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Sample records for average genome size

  1. Quantitative metagenomic analyses based on average genome size normalization

    DEFF Research Database (Denmark)

    Frank, Jeremy Alexander; Sørensen, Søren Johannes

    2011-01-01

    Over the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can...... provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data...... by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different...

  2. Genome size variation in the genus Avena.

    Science.gov (United States)

    Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

    2016-03-01

    Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology. PMID:26881940

  3. Genome size analyses of Pucciniales reveal the largest fungal genomes

    Directory of Open Access Journals (Sweden)

    Silvia eTavares

    2014-08-01

    Full Text Available Rust fungi (Basidiomycota, Pucciniales are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 151.5 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi. In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1,800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp. Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94 %. The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7,000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  4. Genome size of Mycoplasma genitalium.

    OpenAIRE

    Su, C J; Baseman, J B

    1990-01-01

    The genome size of Mycoplasma genitalium was determined by using restriction enzymes that infrequently cut its DNA. The calculated value of 577 to 590 kilobases is one-fourth smaller than the genome of Mycoplasma pneumoniae, which is considered among the smallest genomes of self-replicating organisms.

  5. Sample Size Bias in Judgments of Perceptual Averages

    Science.gov (United States)

    Price, Paul C.; Kimura, Nicole M.; Smith, Andrew R.; Marshall, Lindsay D.

    2014-01-01

    Previous research has shown that people exhibit a sample size bias when judging the average of a set of stimuli on a single dimension. The more stimuli there are in the set, the greater people judge the average to be. This effect has been demonstrated reliably for judgments of the average likelihood that groups of people will experience negative,…

  6. Sauropod dinosaurs evolved moderately sized genomes unrelated to body size

    OpenAIRE

    Organ, Chris L.; Brusatte, Stephen L.; Stein, Koen

    2013-01-01

    Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in di...

  7. Genome Size Dynamics and Evolution in Monocots

    Directory of Open Access Journals (Sweden)

    Ilia J. Leitch

    2010-01-01

    Full Text Available Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small (1C=1.9 pg, there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

  8. A Cluster-Size Averaging Model for Strongly Discontinuous Percolation

    Science.gov (United States)

    Yamada, Yuhei; Yamazaki, Yoshihiro

    2016-05-01

    We propose a network percolation model, called cut-off model, which exhibits strongly discontinuous transition by an averaging effect of cluster sizes. In this model, a randomly selected bond is added if the size of the cluster formed by the bond is less than a times of the mean cluster size. It is shown that the model is strongly discontinuous when a is a finite constant.

  9. Sample size for estimating average productive traits of pigeon pea

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    Giovani Facco

    2016-04-01

    Full Text Available ABSTRACT: The objectives of this study were to determine the sample size, in terms of number of plants, needed to estimate the average values of productive traits of the pigeon pea and to determine whether the sample size needed varies between traits and between crop years. Separate uniformity trials were conducted in 2011/2012 and 2012/2013. In each trial, 360 plants were demarcated, and the fresh and dry masses of roots, stems, and leaves and of shoots and the total plant were evaluated during blossoming for 10 productive traits. Descriptive statistics were calculated, normality and randomness were checked, and the sample size was calculated. There was variability in the sample size between the productive traits and crop years of the pigeon pea culture. To estimate the averages of the productive traits with a 20% maximum estimation error and 95% confidence level, 70 plants are sufficient.

  10. Does Large Genome Size Limit Speciation in Endemic Island Floras?

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    Maxim V. Kapralov

    2011-01-01

    Full Text Available Genome sizes in plants vary by several orders of magnitude, and this diversity may have evolutionary consequences. Large genomes contain mainly noncoding DNA that may impose high energy and metabolic costs for their bearers. Here we test the large genome constraint hypothesis, which assumes that plant lineages with large genomes are diversifying more slowly Knight et al. (2005, using endemic floras of the oceanic archipelagos of the Canaries, Hawaii, and Marquesas Islands. In line with this hypothesis, the number of endemic species per genus is negatively correlated with genus-average genome size for island radiations on Hawaiian and Marquesas archipelagos. However, we do not find this correlation on the Canaries, which are close to the continent and therefore have higher immigration rate and lower endemism compared to Hawaii. Further work on a larger number of floras is required to test the generality of the large genome constraint hypothesis.

  11. On the Relationship between Pollen Size and Genome Size

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    Charles A. Knight

    2010-01-01

    Full Text Available Here we test whether genome size is a predictor of pollen size. If it were, inferences of ancient genome size would be possible using the abundant paleo-palynolgical record. We performed regression analyses across 464 species of pollen width and genome size. We found a significant positive trend. However, regression analysis using phylogentically independent contrasts did not support the correlated evolution of these traits. Instead, a large split between angiosperms and gymnosperms for both pollen width and genome size was revealed. Sister taxa were not more likely to show a positive contrast when compared to deeper nodes. However, significantly more congeneric species had a positive trend than expected by chance. These results may reflect the strong selection pressure for pollen to be small. Also, because pollen grains are not metabolically active when measured, their biology is different than other cells which have been shown to be strongly related to genome size, such as guard cells. Our findings contrast with previously published research. It was our hope that pollen size could be used as a proxy for inferring the genome size of ancient species. However, our results suggest pollen is not a good candidate for such endeavors.

  12. Genome size variation in three Saccharum species

    Science.gov (United States)

    Saccharum species are autopolyploid with ploidy level ranging from 5x to 16x, and is considered one of the most complex genomes among crop plants. In this study, the genome sizes of 28 S. spontaneum accessions, 15 S. officinarum accessions, 28 S. robustum accessions, and 12 Saccharum Hybrids were an...

  13. The evolution of genome size in ants

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    Spagna Joseph C

    2008-02-01

    Full Text Available Abstract Background Despite the economic and ecological importance of ants, genomic tools for this family (Formicidae remain woefully scarce. Knowledge of genome size, for example, is a useful and necessary prerequisite for the development of many genomic resources, yet it has been reported for only one ant species (Solenopsis invicta, and the two published estimates for this species differ by 146.7 Mb (0.15 pg. Results Here, we report the genome size for 40 species of ants distributed across 10 of the 20 currently recognized subfamilies, thus making Formicidae the 4th most surveyed insect family and elevating the Hymenoptera to the 5th most surveyed insect order. Our analysis spans much of the ant phylogeny, from the less derived Amblyoponinae and Ponerinae to the more derived Myrmicinae, Formicinae and Dolichoderinae. We include a number of interesting and important taxa, including the invasive Argentine ant (Linepithema humile, Neotropical army ants (genera Eciton and Labidus, trapjaw ants (Odontomachus, fungus-growing ants (Apterostigma, Atta and Sericomyrmex, harvester ants (Messor, Pheidole and Pogonomyrmex, carpenter ants (Camponotus, a fire ant (Solenopsis, and a bulldog ant (Myrmecia. Our results show that ants possess small genomes relative to most other insects, yet genome size varies three-fold across this insect family. Moreover, our data suggest that two whole-genome duplications may have occurred in the ancestors of the modern Ectatomma and Apterostigma. Although some previous studies of other taxa have revealed a relationship between genome size and body size, our phylogenetically-controlled analysis of this correlation did not reveal a significant relationship. Conclusion This is the first analysis of genome size in ants (Formicidae and the first across multiple species of social insects. We show that genome size is a variable trait that can evolve gradually over long time spans, as well as rapidly, through processes that may

  14. Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid.

    Science.gov (United States)

    Camillo, Julceia; Leão, André P; Alves, Alexandre A; Formighieri, Eduardo F; Azevedo, Ana Ls; Nunes, Juliana D; de Capdeville, Guy; de A Mattos, Jean K; Souza, Manoel T

    2014-01-01

    Aiming at generating a comprehensive genomic database on Elaeis spp., our group is leading several R&D initiatives with Elaeis guineensis (African oil palm) and Elaeis oleifera (American oil palm), including the whole-genome sequencing of the last. Genome size estimates currently available for this genus are controversial, as they indicate that American oil palm genome is about half the size of the African oil palm genome and that the genome of the interspecific hybrid is bigger than both the parental species genomes. We estimated the genome size of three E. guineensis genotypes, five E. oleifera genotypes, and two interspecific hybrids genotypes. On average, the genome size of E. guineensis is 4.32 ± 0.173 pg, while that of E. oleifera is 4.43 ± 0.018 pg. This indicates that both genomes are similar in size, even though E. oleifera is in fact bigger. As expected, the hybrid genome size is around the average of the two genomes, 4.40 ± 0.016 pg. Additionally, we demonstrate that both species present around 38% of GC content. As our results contradict the currently available data on Elaeis spp. genome sizes, we propose that the actual genome size of the Elaeis species is around 4 pg and that American oil palm possesses a larger genome than African oil palm. PMID:26203259

  15. Comparative genomics of brain size evolution

    OpenAIRE

    Enard, Wolfgang

    2014-01-01

    Which genetic changes took place during mammalian, primate and human evolution to build a larger brain? To answer this question, one has to correlate genetic changes with brain size changes across a phylogeny. Such a comparative genomics approach provides unique information to better understand brain evolution and brain development. However, its statistical power is limited for example due to the limited number of species, the presumably complex genetics of brain size evolution and the large ...

  16. Comparative genomics of brain size evolution

    Directory of Open Access Journals (Sweden)

    Wolfgang Enard

    2014-05-01

    Full Text Available Which genetic changes took place during mammalian, primate and human evolution to build a larger brain? To answer this question, one has to correlate genetic changes with brain size changes across a phylogeny. Such a comparative genomics approach provides unique information to better understand brain evolution and brain development. However, its statistical power is limited for example due to the limited number of species, the presumably complex genetics of brain size evolution and the large search space of mammalian genomes. Hence, it is crucial to add functional information, for example by limiting the search space to genes and regulatory elements known to play a role in the relevant cell types during brain development. Similarly, it is crucial to experimentally follow up on hypotheses generated by such a comparative approach. Recent progress in understanding the molecular and cellular mechanisms of mammalian brain development, in genome sequencing and in genome editing, promises to make a close integration of evolutionary and experimental methods a fruitful approach to better understand the genetics of mammalian brain size evolution.

  17. Experimental Warming Decreases the Average Size and Nucleic Acid Content of Marine Bacterial Communities

    KAUST Repository

    Huete-Stauffer, Tamara M.

    2016-05-23

    Organism size reduction with increasing temperature has been suggested as a universal response to global warming. Since genome size is usually correlated to cell size, reduction of genome size in unicells could be a parallel outcome of warming at ecological and evolutionary time scales. In this study, the short-term response of cell size and nucleic acid content of coastal marine prokaryotic communities to temperature was studied over a full annual cycle at a NE Atlantic temperate site. We used flow cytometry and experimental warming incubations, spanning a 6°C range, to analyze the hypothesized reduction with temperature in the size of the widespread flow cytometric bacterial groups of high and low nucleic acid content (HNA and LNA bacteria, respectively). Our results showed decreases in size in response to experimental warming, which were more marked in 0.8 μm pre-filtered treatment rather than in the whole community treatment, thus excluding the role of protistan grazers in our findings. Interestingly, a significant effect of temperature on reducing the average nucleic acid content (NAC) of prokaryotic cells in the communities was also observed. Cell size and nucleic acid decrease with temperature were correlated, showing a common mean decrease of 0.4% per °C. The usually larger HNA bacteria consistently showed a greater reduction in cell and NAC compared with their LNA counterparts, especially during the spring phytoplankton bloom period associated to maximum bacterial growth rates in response to nutrient availability. Our results show that the already smallest planktonic microbes, yet with key roles in global biogeochemical cycling, are likely undergoing important structural shrinkage in response to rising temperatures.

  18. Experimental Warming Decreases the Average Size and Nucleic Acid Content of Marine Bacterial Communities

    Science.gov (United States)

    Huete-Stauffer, Tamara M.; Arandia-Gorostidi, Nestor; Alonso-Sáez, Laura; Morán, Xosé Anxelu G.

    2016-01-01

    Organism size reduction with increasing temperature has been suggested as a universal response to global warming. Since genome size is usually correlated to cell size, reduction of genome size in unicells could be a parallel outcome of warming at ecological and evolutionary time scales. In this study, the short-term response of cell size and nucleic acid content of coastal marine prokaryotic communities to temperature was studied over a full annual cycle at a NE Atlantic temperate site. We used flow cytometry and experimental warming incubations, spanning a 6°C range, to analyze the hypothesized reduction with temperature in the size of the widespread flow cytometric bacterial groups of high and low nucleic acid content (HNA and LNA bacteria, respectively). Our results showed decreases in size in response to experimental warming, which were more marked in 0.8 μm pre-filtered treatment rather than in the whole community treatment, thus excluding the role of protistan grazers in our findings. Interestingly, a significant effect of temperature on reducing the average nucleic acid content (NAC) of prokaryotic cells in the communities was also observed. Cell size and nucleic acid decrease with temperature were correlated, showing a common mean decrease of 0.4% per °C. The usually larger HNA bacteria consistently showed a greater reduction in cell and NAC compared with their LNA counterparts, especially during the spring phytoplankton bloom period associated to maximum bacterial growth rates in response to nutrient availability. Our results show that the already smallest planktonic microbes, yet with key roles in global biogeochemical cycling, are likely undergoing important structural shrinkage in response to rising temperatures. PMID:27242747

  19. Genome size differences in Hyalella cryptic species.

    Science.gov (United States)

    Vergilino, Roland; Dionne, Kaven; Nozais, Christian; Dufresne, France; Belzile, Claude

    2012-02-01

    The Hyalella azteca (Saussure) complex includes numerous amphipod cryptic species in freshwater habitats in America as revealed by DNA barcoding surveys. Two ecomorphs (small and large) have evolved numerous times in this complex. Few phenotypic criteria have been found to differentiate between the numerous species of this complex. The present study aims to explore genome size differences between some species of the H. azteca complex co-occurring in a Canadian boreal lake using flow cytometry. Nuclear DNA content was estimated for 50 individuals belonging to six COI haplotypes corresponding to four provisional species of the H. azteca complex. Species from the large ecomorph had C-values significantly larger than species from the small ecomorph, whereas slight differences were found among species of the small ecomorph. These differences in genome sizes might be linked to ecological and physiological differences among species of the H. azteca complex. PMID:22263854

  20. Finite genome size can halt Muller's ratchet

    CERN Document Server

    Schoenmeyr, T; Schoenmeyr, Tor; Wilke, Claus O.

    2001-01-01

    We study the accumulation of deleterious mutations in a haploid, asexually reproducing population, using analytical models and computer simulations. We find that Muller's ratchet can come to a halt in small populations as a consequence of a finite genome size only, in the complete absence of backward or compensatory mutations, epistasis, or recombination. The origin of this effect lies in the fact that the number of loci at which mutations can create considerable damage decreases with every turn of the ratchet, while the total number of mutations per genome and generation remains constant. Whether the ratchet will come to a halt eventually depends on the ratio of the per-locus deleterious mutation rate $u$ and the selection strength $s$. For sufficiently small $u/s$, the ratchet halts after only a few clicks. We discuss the implications of our results for bacterial and virus evolution.

  1. Evolution of Genome Size in Asexual Digital Organisms

    Science.gov (United States)

    Gupta, Aditi; LaBar, Thomas; Miyagi, Michael; Adami, Christoph

    2016-01-01

    Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in some amoebas. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as mutation rate and population size. While comparative genomics has uncovered how some of these evolutionary factors influence genome size, we still do not understand what drives genome size evolution. Specifically, it is not clear how the primordial mutational processes of base substitutions, insertions, and deletions influence genome size evolution in asexual organisms. Here, we use digital evolution to investigate genome size evolution by tracking genome edits and their fitness effects in real time. In agreement with empirical data, we find that mutation rate is inversely correlated with genome size in asexual populations. We show that at low point mutation rate, insertions are significantly more beneficial than deletions, driving genome expansion and the acquisition of phenotypic complexity. Conversely, the high mutational load experienced at high mutation rates inhibits genome growth, forcing the genomes to compress their genetic information. Our analyses suggest that the inverse relationship between mutation rate and genome size is a result of the tradeoff between evolving phenotypic innovation and limiting the mutational load. PMID:27181837

  2. Evolution of Genome Size in Asexual Digital Organisms.

    Science.gov (United States)

    Gupta, Aditi; LaBar, Thomas; Miyagi, Michael; Adami, Christoph

    2016-01-01

    Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in some amoebas. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as mutation rate and population size. While comparative genomics has uncovered how some of these evolutionary factors influence genome size, we still do not understand what drives genome size evolution. Specifically, it is not clear how the primordial mutational processes of base substitutions, insertions, and deletions influence genome size evolution in asexual organisms. Here, we use digital evolution to investigate genome size evolution by tracking genome edits and their fitness effects in real time. In agreement with empirical data, we find that mutation rate is inversely correlated with genome size in asexual populations. We show that at low point mutation rate, insertions are significantly more beneficial than deletions, driving genome expansion and the acquisition of phenotypic complexity. Conversely, the high mutational load experienced at high mutation rates inhibits genome growth, forcing the genomes to compress their genetic information. Our analyses suggest that the inverse relationship between mutation rate and genome size is a result of the tradeoff between evolving phenotypic innovation and limiting the mutational load. PMID:27181837

  3. Coevolution between simple sequence repeats (SSRs and virus genome size

    Directory of Open Access Journals (Sweden)

    Zhao Xiangyan

    2012-08-01

    Full Text Available Abstract Background Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes. Results In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome  Conclusions We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree.

  4. Plant genome size variation: bloating and purging DNA.

    Science.gov (United States)

    Michael, Todd P

    2014-07-01

    Plant genome size variation is a dynamic process of bloating and purging DNA. While it was thought plants were on a path to obesity through continual DNA bloating, recent research supports that most plants activity purge DNA. Plant genome size research has greatly benefited from the cataloguing of genome size estimates at the Kew Plant DNA C-values Database, and the recent availability of over 50 fully sequenced and published plant genomes. The emerging trend is that plant genomes bloat due to the copy-and-paste proliferation of a few long terminal repeat retrotransposons (LTRs) and aggressively purge these proliferating LTRs through several mechanisms including illegitimate and incomplete recombination, and double-strand break repair through non-homologous end joining. However, ultra-small genomes such as Utricularia gibba (Bladderwort), which is 82 megabases (Mb), purge excess DNA through genome fractionation and neofunctionalization during multiple rounds of whole genome duplication (WGD). In contrast, the largest published genome, Picea abies (Norway Spruce) at 19 800 Mb, has no detectable WGD but has bloated with diverse and diverged LTRs that either have evaded purging mechanisms or these purging mechanism are absent in gymnosperms. Finally, advances in DNA methylation studies suggest that smaller genomes have a more aggressive epigenomic surveillance system to purge young LTR retrotransposons, which is less active or missing in larger genomes like the bloated gymnosperms. While genome size may not reflect genome complexity, evidence is mounting that genome size may reflect evolutionary status. PMID:24651721

  5. 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

    2016-01-01

    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. PMID:27189987

  6. Analysis of litter size and average litter weight in pigs using a recursive model

    DEFF Research Database (Denmark)

    Varona, Luis; Sorensen, Daniel; Thompson, Robin

    2007-01-01

    An analysis of litter size and average piglet weight at birth in Landrace and Yorkshire using a standard two-trait mixed model (SMM) and a recursive mixed model (RMM) is presented. The RMM establishes a one-way link from litter size to average piglet weight. It is shown that there is a one-to-one...

  7. Why size really matters when sequencing plant genomes

    Czech Academy of Sciences Publication Activity Database

    Kelly, L.J.; Leitch, A.R.; Fay, M. F.; Renny-Byfield, S.; Pellicer, J.; Macas, Jiří; Leitch, I.J.

    2012-01-01

    Roč. 5, č. 4 (2012), s. 415-425. ISSN 1755-0874 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : C-value * genome assembly * genome size evolution * genome sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.924, year: 2012

  8. Sample Size Calculation for Time-Averaged Differences in the Presence of Missing Data

    OpenAIRE

    Zhang, Song; Ahn, Chul

    2012-01-01

    Sample size calculations based on two-sample comparisons of slopes in repeated measurements have been reported by many investigators. In contrast, the literature has paid relatively little attention to the sample size calculations for time-averaged differences in the presence of missing data in repeated measurements studies. Diggle et al. (2002) provided a sample size formula comparing time-averaged differences for continuous outcomes in repeated measurement studies assuming no missing data a...

  9. Chironomid midges (Diptera, chironomidae) show extremely small genome sizes.

    Science.gov (United States)

    Cornette, Richard; Gusev, Oleg; Nakahara, Yuichi; Shimura, Sachiko; Kikawada, Takahiro; Okuda, Takashi

    2015-06-01

    Chironomid midges (Diptera; Chironomidae) are found in various environments from the high Arctic to the Antarctic, including temperate and tropical regions. In many freshwater habitats, members of this family are among the most abundant invertebrates. In the present study, the genome sizes of 25 chironomid species were determined by flow cytometry and the resulting C-values ranged from 0.07 to 0.20 pg DNA (i.e. from about 68 to 195 Mbp). These genome sizes were uniformly very small and included, to our knowledge, the smallest genome sizes recorded to date among insects. Small proportion of transposable elements and short intron sizes were suggested to contribute to the reduction of genome sizes in chironomids. We discuss about the possible developmental and physiological advantages of having a small genome size and about putative implications for the ecological success of the family Chironomidae. PMID:26003979

  10. Waif goodbye! Average-size female models promote positive body image and appeal to consumers.

    Science.gov (United States)

    Diedrichs, Phillippa C; Lee, Christina

    2011-10-01

    Despite consensus that exposure to media images of thin fashion models is associated with poor body image and disordered eating behaviours, few attempts have been made to enact change in the media. This study sought to investigate an effective alternative to current media imagery, by exploring the advertising effectiveness of average-size female fashion models, and their impact on the body image of both women and men. A sample of 171 women and 120 men were assigned to one of three advertisement conditions: no models, thin models and average-size models. Women and men rated average-size models as equally effective in advertisements as thin and no models. For women with average and high levels of internalisation of cultural beauty ideals, exposure to average-size female models was associated with a significantly more positive body image state in comparison to exposure to thin models and no models. For men reporting high levels of internalisation, exposure to average-size models was also associated with a more positive body image state in comparison to viewing thin models. These findings suggest that average-size female models can promote positive body image and appeal to consumers. PMID:21500105

  11. Microeconomic principles explain an optimal genome size in bacteria.

    Science.gov (United States)

    Ranea, Juan A G; Grant, Alastair; Thornton, Janet M; Orengo, Christine A

    2005-01-01

    Bacteria can clearly enhance their survival by expanding their genetic repertoire. However, the tight packing of the bacterial genome and the fact that the most evolved species do not necessarily have the biggest genomes suggest there are other evolutionary factors limiting their genome expansion. To clarify these restrictions on size, we studied those protein families contributing most significantly to bacterial-genome complexity. We found that all bacteria apply the same basic and ancestral 'molecular technology' to optimize their reproductive efficiency. The same microeconomics principles that define the optimum size in a factory can also explain the existence of a statistical optimum in bacterial genome size. This optimum is reached when the bacterial genome obtains the maximum metabolic complexity (revenue) for minimal regulatory genes (logistic cost). PMID:15680509

  12. Evolution of genome size and complexity in Pinus.

    Directory of Open Access Journals (Sweden)

    Alison M Morse

    Full Text Available BACKGROUND: Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea. If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA. CONCLUSIONS/SIGNIFICANCE: Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.

  13. DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size

    Directory of Open Access Journals (Sweden)

    Piontkivska Helen

    2005-02-01

    Full Text Available Abstract Background Birds have smaller average genome sizes than other tetrapod classes, and it has been proposed that a relatively low frequency of repeating DNA is one factor in reduction of avian genome sizes. Results DNA repeat arrays in the sequenced portion of the chicken (Gallus gallus autosomes were quantified and compared with those in human autosomes. In the chicken 10.3% of the genome was occupied by DNA repeats, in contrast to 44.9% in human. In the chicken, the percentage of a chromosome occupied by repeats was positively correlated with chromosome length, but even the largest chicken chromosomes had repeat densities much lower than those in human, indicating that avoidance of repeats in the chicken is not confined to minichromosomes. When 294 simple sequence repeat types shared between chicken and human genomes were compared, mean repeat array length and maximum repeat array length were significantly lower in the chicken than in human. Conclusions The fact that the chicken simple sequence repeat arrays were consistently smaller than arrays of the same type in human is evidence that the reduction in repeat array length in the chicken has involved numerous independent evolutionary events. This implies that reduction of DNA repeats in birds is the result of adaptive evolution. Reduction of DNA repeats on minichromosomes may be an adaptation to permit chiasma formation and alignment of small chromosomes. However, the fact that repeat array lengths are consistently reduced on the largest chicken chromosomes supports the hypothesis that other selective factors are at work, presumably related to the reduction of cell size and consequent advantages for the energetic demands of flight.

  14. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa.

    Science.gov (United States)

    Zaitlin, David; Pierce, Andrew J

    2010-12-01

    The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%-26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine-cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10⁶ base pairs, which is approximately 40% of the previously published estimate. PMID:21164539

  15. Evolutionary Dynamics of Intron Size, Genome Size, and Physiological Correlates in Archosaurs

    OpenAIRE

    Waltari, Eric; Edwards, Scott

    2002-01-01

    It has been proposed that intron and genome sizes in birds are reduced in comparison with mammals because of the metabolic demands of flight. To test this hypothesis, we examined the sizes of 14 introns in a nonflying relative of birds, the American alligator (Alligator mississippiensis), and in 19 flighted and flightless birds in 12 taxonomic orders. Our results indicate that a substantial fraction (66%) of the reduction in intron size as well as in genome size had already occurred in nonfly...

  16. Nuclear Genome Size: Are We Getting Closer?

    Czech Academy of Sciences Publication Activity Database

    Doležel, Jaroslav; Greilhuber, J.

    77A, č. 7 (2010), s. 635-642. ISSN 1552-4922 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : cytometric techniques * reference standards * genome sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.749, year: 2010

  17. Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny.

    Science.gov (United States)

    Clark, James; Hidalgo, Oriane; Pellicer, Jaume; Liu, Hongmei; Marquardt, Jeannine; Robert, Yannis; Christenhusz, Maarten; Zhang, Shouzhou; Gibby, Mary; Leitch, Ilia J; Schneider, Harald

    2016-05-01

    The genome evolution of ferns has been considered to be relatively static compared with angiosperms. In this study, we analyse genome size data and chromosome numbers in a phylogenetic framework to explore three hypotheses: the correlation of genome size and chromosome number, the origin of modern ferns from ancestors with high chromosome numbers, and the occurrence of several whole-genome duplications during the evolution of ferns. To achieve this, we generated new genome size data, increasing the percentage of fern species with genome sizes estimated to 2.8% of extant diversity, and ensuring a comprehensive phylogenetic coverage including at least three species from each fern order. Genome size was correlated with chromosome number across all ferns despite some substantial variation in both traits. We observed a trend towards conservation of the amount of DNA per chromosome, although Osmundaceae and Psilotaceae have substantially larger chromosomes. Reconstruction of the ancestral genome traits suggested that the earliest ferns were already characterized by possessing high chromosome numbers and that the earliest divergences in ferns were correlated with substantial karyological changes. Evidence for repeated whole-genome duplications was found across the phylogeny. Fern genomes tend to evolve slowly, albeit genome rearrangements occur in some clades. PMID:26756823

  18. Correlations between the most developed (G7) countries. A moving average window size optimisation

    CERN Document Server

    Miskiewicz, J; Miskiewicz, Janusz; Ausloos, Marcel

    2005-01-01

    Different distance matrices are defined and applied to look for correlations between the gross domestic product of G7 countries. Results are illustrated through displays obtained from various graph methods. Significant similarities between results are obtained. A procedure for choosing the best distance function is proposed taking into account the size of the window in which correlation are averaged.

  19. Correlations Between the Most Developed (G7) Countries. A Moving Average Window Size Optimisation

    International Nuclear Information System (INIS)

    Different distance matrices are defined and applied to look for correlations between the gross domestic product of G7 countries. Results are illustrated through displays obtained from various graph methods. Significant similarities between results are obtained. A procedure for choosing the best distance function is proposed taking into account the size of the window in which correlations are averaged. (author)

  20. Finite size effects in the averaged eigenvalue density of Wigner random-sign real symmetric matrices

    Science.gov (United States)

    Dhesi, G. S.; Ausloos, M.

    2016-06-01

    Nowadays, strict finite size effects must be taken into account in condensed matter problems when treated through models based on lattices or graphs. On the other hand, the cases of directed bonds or links are known to be highly relevant in topics ranging from ferroelectrics to quotation networks. Combining these two points leads us to examine finite size random matrices. To obtain basic materials properties, the Green's function associated with the matrix has to be calculated. To obtain the first finite size correction, a perturbative scheme is hereby developed within the framework of the replica method. The averaged eigenvalue spectrum and the corresponding Green's function of Wigner random sign real symmetric N ×N matrices to order 1 /N are finally obtained analytically. Related simulation results are also presented. The agreement is excellent between the analytical formulas and finite size matrix numerical diagonalization results, confirming the correctness of the first-order finite size expression.

  1. Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.

    Directory of Open Access Journals (Sweden)

    Soichirou Satoh

    Full Text Available Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.

  2. Genome size estimates for six rust (Pucciniales) species

    OpenAIRE

    Talhinhas, Pedro; Ramos, Ana Paula; Tavares, Daniela; Tavares, Sílvia; Loureiro, João

    2015-01-01

    Rust fungi (Basidiomycota, Pucciniales), one of the largest groups of phytopathogenic organisms, are characterised by host specialisation, biotrophy, complex life cycles and enlarged genomes. In this work we have used flow cytometry to determine the genome size of six rust species, Melampsora pulcherrima, Puccinia behenis, P. cichorii, P. pimpinellae, P. vincae and Uromyces dianthi, the causal agents of rust on Mercurialis annua, Silene latifolia, Cichorium intybus, Pimpinella villos...

  3. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

    2011-04-29

    In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

  4. Size and complexity of the nuclear genome of Colletotrichum graminicola.

    OpenAIRE

    Randhir, R J; Hanau, R M

    1997-01-01

    DNA reassociation was used to estimate GC content, size, and complexity of the nuclear genomes of Colletotrichum from maize and sorghum. Melting-temperature analysis indicated that the GC content of the maize pathotype DNA was 51% and that the GC content of the sorghum pathotype was 52%. DNA reassociation kinetics employing S1 nuclease digestion and an appropriately modified second-order equation indicated that the genome sizes of the maize and sorghum pathotypes were 4.8 x 10(7) bp, and 5.0 ...

  5. Genome size diversity in stingless bees (Hymenoptera: Apidae, Meliponini)

    OpenAIRE

    Tavares, Mara; Carvalho, Carlos de; Soares, Fernanda; Oliveira Campos, Lucio

    2012-01-01

    The first studies on the genome size of stingless bee species showed a range from 0.27 pg (Melipona subnitida and Melipona quadrifasciata) to 1.38 pg (Melipona capixaba). Considering this variation, we quantified the DNA content of 26 species of Meliponini, in order to provide input for future comparative studies in this tribe. Haploid genome size (1C) estimates, using flow cytometry analyses (FCM), ranged from 0.26 ± 0.003 pg (Paratrigona subnuda) to 0.98 ± 0.023 pg (Melipona flavolineata), ...

  6. On the time-averaging of ultrafine particle number size spectra in vehicular plumes

    Directory of Open Access Journals (Sweden)

    X. H. Yao

    2006-01-01

    Full Text Available Ultrafine vehicular particle (<100 nm number size distributions presented in the literature are mostly averages of long scan-time (~30 s or more spectra mainly due to the non-availability of commercial instruments that can measure particle distributions in the <10 nm to 100 nm range faster than 30 s even though individual researchers have built faster (1–2.5 s scanning instruments. With the introduction of the Engine Exhaust Particle Sizer (EEPS in 2004, high time-resolution (1 full 32-channel spectrum per second particle size distribution data become possible and allow atmospheric researchers to study the characteristics of ultrafine vehicular particles in rapidly and perhaps randomly varying high concentration environments such as roadside, on-road and tunnel. In this study, particle size distributions in these environments were found to vary as rapidly as one second frequently. This poses the question on the generality of using averages of long scan-time spectra for dynamic and/or mechanistic studies in rapidly and perhaps randomly varying high concentration environments. One-second EEPS data taken at roadside, on roads and in tunnels by a mobile platform are time-averaged to yield 5, 10, 30 and 120 s distributions to answer this question.

  7. Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    Renata T Souza

    Full Text Available BACKGROUND: The Trypanosoma cruzi genome was sequenced from a hybrid strain (CL Brener. However, high allelic variation and the repetitive nature of the genome have prevented the complete linear sequence of chromosomes being determined. Determining the full complement of chromosomes and establishing syntenic groups will be important in defining the structure of T. cruzi chromosomes. A large amount of information is now available for T. cruzi and Trypanosoma brucei, providing the opportunity to compare and describe the overall patterns of chromosomal evolution in these parasites. METHODOLOGY/PRINCIPAL FINDINGS: The genome sizes, repetitive DNA contents, and the numbers and sizes of chromosomes of nine strains of T. cruzi from four lineages (TcI, TcII, TcV and TcVI were determined. The genome of the TcI group was statistically smaller than other lineages, with the exception of the TcI isolate Tc1161 (José-IMT. Satellite DNA content was correlated with genome size for all isolates, but this was not accompanied by simultaneous amplification of retrotransposons. Regardless of chromosomal polymorphism, large syntenic groups are conserved among T. cruzi lineages. Duplicated chromosome-sized regions were identified and could be retained as paralogous loci, increasing the dosage of several genes. By comparing T. cruzi and T. brucei chromosomes, homologous chromosomal regions in T. brucei were identified. Chromosomes Tb9 and Tb11 of T. brucei share regions of syntenic homology with three and six T. cruzi chromosomal bands, respectively. CONCLUSIONS: Despite genome size variation and karyotype polymorphism, T. cruzi lineages exhibit conservation of chromosome structure. Several syntenic groups are conserved among all isolates analyzed in this study. The syntenic regions are larger than expected if rearrangements occur randomly, suggesting that they are conserved owing to positive selection. Mapping of the syntenic regions on T. cruzi chromosomal bands

  8. Nuclear genome size analysis of Agave tequilana Weber

    Czech Academy of Sciences Publication Activity Database

    Palomino, G.; Doležel, Jaroslav; Méndez, I.; Rubluo, A.

    2003-01-01

    Roč. 56, č. 1 (2003), s. 37-46. ISSN 0008-7114 Grant ostatní: Itálie(IT) Z5038910 Institutional research plan: CEZ:AV0Z5038910 Keywords : Flow cytometry * nuclear genome size * Agave tequilana Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.337, year: 2003

  9. GI Joe or Average Joe? The impact of average-size and muscular male fashion models on men's and women's body image and advertisement effectiveness.

    Science.gov (United States)

    Diedrichs, Phillippa C; Lee, Christina

    2010-06-01

    Increasing body size and shape diversity in media imagery may promote positive body image. While research has largely focused on female models and women's body image, men may also be affected by unrealistic images. We examined the impact of average-size and muscular male fashion models on men's and women's body image and perceived advertisement effectiveness. A sample of 330 men and 289 women viewed one of four advertisement conditions: no models, muscular, average-slim or average-large models. Men and women rated average-size models as equally effective in advertisements as muscular models. For men, exposure to average-size models was associated with more positive body image in comparison to viewing no models, but no difference was found in comparison to muscular models. Similar results were found for women. Internalisation of beauty ideals did not moderate these effects. These findings suggest that average-size male models can promote positive body image and appeal to consumers. PMID:20488770

  10. Sample size for estimating average trunk diameter and plant height in eucalyptus hybrids

    Directory of Open Access Journals (Sweden)

    Alberto Cargnelutti Filho

    2016-01-01

    Full Text Available ABSTRACT: In eucalyptus crops, it is important to determine the number of plants that need to be evaluated for a reliable inference of growth. The aim of this study was to determine the sample size needed to estimate average trunk diameter at breast height and plant height of inter-specific eucalyptus hybrids. In 6,694 plants of twelve inter-specific hybrids it was evaluated trunk diameter at breast height at three (DBH3 and seven years (DBH7 and tree height at seven years (H7 of age. The statistics: minimum, maximum, mean, variance, standard deviation, standard error, and coefficient of variation were calculated. The hypothesis of variance homogeneity was tested. The sample size was determined by re sampling with replacement of 10,000 re samples. There was an increase in the sample size from DBH3 to H7 and DBH7. A sample size of 16, 59 and 31 plants is adequate to estimate DBH3, DBH7 and H7 means, respectively, of inter-specific hybrids of eucalyptus, with amplitude of confidence interval of 95% equal to 20% of the estimated mean.

  11. Genome Size in Diploids, Allopolyploids, and Autopolyploids of Mediterranean Triticeae

    Directory of Open Access Journals (Sweden)

    T. Eilam

    2010-01-01

    Full Text Available Nuclear DNA amount, determined by the flow cytometry method, in diploids, natural and synthetic allopolyploids, and natural and synthetic autopolyploids of the tribe Triticeae (Poaceae is reviewed here and discussed. In contrast to the very small and nonsignificant variation in nuclear DNA amount that was found at the intraspecific level, the variation at the interspecific level is very large. Evidently changes in genome size are either the cause or the result of speciation. Typical autopolyploids had the expected additive DNA amount of their diploid parents, whereas natural and synthetic cytologically diploidized autopolyploids and natural and synthetic allopolyploids had significantly less DNA than the sum of their parents. Thus, genome downsizing, occurring during or immediately after the formation of these polyploids, provides the physical basis for their cytological diploidization, that is, diploid-like meiotic behavior. Possible mechanisms that are involved in genome downsizing and the biological significance of this phenomenon are discussed.

  12. Plant DNA flow cytometry and estimation of nuclear genome size

    Czech Academy of Sciences Publication Activity Database

    Doležel, Jaroslav; Bartoš, Jan

    2005-01-01

    Roč. 95, - (2005), s. 99-110. ISSN 0305-7364 R&D Projects: GA ČR GA522/03/0354; GA ČR GA204/04/1207 Institutional research plan: CEZ:AV0Z50380511 Keywords : flow cytometry * nuclear genome size * DNA C-value Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.665, year: 2005

  13. Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid

    OpenAIRE

    Camillo, Julceia; Leão, André P; Alves, Alexandre A; Formighieri, Eduardo F; Azevedo, Ana LS; Nunes, Juliana D; de Capdeville, Guy; de A Mattos, Jean K; Souza, Manoel T

    2014-01-01

    Aiming at generating a comprehensive genomic database on Elaeis spp., our group is leading several R&D initiatives with Elaeis guineensis (African oil palm) and Elaeis oleifera (American oil palm), including the whole-genome sequencing of the last. Genome size estimates currently available for this genus are controversial, as they indicate that American oil palm genome is about half the size of the African oil palm genome and that the genome of the interspecific hybrid is bigger than both the...

  14. A Running Average Method for Predicting the Size and Length of a Solar Cycle

    Institute of Scientific and Technical Information of China (English)

    Zhan-Le Du; Hua-Ning Wang; Li-Yun Zhang

    2008-01-01

    The running correlation coefficient between the solar cycle amplitudes and the max-max cycle lengths at a given cycle lag is found to vary roughly in a cyclical wave with the cycle number, based on the smoothed monthly mean Group sunspot numbers available since 1610. A running average method is proposed to predict the size and length of a solar cycle by the use of the varying trend of the coefficients. It is found that, when a condition (that the correlation becomes stronger) is satisfied, the mean prediction error (16.1) is much smaller than when the condition is not satisfied (38.7). This result can be explained by the fact that the prediction must fall on the regression line and increase the strength of the correlation. The method itself can also indicate whether the prediction is reasonable or not. To obtain a reasonable prediction, it is more important to search.for a running correlation coefficient whose varying trend satisfies the proposed condition, and the result does not depend so much on the size of the correlation coefficient. As an application, the peak sunspot number of cycle 24 is estimated as 140.4±15.7, and the peak as May 2012± 11 months.

  15. Icelandic Birch Polyploids—The Case of a Perfect Fit in Genome Size

    Directory of Open Access Journals (Sweden)

    K. Anamthawat-Jónsson

    2010-01-01

    Full Text Available Two birch species coexist in Iceland, dwarf birch Betula nana and tree birch B. pubescens. Both species are variable morphologically, which has been shown to be due to introgressive hybridization via interspecific hybrids. The aim of this study was to examine if the introgression could be related to genome size. We characterized 42 plants from Bifröst woodland morphologically and cytogenetically. The population consisted of diploid B. nana (38%, tetraploid B. pubescens (55%, and triploid hybrids (7%. Genome size was measured from 12 plants, using Feulgen DNA image densitometry (FDM on spring leaf buds and flow cytometry (FCM with dormant winter twigs. The use of winter twigs for FCM is novel. The average 1C-values for diploid, triploid, and tetraploid plants were 448, 666, and 882 Mbp, respectively. Monoploid genome sizes were found to be statistically constant among ploidy levels. This stability is in contrast to the different taxonomic positions of the di- and tetraploids and also contrasts with the frequent occurrence of genome downsizing in polyploids.

