

    2012-10-05

    ... Methods: Designation of Three New Equivalent Methods AGENCY: Environmental Protection Agency. ACTION: Notice of the designation of three new equivalent methods for monitoring ambient air quality. SUMMARY... equivalent methods, one for measuring concentrations of PM 2.5 , one for measuring concentrations of PM 10...

  8. Analytical and numerical construction of equivalent cables.

    Science.gov (United States)

    Lindsay, K A; Rosenberg, J R; Tucker, G

    2003-08-01

    The mathematical complexity experienced when applying cable theory to arbitrarily branched dendrites has lead to the development of a simple representation of any branched dendrite called the equivalent cable. The equivalent cable is an unbranched model of a dendrite and a one-to-one mapping of potentials and currents on the branched model to those on the unbranched model, and vice versa. The piecewise uniform cable, with a symmetrised tri-diagonal system matrix, is shown to represent the canonical form for an equivalent cable. Through a novel application of the Laplace transform it is demonstrated that an arbitrary branched model of a dendrite can be transformed to the canonical form of an equivalent cable. The characteristic properties of the equivalent cable are extracted from the matrix for the transformed branched model. The one-to-one mapping follows automatically from the construction of the equivalent cable. The equivalent cable is used to provide a new procedure for characterising the location of synaptic contacts on spinal interneurons.

  9. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae

    Directory of Open Access Journals (Sweden)

    Gonthier Lucy

    2010-08-01

    Full Text Available Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L. constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This

  10. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae).

    Science.gov (United States)

    Gonthier, Lucy; Bellec, Arnaud; Blassiau, Christelle; Prat, Elisa; Helmstetter, Nicolas; Rambaud, Caroline; Huss, Brigitte; Hendriks, Theo; Bergès, Hélène; Quillet, Marie-Christine

    2010-08-11

    The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. This indicated that both BAC libraries are valuable tools for molecular

  11. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  12. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  13. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  14. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

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

  15. Geometry of the local equivalence of states

    Energy Technology Data Exchange (ETDEWEB)

    Sawicki, A; Kus, M, E-mail: assawi@cft.edu.pl, E-mail: marek.kus@cft.edu.pl [Center for Theoretical Physics, Polish Academy of Sciences, Al Lotnikow 32/46, 02-668 Warszawa (Poland)

    2011-12-09

    We present a description of locally equivalent states in terms of symplectic geometry. Using the moment map between local orbits in the space of states and coadjoint orbits of the local unitary group, we reduce the problem of local unitary equivalence to an easy part consisting of identifying the proper coadjoint orbit and a harder problem of the geometry of fibers of the moment map. We give a detailed analysis of the properties of orbits of 'equally entangled states'. In particular, we show connections between certain symplectic properties of orbits such as their isotropy and coisotropy with effective criteria of local unitary equivalence. (paper)

  16. A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

    Directory of Open Access Journals (Sweden)

    Guangtu Gao

    2018-04-01

    Full Text Available Single-nucleotide polymorphisms (SNPs are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss, SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD libraries, reduced representation libraries (RRL and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1 which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs and multi-sequence variants (MSVs. Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25. The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and

  17. The Yeast Deletion Collection: A Decade of Functional Genomics

    Science.gov (United States)

    Giaever, Guri; Nislow, Corey

    2014-01-01

    The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general. PMID:24939991

  18. Quantum equivalence principle without mass superselection

    International Nuclear Information System (INIS)

    Hernandez-Coronado, H.; Okon, E.

    2013-01-01

    The standard argument for the validity of Einstein's equivalence principle in a non-relativistic quantum context involves the application of a mass superselection rule. The objective of this work is to show that, contrary to widespread opinion, the compatibility between the equivalence principle and quantum mechanics does not depend on the introduction of such a restriction. For this purpose, we develop a formalism based on the extended Galileo group, which allows for a consistent handling of superpositions of different masses, and show that, within such scheme, mass superpositions behave as they should in order to obey the equivalence principle. - Highlights: • We propose a formalism for consistently handling, within a non-relativistic quantum context, superpositions of states with different masses. • The formalism utilizes the extended Galileo group, in which mass is a generator. • The proposed formalism allows for the equivalence principle to be satisfied without the need of imposing a mass superselection rule

  19. On the equivalence of chaos control systems

    International Nuclear Information System (INIS)

    Wang Xiaofan

    2003-01-01

    For a given chaotic system, different control systems can be constructed depending on which parameter is tuned or where the external input is added. We prove that two different feedback control systems are qualitatively equivalent if they are feedback linearizable

  20. Equivalence relations and the reinforcement contingency.

    Science.gov (United States)

    Sidman, M

    2000-07-01

    Where do equivalence relations come from? One possible answer is that they arise directly from the reinforcement contingency. That is to say, a reinforcement contingency produces two types of outcome: (a) 2-, 3-, 4-, 5-, or n-term units of analysis that are known, respectively, as operant reinforcement, simple discrimination, conditional discrimination, second-order conditional discrimination, and so on; and (b) equivalence relations that consist of ordered pairs of all positive elements that participate in the contingency. This conception of the origin of equivalence relations leads to a number of new and verifiable ways of conceptualizing equivalence relations and, more generally, the stimulus control of operant behavior. The theory is also capable of experimental disproof.

  1. REFractions: The Representing Equivalent Fractions Game

    Science.gov (United States)

    Tucker, Stephen I.

    2014-01-01

    Stephen Tucker presents a fractions game that addresses a range of fraction concepts including equivalence and computation. The REFractions game also improves students' fluency with representing, comparing and adding fractions.

  2. ON THE EQUIVALENCE OF THE ABEL EQUATION

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    This article uses the reflecting function of Mironenko to study some complicated differential equations which are equivalent to the Abel equation. The results are applied to discuss the behavior of solutions of these complicated differential equations.

  3. interpratation: of equivalences and cultural untranslatability

    African Journals Online (AJOL)

    jgmweri

    translatability in cultural diversity in terms equivalences such as –Vocabulary or lexical ..... A KSL interpreter who does not understand this English idiom may literally interpret it .... Nida, E.A. (1958) Analysis of meaning and dictionary making.

  4. Equivalence Principle, Higgs Boson and Cosmology

    Directory of Open Access Journals (Sweden)

    Mauro Francaviglia

    2013-05-01

    Full Text Available We discuss here possible tests for Palatini f(R-theories together with their implications for different formulations of the Equivalence Principle. We shall show that Palatini f(R-theories obey the Weak Equivalence Principle and violate the Strong Equivalence Principle. The violations of the Strong Equivalence Principle vanish in vacuum (and purely electromagnetic solutions as well as on short time scales with respect to the age of the universe. However, we suggest that a framework based on Palatini f(R-theories is more general than standard General Relativity (GR and it sheds light on the interpretation of data and results in a way which is more model independent than standard GR itself.

  5. The gauge principle vs. the equivalence principle

    International Nuclear Information System (INIS)

    Gates, S.J. Jr.

    1984-01-01

    Within the context of field theory, it is argued that the role of the equivalence principle may be replaced by the principle of gauge invariance to provide a logical framework for theories of gravitation

  6. Dark matter and the equivalence principle

    Science.gov (United States)

    Frieman, Joshua A.; Gradwohl, Ben-Ami

    1993-01-01

    A survey is presented of the current understanding of dark matter invoked by astrophysical theory and cosmology. Einstein's equivalence principle asserts that local measurements cannot distinguish a system at rest in a gravitational field from one that is in uniform acceleration in empty space. Recent test-methods for the equivalence principle are presently discussed as bases for testing of dark matter scenarios involving the long-range forces between either baryonic or nonbaryonic dark matter and ordinary matter.

  7. S-equivalents lagrangians in generalized mechanics

    International Nuclear Information System (INIS)

    Negri, L.J.; Silva, Edna G. da.

    1985-01-01

    The problem of s-equivalent lagrangians is considered in the realm of generalized mechanics. Some results corresponding to the ordinary (non-generalized) mechanics are extended to the generalized case. A theorem for the reduction of the higher order lagrangian description to the usual order is found to be useful for the analysis of generalized mechanical systems and leads to a new class of equivalence between lagrangian functions. Some new perspectives are pointed out. (Author) [pt

  8. A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

    Science.gov (United States)

    Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

    2017-07-05

    The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

  9. Ecological equivalency as a tool for endangered species management.

    Science.gov (United States)

    Searcy, Christopher A; Rollins, Hilary B; Shaffer, H Bradley

    2016-01-01

    The use of taxon substitutes for extinct or endangered species is a controversial conservation measure. We use the example of the endangered California tiger salamander (Ambystoma californiense; CTS), which is being replaced by hybrids with the invasive barred tiger salamander (Ambystoma mavortium), to illustrate a strategy for evaluating taxon substitutes based on their position in a multivariate community space. Approximately one-quarter of CTS's range is currently occupied by "full hybrids" with 70% nonnative genes, while another one-quarter is occupied by "superinvasives" where a specific set of 3/68 genes comprising 4% of the surveyed genome is nonnative. Based on previous surveys of natural CTS breeding ponds, we stocked experimental mesocosms with field-verified, realistic densities of tiger salamander larvae and their prey, and used these mesocosms to evaluate ecological equivalency between pure CTS, full hybrids, and superinvasives in experimental pond communities. We also included a fourth treatment with no salamanders present to evaluate the community effects of eliminating Ambystoma larvae altogether. We found that pure CTS and superinvasive larvae were ecologically equivalent, because their positions in the multivariate community space were statistically indistinguishable and they did not differ significantly along any univariate community axes. Full hybrids were ecologically similar, but not equivalent, to the other two genotypes, and the no-Ambystoma treatment was by far the most divergent. We conclude that, at least for the larval stage, superinvasives are adequate taxon substitutes for pure CTS and should probably be afforded protection under the Endangered Species Act. The proper conservation status for full hybrids remains debatable.

  10. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  11. First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc Maxim, a Chinese Traditional Medicinal Plant

    Directory of Open Access Journals (Sweden)

    Gong Xiao

    2013-06-01

    Full Text Available Epimedium sagittatum (Sieb. et Zucc Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12. However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE repeats identified (65.37% of all TE repeats, particularly LTR (Long Terminal Repeat retrotransposons (52.27% of all TE repeats. Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant.

  12. First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant

    Science.gov (United States)

    Liu, Di; Zeng, Shao-Hua; Chen, Jian-Jun; Zhang, Yan-Jun; Xiao, Gong; Zhu, Lin-Yao; Wang, Ying

    2013-01-01

    Epimedium sagittatum (Sieb. et Zucc) Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12). However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE) repeats identified (65.37% of all TE repeats), particularly LTR (Long Terminal Repeat) retrotransposons (52.27% of all TE repeats). Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant. PMID:23807511

  13. The principle of equivalence reconsidered: assessing the relevance of the principle of equivalence in prison medicine.

    Science.gov (United States)

    Jotterand, Fabrice; Wangmo, Tenzin

    2014-01-01

    In this article we critically examine the principle of equivalence of care in prison medicine. First, we provide an overview of how the principle of equivalence is utilized in various national and international guidelines on health care provision to prisoners. Second, we outline some of the problems associated with its applications, and argue that the principle of equivalence should go beyond equivalence to access and include equivalence of outcomes. However, because of the particular context of the prison environment, third, we contend that the concept of "health" in equivalence of health outcomes needs conceptual clarity; otherwise, it fails to provide a threshold for healthy states among inmates. We accomplish this by examining common understandings of the concepts of health and disease. We conclude our article by showing why the conceptualization of diseases as clinical problems provides a helpful approach in the delivery of health care in prison.

  14. Equivalence of Szegedy's and coined quantum walks

    Science.gov (United States)

    Wong, Thomas G.

    2017-09-01

    Szegedy's quantum walk is a quantization of a classical random walk or Markov chain, where the walk occurs on the edges of the bipartite double cover of the original graph. To search, one can simply quantize a Markov chain with absorbing vertices. Recently, Santos proposed two alternative search algorithms that instead utilize the sign-flip oracle in Grover's algorithm rather than absorbing vertices. In this paper, we show that these two algorithms are exactly equivalent to two algorithms involving coined quantum walks, which are walks on the vertices of the original graph with an internal degree of freedom. The first scheme is equivalent to a coined quantum walk with one walk step per query of Grover's oracle, and the second is equivalent to a coined quantum walk with two walk steps per query of Grover's oracle. These equivalences lie outside the previously known equivalence of Szegedy's quantum walk with absorbing vertices and the coined quantum walk with the negative identity operator as the coin for marked vertices, whose precise relationships we also investigate.

  15. Chloroplast microsatellite markers for Pseudotaxus chienii developed from the whole chloroplast genome of Taxus chinensis var. mairei (Taxaceae).

    Science.gov (United States)

    Deng, Qi; Zhang, Hanrui; He, Yipeng; Wang, Ting; Su, Yingjuan

    2017-03-01

    Pseudotaxus chienii (Taxaceae) is an old rare species endemic to China that has adapted well to ecological heterogeneity with high genetic diversity in its nuclear genome. However, the genetic variation in its chloroplast genome is unknown. Eighteen chloroplast microsatellite markers (cpSSRs) were developed from the whole chloroplast genome of Taxus chinensis var. mairei and successfully amplified in four P. chienii populations and one T. chinensis var. mairei population. Of these loci, 10 were polymorphic in P. chienii , whereas six were polymorphic in T. chinensis var. mairei . The unbiased haploid diversity per locus ranged from 0.000 to 0.641 and 0.000 to 0.545 for P. chienii and T. chinensis var. mairei , respectively. The 18 cpSSRs will be used to further investigate the chloroplast genetic structure and adaptive evolution in P. chienii populations.

  16. Quantum mechanics and the equivalence principle

    International Nuclear Information System (INIS)

    Davies, P C W

    2004-01-01

    A quantum particle moving in a gravitational field may penetrate the classically forbidden region of the gravitational potential. This raises the question of whether the time of flight of a quantum particle in a gravitational field might deviate systematically from that of a classical particle due to tunnelling delay, representing a violation of the weak equivalence principle. I investigate this using a model quantum clock to measure the time of flight of a quantum particle in a uniform gravitational field, and show that a violation of the equivalence principle does not occur when the measurement is made far from the turning point of the classical trajectory. The results are then confirmed using the so-called dwell time definition of quantum tunnelling. I conclude with some remarks about the strong equivalence principle in quantum mechanics

  17. Water equivalence of polymer gel dosimeters

    International Nuclear Information System (INIS)

    Sellakumar, P.; James Jebaseelan Samuel, E.; Supe, Sanjay S.

    2007-01-01

    To evaluate the water equivalence and radiation transport properties of polymer gel dosimeters over the wide range of photon and electron energies 14 different types of polymer gels were considered. Their water equivalence was evaluated in terms of effective atomic number (Z eff ), electron density (ρ e ), photon mass attenuation coefficient (μ/ρ), photon mass energy absorption coefficient (μ en /ρ) and total stopping power (S/ρ) tot of electrons using the XCOM and the ESTAR database. The study showed that the effective atomic number of polymer gels were very close ( en /ρ for all polymer gels were in close agreement ( tot of electrons in polymer gel dosimeters were within 1% agreement with that of water. From the study we conclude that at lower energy (<80keV) the polymer gel dosimeters cannot be considered water equivalent and study has to be carried out before using the polymer gel for clinical application

  18. Using frequency equivalency in stability calculations

    Energy Technology Data Exchange (ETDEWEB)

    Gruzdev, I.A.; Temirbulatov, R.A.; Tereshko, L.A.

    1981-01-01

    A methodology for calculating oscillatory instability that involves using frequency equivalency is employed in carrying out the following proceedures: dividing an electric power system into subgroups; determining the adjustments to the automatic excitation control in each subsystem; simplifying the mathematical definition of the separate subsystems by using frequency equivalency; gradually re-tuning the automatic excitation control in the separate subsystems to account for neighboring subsystems by using their equivalent frequency characteristics. The methodology is to be used with a computer program to determine the gain in the stabilization channels of the automatic excitation control unit in which static stability of the entire aggregate of normal and post-breakdown conditions acceptable damping of transient processes are provided. The possibility of reducing the equation series to apply to chosen regions of the existing range of frequencies is demonstrated. The use of the methodology is illustrated in a sample study on stability in a Siberian unified power system.

  19. The equivalence problem for LL- and LR-regular grammars

    NARCIS (Netherlands)

    Nijholt, Antinus; Gecsec, F.

    It will be shown that the equivalence problem for LL-regular grammars is decidable. Apart from extending the known result for LL(k) grammar equivalence to LLregular grammar equivalence, we obtain an alternative proof of the decidability of LL(k) equivalence. The equivalence prob]em for LL-regular

  20. Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch.

    Directory of Open Access Journals (Sweden)

    Raúl A Ortiz-Merino

    2017-05-01

    Full Text Available Many interspecies hybrids have been discovered in yeasts, but most of these hybrids are asexual and can replicate only mitotically. Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility, restoring their ability to perform meiosis and sporulate. Here, we show that this process occurred naturally during the evolution of Zygosaccharomyces parabailii, an interspecies hybrid that was formed by mating between 2 parents that differed by 7% in genome sequence and by many interchromosomal rearrangements. Surprisingly, Z. parabailii has a full sexual cycle and is genetically haploid. It goes through mating-type switching and autodiploidization, followed by immediate sporulation. We identified the key evolutionary event that enabled Z. parabailii to regain fertility, which was breakage of 1 of the 2 homeologous copies of the mating-type (MAT locus in the hybrid, resulting in a chromosomal rearrangement and irreparable damage to 1 MAT locus. This rearrangement was caused by HO endonuclease, which normally functions in mating-type switching. With 1 copy of MAT inactivated, the interspecies hybrid now behaves as a haploid. Our results provide the first demonstration that MAT locus damage is a naturally occurring evolutionary mechanism for whole-genome duplication and restoration of fertility to interspecies hybrids. The events that occurred in Z. parabailii strongly resemble those postulated to have caused ancient whole-genome duplication in an ancestor of Saccharomyces cerevisiae.

  1. In vitro production of haploid cells after coculture of CD49f+ with Sertoli cells from testicular sperm extraction in nonobstructive azoospermic patients.

    Science.gov (United States)

    Riboldi, Marcia; Rubio, Carmen; Pellicer, Antonio; Gil-Salom, Manuel; Simón, Carlos

    2012-09-01

    To isolate CD49f+ cells from testicular sperm extraction (TESE) samples of azoospermic patients and induce meiosis by coculturing these cells with Sertoli cells. Prospective analysis. Research center. Obstructive azoospermic (OA) and nonobstructive azoospermic (NOA) patients. TESE, with enzymatic dissociation of samples to obtain a cell suspension, which was cultured for 4 days with 4 ng/mL GDNF. The CD49f+ cells were sorted using fluorescence-activated cell sorting (FACS) as a marker to identify spermatogonial stem cells (SSCs), which were cocultured with Sertoli cells expressing red fluorescent protein (RFP) in knockout serum replacement (KSR) media with addition of 1,000 IU/mL of follicle-stimulating hormone (FSH), 1 μM testosterone, 40 ng/mL of GDNF, and 2 μM retinoic acid (RA) for 15 days in culture at 37°C and 5% CO(2) to induce meiotic progression. Cells were collected and analyzed by immunofluorescence for meiosis progression with specific markers SCP3 and CREST, and they were confirmed by fluorescence in situ hybridization (FISH). Isolation of CD49f+ cells and coculture with Sertoli cells, meiosis progression in vitro, assessment of SSCs and meiotic markers real-time polymerase chain reaction (RT-PCR), immunohistochemical analysis, and FISH. The CD49f+ isolated from the of total cell count in the TESE samples of azoospermic patients varied from 5.45% in OA to 2.36% in NOA. Sertoli cells were obtained from the same TESE samples, and established protocols were used to characterize them as positive for SCF, rGDNF, WT1, GATA-4, and vimentin, with the presence of tight junctions and lipid droplets shown by oil red staining. After isolation, the CD49f+ cells were cocultured with RFP Sertoli cells in a 15-day time-course experiment. Positive immunostaining for meiosis markers SCP3 and CREST on days 3 to 5 was noted in the samples obtained from one NOA patient. A FISH analysis for chromosomes 13, 18, 21, X, and Y confirmed the presence of haploid cells on day

  2. Fiscal adjustments in Europe and Ricardian equivalence

    Directory of Open Access Journals (Sweden)

    V. DE BONIS

    1998-09-01

    Full Text Available According to the ‘Ricardian’ equivalence hypothesis, consumption is dependent on permanent disposable income and current deficits are equivalent to future tax payments. This hypothesis is tested on 14 European countries in the 1990s. The relationships between private sector savings and general government deficit, and the GDP growth rate and the unemployment rate are determined. The results show the change in consumers' behaviour with respect to government deficit, and that expectations of an increase in future wealth are no longer associated with a decrease in deficit.