  16. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies.

    Science.gov (United States)

    Sessegolo, Camille; Burlet, Nelly; Haudry, Annabelle

    2016-08-01

    While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup. PMID:27576524

  17. Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary

    Science.gov (United States)

    Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation...

  18. Population size changes reshape genomic patterns of diversity

    DEFF Research Database (Denmark)

    Pool, John E; Nielsen, Rasmus

    2007-01-01

    Elucidating the forces responsible for genomic variation is critical for understanding evolution. Under standard conditions, X-linked diversity is expected to be three-quarters the level of autosomal diversity. Empirical data often deviate from this prediction, but the reasons for these departures...... are unclear. We demonstrate that population size changes can greatly alter relative levels of X-linked and autosomal variation: population size reductions lead to particularly low X-linked diversity, whereas growth elevates X-linked relative to autosomal diversity. Genetic variation from a diverse...... array of taxa supports an important role for this effect in accounting for population differences in the ratio of X-linked to autosomal diversity. Consideration of this effect may improve the inference of population history and other evolutionary processes....

  19. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity.

    Directory of Open Access Journals (Sweden)

    Lisa L Ellis

    2014-07-01

    Full Text Available We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

  20. Karyotype and genome size in Euterpe Mart. (Arecaceae) species

    Science.gov (United States)

    Oliveira, Ludmila Cristina; de Oliveira, Maria do Socorro Padilha; Davide, Lisete Chamma; Torres, Giovana Augusta

    2016-01-01

    Abstract Euterpe (Martius, 1823), a genus from Central and South America, has species with high economic importance in Brazil, because of their palm heart and fruits, known as açaí berries. Breeding programs have been conducted to increase yield and establish cultivation systems to replace the extraction of wild material. These programs need basic information about the genome of these species to better explore the available genetic variability. The aim of this study was to compare Euterpe edulis (Martius, 1824), Euterpe oleracea (Martius, 1824) and Euterpe precatoria (Martius, 1842), with regard to karyotype, type of interphase nucleus and nuclear DNA amount. Metaphase chromosomes and interphase nuclei from root tip meristematic cells were obtained by the squashing technique and solid stained for microscope analysis. The DNA amount was estimated by flow cytometry. There were previous reports on the chromosome number of Euterpe edulis and Euterpe oleracea, but chromosome morphology of these two species and the whole karyotype of Euterpe precatoria are reported for the first time. The species have 2n=36, a number considered as a pleisomorphic feature in Arecoideae since the modern species, according to floral morphology, have the lowest chromosome number (2n=28 and 2n=30). The three Euterpe species also have the same type of interphase nuclei, classified as semi-reticulate. The species differed on karyotypic formulas, on localization of secondary constriction and genome size. The data suggest that the main forces driving Euterpe karyotype evolution were structural rearrangements, such as inversions and translocations that alter chromosome morphology, and either deletion or amplification that led to changes in chromosome size. PMID:27186334

  1. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae.

    Science.gov (United States)

    Pellicer, Jaume; Kelly, Laura J; Leitch, Ilia J; Zomlefer, Wendy B; Fay, Michael F

    2014-03-01

    • Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes. PMID:24299166

  2. Genome size of human oral Treponema species by pulsed-field gel electrophoresis.

    Science.gov (United States)

    Correia, F F; Plummer, A R; Paster, B J; Dewhirst, F E

    2004-04-01

    The genome sizes of seven strains of oral treponemes were determined using pulsed-field gel electrophoresis (PFGE). These strains represent members from six of the currently known cultivable oral treponeme groups. The PFGE fragments were digitally recorded and then quantitated using GIMP v 1.2, an image manipulation program. The results show that the six oral treponeme genomes are comparable in size, ranging from approximately 2.2 to 2.5 Mbp. The genome sizes of these strains are 20-25% smaller than Treponema denticola strains, which have genome sizes of approximately 2.8-3.0 Mbp. PMID:14871355

  3. The role of size polydispersity in magnetic fluid hyperthermia: average vs. local infra/over-heating effects.

    Science.gov (United States)

    Munoz-Menendez, Cristina; Conde-Leboran, Ivan; Baldomir, Daniel; Chubykalo-Fesenko, Oksana; Serantes, David

    2015-11-01

    An efficient and safe hyperthermia cancer treatment requires the accurate control of the heating performance of magnetic nanoparticles, which is directly related to their size. However, in any particle system the existence of some size polydispersity is experimentally unavoidable, which results in a different local heating output and consequently a different hyperthermia performance depending on the size of each particle. With the aim to shed some light on this significant issue, we have used a Monte Carlo technique to study the role of size polydispersity in heat dissipation at both the local (single particle) and global (macroscopic average) levels. We have systematically varied size polydispersity, temperature and interparticle dipolar interaction conditions, and evaluated local heating as a function of these parameters. Our results provide a simple guide on how to choose, for a given polydispersity degree, the more adequate average particle size so that the local variation in the released heat is kept within some limits that correspond to safety boundaries for the average-system hyperthermia performance. All together we believe that our results may help in the design of more effective magnetic hyperthermia applications. PMID:26437746

  4. Estimating average tree crown size using high-resolution airborne data

    Czech Academy of Sciences Publication Activity Database

    Brovkina, Olga; Latypov, I.; Cienciala, E.

    2015-01-01

    Roč. 9, may 13 (2015), 096053-1-096053-13. ISSN 1931-3195 R&D Projects: GA MŠk(CZ) LO1415; GA MŠk OC09001 Institutional support: RVO:67179843 Keywords : crown size * airborne data * spruce * granulometry Subject RIV: EH - Ecology, Behaviour Impact factor: 1.183, year: 2014

  5. Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

    OpenAIRE

    Baym, Michael; Kryazhimskiy, Sergey; Lieberman, Tami D; Chung, Hattie; Desai, Michael M; Kishony, Roy

    2015-01-01

    Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnec...

  6. Optimal designs of the median run length based double sampling X chart for minimizing the average sample size.

    Directory of Open Access Journals (Sweden)

    Wei Lin Teoh

    Full Text Available Designs of the double sampling (DS X chart are traditionally based on the average run length (ARL criterion. However, the shape of the run length distribution changes with the process mean shifts, ranging from highly skewed when the process is in-control to almost symmetric when the mean shift is large. Therefore, we show that the ARL is a complicated performance measure and that the median run length (MRL is a more meaningful measure to depend on. This is because the MRL provides an intuitive and a fair representation of the central tendency, especially for the rightly skewed run length distribution. Since the DS X chart can effectively reduce the sample size without reducing the statistical efficiency, this paper proposes two optimal designs of the MRL-based DS X chart, for minimizing (i the in-control average sample size (ASS and (ii both the in-control and out-of-control ASSs. Comparisons with the optimal MRL-based EWMA X and Shewhart X charts demonstrate the superiority of the proposed optimal MRL-based DS X chart, as the latter requires a smaller sample size on the average while maintaining the same detection speed as the two former charts. An example involving the added potassium sorbate in a yoghurt manufacturing process is used to illustrate the effectiveness of the proposed MRL-based DS X chart in reducing the sample size needed.

  7. An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies.

    Science.gov (United States)

    Thompson, Wesley K; Wang, Yunpeng; Schork, Andrew J; Witoelar, Aree; Zuber, Verena; Xu, Shujing; Werge, Thomas; Holland, Dominic; Andreassen, Ole A; Dale, Anders M

    2015-12-01

    Characterizing the distribution of effects from genome-wide genotyping data is crucial for understanding important aspects of the genetic architecture of complex traits, such as number or proportion of non-null loci, average proportion of phenotypic variance explained per non-null effect, power for discovery, and polygenic risk prediction. To this end, previous work has used effect-size models based on various distributions, including the normal and normal mixture distributions, among others. In this paper we propose a scale mixture of two normals model for effect size distributions of genome-wide association study (GWAS) test statistics. Test statistics corresponding to null associations are modeled as random draws from a normal distribution with zero mean; test statistics corresponding to non-null associations are also modeled as normal with zero mean, but with larger variance. The model is fit via minimizing discrepancies between the parametric mixture model and resampling-based nonparametric estimates of replication effect sizes and variances. We describe in detail the implications of this model for estimation of the non-null proportion, the probability of replication in de novo samples, the local false discovery rate, and power for discovery of a specified proportion of phenotypic variance explained from additive effects of loci surpassing a given significance threshold. We also examine the crucial issue of the impact of linkage disequilibrium (LD) on effect sizes and parameter estimates, both analytically and in simulations. We apply this approach to meta-analysis test statistics from two large GWAS, one for Crohn's disease (CD) and the other for schizophrenia (SZ). A scale mixture of two normals distribution provides an excellent fit to the SZ nonparametric replication effect size estimates. While capturing the general behavior of the data, this mixture model underestimates the tails of the CD effect size distribution. We discuss the implications of

  8. Genome size variation and polyploidy incidence in the alpine flora from Spain

    OpenAIRE

    Loureiro, João; Castro, Mariana; Cerca de Oliveira, José; Mota, Lucie; Torices, Rubén

    2013-01-01

    The interest to study genome evolution, in particular genome size variation and polyploid incidence, has increased in recent years. Still, only a few studies have been focused at a community level. Of particular interest are high mountain species, because of the high frequency of narrow endemics and their higher susceptibility to extinction due to the effects of climate change. In the present study we explored genome size variation and polyploidy incidence in the entomophilous plant communiti...

  9. Small-Sized Circular Genomes Similar to Genome of Porcine Circovirus 2

    OpenAIRE

    Luo, Wei; Zhao, Dun; Yu, Xing-Long; Ge, Meng; Li, Run-Cheng; Jiang, Da-Liang

    2013-01-01

    Circular genomes smaller than and similar to the genome of porcine circovirus 2 were obtained from pig tissues along with the full-length genome of porcine circovirus 2. The 922-, 839-, and 617-nucleotide-long genomes exhibit high homology to the rep gene plus the origin of replication sequence of porcine circovirus 2.

  10. Photocatalytic performances of BiFeO{sub 3} particles with the average size in nanometer, submicrometer, and micrometer

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Chunxue; FushengWen,, E-mail: wenfsh03@126.com; Xiang, Jianyong; Hou, Hang; Lv, Weiming; Lv, Yifei; Hu, Wentao; Liu, Zhongyuan

    2014-02-01

    Highlights: • Three different synthesis routes have been taken to successfully prepare the BiFeO{sub 3} particles with the different morphologies and average size in 50, 500 nm, and 15 μm. • For photodegradation of dyes under visible irradiation in the presence of BiFeO{sub 3}, the photocatalytic efficiency increases quickly with the decrease in size. • The enhanced photocatalytic efficiency of BiFeO{sub 3} nanoparticles may attribute to more surface active catalytic-sites and shorter distances carriers have to migrate to the surface reaction sites. - Abstract: Three different synthesis routes were taken to successfully prepare the BiFeO{sub 3} particles with the different morphologies and average size in 50, 500 nm, and 15 μm, respectively. The crystal structure was recognized to be a distorted rhombohedral one with the space group R3c. With the decrease in particle size, obvious decrease in peak intensity and redshift in peak position were observed for the Raman active bands. The narrow band gap was determined from the UV–vis absorption spectra, indicating the semiconducting nature of the BiFeO{sub 3}. For photodegradation of dyes under visible irradiation in the presence of BiFeO{sub 3}, the photocatalytic efficiency increased quickly with the decrease in size which may attribute to more surface active catalytic-sites and shorter distances carriers had to migrate to the surface reaction sites.

  11. Nitrogen limitation as a driver of genome size evolution in a group of karst plants

    Science.gov (United States)

    Kang, Ming; Wang, Jing; Huang, Hongwen

    2015-06-01

    Genome size is of fundamental biological importance with significance in predicting structural and functional attributes of organisms. Although abundant evidence has shown that the genome size can be largely explained by differential proliferation and removal of non-coding DNA of the genome, the evolutionary and ecological basis of genome size variation remains poorly understood. Nitrogen (N) and phosphorus (P) are essential elements of DNA and protein building blocks, yet often subject to environmental limitation in natural ecosystems. Using phylogenetic comparative methods, we test this hypothesis by determining whether leaf N and P availability affects genome sizes in 99 species of Primulina (Gesneriaceae), a group of soil specialists adapted to limestone karst environment in south China. We find that genome sizes in Primulina are strongly positively correlated with plant N content, but the correlation with plant P content is not significant when phylogeny history was taken into account. This study shows for the first time that N limitation might have been a plausible driver of genome size variation in a group of plants. We propose that competition for nitrogen nutrient between DNA synthesis and cellular functions is a possible mechanism for genome size evolution in Primulina under N-limitation.

  12. Genome-wide polygenic scoring for a 14-year long-term average depression phenotype

    OpenAIRE

    Chang, Shun-Chiao; Glymour, M. Maria; Walter, Stefan; Liang, Liming; Koenen, Karestan C.; Tchetgen, Eric J; Cornelis, Marilyn C; Kawachi, Ichiro; Rimm, Eric; Kubzansky, Laura D.

    2014-01-01

    Background: Despite moderate heritability estimates for depression-related phenotypes, few robust genetic predictors have been identified. Potential explanations for this discrepancy include the use of phenotypic measures taken from a single time point, rather than integrating information over longer time periods via multiple assessments, and the possibility that genetic risk is shaped by multiple loci with small effects. Methods: We developed a 14-year long-term average depression measure ba...

  13. Genome-wide polygenic scoring for a 14-year long-term average depression phenotype

    OpenAIRE

    Chang, Shun-Chiao; Glymour, M. Maria; Walter, Stefan; Liang, Liming; Koenen, Karestan C.; Tchetgen, Eric J; Cornelis, Marilyn C; Kawachi, Ichiro; Rimm, Eric; Kubzansky, Laura D.

    2014-01-01

    Background Despite moderate heritability estimates for depression-related phenotypes, few robust genetic predictors have been identified. Potential explanations for this discrepancy include the use of phenotypic measures taken from a single time point, rather than integrating information over longer time periods via multiple assessments, and the possibility that genetic risk is shaped by multiple loci with small effects. Methods We developed a 14-year long-term average depression measure base...

  14. Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla.

    Science.gov (United States)

    Li, Xiu-Qing; Du, Donglei

    2014-01-01

    C+G content (GC content or G+C content) is known to be correlated with genome/chromosome size in bacteria but the relationship for other kingdoms remains unclear. This study analyzed genome size, chromosome size, and base composition in most of the available sequenced genomes in various kingdoms. Genome size tends to increase during evolution in plants and animals, and the same is likely true for bacteria. The genomic C+G contents were found to vary greatly in microorganisms but were quite similar within each animal or plant subkingdom. In animals and plants, the C+G contents are ranked as follows: monocot plants>mammals>non-mammalian animals>dicot plants. The variation in C+G content between chromosomes within species is greater in animals than in plants. The correlation between average chromosome C+G content and chromosome length was found to be positive in Proteobacteria, Actinobacteria (but not in other analyzed bacterial phyla), Ascomycota fungi, and likely also in some plants; negative in some animals, insignificant in two protist phyla, and likely very weak in Archaea. Clearly, correlations between C+G content and chromosome size can be positive, negative, or not significant depending on the kingdoms/groups or species. Different phyla or species exhibit different patterns of correlation between chromosome-size and C+G content. Most chromosomes within a species have a similar pattern of variation in C+G content but outliers are common. The data presented in this study suggest that the C+G content is under genetic control by both trans- and cis- factors and that the correlation between C+G content and chromosome length can be positive, negative, or not significant in different phyla. PMID:24551092

  15. The hidden side of plant invasions: the role of genome size.

    Science.gov (United States)

    Suda, Jan; Meyerson, Laura A; Leitch, Ilia J; Pyšek, Petr

    2015-02-01

    The ecological role of genome size in plant biology, biogeography, and morphology has garnered increasing attention as the methods and technology associated with measuring cytological characteristics have become more reliable and accessible. However, how plant genome size influences plant invasions and at what stage in the invasion this influence occurs have been little explored. Several large-scale analyses of published data have yielded valuable interspecific comparisons, but experimental studies that manipulate environmental factors are needed, particularly below the species level, to fully understand the role that genome size plays in plant invasion. In this review, we summarize the available knowledge, discuss the integration of genome size data into invasion research, and suggest how it can be applied to detect and manage invasive species. We also explore how global climate change could exert selective pressures on plant populations with varying genome sizes, thereby increasing the distribution range and invasiveness of some populations while decreasing others. Finally, we outline avenues for future research, including considerations of large-scale studies of intraspecific variation in genome size of invasive populations, testing the interaction of genome size with other factors in macroecological analyses of invasions, as well as the role this trait may play in plant-enemy interactions. PMID:25323486

  16. Inexpensive multiplexed library preparation for megabase-sized genomes.

    Directory of Open Access Journals (Sweden)

    Michael Baym

    Full Text Available Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the standard Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples. Several hundred samples can then be pooled on the same HiSeq lane via custom barcodes. Our method will be useful for re-sequencing of microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples, as well as for other sequencing applications including large amplicon, open chromosome, artificial chromosomes, and RNA sequencing.

  17. Transcriptome and genome size analysis of the venus flytrap

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Vogt, Josef Korbinian; Bressendorff, Simon;

    2015-01-01

    The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin's studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D...

  18. Statistical mechanics of the ``Chinese restaurant process'': Lack of self-averaging, anomalous finite-size effects, and condensation

    Science.gov (United States)

    Bassetti, Bruno; Zarei, Mina; Cosentino Lagomarsino, Marco; Bianconi, Ginestra

    2009-12-01

    The Pitman-Yor, or Chinese restaurant process, is a stochastic process that generates distributions following a power law with exponents lower than 2, as found in numerous physical, biological, technological, and social systems. We discuss its rich behavior with the tools and viewpoint of statistical mechanics. We show that this process invariably gives rise to a condensation, i.e., a distribution dominated by a finite number of classes. We also evaluate thoroughly the finite-size effects, finding that the lack of stationary state and self-averaging of the process creates realization-dependent cutoffs and behavior of the distributions with no equivalent in other statistical mechanical models.

  19. Genome size of termites (Insecta, Dictyoptera, Isoptera) and wood roaches (Insecta, Dictyoptera, Cryptocercidae)

    Science.gov (United States)

    Koshikawa, Shigeyuki; Miyazaki, Satoshi; Cornette, Richard; Matsumoto, Tadao; Miura, Toru

    2008-09-01

    The evolution of genome size has been discussed in relation to the evolution of various biological traits. In the present study, the genome sizes of 22 dictyopteran species were estimated by Feulgen image analysis densitometry and 6-diamidino-2-phenylindole (DAPI)-based flow cytometry. The haploid genome sizes ( C-values) of termites (Isoptera) ranged from 0.58 to 1.90 pg, and those of Cryptocercus wood roaches (Cryptocercidae) were 1.16 to 1.32 pg. Compared to known values of other cockroaches (Blattaria) and mantids (Mantodea), these values are low. A relatively small genome size appears to be a (syn)apomorphy of Isoptera + Cryptocercus, together with their sociality. In some phylogenetic groups, genome size evolution is thought to be influenced by selective pressure on a particular trait, such as cell size or rate of development. The present results raise the possibility that genome size is influenced by selective pressures on traits associated with the evolution of sociality.

  20. Genome size and sequence composition of moso bamboo: A comparative study

    Institute of Scientific and Technical Information of China (English)

    GUI; YiJie; WANG; Sheng; QUAN; LiYan; ZHOU; ChangPing; LONG; ShiBao; ZHENG; HuaJun; JIN; Liang; ZHANG; XianYin

    2007-01-01

    Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo―over two-thirds of the total bamboo forest area―and the highest economic value in China. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize genome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotransposons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to confirm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.

  1. Genome size correlates with growth form, habitat and phylogeny in the Andean genus Lasiocephalus (Asteraceae)

    Czech Academy of Sciences Publication Activity Database

    Dušková, E.; Kolář, Filip; Sklenář, P.; Rauchová, Jana; Kubešová, Magdalena; Fér, T.; Suda, Jan; Marhold, K.

    2010-01-01

    Roč. 82, č. 1 (2010), s. 127-148. ISSN 0032-7786 Institutional research plan: CEZ:AV0Z60050516 Keywords : cytometry * ploidy * genome size Subject RIV: EF - Botanics Impact factor: 2.792, year: 2010

  2. Karyotype and genome size in Euterpe Mart. (Arecaceae) species

    OpenAIRE

    Oliveira,Ludmila Cristina; de Oliveira, Maria do Socorro Padilha; Davide, Lisete Chamma, 1953-; Torres, Giovana Augusta

    2016-01-01

    Abstract Euterpe (Martius, 1823), a genus from Central and South America, has species with high economic importance in Brazil, because of their palm heart and fruits, known as açaí berries. Breeding programs have been conducted to increase yield and establish cultivation systems to replace the extraction of wild material. These programs need basic information about the genome of these species to better explore the available genetic variability. The aim of this study was to compare Euterpe edu...

  3. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

    Directory of Open Access Journals (Sweden)

    Simon Boitard

    2016-03-01

    Full Text Available Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey, PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

  4. Estimation of (co)variances for genomic regions of flexible sizes

    DEFF Research Database (Denmark)

    Sørensen, Lars P; Janss, Luc; Madsen, Per;

    2012-01-01

    part-whole relationship between these traits. The chromosome-wise genomic proportions of the total variance differed between traits, with some chromosomes explaining higher or lower values than expected in relation to chromosome size. Few chromosomes showed pleiotropic effects and only chromosome 19...... used. There was a clear difference in the region-wise patterns of genomic correlation among combinations of traits, with distinctive peaks indicating the presence of pleiotropic QTL. CONCLUSIONS: The results show that it is possible to estimate, genome-wide and region-wise genomic (co)variances of...

  5. Cytogenetic characterization and genome size of the medicinal plant Catharanthus roseus (L.) G. Don

    Science.gov (United States)

    Guimarães, Guilherme; Cardoso, Luísa; Oliveira, Helena; Santos, Conceição; Duarte, Patrícia; Sottomayor, Mariana

    2012-01-01

    Background and aims Catharanthus roseus is a highly valuable medicinal plant producing several terpenoid indole alkaloids (TIAs) with pharmaceutical applications, including the anticancer agents vinblastine and vincristine. Due to the interest in its TIAs, C. roseus is one of the most extensively studied medicinal plants and has become a model species for the study of plant secondary metabolism. However, very little is known about the cytogenetics and genome size of this species, in spite of their importance for breeding programmes, TIA genetics and emerging genomic research. Therefore, the present paper provides a karyotype description and fluorescence in situ hybridization (FISH) data for C. roseus, as well as a rigorous characterization of its genome size. Methodology The organization of C. roseus chromosomes was characterized using several DNA/chromatin staining techniques and FISH of rDNA. Genome size was investigated by flow cytometry using an optimized methodology. Principal results The C. roseus full chromosome complement of 2n = 16 includes two metacentric, four subtelocentric and two telocentric chromosome pairs, with the presence of a single nucleolus organizer region in chromosome 6. An easy and reliable flow cytometry protocol for nuclear genome analysis of C. roseus was optimized, and the C-value of this species was estimated to be 1C = 0.76 pg, corresponding to 738 Mbp. Conclusions The organization and size of the C. roseus genome were characterized, providing an important basis for future studies of this important medicinal species, including further cytogenetic mapping, genomics, TIA genetics and breeding programmes. PMID:22479673

  6. The Cambrian explosion triggered by critical turning point in genome size evolution.

    Science.gov (United States)

    Li, Dirson Jian; Zhang, Shengli

    2010-02-01

    The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conflicts on nature and timing of metazoan origins. The crux of the matter is that an entire roadmap of the evolution is missing to discern the biological complexity transition and to evaluate the critical role of the Cambrian explosion in the overall evolutionary context. Here, we calculate the time of the Cambrian explosion by a "C-value clock"; our result quite fits the fossil records. We clarify that the intrinsic reason of genome evolution determined the Cambrian explosion. A general formula for evaluating genome size of different species has been found, by which the genome size evolution can be illustrated. The Cambrian explosion, as a major transition of biological complexity, essentially corresponds to a critical turning point in genome size evolution. PMID:20074549

  7. Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta

    Directory of Open Access Journals (Sweden)

    von Dassow Peter

    2010-01-01

    Full Text Available Abstract Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2 possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1. The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is

  8. Evaluation of the mobile content in Magnetospirillum magneticum AMB-1 genome using bioinformatical approaches reveals a new genome size for the magnetosome island

    OpenAIRE

    Ali Bin Thani; Essam Ghanem; Mohamed Bououdina; Salwa Al-Thawadi; Ahmed Al-Saie; Suad Rashdan

    2015-01-01

    After completing its sequence/annotation in 2005, Magnetospirillum magneticum AMB-1 had become one of the most important magnetotactic genomes used to facilitate analysis of the magnetosome formation process. In this paper we investigate the genome contents of AMB-1 and other magnetotactic bacteria to demonstrate the size of mobile genome and number of conserved genes in M. magneticum AMB-1. The preliminary analysis presented here shows the mosaic structure of these genomes. 100 genomic islan...

  9. Intra-event isotope and raindrop size data of tropical rain reveal effects concealed by event averaged data

    Science.gov (United States)

    Managave, S. R.; Jani, R. A.; Narayana Rao, T.; Sunilkumar, K.; Satheeshkumar, S.; Ramesh, R.

    2016-08-01

    Evaporation of rain is known to contribute water vapor, a potent greenhouse gas, to the atmosphere. Stable oxygen and hydrogen isotopic compositions (δ18O and, δD, respectively) of precipitation, usually measured/presented as values integrated over rain events or monthly mean values, are important tools for detecting evaporation effects. The slope ~8 of the linear relationship between such time-averaged values of δD and δ18O (called the meteoric water line) is widely accepted as a proof of condensation under isotopic equilibrium and absence of evaporation of rain during atmospheric fall. Here, through a simultaneous investigation of the isotopic and drop size distributions of seventeen rain events sampled on an intra-event scale at Gadanki (13.5°N, 79.2°E), southern India, we demonstrate that the evaporation effects, not evident in the time-averaged data, are significantly manifested in the sub-samples of individual rain events. We detect this through (1) slopes significantly less than 8 for the δD-δ18O relation on intra-event scale and (2) significant positive correlations between deuterium excess ( d-excess = δD - 8*δ18O; lower values in rain indicate evaporation) and the mass-weighted mean diameter of the raindrops ( D m ). An estimated ~44 % of rain is influenced by evaporation. This study also reveals a signature of isotopic equilibration of rain with the cloud base vapor, the processes important for modeling isotopic composition of precipitation. d-excess values of rain are modified by the post-condensation processes and the present approach offers a way to identify the d-excess values least affected by such processes. Isotope-enabled global circulation models could be improved by incorporating intra-event isotopic data and raindrop size dependent isotopic effects.

  10. Intra-event isotope and raindrop size data of tropical rain reveal effects concealed by event averaged data

    Science.gov (United States)

    Managave, S. R.; Jani, R. A.; Narayana Rao, T.; Sunilkumar, K.; Satheeshkumar, S.; Ramesh, R.

    2015-11-01

    Evaporation of rain is known to contribute water vapor, a potent greenhouse gas, to the atmosphere. Stable oxygen and hydrogen isotopic compositions (δ18O and, δD, respectively) of precipitation, usually measured/presented as values integrated over rain events or monthly mean values, are important tools for detecting evaporation effects. The slope ~8 of the linear relationship between such time-averaged values of δD and δ18O (called the meteoric water line) is widely accepted as a proof of condensation under isotopic equilibrium and absence of evaporation of rain during atmospheric fall. Here, through a simultaneous investigation of the isotopic and drop size distributions of seventeen rain events sampled on an intra-event scale at Gadanki (13.5°N, 79.2°E), southern India, we demonstrate that the evaporation effects, not evident in the time-averaged data, are significantly manifested in the sub-samples of individual rain events. We detect this through (1) slopes significantly less than 8 for the δD-δ18O relation on intra-event scale and (2) significant positive correlations between deuterium excess (d-excess = δD - 8*δ18O; lower values in rain indicate evaporation) and the mass-weighted mean diameter of the raindrops (D m ). An estimated ~44 % of rain is influenced by evaporation. This study also reveals a signature of isotopic equilibration of rain with the cloud base vapor, the processes important for modeling isotopic composition of precipitation. d-excess values of rain are modified by the post-condensation processes and the present approach offers a way to identify the d-excess values least affected by such processes. Isotope-enabled global circulation models could be improved by incorporating intra-event isotopic data and raindrop size dependent isotopic effects.

  11. The Influence of Genome and Cell Size on Brain Morphology in Amphibians.

    Science.gov (United States)

    Roth, Gerhard; Walkowiak, Wolfgang

    2015-09-01

    In amphibians, nerve cell size is highly correlated with genome size, and increases in genome and cell size cause a retardation of the rate of development of nervous (as well as nonnervous) tissue leading to secondary simplification. This yields an inverse relationship between genome and cell size on the one hand and morphological complexity of the tectum mesencephali as the main visual center, the size of the torus semicircularis as the main auditory center, the size of the amphibian papilla as an important peripheral auditory structure, and the size of the cerebellum as a major sensorimotor center. Nervous structures developing later (e.g., torus and cerebellum) are more affected by secondary simplification than those that develop earlier (e.g., the tectum). This effect is more prominent in salamanders and caecilians than in frogs owing to larger genome and cells sizes in the former two taxa. We hypothesize that because of intragenomic evolutionary processes, important differences in brain morphology can arise independently of specific environmental selection. PMID:26261281

  12. Identifying parental chromosomes and genomic rearrangements in animal hybrid complexes of species with small genome size using Genomic In Situ Hybridization (GISH

    Directory of Open Access Journals (Sweden)

    Massimiliano Rampin

    2012-09-01

    Full Text Available Genomic In Situ Hybridization (GISH, a powerful tool to identify and to quantify genomic constituents in allopolyploids, has been widely used in plants but not in animals mainly due to technical problems in obtaining informative results. Using the allopolyploid Squalius alburnoides fish complex as a model system, we succeeded in overcoming methodological constraints when dealing with parental species with a small genome size. This hybridogenetic complex has biotypes with different genome compositions and ploidy levels, but parental chromosomes are small, morphologically very similar and therefore cannot be distinguished by conventional cytogenetic approaches. Specimens have a small genome (C-value = 1.2 pg with a low level of highly and moderate repetitive sequences, mainly located at pericentromeric chromosome regions. Since it is well known that probe annealing depends on probe concentration and hybridization time to obtain uniform hybridization signals along the chromosome arms, we progressively increased the amount of labeled probes from 100ng up to 1µg per slide and the incubation time from overnight up to 72 h, among other minor improvements. Results showed a clear enhancement of signals with respect to previous data, allowing an accurate and reproducible assignment of the parental genomes in both diploid and triploid fish. It was thus evidenced that high probes’ concentrations and long incubation time are the key to obtain, without extra image editing, uniform and reliable hybridization signals in metaphase chromosomes of hybrid fish even involving parental species with small genome size.

  13. Viral genome size distribution does not correlate with the antiquity of the host lineages

    Directory of Open Access Journals (Sweden)

    José Alberto Campillo-Balderas

    2015-12-01

    Full Text Available It has been suggested that RNA viruses and other subcellular entities endowed with RNA genomes are relicts from an ancient RNA/protein World which is believed to have preceded extant DNA/RNA/protein-based cells. According to their proponents, this possibility is supported by the small-genome sizes of RNA viruses and their manifold replication strategies, which have been interpreted as the result of an evolutionary exploration of different alternative genome organizations and replication strategies during early evolutionary stages. At the other extreme are the giant DNA viruses, whose genome sizes can be as large as those of some prokaryotes, and which have been grouped by some authors into a fourth domain of life. As argued here, the comparative analysis of the chemical nature and sizes of the viral genomes reported in GenBank does not reveal any obvious correlation with the phylogenetic history of their hosts. Accordingly, it is somewhat difficult to reconcile the proposal of the putative pre-DNA antiquity of RNA viruses, with their extraordinary diversity in plant hosts and their apparent absence among the Archaea. Other issues related to the genome size of all known viruses and subviral agents and the relationship with their hosts are discussed.

  14. Genome size of Alexandrium catenella and Gracilariopsis lemaneiformis estimated by flow cytometry

    Science.gov (United States)

    Du, Qingwei; Sui, Zhenghong; Chang, Lianpeng; Wei, Huihui; Liu, Yuan; Mi, Ping; Shang, Erlei; Zeeshan, Niaz; Que, Zhou

    2016-08-01

    Flow cytometry (FCM) technique has been widely applied to estimating the genome size of various higher plants. However, there is few report about its application in algae. In this study, an optimized procedure of FCM was exploited to estimate the genome size of two eukaryotic algae. For analyzing Alexandrium catenella, an important red tide species, the whole cell instead of isolated nucleus was studied, and chicken erythrocytes were used as an internal reference. The genome size of A. catenella was estimated to be 56.48 ± 4.14 Gb (1C), approximately nineteen times larger than that of human genome. For analyzing Gracilariopsis lemaneiformis, an important economical red alga, the purified nucleus was employed, and Arabidopsis thaliana and Chondrus crispus were used as internal references, respectively. The genome size of Gp. lemaneiformis was 97.35 ± 2.58 Mb (1C) and 112.73 ± 14.00 Mb (1C), respectively, depending on the different internal references. The results of this research will promote the related studies on the genomics and evolution of these two species.

  15. Genome-wide patterns of large-size presence/absence variants in sorghum

    Institute of Scientific and Technical Information of China (English)

    LiMin Zhang; Hong Luo; ZhiQuan Liu; Yi Zhao; JingChu Luo; DongYun Hao; HaiChun Jing

    2014-01-01

    The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum (Sorghum bicolour L.) genomes, each 12? coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30 kb) PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96 sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.

  16. Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

    Czech Academy of Sciences Publication Activity Database

    Vu, G.T.H.; Schmutzer, T.; Bull, F.; Cao, H.X.; Fuchs, J.; Tran, T.D.; Jovtchev, G.; Pistrick, K.; Stein, N.; Pečinka, A.; Neumann, Pavel; Novák, Petr; Macas, Jiří; Dear, P.H.; Blattner, F.R.; Scholz, U.; Schubert, I.

    2015-01-01

    Roč. 8, č. 3 (2015). ISSN 1940-3372 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Genlisea * genome * repetitive sequences Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.933, year: 2014

  17. Effect of particle size on the average heat-transfer rate from a cylinder in a liquid-penetrated granular bed

    Science.gov (United States)

    Baluev, V. V.; Rzaev, A. I.

    1992-08-01

    Experimental results on the average heat transfer from a cylinder in a liquid-penetrated granular bed are presented and the dependence of the heat transfer rate on the particle size in the bed is found.

  18. Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken

    OpenAIRE

    Kasai, Fumio; O'Brien, Patricia C. M.; Ferguson-Smith, Malcolm A

    2012-01-01

    The genome size in turtles and crocodiles is thought to be much larger than the 1.2 Gb of the chicken (Gallus gallus domesticus, GGA), according to the animal genome size database. However, GGA macrochromosomes show extensive homology in the karyotypes of the red eared slider (Trachemys scripta elegans, TSC) and the Nile crocodile (Crocodylus niloticus, CNI), and bird and reptile genomes have been highly conserved during evolution. In this study, size and GC content of all chromosomes are mea...

  19. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments.

    Science.gov (United States)

    Bentkowski, Piotr; Van Oosterhout, Cock; Mock, Thomas

    2015-08-01

    Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt. PMID:26242601

  20. Exploring Diversification and Genome Size Evolution in Extant Gymnosperms through Phylogenetic Synthesis

    Directory of Open Access Journals (Sweden)

    J. Gordon Burleigh

    2012-01-01

    Full Text Available Gymnosperms, comprising cycads, Ginkgo, Gnetales, and conifers, represent one of the major groups of extant seed plants. Yet compared to angiosperms, little is known about the patterns of diversification and genome evolution in gymnosperms. We assembled a phylogenetic supermatrix containing over 4.5 million nucleotides from 739 gymnosperm taxa. Although 93.6% of the cells in the supermatrix are empty, the data reveal many strongly supported nodes that are generally consistent with previous phylogenetic analyses, including weak support for Gnetales sister to Pinaceae. A lineage through time plot suggests elevated rates of diversification within the last 100 million years, and there is evidence of shifts in diversification rates in several clades within cycads and conifers. A likelihood-based analysis of the evolution of genome size in 165 gymnosperms finds evidence for heterogeneous rates of genome size evolution due to an elevated rate in Pinus.

  1. The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae)

    Czech Academy of Sciences Publication Activity Database

    Leitch, I.J.; Hanson, L.; Lim, K.Y.; Kovařík, Aleš; Chase, M.W.; Clarkson, J.J.; Leitch, A.R.

    2008-01-01

    Roč. 101, č. 6 (2008), s. 805-814. ISSN 0305-7364 R&D Projects: GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : genome size * allopolyploidy * evolution-Nicotiana Subject RIV: BO - Biophysics Impact factor: 2.755, year: 2008

  2. Genome size and phenotypic variation of Nymphaea (Nymphaeaceae) species from Eastern Europe and temperate Asia

    Czech Academy of Sciences Publication Activity Database

    Dąbrowska, M. A.; Rola, K.; Volkova, P.; Suda, Jan; Zalewska-Gałosz, J.

    2015-01-01

    Roč. 84, č. 2 (2015), s. 277-286. ISSN 0001-6977 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : flow cytometry * genome size * morphometrics Subject RIV: EF - Botanics Impact factor: 1.174, year: 2014

  3. On the need for widespread horizontal gene transfers under genome size constraint

    Directory of Open Access Journals (Sweden)

    Stein Richard R

    2009-08-01

    Full Text Available Abstract Background While eukaryotes primarily evolve by duplication-divergence expansion (and reduction of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. Hypothesis We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i their apparent genome size constraint compared to typical eukaryote genomes and ii their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. Implications This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene

  4. Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum.

    Science.gov (United States)

    Bourne, Elizabeth C; Mina, Diogo; Gonçalves, Susana C; Loureiro, João; Freitas, Helena; Muller, Ludo A H

    2014-01-01

    Estimations of genome size and its variation can provide valuable information regarding the genetic diversity of organisms and their adaptation potential to heterogeneous environments. We used flow cytometry to characterize the variation in genome size among 40 isolates of Cenococcum geophilum, an ectomycorrhizal fungus with a wide ecological and geographical distribution, obtained from two serpentine and two non-serpentine sites in Portugal. Besides determining the genome size and its intraspecies variation, we wanted to assess whether a relationship exists between genome size and the edaphic background of the C. geophilum isolates. Our results reveal C. geophilum to have one of the largest genome sizes so far measured in the Ascomycota, with a mean haploid genome size estimate of 0.208 pg (203 Mbp). However, no relationship was found between genome size and the edaphic background of the sampled isolates, indicating genetic and demographic processes to be more important for shaping the genome size variation in this species than environmental selection. The detection of variation in ploidy level among our isolates, including a single individual with both presumed haploid and diploid nuclei, provides supportive evidence for a possible cryptic sexual or parasexual cycle in C. geophilum (although other mechanisms may have caused this variation). The existence of such a cycle would have wide significance, explaining the high levels of genetic diversity and likelihood of recombination previously reported in this species, and adds to the increasing number of studies suggesting sexual cycles in previously assumed asexual fungi. PMID:23754539

  5. Multi-beam raindrop size distributions retrievals on the Doppler spectra: Influence of averaging and mean horizontal wind correction

    OpenAIRE

    Unal, C.M.H.

    2012-01-01

    Acquiring the raindrop size distribution (DSD) from radar data is still a challenge. For profiling radar, this distribution can be estimated from the Doppler spectra. However the Doppler spectrum is not a direct measure of the DSD. The radial component of the wind shifts the Doppler spectrum related to the raindrop size distribution along the Doppler velocity interval. Furthermore, the Doppler spectrum may be broadened by turbulence effect. The Doppler spectra of rain are modelled using Rayle...

  6. Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction

    Directory of Open Access Journals (Sweden)

    Rensing Stephan

    2011-05-01

    Full Text Available Abstract Background The purpose of this work was to study the impact of both the size of genomic reference populations and the inclusion of a residual polygenic effect on dairy cattle genetic evaluations enhanced with genomic information. Methods Direct genomic values were estimated for German Holstein cattle with a genomic BLUP model including a residual polygenic effect. A total of 17,429 genotyped Holstein bulls were evaluated using the phenotypes of 44 traits. The Interbull genomic validation test was implemented to investigate how the inclusion of a residual polygenic effect impacted genomic estimated breeding values. Results As the number of reference bulls increased, both the variance of the estimates of single nucleotide polymorphism effects and the reliability of the direct genomic values of selection candidates increased. Fitting a residual polygenic effect in the model resulted in less biased genome-enhanced breeding values and decreased the correlation between direct genomic values and estimated breeding values of sires in the reference population. Conclusions Genetic evaluation of dairy cattle enhanced with genomic information is highly effective in increasing reliability, as well as using large genomic reference populations. We found that fitting a residual polygenic effect reduced the bias in genome-enhanced breeding values, decreased the correlation between direct genomic values and sire's estimated breeding values and made genome-enhanced breeding values more consistent in mean and variance as is the case for pedigree-based estimated breeding values.

  7. Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses.

    Science.gov (United States)

    Chen, Wenbo; Hasegawa, Daniel K; Arumuganathan, Kathiravetpillai; Simmons, Alvin M; Wintermantel, William M; Fei, Zhangjun; Ling, Kai-Shu

    2015-01-01

    Whiteflies of the Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species complex are among the most important agricultural insect pests in the world. These phloem-feeding insects can colonize over 1000 species of plants worldwide and inflict severe economic losses to crops, mainly through the transmission of pathogenic viruses. Surprisingly, there is very little genomic information about whiteflies. As a starting point to genome sequencing, we report a new estimation of the genome size of the B. tabaci B biotype or Middle East-Asia Minor 1 (MEAM1) population. Using an isogenic whitefly colony with over 6500 haploid male individuals for genomic DNA, three paired-end genomic libraries with insert sizes of ~300 bp, 500 bp and 1 Kb were constructed and sequenced on an Illumina HiSeq 2500 system. A total of ~50 billion base pairs of sequences were obtained from each library. K-mer analysis using these sequences revealed that the genome size of the whitefly was ~682.3 Mb. In addition, the flow cytometric analysis estimated the haploid genome size of the whitefly to be ~690 Mb. Considering the congruency between both estimation methods, we predict the haploid genome size of B. tabaci MEAM1 to be ~680-690 Mb. Our data provide a baseline for ongoing efforts to assemble and annotate the B. tabaci genome. PMID:26463411

  8. Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses

    Directory of Open Access Journals (Sweden)

    Wenbo Chen

    2015-07-01

    Full Text Available Whiteflies of the Bemisia tabaci (Hemiptera: Aleyrodidae cryptic species complex are among the most important agricultural insect pests in the world. These phloem-feeding insects can colonize over 1000 species of plants worldwide and inflict severe economic losses to crops, mainly through the transmission of pathogenic viruses. Surprisingly, there is very little genomic information about whiteflies. As a starting point to genome sequencing, we report a new estimation of the genome size of the B. tabaci B biotype or Middle East-Asia Minor 1 (MEAM1 population. Using an isogenic whitefly colony with over 6500 haploid male individuals for genomic DNA, three paired-end genomic libraries with insert sizes of ~300 bp, 500 bp and 1 Kb were constructed and sequenced on an Illumina HiSeq 2500 system. A total of ~50 billion base pairs of sequences were obtained from each library. K-mer analysis using these sequences revealed that the genome size of the whitefly was ~682.3 Mb. In addition, the flow cytometric analysis estimated the haploid genome size of the whitefly to be ~690 Mb. Considering the congruency between both estimation methods, we predict the haploid genome size of B. tabaci MEAM1 to be ~680–690 Mb. Our data provide a baseline for ongoing efforts to assemble and annotate the B. tabaci genome.

  9. Leveraging wall-sized high-resolution displays for comparative genomics analyses of copy number variation

    OpenAIRE

    Ruddle, RA; Fateen, W; Treanor, D; Quirke, P.; Sondergeld, P

    2013-01-01

    The scale of comparative genomics data frequently overwhelms current data visualization methods on conventional (desktop) displays. This paper describes two types of solution that take advantage of wall-sized high-resolution displays (WHirDs), which have orders of magnitude more display real estate (i.e., pixels) than desktop displays. The first allows users to view detailed graphics of copy number variation (CNV) that were output by existing software. A WHirD's resolution allowed a 10× incre...

  10. Cytogenetic characterization and genome size of the medicinal plant Catharanthus roseus (L.) G. Don

    OpenAIRE

    Guimarães, Guilherme; Cardoso, Luísa; Oliveira, Helena; Santos, Conceição; Duarte, Patrícia; Sottomayor, Mariana

    2012-01-01

    Background and aims Catharanthus roseus is a highly valuable medicinal plant producing several terpenoid indole alkaloids (TIAs) with pharmaceutical applications, including the anticancer agents vinblastine and vincristine. Due to the interest in its TIAs, C. roseus is one of the most extensively studied medicinal plants and has become a model species for the study of plant secondary metabolism. However, very little is known about the cytogenetics and genome size of this species, in spite of ...

  11. Insights into the dynamics of genome size and chromosome evolution in the early diverging angiosperm lineage Nymphaeales (water lilies).

    Science.gov (United States)

    Pellicer, J; Kelly, L J; Magdalena, C; Leitch, I J

    2013-08-01

    Nymphaeales are the most species-rich lineage of the earliest diverging angiosperms known as the ANA grade (Amborellales, Nymphaeales, Austrobaileyales), and they have received considerable attention from morphological, physiological, and ecological perspectives. Although phylogenetic relationships between these three lineages of angiosperms are mainly well resolved, insights at the whole genome level are still limited because of a dearth of information. To address this, genome sizes and chromosome numbers in 34 taxa, comprising 28 species were estimated and analysed together with previously published data to provide an overview of genome size and chromosome diversity in Nymphaeales. Overall, genome sizes were shown to vary 10-fold and chromosome numbers and ploidy levels ranged from 2n = 2x = 18 to 2n = 16x = ∼224. Distinct patterns of genome diversity were apparent, reflecting the differential incidence of polyploidy, changes in repetitive DNA content, and chromosome rearrangements within and between genera. Using model-based approaches, ancestral genome size and basic chromosome numbers were reconstructed to provide insights into the dynamics of genome size and chromosome number evolution. Finally, by combining additional data from Amborellales and Austrobaileyales, a comprehensive overview of genome sizes and chromosome numbers in these early diverging angiosperms is presented. PMID:24168627

  12. Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken.

    Science.gov (United States)

    Kasai, Fumio; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A

    2012-08-23

    The genome size in turtles and crocodiles is thought to be much larger than the 1.2 Gb of the chicken (Gallus gallus domesticus, GGA), according to the animal genome size database. However, GGA macrochromosomes show extensive homology in the karyotypes of the red eared slider (Trachemys scripta elegans, TSC) and the Nile crocodile (Crocodylus niloticus, CNI), and bird and reptile genomes have been highly conserved during evolution. In this study, size and GC content of all chromosomes are measured from the flow karyotypes of GGA, TSC and CNI. Genome sizes estimated from the total chromosome size demonstrate that TSC and CNI are 1.21 Gb and 1.29 Gb, respectively. This refines previous overestimations and reveals similar genome sizes in chicken, turtle and crocodile. Analysis of chromosome GC content in each of these three species shows a higher GC content in smaller chromosomes than in larger chromosomes. This contrasts with mammals and squamates in which GC content does not correlate with chromosome size. These data suggest that a common ancestor of birds, turtles and crocodiles had a small genome size and a chromosomal size-dependent GC bias, distinct from the squamate lineage. PMID:22491763

  13. Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species

    Science.gov (United States)

    Herben, Tomáš; Suda, Jan; Klimešová, Jitka; Mihulka, Stanislav; Říha, Pavel; Šímová, Irena

    2012-01-01

    Background and Aims Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate. Methods Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis. Key Results Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R2 = 0·145) than for perennials (R2 = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance. Conclusions The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes. PMID:22628380

  14. Genome Size Study in the Valerianaceae: First Results and New Hypotheses

    Directory of Open Access Journals (Sweden)

    Oriane Hidalgo

    2010-01-01

    Full Text Available The purpose of this study is to provide a new focus to contribute, from the perspective of genomic evolution, towards a better understanding of the Valerianaceae evolutionary history. Chromosome numbers were determined by Feulgen staining in 24 populations of 18 species (first count for Valerianella multidentata, 2n=2x=14–16, and DNA contents were assessed by flow cytometry in 74 populations of 35 species (first assessments in all taxa but Centranthus ruber. A molecular phylogeny based on the trnL-trnF and including 41 new sequences was established, with the first DNA sequence for Centranthus nevadensis, Valeriana rotundifolia, V. saxatilis, Valerianella multidentata, and V. turgida. This work is the first large genome size study devoted to the Valerianaceae, showing a range of DNA amounts from 2C=0.39 pg (Valerianella turgida to 2C=8.32 pg (Valeriana officinalis. At the family level, changes in basic chromosome number and genome size coincide with or precede major shifts in the evolutionary history of the group, such as those concerning stamen number and floral symmetry.

  15. On Size and Shape of the Average Meson Fields in the Semibosonized Nambu & Jona-Lasinio Model

    CERN Document Server

    Wünsch, R; Meissner, T; Meissner, Th.

    1994-01-01

    We consider a two-flavor Nambu \\& Jona-Lasinio model in Hartree approximation involving scalar-isoscalar and pseudoscalar-isovector quark-quark interactions. Average meson fields are defined by minimizing the effective Euklidean action. The fermionic part of the action, which contains the full Dirac sea, is regularized within Schwinger's proper-time scheme. The meson fields are restricted to the chiral circle and to hedgehog configurations. The only parameter of the model is the constituent quark mass $M$ which simultaneously controls the regularization. We evaluate meson and quark fields self-consistently in dependence on the constituent quark mass. It is shown that the self-consistent fields do practically not depend on the constituent quark mass. This allows us to define a properly parameterized reference field which for physically relevant constituent masses can be used as a good approximation to the exactly calculated one. The reference field is chosen to have correct behaviour for small and large ra...

  16. Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses

    OpenAIRE

    Wenbo Chen; Hasegawa, Daniel K.; Kathiravetpillai Arumuganathan; Simmons, Alvin M.; Wintermantel, William M.; Zhangjun Fei; Kai-Shu Ling

    2015-01-01

    Whiteflies of the Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species complex are among the most important agricultural insect pests in the world. These phloem-feeding insects can colonize over 1000 species of plants worldwide and inflict severe economic losses to crops, mainly through the transmission of pathogenic viruses. Surprisingly, there is very little genomic information about whiteflies. As a starting point to genome sequencing, we report a new estimation of the genome size of ...

  17. An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies

    DEFF Research Database (Denmark)

    Thompson, Wesley K.; Wang, Yunpeng; Schork, Andrew J.;

    2015-01-01

    -wide association study (GWAS) test statistics. Test statistics corresponding to null associations are modeled as random draws from a normal distribution with zero mean; test statistics corresponding to non-null associations are also modeled as normal with zero mean, but with larger variance. The model is fit via...... discovery, and polygenic risk prediction. To this end, previous work has used effect-size models based on various distributions, including the normal and normal mixture distributions, among others. In this paper we propose a scale mixture of two normals model for effect size distributions of genome...... minimizing discrepancies between the parametric mixture model and resampling-based nonparametric estimates of replication effect sizes and variances. We describe in detail the implications of this model for estimation of the non-null proportion, the probability of replication in de novo samples, the local...

  18. Standard practice for determining average grain size using electron backscatter diffraction (EBSD) in fully recrystallized polycrystalline materials

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2010-01-01

    1.1 This practice is used to determine grain size from measurements of grain areas from automated electron backscatter diffraction (EBSD) scans of polycrystalline materials. 1.2 The intent of this practice is to standardize operation of an automated EBSD instrument to measure ASTM G directly from crystal orientation. The guidelines and caveats of E112 apply here, but the focus of this standard is on EBSD practice. 1.3 This practice is only applicable to fully recrystallized materials. 1.4 This practice is applicable to any crystalline material which produces EBSD patterns of sufficient quality that a high percentage of the patterns can be reliably indexed using automated indexing software. 1.5 The practice is applicable to any type of grain structure or grain size distribution. 1.6 The values stated in SI units are to be regarded as standard. No other units of measurement are included in this standard. 1.7 The values stated in inch-pound units are to be regarded as standard. The values given in parenthe...

  19. A simple model for the size and shape dependent Curie temperature of freestanding Ni and Fe nanoparticles based on the average coordination number and atomic cohesive energy

    International Nuclear Information System (INIS)

    Graphical abstract: To study the effect of size and shape of metallic nanoparticle on their Curie temperature of FCC (Fig. A) and BCC clusters (Fig. B), an analytical model is proposed. When variable core coordination number is utilised, a low Curie temperature is observed at a critical cluster size of 2-3 nm in good agreement with experimental results. This critical diameter corresponds to the 50% fractional surface atoms. Display Omitted Highlights: → The Curie temperature (TC) of freestanding Ni and Fe nanoparticles have been examined. → The average coordination number as a geometrical parameter has been considered. → It is found that for even smaller particles, the Curie temperature actually increases. - Abstract: To study the effect of size and shape of metallic nanoparticle on their Curie temperature, an analytical model is proposed. The core average coordination number (CAC) and surface average coordination number (SAC) of freestanding nanoparticles are considered in the model. Clusters of icosahedral (IC) and body centred cubic (BCC) structure without any vacancies and defects are modelled. A critical Curie temperature is introduced for metallic clusters with a diameter of 2-3 nm. This critical diameter is related to clusters which the ratio of surface atoms to total atoms is about 50%. The 'shape effect' is shown to be important at sizes less than 20 nm. The obtained results are supported by available experimental results for nickel and iron nanoparticles.

  20. Evaluation of the mobile content in Magnetospirillum magneticum AMB-1 genome using bioinformatical approaches reveals a new genome size for the magnetosome island

    Directory of Open Access Journals (Sweden)

    Ali Bin Thani

    2015-10-01

    Full Text Available After completing its sequence/annotation in 2005, Magnetospirillum magneticum AMB-1 had become one of the most important magnetotactic genomes used to facilitate analysis of the magnetosome formation process. In this paper we investigate the genome contents of AMB-1 and other magnetotactic bacteria to demonstrate the size of mobile genome and number of conserved genes in M. magneticum AMB-1. The preliminary analysis presented here shows the mosaic structure of these genomes. 100 genomic islands were identified in AMB-1 by IslandPick. Moreover, the size of AMB-1 magnetosome island (MAI, previously known to be 100 kb, was re-estimated to be in the size range of 110 kb. Thus more genes were included to be part of this GI. The investigation included the use of comparative approaches to elucidate conserved protein coding sequences. 13 CDS were identified to be conserved among three magnetotactic genomes. One CDS (amb3135 was conserved in five magnetotactic genomes. The amino acid sequence for this CDS (amb3135 was used to draw a phylogenetic tree among magnetotactic bacteria. The phylogeny based on amb3135 is in concordance with previous studies indicating a close relationship between strain AMB-1 and other Magnetospirillum species.

  1. Genome Sizes in Hepatica Mill: (Ranunculaceae Show a Loss of DNA, Not a Gain, in Polyploids

    Directory of Open Access Journals (Sweden)

    B. J. M. Zonneveld

    2010-01-01

    , and a possible pentaploid. The somatic nuclear DNA contents (2C-value, as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14% loss of nuclear DNA in the natural allopolyploids was found.

  2. Sizing of the Haemophilus influenzae Rd genome by pulsed-field agarose gel electrophoresis.

    OpenAIRE

    Lee, J J; Smith, H O

    1988-01-01

    The four restriction enzymes ApaI (5'-GGGCCC), EagI (5'-CGGCCG), NaeI (5'-GCCGGC), and SmaI (5'-CCCGGG) were found to produce distributions of DNA fragment sizes useful for mapping of the Haemophilus influenzae Rd genome by pulsed-field agarose gel electrophoresis. ApaI produced 21 fragments (range, 1.6 to 305 kilobases [kb]), EagI yielded 30 fragments (0.6 to 339 kb), NaeI produced 32 fragments (2.3 to 290 kb), and SmaI yielded 16 fragments (6.0 to 377 kb). Summation of the fragment lengths ...

  3. Challenges of flow-cytometric estimation of nuclear genome size in orchids, a plant group with both whole-genome and progressively partial endoreplication.

    Science.gov (United States)

    Trávníček, Pavel; Ponert, Jan; Urfus, Tomáš; Jersáková, Jana; Vrána, Jan; Hřibová, Eva; Doležel, Jaroslav; Suda, Jan

    2015-10-01

    Nuclear genome size is an inherited quantitative trait of eukaryotic organisms with both practical and biological consequences. A detailed analysis of major families is a promising approach to fully understand the biological meaning of the extensive variation in genome size in plants. Although Orchidaceae accounts for ∼10% of the angiosperm diversity, the knowledge of patterns and dynamics of their genome size is limited, in part due to difficulties in flow cytometric analyses. Cells in various somatic tissues of orchids undergo extensive endoreplication, either whole-genome or partial, and the G1-phase nuclei with 2C DNA amounts may be lacking, resulting in overestimated genome size values. Interpretation of DNA content histograms is particularly challenging in species with progressively partial endoreplication, in which the ratios between the positions of two neighboring DNA peaks are lower than two. In order to assess distributions of nuclear DNA amounts and identify tissue suitable for reliable estimation of nuclear DNA content, we analyzed six different tissue types in 48 orchid species belonging to all recognized subfamilies. Although traditionally used leaves may provide incorrect C-values, particularly in species with progressively partial endoreplication, young ovaries and pollinaria consistently yield 2C and 1C peaks of their G1-phase nuclei, respectively, and are, therefore, the most suitable parts for genome size studies in orchids. We also provide new DNA C-values for 22 orchid genera and 42 species. Adhering to the proposed methodology would allow for reliable genome size estimates in this largest plant family. Although our research was limited to orchids, the need to find a suitable tissue with dominant 2C peak of G1-phase nuclei applies to all endopolyploid species. PMID:25929591

  4. Genome-Wide Association Study on Male Genital Shape and Size in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Baku Takahara

    Full Text Available Male genital morphology of animals with internal fertilization and promiscuous mating systems have been one of the most diverse and rapidly evolving morphological traits. The male genital morphology in general is known to have low phenotypic and genetic variations, but the genetic basis of the male genital variation remains unclear. Drosophila melanogaster and its closely related species are morphologically very similar, but the shapes of the posterior lobe, a cuticular projection on the male genital arch are distinct from each other, representing a model system for studying the genetic basis of male genital morphology. In this study, we used highly inbred whole genome sequenced strains of D. melanogaster to perform genome wide association analysis on posterior lobe morphology. We quantified the outline shape of posterior lobes with Fourier coefficients obtained from elliptic Fourier analysis and performed principal component analysis, and posterior lobe size. The first and second principal components (PC1 and PC2 explained approximately 88% of the total variation of the posterior lobe shape. We then examined the association between the principal component scores and posterior lobe size and 1902142 single nucleotide polymorphisms (SNPs. As a result, we obtained 15, 14 and 15 SNPs for PC1, PC2 and posterior lobe size with P-values smaller than 10(-5. Based on the location of the SNPs, 13, 13 and six protein coding genes were identified as potential candidates for PC1, PC2 and posterior lobe size, respectively. In addition to the previous findings showing that the intraspecific posterior shape variation are regulated by multiple QTL with strong effects, the present study suggests that the intraspecific variation may be under polygenic regulation with a number of loci with small effects. Further studies are required for investigating whether these candidate genes are responsible for the intraspecific posterior lobe shape variation.

  5. Genome size and ploidy influence angiosperm species' biomass under nitrogen and phosphorus limitation.

    Science.gov (United States)

    Guignard, Maïté S; Nichols, Richard A; Knell, Robert J; Macdonald, Andy; Romila, Catalina-Andreea; Trimmer, Mark; Leitch, Ilia J; Leitch, Andrew R

    2016-06-01

    Angiosperm genome sizes (GS) range c. 2400-fold, and as nucleic acids are amongst the most phosphorus- (P) and nitrogen (N)-demanding cellular biomolecules, we test the hypothesis that a key influence on plant biomass and species composition is the interaction between N and P availability and plant GS. We analysed the impact of different nutrient regimes on above-ground biomass of angiosperm species with different GS, ploidy level and Grime's C-S-R (competitive, stress-tolerant, ruderal) plant strategies growing at the Park Grass Experiment (Rothamsted, UK), established in 1856. The biomass-weighted mean GS of species growing on plots with the addition of both N and P fertilizer were significantly higher than that of plants growing on control plots and plots with either N or P. The plants on these N + P plots are dominated by polyploids with large GS and a competitive plant strategy. The results are consistent with our hypothesis that large genomes are costly to build and maintain under N and P limitation. Hence GS and ploidy are significant traits affecting biomass growth under different nutrient regimes, influencing plant community composition and ecosystem dynamics. We propose that GS is a critical factor needed in models that bridge the knowledge gap between biodiversity and ecosystem functioning. PMID:26875784

  6. Effect of particle size on the average heat-transfer rate from a cylinder in a liquid-penetrated granular bed

    International Nuclear Information System (INIS)

    Data of heat transfer of bodies submerged in a fixed liquid-penetrated granular bed are important for the development of efficient catalytic and helium reactors an hydrogen accumulators based on porous intermetallics. In this work, experimental results on the average heat transfer from a cylinder in a liquid-penetrated granular bed are presented and the dependence of the heat-transfer rate on the particle size in the bed is found. The results of these experiments are important for practical estimation and design of catalytic reactors

  7. Molecular Phylogenetic Analysis of Infidum similis, Including Morphological Data and Estimation of its Genome Size.

    Science.gov (United States)

    Martínez-Salazar, Elizabeth A; Rosas-Valdez, Rogelio; Gregory, T Ryan; Violante-González, Juan

    2016-08-01

    :   Infidum similis Travassos, 1916 (Dicrocoeliidae: Leipertrematinae) was found in the gall bladder of Leptophis diplotropis Günther, 1872 from El Podrido, Acapulco, Guerrero, Mexico. A phylogenetic analysis based on partial sequences of the 28S ribosomal RNA using maximum likelihood (ML) and Bayesian inference (BI) analyses was carried out to assess its phylogenetic position within suborder Xiphidiata, alongside members of the superfamilies Gorgoderoidea and Plagiorchoidea. The phylogenetic trees showed that the genus is most-closely related to the Plagiorchoidea rather than to the Gorgoderoidea, in keeping with previous taxonomic designations. Phylogenies obtained from ML and BI analysis of the 28S rDNA gene revealed a well supported clade in which Choledocystus hepaticus (Lutz, 1928) Sullivan, 1977 is sister to I. similis. On the other hand, a tree obtained using a partial sequence of the cytochrome c oxidase subunit 1 (cox1) mtDNA gene (ML and BI analysis), with species supposed to be closely related to I. similis according to 28S, does not support this relatedness. Based on the independence of Infidum from the subfamily Leipertrematinae Yamaguti, 1958 , our results clearly demonstrated that the genus corresponds to a different family and with species closely related to C. hepaticus within Plagiorchoidea. New data are presented about the tegumental surface of I. similis by scanning electron microscopy as well as the estimation of its haploid genome size using Feulgen Image Analysis Densitometry of sperm nuclei as part of the characterization of this species. This is the first genome size estimated for a member of Plagiorchiida, and these data will provide a new source of knowledge on helminth diversity and evolutionary studies. This constitutes the first host record, and new geographical distribution, for this species in Mexico. PMID:26998629

  8. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size

    Czech Academy of Sciences Publication Activity Database

    Kelly, L.J.; Renny-Byfield, S.; Macas, Jiří; Novák, Petr; Neumann, Pavel; Lysák, M.; Day, P.D.; Berger, M.; Fay, M. F.; Nichols, R. A.; Leitch, A. R.; Leitch, I. J.

    2015-01-01

    Roč. 208, č. 2 (2015), s. 596-607. ISSN 0028-646X R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : DNA deletion * Fritillaria * Liliaceae * genome size evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.672, year: 2014

  9. Challenges of flow-cytometric estimation of nuclear genome size in orchids, a plant group with both whole-genome and progressively partial endoreplication

    Czech Academy of Sciences Publication Activity Database

    Trávníček, Pavel; Ponert, J.; Urfus, Tomáš; Jersáková, Jana; Vrána, Jan; Hřibová, Eva; Doležel, Jaroslav; Suda, Jan

    2015-01-01

    Roč. 87, č. 10 (2015), s. 958-966. ISSN 1552-4922 R&D Projects: GA ČR GAP506/12/1320 Institutional support: RVO:67985939 ; RVO:67179843 ; RVO:61389030 Keywords : flow cytometry * genome size * hyporeduplication Subject RIV: EF - Botanics; EF - Botanics (UEB-Q); EH - Ecology, Behaviour (UEK-B) Impact factor: 2.928, year: 2014

  10. How airlines decide the average size of airplanes in Brazilian market? Study of the determinants and projections for the next decade [paper in Portuguese

    Directory of Open Access Journals (Sweden)

    Thyago Silva Hermeto

    2012-01-01

    Full Text Available In Brazilian market, all airlines companies have a complex problem to solve, regarding the ideal profile for the aircraft fleet: Embraer`s aircraft profile (availability of seats 100 passengers aircraft or Boeing or Airbus profile (available above 140 seats? To answer this question is necessary to think about the following boundary conditions: (1 the organic growth of passangers at a rate of 11,8%/year (2003-2008, (2 physical limitations of the major airports - the ability of the passenger terminal, number of lanes, number of slots in the apron area, (3 the rate of completion of infrastructure works in this short of monitoring the speed of demand growth displayed until the present moment. To address this issue, this econometric study presents the evolution of the average size of aircraft used in Brazil. The middle step practiced by airlines is the variable that causes the choice for larger aircraft, with elasticity of 37,9%, in contrast, GDP growth leads to a choice of smaller aircraft, elasticity of –17,6%. The conclusion is that neutral scenario proved to be more consistent with market reality, there is an initial decrease of 6.5% over the average size of the aircraft in July 2010 and July 2020 shows an increase of 9.8%.

  11. Flow cytometry and K-mer analysis estimates of the genome sizes of Bemisia tabaci B and Q (Hemiptera: Aleyrodidae)

    OpenAIRE

    Guo, Li T.; Wang, Shao L.; Wu, Qing J.; Zhou, Xu G.; Xie, Wen; Zhang, You J.

    2015-01-01

    The genome sizes of the B- and Q-types of the whitefly Bemisia tabaci (Gennnadius) were estimated using flow cytometry (Drosophila melanogaster as the DNA reference standard and propidium iodide (PI) as the fluorochrome) and k-mer analysis. For flow cytometry, the mean nuclear DNA content was 0.686 pg for B-type males, 1.392 pg for B-type females, 0.680 pg for Q-type males, and 1.306 pg for Q-type females. Based on the relationship between DNA content and genome size (1 pg DNA = 980 Mbp), the...

  12. Evolutionary and taxonomic implications of variation in nuclear genome size: lesson from the grass genus Anthoxanthum (Poaceae)

    Czech Academy of Sciences Publication Activity Database

    Chlumová, Z.; Krejčíková, J.; Mandáková, T.; Suda, Jan; Trávníček, Pavel

    2015-01-01

    Roč. 10, č. 7 (2015), no.e0133748,1-17. E-ISSN 1932-6203 Institutional support: RVO:67985939 Keywords : flow cytometry * genome size * polyploidy Subject RIV: EF - Botanics Impact factor: 3.234, year: 2014

  13. Continuous Morphological Variation Correlated with Genome Size Indicates Frequent Introgressive Hybridization among Diphasiastrum Species (Lycopodiaceae) in Central Europe

    Czech Academy of Sciences Publication Activity Database

    Hanušová, K.; Ekrt, L.; Vít, Petr; Kolář, Filip; Urfus, Tomáš

    2014-01-01

    Roč. 9, č. 6 (2014), no.-e99552. E-ISSN 1932-6203 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : genome size * merphometrics * Diphasiastrum Subject RIV: EF - Botanics Impact factor: 3.234, year: 2014

  14. Species boundaries and hybridization in central-European Nymphaea species inferred from genome size and morphometric data

    Czech Academy of Sciences Publication Activity Database

    Kabátová, Klára; Vít, Petr; Suda, Jan

    2014-01-01

    Roč. 86, č. 2 (2014), s. 131-154. ISSN 0032-7786 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : genome size * multivariate morphometrics * Nymphaea Subject RIV: EF - Botanics Impact factor: 4.104, year: 2014

  15. Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules.

    Science.gov (United States)

    Rashid, M Harun-or; Young, J Peter W; Everall, Isobel; Clercx, Pia; Willems, Anne; Santhosh Braun, Markus; Wink, Michael

    2015-09-01

    Rhizobial strains isolated from effective root nodules of field-grown lentil (Lens culinaris) from different parts of Bangladesh were previously analysed using sequences of the 16S rRNA gene, three housekeeping genes (recA, atpD and glnII) and three nodulation genes (nodA, nodC and nodD), DNA fingerprinting and phenotypic characterization. Analysis of housekeeping gene sequences and DNA fingerprints indicated that the strains belonged to three novel clades in the genus Rhizobium. In present study, a representative strain from each clade was further characterized by determination of cellular fatty acid compositions, carbon substrate utilization patterns and DNA-DNA hybridization and average nucleotide identity (ANI) analyses from whole-genome sequences. DNA-DNA hybridization showed 50-62% relatedness to their closest relatives (the type strains of Rhizobium etli and Rhizobium phaseoli) and 50-60% relatedness to each other. These results were further supported by ANI values, based on genome sequencing, which were 87-92% with their close relatives and 88-89% with each other. On the basis of these results, three novel species, Rhizobium lentis sp. nov. (type strain BLR27(T) = LMG 28441(T) = DSM 29286(T)), Rhizobium bangladeshense sp. nov. (type strain BLR175(T) = LMG 28442(T) = DSM 29287(T)) and Rhizobium binae sp. nov. (type strain BLR195(T) = LMG 28443(T) = DSM 29288(T)), are proposed. These species share common nodulation genes (nodA, nodC and nodD) that are similar to those of the symbiovar viciae. PMID:26060217

  16. State Averages

    Data.gov (United States)

    U.S. Department of Health & Human Services — A list of a variety of averages for each state or territory as well as the national average, including each quality measure, staffing, fine amount and number of...

  17. Transcriptional burst frequency and burst size are equally modulated across the human genome

    OpenAIRE

    Dar, Roy D.; Razooky, Brandon S; Singh, Abhyudai; Trimeloni, Thomas V.; McCollum, James M.; Cox, Chris D.; Simpson, Michael L.; Weinberger, Leor S.

    2012-01-01

    Gene expression occurs either as an episodic process, characterized by pulsatile bursts, or as a constitutive process, characterized by a Poisson-like accumulation of gene products. It is not clear which mode of gene expression (constitutive versus bursty) predominates across a genome or how transcriptional dynamics are influenced by genomic position and promoter sequence. Here, we use time-lapse fluorescence microscopy to analyze 8,000 individual human genomic loci and find that at virtually...

  18. Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group

    OpenAIRE

    Zheng, Jinshui; Peng, Donghai; Ruan, Lifang; Sun, Ming

    2013-01-01

    Background Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. However, the origin and evolution of most plasmids remains unclear, especially for megaplasmids. Strains of the Bacillus cereus group contain up to 13 plasmids with genome sizes ranging from 2 kb to 600 kb, and thus can be used to study plasmid dynamics and evolution. Results This work studied the origin and evolution of 31 B. cereus group megaplasmids (>100 kb) focusing on the...

  19. Brain scaling in mammalian evolution as a consequence of concerted and mosaic changes in numbers of neurons and average neuronal cell size

    Directory of Open Access Journals (Sweden)

    Suzana eHerculano-Houzel

    2014-08-01

    Full Text Available Enough species have now been subject to systematic quantitative analysis of the relationship between the morphology and cellular composition of their brain that patterns begin to emerge and shed light on the evolutionary path that led to mammalian brain diversity. Based on an analysis of the shared and clade-specific characteristics of 41 modern mammalian species in 6 clades, and in light of the phylogenetic relationships among them, here we propose that ancestral mammal brains were composed and scaled in their cellular composition like modern afrotherian and glire brains: with an addition of neurons that is accompanied by a decrease in neuronal density and very little modification in glial cell density, implying a significant increase in average neuronal cell size in larger brains, and the allocation of approximately 2 neurons in the cerebral cortex and 8 neurons in the cerebellum for every neuron allocated to the rest of brain. We also propose that in some clades the scaling of different brain structures has diverged away from the common ancestral layout through clade-specific (or clade-defining changes in how average neuronal cell mass relates to numbers of neurons in each structure, and how numbers of neurons are differentially allocated to each structure relative to the number of neurons in the rest of brain. Thus, the evolutionary expansion of mammalian brains has involved both concerted and mosaic patterns of scaling across structures. This is, to our knowledge, the first mechanistic model that explains the generation of brains large and small in mammalian evolution, and it opens up new horizons for seeking the cellular pathways and genes involved in brain evolution.

  20. Quaternion Averaging

    Science.gov (United States)

    Markley, F. Landis; Cheng, Yang; Crassidis, John L.; Oshman, Yaakov

    2007-01-01

    Many applications require an algorithm that averages quaternions in an optimal manner. For example, when combining the quaternion outputs of multiple star trackers having this output capability, it is desirable to properly average the quaternions without recomputing the attitude from the the raw star tracker data. Other applications requiring some sort of optimal quaternion averaging include particle filtering and multiple-model adaptive estimation, where weighted quaternions are used to determine the quaternion estimate. For spacecraft attitude estimation applications, derives an optimal averaging scheme to compute the average of a set of weighted attitude matrices using the singular value decomposition method. Focusing on a 4-dimensional quaternion Gaussian distribution on the unit hypersphere, provides an approach to computing the average quaternion by minimizing a quaternion cost function that is equivalent to the attitude matrix cost function Motivated by and extending its results, this Note derives an algorithm that deterniines an optimal average quaternion from a set of scalar- or matrix-weighted quaternions. Rirthermore, a sufficient condition for the uniqueness of the average quaternion, and the equivalence of the mininiization problem, stated herein, to maximum likelihood estimation, are shown.

  1. Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology

    OpenAIRE

    Whittaker Kerry A; Rignanese Dayna R; Olson Robert J; Rynearson Tatiana A

    2012-01-01

    Abstract Background Marine phytoplankton drift passively with currents, have high dispersal potentials and can be comprised of morphologically cryptic species. To examine molecular subdivision in the marine diatom Thalassiosira rotula, variations in rDNA sequence, genome size, and growth rate were examined among isolates collected from the Atlantic and Pacific Ocean basins. Analyses of rDNA included T. gravida because morphological studies have argued that T. rotula and T. gravida are conspec...

  2. Continuous morphological variation correlated with genome size indicates frequent introgressive hybridization among Diphasiastrum species (Lycopodiaceae in Central Europe.

    Directory of Open Access Journals (Sweden)

    Kristýna Hanušová

    Full Text Available Introgressive hybridization is an important evolutionary process frequently contributing to diversification and speciation of angiosperms. Its extent in other groups of land plants has only rarely been studied, however. We therefore examined the levels of introgression in the genus Diphasiastrum, a taxonomically challenging group of Lycopodiophytes, using flow cytometry and numerical and geometric morphometric analyses. Patterns of morphological and cytological variation were evaluated in an extensive dataset of 561 individuals from 57 populations of six taxa from Central Europe, the region with the largest known taxonomic complexity. In addition, genome size values of 63 individuals from Northern Europe were acquired for comparative purposes. Within Central European populations, we detected a continuous pattern in both morphological variation and genome size (strongly correlated together suggesting extensive levels of interspecific gene flow within this region, including several large hybrid swarm populations. The secondary character of habitats of Central European hybrid swarm populations suggests that man-made landscape changes might have enhanced unnatural contact of species, resulting in extensive hybridization within this area. On the contrary, a distinct pattern of genome size variation among individuals from other parts of Europe indicates that pure populations prevail outside Central Europe. All in all, introgressive hybridization among Diphasiastrum species in Central Europe represents a unique case of extensive interspecific gene flow among spore producing vascular plants that cause serious complications of taxa delimitation.

  3. Genome-wide screens for effective siRNAs through assessing the size of siRNA effects

    Directory of Open Access Journals (Sweden)

    Zhang Xiaohua

    2008-06-01

    Full Text Available Abstract Background RNA interference (RNAi has been seen as a revolution in functional genomics and system biology. Genome-wide RNAi research relies on the development of RNAi high-throughput screening (HTS assays. One of the most fundamental challenges in RNAi HTS is to glean biological significance from mounds of data, which relies on the development of effective analytic methods for selecting effective small interfering RNAs (siRNAs. Findings Based on a recently proposed parameter, strictly standardized mean difference (SSMD, I propose an analytic method for genome-wide screens of effective siRNAs through assessing and testing the size of siRNA effects. Central to this method is the capability of SSMD in quantifying siRNA effects. This method has relied on normal approximation, which works only in the primary screens but not in the confirmatory screens. In this paper, I explore the non-central t-distribution property of SSMD estimates and use this property to extend the SSMD-based method so that it works effectively in either primary or confirmatory screens as well as in any HTS screens with or without replicates. The SSMD-based method maintains a balanced control of false positives and false negatives. Conclusion The central interest in genome-wide RNAi research is the selection of effective siRNAs which relies on the development of analytic methods to measure the size of siRNA effects. The new analytic method for hit selection provided in this paper offers a good analytic tool for selecting effective siRNAs, better than current analytic methods, and thus may have broad utility in genome-wide RNAi research.

  4. Quantitative testing of the methodology for genome size estimation in plants using flow cytometry: a case study of the Primulina genus

    Directory of Open Access Journals (Sweden)

    Jing eWang

    2015-05-01

    Full Text Available Flow cytometry (FCM is a commonly used method for estimating genome size in many organisms. The use of flow cytometry in plants is influenced by endogenous fluorescence inhibitors and may cause an inaccurate estimation of genome size; thus, falsifying the relationship between genome size and phenotypic traits/ecological performance. Quantitative optimization of FCM methodology minimizes such errors, yet there are few studies detailing this methodology. We selected the genus Primulina, one of the most representative and diverse genera of the Old World Gesneriaceae, to evaluate the methodology effect on determining genome size. Our results showed that buffer choice significantly affected genome size estimation in six out of the eight species examined and altered the 2C-value (DNA content by as much as 21.4%. The staining duration and propidium iodide (PI concentration slightly affected the 2C-value. Our experiments showed better histogram quality when the samples were stained for 40 minutes at a PI concentration of 100 µg ml-1. The quality of the estimates was not improved by one-day incubation in the dark at 4 °C or by centrifugation. Thus, our study determined an optimum protocol for genome size measurement in Primulina: LB01 buffer supplemented with 100 µg ml-1 PI and stained for 40 minutes. This protocol also demonstrated a high universality in other Gesneriaceae genera. We report the genome size of nine Gesneriaceae species for the first time. The results showed substantial genome size variation both within and among the species, with the 2C-value ranging between 1.62 and 2.71 pg. Our study highlights the necessity of optimizing the FCM methodology prior to obtaining reliable genome size estimates in a given taxon.

  5. Average Interest

    OpenAIRE

    George Chacko; Sanjiv Ranjan Das

    1997-01-01

    We develop analytic pricing models for options on averages by means of a state-space expansion method. These models augment the class of Asian options to markets where the underlying traded variable follows a mean-reverting process. The approach builds from the digital Asian option on the average and enables pricing of standard Asian calls and puts, caps and floors, as well as other exotica. The models may be used (i) to hedge long period interest rate risk cheaply, (ii) to hedge event risk (...

  6. Notes on genome size in the hybrid Ranunculus x luizetii (Ranunculaceae and its parents by flow cytometry

    Directory of Open Access Journals (Sweden)

    Fernández Prieto, J. A.

    2011-12-01

    Full Text Available Notes on genome size in the hybrid Ranunculus x luizetii (Ranunculaceae and its parents by flow cytometry.- Flow cytometry was used to estimate the nuclear DNA content in the natural hybrid Ranunculus x luizetii and its parents. Our results indicate that the genome size of the hybrid R. x luizetii is closer to R. pyrenaeus than to R. parnassiifolius, providing an evidence of genome downsizing.Notas sobre el tamaño del genoma en el híbrido Ranunculus x luizetii (Ranunculaceae y sus progenitores mediante citometría de flujo.- Se ha empleado la citometría de flujo para estimar el contenido de ADN nuclear en el híbrido Ranunculus x luizetii y sus progenitores. Nuestros resultados indican que el tamaño del genoma del híbrido R. x luizetii se acerca más a R. pyrenaeus que a R. parnassiifolius, con una evidencia de reducción del genoma.