  3. Equivalent circuit analysis of terahertz metamaterial filters

    KAUST Repository

    Zhang, Xueqian

    2011-01-01

    An equivalent circuit model for the analysis and design of terahertz (THz) metamaterial filters is presented. The proposed model, derived based on LMC equivalent circuits, takes into account the detailed geometrical parameters and the presence of a dielectric substrate with the existing analytic expressions for self-inductance, mutual inductance, and capacitance. The model is in good agreement with the experimental measurements and full-wave simulations. Exploiting the circuit model has made it possible to predict accurately the resonance frequency of the proposed structures and thus, quick and accurate process of designing THz device from artificial metamaterials is offered. ©2011 Chinese Optics Letters.

  4. Topological equivalence of nonlinear autonomous dynamical systems

    International Nuclear Information System (INIS)

    Nguyen Huynh Phan; Tran Van Nhung

    1995-12-01

    We show in this paper that the autonomous nonlinear dynamical system Σ(A,B,F): x' = Ax+Bu+F(x) is topologically equivalent to the linear dynamical system Σ(A,B,O): x' = Ax+Bu if the projection of A on the complement in R n of the controllable vectorial subspace is hyperbolic and if lipschitz constant of F is sufficiently small ( * ) and F(x) = 0 when parallel x parallel is sufficiently large ( ** ). In particular, if Σ(A,B,O) is controllable, it is topologically equivalent to Σ(A,B,F) when it is only that F satisfy ( ** ). (author). 18 refs

  5. A neutron dose equivalent meter at CAEP

    International Nuclear Information System (INIS)

    Tian Shihai; Lu Yan; Wang Heyi; Yuan Yonggang; Chen Xu

    2012-01-01

    The measurement of neutron dose equivalent has been a widespread need in industry and research. In this paper, aimed at improving the accuracy of neutron dose equivalent meter: a neutron dose counter is simulated with MCNP5, and the energy response curve is optimized. The results show that the energy response factor is from 0.2 to 1.8 for neutrons in the energy range of 2.53×10 -8 MeV to 10 MeV Compared with other related meters, it turns that the design of this meter is right. (authors)

  6. Measurements of the personal dose equivalent

    International Nuclear Information System (INIS)

    Scarlat, F.; Scarisoreanu, A.; Badita, E.; Oane, M.; Mitru, E.

    2008-01-01

    Full text: The paper presents the results of measurements related to the personal dose equivalent in the rooms adjacent to NILPRP 7 MeV linear accelerator, by means of the secondary standard chamber T34035 Hp(10). The chamber was calibrated by PTB at S- 137 Cs (E av = 661.6 keV, T 1/2 11050 days) and has N H = 3.17x10 6 Sv/C calibration factor for the personal dose equivalent, Hp(10), at a depth of 10 mm in climatic reference conditions. The measurements were made for the two operation mode of the 7 MeV linac: electrons and bremsstrahlung

  7. 77 FR 32632 - Ambient Air Monitoring Reference and Equivalent Methods: Designation of Three New Equivalent Methods

    Science.gov (United States)

    2012-06-01

    ... Methods: Designation of Three New Equivalent Methods AGENCY: Environmental Protection Agency. ACTION... accordance with 40 CFR Part 53, three new equivalent methods: One for measuring concentrations of nitrogen... INFORMATION: In accordance with regulations at 40 CFR Part 53, the EPA evaluates various methods for...

  8. Confluence Modulo Equivalence in Constraint Handling Rules

    DEFF Research Database (Denmark)

    Christiansen, Henning; Kirkeby, Maja Hanne

    2015-01-01

    Previous results on confluence for Constraint Handling Rules, CHR, are generalized to take into account user-defined state equivalence relations. This allows a much larger class of programs to enjoy the advantages of confluence, which include various optimization techniques and simplified...

  9. Free Fall and the Equivalence Principle Revisited

    Science.gov (United States)

    Pendrill, Ann-Marie

    2017-01-01

    Free fall is commonly discussed as an example of the equivalence principle, in the context of a homogeneous gravitational field, which is a reasonable approximation for small test masses falling moderate distances. Newton's law of gravity provides a generalisation to larger distances, and also brings in an inhomogeneity in the gravitational field.…

  10. Estimation of Toxicity Equivalent Concentration (TEQ) of ...

    African Journals Online (AJOL)

    Estimation of Toxicity Equivalent Concentration (TEQ) of carcinogenic polycyclic aromatic hydrocarbons in soils from Idu Ekpeye playground and University of Port ... Effective soil remediation and detoxification method like Dispersion by chemical reaction technology should be deployed to clean-up sites to avoid soil toxicity ...

  11. Chemical equivalence assessment of three brands of ...

    African Journals Online (AJOL)

    Assay for content of active ingredients is a critical test of drug quality; failure to meet up the standard for content of active ingredients will result to sub therapeutic quantities. Three brands (A, B and C) of carbamazepine were assayed to determine their chemical equivalence as well as their anticonvulsant activities. This was ...

  12. On Behavioral Equivalence of Rational Representations

    NARCIS (Netherlands)

    Trentelman, Harry L.; Willems, JC; Hara, S; Ohta, Y; Fujioka, H

    2010-01-01

    This article deals with the equivalence of representations of behaviors of linear differential systems In general. the behavior of a given linear differential system has many different representations. In this paper we restrict ourselves to kernel representations and image representations Two kernel

  13. Visual Equivalence and Amodal Completion in Cuttlefish.

    Science.gov (United States)

    Lin, I-Rong; Chiao, Chuan-Chin

    2017-01-01

    Modern cephalopods are notably the most intelligent invertebrates and this is accompanied by keen vision. Despite extensive studies investigating the visual systems of cephalopods, little is known about their visual perception and object recognition. In the present study, we investigated the visual processing of the cuttlefish Sepia pharaonis , including visual equivalence and amodal completion. Cuttlefish were trained to discriminate images of shrimp and fish using the operant conditioning paradigm. After cuttlefish reached the learning criteria, a series of discrimination tasks were conducted. In the visual equivalence experiment, several transformed versions of the training images, such as images reduced in size, images reduced in contrast, sketches of the images, the contours of the images, and silhouettes of the images, were used. In the amodal completion experiment, partially occluded views of the original images were used. The results showed that cuttlefish were able to treat the training images of reduced size and sketches as the visual equivalence. Cuttlefish were also capable of recognizing partially occluded versions of the training image. Furthermore, individual differences in performance suggest that some cuttlefish may be able to recognize objects when visual information was partly removed. These findings support the hypothesis that the visual perception of cuttlefish involves both visual equivalence and amodal completion. The results from this research also provide insights into the visual processing mechanisms used by cephalopods.

  14. Possibility and necessity measures and integral equivalence

    Czech Academy of Sciences Publication Activity Database

    Chen, T.; Mesiar, Radko; Li, J.; Stupňanová, A.

    2017-01-01

    Roč. 86, č. 1 (2017), s. 62-72 ISSN 0888-613X Institutional support: RVO:67985556 Keywords : Integral equivalence * Necessity measure * Possibility measure * Survival function * Universal integral Subject RIV: BA - General Mathematics OBOR OECD: Statistics and probability Impact factor: 2.845, year: 2016 http://library.utia.cas.cz/separaty/2017/E/mesiar-0477092.pdf

  15. Fuel Cell Equivalent Electric Circuit Parameter Mapping

    DEFF Research Database (Denmark)

    Jeppesen, Christian; Zhou, Fan; Andreasen, Søren Juhl

    In this work a simple model for a fuel cell is investigated for diagnostic purpose. The fuel cell is characterized, with respect to the electrical impedance of the fuel cell at non-faulty conditions and under variations in load current. Based on this the equivalent electrical circuit parameters can...

  16. Weak equivalence classes of complex vector bundles

    Czech Academy of Sciences Publication Activity Database

    Le, Hong-Van

    LXXVII, č. 1 (2008), s. 23-30 ISSN 0862-9544 R&D Projects: GA AV ČR IAA100190701 Institutional research plan: CEZ:AV0Z10190503 Keywords : chern classes * complex Grassmannians weak equivalence Subject RIV: BA - General Mathematics

  17. Violation of Equivalence Principle and Solar Neutrinos

    International Nuclear Information System (INIS)

    Gago, A.M.; Nunokawa, H.; Zukanovich Funchal, R.

    2001-01-01

    We have updated the analysis for the solution to the solar neutrino problem by the long-wavelength neutrino oscillations induced by a tiny breakdown of the weak equivalence principle of general relativity, and obtained a very good fit to all the solar neutrino data

  18. Bilingual Dictionaries and Communicative Equivalence for a ...

    African Journals Online (AJOL)

    This implies that a bilingual dictionary becomes a poly functional instrument, presenting more information than just translation equivalents. ... With the emphasis on the user perspective, metalexicographical criteria are used to investigate problems regarding the access structure and the addressing procedures in Afrikaans ...

  19. Equivalent operator preconditioning for elliptic problems

    Czech Academy of Sciences Publication Activity Database

    Axelsson, Owe; Karátson, J.

    2009-01-01

    Roč. 50, č. 3 (2009), s. 297-380 ISSN 1017-1398 Institutional research plan: CEZ:AV0Z30860518 Keywords : Elliptic problem * Conjugate gradient method * preconditioning * equivalent operators * compact operators Subject RIV: BA - General Mathematics Impact factor: 0.716, year: 2009 http://en.scientificcommons.org/42514649

  20. Superstring field theory equivalence: Ramond sector

    International Nuclear Information System (INIS)

    Kroyter, Michael

    2009-01-01

    We prove that the finite gauge transformation of the Ramond sector of the modified cubic superstring field theory is ill-defined due to collisions of picture changing operators. Despite this problem we study to what extent could a bijective classical correspondence between this theory and the (presumably consistent) non-polynomial theory exist. We find that the classical equivalence between these two theories can almost be extended to the Ramond sector: We construct mappings between the string fields (NS and Ramond, including Chan-Paton factors and the various GSO sectors) of the two theories that send solutions to solutions in a way that respects the linearized gauge symmetries in both sides and keeps the action of the solutions invariant. The perturbative spectrum around equivalent solutions is also isomorphic. The problem with the cubic theory implies that the correspondence of the linearized gauge symmetries cannot be extended to a correspondence of the finite gauge symmetries. Hence, our equivalence is only formal, since it relates a consistent theory to an inconsistent one. Nonetheless, we believe that the fact that the equivalence formally works suggests that a consistent modification of the cubic theory exists. We construct a theory that can be considered as a first step towards a consistent RNS cubic theory.

  1. Equivalence Scales for the Former West Germany

    NARCIS (Netherlands)

    Charlier, E.

    1997-01-01

    Equivalence scales provide answers to questions like how much a household with four children needs to spend compared to a household with two children or how much a childless couple needs to spend compared to a single person household to attain the same welfare level. These are important questions

  2. Confluence Modulo Equivalence in Constraint Handling Rules

    DEFF Research Database (Denmark)

    Christiansen, Henning; Kirkeby, Maja Hanne

    2014-01-01

    Previous results on confluence for Constraint Handling Rules, CHR, are generalized to take into account user-defined state equivalence relations. This allows a much larger class of programs to enjoy the ad- vantages of confluence, which include various optimization techniques and simplified...

  3. Equivalence of rational representations of behaviors

    NARCIS (Netherlands)

    Gottimukkala, Sasanka; Fiaz, Shaik; Trentelman, H.L.

    This article deals with the equivalence of representations of behaviors of linear differential systems. In general, the behavior of a given linear differential system has many different representations. In this paper we restrict ourselves to kernel and image representations. Two kernel

  4. Equivalent physical models and formulation of equivalent source layer in high-resolution EEG imaging

    International Nuclear Information System (INIS)

    Yao Dezhong; He Bin

    2003-01-01

    In high-resolution EEG imaging, both equivalent dipole layer (EDL) and equivalent charge layer (ECL) assumed to be located just above the cortical surface have been proposed as high-resolution imaging modalities or as intermediate steps to estimate the epicortical potential. Presented here are the equivalent physical models of these two equivalent source layers (ESL) which show that the strength of EDL is proportional to the surface potential of the layer when the outside of the layer is filled with an insulator, and that the strength of ECL is the normal current of the layer when the outside is filled with a perfect conductor. Based on these equivalent physical models, closed solutions of ECL and EDL corresponding to a dipole enclosed by a spherical layer are given. These results provide the theoretical basis of ESL applications in high-resolution EEG mapping

  5. Equivalent physical models and formulation of equivalent source layer in high-resolution EEG imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yao Dezhong [School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu City, 610054, Sichuan Province (China); He Bin [The University of Illinois at Chicago, IL (United States)

    2003-11-07

    In high-resolution EEG imaging, both equivalent dipole layer (EDL) and equivalent charge layer (ECL) assumed to be located just above the cortical surface have been proposed as high-resolution imaging modalities or as intermediate steps to estimate the epicortical potential. Presented here are the equivalent physical models of these two equivalent source layers (ESL) which show that the strength of EDL is proportional to the surface potential of the layer when the outside of the layer is filled with an insulator, and that the strength of ECL is the normal current of the layer when the outside is filled with a perfect conductor. Based on these equivalent physical models, closed solutions of ECL and EDL corresponding to a dipole enclosed by a spherical layer are given. These results provide the theoretical basis of ESL applications in high-resolution EEG mapping.

  6. Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.

    Science.gov (United States)

    Leushkin, Evgeny V; Logacheva, Maria D; Penin, Aleksey A; Sutormin, Roman A; Gerasimov, Evgeny S; Kochkina, Galina A; Ivanushkina, Natalia E; Vasilenko, Oleg V; Kondrashov, Alexey S; Ozerskaya, Svetlana M

    2015-05-21

    Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50 Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100-10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.

  7. Novel type of linear mitochondrial genomes with dual flip-flop inversion system in apicomplexan parasites, Babesia microti and Babesia rodhaini

    Directory of Open Access Journals (Sweden)

    Hikosaka Kenji

    2012-11-01

    Full Text Available Abstract Background Mitochondrial (mt genomes vary considerably in size, structure and gene content. The mt genomes of the phylum Apicomplexa, which includes important human pathogens such as the malaria parasite Plasmodium, also show marked diversity of structure. Plasmodium has a concatenated linear mt genome of the smallest size (6-kb; Babesia and Theileria have a linear monomeric mt genome (6.5-kb to 8.2-kb with terminal inverted repeats; Eimeria, which is distantly related to Plasmodium and Babesia/Theileria, possesses a mt genome (6.2-kb with a concatemeric form similar to that of Plasmodium; Cryptosporidium, the earliest branching lineage within the phylum Apicomplexa, has no mt genome. We are interested in the evolutionary origin of linear mt genomes of Babesia/Theileria, and have investigated mt genome structures in members of archaeopiroplasmid, a lineage branched off earlier from Babesia/Theileria. Results The complete mt genomes of archaeopiroplasmid parasites, Babesia microti and Babesia rodhaini, were sequenced. The mt genomes of B. microti (11.1-kb and B. rodhaini (6.9-kb possess two pairs of unique inverted repeats, IR-A and IR-B. Flip-flop inversions between two IR-As and between two IR-Bs appear to generate four distinct genome structures that are present at an equi-molar ratio. An individual parasite contained multiple mt genome structures, with 20 copies and 2 – 3 copies per haploid nuclear genome in B. microti and B. rodhaini, respectively. Conclusion We found a novel linear monomeric mt genome structure of B. microti and B. rhodhaini equipped with dual flip-flop inversion system, by which four distinct genome structures are readily generated. To our knowledge, this study is the first to report the presence of two pairs of distinct IR sequences within a monomeric linear mt genome. The present finding provides insight into further understanding of evolution of mt genome structure.

  8. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  9. Digestive and regenerative cells in the midgut of haploid and diploid males of the stingless bee Melipona quadrifasciata anthidioides (Hymenoptera: Apidae

    Directory of Open Access Journals (Sweden)

    Kenner M. Fernandes

    2012-10-01

    Full Text Available In eusocial bees, workers and queens are diploid (2n, whereas males are haploid (n. However, in some species, including the stingless bee Melipona quadrifasciata anthidioides Lepeletier, 1836, 2n males arise from fertilized eggs resulting from the crossing between a queen and her brother. In the present study, we provide a comparative analysis of the digestive and regenerative cells in n and 2n pupae and adult males of M. quadrifasciata anthidioides. In n and 2n pupae and adult males, the number of regenerative cells/nest was similar. In n and 2n pupae, the mean number of digestive cells/midgut area was 2076 ± 0.60, whereas in adults it was 1234 ± 1.42 digestive cells/midgut area. The nuclear area of the digestive cells was also similar in both n and 2n adult males (~154 µm² and smaller in pupae (~91 µm²; this variation might be a result of DNA amplification in digestive cells during bee development. The results from our current study provide further understanding of the morphological and physiological aspects of the digestive tract of bees and show that the ploidy difference between n and 2n male stages does not affect the number of digestive and regenerative cells in the midgut of M. quadrifasciata anthidioides.

  10. The influence of Glu-1 and Glu-3 loci on dough rheology and bread-making properties in wheat (Triticum aestivum L.) doubled haploid lines.

    Science.gov (United States)

    Langner, Monika; Krystkowiak, Karolina; Salmanowicz, Bolesław P; Adamski, Tadeusz; Krajewski, Paweł; Kaczmarek, Zygmunt; Surma, Maria

    2017-12-01

    The major determinants of wheat quality are Glu-1 and Glu-3 glutenin loci and environmental factors. Additive effects of alleles at the Glu-1 and Glu-3 loci, as well as their interactions, were evaluated for dough rheology and baking properties in four groups of wheat doubled haploid lines differing in high- and low-molecular-weight glutenin composition. Flour quality, Reomixer (Reologica Instruments, Lund, Sweden), dough extension, Farinograph (Brabender GmbH, Duisburg, Germany) and baking parameters were determined. Groups of lines with the alleles Glu-A3b and Glu-B3d were characterized by higher values of dough and baking parameters compared to those with the Glu-A3e and Glu-B3a alleles. Effects of interactions between allelic variants at the Glu-1 and Glu-3 loci on Reomixer parameters, dough extension tests and baking parameters were significant, although additive effects of individual alleles were not always significant. The allelic variants at Glu-B3 had a much greater effect on dough rheological parameters than the variants at Glu-A3 or Glu-D3 loci. The effect of allelic variations at the Glu-D3 loci on rheological parameters and bread-making quality was non-significant, whereas their interactions with a majority of alleles at the other Glu-1 × Glu-3 loci were significant. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  11. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  12. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity.

    Science.gov (United States)

    Schwessinger, Benjamin; Sperschneider, Jana; Cuddy, William S; Garnica, Diana P; Miller, Marisa E; Taylor, Jennifer M; Dodds, Peter N; Figueroa, Melania; Park, Robert F; Rathjen, John P

    2018-02-20

    A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N 50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is

  13. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  14. Genome size evolution at the speciation level: the cryptic species complex Brachionus plicatilis (Rotifera).

    Science.gov (United States)

    Stelzer, Claus-Peter; Riss, Simone; Stadler, Peter

    2011-04-07

    Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels--within and among genealogical species--and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.

  15. Genome size evolution at the speciation level: The cryptic species complex Brachionus plicatilis (Rotifera

    Directory of Open Access Journals (Sweden)

    Riss Simone

    2011-04-01

    Full Text Available Abstract Background Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. Results We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg. Most of this variation (67% could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32% at lower taxonomic levels - within and among genealogical species - and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Conclusions Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.