  7. A genomics approach to understanding the role of auxin in apple (Malus x domestica fruit size control

    Directory of Open Access Journals (Sweden)

    Devoghalaere Fanny

    2012-01-01

    Full Text Available Abstract Background Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. Results High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106. This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. Conclusions The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3 removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

  8. Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.

    Directory of Open Access Journals (Sweden)

    Daniel I Chasman

    2009-11-01

    Full Text Available While conventional LDL-C, HDL-C, and triglyceride measurements reflect aggregate properties of plasma lipoprotein fractions, NMR-based measurements more accurately reflect lipoprotein particle concentrations according to class (LDL, HDL, and VLDL and particle size (small, medium, and large. The concentrations of these lipoprotein sub-fractions may be related to risk of cardiovascular disease and related metabolic disorders. We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women's Genome Health Study (WGHS. Among 36 loci with genome-wide significance (P<5x10(-8 in primary and secondary analysis, ten (PCCB/STAG1 (3q22.3, GMPR/MYLIP (6p22.3, BTNL2 (6p21.32, KLF14 (7q32.2, 8p23.1, JMJD1C (10q21.3, SBF2 (11p15.4, 12q23.2, CCDC92/DNAH10/ZNF664 (12q24.31.B, and WIPI1 (17q24.2 have not been reported in prior genome-wide association studies for plasma lipid concentration. Associations with mean lipoprotein particle size but not cholesterol content were found for LDL at four loci (7q11.23, LPL (8p21.3, 12q24.31.B, and LIPG (18q21.1 and for HDL at one locus (GCKR (2p23.3. In addition, genetic determinants of total IDL and total VLDL concentration were found at many loci, most strongly at LIPC (15q22.1 and APOC-APOE complex (19q13.32, respectively. Associations at seven more loci previously known for effects on conventional plasma lipid measures reveal additional genetic influences on lipoprotein profiles and bring the total number of loci to 43. Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism-including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles-all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay.

  9. Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.

    Science.gov (United States)

    Chasman, Daniel I; Paré, Guillaume; Mora, Samia; Hopewell, Jemma C; Peloso, Gina; Clarke, Robert; Cupples, L Adrienne; Hamsten, Anders; Kathiresan, Sekar; Mälarstig, Anders; Ordovas, José M; Ripatti, Samuli; Parker, Alex N; Miletich, Joseph P; Ridker, Paul M

    2009-11-01

    While conventional LDL-C, HDL-C, and triglyceride measurements reflect aggregate properties of plasma lipoprotein fractions, NMR-based measurements more accurately reflect lipoprotein particle concentrations according to class (LDL, HDL, and VLDL) and particle size (small, medium, and large). The concentrations of these lipoprotein sub-fractions may be related to risk of cardiovascular disease and related metabolic disorders. We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women's Genome Health Study (WGHS). Among 36 loci with genome-wide significance (PKLF14 (7q32.2), 8p23.1, JMJD1C (10q21.3), SBF2 (11p15.4), 12q23.2, CCDC92/DNAH10/ZNF664 (12q24.31.B), and WIPI1 (17q24.2)) have not been reported in prior genome-wide association studies for plasma lipid concentration. Associations with mean lipoprotein particle size but not cholesterol content were found for LDL at four loci (7q11.23, LPL (8p21.3), 12q24.31.B, and LIPG (18q21.1)) and for HDL at one locus (GCKR (2p23.3)). In addition, genetic determinants of total IDL and total VLDL concentration were found at many loci, most strongly at LIPC (15q22.1) and APOC-APOE complex (19q13.32), respectively. Associations at seven more loci previously known for effects on conventional plasma lipid measures reveal additional genetic influences on lipoprotein profiles and bring the total number of loci to 43. Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism-including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles-all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay. PMID:19936222

  10. Karyotype and genome size of Iberochondrostoma almacai (Teleostei, Cyprinidae) and comparison with the sister-species I. lusitanicum

    OpenAIRE

    Rita Monteiro; Cláudia Carvalho; Maria João Collares-Pereira

    2009-01-01

    This study aimed to define the karyotype of the recently described Iberian endemic Iberochondrostoma almacai, to revisit the previously documented chromosome polymorphisms of its sister species I. lusitanicum using C-, Ag-/CMA3 and RE-banding, and to compare the two species genome sizes. A 2n = 50 karyotype (with the exception of a triploid I. lusitanicum specimen) and a corresponding haploid chromosome formula of 7M:15SM:3A (FN = 94) were found. Multiple NORs were observed in both species (i...

  11. Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain

    Science.gov (United States)

    A genome scan was used to detect chromosomal regions and QTL that control quantitative traits of economic importance in chickens. Two unique F2 crosses generated from a commercial broiler male line and 2 genetically distinct inbred lines (Leghorn and Fayoumi) were used to identify QTL affecting BW a...

  12. Genome size estimations on Ulmus minor Mill., Ulmus glabra Huds., and Celtis australis L. using flow cytometry.

    Science.gov (United States)

    Loureiro, J; Rodriguez, E; Gomes, A; Santos, C

    2007-07-01

    The Ulmaceae family is composed of nearly 2000 species widely distributed in the northern hemisphere. Despite their wide distribution area, there are only four native species in the Iberian Peninsula. In this work the genome size of three of those species (ULMUS MINOR, U. GLABRA, and CELTIS AUSTRALIS) was estimated using flow cytometry. The nuclear DNA content of C. AUSTRALIS was estimated as 2.46 +/- 0.061 pg/2C, of U. MINOR as 4.25 +/- 0.158 pg/2C, and of U. GLABRA as 4.37 +/- 0.103 pg/2C of DNA. No statistically significant differences were detected among individuals of the same species. These species revealed to be problematic for flow cytometric analyses, due to the release of mucilaginous compounds into the nuclear suspension. Despite that, the modified protocol here presented ensured high quality analyses (low coefficient of variation and background debris and nuclear fluorescence stability), opening good perspectives on its application to estimate the genome size of species with similar problems. PMID:17642035

  13. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape : A Large-Scale Genome-Wide Interaction Study

    NARCIS (Netherlands)

    Winkler, Thomas W.; Justice, Anne E.; Graff, Mariaelisa; Barata, Llilda; Feitosa, Mary F.; Chu, Su; Czajkowski, Jacek; Esko, Tonu; Fall, Tove; Kilpelainen, Tuomas O.; Lu, Yingchang; Magi, Reedik; Mihailov, Evelin; Pers, Tune H.; Rueeger, Sina; Teumer, Alexander; Ehret, Georg B.; Ferreira, Teresa; Heard-Costa, Nancy L.; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D.; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M.; Jansen, Rick; Westra, Harm-Jan; White, Charles C.; Absher, Devin; Ahluwalia, Tarunveer S.; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L.; de Craen, Anton J. M.; Bis, Joshua C.; Bonnefond, Amelie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W. K.; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E.; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B.; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E.; Jackson, Anne U.; Jacobs, Kevin B.; Johansson, Asa; Kaakinen, Marika; Kleber, Marcus E.; Lahti, Jari; Leach, Irene Mateo; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A. F.; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L.; Montasser, May E.; Mueller, Gabriele; Mueller-Nurasyid, Martina; Nolte, Ilja M.; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W.; Renstrom, Frida; Rizzi, Federica; Rose, Lynda M.; Ryan, Kathy A.; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stancakova, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J.; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P.; Vandenput, Liesbeth; van der Laan, Sander W.; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L.; Wang, Sophie R.; Wang, Zhaoming; Wild, Sarah H.; Willenborg, Christina; Wilson, James F.; Wong, Andrew; Yang, Jian; Yengo, Loic; Yerges-Armstrong, Laura M.; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A.; Bakker, Stephan J. L.; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blueher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L.; Boyd, Heather A.; Bruinenberg, Marcel; Buchman, Aron S.; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S.; Claudi-Boehm, Simone; Cole, John; Collins, Francis S.; de Geus, Eco J. C.; de Groot, Lisette C. P. G. M.; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G.; Friedrich, Nele; Gejman, Pablo V.; Gigante, Bruna; Glorioso, Nicola; Go, Alan S.; Gottesman, Omri; Graessler, Juergen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C.; Hansen, Torben; Harris, Tamara B.; Hartman, Catharina A.; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T.; Heath, Andrew C.; Henders, Anjali K.; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G.; Hui, Jennie; Husemoen, Lise L.; Hutri-Kahonen, Nina; Hysi, Pirro G.; Illig, Thomas; De Jager, Philip L.; Jalilzadeh, Shapour; Jorgensen, Torben; Jukema, J. Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J.; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T.; Kratzer, Wolfgang; Krueger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J.; Leander, Karin; Lindstrom, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stephane; Luben, Robert; Lyssenko, Valeriya; Mannisto, Satu; Magnusson, Patrik K.; McArdle, Wendy L.; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W.; Morris, Andrew P.; Narisu, Narisu; Nelis, Mari; Ong, Ken K.; Palotie, Aarno; Perusse, Louis; Pichler, Irene; Pilia, Maria G.; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M.; Rice, Treva K.; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R.; Sarzynski, Mark A.; Scholtens, Salome; Scott, Robert A.; Scott, William R.; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P. Eline; Smit, Jan H.; Sparso, Thomas H.; Stirrups, Kathleen; Stolk, Ronald P.; Stringham, Heather M.; Swertz, Morris A.; Swift, Amy J.; Syvanen, Ann-Christine; Tan, Sian-Tsung; Thorand, Barbara; Toenjes, Anke; Tremblay, Angelo; Tsafantakis, Emmanouil; van der Most, Peter J.; Voelker, Uwe; Vohl, Marie-Claude; Vonk, Judith M.; Waldenberger, Melanie; Walker, Ryan W.; Wennauer, Roman; Widen, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Wright, Alan F.; Zillikens, M. Carola; van Dijk, Suzanne C.; van Schoor, Natasja M.; Asselbergs, Folkert W.; de Bakker, Paul I. W.; Beckmann, Jacques S.; Beilby, John; Bennett, David A.; Bergman, Richard N.; Bergmann, Sven; Boeger, Carsten A.; Boehm, Bernhard O.; Boerwinkle, Eric; Boomsma, Dorret I.; Bornstein, Stefan R.; Bottinger, Erwin P.; Bouchard, Claude; Chambers, John C.; Chanock, Stephen J.; Chasman, Daniel I.; Cucca, Francesco; Cusi, Daniele; Dedoussis, George; Erdmann, Jeanette; Eriksson, Johan G.; Evans, Denis A.; de Faire, Ulf; Farrall, Martin; Ferrucci, Luigi; Ford, Ian; Franke, Lude; Franks, Paul W.; Froguel, Philippe; Gansevoort, Ron T.; Gieger, Christian; Gronberg, Henrik; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Per; Hamsten, Anders; van der Harst, Pim; Hayward, Caroline; Heliovaara, Markku; Hengstenberg, Christian; Hicks, Andrew A.; Hingorani, Aroon; Hofman, Albert; Hu, Frank; Huikuri, Heikki V.; Hveem, Kristian; James, Alan L.; Jordan, Joanne M.; Jula, Antti; Kaehoenen, Mika; Kajantie, Eero; Kathiresan, Sekar; Kiemeney, Lambertus A. L. M.; Kivimaki, Mika; Knekt, Paul B.; Koistinen, Heikki A.; Kooner, Jaspal S.; Koskinen, Seppo; Kuusisto, Johanna; Maerz, Winfried; Martin, Nicholas G.; Laakso, Markku; Lakka, Timo A.; Lehtimaki, Terho; Lettre, Guillaume; Levinson, Douglas F.; Lind, Lars; Lokki, Marja-Liisa; Mantyselka, Pekka; Melbye, Mads; Metspalu, Andres; Mitchell, Braxton D.; Moll, Frans L.; Murray, Jeffrey C.; Musk, Arthur W.; Nieminen, Markku S.; Njolstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J.; Oostra, Ben A.; Palmer, Lyle J.; Pankow, James S.; Pasterkamp, Gerard; Pedersen, Nancy L.; Pedersen, Oluf; Penninx, Brenda W.; Perola, Markus; Peters, Annette; Polasek, Ozren; Pramstaller, Peter P.; Psaty, Bruce M.; Qi, Lu; Quertermous, Thomas; Raitakari, Olli T.; Rankinen, Tuomo; Rauramaa, Rainer; Ridker, Paul M.; Rioux, John D.; Rivadeneira, Fernando; Rotter, Jerome I.; Rudan, Igor; den Ruijter, Hester M.; Saltevo, Juha; Sattar, Naveed; Schunkert, Heribert; Schwarz, Peter E. H.; Shuldiner, Alan R.; Sinisalo, Juha; Snieder, Harold; Sorensen, Thorkild I. A.; Spector, Tim D.; Staessen, Jan A.; Stefania, Bandinelli; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tardif, Jean-Claude; Tremoli, Elena; Tuomilehto, Jaakko; Uitterlinden, Andre G.; Uusitupa, Matti; Verbeek, Andre L. M.; Vermeulen, Sita H.; Viikari, Jorma S.; Vitart, Veronique; Voelzke, Henry; Vollenweider, Peter; Waeber, Gerard; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J.; Watkins, Hugh; Zeggini, Eleftheria; Chakravarti, Aravinda; Clegg, Deborah J.; Cupples, L. Adrienne; Gordon-Larsen, Penny; Jaquish, Cashell E.; Rao, D. C.; Abecasis, Goncalo R.; Assimes, Themistocles L.; Barroso, Ines; Berndt, Sonja I.; Boehnke, Michael; Deloukas, Panos; Fox, Caroline S.; Groop, Leif C.; Hunter, David J.; Ingelsson, Erik; Kaplan, Robert C.; McCarthy, Mark I.; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Hirschhorn, Joel N.; Lindgren, Cecilia M.; Heid, Iris M.; North, Kari E.; Borecki, Ingrid B.; Kutalik, Zoltan; Loos, Ruth J. F.

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially betw

  14. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

    NARCIS (Netherlands)

    Winkler, T.W.; Justice, A.E.; Graff, M.; Barata, L.; Feitosa, M.F.; Chu, S.; Czajkowski, J.; Esko, T.; Fall, T.; Kilpelainen, T.O.; Lu, Y.; Magi, R.; Mihailov, E.; Pers, T.H.; Rueger, S.; Teumer, A.; Ehret, G.B.; Ferreira, T.; Heard-Costa, N.L.; Karjalainen, J.; Lagou, V.; Mahajan, A.; Neinast, M.D.; Prokopenko, I.; Simino, J.; Teslovich, T.M.; Jansen, R.; Westra, H.J.; White, C.C.; Absher, D.; Ahluwalia, T.S.; Ahmad, S.; Albrecht, E.; Ferreira Alves, A.C.; Bragg-Gresham, J.L.; Craen, A.J. de; Bis, J.C.; Bonnefond, A.; Boucher, G.; Cadby, G.; Cheng, Y.C.; Chiang, C.W.; Delgado, G.; Demirkan, A.; Dueker, N.; Eklund, N.; Eiriksdottir, G.; Eriksson, J.; Feenstra, B.; Fischer, K.; Frau, F.; Galesloot, T.E.; Geller, F.; Goel, A.; Gorski, M.; Grammer, T.B.; Gustafsson, S.; Haitjema, S.; Hottenga, J.J.; Huffman, J.E.; Jackson, A.U.; Jacobs, K.B.; Johansson, A; Kaakinen, M.; Kleber, M.E.; Lahti, J.; Leach, I.M.; Lehne, B.; Liu, Y.; Lo, K.S.; Lorentzon, M.; Luan, J.; Madden, P.A.F.; Mangino, M.; McKnight, B.; Medina-Gomez, C.; Monda, K.L.; Montasser, M.E.; Muller, G.; Muller-Nurasyid, M.; Nolte, I.M.; Panoutsopoulou, K.; Pascoe, L.; Paternoster, L.; Rayner, N.W.; Renstrom, F.; Rizzi, F.; Rose, L.M.; Ryan, K.A.; Salo, P.; Sanna, S.; Scharnagl, H.; Shi, J.; Smith, A.V.; Southam, L.; Stancakova, A.; Steinthorsdottir, V.; Strawbridge, R.J.; Sung, Y.J.; Tachmazidou, I.; Kiemeney, B.; Vermeulen, S.H.

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially betw

  15. Combining site occupancy, breeding population sizes and reproductive success to calculate time-averaged reproductive output of different habitat types: an application to Tricolored Blackbirds.

    Science.gov (United States)

    Holyoak, Marcel; Meese, Robert J; Graves, Emily E

    2014-01-01

    In metapopulations in which habitat patches vary in quality and occupancy it can be complicated to calculate the net time-averaged contribution to reproduction of particular populations. Surprisingly, few indices have been proposed for this purpose. We combined occupancy, abundance, frequency of occurrence, and reproductive success to determine the net value of different sites through time and applied this method to a bird of conservation concern. The Tricolored Blackbird (Agelaius tricolor) has experienced large population declines, is the most colonial songbird in North America, is largely confined to California, and breeds itinerantly in multiple habitat types. It has had chronically low reproductive success in recent years. Although young produced per nest have previously been compared across habitats, no study has simultaneously considered site occupancy and reproductive success. Combining occupancy, abundance, frequency of occurrence, reproductive success and nest failure rate we found that that large colonies in grain fields fail frequently because of nest destruction due to harvest prior to fledging. Consequently, net time-averaged reproductive output is low compared to colonies in non-native Himalayan blackberry or thistles, and native stinging nettles. Cattail marshes have intermediate reproductive output, but their reproductive output might be improved by active management. Harvest of grain-field colonies necessitates either promoting delay of harvest or creating alternative, more secure nesting habitats. Stinging nettle and marsh colonies offer the main potential sources for restoration or native habitat creation. From 2005-2011 breeding site occupancy declined 3x faster than new breeding colonies were formed, indicating a rapid decline in occupancy. Total abundance showed a similar decline. Causes of variation in the value for reproduction of nesting substrates and factors behind continuing population declines merit urgent investigation. The method we

  16. Combining site occupancy, breeding population sizes and reproductive success to calculate time-averaged reproductive output of different habitat types: an application to Tricolored Blackbirds.

    Directory of Open Access Journals (Sweden)

    Marcel Holyoak

    Full Text Available In metapopulations in which habitat patches vary in quality and occupancy it can be complicated to calculate the net time-averaged contribution to reproduction of particular populations. Surprisingly, few indices have been proposed for this purpose. We combined occupancy, abundance, frequency of occurrence, and reproductive success to determine the net value of different sites through time and applied this method to a bird of conservation concern. The Tricolored Blackbird (Agelaius tricolor has experienced large population declines, is the most colonial songbird in North America, is largely confined to California, and breeds itinerantly in multiple habitat types. It has had chronically low reproductive success in recent years. Although young produced per nest have previously been compared across habitats, no study has simultaneously considered site occupancy and reproductive success. Combining occupancy, abundance, frequency of occurrence, reproductive success and nest failure rate we found that that large colonies in grain fields fail frequently because of nest destruction due to harvest prior to fledging. Consequently, net time-averaged reproductive output is low compared to colonies in non-native Himalayan blackberry or thistles, and native stinging nettles. Cattail marshes have intermediate reproductive output, but their reproductive output might be improved by active management. Harvest of grain-field colonies necessitates either promoting delay of harvest or creating alternative, more secure nesting habitats. Stinging nettle and marsh colonies offer the main potential sources for restoration or native habitat creation. From 2005-2011 breeding site occupancy declined 3x faster than new breeding colonies were formed, indicating a rapid decline in occupancy. Total abundance showed a similar decline. Causes of variation in the value for reproduction of nesting substrates and factors behind continuing population declines merit urgent

  17. Molecular subdivision of the marine diatom Thalassiosira rotula in relation to geographic distribution, genome size, and physiology

    Directory of Open Access Journals (Sweden)

    Whittaker Kerry A

    2012-10-01

    Full Text Available Abstract Background Marine phytoplankton drift passively with currents, have high dispersal potentials and can be comprised of morphologically cryptic species. To examine molecular subdivision in the marine diatom Thalassiosira rotula, variations in rDNA sequence, genome size, and growth rate were examined among isolates collected from the Atlantic and Pacific Ocean basins. Analyses of rDNA included T. gravida because morphological studies have argued that T. rotula and T. gravida are conspecific. Results Culture collection isolates of T. gravida and T. rotula diverged by 7.0 ± 0.3% at the ITS1 and by 0.8 ± 0.03% at the 28S. Within T. rotula, field and culture collection isolates were subdivided into three lineages that diverged by 0.6 ± 0.3% at the ITS1 and 0% at the 28S. The predicted ITS1 secondary structure revealed no compensatory base pair changes among lineages. Differences in genome size were observed among isolates, but were not correlated with ITS1 lineages. Maximum acclimated growth rates of isolates revealed genotype by environment effects, but these were also not correlated with ITS1 lineages. In contrast, intra-individual variation in the multi-copy ITS1 revealed no evidence of recombination amongst lineages, and molecular clock estimates indicated that lineages diverged 0.68 Mya. The three lineages exhibited different geographic distributions and, with one exception, each field sample was dominated by a single lineage. Conclusions The degree of inter- and intra-specific divergence between T. gravida and T. rotula suggests they should continue to be treated as separate species. The phylogenetic distinction of the three closely-related T. rotula lineages was unclear. On the one hand, the lineages showed no physiological differences, no consistent genome size differences and no significant changes in the ITS1 secondary structure, suggesting there are no barriers to interbreeding among lineages. In contrast, analysis of intra

  18. Determination of microbial genome sizes by two-dimensional denaturing gradient gel electrophoresis.

    OpenAIRE

    Poddar, S K; Maniloff, J

    1989-01-01

    In two-dimensional denaturing gradient gel electrophoresis, DNA is digested with a restriction endonuclease and the resulting DNA fragments are separated as a function of size by conventional agarose gel electrophoresis. Following this first dimension electrophoresis, the fragment distribution is placed at the top of a denaturing gradient slab gel and electrophoresis is carried out parallel to the gradient direction. This second dimension separation is a complex function of the base sequence ...

  19. A novel mitochondrial genome architecture in thrips (Insecta: Thysanoptera): extreme size asymmetry among chromosomes and possible recent control region duplication

    OpenAIRE

    Dickey, Aaron M.; Kumar, Vivek; Morgan, J. Kent; Jara-Cavieres, Antonella; Robert G Shatters; McKenzie, Cindy L.; Lance S Osborne

    2015-01-01

    Background Multipartite mitochondrial genomes are very rare in animals but have been found previously in two insect orders with highly rearranged genomes, the Phthiraptera (parasitic lice), and the Psocoptera (booklice/barklice). Results We provide the first report of a multipartite mitochondrial genome architecture in a third order with highly rearranged genomes: Thysanoptera (thrips). We sequenced the complete mitochondrial genomes of two divergent members of the Scirtothrips dorsalis crypt...

  20. Silage Collected from Dairy Farms Harbors an Abundance of Listeriaphages with Considerable Host Range and Genome Size Diversity

    Science.gov (United States)

    Vongkamjan, Kitiya; Switt, Andrea Moreno; den Bakker, Henk C.; Fortes, Esther D.

    2012-01-01

    Since the food-borne pathogen Listeria monocytogenes is common in dairy farm environments, it is likely that phages infecting this bacterium (“listeriaphages”) are abundant on dairy farms. To better understand the ecology and diversity of listeriaphages on dairy farms and to develop a diverse phage collection for further studies, silage samples collected on two dairy farms were screened for L. monocytogenes and listeriaphages. While only 4.5% of silage samples tested positive for L. monocytogenes, 47.8% of samples were positive for listeriaphages, containing up to >1.5 × 104 PFU/g. Host range characterization of the 114 phage isolates obtained, with a reference set of 13 L. monocytogenes strains representing the nine major serotypes and four lineages, revealed considerable host range diversity; phage isolates were classified into nine lysis groups. While one serotype 3c strain was not lysed by any phage isolates, serotype 4 strains were highly susceptible to phages and were lysed by 63.2 to 88.6% of phages tested. Overall, 12.3% of phage isolates showed a narrow host range (lysing 1 to 5 strains), while 28.9% of phages represented broad host range (lysing ≥11 strains). Genome sizes of the phage isolates were estimated to range from approximately 26 to 140 kb. The extensive host range and genomic diversity of phages observed here suggest an important role of phages in the ecology of L. monocytogenes on dairy farms. In addition, the phage collection developed here has the potential to facilitate further development of phage-based biocontrol strategies (e.g., in silage) and other phage-based tools. PMID:23042180

  1. A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

    Science.gov (United States)

    Halley, Yvette A.; Dowd, Scot E.; Decker, Jared E.; Seabury, Paul M.; Bhattarai, Eric; Johnson, Charles D.; Rollins, Dale; Tizard, Ian R.; Brightsmith, Donald J.; Peterson, Markus J.; Taylor, Jeremy F.; Seabury, Christopher M.

    2014-01-01

    Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within 14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts. PMID:24621616

  2. Pool Size Adaptive Adjusting Algorithm Based on Average Time%基于平均时间的线程池尺寸自适应调整算法

    Institute of Scientific and Technical Information of China (English)

    黄智泉; 刘正熙

    2013-01-01

      为了实现自适应调整线程池尺寸,提高并发程序处理的运行速度、改善效率和降低系统的资源开销,提出了一种基于任务平均处理时间的线程池尺寸自适应调整算法。首先研究线程池的一些特征数据以及用户请求的任务时间周期,提出了任务平均处理时间的概念。然后研究了不同任务类型下,任务平均处理时间与线程池的尺寸的相关性,提出了一种自适应调整算法。实验结果表明,该算法能够自适应调整线程池尺寸到适当区域,有效地提高应用程序的整体性能。%To realize adaptive adjusting the thread pool size,improve the operation speed of concurrent processing program,efficiency and reduce the system resource spending,a thread pool size adaptive adjusting algorithm based on task average time is presented. Firstly,some characteristics of the thread pool and the task time period of users request are studied,then the concept of task average processing time is put forward. After that,the correlation between the task average processing time and thread pool size under the different types of tasks is analyzed. A kind of adaptive adjustment algorithm is put forward. The experimental results show that the algorithm can adaptively adjust thread pool size to the appropriate area,effectively improving the overall performance of application program.

  3. Robust Averaging Level Control

    OpenAIRE

    Rosander, Peter; Isaksson, Alf; Löfberg, Johan; Forsman, Krister

    2011-01-01

    Frequent inlet flow changes typically cause problems for averaging level controllers. For a frequently changing inlet flow the upsets do not occur when the system is in steady state and the tank level at its set-point. For this reason the tuning of the level controller gets quite complicated, since not only the size of the upsets but also the time in between them relative to the hold up of the tank have to be considered. One way to obtain optimal flow filtering while directly accounting for futur...

  4. Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

    OpenAIRE

    Romiguier, J.; Ranwez, V.; Douzery, E. J. P.; Galtier, N

    2010-01-01

    The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in ...

  5. The influence of age and sex on genetic associations with adult body size and shape: a large-scale genome-wide interaction study

    OpenAIRE

    Winkler, Thomas W; Heid, Iris M.; Gorski, Mathias

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of Eu...

  6. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape : A Large-Scale Genome-Wide Interaction Study

    OpenAIRE

    Winkler, Thomas W; Justice, Anne E; Graff, Mariaelisa; Barata, Llilda; Feitosa, Mary F.; Chu, Su,; Czajkowski, Jacek; Esko, Tonu; Fall, Tove; Kilpelainen, Tuomas O.; Lu, Yingchang; Magi, Reedik; Mihailov, Evelin; Pers, Tune H.; Rueeger, Sina

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age-and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of Eur...

  7. Optimization of AFLP fingerprinting of organisms with a large-sized genome: a study on Alstroemeria spp

    NARCIS (Netherlands)

    Han, T.H.; Eck, van H.J.; Jeu, de M.J.; Jacobsen, E.

    1999-01-01

    The recently introduced PCR-based DNA fingerprinting technique AFLP (amplified fragment length polymorphism) allows the selective amplification of subsets of genomic restriction fragments. AFLP has been used for multiple purposes such as the construction of linkage maps, marker saturation at specifi

  8. Comparative Analysis of Growth, Genome Size, Chromosome Numbers and Phylogeny of Arabidopsis thaliana and Three Cooccurring Species of the Brassicaceae from Uzbekistan

    Directory of Open Access Journals (Sweden)

    Matthias H. Hoffmann

    2010-01-01

    Full Text Available Contrary to literature data Arabidopsis thaliana was rarely observed in Middle Asia during a collection trip in 2001. Instead, three other Brassicaceae species were frequently found at places where A. thaliana was expected. To reveal reasons for this frequency pattern, we studied chromosome numbers, genome sizes, phylogenetic relationships, developmental rates, and reproductive success of A. thaliana, Olimarabidopsis pumila, Arabis montbretiana, and Arabis auriculata from Uzbekistan in two temperature treatments. There are little but partially significant differences between phenotypes. All studied species have very small genomes. The 1Cx-values of different genotypes within the sampled species are correlated with altitude. Developmental rates are also correlated with 1Cx-values. In our growth experiments, Arabidopsis had high seed sterility at higher temperature, which might be one reason for the rarity of A. thaliana in Middle Asia.

  9. Microbial genomic taxonomy

    OpenAIRE

    Cristiane C Thompson; Chimetto, Luciane; Edwards, Robert A.; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes,  70% in silico Genome-to-Genome Hybridization similarity (G...

  10. Determinação em linha de tamanho de partículas na polimerização em suspensão In-line evaluation of average particle sizes in batch styrene suspension polymerizations

    Directory of Open Access Journals (Sweden)

    Alexandre F. Santos

    1999-12-01

    Full Text Available A técnica de espectrofotometria na região do infra-vermelho próximo (NIR é usada nesse trabalho para avaliar e controlar de forma contínua e em linha a evolução do tamanho médio de partícula em polimerizações de estireno em suspensão. Os resultados obtidos mostram que os espectros de NIR são sensíveis a modificações das condições de operação, podendo dessa forma prover informações sobre a evolução dinâmica da distribuição de tamanhos de partícula e sobre a estabilidade da suspensão durante a polimerização. Observa-se que a manipulação das variáveis normalmente utilizadas para modificar as curvas de distribuição de tamanhos, tais como a velocidade de agitação e a concentração de agente estabilizante, não causa modificações significativas na cinética da polimerização. Finalmente, experimentos mostram que a monitoração e controle contínuo da polimerização com a técnica de NIR permite projetar e obter distribuições de tamanho com valores médios pré-especificados, o que aponta para potencial desenvovlvimento de aplicações industriais.This work presents the application of near-infrared (NIR spectroscopy to the in-line monitoring of particle size in styrene suspension polymerizations. Results show that NIR spectra are sensitive to the different operational conditions and may provide information about particle dynamics and suspension stability. It is observed that the manipulation of important variables to the control of particle size distributions, such as stirrer speed and stabilizer concentration, does not cause any change to the polymerization kinetics. Finally, suspension polymerization experiments are carried out with in-line spectrophotometer, in order to obtain a specified average particle size, and results point out to potential industrial applications.

  11. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.

    Directory of Open Access Journals (Sweden)

    Estienne C Swart

    Full Text Available The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5% of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10%, encode 2-8 genes, have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size that vary from 469 bp to 66 kb long (mean ∼3.2 kb and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%, suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing

  12. Neutron resonance averaging

    International Nuclear Information System (INIS)

    The principles of resonance averaging as applied to neutron capture reactions are described. Several illustrations of resonance averaging to problems of nuclear structure and the distribution of radiative strength in nuclei are provided. 30 refs., 12 figs

  13. The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants

    Science.gov (United States)

    The American cranberry (Vaccinium macrocarpon Ait.) mitochondrial genome was assembled and reconstructed from whole genome 454 Roche GS-FLX and Illumina shotgun sequences. Compared with other Asterids, the reconstruction of the genome revealed an average size mitochondrion (459,678 nt) with comparat...

  14. Averaging anisotropic cosmologies

    International Nuclear Information System (INIS)

    We examine the effects of spatial inhomogeneities on irrotational anisotropic cosmologies by looking at the average properties of anisotropic pressure-free models. Adopting the Buchert scheme, we recast the averaged scalar equations in Bianchi-type form and close the standard system by introducing a propagation formula for the average shear magnitude. We then investigate the evolution of anisotropic average vacuum models and those filled with pressureless matter. In the latter case we show that the backreaction effects can modify the familiar Kasner-like singularity and potentially remove Mixmaster-type oscillations. The presence of nonzero average shear in our equations also allows us to examine the constraints that a phase of backreaction-driven accelerated expansion might put on the anisotropy of the averaged domain. We close by assessing the status of these and other attempts to define and calculate 'average' spacetime behaviour in general relativity

  15. Inheritance of the yeast mitochondrial genome

    DEFF Research Database (Denmark)

    Piskur, Jure

    1994-01-01

    Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast......Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast...

  16. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

    Science.gov (United States)

    Winkler, Thomas W; Justice, Anne E; Graff, Mariaelisa; Barata, Llilda; Feitosa, Mary F; Chu, Su; Czajkowski, Jacek; Esko, Tõnu; Fall, Tove; Kilpeläinen, Tuomas O; Lu, Yingchang; Mägi, Reedik; Mihailov, Evelin; Pers, Tune H; Rüeger, Sina; Teumer, Alexander; Ehret, Georg B; Ferreira, Teresa; Heard-Costa, Nancy L; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M; Jansen, Rick; Westra, Harm-Jan; White, Charles C; Absher, Devin; Ahluwalia, Tarunveer S; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L; de Craen, Anton J M; Bis, Joshua C; Bonnefond, Amélie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W K; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E; Jackson, Anne U; Jacobs, Kevin B; Johansson, Åsa; Kaakinen, Marika; Kleber, Marcus E; Lahti, Jari; Mateo Leach, Irene; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A F; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L; Montasser, May E; Müller, Gabriele; Müller-Nurasyid, Martina; Nolte, Ilja M; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W; Renström, Frida; Rizzi, Federica; Rose, Lynda M; Ryan, Kathy A; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stančáková, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P; Vandenput, Liesbeth; van der Laan, Sander W; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L; Wang, Sophie R; Wang, Zhaoming; Wild, Sarah H; Willenborg, Christina; Wilson, James F; Wong, Andrew; Yang, Jian; Yengo, Loïc; Yerges-Armstrong, Laura M; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A; Bakker, Stephan J L; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blüher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L; Boyd, Heather A; Bruinenberg, Marcel; Buchman, Aron S; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S; Claudi-Boehm, Simone; Cole, John; Collins, Francis S; de Geus, Eco J C; de Groot, Lisette C P G M; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G; Friedrich, Nele; Gejman, Pablo V; Gigante, Bruna; Glorioso, Nicola; Go, Alan S; Gottesman, Omri; Gräßler, Jürgen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C; Hansen, Torben; Harris, Tamara B; Hartman, Catharina A; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T; Heath, Andrew C; Henders, Anjali K; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G; Hui, Jennie; Husemoen, Lise L; Hutri-Kähönen, Nina; Hysi, Pirro G; Illig, Thomas; De Jager, Philip L; Jalilzadeh, Shapour; Jørgensen, Torben; Jukema, J Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T; Kratzer, Wolfgang; Krüger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J; Leander, Karin; Lindström, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stéphane; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Magnusson, Patrik K; McArdle, Wendy L; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W; Morris, Andrew P; Narisu, Narisu; Nelis, Mari; Ong, Ken K; Palotie, Aarno; Pérusse, Louis; Pichler, Irene; Pilia, Maria G; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M; Rice, Treva K; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R; Sarzynski, Mark A; Scholtens, Salome; Scott, Robert A; Scott, William R; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P Eline; Smit, Jan H; Sparsø, Thomas H; Stirrups, Kathleen; Stolk, Ronald P; Stringham, Heather M; Swertz, Morris A; Swift, Amy J; Syvänen, Ann-Christine; Tan, Sian-Tsung; Thorand, Barbara; Tönjes, Anke; Tremblay, Angelo; Tsafantakis, Emmanouil; van der Most, Peter J; Völker, Uwe; Vohl, Marie-Claude; Vonk, Judith M; Waldenberger, Melanie; Walker, Ryan W; Wennauer, Roman; Widén, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Wright, Alan F; Zillikens, M Carola; van Dijk, Suzanne C; van Schoor, Natasja M; Asselbergs, Folkert W; de Bakker, Paul I W; Beckmann, Jacques S; Beilby, John; Bennett, David A; Bergman, Richard N; Bergmann, Sven; Böger, Carsten A; Boehm, Bernhard O; Boerwinkle, Eric; Boomsma, Dorret I; Bornstein, Stefan R; Bottinger, Erwin P; Bouchard, Claude; Chambers, John C; Chanock, Stephen J; Chasman, Daniel I; Cucca, Francesco; Cusi, Daniele; Dedoussis, George; Erdmann, Jeanette; Eriksson, Johan G; Evans, Denis A; de Faire, Ulf; Farrall, Martin; Ferrucci, Luigi; Ford, Ian; Franke, Lude; Franks, Paul W; Froguel, Philippe; Gansevoort, Ron T; Gieger, Christian; Grönberg, Henrik; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Per; Hamsten, Anders; van der Harst, Pim; Hayward, Caroline; Heliövaara, Markku; Hengstenberg, Christian; Hicks, Andrew A; Hingorani, Aroon; Hofman, Albert; Hu, Frank; Huikuri, Heikki V; Hveem, Kristian; James, Alan L; Jordan, Joanne M; Jula, Antti; Kähönen, Mika; Kajantie, Eero; Kathiresan, Sekar; Kiemeney, Lambertus A L M; Kivimaki, Mika; Knekt, Paul B; Koistinen, Heikki A; Kooner, Jaspal S; Koskinen, Seppo; Kuusisto, Johanna; Maerz, Winfried; Martin, Nicholas G; Laakso, Markku; Lakka, Timo A; Lehtimäki, Terho; Lettre, Guillaume; Levinson, Douglas F; Lind, Lars; Lokki, Marja-Liisa; Mäntyselkä, Pekka; Melbye, Mads; Metspalu, Andres; Mitchell, Braxton D; Moll, Frans L; Murray, Jeffrey C; Musk, Arthur W; Nieminen, Markku S; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J; Oostra, Ben A; Palmer, Lyle J; Pankow, James S; Pasterkamp, Gerard; Pedersen, Nancy L; Pedersen, Oluf; Penninx, Brenda W; Perola, Markus; Peters, Annette; Polašek, Ozren; Pramstaller, Peter P; Psaty, Bruce M; Qi, Lu; Quertermous, Thomas; Raitakari, Olli T; Rankinen, Tuomo; Rauramaa, Rainer; Ridker, Paul M; Rioux, John D; Rivadeneira, Fernando; Rotter, Jerome I; Rudan, Igor; den Ruijter, Hester M; Saltevo, Juha; Sattar, Naveed; Schunkert, Heribert; Schwarz, Peter E H; Shuldiner, Alan R; Sinisalo, Juha; Snieder, Harold; Sørensen, Thorkild I A; Spector, Tim D; Staessen, Jan A; Stefania, Bandinelli; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tardif, Jean-Claude; Tremoli, Elena; Tuomilehto, Jaakko; Uitterlinden, André G; Uusitupa, Matti; Verbeek, André L M; Vermeulen, Sita H; Viikari, Jorma S; Vitart, Veronique; Völzke, Henry; Vollenweider, Peter; Waeber, Gérard; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J; Watkins, Hugh; Zeggini, Eleftheria; Chakravarti, Aravinda; Clegg, Deborah J; Cupples, L Adrienne; Gordon-Larsen, Penny; Jaquish, Cashell E; Rao, D C; Abecasis, Goncalo R; Assimes, Themistocles L; Barroso, Inês; Berndt, Sonja I; Boehnke, Michael; Deloukas, Panos; Fox, Caroline S; Groop, Leif C; Hunter, David J; Ingelsson, Erik; Kaplan, Robert C; McCarthy, Mark I; Mohlke, Karen L; O'Connell, Jeffrey R; Schlessinger, David; Strachan, David P; Stefansson, Kari; van Duijn, Cornelia M; Hirschhorn, Joel N; Lindgren, Cecilia M; Heid, Iris M; North, Kari E; Borecki, Ingrid B; Kutalik, Zoltán; Loos, Ruth J F

    2015-10-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape. PMID:26426971

  17. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

    Science.gov (United States)

    Feitosa, Mary F.; Chu, Su; Czajkowski, Jacek; Esko, Tõnu; Fall, Tove; Kilpeläinen, Tuomas O.; Lu, Yingchang; Mägi, Reedik; Mihailov, Evelin; Pers, Tune H.; Rüeger, Sina; Teumer, Alexander; Ehret, Georg B.; Ferreira, Teresa; Heard-Costa, Nancy L.; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D.; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M.; Jansen, Rick; Westra, Harm-Jan; White, Charles C.; Absher, Devin; Ahluwalia, Tarunveer S.; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L.; de Craen, Anton J. M.; Bis, Joshua C.; Bonnefond, Amélie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W. K.; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E.; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B.; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E.; Jackson, Anne U.; Jacobs, Kevin B.; Johansson, Åsa; Kaakinen, Marika; Kleber, Marcus E.; Lahti, Jari; Leach, Irene Mateo; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A. F.; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L.; Montasser, May E.; Müller, Gabriele; Müller-Nurasyid, Martina; Nolte, Ilja M.; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W.; Renström, Frida; Rizzi, Federica; Rose, Lynda M.; Ryan, Kathy A.; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stančáková, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J.; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P.; Vandenput, Liesbeth; van der Laan, Sander W; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L.; Wang, Sophie R.; Wang, Zhaoming; Wild, Sarah H.; Willenborg, Christina; Wilson, James F.; Wong, Andrew; Yang, Jian; Yengo, Loïc; Yerges-Armstrong, Laura M.; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A.; Bakker, Stephan J. L.; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blüher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L.; Boyd, Heather A.; Bruinenberg, Marcel; Buchman, Aron S; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S.; Claudi-Boehm, Simone; Cole, John; Collins, Francis S.; de Geus, Eco J. C.; de Groot, Lisette C. P. G. M.; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G.; Friedrich, Nele; Gejman, Pablo V.; Gigante, Bruna; Glorioso, Nicola; Go, Alan S.; Gottesman, Omri; Gräßler, Jürgen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C.; Hansen, Torben; Harris, Tamara B.; Hartman, Catharina A.; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T.; Heath, Andrew C.; Henders, Anjali K.; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G; Hui, Jennie; Husemoen, Lise L.; Hutri-Kähönen, Nina; Hysi, Pirro G.; Illig, Thomas; De Jager, Philip L.; Jalilzadeh, Shapour; Jørgensen, Torben; Jukema, J. Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J.; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T.; Kratzer, Wolfgang; Krüger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J.; Leander, Karin; Lindström, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stéphane; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Magnusson, Patrik K.; McArdle, Wendy L.; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W.; Morris, Andrew P.; Narisu, Narisu; Nelis, Mari; Ong, Ken K.; Palotie, Aarno; Pérusse, Louis; Pichler, Irene; Pilia, Maria G.; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M.; Rice, Treva K.; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R.; Sarzynski, Mark A.; Scholtens, Salome; Scott, Robert A.; Scott, William R.; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P. Eline; Smit, Jan H.; Sparsø, Thomas H.; Stirrups, Kathleen; Stolk, Ronald P.; Stringham, Heather M.; Swertz, Morris A; Swift, Amy J.; Syvänen, Ann-Christine; Tan, Sian-Tsung; Thorand, Barbara; Tönjes, Anke; Tremblay, Angelo; Tsafantakis, Emmanouil; van der Most, Peter J.; Völker, Uwe; Vohl, Marie-Claude; Vonk, Judith M.; Waldenberger, Melanie; Walker, Ryan W.; Wennauer, Roman; Widén, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Wright, Alan F.; Zillikens, M. Carola; van Dijk, Suzanne C.; van Schoor, Natasja M.; Asselbergs, Folkert W.; de Bakker, Paul I. W.; Beckmann, Jacques S.; Beilby, John; Bennett, David A.; Bergman, Richard N.; Bergmann, Sven; Böger, Carsten A.; Boehm, Bernhard O.; Boerwinkle, Eric; Boomsma, Dorret I.; Bornstein, Stefan R.; Bottinger, Erwin P.; Bouchard, Claude; Chambers, John C.; Chanock, Stephen J.; Chasman, Daniel I.; Cucca, Francesco; Cusi, Daniele; Dedoussis, George; Erdmann, Jeanette; Eriksson, Johan G.; Evans, Denis A.; de Faire, Ulf; Farrall, Martin; Ferrucci, Luigi; Ford, Ian; Franke, Lude; Franks, Paul W.; Froguel, Philippe; Gansevoort, Ron T.; Gieger, Christian; Grönberg, Henrik; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Per; Hamsten, Anders; van der Harst, Pim; Hayward, Caroline; Heliövaara, Markku; Hengstenberg, Christian; Hicks, Andrew A; Hingorani, Aroon; Hofman, Albert; Hu, Frank; Huikuri, Heikki V.; Hveem, Kristian; James, Alan L.; Jordan, Joanne M.; Jula, Antti; Kähönen, Mika; Kajantie, Eero; Kathiresan, Sekar; Kiemeney, Lambertus A. L. M.; Kivimaki, Mika; Knekt, Paul B.; Koistinen, Heikki A.; Kooner, Jaspal S.; Koskinen, Seppo; Kuusisto, Johanna; Maerz, Winfried; Martin, Nicholas G; Laakso, Markku; Lakka, Timo A.; Lehtimäki, Terho; Lettre, Guillaume; Levinson, Douglas F.; Lind, Lars; Lokki, Marja-Liisa; Mäntyselkä, Pekka; Melbye, Mads; Metspalu, Andres; Mitchell, Braxton D.; Moll, Frans L.; Murray, Jeffrey C.; Musk, Arthur W.; Nieminen, Markku S.; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J.; Oostra, Ben A.; Palmer, Lyle J; Pankow, James S.; Pasterkamp, Gerard; Pedersen, Nancy L.; Pedersen, Oluf; Penninx, Brenda W.; Perola, Markus; Peters, Annette; Polašek, Ozren; Pramstaller, Peter P.; Psaty, Bruce M.; Qi, Lu; Quertermous, Thomas; Raitakari, Olli T.; Rankinen, Tuomo; Rauramaa, Rainer; Ridker, Paul M.; Rioux, John D.; Rivadeneira, Fernando; Rotter, Jerome I.; Rudan, Igor; den Ruijter, Hester M.; Saltevo, Juha; Sattar, Naveed; Schunkert, Heribert; Schwarz, Peter E. H.; Shuldiner, Alan R.; Sinisalo, Juha; Snieder, Harold; Sørensen, Thorkild I. A.; Spector, Tim D.; Staessen, Jan A.; Stefania, Bandinelli; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tardif, Jean-Claude; Tremoli, Elena; Tuomilehto, Jaakko; Uitterlinden, André G.; Uusitupa, Matti; Verbeek, André L. M.; Vermeulen, Sita H.; Viikari, Jorma S.; Vitart, Veronique; Völzke, Henry; Vollenweider, Peter; Waeber, Gérard; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J.; Watkins, Hugh; Zeggini, Eleftheria; Chakravarti, Aravinda; Clegg, Deborah J.; Cupples, L. Adrienne; Gordon-Larsen, Penny; Jaquish, Cashell E.; Rao, D. C.; Abecasis, Goncalo R.; Assimes, Themistocles L.; Barroso, Inês; Berndt, Sonja I.; Boehnke, Michael; Deloukas, Panos; Fox, Caroline S.; Groop, Leif C.; Hunter, David J.; Ingelsson, Erik; Kaplan, Robert C.; McCarthy, Mark I.; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Hirschhorn, Joel N.; Lindgren, Cecilia M.; Heid, Iris M.; North, Kari E.; Borecki, Ingrid B.; Kutalik, Zoltán; Loos, Ruth J. F.

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape. PMID:26426971

  18. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

    Directory of Open Access Journals (Sweden)

    Thomas W Winkler

    2015-10-01

    Full Text Available Genome-wide association studies (GWAS have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI, a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE, sex-specific effects (G x SEX or age-specific effects that differed between men and women (G x AGE x SEX. For BMI, we identified 15 loci (11 previously established for main effects, four novel that showed significant (FDR<5% age-specific effects, of which 11 had larger effects in younger (<50y than in older adults (≥50y. No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.

  19. Averages of Values of L-Series

    OpenAIRE

    Alkan, Emre; Ono, Ken

    2013-01-01

    We obtain an exact formula for the average of values of L-series over two independent odd characters. The average of any positive moment of values at s = 1 is then expressed in terms of finite cotangent sums subject to congruence conditions. As consequences, bounds on such cotangent sums, limit points for the average of first moment of L-series at s = 1 and the average size of positive moments of character sums related to the class number are deduced.

  20. Average-energy games

    OpenAIRE

    Bouyer, Patricia; Markey, Nicolas; Randour, Mickael; Larsen, Kim G.; Laursen, Simon

    2015-01-01

    Two-player quantitative zero-sum games provide a natural framework to synthesize controllers with performance guarantees for reactive systems within an uncontrollable environment. Classical settings include mean-payoff games, where the objective is to optimize the long-run average gain per action, and energy games, where the system has to avoid running out of energy. We study average-energy games, where the goal is to optimize the long-run average of the accumulated energy. We show that this ...

  1. On Averaging Rotations

    DEFF Research Database (Denmark)

    Gramkow, Claus

    In this article two common approaches to averaging rotations are compared to a more advanced approach based on a Riemannian metric. Very offten the barycenter of the quaternions or matrices that represent the rotations are used as an estimate of the mean. These methods neglect that rotations belong...... natural approximations to the Riemannian metric, and that the subsequent corrections are inherient in the least squares estimation. Keywords: averaging rotations, Riemannian metric, matrix, quaternion...

  2. Average Angular Velocity

    OpenAIRE

    Van Essen, H.

    2004-01-01

    This paper addresses the problem of the separation of rotational and internal motion. It introduces the concept of average angular velocity as the moment of inertia weighted average of particle angular velocities. It extends and elucidates the concept of Jellinek and Li (1989) of separation of the energy of overall rotation in an arbitrary (non-linear) $N$-particle system. It generalizes the so called Koenig's theorem on the two parts of the kinetic energy (center of mass plus internal) to th...

  3. On the Averaging Principle

    OpenAIRE

    Fibich, Gadi; Gavious, Arieh; Solan, Eilon

    2012-01-01

    Typically, models with a heterogeneous property are considerably harder to analyze than the corresponding homogeneous models, in which the heterogeneous property is replaced with its average value. In this study we show that any outcome of a heterogeneous model that satisfies the two properties of differentiability and interchangibility is O(\\epsilon^2) equivalent to the outcome of the corresponding homogeneous model, where \\epsilon is the level of heterogeneity. We then use this averaging pr...

  4. On Averaging Rotations

    DEFF Research Database (Denmark)

    Gramkow, Claus

    1999-01-01

    In this article two common approaches to averaging rotations are compared to a more advanced approach based on a Riemannian metric. Very offten the barycenter of the quaternions or matrices that represent the rotations are used as an estimate of the mean. These methods neglect that rotations belong...... natural approximations to the Riemannian metric, and that the subsequent corrections are inherient in the least squares estimation. Keywords: averaging rotations, Riemannian metric, matrix, quaternion...

  5. Averaged extreme regression quantile

    OpenAIRE

    Jureckova, Jana

    2015-01-01

    Various events in the nature, economics and in other areas force us to combine the study of extremes with regression and other methods. A useful tool for reducing the role of nuisance regression, while we are interested in the shape or tails of the basic distribution, is provided by the averaged regression quantile and namely by the average extreme regression quantile. Both are weighted means of regression quantile components, with weights depending on the regressors. Our primary interest is ...

  6. Genomic Copy Number Variations in the Genomes of Leukocytes Predict Prostate Cancer Clinical Outcomes.

    Directory of Open Access Journals (Sweden)

    Yan P Yu

    Full Text Available Accurate prediction of prostate cancer clinical courses remains elusive. In this study, we performed whole genome copy number analysis on leukocytes of 273 prostate cancer patients using Affymetrix SNP6.0 chip. Copy number variations (CNV were found across all chromosomes of the human genome. An average of 152 CNV fragments per genome was identified in the leukocytes from prostate cancer patients. The size distributions of CNV in the genome of leukocytes were highly correlative with prostate cancer aggressiveness. A prostate cancer outcome prediction model was developed based on large size ratio of CNV from the leukocyte genomes. This prediction model generated an average prediction rate of 75.2%, with sensitivity of 77.3% and specificity of 69.0% for prostate cancer recurrence. When combined with Nomogram and the status of fusion transcripts, the average prediction rate was improved to 82.5% with sensitivity of 84.8% and specificity of 78.2%. In addition, the leukocyte prediction model was 62.6% accurate in predicting short prostate specific antigen doubling time. When combined with Gleason's grade, Nomogram and the status of fusion transcripts, the prediction model generated a correct prediction rate of 77.5% with 73.7% sensitivity and 80.1% specificity. To our knowledge, this is the first study showing that CNVs in leukocyte genomes are predictive of clinical outcomes of a human malignancy.

  7. Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.

    Directory of Open Access Journals (Sweden)

    Nicole Soranzo

    2009-04-01

    Full Text Available Recent genome-wide (GW scans have identified several independent loci affecting human stature, but their contribution through the different skeletal components of height is still poorly understood. We carried out a genome-wide scan in 12,611 participants, followed by replication in an additional 7,187 individuals, and identified 17 genomic regions with GW-significant association with height. Of these, two are entirely novel (rs11809207 in CATSPER4, combined P-value = 6.1x10(-8 and rs910316 in TMED10, P-value = 1.4x10(-7 and two had previously been described with weak statistical support (rs10472828 in NPR3, P-value = 3x10(-7 and rs849141 in JAZF1, P-value = 3.2x10(-11. One locus (rs1182188 at GNA12 identifies the first height eQTL. We also assessed the contribution of height loci to the upper- (trunk and lower-body (hip axis and femur skeletal components of height. We find evidence for several loci associated with trunk length (including rs6570507 in GPR126, P-value = 4x10(-5 and rs6817306 in LCORL, P-value = 4x10(-4, hip axis length (including rs6830062 at LCORL, P-value = 4.8x10(-4 and rs4911494 at UQCC, P-value = 1.9x10(-4, and femur length (including rs710841 at PRKG2, P-value = 2.4x10(-5 and rs10946808 at HIST1H1D, P-value = 6.4x10(-6. Finally, we used conditional analyses to explore a possible differential contribution of the height loci to these different skeletal size measurements. In addition to validating four novel loci controlling adult stature, our study represents the first effort to assess the contribution of genetic loci to three skeletal components of height. Further statistical tests in larger numbers of individuals will be required to verify if the height loci affect height preferentially through these subcomponents of height.

  8. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  9. Averaging anisotropic cosmologies

    CERN Document Server

    Barrow, J D; Barrow, John D.; Tsagas, Christos G.

    2006-01-01

    We examine the effects of spatial inhomogeneities on irrotational anisotropic cosmologies by looking at the average properties of pressure-free Bianchi-type models. Adopting the Buchert averaging scheme, we identify the kinematic backreaction effects by focussing on spacetimes with zero or isotropic spatial curvature. This allows us to close the system of the standard scalar formulae with a propagation equation for the shear magnitude. We find no change in the already known conditions for accelerated expansion. The backreaction terms are expressed as algebraic relations between the mean-square fluctuations of the models' irreducible kinematical variables. Based on these we investigate the early evolution of averaged vacuum Bianchi type $I$ universes and those filled with pressureless matter. In the latter case we show that the backreaction effects can modify the familiar Kasner-like singularity and potentially remove Mixmaster-type oscillations. We also discuss the possibility of accelerated expansion due to ...

  10. 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.

  11. Average Angular Velocity

    CERN Document Server

    Essén, H

    2003-01-01

    This paper addresses the problem of the separation of rotational and internal motion. It introduces the concept of average angular velocity as the moment of inertia weighted average of particle angular velocities. It extends and elucidates the concept of Jellinek and Li (1989) of separation of the energy of overall rotation in an arbitrary (non-linear) $N$-particle system. It generalizes the so called Koenig's theorem on the two parts of the kinetic energy (center of mass plus internal) to three parts: center of mass, rotational, plus the remaining internal energy relative to an optimally translating and rotating frame.

  12. On sparsity averaging

    CERN Document Server

    Carrillo, Rafael E; Wiaux, Yves

    2013-01-01

    Recent developments in Carrillo et al. (2012) and Carrillo et al. (2013) introduced a novel regularization method for compressive imaging in the context of compressed sensing with coherent redundant dictionaries. The approach relies on the observation that natural images exhibit strong average sparsity over multiple coherent frames. The associated reconstruction algorithm, based on an analysis prior and a reweighted $\\ell_1$ scheme, is dubbed Sparsity Averaging Reweighted Analysis (SARA). We review these advances and extend associated simulations establishing the superiority of SARA to regularization methods based on sparsity in a single frame, for a generic spread spectrum acquisition and for a Fourier acquisition of particular interest in radio astronomy.

  13. Comprehensive human genome amplification using multiple displacement amplification

    OpenAIRE

    Dean, Frank B.; Hosono, Seiyu; Fang, Linhua; Wu, Xiaohong; Faruqi, A. Fawad; Bray-Ward, Patricia; Zhenyu SUN; Zong, Qiuling; Du, Yuefen; Du, Jing; Driscoll, Mark; Song, Wanmin; Kingsmore, Stephen F.; Egholm, Michael; Lasken, Roger S.

    2002-01-01

    Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multi...

  14. On Averaging Rotations

    DEFF Research Database (Denmark)

    Gramkow, Claus

    2001-01-01

    In this paper two common approaches to averaging rotations are compared to a more advanced approach based on a Riemannian metric. Very often the barycenter of the quaternions or matrices that represent the rotations are used as an estimate of the mean. These methods neglect that rotations belong to...

  15. Labour Turnover Costs and Average Labour Demand

    OpenAIRE

    Bertola, Giuseppe

    1991-01-01

    The effect of labour turnover costs on average employment in a partial equilibrium model of labour demand, depends on the form of the revenue function, on the rates of discount and labour attrition, and on the relative size of hiring and firing costs. If discount and attrition rates are strictly positive, firing costs may well increase average employment even when hiring costs reduce it.

  16. Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples

    OpenAIRE

    Brittan S Scales; Erb-Downward, John R.; LiPuma, John J.; Huffnagle, Gary B.

    2015-01-01

    We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical samples. Phylogenetic analysis places three in subclade I and two in subclade II of the P. fluorescens species complex. The average G+C content and genomic size are 63% and 7.1 Mbp (subclade I) and 59.6% and 6.14 Mbp (subclade II), respectively.

  17. Covariant approximation averaging

    CERN Document Server

    Shintani, Eigo; Blum, Thomas; Izubuchi, Taku; Jung, Chulwoo; Lehner, Christoph

    2014-01-01

    We present a new class of statistical error reduction techniques for Monte-Carlo simulations. Using covariant symmetries, we show that correlation functions can be constructed from inexpensive approximations without introducing any systematic bias in the final result. We introduce a new class of covariant approximation averaging techniques, known as all-mode averaging (AMA), in which the approximation takes account of contributions of all eigenmodes through the inverse of the Dirac operator computed from the conjugate gradient method with a relaxed stopping condition. In this paper we compare the performance and computational cost of our new method with traditional methods using correlation functions and masses of the pion, nucleon, and vector meson in $N_f=2+1$ lattice QCD using domain-wall fermions. This comparison indicates that AMA significantly reduces statistical errors in Monte-Carlo calculations over conventional methods for the same cost.

  18. The averaging principle

    OpenAIRE

    Fibich, Gadi; Gavious, Arieh; Solan, Eilon

    2012-01-01

    Typically, models with a heterogeneous property are considerably harder to analyze than the corresponding homogeneous models, in which the heterogeneous property is replaced with its average value. In this study we show that any outcome of a heterogeneous model that satisfies the two properties of \\emph{differentiability} and \\emph{interchangibility}, is $O(\\epsilon^2)$ equivalent to the outcome of the corresponding homogeneous model, where $\\epsilon$ is the level of heterogeneity. We then us...

  19. Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information

    Directory of Open Access Journals (Sweden)

    Aguilar Ignacio

    2011-01-01

    Full Text Available Abstract Background The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships, there is a question of which is optimal and what the effects of deviations from optimality are. Methods Data of litter size (total number born per litter for 338,346 sows were analyzed. Illumina PorcineSNP60 BeadChip genotypes were available for 1,989. Analyses were carried out with the complete data set and with a subset of genotyped animals and three generations pedigree (5,090 animals. A single-trait animal model was used to estimate variance components and breeding values. Genomic relationship matrices were constructed using allele frequencies equal to 0.5 (G05, equal to the average minor allele frequency (GMF, or equal to observed frequencies (GOF. A genomic matrix considering random ascertainment of allele frequencies was also used (GOF*. A normalized matrix (GN was obtained to have average diagonal coefficients equal to 1. The genomic matrices were combined with the numerator relationship matrix creating H matrices. Results In G05 and GMF, both diagonal and off-diagonal elements were on average greater than the pedigree-based coefficients. In GOF and GOF*, the average diagonal elements were smaller than pedigree-based coefficients. The mean of off-diagonal coefficients was zero in GOF and GOF*. Choices of G with average diagonal coefficients different from 1 led to greater estimates of additive variance in the smaller data set. The correlation between EBV and genomic EBV (n = 1,989 were: 0.79 using G05, 0.79 using GMF, 0.78 using GOF, 0.79 using GOF*, and 0.78 using GN. Accuracies calculated by inversion increased with all genomic matrices. The accuracies of genomic-assisted EBV

  20. Average Equivalent Diameter of A Particulate Material

    OpenAIRE

    AL-MAGHRABI, Mohammed-Noor N. H.

    2010-01-01

    In the field of mineral processing, it is important to determine the size of a particle. A method of defining an average diameter for a collection of particles is presented. The theoretical basis developed for the purpose is verified by a specially designed experimental technique.  Key words: mineral processing, particle size, equivalent diameter

  1. 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...

  2. Negative Average Preference Utilitarianism

    Directory of Open Access Journals (Sweden)

    Roger Chao

    2012-03-01

    Full Text Available For many philosophers working in the area of Population Ethics, it seems that either they have to confront the Repugnant Conclusion (where they are forced to the conclusion of creating massive amounts of lives barely worth living, or they have to confront the Non-Identity Problem (where no one is seemingly harmed as their existence is dependent on the “harmful” event that took place. To them it seems there is no escape, they either have to face one problem or the other. However, there is a way around this, allowing us to escape the Repugnant Conclusion, by using what I will call Negative Average Preference Utilitarianism (NAPU – which though similar to anti-frustrationism, has some important differences in practice. Current “positive” forms of utilitarianism have struggled to deal with the Repugnant Conclusion, as their theory actually entails this conclusion; however, it seems that a form of Negative Average Preference Utilitarianism (NAPU easily escapes this dilemma (it never even arises within it.

  3. Average nuclear surface properties

    International Nuclear Information System (INIS)

    The definition of the nuclear surface energy is discussed for semi-infinite matter. This definition is extended also for the case that there is a neutron gas instead of vacuum on the one side of the plane surface. The calculations were performed with the Thomas-Fermi Model of Syler and Blanchard. The parameters of the interaction of this model were determined by a least squares fit to experimental masses. The quality of this fit is discussed with respect to nuclear masses and density distributions. The average surface properties were calculated for different particle asymmetry of the nucleon-matter ranging from symmetry beyond the neutron-drip line until the system no longer can maintain the surface boundary and becomes homogeneous. The results of the calculations are incorporated in the nuclear Droplet Model which then was fitted to experimental masses. (orig.)

  4. Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite Begomoviruses

    OpenAIRE

    Ho, Eric S; Kuchie, Joan; Duffy, Siobain

    2014-01-01

    Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss, particularly in developing countries. The bipartite genome of begomoviruses prevalent in the New World and their counterparts in the Old World share a high degree of genome homology except for a ...

  5. A genome-wide survey of switchgrass genome structure and organization.

    Directory of Open Access Journals (Sweden)

    Manoj K Sharma

    Full Text Available The perennial grass, switchgrass (Panicum virgatum L., is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated and 110 kb (BstYI-generated. A total of 330,297 high quality BAC-end sequences (BES were generated, accounting for 263.2 Mbp (16.4% of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs. Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.

  6. Modeling and Instability of Average Current Control

    OpenAIRE

    Fang, Chung-Chieh

    2012-01-01

    Dynamics and stability of average current control of DC-DC converters are analyzed by sampled-data modeling. Orbital stability is studied and it is found unrelated to the ripple size of the orbit. Compared with the averaged modeling, the sampled-data modeling is more accurate and systematic. An unstable range of compensator pole is found by simulations, and is predicted by sampled-data modeling and harmonic balance modeling.

  7. Disk-averaged synthetic spectra of Mars

    OpenAIRE

    Tinetti, Giovanna; Meadows, Victoria S.; Crisp, David; Fong, William; Velusamy, Thangasamy; Snively, Heather

    2004-01-01

    The principal goal of the NASA Terrestrial Planet Finder (TPF) and ESA Darwin mission concepts is to directly detect and characterize extrasolar terrestrial (Earth-sized) planets. This first generation of instruments is expected to provide disk-averaged spectra with modest spectral resolution and signal-to-noise. Here we use a spatially and spectrally resolved model of the planet Mars to study the detectability of a planet's surface and atmospheric properties from disk-averaged spectra as a f...

  8. Survey of genome size in 10 invertebrates from hydrothermal vent and cold seep%热液和冷泉10种无脊椎动物基因组大小测定及比较

    Institute of Scientific and Technical Information of China (English)

    郑平; 王敏晓; 李超伦; 孙松

    2016-01-01

    Knowledge of genome size is an important prerequisite for the development of many genomic resources. To better understand the evolution of genome size and their roles in environmental adaption,it is necessary to col-lect data covering a broad taxonomic base,especially from particular ecosystems.With high disturbance and unique environmental features,hydrothermal vent and cold seep offer a typical model to investigate the variation of genome size under extreme environments.Here we measured 10 deep-sea invertebrates from hydrothermal vent and cold seep by flow cytometry.The C-value ranged from 0.87 pg to 12.28 pg,and the crustaceans have larger genomes. Then we compared the three common species (Bathymodiolus platifrons ,Shinkaia crosnieri and Alvinocaris lon-girostris )in both environments.Though with high level of intraspecific variations,no significant differences were revealed between two populations.We also compared the obtained genome sizes to their corresponding taxonomic relatives (at family or order level).No evidence of genome size expansion or reduction were found in invertebrates from chemosynthetic environments.In our study,there are no clear trends of the genome size variations under the extreme deep-sea ecological conditions.%基因组大小(或称 C 值)作为生物单倍体细胞中全套染色体的 DNA 总量,在一定程度上是恒定的,因而 C 值可以作为生物物种的一个特定参数。深海热液和冷泉为更好地理解 C 值与不同环境之间的关系提供了一个特征性的模型。本文采用流式细胞术,测定了来自热液和冷泉环境中的10种深海无脊椎动物的 C 值,其分布范围从0.87 pg 到12.28 pg,其中,相比于软体动物和多毛类,甲壳生物基因组大小及变异均较大。对比热液和冷泉两个群落中共有种(深海偏顶蛤 Bathymodiolus plati-frons 、柯氏潜铠虾 Shinkaia crosnieri 以及长角阿尔文虾Alvinocaris longirostris

  9. Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea

    Directory of Open Access Journals (Sweden)

    Joon-Hee Han

    2016-06-01

    Full Text Available Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760 bp in size with a G + C content of 51.73% in 27 scaffolds and to contain 13,559 genes with an average length of 1516 bp. Gene prediction and annotation were performed by incorporating RNA-Seq data. The genome sequence of the KC05 was deposited at DDBJ/ENA/GenBank under the accession number LUXP00000000.

  10. Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea.

    Science.gov (United States)

    Han, Joon-Hee; Chon, Jae-Kyung; Ahn, Jong-Hwa; Choi, Ik-Young; Lee, Yong-Hwan; Kim, Kyoung Su

    2016-06-01

    Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760 bp in size with a G + C content of 51.73% in 27 scaffolds and to contain 13,559 genes with an average length of 1516 bp. Gene prediction and annotation were performed by incorporating RNA-Seq data. The genome sequence of the KC05 was deposited at DDBJ/ENA/GenBank under the accession number LUXP00000000. PMID:27114908

  11. Average Drift Analysis and Population Scalability

    OpenAIRE

    He, Jun; Yao, Xin

    2013-01-01

    This paper aims to study how the population size affects the computation time of evolutionary algorithms in a rigorous way. The computation time of an evolutionary algorithm can be measured by either the expected number of generations (hitting time) or the expected number of fitness evaluations (running time) to find an optimal solution. Population scalability is the ratio of the expected hitting time between a benchmark algorithm and an algorithm using a larger population size. Average drift...

  12. Otero County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  13. Santa Fe County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  14. Quay County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  15. Bernalillo County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  16. Dona Ana County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  17. Chaves County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  18. Curry County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  19. San Miguel County Blocks, Average Household Size by Tenure (2010)

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The once-a-decade decennial census was conducted in April 2010 by the U.S. Census Bureau. This count of every resident in the United States was mandated by Article...

  20. Virtual Averaging Making Nonframe-Averaged Optical Coherence Tomography Images Comparable to Frame-Averaged Images

    OpenAIRE

    Chen, Chieh-Li; Ishikawa, Hiroshi; Wollstein, Gadi; Bilonick, Richard A.; Kagemann, Larry; Schuman, Joel S.

    2016-01-01

    Purpose Developing a novel image enhancement method so that nonframe-averaged optical coherence tomography (OCT) images become comparable to active eye-tracking frame-averaged OCT images. Methods Twenty-one eyes of 21 healthy volunteers were scanned with noneye-tracking nonframe-averaged OCT device and active eye-tracking frame-averaged OCT device. Virtual averaging was applied to nonframe-averaged images with voxel resampling and adding amplitude deviation with 15-time repetitions. Signal-to...

  1. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

    Directory of Open Access Journals (Sweden)

    Muehlbauer Gary J

    2010-12-01

    Full Text Available Abstract Background Considerations in applying association mapping (AM to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102 assembled at the start of the Barley Coordinated Agricultural Project (CAP. This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608. Results Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without a priori knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We

  2. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.;

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of...... tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios....... RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a...

  3. Construction of Oryza Sativa genome contigs by fingerprint strategy

    Institute of Scientific and Technical Information of China (English)

    TAOQUAZHOU; GUOFANHONG; 等

    1995-01-01

    We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa.Guang Lu Ai 4. An entire representative(Sixfold coverage of rice chromosomes)and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis.And all the images thus obtained were subject to image-processing,which consisted of preliminary location of bands,cooperative tracking of lanes by correlation of adjacent bads.a precise densitometric pass,alignment at the marker bands with the standard,optional interactive editing,and normalization of the accepted bands.The contigs were generated based on the Computer Software specially designed for genome mapping.The number of contigs with 600 kb in length on average was 464.of contigs with 1000kb in length on average was 107; of contigs with 1500 kb in length on average was Construction of Oryza Sativa genome contigs.23.Therefor,all the contigs we have obtained ampunted up to 420 megabases in length.Considering the size of rice genome(430 megabased),the contigs generated in this lab have covered nearly 98% of the rice genome.We are now in the process of mapping the contigs to chromosomes.

  4. Microbial genomic taxonomy.

    Science.gov (United States)

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes,  70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  5. Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation.

    Science.gov (United States)

    Ciandrini, Luca; Stansfield, Ian; Romano, M Carmen

    2013-01-01

    To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function. PMID:23382661

  6. Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture

    OpenAIRE

    Bhatia, Gaurav; Tandon, Arti; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; William J Blot; Bock, Cathryn H.; Caporaso, Neil; Casey, Graham; Deming, Sandra L.; Diver, W Ryan; Gapstur, Susan M

    2013-01-01

    We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent study of selection in...

  7. Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

    OpenAIRE

    Ciandrini, Luca; Stansfield, Ian; Romano, M. Carmen

    2013-01-01

    To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and...

  8. Extensive variation in chromosome number and genome size in sexual and parthenogenetic species of the jumping-bristletail genus Machilis (Archaeognatha)

    Czech Academy of Sciences Publication Activity Database

    Gassner, M.; Dejaco, T.; Schönswetter, P.; Marec, František; Arthofer, W.; Schlick-Steiner, B. C.; Steiner, F. M.

    2014-01-01

    Roč. 4, č. 21 (2014), s. 4093-4105. ISSN 2045-7758 R&D Projects: GA ČR(CZ) GA14-22765S Grant ostatní: University of Innsbruck(AT) 40.3/22306/27.01.2014 Institutional support: RVO:60077344 Keywords : asexuality * chromosomal speciation * genome downsizing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.320, year: 2014

  9. Human facial beauty : Averageness, symmetry, and parasite resistance.

    Science.gov (United States)

    Thornhill, R; Gangestad, S W

    1993-09-01

    It is hypothesized that human faces judged to be attractive by people possess two features-averageness and symmetry-that promoted adaptive mate selection in human evolutionary history by way of production of offspring with parasite resistance. Facial composites made by combining individual faces are judged to be attractive, and more attractive than the majority of individual faces. The composites possess both symmetry and averageness of features. Facial averageness may reflect high individual protein heterozygosity and thus an array of proteins to which parasites must adapt. Heterozygosity may be an important defense of long-lived hosts against parasites when it occurs in portions of the genome that do not code for the essential features of complex adaptations. In this case heterozygosity can create a hostile microenvironment for parasites without disrupting adaptation. Facial bilateral symmetry is hypothesized to affect positive beauty judgments because symmetry is a certification of overall phenotypic quality and developmental health, which may be importantly influenced by parasites. Certain secondary sexual traits are influenced by testosterone, a hormone that reduces immunocompetence. Symmetry and size of the secondary sexual traits of the face (e.g., cheek bones) are expected to correlate positively and advertise immunocompetence honestly and therefore to affect positive beauty judgments. Facial attractiveness is predicted to correlate with attractive, nonfacial secondary sexual traits; other predictions from the view that parasite-driven selection led to the evolution of psychological adaptations of human beauty perception are discussed. The view that human physical attractiveness and judgments about human physical attractiveness evolved in the context of parasite-driven selection leads to the hypothesis that both adults and children have a species-typical adaptation to the problem of identifying and favoring healthy individuals and avoiding parasite

  10. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.

    Directory of Open Access Journals (Sweden)

    Mirte Bosse

    Full Text Available Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand

  11. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine.

    Science.gov (United States)

    Chaitanya, Lakshmi; Ralf, Arwin; van Oven, Mannis; Kupiec, Tomasz; Chang, Joseph; Lagacé, Robert; Kayser, Manfred

    2015-12-01

    Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications. PMID:26387877

  12. Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation.

    Directory of Open Access Journals (Sweden)

    Luca Ciandrini

    Full Text Available To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function.

  13. Tamanho da leitegada e pesos médios, ao nascer e aos 21 dias de idade, de leitões da raça Large White Litter size and average weights at birth and at 21 days of age of Large White piglets

    Directory of Open Access Journals (Sweden)

    M.C.R. Holanda

    2005-08-01

    Full Text Available Avaliaram-se os efeitos da época de parto e idade da matriz ao parto (IMP sobre o tamanho da leitegada (TL, da época de parto, idade da matriz ao parto e tamanho da leitegada sobre o peso médio ao nascer (PMN, e da época de parto, idade da matriz ao parto, número de nascidos vivos (NV e percentual de machos na leitegada (PERCM sobre o peso aos 21 dias de idade (PM21 de leitões Large White. Utilizaram-se dados de 3259 leitões nascidos no período de junho/85 a junho/96. A avaliação foi feita por meio de regressão múltipla. Para TL apenas o efeito de IMP determinou modificações significativas sobre o número de leitões nascidos. TL médio foi 9,73±2,78, observando-se maiores leitegadas em fêmeas de 2,84 a 3,83 anos. PMN e PM21 foram 1,35kg±0,18 e 5,06kg±1,00, respectivamente. Para PMN foram significativos os efeitos de IMP e TL, com redução do peso em 20g para cada leitão adicional. Para PM21 apenas o número de NV apresentou efeito significativo.The effects of season of birth (PE and age of sow at birth (IMP on litter size (TL; season of birth, age of sow and litter size on average weight at birth (PMN; season of birth age of sow, number of alive piglets at birth (NV, and percentage of alive males on average weight at 21 days of age (PM21 of 3259 Large White piglets born from June/85 to June/96 were evaluated by multiple regression analyses. The IMP effect on TL was significant. The average TL was 9.73±2.78. Larger litters were observed for sows from 2.84 to 3.83 years of age. The average PMN and PM21 were 1.35kg±0.18 e 5.06kg±1.00, respectively. The IMP and TL effects on PMN traits were linear and significant. A decrease of 20g on piglet weight was estimated for each additional piglet in the litter. The effect of NV was significant only for PM21 trait.

  14. Average Range and Network Synchronizability

    International Nuclear Information System (INIS)

    The influence of structural properties of a network on the network synchronizability is studied by introducing a new concept of average range of edges. For both small-world and scale-free networks, the effect of average range on the synchronizability of networks with bounded or unbounded synchronization regions is illustrated through numerical simulations. The relations between average range, range distribution, average distance, and maximum betweenness are also explored, revealing the effects of these factors on the network synchronizability of the small-world and scale-free networks, respectively. (general)

  15. Physical Theories with Average Symmetry

    CERN Document Server

    Alamino, Roberto C

    2013-01-01

    This Letter probes the existence of physical laws invariant only in average when subjected to some transformation. The concept of a symmetry transformation is broadened to include corruption by random noise and average symmetry is introduced by considering functions which are invariant only in average under these transformations. It is then shown that actions with average symmetry obey a modified version of Noether's Theorem with dissipative currents. The relation of this with possible violations of physical symmetries, as for instance Lorentz invariance in some quantum gravity theories, is briefly commented.

  16. Genome sequence of Aedes aegypti, a major arbovirus vector.

    Science.gov (United States)

    Nene, Vishvanath; Wortman, Jennifer R; Lawson, Daniel; Haas, Brian; Kodira, Chinnappa; Tu, Zhijian Jake; Loftus, Brendan; Xi, Zhiyong; Megy, Karyn; Grabherr, Manfred; Ren, Quinghu; Zdobnov, Evgeny M; Lobo, Neil F; Campbell, Kathryn S; Brown, Susan E; Bonaldo, Maria F; Zhu, Jingsong; Sinkins, Steven P; Hogenkamp, David G; Amedeo, Paolo; Arensburger, Peter; Atkinson, Peter W; Bidwell, Shelby; Biedler, Jim; Birney, Ewan; Bruggner, Robert V; Costas, Javier; Coy, Monique R; Crabtree, Jonathan; Crawford, Matt; Debruyn, Becky; Decaprio, David; Eiglmeier, Karin; Eisenstadt, Eric; El-Dorry, Hamza; Gelbart, William M; Gomes, Suely L; Hammond, Martin; Hannick, Linda I; Hogan, James R; Holmes, Michael H; Jaffe, David; Johnston, J Spencer; Kennedy, Ryan C; Koo, Hean; Kravitz, Saul; Kriventseva, Evgenia V; Kulp, David; Labutti, Kurt; Lee, Eduardo; Li, Song; Lovin, Diane D; Mao, Chunhong; Mauceli, Evan; Menck, Carlos F M; Miller, Jason R; Montgomery, Philip; Mori, Akio; Nascimento, Ana L; Naveira, Horacio F; Nusbaum, Chad; O'leary, Sinéad; Orvis, Joshua; Pertea, Mihaela; Quesneville, Hadi; Reidenbach, Kyanne R; Rogers, Yu-Hui; Roth, Charles W; Schneider, Jennifer R; Schatz, Michael; Shumway, Martin; Stanke, Mario; Stinson, Eric O; Tubio, Jose M C; Vanzee, Janice P; Verjovski-Almeida, Sergio; Werner, Doreen; White, Owen; Wyder, Stefan; Zeng, Qiandong; Zhao, Qi; Zhao, Yongmei; Hill, Catherine A; Raikhel, Alexander S; Soares, Marcelo B; Knudson, Dennis L; Lee, Norman H; Galagan, James; Salzberg, Steven L; Paulsen, Ian T; Dimopoulos, George; Collins, Frank H; Birren, Bruce; Fraser-Liggett, Claire M; Severson, David W

    2007-06-22

    We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species. PMID:17510324

  17. Matrix averages relating to Ginibre ensembles

    Energy Technology Data Exchange (ETDEWEB)

    Forrester, Peter J [Department of Mathematics and Statistics, University of Melbourne, Victoria 3010 (Australia); Rains, Eric M [Department of Mathematics, California Institute of Technology, Pasadena, CA 91125 (United States)], E-mail: p.forrester@ms.unimelb.edu.au

    2009-09-25

    The theory of zonal polynomials is used to compute the average of a Schur polynomial of argument AX, where A is a fixed matrix and X is from the real Ginibre ensemble. This generalizes a recent result of Sommers and Khoruzhenko (2009 J. Phys. A: Math. Theor. 42 222002), and furthermore allows analogous results to be obtained for the complex and real quaternion Ginibre ensembles. As applications, the positive integer moments of the general variance Ginibre ensembles are computed in terms of generalized hypergeometric functions; these are written in terms of averages over matrices of the same size as the moment to give duality formulas, and the averages of the power sums of the eigenvalues are expressed as finite sums of zonal polynomials.