  16. Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes.

    Science.gov (United States)

    Song, Yutong; Gorbatsevych, Oleksandr; Liu, Ying; Mugavero, JoAnn; Shen, Sam H; Ward, Charles B; Asare, Emmanuel; Jiang, Ping; Paul, Aniko V; Mueller, Steffen; Wimmer, Eckard

    2017-10-10

    Computer design and chemical synthesis generated viable variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutations (excess of overrepresented synonymous codon pairs) or up to 2,104 "SD" mutations (randomly scrambled synonymous codons). "Min" variants (excess of underrepresented synonymous codon pairs) are nonviable except for P2 Min , a variant temperature-sensitive at 33 and 39.5 °C. Compared with WT PV1, P2 Min displayed a vastly reduced specific infectivity (si) (WT, 1 PFU/118 particles vs. P2 Min , 1 PFU/35,000 particles), a phenotype that will be discussed broadly. Si of haploid PV presents cellular infectivity of a single genotype. We performed a comprehensive analysis of sequence and structures of the PV genome to determine if evolutionary conserved cis-acting packaging signal(s) were preserved after recoding. We showed that conserved synonymous sites and/or local secondary structures that might play a role in determining packaging specificity do not survive codon pair recoding. This makes it unlikely that numerous "cryptic, sequence-degenerate, dispersed RNA packaging signals mapping along the entire viral genome" [Patel N, et al. (2017) Nat Microbiol 2:17098] play the critical role in poliovirus packaging specificity. Considering all available evidence, we propose a two-step assembly strategy for +ssRNA viruses: step I, acquisition of packaging specificity, either ( a ) by specific recognition between capsid protein(s) and replication proteins (poliovirus), or ( b ) by the high affinity interaction of a single RNA packaging signal (PS) with capsid protein(s) (most +ssRNA viruses so far studied); step II, cocondensation of genome/capsid precursors in which an array of hairpin structures plays a role in virion formation.

  17. Genomic Predictability of Interconnected Biparental Maize Populations

    Science.gov (United States)

    Riedelsheimer, Christian; Endelman, Jeffrey B.; Stange, Michael; Sorrells, Mark E.; Jannink, Jean-Luc; Melchinger, Albrecht E.

    2013-01-01

    Intense structuring of plant breeding populations challenges the design of the training set (TS) in genomic selection (GS). An important open question is how the TS should be constructed from multiple related or unrelated small biparental families to predict progeny from individual crosses. Here, we used a set of five interconnected maize (Zea mays L.) populations of doubled-haploid (DH) lines derived from four parents to systematically investigate how the composition of the TS affects the prediction accuracy for lines from individual crosses. A total of 635 DH lines genotyped with 16,741 polymorphic SNPs were evaluated for five traits including Gibberella ear rot severity and three kernel yield component traits. The populations showed a genomic similarity pattern, which reflects the crossing scheme with a clear separation of full sibs, half sibs, and unrelated groups. Prediction accuracies within full-sib families of DH lines followed closely theoretical expectations, accounting for the influence of sample size and heritability of the trait. Prediction accuracies declined by 42% if full-sib DH lines were replaced by half-sib DH lines, but statistically significantly better results could be achieved if half-sib DH lines were available from both instead of only one parent of the validation population. Once both parents of the validation population were represented in the TS, including more crosses with a constant TS size did not increase accuracies. Unrelated crosses showing opposite linkage phases with the validation population resulted in negative or reduced prediction accuracies, if used alone or in combination with related families, respectively. We suggest identifying and excluding such crosses from the TS. Moreover, the observed variability among populations and traits suggests that these uncertainties must be taken into account in models optimizing the allocation of resources in GS. PMID:23535384

  18. Equivalent Gene Expression Profiles between Glatopa™ and Copaxone®.

    Directory of Open Access Journals (Sweden)

    Josephine S D'Alessandro

    Full Text Available Glatopa™ is a generic glatiramer acetate recently approved for the treatment of patients with relapsing forms of multiple sclerosis. Gene expression profiling was performed as a means to evaluate equivalence of Glatopa and Copaxone®. Microarray analysis containing 39,429 unique probes across the entire genome was performed in murine glatiramer acetate--responsive Th2-polarized T cells, a test system highly relevant to the biology of glatiramer acetate. A closely related but nonequivalent glatiramoid molecule was used as a control to establish assay sensitivity. Multiple probe-level (Student's t-test and sample-level (principal component analysis, multidimensional scaling, and hierarchical clustering statistical analyses were utilized to look for differences in gene expression induced by the test articles. The analyses were conducted across all genes measured, as well as across a subset of genes that were shown to be modulated by Copaxone. The following observations were made across multiple statistical analyses: the expression of numerous genes was significantly changed by treatment with Copaxone when compared against media-only control; gene expression profiles induced by Copaxone and Glatopa were not significantly different; and gene expression profiles induced by Copaxone and the nonequivalent glatiramoid were significantly different, underscoring the sensitivity of the test system and the multiple analysis methods. Comparative analysis was also performed on sets of transcripts relevant to T-cell biology and antigen presentation, among others that are known to be modulated by glatiramer acetate. No statistically significant differences were observed between Copaxone and Glatopa in the expression levels (magnitude and direction of these glatiramer acetate-regulated genes. In conclusion, multiple methods consistently supported equivalent gene expression profiles between Copaxone and Glatopa.

  19. On the equivalence of GPD representations

    International Nuclear Information System (INIS)

    Müller, Dieter; Semenov-Tian-Shansky, Kirill

    2016-01-01

    Phenomenological representations of generalized parton distributions (GPDs) implementing the non-trivial field theoretical requirements are employed in the present day strategies for extracting of hadron structure information encoded in GPDs from the observables of hard exclusive reactions. Showing out the equivalence of various GPD representations can help to get more insight into GPD properties and allow to build up flexible GPD models capable of satisfactory description of the whole set of available experimental data. Below we review the mathematical aspects of establishing equivalence between the the double partial wave expansion of GPDs in the conformal partial waves and in the t-channel SO(3) partial waves and the double distribution representation of GPDs

  20. Developing equivalent circuits for radial distribution networks

    Energy Technology Data Exchange (ETDEWEB)

    Prada, Ricardo; Coelho, Agnelo; Rodrigues, Anselmo [Catholic University of Rio de Janeiro (PUC-Rio), RJ (Brazil). Dept. of Electrical Engineering], Emails: prada@ele.puc-rio.br, agnelo@ele.puc-rio.br, nebulok_99@yahoo.com; Silva, Maria da Guia da [Federal University of Maranhao, Sao Luiz, MA (Brazil). Dept. of Electrical Engineering

    2009-07-01

    This paper presents a method for evaluating External Equivalent in Electric Distribution Networks (EDN).The proposed method has as its main objectives the reduction of the computational costs in distribution network reconfiguration, investigation of the optimal allocation of banks of capacitors, investigation of the allocation of distributed generation, etc. In these sorts of problems a large number of alternative projects must be assessed in order to identify the optimal solution. The optimal solution comes up with the voltage level in the load points within specified limits. Consequently, the EDN must retain the external network load points but without major increasing in the dimension of the equivalent circuit. The proposed method has been tested and validated in a substation of the Electricity Utility of Maranhao - CEMAR, in Brazil. (author)

  1. Thermoluminescence dosemeter for personal dose equivalent assessment

    International Nuclear Information System (INIS)

    Silva, T.A. da; Rosa, L.A.R. da; Campos, L.L.

    1995-01-01

    The possibility was investigated of utilising a Brazilian thermoluminescence individual dosemeter, usually calibrated in terms of photon dose equivalent, for the assessment of the personal dose equivalent, H p (d), at depths of 0.07 and 10 mm. The dosemeter uses four CaSO 4 :Dy thermoluminescent detectors, between different filters, as the sensitive materials. It was calibrated in gamma and X radiation fields in the energy range from 17 to 1250 keV. Linear combinations of the responses of three detectors, in this energy range, allow the evaluation of H p (0.07) and H p (10), for radiation incidence angles varying from 0 to 60 degrees, with an accuracy better than 35%. The method is not applicable to mixed photon-beta fields. (author)

  2. Thevenin Equivalent Method for Dynamic Contingency Assessment

    DEFF Research Database (Denmark)

    Møller, Jakob Glarbo; Jóhannsson, Hjörtur; Østergaard, Jacob

    2015-01-01

    A method that exploits Thevenin equivalent representation for obtaining post-contingency steady-state nodal voltages is integrated with a method of detecting post-contingency aperiodic small-signal instability. The task of integrating stability assessment with contingency assessment is challenged...... by the cases of unstable post-contingency conditions. For unstable postcontingency conditions there exists no credible steady-state which can be used for basis of a stability assessment. This paper demonstrates how Thevenin Equivalent methods can be applied in algebraic representation of such bifurcation...... points which may be used in assessment of post-contingency aperiodic small-signal stability. The assessment method is introduced with a numeric example....

  3. The Logic of Equivalence in Academic Discourse?

    DEFF Research Database (Denmark)

    Madsen, Dorte

    2017-01-01

    of discourse to distinguish between the scientific field, where interrelationships among academic disciplines are taken as an object of research, and the widespread uses of ‘interdisciplinary’ and ‘interdisciplinarity’ in academic discourse more generally, typically for legitimation purposes. The assumption......-discourses meet. It is suggested that the logics of signification, and the tension between difference and equivalence, may be important tools for theorizing this borderland. It is argued that whereas the logic of equivalence and the production of empty signifiers appears to be of marginal interest...... to the scientific field, the logic of difference as a more complex articulation of elements, seems to be more in line with the ideals of academic discourse....

  4. On equivalent resistance of electrical circuits

    Science.gov (United States)

    Kagan, Mikhail

    2015-01-01

    While the standard (introductory physics) way of computing the equivalent resistance of nontrivial electrical circuits is based on Kirchhoff's rules, there is a mathematically and conceptually simpler approach, called the method of nodal potentials, whose basic variables are the values of the electric potential at the circuit's nodes. In this paper, we review the method of nodal potentials and illustrate it using the Wheatstone bridge as an example. We then derive a closed-form expression for the equivalent resistance of a generic circuit, which we apply to a few sample circuits. The result unveils a curious interplay between electrical circuits, matrix algebra, and graph theory and its applications to computer science. The paper is written at a level accessible by undergraduate students who are familiar with matrix arithmetic. Additional proofs and technical details are provided in appendices.

  5. Symmetry adaptation, operator equivalents and magnetic resonance

    International Nuclear Information System (INIS)

    Kibler, M.; Chatterjee, R.

    1977-12-01

    Basic quantities for symmetry adaptation are discussed in connection with molecular and solid state physics. This gives rise to a formalism whose the central elements are operator equivalents adapted to a point group. Such symmetry adapted operator equivalents are defined in terms of Schwinger operators so that they cover the off-diagonal and diagonal cases. Special emphasis is put on the applications of the formalism to magnetic resonance. More specifically, it is shown how to apply the formalism to the construction, the study of the transformation properties, and the determination of the eigenstates of a generalized spin hamiltonian. Numerous examples are given as well as key tables relative to the chain SO(3) for making easy the application of the formalism to electron paramagnetic resonance [fr

  6. 3D modeling of genome macroorganization on the basis of its structural changes after action of radiation

    International Nuclear Information System (INIS)

    Aleksandrov, I.D.; Aleksandrova, M.V.; Zaikin, N.S.; Koren'kov, V.V.; Pervushova, O.V.; Stepanenko, V.A.

    2006-01-01

    At present, after 120 years of the theoretical and experimental works, the issue of the genome macroarchitecture as the highest level of interphase chromosome organization in somatic cell nuclei remains still unresolved. The problem of the spatial arrangement of interphase chromosomes in haploid germ cells has never even been studied. A 3D simulation of packaging of the entire second chromosome in Drosophila mature sperms has been performed by using mathematical approaches and visualization methods to present macromolecular structure data. As genetic markers for simulation, frequency and location of the second inversion breakpoints for 72 structural υg mutants induced by ionizing radiation were used supposing that both ends of each inversion are topologically brought together forming loop of appropriate size. For the account of a degree of spatial affinity and visualization of chromosomal loops modern 3D-modeling methods with application of splines, libraries OpenGL, language Delphi, program Gmax were used. According to the model proposed, the entire second chromosome within mature sperm nuclei seems to be packaged in the form of a megarosette-loop structure which may be a basic principle of organization of the genome macro-architecture in animal haploid germ cells

  7. A Logical Characterisation of Static Equivalence

    DEFF Research Database (Denmark)

    Hüttel, Hans; Pedersen, Michael D.

    2007-01-01

    -order logic for frames with quantification over environment knowledge which, under certain general conditions, characterizes static equivalence and is amenable to construction of characteristic formulae. The logic can be used to reason about environment knowledge and can be adapted to a particular application...... by defining a suitable signature and associated equational theory. The logic can furthermore be extended with modalities to yield a modal logic for e.g. the Applied Pi calculus....

  8. Global equivalent magnetization of the oceanic lithosphere

    Science.gov (United States)

    Dyment, J.; Choi, Y.; Hamoudi, M.; Lesur, V.; Thebault, E.

    2015-11-01

    As a by-product of the construction of a new World Digital Magnetic Anomaly Map over oceanic areas, we use an original approach based on the global forward modeling of seafloor spreading magnetic anomalies and their comparison to the available marine magnetic data to derive the first map of the equivalent magnetization over the World's ocean. This map reveals consistent patterns related to the age of the oceanic lithosphere, the spreading rate at which it was formed, and the presence of mantle thermal anomalies which affects seafloor spreading and the resulting lithosphere. As for the age, the equivalent magnetization decreases significantly during the first 10-15 Myr after its formation, probably due to the alteration of crustal magnetic minerals under pervasive hydrothermal alteration, then increases regularly between 20 and 70 Ma, reflecting variations in the field strength or source effects such as the acquisition of a secondary magnetization. As for the spreading rate, the equivalent magnetization is twice as strong in areas formed at fast rate than in those formed at slow rate, with a threshold at ∼40 km/Myr, in agreement with an independent global analysis of the amplitude of Anomaly 25. This result, combined with those from the study of the anomalous skewness of marine magnetic anomalies, allows building a unified model for the magnetic structure of normal oceanic lithosphere as a function of spreading rate. Finally, specific areas affected by thermal mantle anomalies at the time of their formation exhibit peculiar equivalent magnetization signatures, such as the cold Australian-Antarctic Discordance, marked by a lower magnetization, and several hotspots, marked by a high magnetization.

  9. Visual Equivalence and Amodal Completion in Cuttlefish

    OpenAIRE

    Lin, I-Rong; Chiao, Chuan-Chin

    2017-01-01

    Modern cephalopods are notably the most intelligent invertebrates and this is accompanied by keen vision. Despite extensive studies investigating the visual systems of cephalopods, little is known about their visual perception and object recognition. In the present study, we investigated the visual processing of the cuttlefish Sepia pharaonis, including visual equivalence and amodal completion. Cuttlefish were trained to discriminate images of shrimp and fish using the operant conditioning pa...

  10. Canonizing certain Borel equivalences for Silver forcing

    Czech Academy of Sciences Publication Activity Database

    Doucha, Michal

    2012-01-01

    Roč. 159, č. 13 (2012), s. 2973-2979 ISSN 0166-8641. [Prague Symposium on General Topology and its Relations to Modern Analysis and Algebra /11./. Prague, 07.08.2011-12.08.2011] Institutional research plan: CEZ:AV0Z10190503 Keywords : Borel equivalence relations * silver ideal * canonical Ramsey theorem Subject RIV: BA - General Mathematics Impact factor: 0.562, year: 2012 http://www.sciencedirect.com/science/article/pii/S0166864112002180#

  11. Quantum mechanics from an equivalence principle

    International Nuclear Information System (INIS)

    Faraggi, A.E.

    1997-01-01

    The authors show that requiring diffeomorphic equivalence for one-dimensional stationary states implies that the reduced action S 0 satisfies the quantum Hamilton-Jacobi equation with the Planck constant playing the role of a covariantizing parameter. The construction shows the existence of a fundamental initial condition which is strictly related to the Moebius symmetry of the Legendre transform and to its involutive character. The universal nature of the initial condition implies the Schroedinger equation in any dimension

  12. Equivalency of two-dimensional algebras

    International Nuclear Information System (INIS)

    Santos, Gildemar Carneiro dos; Pomponet Filho, Balbino Jose S.

    2011-01-01

    Full text: Let us consider a vector z = xi + yj over the field of real numbers, whose basis (i,j) satisfy a given algebra. Any property of this algebra will be reflected in any function of z, so we can state that the knowledge of the properties of an algebra leads to more general conclusions than the knowledge of the properties of a function. However structural properties of an algebra do not change when this algebra suffers a linear transformation, though the structural constants defining this algebra do change. We say that two algebras are equivalent to each other whenever they are related by a linear transformation. In this case, we have found that some relations between the structural constants are sufficient to recognize whether or not an algebra is equivalent to another. In spite that the basis transform linearly, the structural constants change like a third order tensor, but some combinations of these tensors result in a linear transformation, allowing to write the entries of the transformation matrix as function of the structural constants. Eventually, a systematic way to find the transformation matrix between these equivalent algebras is obtained. In this sense, we have performed the thorough classification of associative commutative two-dimensional algebras, and find that even non-division algebra may be helpful in solving non-linear dynamic systems. The Mandelbrot set was used to have a pictorial view of each algebra, since equivalent algebras result in the same pattern. Presently we have succeeded in classifying some non-associative two-dimensional algebras, a task more difficult than for associative one. (author)

  13. Cryogenic test of the equivalence principle

    International Nuclear Information System (INIS)

    Worden, P.W. Jr.

    1976-01-01

    The weak equivalence principle is the hypothesis that the ratio of internal and passive gravitational mass is the same for all bodies. A greatly improved test of this principle is possible in an orbiting satellite. The most promising experiments for an orbital test are adaptations of the Galilean free-fall experiment and the Eotvos balance. Sensitivity to gravity gradient noise, both from the earth and from the spacecraft, defines a limit to the sensitivity in each case. This limit is generally much worse for an Eotvos balance than for a properly designed free-fall experiment. The difference is related to the difficulty of making a balance sufficiently isoinertial. Cryogenic technology is desirable to take full advantage of the potential sensitivity, but tides in the liquid helium refrigerant may produce a gravity gradient that seriously degrades the ultimate sensitivity. The Eotvos balance appears to have a limiting sensitivity to relative difference of rate of fall of about 2 x 10 -14 in orbit. The free-fall experiment is limited by helium tide to about 10 -15 ; if the tide can be controlled or eliminated the limit may approach 10 -18 . Other limitations to equivalence principle experiments are discussed. An experimental test of some of the concepts involved in the orbital free-fall experiment is continuing. The experiment consists in comparing the motions of test masses levitated in a superconducting magnetic bearing, and is itself a sensitive test of the equivalence principle. At present the levitation magnets, position monitors and control coils have been tested and major noise sources identified. A measurement of the equivalence principle is postponed pending development of a system for digitizing data. The experiment and preliminary results are described

  14. Extended equivalent dipole model for radiated emissions

    OpenAIRE

    Obiekezie, Chijioke S.

    2016-01-01

    This work is on the characterisation of radiated fields from electronic devices. An equivalent dipole approach is used. Previous work showed that this was an effective approach for single layer printed circuit boards where an infinite ground plane can be assumed. In this work, this approach is extended for the characterisation of more complex circuit boards or electronic systems.\\ud For complex electronic radiators with finite ground planes, the main challenge is characterising field diffract...

  15. Equivalence of Lagrangian and Hamiltonian BRST quantizations

    International Nuclear Information System (INIS)

    Grigoryan, G.V.; Grigoryan, R.P.; Tyutin, I.V.