  18. Comparative genomics of Lactobacillus and other LAB

    DEFF Research Database (Denmark)

    Wassenaar, Trudy M.; Lukjancenko, Oksana

    2014-01-01

    The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...... that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively...... high for Lb. sanfransiscensis and Lb. salivarius, with respect to their moderate gene size. The phylogenetic relationship of the 16S ribosomal RNA genes of these genomes was established and pan- and core genomes were defined for each genus. In addition, core genome analysis was performed on all food...

  19. "Pricing Average Options on Commodities"

    OpenAIRE

    Kenichiro Shiraya; Akihiko Takahashi

    2010-01-01

    This paper proposes a new approximation formula for pricing average options on commodities under a stochastic volatility environment. In particular, it derives an option pricing formula under Heston and an extended lambda-SABR stochastic volatility models (which includes an extended SABR model as a special case). Moreover, numerical examples support the accuracy of the proposed average option pricing formula.

  20. Comparative Analysis of Genome Diversity in Bullmastiff Dogs.

    Science.gov (United States)

    Mortlock, Sally-Anne; Khatkar, Mehar S; Williamson, Peter

    2016-01-01

    Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial. PMID:26824579

  1. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  2. Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

    Science.gov (United States)

    Nabholz, Benoit; Lartillot, Nicolas

    2013-01-01

    The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more

  3. Standard Metabolic Rate (SMR) is inversely related to erythrocyte and genome size in allopolyploid fish of the Cobitis taenia hybrid complex

    Czech Academy of Sciences Publication Activity Database

    Maciak, S.; Janko, Karel; Kotusz, J.; Choleva, Lukáš; Boron, A.; Juchno, D.; Kujawa, R.; Kozlowski, J.; Konarzewski, M.

    2011-01-01

    Roč. 25, č. 5 (2011), s. 1072-1078. ISSN 0269-8463 R&D Projects: GA AV ČR KJB600450902; GA ČR GA206/09/1298 Institutional research plan: CEZ:AV0Z50450515 Keywords : CELL-SIZE * C-VALUE * PASSERINE BIRDS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.567, year: 2011

  4. Power convergence of Abel averages

    OpenAIRE

    Kozitsky, Yuri; Shoikhet, David; Zemanek, Jaroslav

    2012-01-01

    Necessary and sufficient conditions are presented for the Abel averages of discrete and strongly continuous semigroups, $T^k$ and $T_t$, to be power convergent in the operator norm in a complex Banach space. These results cover also the case where $T$ is unbounded and the corresponding Abel average is defined by means of the resolvent of $T$. They complement the classical results by Michael Lin establishing sufficient conditions for the corresponding convergence for a bounded $T$.

  5. High-average-power lasers

    International Nuclear Information System (INIS)

    The goals of the High-Average-Power Laser Program at LLNL are to develop a broad technology base for solid state lasers and to demonstrate high-average-power laser operation with more efficiency and higher beam quality than has been possible with current technology. Major activities are the zig-zag laser testbed and the gas-cooled-slab laser test bed. This section describes these activities as well as discussion of material development; nonlinear optics; laser materials, and applications

  6. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

    Directory of Open Access Journals (Sweden)

    Hayes Ben

    2009-04-01

    Full Text Available Abstract Background Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection. With the completion of the cattle genome, private companies are now providing large numbers of polymorphic markers for probing variation in domestic cattle (Bos taurus. We analysed over 7,500 polymorphic single nucleotide polymorphisms (SNP in beef (Angus and dairy (Holstein cattle and outgroup species Bison, Yak and Banteng in an indirect test of inbreeding and positive selection in Domestic cattle. Results Outgroup species: Bison, Yak and Banteng, were genotyped with high levels of success (90% and used to determine ancestral and derived allele states in domestic cattle. Frequency spectrums of the derived alleles in Angus and Holstein were examined using Fay and Wu's H test. Significant divergences from the predicted frequency spectrums expected under neutrality were identified. This appeared to be the result of combined influences of positive selection, inbreeding and ascertainment bias for moderately frequent SNP. Approximately 10% of all polymorphisms identified as segregating in B. taurus were also segregating in Bison, Yak or Banteng; highlighting a large number of polymorphisms that are ancient in origin. Conclusion These results suggest that a large effective population size (Ne of approximately 90,000 or more existed in B. taurus since they shared a common ancestor with Bison, Yak and Banteng ~1–2 million years ago (MYA. More recently Ne decreased sharply probably associated with domestication. This may partially explain the paradox of high levels of polymorphism in Domestic cattle and the relatively small recent Ne in this species. The period of inbreeding caused Fay and Wu's H statistic to depart from its expectation under neutrality mimicking the effect of selection. However, there was also evidence for selection

  7. Nothing special in the specialist? Draft genome sequence of Cryomyces antarcticus, the most extremophilic fungus from Antarctica.

    Directory of Open Access Journals (Sweden)

    Katja Sterflinger

    Full Text Available The draft genome of the Antarctic endemic fungus Cryomyces antarcticus is presented. This rock inhabiting, microcolonial fungus is extremely stress tolerant and it is a model organism for exobiology and studies on stress resistance in Eukaryots. Since this fungus is a specialist in the most extreme environment of the Earth, the analysis of its genome is of important value for the understanding of fungal genome evolution and stress adaptation. A comparison with Neurospora crassa as well as with other microcolonial fungi shows that the fungus has a genome size of 24 Mbp, which is the average in the fungal kingdom. Although sexual reproduction was never observed in this fungus, 34 mating genes are present with protein homologs in the classes Eurotiomycetes, Sordariomycetes and Dothideomycetes. The first analysis of the draft genome did not reveal any significant deviations of this genome from comparative species and mesophilic hyphomycetes.

  8. Nothing Special in the Specialist? Draft Genome Sequence of Cryomyces antarcticus, the Most Extremophilic Fungus from Antarctica

    Science.gov (United States)

    Sterflinger, Katja; Lopandic, Ksenija; Pandey, Ram Vinay; Blasi, Barbara; Kriegner, Albert

    2014-01-01

    The draft genome of the Antarctic endemic fungus Cryomyces antarcticus is presented. This rock inhabiting, microcolonial fungus is extremely stress tolerant and it is a model organism for exobiology and studies on stress resistance in Eukaryots. Since this fungus is a specialist in the most extreme environment of the Earth, the analysis of its genome is of important value for the understanding of fungal genome evolution and stress adaptation. A comparison with Neurospora crassa as well as with other microcolonial fungi shows that the fungus has a genome size of 24 Mbp, which is the average in the fungal kingdom. Although sexual reproduction was never observed in this fungus, 34 mating genes are present with protein homologs in the classes Eurotiomycetes, Sordariomycetes and Dothideomycetes. The first analysis of the draft genome did not reveal any significant deviations of this genome from comparative species and mesophilic hyphomycetes. PMID:25296285

  9. Vocal attractiveness increases by averaging.

    Science.gov (United States)

    Bruckert, Laetitia; Bestelmeyer, Patricia; Latinus, Marianne; Rouger, Julien; Charest, Ian; Rousselet, Guillaume A; Kawahara, Hideki; Belin, Pascal

    2010-01-26

    Vocal attractiveness has a profound influence on listeners-a bias known as the "what sounds beautiful is good" vocal attractiveness stereotype [1]-with tangible impact on a voice owner's success at mating, job applications, and/or elections. The prevailing view holds that attractive voices are those that signal desirable attributes in a potential mate [2-4]-e.g., lower pitch in male voices. However, this account does not explain our preferences in more general social contexts in which voices of both genders are evaluated. Here we show that averaging voices via auditory morphing [5] results in more attractive voices, irrespective of the speaker's or listener's gender. Moreover, we show that this phenomenon is largely explained by two independent by-products of averaging: a smoother voice texture (reduced aperiodicities) and a greater similarity in pitch and timbre with the average of all voices (reduced "distance to mean"). These results provide the first evidence for a phenomenon of vocal attractiveness increases by averaging, analogous to a well-established effect of facial averaging [6, 7]. They highlight prototype-based coding [8] as a central feature of voice perception, emphasizing the similarity in the mechanisms of face and voice perception. PMID:20129047

  10. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from...... Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  11. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from...... Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  12. Sparsity Averaging for Compressive Imaging

    CERN Document Server

    Carrillo, Rafael E; Van De Ville, Dimitri; Thiran, Jean-Philippe; Wiaux, Yves

    2012-01-01

    We propose a novel regularization method for sparse image reconstruction from compressive measurements. The approach relies on the conjecture that natural images exhibit strong average sparsity over multiple coherent frames. The associated reconstruction algorithm, based on an analysis prior and a reweighted $\\ell_1$ scheme, is dubbed Sparsity Averaging Reweighted Analysis (SARA). We test our prior and the associated algorithm through extensive numerical simulations for spread spectrum and Gaussian acquisition schemes suggested by the recent theory of compressed sensing with coherent and redundant dictionaries. Our results show that average sparsity outperforms state-of-the-art priors that promote sparsity in a single orthonormal basis or redundant frame, or that promote gradient sparsity. We also illustrate the performance of SARA in the context of Fourier imaging, for particular applications in astronomy and medicine.

  13. On generalized averaged Gaussian formulas

    Science.gov (United States)

    Spalevic, Miodrag M.

    2007-09-01

    We present a simple numerical method for constructing the optimal (generalized) averaged Gaussian quadrature formulas which are the optimal stratified extensions of Gauss quadrature formulas. These extensions exist in many cases in which real positive Kronrod formulas do not exist. For the Jacobi weight functions w(x)equiv w^{(alpha,beta)}(x)D(1-x)^alpha(1+x)^beta ( alpha,beta>-1 ) we give a necessary and sufficient condition on the parameters alpha and beta such that the optimal averaged Gaussian quadrature formulas are internal.

  14. On T-matrix averaging

    International Nuclear Information System (INIS)

    The T-matrix averaging procedure advocated by Burke, Berrington and Sukumar [1981, J. Phys. B. At. Mol. Phys. 14, 289] is demonstrated to hold in a class of soluble models for two different L2 basis expansions. The convergence rates as the bases are extended to completeness are determined. (author)

  15. Between two fern genomes.

    Science.gov (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  16. Independence, Odd Girth, and Average Degree

    DEFF Research Database (Denmark)

    Löwenstein, Christian; Pedersen, Anders Sune; Rautenbach, Dieter;

    2011-01-01

      We prove several tight lower bounds in terms of the order and the average degree for the independence number of graphs that are connected and/or satisfy some odd girth condition. Our main result is the extension of a lower bound for the independence number of triangle-free graphs of maximum...... degree at most three due to Heckman and Thomas [Discrete Math 233 (2001), 233–237] to arbitrary triangle-free graphs. For connected triangle-free graphs of order n and size m, our result implies the existence of an independent set of order at least (4n−m−1) / 7.  ...

  17. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø;

    2012-01-01

    Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven...... as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casual mutation alleles are reversed across populations, or the actual...... casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...

  18. Draft Genome Sequence of "Rathayibacter tanaceti" Strain VKM Ac-2596 Isolated from Tanacetum vulgare Infested by a Foliar Nematode.

    Science.gov (United States)

    Vasilenko, Oleg V; Starodumova, Irina P; Tarlachkov, Sergey V; Dorofeeva, Lubov V; Avtukh, Alexander N; Evtushenko, Lyudmila I

    2016-01-01

    The draft genome of "Rathayibacter tanaceti" VKM Ac-2596 is 3.17 Mb in size with an average G+C content of 70.7% and comprises at least two nonidentical copies of ribosomal small subunit (SSU-rRNA) genes. The semiconductor sequencing platform Ion Torrent was used. PMID:27313291

  19. Average-Consensus Algorithms in a Deterministic Framework

    OpenAIRE

    Topley, Kevin; Krishnamurthy, Vikram

    2011-01-01

    We consider the average-consensus problem in a multi-node network of finite size. Communication between nodes is modeled by a sequence of directed signals with arbitrary communication delays. Four distributed algorithms that achieve average-consensus are proposed. Necessary and sufficient communication conditions are given for each algorithm to achieve average-consensus. Resource costs for each algorithm are derived based on the number of scalar values that are required for communication and ...

  20. Treponema pallidum subsp. pallidum has a single, circular chromosome with a size of approximately 900 kilobase pairs.

    OpenAIRE

    Walker, E M; Arnett, J K; Heath, J D; Norris, S J

    1991-01-01

    The genome size and chromosome conformation of Treponema pallidum subsp. pallidum, Nichols strain, were determined by contour-clamped homogeneous electric field electrophoresis, a pulsed-field gel electrophoresis technique. Digestion of T. pallidum subsp. pallidum DNA with the restriction endonucleases NotI and SpeI produced 12 and 26 fragments, respectively. Summation of the physical lengths of the fragments produced by NotI and SpeI cleavage yielded average sizes of 900 and 913 kbp, respect...

  1. Stochastic Approximation with Averaging Innovation

    CERN Document Server

    Laruelle, Sophie

    2010-01-01

    The aim of the paper is to establish a convergence theorem for multi-dimensional stochastic approximation in a setting with innovations satisfying some averaging properties and to study some applications. The averaging assumptions allow us to unify the framework where the innovations are generated (to solve problems from Numerical Probability) and the one with exogenous innovations (market data, output of "device" $e.g.$ an Euler scheme) with stationary or ergodic properties. We propose several fields of applications with random innovations or quasi-random numbers. In particular we provide in both setting a rule to tune the step of the algorithm. At last we illustrate our results on five examples notably in Finance.

  2. High average power supercontinuum sources

    Indian Academy of Sciences (India)

    J C Travers

    2010-11-01

    The physical mechanisms and basic experimental techniques for the creation of high average spectral power supercontinuum sources is briefly reviewed. We focus on the use of high-power ytterbium-doped fibre lasers as pump sources, and the use of highly nonlinear photonic crystal fibres as the nonlinear medium. The most common experimental arrangements are described, including both continuous wave fibre laser systems with over 100 W pump power, and picosecond mode-locked, master oscillator power fibre amplifier systems, with over 10 kW peak pump power. These systems can produce broadband supercontinua with over 50 and 1 mW/nm average spectral power, respectively. Techniques for numerical modelling of the supercontinuum sources are presented and used to illustrate some supercontinuum dynamics. Some recent experimental results are presented.

  3. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAOGuo-ping

    2004-01-01

    Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  4. Evolution of plant genome architecture.

    Science.gov (United States)

    Wendel, Jonathan F; Jackson, Scott A; Meyers, Blake C; Wing, Rod A

    2016-01-01

    We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement. PMID:26926526

  5. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Guo-ping

    2004-01-01

    @@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  6. Identification of a large genomic region in UV-irradiated human cells which has fewer cyclobutane pyrimidine dimers than most genomic regions

    International Nuclear Information System (INIS)

    Size separation after UV-endonuclease digestion of DNA from UV-irradiated human cells using denaturing conditions fractionates the genome based on cyclobutane pyrimidine dimer content. We have examined the largest molecules available (50-80 kb; about 5% of the DNA) after fractionation and those of average size (5-15 kb) for content of some specific genes. We find that the largest molecules are not a representative sampling of the genome. Three contiguous genes located in a G+C-rich isochore (tyrosine hydroxylase, insulin, insulin-like growth factor II) have concentrations two to three times greater in the largest molecules. This shows that this genomic region has fewer pyrimidine dimers than most other genomic regions. In contrast, the β-actin genomic region, which has a similar G+C content, has an equal concentration in both fractions as do the p53 and β-globin genomic regions, which are A+T-rich. These data show that DNA damage in the form of cyclobutane pyrimidine dimers occurs with different probabilities in specific isochores. Part of the reason may be the relative G-C content, but other factors must play a significant role. We also report that the transcriptionally inactive insulin region is repaired at the genome-overall rate in normal cells and is not repaired in xeroderma pigmentosum complementation group C cells. (author)

  7. Architecture and evolution of a minute plant genome.

    OpenAIRE

    Ibarra-Laclette, E.; Lyons, E.; Hernández-Guzmán, G.; Pérez-Torres, C.A.; L. Carretero-Paulet; Chang, T.-H.; Lan, T.; Welch, A.J.; Abraham Juárez, M.J.; Simpson, J; Fernández-Cortés, A.; Arteaga-Vázquez, M.; Góngora-Castillo, E.; Acevedo-Hernández, A.; Schuster, S.C.

    2013-01-01

    It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, ...

  8. Correlations of plant seed dispersal pattern with genome size and 1000-seed mass%植物种子传播途径与基因组值和千粒重的相关性

    Institute of Scientific and Technical Information of China (English)

    白成科; 曹博; 李桂双

    2013-01-01

    Seed dispersal is essential to the reproduction, distribution, and evolution of plants. To study the correlations of plant seed dispersal pattern with genome size and 1000-seed mass is of significance for revealing the invasion of plant seeds and the mechanisms of genome evolution. In this paper, statistics and correlation analysis were conducted on 235 plant species with complete genome information (chromosomes number, ploidy, and C-value) , 1000-seed mass, and seed dispersal patterns, based on the previous estimation of some plant species C-values and the searching of plant C-value database and seed information database. The ANOVA analysis indicated that for the plants whose seeds were dispersed by water, bird, and wind, the C-values (Cwater = 1.3 pg, Cbird = 1.6 pg, and Cwingd=2.0 pg) and genome sizes (1Cxwater = 1. 1 pg, lCxbird = 1.3 pg, and 1Cxwind = 1.6 pg) were significantly lower than those whose seeds were dispersed by animal-eating (1Canimal=4.9 pg, and lCxanimal=4.7 pg) (P 0. 05). The 1000-seed mass of the 235 species varied greatly. The 1000-seed mass of the plants with seed dispersal by wind and animal-carrying (7. 2 g and 13. 5 g, respectively) were obviously lower than that with seed dispersal by water and animal-eating (85. 8 g and 92. 5 g, respectively) , but the 1000-seed mass of the plants with unassisted dispersal had no significant differences with that of other dispersal patterns. The further correlation analysis showed that there existed positive correlations between the genome size and 1000-seed mass of the plants whose seeds were dispersed by animal-eating and water (γ = 0. 33) , in which, the correlation for the plants whose seeds were dispersed by animal-eating was significant (γ = 0. 67 x + 3. 23, R2 =0.11, P = 0. 04). These findings would provide references to reveal the mechanisms of plant seed dispersal, distribution, and genome evolution.%种子传播对植物的繁殖、分布和进化至关重要,研究植物基因组、种子

  9. Disk-averaged synthetic spectra of Mars

    CERN Document Server

    Tinetti, G; Fong, W; Meadows, V S; Snively, H; Velusamy, T; Crisp, David; Fong, William; Meadows, Victoria S.; Snively, Heather; Tinetti, Giovanna; Velusamy, Thangasamy

    2004-01-01

    The principal goal of the NASA Terrestrial Planet Finder (TPF) and ESA Darwin mission concepts is to directly detect and characterize extrasolar terrestrial (Earth-sized) planets. This first generation of instruments is expected to provide disk-averaged spectra with modest spectral resolution and signal-to-noise. Here we use a spatially and spectrally resolved model of the planet Mars to study the detectability of a planet's surface and atmospheric properties from disk-averaged spectra as a function of spectral resolution and wavelength range, for both the proposed visible coronograph (TPF-C) and mid-infrared interferometer (TPF-I/Darwin) architectures. At the core of our model is a spectrum-resolving (line-by-line) atmospheric/surface radiative transfer model which uses observational data as input to generate a database of spatially-resolved synthetic spectra for a range of illumination conditions (phase angles) and viewing geometries. Results presented here include disk averaged synthetic spectra, light-cur...

  10. Michel Parameters averages and interpretation

    International Nuclear Information System (INIS)

    The new measurements of Michel parameters in τ decays are combined to world averages. From these measurements model independent limits on non-standard model couplings are derived and interpretations in the framework of specific models are given. A lower limit of 2.5 tan β GeV on the mass of a charged Higgs boson in models with two Higgs doublets can be set and a 229 GeV limit on a right-handed W-boson in left-right symmetric models (95 % c.l.)

  11. Flexible time domain averaging technique

    Science.gov (United States)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng

    2013-09-01

    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  12. 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

  13. Burst speciation processes and genomic expansion in the neotropical annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae).

    Science.gov (United States)

    García, G; Gutiérrez, V; Ríos, N; Turner, B; Santiñaque, F; López-Carro, B; Folle, G

    2014-02-01

    The extent to which genome sizes and other nucleotypic factors influence the phyletic diversification of lineages has long been discussed but remains largely unresolved. In the present work, we present evidence that the genomes of at least 16 species of the neotropical rivulid killifish genus Austrolebias are unusually large, with an average DNA content of about 5.95 ± 0.45 picograms per diploid cell (mean C-value of about 2.98 pg). They are thus larger than the genomes of very nearly all other diploid, i.e. non-(paleo) polyploid species of actinopterygian fishes so far reported. Austrolebias species appear to be conventional diploids in all other respects and there is no reason to believe that they arise from polyploid ancestors. The genome sizes reported for other rivulid killifishes, including a putative sister group, are considerably smaller and fall within the range typical of most other cyprinodontoid species. Therefore, it appears that the ancestor(s) of contemporary Austrolebias have undergone one or more episodes of genome expansion encompassing sudden speciation process during the Pleistocene. In addition, these findings are consistent with the hypothesis of a positive correlation between species richness and genome size. PMID:24452909

  14. Genome digging: insight into the mitochondrial genome of Homo.

    Directory of Open Access Journals (Sweden)

    Igor V Ovchinnikov

    Full Text Available BACKGROUND: A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1 into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split. PRINCIPAL FINDINGS: Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2 with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively. CONCLUSIONS: This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N/d(S dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective

  15. Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes.

    Directory of Open Access Journals (Sweden)

    Barbora Staudová

    Full Text Available T. pallidum subsp. endemicum (TEN is the causative agent of bejel (also known as endemic syphilis. Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA, TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe.The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina. Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.

  16. Averaging along Uniform Random Integers

    CERN Document Server

    Janvresse, Élise

    2011-01-01

    Motivated by giving a meaning to "The probability that a random integer has initial digit d", we define a URI-set as a random set E of natural integers such that each n>0 belongs to E with probability 1/n, independently of other integers. This enables us to introduce two notions of densities on natural numbers: The URI-density, obtained by averaging along the elements of E, and the local URI-density, which we get by considering the k-th element of E and letting k go to infinity. We prove that the elements of E satisfy Benford's law, both in the sense of URI-density and in the sense of local URI-density. Moreover, if b_1 and b_2 are two multiplicatively independent integers, then the mantissae of a natural number in base b_1 and in base b_2 are independent. Connections of URI-density and local URI-density with other well-known notions of densities are established: Both are stronger than the natural density, and URI-density is equivalent to log-density. We also give a stochastic interpretation, in terms of URI-...

  17. Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae).

    Science.gov (United States)

    García, G; Ríos, N; Gutiérrez, V

    2015-06-01

    Among Neotropical fish fauna, the South American killifish genus Austrolebias (Cyprinodontiformes: Rivulidae) constitutes an excellent model to study the genomic evolutionary processes underlying speciation events. Recently, unusually large genome size has been described in 16 species of this genus, with an average DNA content of about 5.95 ± 0.45 pg per diploid cell (mean C-value of about 2.98 pg). In the present paper we explore the possible origin of this unparallel genomic increase by means of comparative analysis of the repetitive components using NGS (454-Roche) technology in the lowest and highest Rivulidae genomes. Here, we provide the first annotated Rivulidae-repeated sequences composition and their relative repetitive fraction in both genomes. Remarkably, the genomic proportion of the moderately repetitive DNA in Austrolebias charrua genome represents approximately twice (45%) of the repetitive components of the highly related rivulinae taxon Cynopoecilus melanotaenia (25%). Present work provides evidence about the impact of the repeat families that could be distinctly proliferated among sublineages within Rivulidae fish group, explaining the great genome size differences encompassing the differentiation and speciation events in this family. PMID:25792372

  18. 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...

  19. Draft Genome Sequence of “Rathayibacter tanaceti” Strain VKM Ac-2596 Isolated from Tanacetum vulgare Infested by a Foliar Nematode

    Science.gov (United States)

    Starodumova, Irina P.; Tarlachkov, Sergey V.; Dorofeeva, Lubov V.; Avtukh, Alexander N.; Evtushenko, Lyudmila I.

    2016-01-01

    The draft genome of “Rathayibacter tanaceti” VKM Ac-2596 is 3.17 Mb in size with an average G+C content of 70.7% and comprises at least two nonidentical copies of ribosomal small subunit (SSU-rRNA) genes. The semiconductor sequencing platform Ion Torrent was used. PMID:27313291

  20. The diploid genome sequence of an Asian individual

    DEFF Research Database (Denmark)

    Wang, Jun; Wang, Wei; Li, Ruiqiang;

    2008-01-01

    Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we...

  1. Leaner and meaner genomes in Escherichia coli

    DEFF Research Database (Denmark)

    Ussery, David

    2006-01-01

    A 'better' Escherichia coli K-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. Comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions....

  2. Evolution of genome architecture.

    Science.gov (United States)

    Koonin, Eugene V

    2009-02-01

    Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome

  3. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  4. Genomic Aspects of Research Involving Polyploid Plants

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  5. Genic regions of a large salamander genome contain long introns and novel genes

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

  6. Bootstrapping pre-averaged realized volatility under market microstructure noise

    DEFF Research Database (Denmark)

    Hounyo, Ulrich; Goncalves, Sílvia; Meddahi, Nour

    The main contribution of this paper is to propose a bootstrap method for inference on integrated volatility based on the pre-averaging approach of Jacod et al. (2009), where the pre-averaging is done over all possible overlapping blocks of consecutive observations. The overlapping nature of the pre......-averaged returns implies that these are kn-dependent with kn growing slowly with the sample size n. This motivates the application of a blockwise bootstrap method. We show that the "blocks of blocks" bootstrap method suggested by Politis and Romano (1992) (and further studied by Bühlmann and Künsch (1995)) is...... valid only when volatility is constant. The failure of the blocks of blocks bootstrap is due to the heterogeneity of the squared pre-averaged returns when volatility is stochastic. To preserve both the dependence and the heterogeneity of squared pre-averaged returns, we propose a novel procedure that...

  7. Construction and Preliminary Characterization Analysis of Wuzhishan Miniature Pig Bacterial Artificial Chromosome Library with Approximately 8-Fold Genome Equivalent Coverage

    Directory of Open Access Journals (Sweden)

    Changqing Liu

    2013-01-01

    Full Text Available Bacterial artificial chromosome (BAC libraries have been invaluable tools for the genome-wide genetic dissection of complex organisms. Here, we report the construction and characterization of a high-redundancy BAC library from a very valuable pig breed in China, Wuzhishan miniature pig (Sus scrofa, using its blood cells and fibroblasts, respectively. The library contains approximately 153,600 clones ordered in 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 152.3 kb, representing approximately 7.68 genome equivalents of the porcine haploid genome and a 99.93% statistical probability of obtaining at least one clone containing a unique DNA sequence in the library. 19 pairs of microsatellite marker primers covering porcine chromosomes were used for screening the BAC library, which showed that each of these markers was positive in the library; the positive clone number was 2 to 9, and the average number was 7.89, which was consistent with 7.68-fold coverage of the porcine genome. And there were no significant differences of genomic BAC library from blood cells and fibroblast cells. Therefore, we identified 19 microsatellite markers that could potentially be used as genetic markers. As a result, this BAC library will serve as a valuable resource for gene identification, physical mapping, and comparative genomics and large-scale genome sequencing in the porcine.

  8. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj;

    2014-01-01

    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also...... heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting...... in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome...

  9. Analysing complex Triticeae genomes – concepts and strategies

    OpenAIRE

    Spannagl, Manuel; Martis, Mihaela M.; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus FX

    2013-01-01

    The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access t...

  10. Análisis del tamaño del genoma y cariotipo de Agave aktites Gentry (Agavaceae de Sonora, México Genome size and karyotype analysis of Agave aktites Gentry (Agavaceae from Sonora, Mexico

    Directory of Open Access Journals (Sweden)

    Guadalupe Palomino

    2010-12-01

    Full Text Available Se determinó el tamaño del genoma y la estructura del cariotipo de 2 poblaciones silvestres de Agave aktites Gentry de Las Bocas y San Carlos, Sonora, México. El contenido de ADN nuclear en tejido foliar se determinó por citometría de flujo y los cromosomas se observaron en metafase mitótica de meristemos radiculares. Las plantas en ambas poblaciones son diploides (2n= 2x= 60. El contenido promedio 2C de ADN nuclear fue de 8.404 pg; 1Cx= 4 120 millones de pares de nucleótidos. El cariotipo bimodal fue similar en las 2 poblaciones y consistió de 10 cromosomas grandes y 50 pequeños y correspondió a 46m+6st+8t: también mostró un par de cromosomas telocéntricos grandes con constricción secundaria. El cociente de los brazos cromosómicos fue diferente en los pares 7, 8, 14 y 16 del grupo de cromosomas pequeños que presentan diferencias morfológicas entre las 2 poblaciones. Estos rearreglos cromosómicos podrían deberse a intercambios cromosómicos heterocigóticos espontáneos y son evidencia de que los genomas de distintas poblaciones de A. aktites se encuentran en un activo proceso de diferenciación que podría llevar a la especiación. Los análisis son básicos para conocer la diversidad genética intraespecífica de A. aktites y para establecer estrategias de conservación in situ y ex situ para esta especie.Genome size and karyotype structure of 2 wild populations of Agave aktites Gentry from Las Bocas and San Carlos, Sonora, Mexico were determined. Nuclear DNA content of leaf tissue was measured through flow cytometry, and chromosomes were observed in mitotic metaphase of root tips. All individual plants studied in both populations are diploids (2n= 2x= 60. The mean 2C nuclear DNA content was 8.404 pg; 1Cx= 4 120 million of base pairs. All plants of the 2 populations of A. aktites show a bimodal karyotype consisting of 10 large + 50 small chromosomes and corresponded to 46m+6st+8t; they also have a pair of large telocentric

  11. The Averaged Fokker - Planck equation in tokamak plasma

    International Nuclear Information System (INIS)

    In this paper the numerical code which has been developed to solve averaged Fokker-Planck equation, and its applications for studying the time evolution of the electron distribution function in tokamak device of medium size and performances are discussed. The electron collisions and DC electric field effects are analysed in details

  12. Comparative genomic data of the Avian Phylogenomics Project

    DEFF Research Database (Denmark)

    Zhang, Guojie; Li, Bo; Li, Cai;

    2014-01-01

    in phylogenomics and comparative genomics. FINDINGS: The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23...

  13. A BAC-based physical map of the Drosophila buzzatii genome

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Josefa; Nefedov, Michael; Bosdet, Ian; Casals, Ferran; Calvete, Oriol; Delprat, Alejandra; Shin, Heesun; Chiu, Readman; Mathewson, Carrie; Wye, Natasja; Hoskins, Roger A.; Schein, JacquelineE.; de Jong, Pieter; Ruiz, Alfredo

    2005-03-18

    Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophilabuzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and a {approx}18X expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

  14. Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes.

    Science.gov (United States)

    Lu, D; Akanno, E C; Crowley, J J; Schenkel, F; Li, H; De Pauw, M; Moore, S S; Wang, Z; Li, C; Stothard, P; Plastow, G; Miller, S P; Basarab, J A

    2016-04-01

    The accuracy of genomic predictions can be used to assess the utility of dense marker genotypes for genetic improvement of beef efficiency traits. This study was designed to test the impact of genomic distance between training and validation populations, training population size, statistical methods, and density of genetic markers on prediction accuracy for feed efficiency traits in multibreed and crossbred beef cattle. A total of 6,794 beef cattle data collated from various projects and research herds across Canada were used. Illumina BovineSNP50 (50K) and imputed Axiom Genome-Wide BOS 1 Array (HD) genotypes were available for all animals. The traits studied were DMI, ADG, and residual feed intake (RFI). Four validation groups of 150 animals each, including Angus (AN), Charolais (CH), Angus-Hereford crosses (ANHH), and a Charolais-based composite (TX) were created by considering the genomic distance between pairs of individuals in the validation groups. Each validation group had 7 corresponding training groups of increasing sizes ( = 1,000, 1,999, 2,999, 3,999, 4,999, 5,998, and 6,644), which also represent increasing average genomic distance between pairs of individuals in the training and validations groups. Prediction of genomic estimated breeding values (GEBV) was performed using genomic best linear unbiased prediction (GBLUP) and Bayesian method C (BayesC). The accuracy of genomic predictions was defined as the Pearson's correlation between adjusted phenotype and GEBV (), unless otherwise stated. Using 50K genotypes, the highest average achieved in purebreds (AN, CH) was 0.41 for DMI, 0.34 for ADG, and 0.35 for RFI, whereas in crossbreds (ANHH, TX) it was 0.38 for DMI, 0.21 for ADG, and 0.25 for RFI. Similarly, when imputed HD genotypes were applied in purebreds (AN, CH), the highest average was 0.14 for DMI, 0.15 for ADG, and 0.14 for RFI, whereas in crossbreds (ANHH, TX) it was 0.38 for DMI, 0.22 for ADG, and 0.24 for RFI. The of GBLUP predictions were

  15. Genomic legacy of the African cheetah, Acinonyx jubatus

    OpenAIRE

    Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren; Kuderna, Lukas F.K.; García-Pérez, Raquel; de Manuel, Marc; Godinez, Ricardo; Komissarov, Aleksey

    2015-01-01

    Background: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain ...

  16. Rhipicephalus (Boophilus) microplus strain Deutsch, whole genome shotgun sequencing project first submission of genome sequence

    Science.gov (United States)

    The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence difficult. Cot filtration/selection techniques were used to reduce the repetitive fraction of the tick genome and enrich for the fraction of DNA with gene-containing regions. The Cot-selected ...

  17. Spectral averaging techniques for Jacobi matrices

    CERN Document Server

    del Rio, Rafael; Schulz-Baldes, Hermann

    2008-01-01

    Spectral averaging techniques for one-dimensional discrete Schroedinger operators are revisited and extended. In particular, simultaneous averaging over several parameters is discussed. Special focus is put on proving lower bounds on the density of the averaged spectral measures. These Wegner type estimates are used to analyze stability properties for the spectral types of Jacobi matrices under local perturbations.

  18. The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics.

    Science.gov (United States)

    Lufino, Michele M P; Edser, Pauline A H; Quail, Michael A; Rice, Stephen; Adams, David J; Wade-Martins, Richard

    2016-01-01

    Gene dosage plays a critical role in a range of cellular phenotypes, yet most cellular expression systems use heterologous cDNA-based vectors which express proteins well above physiological levels. In contrast, genomic DNA expression vectors generate physiologically-relevant levels of gene expression by carrying the whole genomic DNA locus of a gene including its regulatory elements. Here we describe the first genomic DNA expression library generated using the high-capacity herpes simplex virus-1 amplicon technology to deliver bacterial artificial chromosomes (BACs) into cells by viral transduction. The infectious BAC (iBAC) library contains 184,320 clones with an average insert size of 134.5 kb. We show in a Chinese hamster ovary (CHO) disease model cell line and mouse embryonic stem (ES) cells that this library can be used for genetic rescue studies in a range of contexts including the physiological restoration of Ldlr deficiency, and viral receptor expression. The iBAC library represents an important new genetic analysis tool openly available to the research community. PMID:27353647

  19. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae

    Science.gov (United States)

    2011-01-01

    Background The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level. Results The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG. Conclusions This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae. PMID:21247459

  20. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758 reveals slow genome and chromosome evolution in the Apidae

    Directory of Open Access Journals (Sweden)

    Kube Michael

    2011-01-01

    Full Text Available Abstract Background The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level. Results The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG. Conclusions This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.

  1. DNA sequence comparative analysis of the 3pter-p26 region of human genome

    Institute of Scientific and Technical Information of China (English)

    LUO; Chunqing; LI; Yan; ZHANG; Xiaowei; ZHANG; Yilin; ZHAN

    2005-01-01

    Most proterminal regions of human chromosomes are GC-rich and gene-rich. Chromosome 3p is an exception. Its proterminal region is GC-poor, and likely to lose heterozygosity, thus causing a number of fatal diseases. Except one gap left in the telomeric position, the proterminal region of human chromosome 3p has been completely sequenced. The detailed sequence analysis showed: (i) the GC content of this region was 38.5%, being the lowest among all the human proterminal regions; (ii) this region contained 20 known genes and 22 predicted genes, with an average gene size of 97.5 kb. The previously mapped gene Cntn3 was not found in this region, but instead located in the 74 Mb position of human chromosome 3p; (iii) the interspersed repeats of this region were more active than the average level of the whole human genome, especially (TA)n, the content of which was twice the genome average; (iv) this region had a conserved synteny extending from 104.1 Mb to 112.4 Mb on the mouse chromosome 6, which was 8% larger in size, not in accordance with the whole genome comparison, probably because the 3pter-p26 region was more likely to lose neocleitides and its mouse synteny had more active interspersed repeats.

  2. Construction and characterization of a Lipotes vexillifer genomic DNA BAC library.

    Science.gov (United States)

    Du, Bo; Zhang, Xian-Feng; Fang, Sheng-Guo; Wang, Ding

    2007-04-01

    We constructed a genomic DNA library for Lipotes vexillifer (L. vexillifer), the Baiji or Yangtze River dolphin, one of the most endangered mammals in the world. The library consists of 149,000 BAC clones, with an average insert size of 83 kb, representing approximately 3.4 haploid genome equivalents. PCR amplification of four known L. vexillifer genes yielded two to four positive clones each. To demonstrate the utility of this library, we isolated and sequenced the L. vexillifer alpha lactalbumin gene, which is a gene specific to mammals and one which has been widely used as molecular tool in phylogenetic analysis. We also end-sequenced 20 randomly selected clones, resulting in the identification of at least five new L. vexillifer genes, five SSR loci, and one SINE locus. These results suggest that this library is a valuable resource for candidate gene cloning, physical mapping, and genome sequencing of this important and threatened species. PMID:17867838

  3. Fungal genome sequencing: basic biology to biotechnology.

    Science.gov (United States)

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research. PMID:25721271

  4. Average-cost based robust structural control

    Science.gov (United States)

    Hagood, Nesbitt W.

    1993-01-01

    A method is presented for the synthesis of robust controllers for linear time invariant structural systems with parameterized uncertainty. The method involves minimizing quantities related to the quadratic cost (H2-norm) averaged over a set of systems described by real parameters such as natural frequencies and modal residues. Bounded average cost is shown to imply stability over the set of systems. Approximations for the exact average are derived and proposed as cost functionals. The properties of these approximate average cost functionals are established. The exact average and approximate average cost functionals are used to derive dynamic controllers which can provide stability robustness. The robustness properties of these controllers are demonstrated in illustrative numerical examples and tested in a simple SISO experiment on the MIT multi-point alignment testbed.

  5. Coherent ensemble averaging techniques for impedance cardiography

    OpenAIRE

    Hurwitz, Barry E.; Shyu, Liang-Yu; Reddy, Sridhar P; Schneiderman, Neil; Nagel, Joachim H.

    1990-01-01

    EKG synchronized ensemble averaging of the impedance cardiogram tends to blur or suppress signal events due to signal jitter or event latency variability. Although ensemble averaging provides some improvement in the stability of the signal and signal to noise ratio under conditions of nonperiodic influences of respiration and motion, coherent averaging techniques were developed to determine whether further enhancement of the impedance cardiogram could be obtained. Physiological signals were o...

  6. MEASUREMENT AND MODELLING AVERAGE PHOTOSYNTHESIS OF MAIZE

    OpenAIRE

    ZS LÕKE

    2005-01-01

    The photosynthesis of fully developed maize was investigated in the Agrometeorological Research Station Keszthely, in 2000. We used LI-6400 type measurement equipment to locate measurement points where the intensity of photosynthesis mostly nears the average. So later we could obtain average photosynthetic activities featuring the crop, with only one measurement. To check average photosynthesis of maize we used Goudriaan’s simulation model (CMSM) as well to calculate values on cloudless sampl...

  7. Complete genome sequence of an attenuated Sparfloxacin-resistant Streptococcus agalactiae strain 138spar

    Science.gov (United States)

    The complete genome of a sparfloxacin-resistant Streptococcus agalactiae vaccine strain 138spar is 1,838,126 bp in size. The genome has 1892 coding sequences and 82 RNAs. The annotation of the genome is added by the NCBI Prokaryotic Genome Annotation Pipeline. The publishing of this genome will allo...

  8. NOAA Average Annual Salinity (3-Zone)

    Data.gov (United States)

    California Department of Resources — The 3-Zone Average Annual Salinity Digital Geography is a digital spatial framework developed using geographic information system (GIS) technology. These salinity...

  9. FUNDAMENTALS OF TRANSMISSION FLUCTUATION SPECTROMETRY WITH VARIABLE SPATIAL AVERAGING

    Institute of Scientific and Technical Information of China (English)

    Jianqi Shen; Ulrich Riebel; Marcus Breitenstein; Udo Kr(a)uter

    2003-01-01

    Transmission signal of radiation in suspension of particles performed with a high spatial and temporal resolution shows significant fluctuations, which are related to the physical properties of the particles and the process of spatial and temporal averaging. Exploiting this connection, it is possible to calculate the parti cie size distribution (PSD)and particle concentration. This paper provides an approach of transmission fluctuation spectrometry (TFS) with variable spatial averaging. The transmission fluctuations are expressed in terms of the expectancy of transmission square (ETS)and are obtained as a spectrum, which is a function of the variable beam diameter. The reversal point and the depth of the spectrum contain the information of particle size and particle concentration, respectively.

  10. Improving consensus structure by eliminating averaging artifacts

    Directory of Open Access Journals (Sweden)

    KC Dukka B

    2009-03-01

    Full Text Available Abstract Background Common structural biology methods (i.e., NMR and molecular dynamics often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures. However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%; in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38 of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA 1, our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction 2, which

  11. Comparative genomics of two independently enriched ‘Candidatus Kuenenia stuttgartiensis’ anammox bacteria

    Directory of Open Access Journals (Sweden)

    DaanRSpeth

    2012-08-01

    Here we present a comparative genomic analysis of two ‘Ca. K. stuttgartiensis’ anammox bacteria that were independently enriched, with the aim to understand more about the evolution, cell plan and metabolism of these important microbes and to further improve and complete the reference genome. The two anammox bacteria used are ‘Ca. K. stuttgartiensis’ RU1, which was originally sequenced for the reference genome in 2002, and for the present study resequenced after seven (2002-2009 years in continuous culture. Furthermore ‘Ca. K. stuttgartiensis’ CH1, enriched from a Chinese wastewater treatment plant was used as an independent source of genomic information. The two different ‘Ca. Kuenenia’ bacteria showed a very high sequence identity (> 99 % at nucleotide level over the entire genome, but 31 genomic regions (average size 11 kb were absent from strain CH1 and 220 kb of sequence was specifically found in the CH1 assembly. The high sequence homology between these two bacteria indicates that mobile genetic elements are the main source of variation between these geographically widely separated strains.

  12. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong

    2011-12-21

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  13. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

  14. The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications.

    Directory of Open Access Journals (Sweden)

    Karina Stucken

    Full Text Available Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N(2 fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes. Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N(2 fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP. Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505 and 3.2 (D9 Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N(2 fixation capacity. Further comparisons to all available cyanobacterial

  15. The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications

    Science.gov (United States)

    Stucken, Karina; John, Uwe; Cembella, Allan; Murillo, Alejandro A.; Soto-Liebe, Katia; Fuentes-Valdés, Juan J.; Friedel, Maik; Plominsky, Alvaro M.; Vásquez, Mónica; Glöckner, Gernot

    2010-01-01

    Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N2) fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes). Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N2 fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP). Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505) and 3.2 (D9) Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny) between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N2 fixation capacity. Further comparisons to all available cyanobacterial genomes covering

  16. The inhomogeneous Universe : its average expansion and cosmic variance

    OpenAIRE

    Wiegand, Alexander

    2012-01-01

    Despite its global homogeneity and isotropy, the local matter distribution in the late Universe is manifestly inhomogeneous. Understanding the various effects resulting from these inhomogeneities is one of the most important tasks of modern cosmology. In this thesis, we investigate two aspects of the influence of local structure: firstly, to what extent do local structures modify the average expansion of spatial regions with a given size, and secondly, how strongly does the presence of struct...

  17. Draft Genome Sequence of Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556.

    Science.gov (United States)

    Komaki, Hisayuki; Ichikawa, Natsuko; Oguchi, Akio; Hamada, Moriyuki; Tamura, Tomohiko; Suzuki, Ken-Ichiro; Fujita, Nobuyuki

    2016-01-01

    Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces hygroscopicus subsp. hygroscopicus into the NBRC culture collection. An average nucleotide identity analysis confirmed that the taxonomic identification is correct. The genome sequence will serve as a valuable reference for genome mining to search new secondary metabolites. PMID:27198007

  18. Genome position specific priors for genomic prediction

    Directory of Open Access Journals (Sweden)

    Brøndum Rasmus

    2012-10-01

    Full Text Available Abstract Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casuative mutation alleles are reversed across populations, or the actual casuative mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed. Results Results showed an increase in accuracy of up to 3.5% for the Jersey population when using BayesRS with a prior derived from Australian Holstein compared to a model without location specific priors. The increase in accuracy was however lower than was achieved when reference populations were combined to estimate SNP effects, except in the case of fat yield. The small size of the Jersey validation set meant that these improvements in accuracy were not significant using a Hotelling-Williams t-test at the 5% level. An increase in accuracy of 1-2% for all traits was observed in the Australian Holstein population when using a prior derived from the Nordic Holstein population compared to using no prior information. These improvements were significant (P

  19. A note on generalized averaged Gaussian formulas

    Science.gov (United States)

    Spalevic, Miodrag

    2007-11-01

    We have recently proposed a very simple numerical method for constructing the averaged Gaussian quadrature formulas. These formulas exist in many more cases than the real positive Gauss?Kronrod formulas. In this note we try to answer whether the averaged Gaussian formulas are an adequate alternative to the corresponding Gauss?Kronrod quadrature formulas, to estimate the remainder term of a Gaussian rule.

  20. Average Transmission Probability of a Random Stack

    Science.gov (United States)

    Lu, Yin; Miniatura, Christian; Englert, Berthold-Georg

    2010-01-01

    The transmission through a stack of identical slabs that are separated by gaps with random widths is usually treated by calculating the average of the logarithm of the transmission probability. We show how to calculate the average of the transmission probability itself with the aid of a recurrence relation and derive analytical upper and lower…

  1. 40 CFR 76.11 - Emissions averaging.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Emissions averaging. 76.11 Section 76...) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.11 Emissions averaging. (a) General provisions. In lieu of complying with the applicable emission limitation in § 76.5, 76.6, or 76.7,...

  2. Adaptive Spontaneous Transitions between Two Mechanisms of Numerical Averaging.

    Science.gov (United States)

    Brezis, Noam; Bronfman, Zohar Z; Usher, Marius

    2015-01-01

    We investigated the mechanism with which humans estimate numerical averages. Participants were presented with 4, 8 or 16 (two-digit) numbers, serially and rapidly (2 numerals/second) and were instructed to convey the sequence average. As predicted by a dual, but not a single-component account, we found a non-monotonic influence of set-size on accuracy. Moreover, we observed a marked decrease in RT as set-size increases and RT-accuracy tradeoff in the 4-, but not in the 16-number condition. These results indicate that in accordance with the normative directive, participants spontaneously employ analytic/sequential thinking in the 4-number condition and intuitive/holistic thinking in the 16-number condition. When the presentation rate is extreme (10 items/sec) we find that, while performance still remains high, the estimations are now based on intuitive processing. The results are accounted for by a computational model postulating population-coding underlying intuitive-averaging and working-memory-mediated symbolic procedures underlying analytical-averaging, with flexible allocation between the two. PMID:26041580

  3. Analysis of intra-genomic GC content homogeneity within prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J; Snipen, L; Hardy, S.P.;

    2010-01-01

    Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how...... the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of...

  4. New results on averaging theory and applications

    Science.gov (United States)

    Cândido, Murilo R.; Llibre, Jaume

    2016-08-01

    The usual averaging theory reduces the computation of some periodic solutions of a system of ordinary differential equations, to find the simple zeros of an associated averaged function. When one of these zeros is not simple, i.e., the Jacobian of the averaged function in it is zero, the classical averaging theory does not provide information about the periodic solution associated to a non-simple zero. Here we provide sufficient conditions in order that the averaging theory can be applied also to non-simple zeros for studying their associated periodic solutions. Additionally, we do two applications of this new result for studying the zero-Hopf bifurcation in the Lorenz system and in the Fitzhugh-Nagumo system.

  5. The Hubble rate in averaged cosmology

    International Nuclear Information System (INIS)

    The calculation of the averaged Hubble expansion rate in an averaged perturbed Friedmann-Lemaître-Robertson-Walker cosmology leads to small corrections to the background value of the expansion rate, which could be important for measuring the Hubble constant from local observations. It also predicts an intrinsic variance associated with the finite scale of any measurement of H0, the Hubble rate today. Both the mean Hubble rate and its variance depend on both the definition of the Hubble rate and the spatial surface on which the average is performed. We quantitatively study different definitions of the averaged Hubble rate encountered in the literature by consistently calculating the backreaction effect at second order in perturbation theory, and compare the results. We employ for the first time a recently developed gauge-invariant definition of an averaged scalar. We also discuss the variance of the Hubble rate for the different definitions

  6. Average luminosity distance in inhomogeneous universes

    CERN Document Server

    Kostov, Valentin

    2010-01-01

    Using numerical ray tracing, the paper studies how the average distance modulus in an inhomogeneous universe differs from its homogeneous counterpart. The averaging is over all directions from a fixed observer not over all possible observers (cosmic), thus it is more directly applicable to our observations. Unlike previous studies, the averaging is exact, non-perturbative, and includes all possible non-linear effects. The inhomogeneous universes are represented by Sweese-cheese models containing random and simple cubic lattices of mass-compensated voids. The Earth observer is in the homogeneous cheese which has an Einstein - de Sitter metric. For the first time, the averaging is widened to include the supernovas inside the voids by assuming the probability for supernova emission from any comoving volume is proportional to the rest mass in it. Despite the well known argument for photon flux conservation, the average distance modulus correction at low redshifts is not zero due to the peculiar velocities. A form...

  7. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

    Science.gov (United States)

    Grenier, Cécile; Cao, Tuong-Vi; Ospina, Yolima; Quintero, Constanza; Châtel, Marc Henri; Tohme, Joe; Courtois, Brigitte; Ahmadi, Nourollah

    2015-01-01

    Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed. PMID:26313446

  8. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

    Directory of Open Access Journals (Sweden)

    Cécile Grenier

    Full Text Available Genomic selection (GS is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD and minor allele frequency (MAF thresholds for selecting markers, the relative size of the training population (TP and of the validation population (VP, the selected trait and the genomic prediction models (frequentist and Bayesian on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%, and differentiation between the four synthetic populations was low (FST ≤0.06. The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.

  9. Short-Term Auditory Memory of Above-Average and Below-Average Grade Three Readers.

    Science.gov (United States)

    Caruk, Joan Marie

    To determine if performance on short term auditory memory tasks is influenced by reading ability or sex differences, 62 third grade reading students (16 above average boys, 16 above average girls, 16 below average boys, and 14 below average girls) were administered four memory tests--memory for consonant names, memory for words, memory for…

  10. The smallest avian genomes are found in hummingbirds

    OpenAIRE

    Gregory, T. Ryan; Andrews, Chandler B; McGuire, Jimmy A.; Witt, Christopher C.

    2009-01-01

    It has often been suggested that the genome sizes of birds are constrained relative to other tetrapods owing to the high metabolic demands of powered flight and the link between nuclear DNA content and red blood cell size. This hypothesis predicts that hummingbirds, which engage in energy-intensive hovering flight, will display especially constrained genomes even relative to other birds. We report genome size measurements for 37 species of hummingbirds that confirm this prediction. Our result...

  11. Time averaging of instantaneous quantities in HYDRA

    Energy Technology Data Exchange (ETDEWEB)

    McCallen, R.C.

    1996-09-01

    For turbulent flow the evaluation of direct numerical simulations (DNS) where all scales are resolved and large-eddy simulation (LES) where only large-scales are resolved is difficult because the results are three-dimensional and transient. To simplify the analysis, the instantaneous flow field can be averaged in time for evaluation and comparison to experimental results. The incompressible Navier-Stokes flow code HYDRA has been modified for calculation of time-average quantities for both DNS and LES. This report describes how time averages of instantaneous quantities are generated during program execution (i.e., while generating the instantaneous quantities, instead of as a postprocessing operation). The calculations are performed during program execution to avoid storing values at each time step and thus to reduce storage requirements. The method used in calculating the time-average velocities, turbulent intensities, <{ital u}{sup ``}{sup 2}>, <{ital va}{sup ``}{sup 2}>, and <{ital w}{sup ``}{sup 2}>, and turbulent shear, <{ital u}{sup ``}{ital v}{sup ``}> are outlined. The brackets <> used here represent a time average. the described averaging methods were implemented in the HYDRA code for three-dimensional problem solutions. Also presented is a method for taking the time averages for a number of consecutive intervals and calculating the time average for the sum of the intervals. This method could be used for code restarts or further postprocessing of the timer averages from consecutive intervals. This method was not used in the HYDRA implementation, but is included here for completeness. In HYDRA, the running sums needed fro time averaging are simply written to the restart dump.

  12. Single virus genomics: a new tool for virus discovery.

    Directory of Open Access Journals (Sweden)

    Lisa Zeigler Allen

    Full Text Available Whole genome amplification and sequencing of single microbial cells has significantly influenced genomics and microbial ecology by facilitating direct recovery of reference genome data. However, viral genomics continues to suffer due to difficulties related to the isolation and characterization of uncultivated viruses. We report here on a new approach called 'Single Virus Genomics', which enabled the isolation and complete genome sequencing of the first single virus particle. A mixed assemblage comprised of two known viruses; E. coli bacteriophages lambda and T4, were sorted using flow cytometric methods and subsequently immobilized in an agarose matrix. Genome amplification was then achieved in situ via multiple displacement amplification (MDA. The complete lambda phage genome was recovered with an average depth of coverage of approximately 437X. The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable.

  13. Clarifying the Relationship between Average Excesses and Average Effects of Allele Substitutions.

    Science.gov (United States)

    Alvarez-Castro, José M; Yang, Rong-Cai

    2012-01-01

    Fisher's concepts of average effects and average excesses are at the core of the quantitative genetics theory. Their meaning and relationship have regularly been discussed and clarified. Here we develop a generalized set of one locus two-allele orthogonal contrasts for average excesses and average effects, based on the concept of the effective gene content of alleles. Our developments help understand the average excesses of alleles for the biallelic case. We dissect how average excesses relate to the average effects and to the decomposition of the genetic variance. PMID:22509178

  14. Clarifying the relationship between average excesses and average effects of allele substitutions

    Directory of Open Access Journals (Sweden)

    Jose M eÁlvarez-Castro

    2012-03-01

    Full Text Available Fisher’s concepts of average effects and average excesses are at the core of the quantitative genetics theory. Their meaning and relationship have regularly been discussed and clarified. Here we develop a generalized set of one-locus two-allele orthogonal contrasts for average excesses and average effects, based on the concept of the effective gene content of alleles. Our developments help understand the average excesses of alleles for the biallelic case. We dissect how average excesses relate to the average effects and to the decomposition of the genetic variance.

  15. Genome-based peptide fingerprint scanning

    OpenAIRE

    Giddings, Michael C.; Shah, Atul A.; Gesteland, Ray; Moore, Barry

    2002-01-01

    We have implemented a method that identifies the genomic origins of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. Unlike previously reported techniques, this method requires no predefined ORF or protein annotations. Fixed-size windows along the genome sequence are scored by an equation accounting for the number of matching peptides, the number of missed enzymatic cleavages in each peptide, the number ...

  16. Characterization of genome-wide microsatellites of Saccharina japonica based on a preliminary assembly of Illumina sequencing reads

    Science.gov (United States)

    Zhang, Linan; Peng, Jie; Li, Xiaojie; Cui, Cuiju; Sun, Juan; Yang, Guanpin

    2016-06-01

    Microsatellites or simple sequence repeats (SSR) function widely and locate dependently in genome. However, their characteristics are often ignored due to the lack of genomic sequences of most species. Kelp ( Saccharina japonica), a brown macroalga, is extensively cultured in China. In this study, the genome of S. japonica was surveyed using an Illumina sequencing platform, and its microsatellites were characterized. The preliminarily assembled genome was 469.4 Mb in size, with a scaffold N50 of 20529 bp. Among the 128370 identified microsatellites, 90671, 25726 and 11973 were found in intergenic regions, introns and exons, averaging 339.3, 178.8 and 205.4 microsatellites per Mb, respectively. These microsatellites distributed unevenly in S. japonica genome. Mononucleotide motifs were the most abundant in the genome, while trinucleotide ones were the most prevalent in exons. The microsatellite abundance decreased significantly with the increase of motif repeat numbers, and the microsatellites with a small number of repeats accounted for a higher proportion of the exons than those of the intergenic regions and introns. C/G-rich motifs were more common in exons than in intergenic regions and introns. These characteristics of microsatellites in S. japonica genome may associate with their functions, and ultimately their adaptation and evolution. Among the 120140 pairs of designed microsatellite primers, approximately 75% were predicted to be able to amplify S. japonica DNA. These microsatellite markers will be extremely useful for the genetic breeding and population evolution studies of kelp.

  17. Size matter!

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg; Jespersen, Andreas Maaløe; Skov, Laurits Rhoden

    2015-01-01

    Objectives We examined how a reduction in plate size would affect the amount of food waste from leftovers in a field experiment at a standing lunch for 220 CEOs. Methods A standing lunch for 220 CEOs in the Danish Opera House was arranged to feature two identical buffets with plates of two differ...

  18. Value of a newly sequenced bacterial genome.

    Science.gov (United States)

    Barbosa, Eudes Gv; Aburjaile, Flavia F; Ramos, Rommel Tj; Carneiro, Adriana R; Le Loir, Yves; Baumbach, Jan; Miyoshi, Anderson; Silva, Artur; Azevedo, Vasco

    2014-05-26

    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information. PMID:24921006

  19. Value of a newly sequenced bacterial genome

    Institute of Scientific and Technical Information of China (English)

    Eudes; GV; Barbosa; Flavia; F; Aburjaile; Rommel; TJ; Ramos; Adriana; R; Carneiro; Yves; Le; Loir; Jan; Baumbach; Anderson; Miyoshi; Artur; Silva; Vasco; Azevedo

    2014-01-01

    Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

  20. Small scale magnetic flux-averaged magnetohydrodynamics

    International Nuclear Information System (INIS)

    By relaxing exact magnetic flux conservation below a scale λ a system of flux-averaged magnetohydrodynamic equations are derived from Hamilton's principle with modified constraints. An energy principle can be derived from the linearized averaged system because the total system energy is conserved. This energy principle is employed to treat the resistive tearing instability and the exact growth rate is recovered when λ is identified with the resistive skin depth. A necessary and sufficient stability criteria of the tearing instability with line tying at the ends for solar coronal loops is also obtained. The method is extended to both spatial and temporal averaging in Hamilton's principle. The resulting system of equations not only allows flux reconnection but introduces irreversibility for appropriate choice of the averaging function. Except for boundary contributions which are modified by the time averaging process total energy and momentum are conserved over times much longer than the averaging time τ but not for less than τ. These modified boundary contributions correspond to the existence, also, of damped waves and shock waves in this theory. Time and space averaging is applied to electron magnetohydrodynamics and in one-dimensional geometry predicts solitons and shocks in different limits

  1. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence...... increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  2. 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 in...

  3. Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery

    Directory of Open Access Journals (Sweden)

    Baldwin Samantha

    2011-02-01

    Full Text Available Abstract Background Arabidopsis thaliana is a useful model organism for deciphering the genetic determinants of seed size; however the small size of its seeds makes measurements difficult. Bulk seed weights are often used as an indicator of average seed size, but details of individual seed is obscured. Analysis of seed images is possible but issues arise from variations in seed pigmentation and shadowing making analysis laborious. We therefore investigated the use of a consumer level scanner to facilitate seed size measurements in conjunction with open source image-processing software. Results By using the transmitted light from the slide scanning function of a flatbed scanner and particle analysis of the resulting images, we have developed a method for the rapid and high throughput analysis of seed size and seed size distribution. The technical variation due to the approach was negligible enabling us to identify aspects of maternal plant growth that contribute to biological variation in seed size. By controlling for these factors, differences in seed size caused by altered parental genome dosage and mutation were easily detected. The method has high reproducibility and sensitivity, such that a mutant with a 10% reduction in seed size was identified in a screen of endosperm-expressed genes. Our study also generated average seed size data for 91 Arabidopsis accessions and identified a number of quantitative trait loci from two recombinant inbred line populations, generated from Cape Verde Islands and Burren accessions crossed with Columbia. Conclusions This study describes a sensitive, high-throughput approach for measuring seed size and seed size distribution. The method provides a low cost and robust solution that can be easily implemented into the workflow of studies relating to various aspects of seed development.

  4. Comparative genomics reveals insights into avian genome evolution and adaptation

    DEFF Research Database (Denmark)

    Zhang, Guojie; Li, Cai; Li, Qiye;

    2014-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size......, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this...... pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits....

  5. RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes.

    Science.gov (United States)

    Buza, Krisztian; Wilczynski, Bartek; Dojer, Norbert

    2015-01-01

    Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used. Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge. Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software. PMID:26558255

  6. Self-averaging characteristics of spectral fluctuations

    OpenAIRE

    Braun, Petr; Haake, Fritz

    2014-01-01

    The spectral form factor as well as the two-point correlator of the density of (quasi-)energy levels of individual quantum dynamics are not self-averaging. Only suitable smoothing turns them into useful characteristics of spectra. We present numerical data for a fully chaotic kicked top, employing two types of smoothing: one involves primitives of the spectral correlator, the second a small imaginary part of the quasi-energy. Self-averaging universal (like the CUE average) behavior is found f...

  7. Averaged Lema\\^itre-Tolman-Bondi dynamics

    CERN Document Server

    Isidro, Eddy G Chirinos; Piattella, Oliver F; Zimdahl, Winfried

    2016-01-01

    We consider cosmological backreaction effects in Buchert's averaging formalism on the basis of an explicit solution of the Lema\\^itre-Tolman-Bondi (LTB) dynamics which is linear in the LTB curvature parameter and has an inhomogeneous bang time. The volume Hubble rate is found in terms of the volume scale factor which represents a derivation of the simplest phenomenological solution of Buchert's equations in which the fractional densities corresponding to average curvature and kinematic backreaction are explicitly determined by the parameters of the underlying LTB solution at the boundary of the averaging volume. This configuration represents an exactly solvable toy model but it does not adequately describe our "real" Universe.

  8. Experimental Demonstration of Squeezed State Quantum Averaging

    CERN Document Server

    Lassen, Mikael; Sabuncu, Metin; Filip, Radim; Andersen, Ulrik L

    2010-01-01

    We propose and experimentally demonstrate a universal quantum averaging process implementing the harmonic mean of quadrature variances. The harmonic mean protocol can be used to efficiently stabilize a set of fragile squeezed light sources with statistically fluctuating noise levels. The averaged variances are prepared probabilistically by means of linear optical interference and measurement induced conditioning. We verify that the implemented harmonic mean outperforms the standard arithmetic mean strategy. The effect of quantum averaging is experimentally tested both for uncorrelated and partially correlated noise sources with sub-Poissonian shot noise or super-Poissonian shot noise characteristics.

  9. Average Shape of Transport-Limited Aggregates

    Science.gov (United States)

    Davidovitch, Benny; Choi, Jaehyuk; Bazant, Martin Z.

    2005-08-01

    We study the relation between stochastic and continuous transport-limited growth models. We derive a nonlinear integro-differential equation for the average shape of stochastic aggregates, whose mean-field approximation is the corresponding continuous equation. Focusing on the advection-diffusion-limited aggregation (ADLA) model, we show that the average shape of the stochastic growth is similar, but not identical, to the corresponding continuous dynamics. Similar results should apply to DLA, thus explaining the known discrepancies between average DLA shapes and viscous fingers in a channel geometry.

  10. 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...

  11. Orientation-averaged optical properties of natural aerosol aggregates

    International Nuclear Information System (INIS)

    Orientation-averaged optical properties of natural aerosol aggregates were analyzed by using discrete dipole approximation (DDA) for the effective radius in the range of 0.01 to 2 μm with the corresponding size parameter from 0.1 to 23 for the wavelength of 0.55 μm. Effects of the composition and morphology on the optical properties were also investigated. The composition show small influence on the extinction-efficiency factor in Mie scattering region, scattering- and backscattering-efficiency factors. The extinction-efficiency factor with the size parameter from 9 to 23 and asymmetry factor with the size parameter below 2.3 are almost independent of the natural aerosol composition. The extinction-, absorption, scattering-, and backscattering-efficiency factors with the size parameter below 0.7 are irrespective of the aggregate morphology. The intrinsic symmetry and discontinuity of the normal direction of the particle surface have obvious effects on the scattering properties for the size parameter above 4.6. Furthermore, the scattering phase functions of natural aerosol aggregates are enhanced at the backscattering direction (opposition effect) for large size parameters in the range of Mie scattering. (authors)

  12. Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda

    Directory of Open Access Journals (Sweden)

    Andrea Gloria-Soria

    2016-06-01

    Full Text Available The tsetse fly Glossina fuscipes fuscipes (Gff is the insect vector of the two forms of Human African Trypanosomiasis (HAT that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of ∼73,000 single-nucleotide polymorphisms (SNPs distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies. We used these markers to estimate genomic patterns of linkage disequilibrium (LD in Gff, and used the information, in combination with outlier-locus detection tests, to identify candidate regions of the genome under selection. LD in individual populations decays to half of its maximum value (r2max/2 between 1359 and 2429 bp. The overall LD estimated for the species reaches r2max/2 at 708 bp, an order of magnitude slower than in Drosophila. Using 53 infected (Trypanosoma spp. and uninfected flies from four genetically distinct Ugandan populations adapted to different environmental conditions, we were able to identify SNPs associated with the infection status of the fly and local environmental adaptation. The extent of LD in Gff likely facilitated the detection of loci under selection, despite the small sample size. Furthermore, it is probable that LD in the regions identified is much higher than the average genomic LD due to strong selection. Our results show that even modest sample sizes can reveal significant genetic associations in this species, which has implications for future studies given the difficulties of collecting field specimens with contrasting phenotypes for association analysis.

  13. Genomic analysis for managing small and endangered populations: A case study in Tyrol Grey cattle

    Directory of Open Access Journals (Sweden)

    Gábor eMészáros

    2015-05-01

    Full Text Available Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore the routine collection of genomic information would be an invaluable resource for management of breeding programs in small, endangered populations. The objectives of this project were to analyse 1. linkage disequlibrium decay and the effective population size; 2. Inbreeding level and effective population size (NeROH based on runs of homozygosity (ROH; 3. Prediction of genomic breeding values (GEBV within and across breeds. In addition, the use of genomic information for breed management is discussed. The study was based on all available genotypes of Tyrol Grey AI bulls. ROHs were derived based on regions covering at least 4 Mb, 8 Mb and 16 Mb regions, with the corresponding mean inbreeding coefficients 4.0%, 2.9% and 1.6%, respectively. The NeROH was 125 (NeROH>16Mb, 186 (NeROH>8Mb and 370 (NeROH>4Mb, indicating strict avoidance of close inbreeding in the population.The genomic selection was developed for and is working well in large breeds. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when EBVs and dEBVs were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

  14. Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda.

    Science.gov (United States)

    Gloria-Soria, Andrea; Dunn, W Augustine; Telleria, Erich L; Evans, Benjamin R; Okedi, Loyce; Echodu, Richard; Warren, Wesley C; Montague, Michael J; Aksoy, Serap; Caccone, Adalgisa

    2016-01-01

    The tsetse fly Glossina fuscipes fuscipes (Gff) is the insect vector of the two forms of Human African Trypanosomiasis (HAT) that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of ∼73,000 single-nucleotide polymorphisms (SNPs) distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies. We used these markers to estimate genomic patterns of linkage disequilibrium (LD) in Gff, and used the information, in combination with outlier-locus detection tests, to identify candidate regions of the genome under selection. LD in individual populations decays to half of its maximum value (r(2) max/2) between 1359 and 2429 bp. The overall LD estimated for the species reaches r(2) max/2 at 708 bp, an order of magnitude slower than in Drosophila Using 53 infected (Trypanosoma spp.) and uninfected flies from four genetically distinct Ugandan populations adapted to different environmental conditions, we were able to identify SNPs associated with the infection status of the fly and local environmental adaptation. The extent of LD in Gff likely facilitated the detection of loci under selection, despite the small sample size. Furthermore, it is probable that LD in the regions identified is much higher than the average genomic LD due to strong selection. Our results show that even modest sample sizes can reveal significant genetic associations in this species, which has implications for future studies given the difficulties of collecting field specimens with contrasting phenotypes for association analysis. PMID:27172181

  15. 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.

  16. Characterization of Interspecific Hybrids Between Oryza sativa L. and Three Wild Rice Species of China by Genomic In Situ Hybridization

    Institute of Scientific and Technical Information of China (English)

    Guang-Xuan Tan; Zhi-Yong Xiong; Hua-Jun Jin; Gang Li; Li-Li Zhu; Li-Hui Shu; Guang-Cun He

    2006-01-01

    In the genus Oryza, interspecific hybrids are useful bridges for transferring the desired genes from wild species to cultivated rice (Oryza sativa L.). In the present study, hybrids between O. sativa (AA genome)and three Chinese wild rices, namely O. rufipogon (AA genome), O. officinalis (CC genome), and O. meyeriana (GG genome), were produced. Agricultural traits of the F1 hybrids surveyed were intermediate between their parents and appreciably resembled wild rice parents. Except for the O. sativa × O. rufipogon hybrid,the other F1 hybrids were completely sterile. Genomic in situ hybridization (GISH) was used for hybrid verification. Wild rice genomic DNAs were used as probes and cultivated rice DNA was used as a block. With the exception of O. rufipogon chromosomes, this method distinguished the other two wild rice and cultivated rice chromosomes at the stage of mitotic metaphase with different blocking ratios. The results suggest that a more distant phylogenetic relationship exists between O. meyeriana and O. sativa and that O. rufipogon and O. sativa share a high degree of sequence homology. The average mitotic chromosome length of O. officinalis and O. meyeriana was 1.25- and 1.51-fold that of O. sativa, respectively. 4',6'-Diamidino2-phenylindole staining showed that the chromosomes of O. officinalis and O. meyeriana harbored more heterochromatin, suggesting that the C and G genomes were amplified with repetitive sequences compared with the A genome. Although chromocenters formed by chromatln compaction were detected with wild rice-specific signals corresponding to the C and G genomes in discrete domains of the F1 hybrid interphase nuclei, the size and number of O. meyeriana chromocenters were bigger and greater than those of O. officinalis. The present results provide an important understanding of the genomic relationships and a tool for the transfer of useful genes from three native wild rice species in China to cultivars.

  17. Average Vegetation Growth 1992 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1992 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  18. Average Vegetation Growth 1994 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1994 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  19. Average Vegetation Growth 1991 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1991 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  20. Average Vegetation Growth 1993 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1993 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  1. Average Vegetation Growth 1998 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1998 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  2. Average Vegetation Growth 1999 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1999 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  3. Average Vegetation Growth 1990 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1990 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  4. Average Vegetation Growth 2003 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 2003 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  5. A practical guide to averaging functions

    CERN Document Server

    Beliakov, Gleb; Calvo Sánchez, Tomasa

    2016-01-01

    This book offers an easy-to-use and practice-oriented reference guide to mathematical averages. It presents different ways of aggregating input values given on a numerical scale, and of choosing and/or constructing aggregating functions for specific applications. Building on a previous monograph by Beliakov et al. published by Springer in 2007, it outlines new aggregation methods developed in the interim, with a special focus on the topic of averaging aggregation functions. It examines recent advances in the field, such as aggregation on lattices, penalty-based aggregation and weakly monotone averaging, and extends many of the already existing methods, such as: ordered weighted averaging (OWA), fuzzy integrals and mixture functions. A substantial mathematical background is not called for, as all the relevant mathematical notions are explained here and reported on together with a wealth of graphical illustrations of distinct families of aggregation functions. The authors mainly focus on practical applications ...

  6. Sea Surface Temperature Average_SST_Master

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Sea surface temperature collected via satellite imagery from http://www.esrl.noaa.gov/psd/data/gridded/data.noaa.ersst.html and averaged for each region using...

  7. Averaging procedure in variable-G cosmologies

    CERN Document Server

    Cardone, Vincenzo F

    2008-01-01

    Previous work in the literature had built a formalism for spatially averaged equations for the scale factor, giving rise to an averaged Raychaudhuri equation and averaged Hamiltonian constraint, which involve a backreaction source term. The present paper extends these equations to include models with variable Newton parameter and variable cosmological term, motivated by the non-perturbative renormalization program for quantum gravity based upon the Einstein--Hilbert action. The coupling between backreaction and spatially averaged three-dimensional scalar curvature is found to survive, and all equations involving contributions of a variable Newton parameter are worked out in detail. Interestingly, under suitable assumptions, an approximate solution can be found where the universe tends to a FLRW model, while keeping track of the original inhomogeneities through two effective fluids.

  8. MN Temperature Average (1961-1990) - Line

    Data.gov (United States)

    Minnesota Department of Natural Resources — This data set depicts 30-year averages (1961-1990) of monthly and annual temperatures for Minnesota. Isolines and regions were created using kriging and...

  9. Monthly snow/ice averages (ISCCP)

    Data.gov (United States)

    National Aeronautics and Space Administration — September Arctic sea ice is now declining at a rate of 11.5 percent per decade, relative to the 1979 to 2000 average. Data from NASA show that the land ice sheets...

  10. Average Vegetation Growth 1997 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 1997 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  11. Average Vegetation Growth 2001 - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map layer is a grid map of 2001 average vegetation growth for Alaska and the conterminous United States. The nominal spatial resolution is 1 kilometer and the...

  12. MN Temperature Average (1961-1990) - Polygon

    Data.gov (United States)

    Minnesota Department of Natural Resources — This data set depicts 30-year averages (1961-1990) of monthly and annual temperatures for Minnesota. Isolines and regions were created using kriging and...

  13. Average Bandwidth Allocation Model of WFQ

    Directory of Open Access Journals (Sweden)

    Tomáš Balogh

    2012-01-01

    Full Text Available We present a new iterative method for the calculation of average bandwidth assignment to traffic flows using a WFQ scheduler in IP based NGN networks. The bandwidth assignment calculation is based on the link speed, assigned weights, arrival rate, and average packet length or input rate of the traffic flows. We prove the model outcome with examples and simulation results using NS2 simulator.

  14. Development of average wages in CR regions

    OpenAIRE

    Bejvlová, Jana

    2013-01-01

    The purpose of this study is to analyse trends in average gross monthly earnings of employees – individuals - in particular regions of the Czech Republic. The analysed time series begin in 2000 as the regions were decisively established on 1st January 2000. Moreover the self-governing competencies were introduced by the Act No. 129/2000 Coll., on Regions (Establishment of Regions). The researched period ends in 2010. Based on model construction of referential sets, the study predicts average ...

  15. Grassmann Averages for Scalable Robust PCA

    DEFF Research Database (Denmark)

    Hauberg, Søren; Feragen, Aasa; Black, Michael J.

    vectors (subspaces) or elements of vectors; we focus on the latter and use a trimmed average. The resulting Trimmed Grassmann Average (TGA) is particularly appropriate for computer vision because it is robust to pixel outliers. The algorithm has low computational complexity and minimal memory requirements......, making it scalable to “big noisy data.” We demonstrate TGA for background modeling, video restoration, and shadow removal. We show scalability by performing robust PCA on the entire Star Wars IV movie....

  16. Hyperplane Arrangements with Large Average Diameter

    OpenAIRE

    Deza, Antoine; Xie, Feng

    2007-01-01

    The largest possible average diameter of a bounded cell of a simple hyperplane arrangement is conjectured to be not greater than the dimension. We prove that this conjecture holds in dimension 2, and is asymptotically tight in fixed dimension. We give the exact value of the largest possible average diameter for all simple arrangements in dimension 2, for arrangements having at most the dimension plus 2 hyperplanes, and for arrangements having 6 hyperplanes in dimension 3. In dimension 3, we g...

  17. The Hubble rate in averaged cosmology

    OpenAIRE

    Umeh, Obinna; Larena, Julien; Clarkson, Chris

    2010-01-01

    The calculation of the averaged Hubble expansion rate in an averaged perturbed Friedmann-Lemaitre-Robertson-Walker cosmology leads to small corrections to the background value of the expansion rate, which could be important for measuring the Hubble constant from local observations. It also predicts an intrinsic variance associated with the finite scale of any measurement of H_0, the Hubble rate today. Both the mean Hubble rate and its variance depend on both the definition of the Hubble rate ...

  18. Nonequilibrium statistical averages and thermo field dynamics

    International Nuclear Information System (INIS)

    An extension of thermo field dynamics is proposed, which permits the computation of nonequilibrium statistical averages. The Brownian motion of a quantum oscillator is treated as an example. In conclusion it is pointed out that the procedure proposed to computation of time-dependent statistical average gives the correct two-point Green function for the damped oscillator. A simple extension can be used to compute two-point Green functions of free particles

  19. Averaging Problem in Cosmology and Macroscopic Gravity

    OpenAIRE

    Zalaletdinov, Roustam

    2007-01-01

    The Averaging problem in general relativity and cosmology is discussed. The approach of macroscopic gravity to resolve the problem is presented. An exact cosmological solution to the equations of macroscopic gravity is given and its properties are discussed. Contents: 1. Introduction to General Relativity 2. General Relativity -> Relativistic Cosmology 3. Introduction to Relativistic Cosmology 4. Relativistic Cosmology -> Mathematical Cosmology 5. Averaging Problem in Relativistic Cosmology 6...

  20. Method of averaging in Clifford algebras

    OpenAIRE

    Shirokov, D. S.

    2014-01-01

    In this paper we consider different operators acting on Clifford algebras. We consider Reynolds operator of Salingaros' vee group. This operator average" an action of Salingaros' vee group on Clifford algebra. We consider conjugate action on Clifford algebra. We present a relation between these operators and projection operators onto fixed subspaces of Clifford algebras. Using method of averaging we present solutions of system of commutator equations.

  1. The genome of Eucalyptus grandis

    Energy Technology Data Exchange (ETDEWEB)

    Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; Van de Peer, Yves; Rokhsar, Daniel S.; Schmutz, Jeremy

    2014-06-11

    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  2. Self-averaging characteristics of spectral fluctuations

    Science.gov (United States)

    Braun, Petr; Haake, Fritz

    2015-04-01

    The spectral form factor as well as the two-point correlator of the density of (quasi-)energy levels of individual quantum dynamics are not self-averaging. Only suitable smoothing turns them into useful characteristics of spectra. We present numerical data for a fully chaotic kicked top, employing two types of smoothing: one involves primitives of the spectral correlator, the second, a small imaginary part of the quasi-energy. Self-averaging universal (like the circular unitary ensemble (CUE) average) behavior is found for the smoothed correlator, apart from noise which shrinks like 1/\\sqrt{N} as the dimension N of the quantum Hilbert space grows. There are periodically repeated quasi-energy windows of correlation decay and revival wherein the smoothed correlation remains finite as N\\to ∞ such that the noise is negligible. In between those windows (where the CUE averaged correlator takes on values of the order 1/{{N}2}) the noise becomes dominant and self-averaging is lost. We conclude that the noise forbids distinction of CUE and GUE-type behavior. Surprisingly, the underlying smoothed generating function does not enjoy any self-averaging outside the range of its variables relevant for determining the two-point correlator (and certain higher-order ones). We corroborate our numerical findings for the noise by analytically determining the CUE variance of the smoothed single-matrix correlator.