    1992-01-01

    Two approaches to the quantization of gauge theories using BRST symmetry are widely used nowadays: the Lagrangian quantization, developed in (BV-quantization) and Hamiltonian quantization, formulated in (BFV-quantization). For all known examples of field theory (Yang-Mills theory, gravitation etc.) both schemes give equivalent results. However the equivalence of these approaches in general wasn't proved. The main obstacle in comparing of these formulations consists in the fact, that in Hamiltonian approach the number of ghost fields is equal to the number of all first-class constraints, while in the Lagrangian approach the number of ghosts is equal to the number of independent gauge symmetries, which is equal to the number of primary first-class constraints only. This paper is devoted to the proof of the equivalence of Lagrangian and Hamiltonian quantizations for the systems with first-class constraints only. This is achieved by a choice of special gauge in the Hamiltonian approach. It's shown, that after integration over redundant variables on the functional integral we come to effective action which is constructed according to rules for construction of the effective action in Lagrangian quantization scheme

  16. Energy conservation and the principle of equivalence

    International Nuclear Information System (INIS)

    Haugan, M.P.

    1979-01-01

    If the equivalence principle is violated, then observers performing local experiments can detect effects due to their position in an external gravitational environment (preferred-location effects) or can detect effects due to their velocity through some preferred frame (preferred frame effects). We show that the principle of energy conservation implies a quantitative connection between such effects and structure-dependence of the gravitational acceleration of test bodies (violation of the Weak Equivalence Principle). We analyze this connection within a general theoretical framework that encompasses both non-gravitational local experiments and test bodies as well as gravitational experiments and test bodies, and we use it to discuss specific experimental tests of the equivalence principle, including non-gravitational tests such as gravitational redshift experiments, Eoetvoes experiments, the Hughes-Drever experiment, and the Turner-Hill experiment, and gravitational tests such as the lunar-laser-ranging ''Eoetvoes'' experiment, and measurements of anisotropies and variations in the gravitational constant. This framework is illustrated by analyses within two theoretical formalisms for studying gravitational theories: the PPN formalism, which deals with the motion of gravitating bodies within metric theories of gravity, and the THepsilonμ formalism that deals with the motion of charged particles within all metric theories and a broad class of non-metric theories of gravity

  17. Genomic-based-breeding tools for tropical maize improvement.

    Science.gov (United States)

    Chakradhar, Thammineni; Hindu, Vemuri; Reddy, Palakolanu Sudhakar

    2017-12-01

    Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in

  18. Gauge equivalence of the Gross Pitaevskii equation and the equivalent Heisenberg spin chain

    Science.gov (United States)

    Radha, R.; Kumar, V. Ramesh

    2007-11-01

    In this paper, we construct an equivalent spin chain for the Gross-Pitaevskii equation with quadratic potential and exponentially varying scattering lengths using gauge equivalence. We have then generated the soliton solutions for the spin components S3 and S-. We find that the spin solitons for S3 and S- can be compressed for exponentially growing eigenvalues while they broaden out for decaying eigenvalues.

  19. Equivalent models of wind farms by using aggregated wind turbines and equivalent winds

    International Nuclear Information System (INIS)

    Fernandez, L.M.; Garcia, C.A.; Saenz, J.R.; Jurado, F.

    2009-01-01

    As a result of the increasing wind farms penetration on power systems, the wind farms begin to influence power system, and therefore the modeling of wind farms has become an interesting research topic. In this paper, new equivalent models of wind farms equipped with wind turbines based on squirrel-cage induction generators and doubly-fed induction generators are proposed to represent the collective behavior on large power systems simulations, instead of using a complete model of wind farms where all the wind turbines are modeled. The models proposed here are based on aggregating wind turbines into an equivalent wind turbine which receives an equivalent wind of the ones incident on the aggregated wind turbines. The equivalent wind turbine presents re-scaled power capacity and the same complete model as the individual wind turbines, which supposes the main feature of the present equivalent models. Two equivalent winds are evaluated in this work: (1) the average wind from the ones incident on the aggregated wind turbines with similar winds, and (2) an equivalent incoming wind derived from the power curve and the wind incident on each wind turbine. The effectiveness of the equivalent models to represent the collective response of the wind farm at the point of common coupling to grid is demonstrated by comparison with the wind farm response obtained from the detailed model during power system dynamic simulations, such as wind fluctuations and a grid disturbance. The present models can be used for grid integration studies of large power system with an important reduction of the model order and the computation time

  20. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  1. Mutation induction in haploid yeast after split-dose radiation exposure. II. Combination of UV-irradiation and X-rays.

    Science.gov (United States)

    Keller, B; Zölzer, F; Kiefer, J

    2004-01-01

    Split-dose protocols can be used to investigate the kinetics of recovery from radiation damage and to elucidate the mechanisms of cell inactivation and mutation induction. In this study, a haploid strain of the yeast, Saccharomyces cerevisiae, wild-type with regard to radiation sensitivity, was irradiated with 254-nm ultraviolet (UV) light and then exposed to X-rays after incubation for 0-6 hr. The cells were incubated either on nutrient medium or salt agar between the treatments. Loss of reproductive ability and mutation to canavanine resistance were measured. When the X-ray exposure immediately followed UV-irradiation, the X-ray survival curves had the same slope irrespective of the pretreatment, while the X-ray mutation induction curves were changed from linear to linear quadratic with increasing UV fluence. Incubations up to about 3 hr on nutrient medium between the treatments led to synergism with respect to cell inactivation and antagonism with respect to mutation, but after 4-6 hr the two treatments acted independently. Incubation on salt agar did not cause any change in the survival curves, but there was a strong suppression of X-ray-induced mutation with increasing UV fluence. On the basis of these results, we suggest that mutation after combined UV and X-ray exposure is affected not only by the induction and suppression of DNA repair processes, but also by radiation-induced modifications of cell-cycle progression and changes in the expression of the mutant phenotype. Copyright 2004 Wiley-Liss, Inc.

  2. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  3. Generating carbyne equivalents with photoredox catalysis

    Science.gov (United States)

    Wang, Zhaofeng; Herraiz, Ana G.; Del Hoyo, Ana M.; Suero, Marcos G.

    2018-02-01

    Carbon has the unique ability to bind four atoms and form stable tetravalent structures that are prevalent in nature. The lack of one or two valences leads to a set of species—carbocations, carbanions, radicals and carbenes—that is fundamental to our understanding of chemical reactivity. In contrast, the carbyne—a monovalent carbon with three non-bonded electrons—is a relatively unexplored reactive intermediate; the design of reactions involving a carbyne is limited by challenges associated with controlling its extreme reactivity and the lack of efficient sources. Given the innate ability of carbynes to form three new covalent bonds sequentially, we anticipated that a catalytic method of generating carbynes or related stabilized species would allow what we term an ‘assembly point’ disconnection approach for the construction of chiral centres. Here we describe a catalytic strategy that generates diazomethyl radicals as direct equivalents of carbyne species using visible-light photoredox catalysis. The ability of these carbyne equivalents to induce site-selective carbon-hydrogen bond cleavage in aromatic rings enables a useful diazomethylation reaction, which underpins sequencing control for the late-stage assembly-point functionalization of medically relevant agents. Our strategy provides an efficient route to libraries of potentially bioactive molecules through the installation of tailored chiral centres at carbon-hydrogen bonds, while complementing current translational late-stage functionalization processes. Furthermore, we exploit the dual radical and carbene character of the generated carbyne equivalent in the direct transformation of abundant chemical feedstocks into valuable chiral molecules.

  4. Equivalent conserved currents and generalized Noether's theorem

    International Nuclear Information System (INIS)

    Gordon, T.J.

    1984-01-01

    A generalized Noether theorem is presented, relating symmetries and equivalence classes of local) conservation laws in classical field theories; this is contrasted with the standard theorem. The concept of a ''Noether'' field theory is introduced, being a theory for which the generalized theorem applies; not only does this include the cases of Lagrangian and Hamiltonian field theories, these structures are ''derived'' from the Noether property in a natural way. The generalized theorem applies to currents and symmetries that contain derivatives of the fields up to an arbitrarily high order

  5. Gravitational leptogenesis, C, CP and strong equivalence

    International Nuclear Information System (INIS)

    McDonald, Jamie I.; Shore, Graham M.

    2015-01-01

    The origin of matter-antimatter asymmetry is one of the most important outstanding problems at the interface of particle physics and cosmology. Gravitational leptogenesis (baryogenesis) provides a possible mechanism through explicit couplings of spacetime curvature to appropriate lepton (or baryon) currents. In this paper, the idea that these strong equivalence principle violating interactions could be generated automatically through quantum loop effects in curved spacetime is explored, focusing on the realisation of the discrete symmetries C, CP and CPT which must be broken to induce matter-antimatter asymmetry. The related issue of quantum corrections to the dispersion relation for neutrino propagation in curved spacetime is considered within a fully covariant framework.

  6. European Equivalencies in Legal Interpreting and Translation

    DEFF Research Database (Denmark)

    Corsellis, Ann; Hertog, Erik; Martinsen, Bodil

    2002-01-01

    Within Europe there is increasing freedom of movement between countries and increasing inward migration. As a result, equivalent standards of legl interpreting and translation are required to allow reliable communication for judicial cooperation between member states, for criminal and civil matters...... which cross national borders and for the needs of multilingual populations. The European Convention of Human Rights (article 6, paragrph 3) is one of the main planks of relevant legislation. This international, two year project has been funded by the EU Grotius programme to set out what is required...

  7. Testing efficiency transfer codes for equivalence

    International Nuclear Information System (INIS)

    Vidmar, T.; Celik, N.; Cornejo Diaz, N.; Dlabac, A.; Ewa, I.O.B.; Carrazana Gonzalez, J.A.; Hult, M.; Jovanovic, S.; Lepy, M.-C.; Mihaljevic, N.; Sima, O.; Tzika, F.; Jurado Vargas, M.; Vasilopoulou, T.; Vidmar, G.

    2010-01-01

    Four general Monte Carlo codes (GEANT3, PENELOPE, MCNP and EGS4) and five dedicated packages for efficiency determination in gamma-ray spectrometry (ANGLE, DETEFF, GESPECOR, ETNA and EFFTRAN) were checked for equivalence by applying them to the calculation of efficiency transfer (ET) factors for a set of well-defined sample parameters, detector parameters and energies typically encountered in environmental radioactivity measurements. The differences between the results of the different codes never exceeded a few percent and were lower than 2% in the majority of cases.

  8. The equivalence principle in a quantum world

    DEFF Research Database (Denmark)

    Bjerrum-Bohr, N. Emil J.; Donoghue, John F.; El-Menoufi, Basem Kamal

    2015-01-01

    the energy is small, we now have the tools to address this conflict explicitly. Despite the violation of some classical concepts, the EP continues to provide the core of the quantum gravity framework through the symmetry - general coordinate invariance - that is used to organize the effective field theory......We show how modern methods can be applied to quantum gravity at low energy. We test how quantum corrections challenge the classical framework behind the equivalence principle (EP), for instance through introduction of nonlocality from quantum physics, embodied in the uncertainty principle. When...

  9. Equivalent Circuit Modeling of Hysteresis Motors

    Energy Technology Data Exchange (ETDEWEB)

    Nitao, J J; Scharlemann, E T; Kirkendall, B A

    2009-08-31

    We performed a literature review and found that many equivalent circuit models of hysteresis motors in use today are incorrect. The model by Miyairi and Kataoka (1965) is the correct one. We extended the model by transforming it to quadrature coordinates, amenable to circuit or digital simulation. 'Hunting' is an oscillatory phenomenon often observed in hysteresis motors. While several works have attempted to model the phenomenon with some partial success, we present a new complete model that predicts hunting from first principles.

  10. Money and bonds: an equivalence theorem

    OpenAIRE

    Narayana R. Kocherlakota

    2007-01-01

    This paper considers four models in which immortal agents face idiosyncratic shocks and trade only a single risk-free asset over time. The four models specify this single asset to be private bonds, public bonds, public money, or private money respectively. I prove that, given an equilibrium in one of these economies, it is possible to pick the exogenous elements in the other three economies so that there is an outcome-equivalent equilibrium in each of them. (The term ?exogenous variables? ref...

  11. Gravitational leptogenesis, C, CP and strong equivalence

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, Jamie I.; Shore, Graham M. [Department of Physics, Swansea University,Swansea, SA2 8PP (United Kingdom)

    2015-02-12

    The origin of matter-antimatter asymmetry is one of the most important outstanding problems at the interface of particle physics and cosmology. Gravitational leptogenesis (baryogenesis) provides a possible mechanism through explicit couplings of spacetime curvature to appropriate lepton (or baryon) currents. In this paper, the idea that these strong equivalence principle violating interactions could be generated automatically through quantum loop effects in curved spacetime is explored, focusing on the realisation of the discrete symmetries C, CP and CPT which must be broken to induce matter-antimatter asymmetry. The related issue of quantum corrections to the dispersion relation for neutrino propagation in curved spacetime is considered within a fully covariant framework.

  12. Isolation of BAC Clones Containing Conserved Genes from Libraries of Three Distantly Related Moths: A Useful Resource for Comparative Genomics of Lepidoptera

    Directory of Open Access Journals (Sweden)

    Yuji Yasukochi

    2011-01-01

    Full Text Available Lepidoptera, butterflies and moths, is the second largest animal order and includes numerous agricultural pests. To facilitate comparative genomics in Lepidoptera, we isolated BAC clones containing conserved and putative single-copy genes from libraries of three pests, Heliothis virescens, Ostrinia nubilalis, and Plutella xylostella, harboring the haploid chromosome number, =31, which are not closely related with each other or with the silkworm, Bombyx mori, (=28, the sequenced model lepidopteran. A total of 108–184 clones representing 101–182 conserved genes were isolated for each species. For 79 genes, clones were isolated from more than two species, which will be useful as common markers for analysis using fluorescence in situ hybridization (FISH, as well as for comparison of genome sequence among multiple species. The PCR-based clone isolation method presented here is applicable to species which lack a sequenced genome but have a significant collection of cDNA or EST sequences.

  13. Integrable topological billiards and equivalent dynamical systems

    Science.gov (United States)

    Vedyushkina, V. V.; Fomenko, A. T.

    2017-08-01

    We consider several topological integrable billiards and prove that they are Liouville equivalent to many systems of rigid body dynamics. The proof uses the Fomenko-Zieschang theory of invariants of integrable systems. We study billiards bounded by arcs of confocal quadrics and their generalizations, generalized billiards, where the motion occurs on a locally planar surface obtained by gluing several planar domains isometrically along their boundaries, which are arcs of confocal quadrics. We describe two new classes of integrable billiards bounded by arcs of confocal quadrics, namely, non-compact billiards and generalized billiards obtained by gluing planar billiards along non-convex parts of their boundaries. We completely classify non-compact billiards bounded by arcs of confocal quadrics and study their topology using the Fomenko invariants that describe the bifurcations of singular leaves of the additional integral. We study the topology of isoenergy surfaces for some non-convex generalized billiards. It turns out that they possess exotic Liouville foliations: the integral trajectories of the billiard that lie on some singular leaves admit no continuous extension. Such billiards appear to be leafwise equivalent to billiards bounded by arcs of confocal quadrics in the Minkowski metric.

  14. Twisted conformal field theories and Morita equivalence

    Energy Technology Data Exchange (ETDEWEB)

    Marotta, Vincenzo [Dipartimento di Scienze Fisiche, Universita di Napoli ' Federico II' and INFN, Sezione di Napoli, Compl. universitario M. Sant' Angelo, Via Cinthia, 80126 Napoli (Italy); Naddeo, Adele [CNISM, Unita di Ricerca di Salerno and Dipartimento di Fisica ' E.R. Caianiello' , Universita degli Studi di Salerno, Via Salvador Allende, 84081 Baronissi (Italy); Dipartimento di Scienze Fisiche, Universita di Napoli ' Federico II' , Compl. universitario M. Sant' Angelo, Via Cinthia, 80126 Napoli (Italy)], E-mail: adelenaddeo@yahoo.it

    2009-04-01

    The Morita equivalence for field theories on noncommutative two-tori is analysed in detail for rational values of the noncommutativity parameter {theta} (in appropriate units): an isomorphism is established between an Abelian noncommutative field theory (NCFT) and a non-Abelian theory of twisted fields on ordinary space. We focus on a particular conformal field theory (CFT), the one obtained by means of the m-reduction procedure [V. Marotta, J. Phys. A 26 (1993) 3481; V. Marotta, Mod. Phys. Lett. A 13 (1998) 853; V. Marotta, Nucl. Phys. B 527 (1998) 717; V. Marotta, A. Sciarrino, Mod. Phys. Lett. A 13 (1998) 2863], and show that it is the Morita equivalent of a NCFT. Finally, the whole m-reduction procedure is shown to be the image in the ordinary space of the Morita duality. An application to the physics of a quantum Hall fluid at Jain fillings {nu}=m/(2pm+1) is explicitly discussed in order to further elucidate such a correspondence and to clarify its role in the physics of strongly correlated systems. A new picture emerges, which is very different from the existing relationships between noncommutativity and many body systems [A.P. Polychronakos, arXiv: 0706.1095].

  15. Planck Constant Determination from Power Equivalence

    Science.gov (United States)

    Newell, David B.

    2000-04-01

    Equating mechanical to electrical power links the kilogram, the meter, and the second to the practical realizations of the ohm and the volt derived from the quantum Hall and the Josephson effects, yielding an SI determination of the Planck constant. The NIST watt balance uses this power equivalence principle, and in 1998 measured the Planck constant with a combined relative standard uncertainty of 8.7 x 10-8, the most accurate determination to date. The next generation of the NIST watt balance is now being assembled. Modification to the experimental facilities have been made to reduce the uncertainty components from vibrations and electromagnetic interference. A vacuum chamber has been installed to reduce the uncertainty components associated with performing the experiment in air. Most of the apparatus is in place and diagnostic testing of the balance should begin this year. Once a combined relative standard uncertainty of one part in 10-8 has been reached, the power equivalence principle can be used to monitor the possible drift in the artifact mass standard, the kilogram, and provide an accurate alternative definition of mass in terms of fundamental constants. *Electricity Division, Electronics and Electrical Engineering Laboratory, Technology Administration, U.S. Department of Commerce. Contribution of the National Institute of Standards and Technology, not subject to copyright in the U.S.

  16. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  17. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  18. Resource allocation for maximizing prediction accuracy and genetic gain of genomic selection in plant breeding: a simulation experiment.

    Science.gov (United States)

    Lorenz, Aaron J

    2013-03-01

    Allocating resources between population size and replication affects both genetic gain through phenotypic selection and quantitative trait loci detection power and effect estimation accuracy for marker-assisted selection (MAS). It is well known that because alleles are replicated across individuals in quantitative trait loci mapping and MAS, more resources should be allocated to increasing population size compared with phenotypic selection. Genomic selection is a form of MAS using all marker information simultaneously to predict individual genetic values for complex traits and has widely been found superior to MAS. No studies have explicitly investigated how resource allocation decisions affect success of genomic selection. My objective was to study the effect of resource allocation on response to MAS and genomic selection in a single biparental population of doubled haploid lines by using computer simulation. Simulation results were compared with previously derived formulas for the calculation of prediction accuracy under different levels of heritability and population size. Response of prediction accuracy to resource allocation strategies differed between genomic selection models (ridge regression best linear unbiased prediction [RR-BLUP], BayesCπ) and multiple linear regression using ordinary least-squares estimation (OLS), leading to different optimal resource allocation choices between OLS and RR-BLUP. For OLS, it was always advantageous to maximize population size at the expense of replication, but a high degree of flexibility was observed for RR-BLUP. Prediction accuracy of doubled haploid lines included in the training set was much greater than of those excluded from the training set, so there was little benefit to phenotyping only a subset of the lines genotyped. Finally, observed prediction accuracies in the simulation compared well to calculated prediction accuracies, indicating these theoretical formulas are useful for making resource allocation

  19. Genome Size Diversity in Lilium (Liliaceae Is Correlated with Karyotype and Environmental Traits

    Directory of Open Access Journals (Sweden)

    Yun-peng Du

    2017-07-01

    Full Text Available Genome size (GS diversity is of fundamental biological importance. The occurrence of giant genomes in angiosperms is restricted to just a few lineages in the analyzed genome size of plant species so far. It is still an open question whether GS diversity is shaped by neutral or natural selection. The genus Lilium, with giant genomes, is phylogenetically and horticulturally important and is distributed throughout the northern hemisphere. GS diversity in Lilium and the underlying evolutionary mechanisms are poorly understood. We performed a comprehensive study involving phylogenetically independent analysis on 71 species to explore the diversity and evolution of GS and its correlation with karyological and environmental traits within Lilium (including Nomocharis. The strong phylogenetic signal detected for GS in the genus provides evidence consistent with that the repetitive DNA may be the primary contributors to the GS diversity, while the significant positive relationships detected between GS and the haploid chromosome length (HCL provide insights into patterns of genome evolution. The relationships between GS and karyotypes indicate that ancestral karyotypes of Lilium are likely to have exhibited small genomes, low diversity in centromeric index (CVCI values and relatively high relative variation in chromosome length (CVCL values. Significant relationships identified between GS and annual temperature and between GS and annual precipitation suggest that adaptation to habitat strongly influences GS diversity. We conclude that GS in Lilium is shaped by both neutral (genetic drift and adaptive evolution. These findings will have important consequences for understanding the evolution of giant plant genomes, and exploring the role of repetitive DNA fraction and chromosome changes in a plant group with large genomes and conservation of chromosome number.

  20. Borel equivalence relations structure and classification

    CERN Document Server

    Kanovei, Vladimir

    2008-01-01

    Over the last 20 years, the theory of Borel equivalence relations and related topics have been very active areas of research in set theory and have important interactions with other fields of mathematics, like ergodic theory and topological dynamics, group theory, combinatorics, functional analysis, and model theory. The book presents, for the first time in mathematical literature, all major aspects of this theory and its applications. This book should be of interest to a wide spectrum of mathematicians working in set theory as well as the other areas mentioned. It provides a systematic exposition of results that so far have been only available in journals or are even unpublished. The book presents unified and in some cases significantly streamlined proofs of several difficult results, especially dichotomy theorems. It has rather minimal overlap with other books published in this subject.

  1. Characterization of Destrins with Different Dextrose Equivalents

    Directory of Open Access Journals (Sweden)

    Guanglei Li

    2010-07-01

    Full Text Available Dextrins are widely used for their functional properties and prepared by partial hydrolysis of starch using acid, enzymes, or combinations of both. The physiochemical properties of dextrins are dependent on their molecular distribution and oligosaccharide profiles. In this study, scanning electron microscopy (SEM, X-ray diffractometry (XRD, rapid viscoanalysis (RVA, high-performance Liquid Chromatography (HPLC and gel permeation chromatography (GPC were used to characterize dextrins prepared by common neutral and thermostable α-amylase hydrolysis. The dextrin granules displayed irregular surfaces and were badly damaged by the enzyme treatment. They displayed A-type X-ray diffraction patterns with a decrease of intensity of the characteristic diffraction peaks. The RVA profiles showed that the viscosity of dextrin decreased with the increase of its Dextrose Equivalent (DE value. According to HPLC analysis, the molecular weight, degree of polymerization and the composition of oligosaccharides in dextrins were different.

  2. Multiplicities of states od equivalent fermion shells

    International Nuclear Information System (INIS)

    Savukinas, A.Yu.; Glembotskij, I.I.

    1980-01-01

    Classification of states of three or four equivalent fermions has been studied, i.e. possible terms and their multiplicities have been determined. For this purpose either the group theory or evident expressions for the fractional-parentage coefficients have been used. In the first approach the formulas obtained by other authors for the multiplicities of terms through the characters of the transformation matrices of bond moments have been used. This approach happens to be more general as compared with the second one, as expressions for the fractional-parentage coefficients in many cases are not known. The multiplicities of separate terms have been determined. It has been shown that the number of terms of any multiplicity becomes constant when l or j is increased [ru

  3. Sample size allocation in multiregional equivalence studies.

    Science.gov (United States)

    Liao, Jason J Z; Yu, Ziji; Li, Yulan

    2018-06-17

    With the increasing globalization of drug development, the multiregional clinical trial (MRCT) has gained extensive use. The data from MRCTs could be accepted by regulatory authorities across regions and countries as the primary sources of evidence to support global marketing drug approval simultaneously. The MRCT can speed up patient enrollment and drug approval, and it makes the effective therapies available to patients all over the world simultaneously. However, there are many challenges both operationally and scientifically in conducting a drug development globally. One of many important questions to answer for the design of a multiregional study is how to partition sample size into each individual region. In this paper, two systematic approaches are proposed for the sample size allocation in a multiregional equivalence trial. A numerical evaluation and a biosimilar trial are used to illustrate the characteristics of the proposed approaches. Copyright © 2018 John Wiley & Sons, Ltd.

  4. Equivalence principle and the baryon acoustic peak

    Science.gov (United States)

    Baldauf, Tobias; Mirbabayi, Mehrdad; Simonović, Marko; Zaldarriaga, Matias

    2015-08-01

    We study the dominant effect of a long wavelength density perturbation δ (λL) on short distance physics. In the nonrelativistic limit, the result is a uniform acceleration, fixed by the equivalence principle, and typically has no effect on statistical averages due to translational invariance. This same reasoning has been formalized to obtain a "consistency condition" on the cosmological correlation functions. In the presence of a feature, such as the acoustic peak at ℓBAO, this naive expectation breaks down for λLexplicitly applied to the one-loop calculation of the power spectrum. Finally, the success of baryon acoustic oscillation reconstruction schemes is argued to be another empirical evidence for the validity of the results.

  5. Development of air equivalent gamma dose monitor

    International Nuclear Information System (INIS)

    Alex, Mary; Bhattacharya, Sadhana; Karpagam, R.; Prasad, D.N.; Jakati, R.K.; Mukhopadhyay, P.K.; Patil, R.K.

    2010-01-01

    The paper describes design and development of air equivalent gamma absorbed dose monitor. The monitor has gamma sensitivity of 84 pA/R/h for 60 Co source. The characterization of the monitor has been done to get energy dependence on gamma sensitivity and response to gamma radiation field from 1 R/hr to 5000 R/hr. The gamma sensitivity in the energy range of 0.06 to 1.25MeV relative to 137 Cs nuclide was within 2.5%. The linearity of the monitor response as a function of gamma field from 10 R/h to 3.8 kR/h was within 6%. The monitor has been designed for its application in harsh environment. It has been successfully qualified to meet environmental requirements of shock. (author)

  6. A new concept of equivalent homogenization method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Jin; Pogoskekyan, Leonid; Kim, Young Il; Ju, Hyung Kook; Chang, Moon Hee [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-07-01

    A new concept of equivalent homogenization is proposed. The concept employs new set of homogenized parameters: homogenized cross sections (XS) and interface matrix (IM), which relates partial currents at the cell interfaces. The idea of interface matrix generalizes the idea of discontinuity factors (DFs), proposed and developed by K. Koebke and K. Smith. The offered concept covers both those of K. Koebke and K. Smith; both of them can be simulated within framework of new concept. Also, the offered concept covers Siemens KWU approach for baffle/reflector simulation, where the equivalent homogenized reflector XS are derived from the conservation of response matrix at the interface in 1D simi-infinite slab geometry. The IM and XS of new concept satisfy the same assumption about response matrix conservation in 1D semi-infinite slab geometry. It is expected that the new concept provides more accurate approximation of heterogeneous cell, especially in case of the steep flux gradients at the cell interfaces. The attractive shapes of new concept are: improved accuracy, simplicity of incorporation in the existing codes, equal numerical expenses in comparison to the K. Smith`s approach. The new concept is useful for: (a) explicit reflector/baffle simulation; (b) control blades simulation; (c) mixed UO{sub 2}/MOX core simulation. The offered model has been incorporated in the finite difference code and in the nodal code PANDOX. The numerical results show good accuracy of core calculations and insensitivity of homogenized parameters with respect to in-core conditions. 9 figs., 7 refs. (Author).

  7. Equivalence principle implications of modified gravity models

    International Nuclear Information System (INIS)

    Hui, Lam; Nicolis, Alberto; Stubbs, Christopher W.

    2009-01-01

    Theories that attempt to explain the observed cosmic acceleration by modifying general relativity all introduce a new scalar degree of freedom that is active on large scales, but is screened on small scales to match experiments. We demonstrate that if such screening occurs via the chameleon mechanism, such as in f(R) theory, it is possible to have order unity violation of the equivalence principle, despite the absence of explicit violation in the microscopic action. Namely, extended objects such as galaxies or constituents thereof do not all fall at the same rate. The chameleon mechanism can screen the scalar charge for large objects but not for small ones (large/small is defined by the depth of the gravitational potential and is controlled by the scalar coupling). This leads to order one fluctuations in the ratio of the inertial mass to gravitational mass. We provide derivations in both Einstein and Jordan frames. In Jordan frame, it is no longer true that all objects move on geodesics; only unscreened ones, such as test particles, do. In contrast, if the scalar screening occurs via strong coupling, such as in the Dvali-Gabadadze-Porrati braneworld model, equivalence principle violation occurs at a much reduced level. We propose several observational tests of the chameleon mechanism: 1. small galaxies should accelerate faster than large galaxies, even in environments where dynamical friction is negligible; 2. voids defined by small galaxies would appear larger compared to standard expectations; 3. stars and diffuse gas in small galaxies should have different velocities, even if they are on the same orbits; 4. lensing and dynamical mass estimates should agree for large galaxies but disagree for small ones. We discuss possible pitfalls in some of these tests. The cleanest is the third one where the mass estimate from HI rotational velocity could exceed that from stars by 30% or more. To avoid blanket screening of all objects, the most promising place to look is in

  8. Functional equivalency inferred from "authoritative sources" in networks of homologous proteins.

    Science.gov (United States)

    Natarajan, Shreedhar; Jakobsson, Eric

    2009-06-12

    A one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key feature of our algorithm is utilization of the user's knowledge to assign high confidence to selected functional identification. We show use of the algorithm to retrieve functional equivalents for 7 membrane proteins, from an exploration of almost 40 genomes form multiple online resources. We verify the functional equivalency of our dataset through a series of tests that include sequence, structure and function comparisons. Comparison is made to the OMA methodology, which also identifies one-on-one mapping between proteins from different species. Based on that comparison, we believe that incorporation of user's knowledge as a key aspect of the technique adds value to purely statistical formal methods.

  9. 49 CFR 391.33 - Equivalent of road test.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 5 2010-10-01 2010-10-01 false Equivalent of road test. 391.33 Section 391.33... AND LONGER COMBINATION VEHICLE (LCV) DRIVER INSTRUCTORS Tests § 391.33 Equivalent of road test. (a) In place of, and as equivalent to, the road test required by § 391.31, a person who seeks to drive a...

  10. A bicategorical approach to Morita equivalence for Von Neumann algebras

    NARCIS (Netherlands)

    R.M. Brouwer (Rachel)

    2003-01-01

    textabstractWe relate Morita equivalence for von Neumann algebras to the ``Connes fusion'' tensor product between correspondences. In the purely algebraic setting, it is well known that rings are Morita equivalent if and only if they are equivalent objects in a bicategory whose 1-cells are

  11. Problems of Equivalence in Shona- English Bilingual Dictionaries

    African Journals Online (AJOL)

    rbr

    Page 1 ... translation equivalents in Shona-English dictionaries where lexicographers will be dealing with divergent languages and cultures, traditional practices of lexicography and the absence of reliable ... ideal in translation is to achieve structural and semantic equivalence. Absolute equivalence between any two ...

  12. The equivalence principle in classical mechanics and quantum mechanics

    OpenAIRE

    Mannheim, Philip D.

    1998-01-01

    We discuss our understanding of the equivalence principle in both classical mechanics and quantum mechanics. We show that not only does the equivalence principle hold for the trajectories of quantum particles in a background gravitational field, but also that it is only because of this that the equivalence principle is even to be expected to hold for classical particles at all.

  13. Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey.

    Science.gov (United States)

    Luo, Meizhong; Kim, Hyeran; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A; Ohta, Yuko

    2006-05-03

    Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

  14. Construction of a nurse shark (Ginglymostoma cirratum bacterial artificial chromosome (BAC library and a preliminary genome survey

    Directory of Open Access Journals (Sweden)

    Inoko Hidetoshi

    2006-05-01

    Full Text Available Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC library for the nurse shark, Ginglymostoma cirratum. Results The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. Conclusion We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

  15. Contrasting behavior of heterochromatic and euchromatic chromosome portions and pericentric genome separation in pre-bouquet spermatocytes of hybrid mice.

    Science.gov (United States)

    Scherthan, Harry; Schöfisch, Karina; Dell, Thomas; Illner, Doris

    2014-12-01

    The spatial distribution of parental genomes has attracted much interest because intranuclear chromosome distribution can modulate the transcriptome of cells and influence the efficacy of meiotic homologue pairing. Pairing of parental chromosomes is imperative to sexual reproduction as it translates into homologue segregation and genome haploidization to counteract the genome doubling at fertilization. Differential FISH tagging of parental pericentromeric genome portions and specific painting of euchromatic chromosome arms in Mus musculus (MMU) × Mus spretus (MSP) hybrid spermatogenesis disclosed a phase of homotypic non-homologous pericentromere clustering that led to parental pericentric genome separation from the pre-leptoteneup to zygotene stages. Preferential clustering of MMU pericentromeres correlated with particular enrichment of epigenetic marks (H3K9me3), HP1-γ and structural maintenance of chromosomes SMC6 complex proteins at the MMU major satellite DNA repeats. In contrast to the separation of heterochromatic pericentric genome portions, the euchromatic arms of homeologous chromosomes showed considerable presynaptic pairing already during leptotene stage of all mice investigated. Pericentric genome separation was eventually disbanded by telomere clustering that concentrated both parental pericentric genome portions in a limited nuclear sector of the bouquet nucleus. Our data disclose the differential behavior of pericentromeric heterochromatin and the euchromatic portions of the parental genomes during homologue search. Homotypic pericentromere clustering early in prophase I may contribute to the exclusion of large repetitive DNA domains from homology search, while the telomere bouquet congregates and registers spatially separated portions of the genome to fuel synapsis initiation and high levels of homologue pairing, thus contributing to the fidelity of meiosis and reproduction.

  16. Meraculous: De Novo Genome Assembly with Short Paired-End Reads

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha; Luo, Shujun; Schroth, Gary P.; Rokhsar, Daniel S.; Salzberg, Steven L.

    2011-08-18

    We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ~280 bp or ~3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.

  17. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

    Science.gov (United States)

    D'Hont, Angélique; Denoeud, France; Aury, Jean-Marc; Baurens, Franc-Christophe; Carreel, Françoise; Garsmeur, Olivier; Noel, Benjamin; Bocs, Stéphanie; Droc, Gaëtan; Rouard, Mathieu; Da Silva, Corinne; Jabbari, Kamel; Cardi, Céline; Poulain, Julie; Souquet, Marlène; Labadie, Karine; Jourda, Cyril; Lengellé, Juliette; Rodier-Goud, Marguerite; Alberti, Adriana; Bernard, Maria; Correa, Margot; Ayyampalayam, Saravanaraj; Mckain, Michael R; Leebens-Mack, Jim; Burgess, Diane; Freeling, Mike; Mbéguié-A-Mbéguié, Didier; Chabannes, Matthieu; Wicker, Thomas; Panaud, Olivier; Barbosa, Jose; Hribova, Eva; Heslop-Harrison, Pat; Habas, Rémy; Rivallan, Ronan; Francois, Philippe; Poiron, Claire; Kilian, Andrzej; Burthia, Dheema; Jenny, Christophe; Bakry, Frédéric; Brown, Spencer; Guignon, Valentin; Kema, Gert; Dita, Miguel; Waalwijk, Cees; Joseph, Steeve; Dievart, Anne; Jaillon, Olivier; Leclercq, Julie; Argout, Xavier; Lyons, Eric; Almeida, Ana; Jeridi, Mouna; Dolezel, Jaroslav; Roux, Nicolas; Risterucci, Ange-Marie; Weissenbach, Jean; Ruiz, Manuel; Glaszmann, Jean-Christophe; Quétier, Francis; Yahiaoui, Nabila; Wincker, Patrick

    2012-08-09

    Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.

  18. Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

    Science.gov (United States)

    Neuer-Nitsche, B; Lu, X N; Werner, D

    1988-09-12

    The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

  19. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  1. The one-dimensional normalised generalised equivalence theory (NGET) for generating equivalent diffusion theory group constants for PWR reflector regions

    International Nuclear Information System (INIS)

    Mueller, E.Z.

    1991-01-01

    An equivalent diffusion theory PWR reflector model is presented, which has as its basis Smith's generalisation of Koebke's Equivalent Theory. This method is an adaptation, in one-dimensional slab geometry, of the Generalised Equivalence Theory (GET). Since the method involves the renormalisation of the GET discontinuity factors at nodal interfaces, it is called the Normalised Generalised Equivalence Theory (NGET) method. The advantages of the NGET method for modelling the ex-core nodes of a PWR are summarized. 23 refs

  2. Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

    KAUST Repository

    Lightfoot, D. J.; Jarvis, David Erwin; Ramaraj, T.; Lee, R.; Jellen, E. N.; Maughan, P. J.

    2017-01-01

    Background: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species.Results: Utilizing single-molecule, real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C) to close assembly gaps and scaffold contigs, respectively, we improved our previously reported Illumina-based assembly to produce a chromosome-scale assembly with a scaffold N50 of 24.4 Mb. The 16 largest scaffolds contain 98% of the assembly and likely represent the haploid chromosomes (n = 16). To demonstrate the accuracy and utility of this approach, we produced physical and genetic maps and identified candidate genes for the betalain pigmentation pathway. The chromosome-scale assembly facilitated a genome-wide syntenic comparison of amaranth with other Amaranthaceae species, revealing chromosome loss and fusion events in amaranth that explain the reduction from the ancestral haploid chromosome number (n = 18) for a tetraploid member of the Amaranthaceae. as major evolutionary events in the 2n = 32 amaranths and clearly establish the homoeologous relationship among most of the subgenome chromosomes, which will facilitate future investigations of intragenomic changes that occurred post polyploidization.

  3. A bicategorical approach to Morita equivalence for von Neumann algebras

    International Nuclear Information System (INIS)

    Brouwer, R. M.

    2003-01-01

    We relate Morita equivalence for von Neumann algebras to the ''Connes fusion'' tensor product between correspondences. In the purely algebraic setting, it is well known that rings are Morita equivalent if they are equivalent objects in a bicategory whose 1-cells are bimodules. We present a similar result for von Neumann algebras. We show that von Neumann algebras form a bicategory, having Connes's correspondences as 1-morphisms, and (bounded) intertwiners as 2-morphisms. Further, we prove that two von Neumann algebras are Morita equivalent iff they are equivalent objects in the bicategory. The proofs make extensive use of the Tomita-Takesaki modular theory

  4. Theoretical aspects of the equivalence principle

    International Nuclear Information System (INIS)

    Damour, Thibault

    2012-01-01

    We review several theoretical aspects of the equivalence principle (EP). We emphasize the unsatisfactory fact that the EP maintains the absolute character of the coupling constants of physics, while general relativity and its generalizations (Kaluza–Klein, …, string theory) suggest that all absolute structures should be replaced by dynamical entities. We discuss the EP-violation phenomenology of dilaton-like models, which is likely to be dominated by the linear superposition of two effects: a signal proportional to the nuclear Coulomb energy, related to the variation of the fine-structure constant, and a signal proportional to the surface nuclear binding energy, related to the variation of the light quark masses. We recall various theoretical arguments (including a recently proposed anthropic argument) suggesting that the EP be violated at a small, but not unmeasurably small level. This motivates the need for improved tests of the EP. These tests are probing new territories in physics that are related to deep, and mysterious, issues in fundamental physics. (paper)

  5. Biomonitoring Equivalents for interpretation of urinary fluoride.

    Science.gov (United States)

    Aylward, L L; Hays, S M; Vezina, A; Deveau, M; St-Amand, A; Nong, A

    2015-06-01

    Exposure to fluoride is widespread due to its natural occurrence in the environment and addition to drinking water and dental products for the prevention of dental caries. The potential health risks of excess fluoride exposure include aesthetically unacceptable dental fluorosis (tooth mottling) and increased skeletal fragility. Numerous organizations have conducted risk assessments and set guidance values to represent maximum recommended exposure levels as well as recommended adequate intake levels based on potential public health benefits of fluoride exposure. Biomonitoring Equivalents (BEs) are estimates of the average biomarker concentrations corresponding to such exposure guidance values. The literature on daily urinary fluoride excretion rates as a function of daily fluoride exposure was reviewed and BE values corresponding to the available US and Canadian exposure guidance values were derived for fluoride in urine. The derived BE values range from 1.1 to 2.1mg/L (1.2-2.5μg/g creatinine). Concentrations of fluoride in single urinary spot samples from individuals, even under exposure conditions consistent with the exposure guidance values, may vary from the predicted average concentrations by several-fold due to within- and across-individual variation in urinary flow and creatinine excretion rates and due to the rapid elimination kinetics of fluoride. Thus, the BE values are most appropriately applied to screen population central tendency estimates for biomarker concentrations rather than interpretation of individual spot sample concentrations. Copyright © 2015. Published by Elsevier Inc.

  6. VERSE - Virtual Equivalent Real-time Simulation

    Science.gov (United States)

    Zheng, Yang; Martin, Bryan J.; Villaume, Nathaniel

    2005-01-01

    Distributed real-time simulations provide important timing validation and hardware in the- loop results for the spacecraft flight software development cycle. Occasionally, the need for higher fidelity modeling and more comprehensive debugging capabilities - combined with a limited amount of computational resources - calls for a non real-time simulation environment that mimics the real-time environment. By creating a non real-time environment that accommodates simulations and flight software designed for a multi-CPU real-time system, we can save development time, cut mission costs, and reduce the likelihood of errors. This paper presents such a solution: Virtual Equivalent Real-time Simulation Environment (VERSE). VERSE turns the real-time operating system RTAI (Real-time Application Interface) into an event driven simulator that runs in virtual real time. Designed to keep the original RTAI architecture as intact as possible, and therefore inheriting RTAI's many capabilities, VERSE was implemented with remarkably little change to the RTAI source code. This small footprint together with use of the same API allows users to easily run the same application in both real-time and virtual time environments. VERSE has been used to build a workstation testbed for NASA's Space Interferometry Mission (SIM PlanetQuest) instrument flight software. With its flexible simulation controls and inexpensive setup and replication costs, VERSE will become an invaluable tool in future mission development.

  7. Challenging a culture of racial equivalence.

    Science.gov (United States)

    Song, Miri

    2014-03-01

    We live at a time when our understandings and conceptualizations of 'racism' are often highly imprecise, broad, and used to describe a wide range of racialized phenomena. In this article, I raise some important questions about how the term racism is used and understood in contemporary British society by drawing on some recent cases of alleged racism in football and politics, many of which have been played out via new media technologies. A broader understanding of racism, through the use of the term 'racialization', has been helpful in articulating a more nuanced and complex understanding of racial incidents, especially of people's (often ambivalent) beliefs and behaviours. However, the growing emphasis upon 'racialization' has led to a conceptualization of racism which increasingly involves multiple perpetrators, victims, and practices without enough consideration of how and why particular interactions and practices constitute racism as such. The trend toward a growing culture of racial equivalence is worrying, as it denudes the idea of racism of its historical basis, severity and power. These frequent and commonplace assertions of racism in the public sphere paradoxically end up trivializing and homogenizing quite different forms of racialized interactions. I conclude that we need to retain the term 'racism', but we need to differentiate more clearly between 'racism' (as an historical and structured system of domination) from the broader notion of 'racialization'. © London School of Economics and Political Science 2014.

  8. Testing the equivalence principle on a trampoline

    Science.gov (United States)

    Reasenberg, Robert D.; Phillips, James D.

    2001-07-01

    We are developing a Galilean test of the equivalence principle in which two pairs of test mass assemblies (TMA) are in free fall in a comoving vacuum chamber for about 0.9 s. The TMA are tossed upward, and the process repeats at 1.2 s intervals. Each TMA carries a solid quartz retroreflector and a payload mass of about one-third of the total TMA mass. The relative vertical motion of the TMA of each pair is monitored by a laser gauge working in an optical cavity formed by the retroreflectors. Single-toss precision of the relative acceleration of a single pair of TMA is 3.5×10-12 g. The project goal of Δg/g = 10-13 can be reached in a single night's run, but repetition with altered configurations will be required to ensure the correction of systematic error to the nominal accuracy level. Because the measurements can be made quickly, we plan to study several pairs of materials.

  9. Testing the equivalence principle on cosmological scales

    Science.gov (United States)

    Bonvin, Camille; Fleury, Pierre

    2018-05-01

    The equivalence principle, that is one of the main pillars of general relativity, is very well tested in the Solar system; however, its validity is more uncertain on cosmological scales, or when dark matter is concerned. This article shows that relativistic effects in the large-scale structure can be used to directly test whether dark matter satisfies Euler's equation, i.e. whether its free fall is characterised by geodesic motion, just like baryons and light. After having proposed a general parametrisation for deviations from Euler's equation, we perform Fisher-matrix forecasts for future surveys like DESI and the SKA, and show that such deviations can be constrained with a precision of order 10%. Deviations from Euler's equation cannot be tested directly with standard methods like redshift-space distortions and gravitational lensing, since these observables are not sensitive to the time component of the metric. Our analysis shows therefore that relativistic effects bring new and complementary constraints to alternative theories of gravity.

  10. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.

    Directory of Open Access Journals (Sweden)

    John E Pool

    Full Text Available Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia, while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST were found to be enriched in genomic regions of locally

  11. Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

    Science.gov (United States)

    Pool, John E.; Corbett-Detig, Russell B.; Sugino, Ryuichi P.; Stevens, Kristian A.; Cardeno, Charis M.; Crepeau, Marc W.; Duchen, Pablo; Emerson, J. J.; Saelao, Perot; Begun, David J.; Langley, Charles H.

    2012-01-01

    Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan

  12. Efficient privacy-preserving string search and an application in genomics.

    Science.gov (United States)

    Shimizu, Kana; Nuida, Koji; Rätsch, Gunnar

    2016-06-01

    Personal genomes carry inherent privacy risks and protecting privacy poses major social and technological challenges. We consider the case where a user searches for genetic information (e.g. an allele) on a server that stores a large genomic database and aims to receive allele-associated information. The user would like to keep the query and result private and the server the database. We propose a novel approach that combines efficient string data structures such as the Burrows-Wheeler transform with cryptographic techniques based on additive homomorphic encryption. We assume that the sequence data is searchable in efficient iterative query operations over a large indexed dictionary, for instance, from large genome collections and employing the (positional) Burrows-Wheeler transform. We use a technique called oblivious transfer that is based on additive homomorphic encryption to conceal the sequence query and the genomic region of interest in positional queries. We designed and implemented an efficient algorithm for searching sequences of SNPs in large genome databases. During search, the user can only identify the longest match while the server does not learn which sequence of SNPs the user queried. In an experiment based on 2184 aligned haploid genomes from the 1000 Genomes Project, our algorithm was able to perform typical queries within [Formula: see text] 4.6 s and [Formula: see text] 10.8 s for client and server side, respectively, on laptop computers. The presented algorithm is at least one order of magnitude faster than an exhaustive baseline algorithm. https://github.com/iskana/PBWT-sec and https://github.com/ratschlab/PBWT-sec shimizu-kana@aist.go.jp or Gunnar.Ratsch@ratschlab.org Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  13. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  14. A Bayesian equivalency test for two independent binomial proportions.

    Science.gov (United States)

    Kawasaki, Yohei; Shimokawa, Asanao; Yamada, Hiroshi; Miyaoka, Etsuo

    2016-01-01

    In clinical trials, it is often necessary to perform an equivalence study. The equivalence study requires actively denoting equivalence between two different drugs or treatments. Since it is not possible to assert equivalence that is not rejected by a superiority test, statistical methods known as equivalency tests have been suggested. These methods for equivalency tests are based on the frequency framework; however, there are few such methods in the Bayesian framework. Hence, this article proposes a new index that suggests the equivalency of binomial proportions, which is constructed based on the Bayesian framework. In this study, we provide two methods for calculating the index and compare the probabilities that have been calculated by these two calculation methods. Moreover, we apply this index to the results of actual clinical trials to demonstrate the utility of the index.

  15. Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae.

    Science.gov (United States)

    Oud, Bart; Guadalupe-Medina, Victor; Nijkamp, Jurgen F; de Ridder, Dick; Pronk, Jack T; van Maris, Antonius J A; Daran, Jean-Marc

    2013-11-05

    Laboratory evolution of the yeast Saccharomyces cerevisiae in bioreactor batch cultures yielded variants that grow as multicellular, fast-sedimenting clusters. Knowledge of the molecular basis of this phenomenon may contribute to the understanding of natural evolution of multicellularity and to manipulating cell sedimentation in laboratory and industrial applications of S. cerevisiae. Multicellular, fast-sedimenting lineages obtained from a haploid S. cerevisiae strain in two independent evolution experiments were analyzed by whole genome resequencing. The two evolved cell lines showed different frameshift mutations in a stretch of eight adenosines in ACE2, which encodes a transcriptional regulator involved in cell cycle control and mother-daughter cell separation. Introduction of the two ace2 mutant alleles into the haploid parental strain led to slow-sedimenting cell clusters that consisted of just a few cells, thus representing only a partial reconstruction of the evolved phenotype. In addition to single-nucleotide mutations, a whole-genome duplication event had occurred in both evolved multicellular strains. Construction of a diploid reference strain with two mutant ace2 alleles led to complete reconstruction of the multicellular-fast sedimenting phenotype. This study shows that whole-genome duplication and a frameshift mutation in ACE2 are sufficient to generate a fast-sedimenting, multicellular phenotype in S. cerevisiae. The nature of the ace2 mutations and their occurrence in two independent evolution experiments encompassing fewer than 500 generations of selective growth suggest that switching between unicellular and multicellular phenotypes may be relevant for competitiveness of S. cerevisiae in natural environments.

  16. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  17. The draft genome and transcriptome of Cannabis sativa.

    Science.gov (United States)

    van Bakel, Harm; Stout, Jake M; Cote, Atina G; Tallon, Carling M; Sharpe, Andrew G; Hughes, Timothy R; Page, Jonathan E

    2011-10-20

    Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored. We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp. The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.

  18. Radiation equivalency: For the radiation recall phenomenon

    International Nuclear Information System (INIS)

    Stevens, R.H.; Cole, D.A.

    1983-01-01

    Experimental and clinico-epidemiological investigations have unequivocally established the risk of an offspring in later years developing cancer after experiencing an in utero carcinogenic insult. The present studies have focused upon identifying whether the biological effects of iodine-131 and the colon carcinogen 1,2-dimethylhydrazine (DMH) when administered during pregnancy in the Fischer F344 inbred rat are remembered in the offsprings at a later age. The investigations have been based upon the premise that after exposure to a carcinogen ''foreign-like'' tumor cells develop which result in the host mounting active antitumor immune responses. The authors have now measured at 2 to 3 months post-exposure, the antitumor cell-mediated immunity (CMI) induced by intraperitoneal administration of the radionuclide or chemical at 16-18 days of gestation. Their findings indicate a positive sex relationship existing in those offsprings exposed to the radioiodine with the female being much less sensitive. In contrast, no such difference was observed between responsiveness of the males and females born from dams exposed to the DMH. Significantly, the dams exposed to either the radionuclide or DMH expressed no measurable CMI suggesting that either the fetus acted as a carcinogen trap or else the state of pregnancy altered the mother's immune system in such a fashion to no longer respond to the insult. A Radiation Equivalency value has now been determined for the transplacental DMH exposures with the calculations suggesting the fetus is significantly more sensitive (over 10 times) than the adult animals. The results of this study now demonstrate that carcinogenic memory remains for exposures to both the iodine-131 and DMH in the first offspring generation and suggest that the effects may be recalled at a later age with the expected overt results being the development of cancer

  19. Biomonitoring Equivalents for bisphenol A (BPA).

    Science.gov (United States)

    Krishnan, Kannan; Gagné, Michelle; Nong, Andy; Aylward, Lesa L; Hays, Sean M

    2010-10-01

    Recent efforts worldwide have resulted in a growing database of measured concentrations of chemicals in blood and urine samples taken from the general population. However, few tools exist to assist in the interpretation of the measured values in a health risk context. Biomonitoring Equivalents (BEs) are defined as the concentration or range of concentrations of a chemical or its metabolite in a biological medium (blood, urine, or other medium) that is consistent with an existing health-based exposure guideline. BE values are derived by integrating available data on pharmacokinetics with existing chemical risk assessments. This study reviews available health-based exposure guidance values for bisphenol A (BPA) from Health Canada, the United States Environmental Protection Agency (USEPA) and the European Food Safety Authority (EFSA). BE values were derived based on data on BPA urinary excretion in humans. The BE value corresponding to the oral provisional tolerable daily intake (pTDI) of 25 microg/kg-d from Health Canada is 1mg/L (1.3mg/g creatinine); value corresponding to the US EPA reference dose (RfD) and EFSA tolerable daily intake (TDI) estimates (both of which are equal to 50 microg/kg-d) is 2mg/L (2.6 mg/g creatinine). These values are estimates of the 24-h average urinary BPA concentrations that are consistent with steady-state exposure at the respective exposure guidance values. These BE values may be used as screening tools for evaluation of central tendency measures of population biomonitoring data for BPA in a risk assessment context and can assist in prioritization of the potential need for additional risk assessment efforts for BPA relative to other chemicals. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  20. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

    Science.gov (United States)

    Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

    2012-05-01

    Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

  1. General Dynamic Equivalent Modeling of Microgrid Based on Physical Background

    Directory of Open Access Journals (Sweden)

    Changchun Cai

    2015-11-01

    Full Text Available Microgrid is a new power system concept consisting of small-scale distributed energy resources; storage devices and loads. It is necessary to employ a simplified model of microgrid in the simulation of a distribution network integrating large-scale microgrids. Based on the detailed model of the components, an equivalent model of microgrid is proposed in this paper. The equivalent model comprises two parts: namely, equivalent machine component and equivalent static component. Equivalent machine component describes the dynamics of synchronous generator, asynchronous wind turbine and induction motor, equivalent static component describes the dynamics of photovoltaic, storage and static load. The trajectory sensitivities of the equivalent model parameters with respect to the output variables are analyzed. The key parameters that play important roles in the dynamics of the output variables of the equivalent model are identified and included in further parameter estimation. Particle Swarm Optimization (PSO is improved for the parameter estimation of the equivalent model. Simulations are performed in different microgrid operation conditions to evaluate the effectiveness of the equivalent model of microgrid.

  2. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  3. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  4. Dose sculpting with generalized equivalent uniform dose

    International Nuclear Information System (INIS)

    Wu Qiuwen; Djajaputra, David; Liu, Helen H.; Dong Lei; Mohan, Radhe; Wu, Yan

    2005-01-01

    With intensity-modulated radiotherapy (IMRT), a variety of user-defined dose distribution can be produced using inverse planning. The generalized equivalent uniform dose (gEUD) has been used in IMRT optimization as an alternative objective function to the conventional dose-volume-based criteria. The purpose of this study was to investigate the effectiveness of gEUD optimization to fine tune the dose distributions of IMRT plans. We analyzed the effect of gEUD-based optimization parameters on plan quality. The objective was to determine whether dose distribution to selected structures could be improved using gEUD optimization without adversely altering the doses delivered to other structures, as in sculpting. We hypothesized that by carefully defining gEUD parameters (EUD 0 and n) based on the current dose distributions, the optimization system could be instructed to search for alternative solutions in the neighborhood, and we could maintain the dose distributions for structures already satisfactory and improve dose for structures that need enhancement. We started with an already acceptable IMRT plan optimized with any objective function. The dose distribution was analyzed first. For structures that dose should not be changed, a higher value of n was used and EUD 0 was set slightly higher/lower than the EUD value at the current dose distribution for critical structures/targets. For structures that needed improvement in dose, a higher to medium value of n was used, and EUD 0 was set to the EUD value or slightly lower/higher for the critical structure/target at the current dose distribution. We evaluated this method in one clinical case each of head and neck, lung and prostate cancer. Dose volume histograms, isodose distributions, and relevant tolerance doses for critical structures were used for the assessment. We found that by adjusting gEUD optimization parameters, the dose distribution could be improved with only a few iterations. A larger value of n could lead to

  5. GFVO: the Genomic Feature and Variation Ontology

    KAUST Repository

    Baran, Joachim

    2015-05-05

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  6. Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus

    OpenAIRE

    Spence, Robert J.; Noune, Christopher; Hauxwell, Caroline

    2016-01-01

    Granuloviruses are widespread pathogens of Plutella xylostella L. (diamondback moth) and potential biopesticides for control of this global insect pest. We report the complete genomes of four Plutella xylostella granulovirus isolates from China, Malaysia, and Taiwan exhibiting pairs of noncoding, homologous repeat regions with significant sequence variation but equivalent length.

  7. Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus.

    Science.gov (United States)

    Spence, Robert J; Noune, Christopher; Hauxwell, Caroline

    2016-06-30

    Granuloviruses are widespread pathogens of Plutella xylostella L. (diamondback moth) and potential biopesticides for control of this global insect pest. We report the complete genomes of four Plutella xylostella granulovirus isolates from China, Malaysia, and Taiwan exhibiting pairs of noncoding, homologous repeat regions with significant sequence variation but equivalent length. Copyright © 2016 Spence et al.

  8. The radiobiology of boron neutron capture therapy: Are ''photon-equivalent'' doses really photon-equivalent?

    International Nuclear Information System (INIS)

    Coderre, J.A.; Diaz, A.Z.; Ma, R.

    2001-01-01

    Boron neutron capture therapy (BNCT) produces a mixture of radiation dose components. The high-linear energy transfer (LET) particles are more damaging in tissue than equal doses of low-LET radiation. Each of the high-LET components can multiplied by an experimentally determined factor to adjust for the increased biological effectiveness and the resulting sum expressed in photon-equivalent units (Gy-Eq). BNCT doses in photon-equivalent units are based on a number of assumptions. It may be possible to test the validity of these assumptions and the accuracy of the calculated BNCT doses by 1) comparing the effects of BNCT in other animal or biological models where the effects of photon radiation are known, or 2) if there are endpoints reached in the BNCT dose escalation clinical trials that can be related to the known response to photons of the tissue in question. The calculated Gy-Eq BNCT doses delivered to dogs and to humans with BPA and the epithermal neutron beam of the Brookhaven Medical Research Reactor were compared to expected responses to photon irradiation. The data indicate that Gy-Eq doses in brain may be underestimated. Doses to skin are consistent with the expected response to photons. Gy-Eq doses to tumor are significantly overestimated. A model system of cells in culture irradiated at various depths in a lucite phantom using the epithermal beam is under development. Preliminary data indicate that this approach can be used to detect differences in the relative biological effectiveness of the beam. The rat 9L gliosarcoma cell survival data was converted to photon-equivalent doses using the same factors assumed in the clinical studies. The results superimposed on the survival curve derived from irradiation with Cs-137 photons indicating the potential utility of this model system. (author)

  9. Dynamic equivalence relation on the fuzzy measure algebras

    Directory of Open Access Journals (Sweden)

    Roya Ghasemkhani

    2017-04-01

    Full Text Available The main goal of the present paper is to extend classical results from the measure theory and dynamical systems to the fuzzy subset setting. In this paper, the notion of  dynamic equivalence relation is introduced and then it is proved that this relation is an equivalence relation. Also, a new metric on the collection of all equivalence classes is introduced and it is proved that this metric is complete.

  10. Dose equivalent distributions in the AAEC total body nitrogen facility

    International Nuclear Information System (INIS)

    Allen, B.J.; Bailey, G.M.; McGregor, B.J.

    1985-01-01

    The incident neutron dose equivalent in the AAEC total body nitrogen facility is measured by a calibrated remmeter. Dose equivalent rates and distributions are calculated by Monte Carlo techniques which take account of the secondary neutron flux from the collimator. Experiment and calculation are found to be in satisfactory agreement. The effective dose equivalent per exposure is determined by weighting organ doses, and the potential detriment per exposure is calculated from ICRP risk factors

  11. Equivalence principle violations and couplings of a light dilaton

    International Nuclear Information System (INIS)

    Damour, Thibault; Donoghue, John F.

    2010-01-01

    We consider possible violations of the equivalence principle through the exchange of a light 'dilaton-like' scalar field. Using recent work on the quark-mass dependence of nuclear binding, we find that the dilaton-quark-mass coupling induces significant equivalence-principle-violating effects varying like the inverse cubic root of the atomic number - A -1/3 . We provide a general parametrization of the scalar couplings, but argue that two parameters are likely to dominate the equivalence-principle phenomenology. We indicate the implications of this framework for comparing the sensitivities of current and planned experimental tests of the equivalence principle.

  12. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  13. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  14. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar

    Directory of Open Access Journals (Sweden)

    Jurman Irena

    2010-03-01

    Full Text Available Abstract Background Most of the grapevine (Vitis vinifera L. cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. Results We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. Conclusions We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.

  15. Chromosome End Repair and Genome Stability in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Susannah F. Calhoun

    2017-08-01

    Full Text Available The human malaria parasite Plasmodium falciparum replicates within circulating red blood cells, where it is subjected to conditions that frequently cause DNA damage. The repair of DNA double-stranded breaks (DSBs is thought to rely almost exclusively on homologous recombination (HR, due to a lack of efficient nonhomologous end joining. However, given that the parasite is haploid during this stage of its life cycle, the mechanisms involved in maintaining genome stability are poorly understood. Of particular interest are the subtelomeric regions of the chromosomes, which contain the majority of the multicopy variant antigen-encoding genes responsible for virulence and disease severity. Here, we show that parasites utilize a competitive balance between de novo telomere addition, also called “telomere healing,” and HR to stabilize chromosome ends. Products of both repair pathways were observed in response to DSBs that occurred spontaneously during routine in vitro culture or resulted from experimentally induced DSBs, demonstrating that both pathways are active in repairing DSBs within subtelomeric regions and that the pathway utilized was determined by the DNA sequences immediately surrounding the break. In combination, these two repair pathways enable parasites to efficiently maintain chromosome stability while also contributing to the generation of genetic diversity.

  16. Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina.

    Directory of Open Access Journals (Sweden)

    Volker U Schwartze

    2014-08-01

    Full Text Available Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD, (ii despite the relatively high incidence of introns, alternative splicing (AS is not frequently observed for the generation of paralogs and in response to stress, (iii the content of repetitive elements is strikingly low (<5%, (iv L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i lower content of tRNAs, but unique codons in L. corymbifera, (ii Over 25% of the proteins are apparently specific for L. corymbifera. (iii L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

  17. Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina).

    Science.gov (United States)

    Schwartze, Volker U; Winter, Sascha; Shelest, Ekaterina; Marcet-Houben, Marina; Horn, Fabian; Wehner, Stefanie; Linde, Jörg; Valiante, Vito; Sammeth, Michael; Riege, Konstantin; Nowrousian, Minou; Kaerger, Kerstin; Jacobsen, Ilse D; Marz, Manja; Brakhage, Axel A; Gabaldón, Toni; Böcker, Sebastian; Voigt, Kerstin

    2014-08-01

    Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

  18. Parallel or convergent evolution in human population genomic data revealed by genotype networks.

    Science.gov (United States)

    R Vahdati, Ali; Wagner, Andreas

    2016-08-02

    Genotype networks are representations of genetic variation data that are complementary to phylogenetic trees. A genotype network is a graph whose nodes are genotypes (DNA sequences) with the same broadly defined phenotype. Two nodes are connected if they differ in some minimal way, e.g., in a single nucleotide. We analyze human genome variation data from the 1,000 genomes project, and construct haploid genotype (haplotype) networks for 12,235 protein coding genes. The structure of these networks varies widely among genes, indicating different patterns of variation despite a shared evolutionary history. We focus on those genes whose genotype networks show many cycles, which can indicate homoplasy, i.e., parallel or convergent evolution, on the sequence level. For 42 genes, the observed number of cycles is so large that it cannot be explained by either chance homoplasy or recombination. When analyzing possible explanations, we discovered evidence for positive selection in 21 of these genes and, in addition, a potential role for constrained variation and purifying selection. Balancing selection plays at most a small role. The 42 genes with excess cycles are enriched in functions related to immunity and response to pathogens. Genotype networks are representations of genetic variation data that can help understand unusual patterns of genomic variation.

  19. Equivalent Sensor Radiance Generation and Remote Sensing from Model Parameters. Part 1; Equivalent Sensor Radiance Formulation

    Science.gov (United States)

    Wind, Galina; DaSilva, Arlindo M.; Norris, Peter M.; Platnick, Steven E.

    2013-01-01

    In this paper we describe a general procedure for calculating equivalent sensor radiances from variables output from a global atmospheric forecast model. In order to take proper account of the discrepancies between model resolution and sensor footprint the algorithm takes explicit account of the model subgrid variability, in particular its description of the probably density function of total water (vapor and cloud condensate.) The equivalent sensor radiances are then substituted into an operational remote sensing algorithm processing chain to produce a variety of remote sensing products that would normally be produced from actual sensor output. This output can then be used for a wide variety of purposes such as model parameter verification, remote sensing algorithm validation, testing of new retrieval methods and future sensor studies. We show a specific implementation using the GEOS-5 model, the MODIS instrument and the MODIS Adaptive Processing System (MODAPS) Data Collection 5.1 operational remote sensing cloud algorithm processing chain (including the cloud mask, cloud top properties and cloud optical and microphysical properties products.) We focus on clouds and cloud/aerosol interactions, because they are very important to model development and improvement.

  20. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  1. Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

    Science.gov (United States)

    Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A; Janke, Axel

    2015-05-27

    The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

    Science.gov (United States)

    Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A.; Janke, Axel

    2015-01-01

    The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. PMID:26019166

  3. Computer simulation of arising of diploid genomes

    Science.gov (United States)

    Tretyakov, Victor S.; Tretyakov, Nikolay P.

    2008-07-01

    The haploid-diploid cycle where, under unfavorable conditions the population becomes diploid, is modeled by a Monte-Carlo method in the framework of the Jan-Stauffer-Moseley hypothesis. Diploidy and sex may have first arisen as a way to escape death, when a simple unicellular individual is threatened by too many deleterious mutations. Using a bit string model, we find that in a system where competition is present (through the Verhulst factor), diploids dominate. In this case the transition from haploid to essentially diploid population takes place in a short time interval reminiscent of phase transitions in physical systems.

  4. Development of solid water-equivalent radioactive certified reference materials

    International Nuclear Information System (INIS)

    Finke, E.; Greupner, H.; Groche, K.; Rittwag, R.; Geske, G.

    1991-01-01

    This paper presents a brief description of the development of solid water-equivalent beta volume radioactive certified reference materials. These certified reference materials were prepared for the beta fission nuclides 90 Sr/ 90 Y, 137 Cs, 147 Pm and 204 Tl. Comparative measurements of liquid and solid water-equivalent beta volume radioactive certified reference materials are discussed. (author)

  5. Equivalence of quantum states under local unitary transformations

    International Nuclear Information System (INIS)

    Fei Shaoming; Jing Naihuan

    2005-01-01

    In terms of the analysis of fixed point subgroup and tensor decomposability of certain matrices, we study the equivalence of quantum bipartite mixed states under local unitary transformations. For non-degenerate case an operational criterion for the equivalence of two such mixed bipartite states under local unitary transformations is presented

  6. 40 CFR 133.105 - Treatment equivalent to secondary treatment.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Treatment equivalent to secondary treatment. 133.105 Section 133.105 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS SECONDARY TREATMENT REGULATION § 133.105 Treatment equivalent to secondary treatment...

  7. Microcystin-LR equivalent concentrations in fish tissue during a ...

    African Journals Online (AJOL)

    The effects of a decomposing cyanobacteria bloom on water quality and the accumulation of microcystin-LR equivalent toxin in fish at Loskop Dam were studied in May 2012. Enzyme-linked immunosorbent assay [ELISA] was used to confirm the presence of microcystin-LR equivalent in the water and to determine the ...

  8. Decompositional equivalence: A fundamental symmetry underlying quantum theory

    OpenAIRE

    Fields, Chris

    2014-01-01

    Decompositional equivalence is the principle that there is no preferred decomposition of the universe into subsystems. It is shown here, by using simple thought experiments, that quantum theory follows from decompositional equivalence together with Landauer's principle. This demonstration raises within physics a question previously left to psychology: how do human - or any - observers agree about what constitutes a "system of interest"?

  9. Preparation of A-150 tissue-equivalent plastic films

    International Nuclear Information System (INIS)

    Saion, E.B.; Shaari, A.H.; Watt, D.E.

    1992-01-01

    A-150 tissue-equivalent (TE) plastic is widely used as a wall material for tissue-equivalent proportional counters (TEPCS) used in experimental microdosimetry. The objective of this note is to give a technical account of how A-150 TE plastic film can be fabricated in the laboratory from commercially available A-150 TE plastic. (author)

  10. Equivalence of several Chern-Simons matter models

    International Nuclear Information System (INIS)

    Chen, W.; Itoi, C.

    1994-01-01

    Chern-Simons (CS) coupling characterizes not only statistics, but also spin and scaling dimension of matter fields. We demonstrate spin transmutation in relativistic CS matter theory, and moreover show equivalence of several models. We study the CS vector model in some detail, which provides a consistent check to the assertion of the equivalence

  11. 29 CFR 4.170 - Furnishing fringe benefits or equivalents.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Furnishing fringe benefits or equivalents. 4.170 Section 4... Standards Compliance with Compensation Standards § 4.170 Furnishing fringe benefits or equivalents. (a) General. Fringe benefits required under the Act shall be furnished, separate from and in addition to the...

  12. Theory of Covariance Equivalent ARMAV Models of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Andersen, P.; Brincker, Rune; Kirkegaard, Poul Henning

    1996-01-01

    In this paper the theoretical background for using covariance equivalent ARMAV models in modal analysis is discussed. It is shown how to obtain a covariance equivalent ARMA model for a univariate linear second order continous-time system excited by Gaussian white noise. This result is generalized...

  13. Theory of Covariance Equivalent ARMAV Models of Civil Engineering Structures

    DEFF Research Database (Denmark)

    Andersen, P.; Brincker, Rune; Kirkegaard, Poul Henning

    In this paper the theoretical background for using covariance equivalent ARMAV models in modal analysis is discussed. It is shown how to obtain a covariance equivalent ARMA model for a univariate linear second order continuous-time system excited by Gaussian white noise. This result is generalize...

  14. Graphene-based THz modulator analyzed by equivalent circuit model

    DEFF Research Database (Denmark)

    Xiao, Binggang; Chen, Jing; Xie, Zhiyi

    2016-01-01

    A terahertz (THz) modulator based on graphene is proposed and analysed by use of equivalent transmission line of a homogeneous mediumand the local anisotropic model of the graphene conductivity. The result calculated by the equivalent circuit is consistent with that obtained byFresnel transfer...

  15. The lexicographical handling of grammatical equivalence: the case ...

    African Journals Online (AJOL)

    Lexicographers compiling translating dictionaries are not exclusively concerned with semantic equivalence when selecting translating equivalents for lemmata, but often include also grammatical information in illustrative examples when the lexical item to be translated does not have an exact grammatical counterpart in the ...

  16. 30 CFR 90.206 - Approved sampling devices; equivalent concentrations.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Approved sampling devices; equivalent... LABOR COAL MINE SAFETY AND HEALTH MANDATORY HEALTH STANDARDS-COAL MINERS WHO HAVE EVIDENCE OF THE DEVELOPMENT OF PNEUMOCONIOSIS Sampling Procedures § 90.206 Approved sampling devices; equivalent...

  17. Teaching Brain-Behavior Relations Economically with Stimulus Equivalence Technology

    Science.gov (United States)

    Fienup, Daniel M.; Covey, Daniel P.; Critchfield, Thomas S.

    2010-01-01

    Instructional interventions based on stimulus equivalence provide learners with the opportunity to acquire skills that are not directly taught, thereby improving the efficiency of instructional efforts. The present report describes a study in which equivalence-based instruction was used to teach college students facts regarding brain anatomy and…

  18. Foundations of gravitation theory: the principle of equivalence

    International Nuclear Information System (INIS)

    Haugan, M.P.

    1978-01-01

    A new framework is presented within which to discuss the principle of equivalence and its experimental tests. The framework incorporates a special structure imposed on the equivalence principle by the principle of energy conservation. This structure includes relations among the conceptual components of the equivalence principle as well as quantitative relations among the outcomes of its experimental tests. One of the most striking new results obtained through use of this framework is a connection between the breakdown of local Lorentz invariance and the breakdown of the principle that all bodies fall with the same acceleration in a gravitational field. An extensive discussion of experimental tests of the equivalence principle and their significance is also presented. Within the above framework, theory-independent analyses of a broad range of equivalence principle tests are possible. Gravitational redshift experiments. Doppler-shift experiments, the Turner-Hill and Hughes-Drever experiments, and a number of solar-system tests of gravitation theories are analyzed. Application of the techniques of theoretical nuclear physics to the quantitative interpretation of equivalence principle tests using laboratory materials of different composition yields a number of important results. It is found that current Eotvos experiments significantly demonstrate the compatibility of the weak interactions with the equivalence principle. It is also shown that the Hughes-Drever experiment is the most precise test of local Lorentz invariance yet performed. The work leads to a strong, tightly knit empirical basis for the principle of equivalence, the central pillar of the foundations of gravitation theory

  19. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  20. Multifunctional Role of ATM/Tel1 Kinase in Genome Stability: From the DNA Damage Response to Telomere Maintenance

    Science.gov (United States)

    2014-01-01

    The mammalian protein kinase ataxia telangiectasia mutated (ATM) is a key regulator of the DNA double-strand-break response and belongs to the evolutionary conserved phosphatidylinositol-3-kinase-related protein kinases. ATM deficiency causes ataxia telangiectasia (AT), a genetic disorder that is characterized by premature aging, cerebellar neuropathy, immunodeficiency, and predisposition to cancer. AT cells show defects in the DNA damage-response pathway, cell-cycle control, and telomere maintenance and length regulation. Likewise, in Saccharomyces cerevisiae, haploid strains defective in the TEL1 gene, the ATM ortholog, show chromosomal aberrations and short telomeres. In this review, we outline the complex role of ATM/Tel1 in maintaining genomic stability through its control of numerous aspects of cellular survival. In particular, we describe how ATM/Tel1 participates in the signal transduction pathways elicited by DNA damage and in telomere homeostasis and its importance as a barrier to cancer development. PMID:25247188

  1. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  2. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  3. Calculation simulation of equivalent irradiation swelling for dispersion nuclear fuel

    International Nuclear Information System (INIS)

    Cai Wei; Zhao Yunmei; Gong Xin; Ding Shurong; Huo Yongzhong

    2015-01-01

    The dispersion nuclear fuel was regarded as a kind of special particle composites. Assuming that the fuel particles are periodically distributed in the dispersion nuclear fuel meat, the finite element model to calculate its equivalent irradiation swelling was developed with the method of computational micro-mechanics. Considering irradiation swelling in the fuel particles and the irradiation hardening effect in the metal matrix, the stress update algorithms were established respectively for the fuel particles and metal matrix. The corresponding user subroutines were programmed, and the finite element simulation of equivalent irradiation swelling for the fuel meat was performed in Abaqus. The effects of the particle size and volume fraction on the equivalent irradiation swelling were investigated, and the fitting formula of equivalent irradiation swelling was obtained. The results indicate that the main factors to influence equivalent irradiation swelling of the fuel meat are the irradiation swelling and volume fraction of fuel particles. (authors)

  4. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  5. On identifying name equivalences in digital libraries. Name equivalence, Surname matching, Author identification, Databases

    Directory of Open Access Journals (Sweden)

    Dror G. Feitelson

    2004-01-01

    Full Text Available The services provided by digital libraries can be much improved by correctly identifying variants of the same name. For example, this will allow for better retrieval of all the works by a certain author. We focus on variants caused by abbreviations of first names, and show that significant achievements are possible by simple lexical analysis and comparison of names. This is done in two steps: first a pairwise matching of names is performed, and then these are used to find cliques of equivalent names. However, these steps can each be performed in a variety of ways. We therefore conduct an experimental analysis using two real datasets to find which approaches actually work well in practice. Interestingly, this depends on the size of the repository, as larger repositories may have many more similar names.

  6. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  7. A mutation in the centriole-associated protein centrin causes genomic instability via increased chromosome loss in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Marshall Wallace F

    2005-05-01

    Full Text Available Abstract Background The role of centrioles in mitotic spindle function remains unclear. One approach to investigate mitotic centriole function is to ask whether mutation of centriole-associated proteins can cause genomic instability. Results We addressed the role of the centriole-associated EF-hand protein centrin in genomic stability using a Chlamydomonas reinhardtii centrin mutant that forms acentriolar bipolar spindles and lacks the centrin-based rhizoplast structures that join centrioles to the nucleus. Using a genetic assay for loss of heterozygosity, we found that this centrin mutant showed increased genomic instability compared to wild-type cells, and we determined that the increase in genomic instability was due to a 100-fold increase in chromosome loss rates compared to wild type. Live cell imaging reveals an increased rate in cell death during G1 in haploid cells that is consistent with an elevated rate of chromosome loss, and analysis of cell death versus centriole copy number argues against a role for multipolar spindles in this process. Conclusion The increased chromosome loss rates observed in a centrin mutant that forms acentriolar spindles suggests a role for centrin protein, and possibly centrioles, in mitotic fidelity.

  8. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  9. The performance of low pressure tissue-equivalent chambers and a new method for parameterising the dose equivalent

    International Nuclear Information System (INIS)

    Eisen, Y.

    1986-01-01

    The performance of Rossi-type spherical tissue-equivalent chambers with equivalent diameters between 0.5 μm and 2 μm was tested experimentally using monoenergetic and polyenergetic neutron sources in the energy region of 10 keV to 14.5 MeV. In agreement with theoretical predictions both chambers failed to provide LET information at low neutron energies. A dose equivalent algorithm was derived that utilises the event distribution but does not attempt to correlate event size with LET. The algorithm was predicted theoretically and confirmed by experiment. The algorithm that was developed determines the neutron dose equivalent, from the data of the 0.5 μm chamber, to better than +-20% over the energy range of 30 keV to 14.5 MeV. The same algorithm also determines the dose equivalent from the data of the 2 μm chamber to better than +-20% over the energy range of 60 keV to 14.5 MeV. The efficiency of the chambers is 33 counts per μSv, or equivalently about 10 counts s -1 per mSv.h -1 . This efficiency enables the measurement of dose equivalent rates above 1 mSv.h -1 for an integration period of 3 s. Integrated dose equivalents can be measured as low as 1 μSv. (author)

  10. Coconut genome size determined by flow cytometry: Tall versus Dwarf types.

    Science.gov (United States)

    Freitas Neto, M; Pereira, T N S; Geronimo, I G C; Azevedo, A O N; Ramos, S R R; Pereira, M G

    2016-02-11

    Coconuts (Cocos nucifera L.) are tropical palm trees that are classified into Tall and Dwarf types based on height, and both types are diploid (2n = 2x = 32 chromosomes). The reproduction mode is autogamous for Dwarf types and allogamous for Tall types. One hypothesis for the origin of the Dwarf coconut suggests that it is a Tall variant that resulted from either mutation or inbreeding, and differences in genome size between the two types would support this hypothesis. In this study, we estimated the genome sizes of 14 coconut accessions (eight Tall and six Dwarf types) using flow cytometry. Nuclei were extracted from leaf discs and stained with propidium iodide, and Pisum sativum (2C = 9.07 pg DNA) was used as an internal standard. Histograms with good resolution and low coefficients of variation (2.5 to 3.2%) were obtained. The 2C DNA content ranged from 5.72 to 5.48 pg for Tall accessions and from 5.58 to 5.52 pg for Dwarf accessions. The mean genome sizes for Tall and Dwarf specimens were 5.59 and 5.55 pg, respectively. Among all accessions, Rennel Island Tall had the highest mean DNA content (5.72 pg), whereas West African Tall had the lowest (5.48 pg). The mean coconut genome size (2C = 5.57 pg, corresponding to 2723.73 Mbp/haploid set) was classified as small. Only small differences in genome size existed among the coconut accessions, suggesting that the Dwarf type did not evolve from the Tall type.

  11. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  12. Determination of equivalent copper thickness of patient equivalent phantoms in terms of attenuation, used in radiology

    International Nuclear Information System (INIS)

    Jansen, J.Th.M.; Suliman, I.I.; Zoetelief, J.

    2002-01-01

    Full text: In the radiation protection research programme of the European Union, as part of the DIMOND concerted action, constancy check protocols for fluoroscopic systems have been developed. For practical reasons copper filters are preferred to patients and tissue equivalent, water or PMMA, phantoms. The objectives are to derive patient entrance surface dose rates and the dose rate at the image intensifier input. The protocol states that copper sheets of either 1 mm or 1.5 mm thick may be used. The present study investigates the equivalent thickness of copper filters compared to PMMA phantoms in terms of attenuation for both geometries and different tube voltage and filter combinations. The geometry to determine the patient entrance surface dose is with the copper filter close to the image intensifier. The ionisation chamber is placed on the side of the copper sheet nearest to the X-ray tube. The inverse square law is used to correct for differences in position. Measurements are performed with different settings and with and without the use of an anti-scatter grid. The geometry to determine the air kerma rate at the image intensifier is with the copper filter attached to the X-ray tube diaphragm. The ionisation chamber is placed on the surface of the image intensifier housing. Again measurements are performed with different settings and with and without anti-scatter grid. If necessary, the inverse square law correction is applied. Two different radiation beam sizes are used, i.e., a small beam with a diameter of 0.10 m at a distance of 1.00 m from the focus and a large beam with a diameter of 0.23 m at a distance of 1.00 m from the focus. The applied tube voltages and PMMA phantom thickness combinations are 60 kV, 13 cm; 80 kV, 14 cm; 100 kV, 16 cm; 120 kV, 17 cm; 150 kV, 18 cm; 150 kV, 20 cm and 150 kV, 30 cm. The spectra for the different tube voltages are generated with the IPEM Report 78 software at an anode angle of 16 degree, 0% ripple and 2.5 mm added

  13. Mathematical simulation of biologically equivalent doses for LDR-HDR

    International Nuclear Information System (INIS)

    Slosarek, K.; Zajusz, A.

    1996-01-01

    Based on the LQ model examples of biologically equivalent doses LDR, HDR and external beams were calculated. The biologically equivalent doses for LDR were calculated by appending to the LQ model the corrector for the time of repair of radiation sublethal damages. For radiation continuously delivered at a low dose rate the influence of sublethal damage repair time changes on biologically equivalent doses were analysed. For fractionated treatment with high dose rate the biologically equivalent doses were calculated by adding to the LQ model the formula of accelerated repopulation. For total biologically equivalent dose calculation for combine LDR-HDR-Tele irradiation examples are presented with the use of different parameters of the time of repair of sublethal damages and accelerated repopulation. The calculations performed show, that the same biologically equivalent doses can be obtained for different parameters of cell kinetics changes during radiation treatment. It also shows, that during biologically equivalent dose calculations for different radiotherapy schedules, ignorance of cell kinetics parameters can lead to relevant errors

  14. Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc. Using a Hybrid Assembly Approach

    Directory of Open Access Journals (Sweden)

    Tokurou Shimizu

    2017-12-01

    Full Text Available Satsuma (Citrus unshiu Marc. is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma (“Miyagawa Wase” was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.

  15. Histone variant H3.3-mediated chromatin remodeling is essential for paternal genome activation in mouse preimplantation embryos.

    Science.gov (United States)

    Kong, Qingran; Banaszynski, Laura A; Geng, Fuqiang; Zhang, Xiaolei; Zhang, Jiaming; Zhang, Heng; O'Neill, Claire L; Yan, Peidong; Liu, Zhonghua; Shido, Koji; Palermo, Gianpiero D; Allis, C David; Rafii, Shahin; Rosenwaks, Zev; Wen, Duancheng

    2018-03-09

    Derepression of chromatin-mediated transcriptional repression of paternal and maternal genomes is considered the first major step that initiates zygotic gene expression after fertilization. The histone variant H3.3 is present in both male and female gametes and is thought to be important for remodeling the paternal and maternal genomes for activation during both fertilization and embryogenesis. However, the underlying mechanisms remain poorly understood. Using our H3.3B-HA-tagged mouse model, engineered to report H3.3 expression in live animals and to distinguish different sources of H3.3 protein in embryos, we show here that sperm-derived H3.3 (sH3.3) protein is removed from the sperm genome shortly after fertilization and extruded from the zygotes via the second polar bodies (PBII) during embryogenesis. We also found that the maternal H3.3 (mH3.3) protein is incorporated into the paternal genome as early as 2 h postfertilization and is detectable in the paternal genome until the morula stage. Knockdown of maternal H3.3 resulted in compromised embryonic development both of fertilized embryos and of androgenetic haploid embryos. Furthermore, we report that mH3.3 depletion in oocytes impairs both activation of the Oct4 pluripotency marker gene and global de novo transcription from the paternal genome important for early embryonic development. Our results suggest that H3.3-mediated paternal chromatin remodeling is essential for the development of preimplantation embryos and the activation of the paternal genome during embryogenesis. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12.

    Science.gov (United States)

    Miki, Takeyoshi; Yamamoto, Yoshihiro; Matsuda, Hideo

    2008-01-01

    We developed a novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12. The basic idea of the method is to randomly disrupt the genes on the DNA fragments cloned on the Kohara library by inserting a mini-transposon first, and then transfer the disrupted genes from the lambda vector to the E. coli chromosome by homologous recombination. Using this method, we constructed a set of 8402 Km(r) cis-diploid mutants harboring a mini-Tn10 insertion mutation and the corresponding wild-type gene on a chromosome, as well as a set of 6954 haploid mutants derived from the cis-diploid mutants. The major advantage of the strategy used is that the indispensable genes or sites for growth can be identified. Preliminary results suggest that 415 open reading frames are indispensable for growth in E. coli cells. A total of 6404 haploid mutants were deposited to Genetic Strains Research Center, National Institute of Genetics, Japan (Chapter 26) and are available for public distribution upon request (http://shigen.lab.nig.ac.jp/ecoli/strain/nbrp/resource.jsp).

  17. Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; ZHANG Xiaojun; Chantel F.SCHEURING; ZHANG Hongbin; LI Fuhua; XIANG Jianhai

    2008-01-01

    Two Large-insert genomic bacterial artificial chromosome (BAC) libraries of Zhikong scallop Chlamys farreri were constructed to promote our genetic and genomic research.High-quality megabase-sized DNA was isolated from the adductor muscle of the scallop and partially digested by BamH I and Mbo I,respectively.The BamH I library consisted of 53760 clones while the Mbo I library consisted of 7680 clones.Approximately 96% of the clones in BamH I library contained nuclear DNA inserts in average size of 100 kb,providing a coverage of 5.3 haploid genome equivalents.Similarly,the Mbo I library with an average insert of 145 kb and no insert-empty clones,thus providing a genome coverage of 1.1 haploid genome equivalents.

  18. Modelling of dynamic equivalents in electric power grids

    International Nuclear Information System (INIS)

    Craciun, Diana Iuliana

    2010-01-01

    In a first part, this research thesis proposes a description of the context and new constraints of electric grids: architecture, decentralized production with the impact of distributed energy resource systems, dynamic simulation, and interest of equivalent models. Then, the author discusses the modelling of the different components of electric grids: synchronous and asynchronous machines, distributed energy resource with power electronic interface, loading models. She addresses the techniques of reduction of electric grid models: conventional reduction methods, dynamic equivalence methods using non linear approaches or evolutionary algorithm-based methods of assessment of parameters. This last approach is then developed and implemented, and a new method of computation of dynamic equivalents is described

  19. Asymptotically double lacunry equivalent sequences defined by Orlicz functions

    Directory of Open Access Journals (Sweden)

    Ayhan Esi

    2014-04-01

    Full Text Available This paper presents the following definition which is natural combition of the definition for asymptotically equivalent and Orlicz function. The two nonnegative double sequences x=(x_{k,l} and y=(y_{k,l} are said to be M-asymptotically double equivalent to multiple L provided that for every ε>0, P-lim_{k,l}M(((|((x_{k,l}/(y_{k,l}-L|/ρ=0, for some ρ>0, (denoted by x∽y and simply M-asymptotically double equivalent if L=1. Also we give some new concepts related to this definition and some inclusion theorems.

  20. Calculation of committed dose equivalent from intake of tritiated water

    International Nuclear Information System (INIS)

    Law, D.V.

    1978-08-01

    A new computerized method of calculating the committed dose equivalent from the intake of tritiated water at Harwell is described in this report. The computer program has been designed to deal with a variety of intake patterns and urine sampling schemes, as well as to produce committed dose equivalents corresponding to any periods for which individual monitoring for external radiation is undertaken. Details of retrospective doses are added semi-automatically to the Radiation Dose Records and committed dose equivalents are retained on a separate file. (author)

  1. The Application of Equivalence Theory to Advertising Translation

    Institute of Scientific and Technical Information of China (English)

    张颖

    2017-01-01

    Through analyzing equivalence theory, the author tries to find a solution to the problems arising in the process of ad?vertising translation. These problems include cultural diversity, language diversity and special requirement of advertisement. The author declares that Nida''s functional equivalence is one of the most appropriate theories to deal with these problems. In this pa?per, the author introduces the principles of advertising translation and culture divergences in advertising translation, and then gives some advertising translation practices to explain and analyze how to create good advertising translation by using functional equivalence. At last, the author introduces some strategies in advertising translation.

  2. Spaces of homotopy self-equivalences a survey

    CERN Document Server

    Rutter, John W

    1997-01-01

    This survey covers groups of homotopy self-equivalence classes of topological spaces, and the homotopy type of spaces of homotopy self-equivalences. For manifolds, the full group of equivalences and the mapping class group are compared, as are the corresponding spaces. Included are methods of calculation, numerous calculations, finite generation results, Whitehead torsion and other areas. Some 330 references are given. The book assumes familiarity with cell complexes, homology and homotopy. Graduate students and established researchers can use it for learning, for reference, and to determine the current state of knowledge.

  3. Apparent violation of the principle of equivalence and Killing horizons

    International Nuclear Information System (INIS)

    Zimmerman, R.L.; Farhoosh, H.; Oregon Univ., Eugene

    1980-01-01

    By means of the principle of equivalence it is deduced that the qualitative behavior of the Schwarzschild horizon about a uniformly accelerating particle. This result is confirmed for an exact solution of a uniformly accelerating object in the limit of small accelerations. For large accelerations the Schwarzschild horizon appears to violate the qualitative behavior established via the principle of equivalence. When similar arguments are extended to an observable such as the red shift between two observers, there is no departure from the results expected from the principle of equivalence. The resolution of the paradox is brought about by a compensating effect due to the Rindler horizon. (author)

  4. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.

    Directory of Open Access Journals (Sweden)

    Jennifer L Guler

    Full Text Available Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes.

  5. Genetic variation and inheritance of phytosterol and oil content in a doubled haploid population derived from the winter oilseed rape Sansibar × Oase cross.

    Science.gov (United States)

    Teh, Lishia; Möllers, Christian

    2016-01-01

    Identification of QTL for phytosterol content, oil content, fatty acids content, protein content of defatted meal, and seed weight by multiple interval mapping in a Brassica napus DH population. Phytosterols are minor seed constituents in oilseed rape which have recently drawn wide-interest from the food and nutrition industry due to their health benefit in lowering LDL cholesterol in humans. To understand the genetic basis of phytosterol content and its relationship with other seed quality traits in oilseed rape, QTL mapping was performed in a segregating DH population derived from the cross of two winter oilseed rape varieties, Sansibar and Oase, termed SODH population. Both parental lines are of canola quality which differ in phytosterol and oil content in seed. A genetic map was constructed for SODH population based on a total of 1638 markers organized in 23 linkage groups and covering a map length of 2350 cM with a mean marker interval of 2.0 cM. The SODH population and the parental lines were cultivated at six environments in Europe and were phenotyped for phytosterol content, oil content, fatty acids content, protein content of the defatted meal, and seed weight. Multiple interval mapping identified between one and six QTL for nine phytosterol traits, between two and six QTL for four fatty acids, five QTL for oil content, four QTL for protein content of defatted meal, and three QTL for seed weight. Colocalizations of QTL for different traits were more frequently observed than individual isolated QTL. Major QTL (R (2) ≥ 25%) were all located in the A genome, and the possible candidate genes were investigated by physical localization of the QTL to the reference genome sequence of Brassica rapa.

  6. Deciding Type Equivalence in a Language with Singleton Kinds

    National Research Council Canada - National Science Library

    Stone, Christopher

    1999-01-01

    ...: S(A) is the kind of all types provably equivalent to the type A. Singletons are interesting because they provide a very general form of definitions for type variables and allow fine-grained control of type computations...

  7. Lipschitz equivalence of self-similar sets with touching structures

    International Nuclear Information System (INIS)

    Ruan, Huo-Jun; Wang, Yang; Xi, Li-Feng

    2014-01-01

    Lipschitz equivalence of self-similar sets is an important area in the study of fractal geometry. It is known that two dust-like self-similar sets with the same contraction ratios are always Lipschitz equivalent. However, when self-similar sets have touching structures the problem of Lipschitz equivalence becomes much more challenging and intriguing at the same time. So far, all the known results only cover self-similar sets in R with no more than three branches. In this study we establish results for the Lipschitz equivalence of self-similar sets with touching structures in R with arbitrarily many branches. Key to our study is the introduction of a geometric condition for self-similar sets called substitutable. (paper)

  8. Approved Drug Products with Therapuetic Equivalence Evaluations (Orange Book)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The publication Approved Drug Products with Therapeutic Equivalence Evaluations (the List, commonly known as the Orange Book) identifies drug products approved on...

  9. ESA GlobSnow Snow Water Equivalent (SWE)

    Data.gov (United States)

    National Aeronautics and Space Administration — The European Space Agency (ESA) Global Snow Monitoring for Climate Research (GlobSnow) snow water equivalent (SWE) v2.0 data record contains snow information derived...

  10. Bisimulation Meet PCTL Equivalences for Probabilistic Automata (Journal Version)

    DEFF Research Database (Denmark)

    Song, Lei; Zhang, Lijun; Godskesen, Jens Christian

    2013-01-01

    Probabilistic automata (PA) have been successfully applied in the formal verification of concurrent and stochastic systems. Efficient model checking algorithms have been studied, where the most often used logics for expressing properties are based on PCTL and its extension PCTL*. Various behavioral...... equivalences are proposed for PAs, as a powerful tool for abstraction and compositional minimization for PAs. Unfortunately, the behavioral equivalences are well-known to be strictly stronger than the logical equivalences induced by PCTL or PCTL*. This paper introduces novel notions of strong bisimulation...... relations, which characterizes PCTL and PCTL* exactly. We also extend weak bisimulations characterizing PCTL and PCTL* without next operator, respectively. Thus, our paper bridges the gap between logical and behavioral equivalences in this setting....

  11. Noncommutative Yang-Mills from equivalence of star products

    International Nuclear Information System (INIS)

    Jurco, B.; Schupp, P.

    2000-01-01

    It is shown that the transformation between ordinary and noncommutative Yang-Mills theory as formulated by Seiberg and Witten is due to the equivalence of certain star products on the D-brane world-volume. (orig.)

  12. Noncommutative Yang-Mills from equivalence of star products

    Energy Technology Data Exchange (ETDEWEB)

    Jurco, B. [Max-Planck-Institut fuer Mathematik, Bonn (Germany); Schupp, P. [Sektion Physik, Universitaet Muenchen, Theresienstrasse 37, 80333 Muenchen (Germany)

    2000-05-01

    It is shown that the transformation between ordinary and noncommutative Yang-Mills theory as formulated by Seiberg and Witten is due to the equivalence of certain star products on the D-brane world-volume. (orig.)

  13. Existence and equivalence of twisted products on a symplectic manifold

    International Nuclear Information System (INIS)

    Lichnerowicz, A.

    1979-01-01

    The twisted products play an important role in Quantum Mechanics. A distinction is introduced between Vey *sub(γ) products and strong Vey *sub(γ) products and it is proved that each *sub(γ) product is equivalent to a Vey *sub(γ) product. If b 3 (W) = 0, the symplectic manifold (W,F) admits strong Vey *sub(Gn) products. If b 2 (W) = 0, all *sub(γ) products are equivalent as well as the Vey Lie algebras. In the general case the formal Lie algebras are characterized which are generated by a *sub(γ) product and it proved that the existance of a *sub(γ)-product is equivalent to the existance of a formal Lie algebra infinitesimally equivalent to a Vey Lie algebra at the first order. (Auth.)

  14. On conjugate points and the Leitmann equivalent problem approach

    NARCIS (Netherlands)

    Wagener, F.O.O.

    2009-01-01

    This article extends the Leitmann equivalence method to a class of problems featuring conjugate points. The class is characterised by the requirement that the set of indifference points of a given problem forms a finite stratification.

  15. Thévenin equivalent based static contingency assessment

    DEFF Research Database (Denmark)

    2015-01-01

    of the determined present state of the power system and determining a first representation of the network based on the determined Thevenin equivalents, determining a modified representation of the network, wherein the modified representation is a representation of the network having at least one contingency......, wherein at least one Thevenin equivalent of at least one voltage controlled node is modified due to the at least one contingency, the modified network representation being determined on the basis of the modified Thevenin equivalents, calculating voltage angles of the modified Thevenin equivalents......, and evaluating the voltage angles to determine whether the network having at least one contingency admit a steady state. Also a method of providing information on a real time static security assessment of a power system is disclosed....

  16. Evaluation of pharmaceutical and chemical equivalence of selected ...

    African Journals Online (AJOL)

    Personal

    Evaluation of Pharmaceutical and Chemical Equivalence of Selected Brands of Diclofenac Sodium .... strength- friability. /disintegration time ratio. (CSFR/DT). Drug content. % w/w ... Table 3: Parameters obtained from Kitazawa analysis. Brand.

  17. Do positrons and antiprotons respect the weak equivalence principle?

    International Nuclear Information System (INIS)

    Hughes, R.J.

    1990-01-01

    We resolve the difficulties which Morrison identified with energy conservation and the gravitational red-shift when particles of antimatter, such as the positron and antiproton, do not respect the weak equivalence principle. 13 refs

  18. Characteristics of natural background external radiation and effective dose equivalent

    International Nuclear Information System (INIS)

    Fujimoto, Kenzo

    1989-01-01

    The two sources of natural radiation - cosmic rays and primordial radionuclides - are described. The factors affecting radiation doses received from natural radiation and the calculation of effective dose equivalent due to natural radiation are discussed. 10 figs., 3 tabs

  19. Estimating water equivalent snow depth from related meteorological variables

    International Nuclear Information System (INIS)

    Steyaert, L.T.; LeDuc, S.K.; Strommen, N.D.; Nicodemus, M.L.; Guttman, N.B.

    1980-05-01

    Engineering design must take into consideration natural loads and stresses caused by meteorological elements, such as, wind, snow, precipitation and temperature. The purpose of this study was to determine a relationship of water equivalent snow depth measurements to meteorological variables. Several predictor models were evaluated for use in estimating water equivalent values. These models include linear regression, principal component regression, and non-linear regression models. Linear, non-linear and Scandanavian models are used to generate annual water equivalent estimates for approximately 1100 cooperative data stations where predictor variables are available, but which have no water equivalent measurements. These estimates are used to develop probability estimates of snow load for each station. Map analyses for 3 probability levels are presented

  20. The principle of equivalence and the Trojan asteroids

    International Nuclear Information System (INIS)

    Orellana, R.; Vucetich, H.

    1986-05-01

    An analysis of the Trojan asteroids motion has been carried out in order to set limits to possible violations to the principle of equivalence. Preliminary results, in agreement with general relativity, are reported. (author)