  3. Construction of average adult Japanese voxel phantoms for dose assessment

    International Nuclear Information System (INIS)

    The International Commission on Radiological Protection (ICRP) adopted the adult reference voxel phantoms based on the physiological and anatomical reference data of Caucasian on October, 2007. The organs and tissues of these phantoms were segmented on the basis of ICRP Publication 103. In future, the dose coefficients for internal dose and dose conversion coefficients for external dose calculated using the adult reference voxel phantoms will be widely used for the radiation protection fields. On the other hand, the body sizes and organ masses of adult Japanese are generally smaller than those of adult Caucasian. In addition, there are some cases that the anatomical characteristics such as body sizes, organ masses and postures of subjects influence the organ doses in dose assessment for medical treatments and radiation accident. Therefore, it was needed to use human phantoms with average anatomical characteristics of Japanese. The authors constructed the averaged adult Japanese male and female voxel phantoms by modifying the previously developed high-resolution adult male (JM) and female (JF) voxel phantoms. It has been modified in the following three aspects: (1) The heights and weights were agreed with the Japanese averages; (2) The masses of organs and tissues were adjusted to the Japanese averages within 10%; (3) The organs and tissues, which were newly added for evaluation of the effective dose in ICRP Publication 103, were modeled. In this study, the organ masses, distances between organs, specific absorbed fractions (SAFs) and dose conversion coefficients of these phantoms were compared with those evaluated using the ICRP adult reference voxel phantoms. This report provides valuable information on the anatomical and dosimetric characteristics of the averaged adult Japanese male and female voxel phantoms developed as reference phantoms of adult Japanese. (author)

  4. Targeted Cancer Screening in Average-Risk Individuals.

    Science.gov (United States)

    Marcus, Pamela M; Freedman, Andrew N; Khoury, Muin J

    2015-11-01

    Targeted cancer screening refers to use of disease risk information to identify those most likely to benefit from screening. Researchers have begun to explore the possibility of refining screening regimens for average-risk individuals using genetic and non-genetic risk factors and previous screening experience. Average-risk individuals are those not known to be at substantially elevated risk, including those without known inherited predisposition, without comorbidities known to increase cancer risk, and without previous diagnosis of cancer or pre-cancer. In this paper, we describe the goals of targeted cancer screening in average-risk individuals, present factors on which cancer screening has been targeted, discuss inclusion of targeting in screening guidelines issued by major U.S. professional organizations, and present evidence to support or question such inclusion. Screening guidelines for average-risk individuals currently target age; smoking (lung cancer only); and, in some instances, race; family history of cancer; and previous negative screening history (cervical cancer only). No guidelines include common genomic polymorphisms. RCTs suggest that targeting certain ages and smoking histories reduces disease-specific cancer mortality, although some guidelines extend ages and smoking histories based on statistical modeling. Guidelines that are based on modestly elevated disease risk typically have either no or little evidence of an ability to affect a mortality benefit. In time, targeted cancer screening is likely to include genetic factors and past screening experience as well as non-genetic factors other than age, smoking, and race, but it is of utmost importance that clinical implementation be evidence-based. PMID:26165196

  5. Comparison of Mouse Brain DTI Maps Using K-space Average, Image-space Average, or No Average Approach

    OpenAIRE

    Sun, Shu-Wei; Mei, Jennifer; Tuel, Keelan

    2013-01-01

    Diffusion tensor imaging (DTI) is achieved by collecting a series of diffusion-weighted images (DWIs). Signal averaging of multiple repetitions can be performed in the k-space (k-avg) or in the image space (m-avg) to improve the image quality. Alternatively, one can treat each acquisition as an independent image and use all of the data to reconstruct the DTI without doing any signal averaging (no-avg). To compare these three approaches, in this study, in vivo DTI data was collected from five ...

  6. The characterization of twenty sequenced human genomes.

    Directory of Open Access Journals (Sweden)

    Kimberly Pelak

    2010-09-01

    Full Text Available We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and ten "control" genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.

  7. Draft Genome Sequence of Alternaria alternata ATCC 34957.

    Science.gov (United States)

    Nguyen, Hai D T; Lewis, Christopher T; Lévesque, C André; Gräfenhan, Tom

    2016-01-01

    We report the draft genome sequence of Alternaria alternata ATCC 34957. This strain was previously reported to produce alternariol and alternariol monomethyl ether on weathered grain sorghum. The genome was sequenced with PacBio technology and assembled into 27 scaffolds with a total genome size of 33.5 Mb. PMID:26769939

  8. Basics of averaging of the Maxwell equations

    CERN Document Server

    Chipouline, A; Tretyakov, S

    2011-01-01

    Volume or statistical averaging of the microscopic Maxwell equations (MEs), i.e. transition from microscopic MEs to their macroscopic counterparts, is one of the main steps in electrodynamics of materials. In spite of the fundamental importance of the averaging procedure, it is quite rarely properly discussed in university courses and respective books; up to now there is no established consensus about how the averaging procedure has to be performed. In this paper we show that there are some basic principles for the averaging procedure (irrespective to what type of material is studied) which have to be satisfied. Any homogenization model has to be consistent with the basic principles. In case of absence of this correlation of a particular model with the basic principles the model could not be accepted as a credible one. Another goal of this paper is to establish the averaging procedure for metamaterials, which is rather close to the case of compound materials but should include magnetic response of the inclusi...

  9. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Vattipally B Sreenu; Pankaj Kumar; Javaregowda Nagaraju; Hampapathalu A Nagarajaram

    2007-01-01

    Simple sequence repeats (SSRs) or microsatellites are the repetitive nucleotide sequences of motifs of length 1–6 bp. They are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes. Microsatellites undergo mutations in the form of insertions and deletions (INDELS) of their repeat units with some bias towards insertions that lead to microsatellite tract expansion. Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these enzymes and as a null hypothesis one could expect these genomes to harbour many long tracts. It is therefore interesting to analyse the mycobacterial genomes for distribution and abundance of microsatellites tracts and to look for potentially polymorphic microsatellites. Available mycobacterial genomes, Mycobacterium avium, M. leprae, M. bovis and the two strains of M. tuberculosis (CDC1551 and H37Rv) were analysed for frequencies and abundance of SSRs. Our analysis revealed that the SSRs are distributed throughout the mycobacterial genomes at an average of 220–230 SSR tracts per kb. All the mycobacterial genomes contain few regions that are conspicuously denser or poorer in microsatellites compared to their expected genome averages. The genomes distinctly show scarcity of long microsatellites despite the absence of a post-replicative DNA repair system. Such severe scarcity of long microsatellites could arise as a result of strong selection pressures operating against long and unstable sequences although influence of GC-content and role of point mutations in arresting microsatellite expansions can not be ruled out. Nonetheless, the long tracts occasionally found in coding as well as non-coding regions may account for limited genome plasticity in these genomes.

  10. 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)

    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)

  11. Comparative genomic analyses in Asparagus.

    Science.gov (United States)

    Kuhl, Joseph C; Havey, Michael J; Martin, William J; Cheung, Foo; Yuan, Qiaoping; Landherr, Lena; Hu, Yi; Leebens-Mack, James; Town, Christopher D; Sink, Kenneth C

    2005-12-01

    Garden asparagus (Asparagus officinalis L.) belongs to the monocot family Asparagaceae in the order Asparagales. Onion (Allium cepa L.) and Asparagus officinalis are 2 of the most economically important plants of the core Asparagales, a well supported monophyletic group within the Asparagales. Coding regions in onion have lower GC contents than the grasses. We compared the GC content of 3374 unique expressed sequence tags (ESTs) from A. officinalis with Lycoris longituba and onion (both members of the core Asparagales), Acorus americanus (sister to all other monocots), the grasses, and Arabidopsis. Although ESTs in A. officinalis and Acorus had a higher average GC content than Arabidopsis, Lycoris, and onion, all were clearly lower than the grasses. The Asparagaceae have the smallest nuclear genomes among all plants in the core Asparagales, which typically have huge genomes. Within the Asparagaceae, European Asparagus species have approximately twice the nuclear DNA of that of southern African Asparagus species. We cloned and sequenced 20 genomic amplicons from European A. officinalis and the southern African species Asparagus plumosus and observed no clear evidence for a recent genome doubling in A. officinalis relative to A. plumosus. These results indicate that members of the genus Asparagus with smaller genomes may be useful genomic models for plants in the core Asparagales. PMID:16391674

  12. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Bansal Manju

    2011-07-01

    Full Text Available Abstract Background As more and more genomes are being sequenced, an overview of their genomic features and annotation of their functional elements, which control the expression of each gene or transcription unit of the genome, is a fundamental challenge in genomics and bioinformatics. Findings Relative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability in the vicinity of all annotated translation start sites (TLS. Conclusion PromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web http://nucleix.mbu.iisc.ernet.in/prombase/.

  13. Large interface simulation in an averaged two-fluid code

    International Nuclear Information System (INIS)

    Different ranges of size of interfaces and eddies are involved in multiphase flow phenomena. Classical formalisms focus on a specific range of size. This study presents a Large Interface Simulation (LIS) two-fluid compressible formalism taking into account different sizes of interfaces. As in the single-phase Large Eddy Simulation, a filtering process is used to point out Large Interface (LI) simulation and Small interface (SI) modelization. The LI surface tension force is modelled adapting the well-known CSF method. The modelling of SI transfer terms is done calling for classical closure laws of the averaged approach. To simulate accurately LI transfer terms, we develop a LI recognition algorithm based on a dimensionless criterion. The LIS model is applied in a classical averaged two-fluid code. The LI transfer terms modelling and the LI recognition are validated on analytical and experimental tests. A square base basin excited by a horizontal periodic movement is studied with the LIS model. The capability of the model is also shown on the case of the break-up of a bubble in a turbulent liquid flow. The break-up of a large bubble at a grid impact performed regime transition between two different scales of interface from LI to SI and from PI to LI. (author)

  14. Books average previous decade of economic misery.

    Directory of Open Access Journals (Sweden)

    R Alexander Bentley

    Full Text Available For the 20(th century since the Depression, we find a strong correlation between a 'literary misery index' derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade.

  15. Books average previous decade of economic misery.

    Science.gov (United States)

    Bentley, R Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20(th) century since the Depression, we find a strong correlation between a 'literary misery index' derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade. PMID:24416159

  16. Cosmic structure, averaging and dark energy

    CERN Document Server

    Wiltshire, David L

    2013-01-01

    These lecture notes review the theoretical problems associated with coarse-graining the observed inhomogeneous structure of the universe at late epochs, of describing average cosmic evolution in the presence of growing inhomogeneity, and of relating average quantities to physical observables. In particular, a detailed discussion of the timescape scenario is presented. In this scenario, dark energy is realized as a misidentification of gravitational energy gradients which result from gradients in the kinetic energy of expansion of space, in the presence of density and spatial curvature gradients that grow large with the growth of structure. The phenomenology and observational tests of the timescape model are discussed in detail, with updated constraints from Planck satellite data. In addition, recent results on the variation of the Hubble expansion on < 100/h Mpc scales are discussed. The spherically averaged Hubble law is significantly more uniform in the rest frame of the Local Group of galaxies than in t...

  17. Average Cycle Period in Asymmetrical Flashing Ratchet

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-Yan; HE Hou-Sheng; BAO Jing-Dong

    2005-01-01

    The directed motion of a Brownian particle in a flashing potential with various transition probabilities and waiting times in one of two states is studied. An expression for the average cycle period is proposed and the steady current J of the particle is calculated via Langevin simulation. The results show that the optimal cycle period rm,which takes the maximum of J, is shifted to a small value when the transition probability λ from the potential on to the potential off decreases, the maximalcurrent appears in the case of the average waiting time in the potential on being longer than in the potential off, and the direction of current depends on the ratio of the average times waiting in two states.

  18. Stochastic Averaging and Stochastic Extremum Seeking

    CERN Document Server

    Liu, Shu-Jun

    2012-01-01

    Stochastic Averaging and Stochastic Extremum Seeking develops methods of mathematical analysis inspired by the interest in reverse engineering  and analysis of bacterial  convergence by chemotaxis and to apply similar stochastic optimization techniques in other environments. The first half of the text presents significant advances in stochastic averaging theory, necessitated by the fact that existing theorems are restricted to systems with linear growth, globally exponentially stable average models, vanishing stochastic perturbations, and prevent analysis over infinite time horizon. The second half of the text introduces stochastic extremum seeking algorithms for model-free optimization of systems in real time using stochastic perturbations for estimation of their gradients. Both gradient- and Newton-based algorithms are presented, offering the user the choice between the simplicity of implementation (gradient) and the ability to achieve a known, arbitrary convergence rate (Newton). The design of algorithms...

  19. High Average Power Yb:YAG Laser

    Energy Technology Data Exchange (ETDEWEB)

    Zapata, L E; Beach, R J; Payne, S A

    2001-05-23

    We are working on a composite thin-disk laser design that can be scaled as a source of high brightness laser power for tactical engagement and other high average power applications. The key component is a diffusion-bonded composite comprising a thin gain-medium and thicker cladding that is strikingly robust and resolves prior difficulties with high average power pumping/cooling and the rejection of amplified spontaneous emission (ASE). In contrast to high power rods or slabs, the one-dimensional nature of the cooling geometry and the edge-pump geometry scale gracefully to very high average power. The crucial design ideas have been verified experimentally. Progress this last year included: extraction with high beam quality using a telescopic resonator, a heterogeneous thin film coating prescription that meets the unusual requirements demanded by this laser architecture, thermal management with our first generation cooler. Progress was also made in design of a second-generation laser.

  20. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

    DEFF Research Database (Denmark)

    Li, Yingrui; Zheng, Hancheng; Luo, Ruibang; Wu, Honglong; Zhu, Hongmei; Li, Ruiqiang; Cao, Hongzhi; Wu, Boxin; Huang, Shujia; Shao, Haojing; Ma, Hanzhou; Zhang, Fan; Feng, Shuijian; Zhang, Wei; Du, Hongli; Tian, Geng; Li, Jingxiang; Zhang, Xiuqing; Li, Songgang; Bolund, Lars; Kristiansen, Karsten; de Smith, Adam J; Blakemore, Alexandra I F; Coin, Lachlan J M; Yang, Huanming; Wang, Jian; Wang, Jun

    2011-01-01

    Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1-50 kb) including insertions, deletions, inversions and their precise...

  1. Books Average Previous Decade of Economic Misery

    OpenAIRE

    R Alexander Bentley; Alberto Acerbi; Paul Ormerod; Vasileios Lampos

    2014-01-01

    For the 20(th) century since the Depression, we find a strong correlation between a 'literary misery index' derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is signific...

  2. On the average pairing energy in nuclei

    International Nuclear Information System (INIS)

    The macroscopic-microscopic method is applied to calculate the nuclear energies, especially the microscopic shell and pairing corrections. The single-particle levels are obtained with the Yukawa folded mean-field potential. The macroscopic energy is evaluated using the Lublin-Strasbourg Drop model. The shell corrections are obtained using the Strutinsky method with smoothing in nucleon number space. The average nuclear pairing energy is also determined by folding the BCS sums in nucleon number space. The average pairing energy dependence on the nuclear elongation is investigated. (author)

  3. A singularity theorem based on spatial averages

    Indian Academy of Sciences (India)

    J M M Senovilla

    2007-07-01

    Inspired by Raychaudhuri's work, and using the equation named after him as a basic ingredient, a new singularity theorem is proved. Open non-rotating Universes, expanding everywhere with a non-vanishing spatial average of the matter variables, show severe geodesic incompletness in the past. Another way of stating the result is that, under the same conditions, any singularity-free model must have a vanishing spatial average of the energy density (and other physical variables). This is very satisfactory and provides a clear decisive difference between singular and non-singular cosmologies.

  4. Changing mortality and average cohort life expectancy

    DEFF Research Database (Denmark)

    Schoen, Robert; Canudas-Romo, Vladimir

    2005-01-01

    Period life expectancy varies with changes in mortality, and should not be confused with the life expectancy of those alive during that period. Given past and likely future mortality changes, a recent debate has arisen on the usefulness of the period life expectancy as the leading measure of......, the average cohort life expectancy (ACLE), to provide a precise measure of the average length of life of cohorts alive at a given time. To compare the performance of ACLE with CAL and with period and cohort life expectancy, we first use population models with changing mortality. Then the four...

  5. Average-case analysis of numerical problems

    CERN Document Server

    2000-01-01

    The average-case analysis of numerical problems is the counterpart of the more traditional worst-case approach. The analysis of average error and cost leads to new insight on numerical problems as well as to new algorithms. The book provides a survey of results that were mainly obtained during the last 10 years and also contains new results. The problems under consideration include approximation/optimal recovery and numerical integration of univariate and multivariate functions as well as zero-finding and global optimization. Background material, e.g. on reproducing kernel Hilbert spaces and random fields, is provided.

  6. An improved moving average technical trading rule

    Science.gov (United States)

    Papailias, Fotis; Thomakos, Dimitrios D.

    2015-06-01

    This paper proposes a modified version of the widely used price and moving average cross-over trading strategies. The suggested approach (presented in its 'long only' version) is a combination of cross-over 'buy' signals and a dynamic threshold value which acts as a dynamic trailing stop. The trading behaviour and performance from this modified strategy are different from the standard approach with results showing that, on average, the proposed modification increases the cumulative return and the Sharpe ratio of the investor while exhibiting smaller maximum drawdown and smaller drawdown duration than the standard strategy.

  7. Architecture and evolution of a minute plant genome.

    Science.gov (United States)

    Ibarra-Laclette, Enrique; Lyons, Eric; Hernández-Guzmán, Gustavo; Pérez-Torres, Claudia Anahí; Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Lan, Tianying; Welch, Andreanna J; Juárez, María Jazmín Abraham; Simpson, June; Fernández-Cortés, Araceli; Arteaga-Vázquez, Mario; Góngora-Castillo, Elsa; Acevedo-Hernández, Gustavo; Schuster, Stephan C; Himmelbauer, Heinz; Minoche, André E; Xu, Sen; Lynch, Michael; Oropeza-Aburto, Araceli; Cervantes-Pérez, Sergio Alan; de Jesús Ortega-Estrada, María; Cervantes-Luevano, Jacob Israel; Michael, Todd P; Mockler, Todd; Bryant, Douglas; Herrera-Estrella, Alfredo; Albert, Victor A; Herrera-Estrella, Luis

    2013-06-01

    It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism. PMID:23665961

  8. Architecture and evolution of a minute plant genome

    Science.gov (United States)

    Ibarra-Laclette, Enrique; Lyons, Eric; Hernández-Guzmán, Gustavo; Pérez-Torres, Claudia Anahí; Carretero-Paulet, Lorenzo; Chang, Tien-Hao; Lan, Tianying; Welch, Andreanna J.; Juárez, María Jazmín Abraham; Simpson, June; Fernández-Cortés, Araceli; Arteaga-Vázquez, Mario; Góngora-Castillo, Elsa; Acevedo-Hernández, Gustavo; Schuster, Stephan C.; Himmelbauer, Heinz; Minoche, André E.; Xu, Sen; Lynch, Michael; Oropeza-Aburto, Araceli; Cervantes-Pérez, Sergio Alan; de Jesús Ortega-Estrada, María; Cervantes-Luevano, Jacob Israel; Michael, Todd P.; Mockler, Todd; Bryant, Douglas; Herrera-Estrella, Alfredo; Albert, Victor A.; Herrera-Estrella, Luis

    2016-01-01

    It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism. PMID:23665961

  9. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  10. Refined similarity hypothesis using three-dimensional local averages

    Science.gov (United States)

    Iyer, Kartik P.; Sreenivasan, Katepalli R.; Yeung, P. K.

    2015-12-01

    The refined similarity hypotheses of Kolmogorov, regarded as an important ingredient of intermittent turbulence, has been tested in the past using one-dimensional data and plausible surrogates of energy dissipation. We employ data from direct numerical simulations, at the microscale Reynolds number Rλ˜650 , on a periodic box of 40963 grid points to test the hypotheses using three-dimensional averages. In particular, we study the small-scale properties of the stochastic variable V =Δ u (r ) /(rɛr) 1 /3 , where Δ u (r ) is the longitudinal velocity increment and ɛr is the dissipation rate averaged over a three-dimensional volume of linear size r . We show that V is universal in the inertial subrange. In the dissipation range, the statistics of V are shown to depend solely on a local Reynolds number.

  11. Refined similarity hypothesis using 3D local averages

    CERN Document Server

    Iyer, Kartik P; Yeung, P K

    2015-01-01

    The refined similarity hypotheses of Kolmogorov, regarded as an important ingredient of intermittent turbulence, has been tested in the past using one-dimensional data and plausible surrogates of energy dissipation. We employ data from direct numerical simulations, at the microscale Reynolds number $R_\\lambda \\sim 650$, on a periodic box of $4096^3$ grid points to test the hypotheses using 3D averages. In particular, we study the small-scale properties of the stochastic variable $V = \\Delta u(r)/(r \\epsilon_r)^{1/3}$, where $\\Delta u(r)$ is the longitudinal velocity increment and $\\epsilon_r$ is the dissipation rate averaged over a three-dimensional volume of linear size $r$. We show that $V$ is universal in the inertial subrange. In the dissipation range, the statistics of $V$ are shown to depend solely on a local Reynolds number.

  12. Averaging processes in granular flows driven by gravity

    Science.gov (United States)

    Rossi, Giulia; Armanini, Aronne

    2016-04-01

    One of the more promising theoretical frames to analyse the two-phase granular flows is offered by the similarity of their rheology with the kinetic theory of gases [1]. Granular flows can be considered a macroscopic equivalent of the molecular case: the collisions among molecules are compared to the collisions among grains at a macroscopic scale [2,3]. However there are important statistical differences in dealing with the two applications. In the two-phase fluid mechanics, there are two main types of average: the phasic average and the mass weighed average [4]. The kinetic theories assume that the size of atoms is so small, that the number of molecules in a control volume is infinite. With this assumption, the concentration (number of particles n) doesn't change during the averaging process and the two definitions of average coincide. This hypothesis is no more true in granular flows: contrary to gases, the dimension of a single particle becomes comparable to that of the control volume. For this reason, in a single realization the number of grain is constant and the two averages coincide; on the contrary, for more than one realization, n is no more constant and the two types of average lead to different results. Therefore, the ensamble average used in the standard kinetic theory (which usually is the phasic average) is suitable for the single realization, but not for several realization, as already pointed out in [5,6]. In the literature, three main length scales have been identified [7]: the smallest is the particles size, the intermediate consists in the local averaging (in order to describe some instability phenomena or secondary circulation) and the largest arises from phenomena such as large eddies in turbulence. Our aim is to solve the intermediate scale, by applying the mass weighted average, when dealing with more than one realizations. This statistical approach leads to additional diffusive terms in the continuity equation: starting from experimental

  13. Citrus Genomics

    OpenAIRE

    Talon, Manuel; Gmitter, Fred G.Jr.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The hist...

  14. Light-cone averages in a Swiss-cheese universe

    International Nuclear Information System (INIS)

    We analyze a toy Swiss-cheese cosmological model to study the averaging problem. In our Swiss-cheese model, the cheese is a spatially flat, matter only, Friedmann-Robertson-Walker solution (i.e., the Einstein-de Sitter model), and the holes are constructed from a Lemaitre-Tolman-Bondi solution of Einstein's equations. We study the propagation of photons in the Swiss-cheese model, and find a phenomenological homogeneous model to describe observables. Following a fitting procedure based on light-cone averages, we find that the expansion scalar is unaffected by the inhomogeneities (i.e., the phenomenological homogeneous model is the cheese model). This is because of the spherical symmetry of the model; it is unclear whether the expansion scalar will be affected by nonspherical voids. However, the light-cone average of the density as a function of redshift is affected by inhomogeneities. The effect arises because, as the universe evolves, a photon spends more and more time in the (large) voids than in the (thin) high-density structures. The phenomenological homogeneous model describing the light-cone average of the density is similar to the ΛCDM concordance model. It is interesting that, although the sole source in the Swiss-cheese model is matter, the phenomenological homogeneous model behaves as if it has a dark-energy component. Finally, we study how the equation of state of the phenomenological homogeneous model depends on the size of the inhomogeneities, and find that the equation-of-state parameters w0 and wa follow a power-law dependence with a scaling exponent equal to unity. That is, the equation of state depends linearly on the distance the photon travels through voids. We conclude that, within our toy model, the holes must have a present size of about 250 Mpc to be able to mimic the concordance model

  15. HIGH AVERAGE POWER OPTICAL FEL AMPLIFIERS

    International Nuclear Information System (INIS)

    Historically, the first demonstration of the optical FEL was in an amplifier configuration at Stanford University [l]. There were other notable instances of amplifying a seed laser, such as the LLNL PALADIN amplifier [2] and the BNL ATF High-Gain Harmonic Generation FEL [3]. However, for the most part FELs are operated as oscillators or self amplified spontaneous emission devices. Yet, in wavelength regimes where a conventional laser seed can be used, the FEL can be used as an amplifier. One promising application is for very high average power generation, for instance FEL's with average power of 100 kW or more. The high electron beam power, high brightness and high efficiency that can be achieved with photoinjectors and superconducting Energy Recovery Linacs (ERL) combine well with the high-gain FEL amplifier to produce unprecedented average power FELs. This combination has a number of advantages. In particular, we show that for a given FEL power, an FEL amplifier can introduce lower energy spread in the beam as compared to a traditional oscillator. This properly gives the ERL based FEL amplifier a great wall-plug to optical power efficiency advantage. The optics for an amplifier is simple and compact. In addition to the general features of the high average power FEL amplifier, we will look at a 100 kW class FEL amplifier is being designed to operate on the 0.5 ampere Energy Recovery Linac which is under construction at Brookhaven National Laboratory's Collider-Accelerator Department

  16. Bayesian Model Averaging for Propensity Score Analysis

    Science.gov (United States)

    Kaplan, David; Chen, Jianshen

    2013-01-01

    The purpose of this study is to explore Bayesian model averaging in the propensity score context. Previous research on Bayesian propensity score analysis does not take into account model uncertainty. In this regard, an internally consistent Bayesian framework for model building and estimation must also account for model uncertainty. The…

  17. Average utility maximization: A preference foundation

    NARCIS (Netherlands)

    A.V. Kothiyal (Amit); V. Spinu (Vitalie); P.P. Wakker (Peter)

    2014-01-01

    textabstractThis paper provides necessary and sufficient preference conditions for average utility maximization over sequences of variable length. We obtain full generality by using a new algebraic technique that exploits the richness structure naturally provided by the variable length of the sequen

  18. Average beta measurement in EXTRAP T1

    International Nuclear Information System (INIS)

    Beginning with the ideal MHD pressure balance equation, an expression for the average poloidal beta, ΒΘ, is derived. A method for unobtrusively measuring the quantities used to evaluate ΒΘ in Extrap T1 is described. The results if a series of measurements yielding ΒΘ as a function of externally applied toroidal field are presented. (author)

  19. A Gaussian Average Property for Banach Spaces

    OpenAIRE

    Casazza, Peter G.; Nielsen, Niels Jorgen

    1996-01-01

    In this paper we investigate a Gaussian average property of Banach spaces. This property is weaker than the Gordon Lewis property but closely related to this and other unconditional structures. It is also shown that this property implies that certain Hilbert space valued operators defined on subspaces of the given space can be extended.

  20. Bayesian Averaging is Well-Temperated

    DEFF Research Database (Denmark)

    Hansen, Lars Kai

    2000-01-01

    Bayesian predictions are stochastic just like predictions of any other inference scheme that generalize from a finite sample. While a simple variational argument shows that Bayes averaging is generalization optimal given that the prior matches the teacher parameter distribution the situation is l...

  1. Quantum Averaging of Squeezed States of Light

    DEFF Research Database (Denmark)

    Squeezing has been recognized as the main resource for quantum information processing and an important resource for beating classical detection strategies. It is therefore of high importance to reliably generate stable squeezing over longer periods of time. The averaging procedure for a single...

  2. A Functional Measurement Study on Averaging Numerosity

    Science.gov (United States)

    Tira, Michael D.; Tagliabue, Mariaelena; Vidotto, Giulio

    2014-01-01

    In two experiments, participants judged the average numerosity between two sequentially presented dot patterns to perform an approximate arithmetic task. In Experiment 1, the response was given on a 0-20 numerical scale (categorical scaling), and in Experiment 2, the response was given by the production of a dot pattern of the desired numerosity…

  3. Reformulation of Ensemble Averages via Coordinate Mapping.

    Science.gov (United States)

    Schultz, Andrew J; Moustafa, Sabry G; Lin, Weisong; Weinstein, Steven J; Kofke, David A

    2016-04-12

    A general framework is established for reformulation of the ensemble averages commonly encountered in statistical mechanics. This "mapped-averaging" scheme allows approximate theoretical results that have been derived from statistical mechanics to be reintroduced into the underlying formalism, yielding new ensemble averages that represent exactly the error in the theory. The result represents a distinct alternative to perturbation theory for methodically employing tractable systems as a starting point for describing complex systems. Molecular simulation is shown to provide one appealing route to exploit this advance. Calculation of the reformulated averages by molecular simulation can proceed without contamination by noise produced by behavior that has already been captured by the approximate theory. Consequently, accurate and precise values of properties can be obtained while using less computational effort, in favorable cases, many orders of magnitude less. The treatment is demonstrated using three examples: (1) calculation of the heat capacity of an embedded-atom model of iron, (2) calculation of the dielectric constant of the Stockmayer model of dipolar molecules, and (3) calculation of the pressure of a Lennard-Jones fluid. It is observed that improvement in computational efficiency is related to the appropriateness of the underlying theory for the condition being simulated; the accuracy of the result is however not impacted by this. The framework opens many avenues for further development, both as a means to improve simulation methodology and as a new basis to develop theories for thermophysical properties. PMID:26950263

  4. Bootstrapping Density-Weighted Average Derivatives

    DEFF Research Database (Denmark)

    Cattaneo, Matias D.; Crump, Richard K.; Jansson, Michael

    Employing the "small bandwidth" asymptotic framework of Cattaneo, Crump, and Jansson (2009), this paper studies the properties of a variety of bootstrap-based inference procedures associated with the kernel-based density-weighted averaged derivative estimator proposed by Powell, Stock, and Stoker...

  5. A Measure of the Average Intercorrelation

    Science.gov (United States)

    Meyer, Edward P.

    1975-01-01

    Bounds are obtained for a coefficient proposed by Kaiser as a measure of average correlation and the coefficient is given an interpretation in the context of reliability theory. It is suggested that the root-mean-square intercorrelation may be a more appropriate measure of degree of relationships among a group of variables. (Author)

  6. Full averaging of fuzzy impulsive differential inclusions

    Directory of Open Access Journals (Sweden)

    Natalia V. Skripnik

    2010-09-01

    Full Text Available In this paper the substantiation of the method of full averaging for fuzzy impulsive differential inclusions is studied. We extend the similar results for impulsive differential inclusions with Hukuhara derivative (Skripnik, 2007, for fuzzy impulsive differential equations (Plotnikov and Skripnik, 2009, and for fuzzy differential inclusions (Skripnik, 2009.

  7. An approximate analytical approach to resampling averages

    DEFF Research Database (Denmark)

    Malzahn, Dorthe; Opper, M.

    2004-01-01

    Using a novel reformulation, we develop a framework to compute approximate resampling data averages analytically. The method avoids multiple retraining of statistical models on the samples. Our approach uses a combination of the replica "trick" of statistical physics and the TAP approach for appr...

  8. Generalized Jackknife Estimators of Weighted Average Derivatives

    DEFF Research Database (Denmark)

    Cattaneo, Matias D.; Crump, Richard K.; Jansson, Michael

    With the aim of improving the quality of asymptotic distributional approximations for nonlinear functionals of nonparametric estimators, this paper revisits the large-sample properties of an important member of that class, namely a kernel-based weighted average derivative estimator. Asymptotic li...

  9. High average-power induction linacs

    International Nuclear Information System (INIS)

    Induction linear accelerators (LIAs) are inherently capable of accelerating several thousand amperes of /approximately/ 50-ns duration pulses to > 100 MeV. In this paper we report progress and status in the areas of duty factor and stray power management. These technologies are vital if LIAs are to attain high average power operation. 13 figs

  10. Error estimates on averages of correlated data

    International Nuclear Information System (INIS)

    We describe how the true statistical error on an average of correlated data can be obtained with ease and efficiency by a renormalization group method. The method is illustrated with numerical and analytical examples, having finite as well as infinite range correlations. (orig.)

  11. An approximate analytical approach to resampling averages

    DEFF Research Database (Denmark)

    Malzahn, Dorthe; Opper, M.

    2004-01-01

    Using a novel reformulation, we develop a framework to compute approximate resampling data averages analytically. The method avoids multiple retraining of statistical models on the samples. Our approach uses a combination of the replica "trick" of statistical physics and the TAP approach for...

  12. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

    Directory of Open Access Journals (Sweden)

    Chapple Clint

    2005-06-01

    Full Text Available Abstract Background The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. Results Here we describe the construction of a large-insert bacterial artificial chromosome (BAC library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes. Conclusion The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.

  13. Quenched effective population size

    CERN Document Server

    Sagitov, Serik; Vatutin, Vladimir

    2010-01-01

    We study the genealogy of a geographically - or otherwise - structured version of the Wright-Fisher population model with fast migration. The new feature is that migration probabilities may change in a random fashion. Applying Takahashi's results on Markov chains with random transition matrices, we establish convergence to the Kingman coalescent, as the population size goes to infinity. This brings a novel formula for the coalescent effective population size (EPS). We call it a quenched EPS to emphasize the key feature of our model - random environment. The quenched EPS is compared with an annealed (mean-field) EPS which describes the case of constant migration probabilities obtained by averaging the random migration probabilities over possible environments.

  14. Complete Genome Sequencing of Protease-Producing Novel Arthrobacter sp. Strain IHBB 11108 Using PacBio Single-Molecule Real-Time Sequencing Technology

    OpenAIRE

    Kiran, Shashi; Swarnkar, Mohit K.; Pal, Mohinder; Thakur, Rishu; Tewari, Rupinder; Singh, Anil Kumar; Gulati, Arvind

    2015-01-01

    A previously uncharacterized species of the genus Arthrobacter, strain IHBB 11108 (MCC 2780), is a Gram-positive, strictly aerobic, nonmotile, cold-adapted, and protease-producing alkaliphilic actinobacterium, isolated from shallow undersurface water from Chandra Tal Lake, Lahaul-Spiti, India. The complete genome of the strain is 3.6 Mb in size with an average 58.97% G+C content.

  15. Degenerative minimalism in the genome of a psyllid endosymbiont.

    Science.gov (United States)

    Clark, M A; Baumann, L; Thao, M L; Moran, N A; Baumann, P

    2001-03-01

    Psyllids, like aphids, feed on plant phloem sap and are obligately associated with prokaryotic endosymbionts acquired through vertical transmission from an ancestral infection. We have sequenced 37 kb of DNA of the genome of Carsonella ruddii, the endosymbiont of psyllids, and found that it has a number of unusual properties revealing a more extreme case of degeneration than was previously reported from studies of eubacterial genomes, including that of the aphid endosymbiont Buchnera aphidicola. Among the unusual properties are an exceptionally low guanine-plus-cytosine content (19.9%), almost complete absence of intergenic spaces, operon fusion, and lack of the usual promoter sequences upstream of 16S rDNA. These features suggest the synthesis of long mRNAs and translational coupling. The most extreme instances of base compositional bias occur in the genes encoding proteins that have less highly conserved amino acid sequences; the guanine-plus-cytosine content of some protein-coding sequences is as low as 10%. The shift in base composition has a large effect on proteins: in polypeptides of C. ruddii, half of the residues consist of five amino acids with codons low in guanine plus cytosine. Furthermore, the proteins of C. ruddii are reduced in size, with an average of about 9% fewer amino acids than in homologous proteins of related bacteria. These observations suggest that the C. ruddii genome is not subject to constraints that limit the evolution of other known eubacteria. PMID:11222582

  16. Genome evolution and systems biology in bacterial endosymbionts of insects

    OpenAIRE

    Belda Cuesta, Eugeni

    2010-01-01

    Gene loss is the most important event in the process of genome reduction that appears associated with bacterial endosymbionts of insects. These small genomes were derived features evolved from ancestral prokaryotes with larger genome sizes, consequence of a massive process of genome reduction due to drastic changes in the ecological conditions and evolutionary pressures acting on these prokaryotic lineages during their ecological transition to host-dependent lifestyle. In the present thesis, ...

  17. Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research.

    Science.gov (United States)

    Coates, Brad S; Sumerford, Douglas V; Hellmich, Richard L; Lewis, Leslie C

    2009-01-01

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies. PMID:19132072

  18. Voter dynamics on an adaptive network with finite average connectivity

    Science.gov (United States)

    Mukhopadhyay, Abhishek; Schmittmann, Beate

    2009-03-01

    We study a simple model for voter dynamics in a two-party system. The opinion formation process is implemented in a random network of agents in which interactions are not restricted by geographical distance. In addition, we incorporate the rapidly changing nature of the interpersonal relations in the model. At each time step, agents can update their relationships, so that there is no history dependence in the model. This update is determined by their own opinion, and by their preference to make connections with individuals sharing the same opinion and with opponents. Using simulations and analytic arguments, we determine the final steady states and the relaxation into these states for different system sizes. In contrast to earlier studies, the average connectivity (``degree'') of each agent is constant here, independent of the system size. This has significant consequences for the long-time behavior of the model.

  19. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  20. Inefficiency of orientation averaging: Evidence for hybrid serial/parallel temporal integration.

    Science.gov (United States)

    Solomon, Joshua A; May, Keith A; Tyler, Christopher W

    2016-01-01

    Intuition suggests that increased viewing time should allow for the accumulation of more visual information, but scant support for this idea has been found in studies of voluntary averaging, where observers are asked to make decisions based on perceived average size. In this paper we examine the dynamics of information accrual in an orientation-averaging task. With orientation (unlike intensive dimensions such as size), it is relatively safe to use an item's physical value as an approximation for its average perceived value. We displayed arrays containing eight iso-eccentric Gabor patterns, and asked six trained psychophysical observers to compare their average orientation with that of probe stimuli that were visible before, during, or only after the presentation of the Gabor array. From the relationship between orientation variance and human performance, we obtained estimates of effective set size, i.e., the number of items that an ideal observer would need to assess in order to estimate average orientation as well as our human observers did. We found that display duration had only a modest influence on effective set size. It rose from an average of ∼2 for 0.1-s displays to an average of ∼3 for 3.3-s displays. These results suggest that the visual computation is neither purely serial nor purely parallel. Computations of this nature can be made with a hybrid process that takes a series of subsamples of a few elements at a time. PMID:26790845

  1. Development of genomic resources for the prairie vole (Microtus ochrogaster: construction of a BAC library and vole-mouse comparative cytogenetic map

    Directory of Open Access Journals (Sweden)

    Young Larry J

    2010-01-01

    Full Text Available Abstract Background The prairie vole (Microtus ochrogaster is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC library from a single male prairie vole and a prairie vole-mouse (Mus musculus comparative cytogenetic map. Results We constructed a prairie vole BAC library (CHORI-232 consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements. Conclusions The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this

  2. Optimal step-size LMS algorithm using exponentially averaged gradient vector

    Czech Academy of Sciences Publication Activity Database

    Malenovský, V.; Smékal, Z.; Koula, Ivan

    Piscataway : Institute of Electrical and Electronics Engineers, 2005, s. 1554-1557. ISBN 1-4244-0050-3. [EUROCON 2005. Beograd (CS), 21.11.2005-24.11.2005] R&D Projects: GA AV ČR(CZ) 1ET301710509 Institutional research plan: CEZ:AV0Z20670512 Keywords : adaptive filters * least mean squares methods * convergence numerical methods Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  3. Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities

    Directory of Open Access Journals (Sweden)

    Fast Naomi M

    2008-04-01

    Full Text Available Abstract Background Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but genomes of different species range in size from 2.3 Mb to 19.5 Mb and the nature of the larger genomes remains unknown. Results Here we have undertaken genome sequence surveys of two diverse microsporidia, Brachiola algerae and Edhazardia aedis. In both species we find very large intergenic regions, many transposable elements, and a low gene-density, all in contrast to the small, model microsporidian genomes. We also find no recognizable genes that are not also found in other surveyed or sequenced microsporidian genomes. Conclusion Our results demonstrate that microsporidian genome architecture varies greatly between microsporidia. Much of the genome size difference could be accounted for by non-coding material, such as intergenic spaces and retrotransposons, and this suggests that the forces dictating genome size may vary across the phylum.

  4. Mathematical Analysis of Genomic Evolution

    Directory of Open Access Journals (Sweden)

    Cedric Green

    2011-01-01

    Full Text Available Changes in nucleotide sequences, or mutations, accumulate from generation to generation in the genomes of all living organisms. The mutations can be advantageous, deleterious, or neutral. The goal of this project is to determine the amount of advantageous mutations it takes to get human (Homo sapiens DNA from the DNA of genetically distinct organisms. We do this by collecting the genomic data of such organisms, and estimating the amount of mutations it takes to transform yeast (Saccharomyces cerevisiae DNA to the DNA of a human. We calculate the typical number of mutations occurring annually through the organism's average life span and the average mutation rate. This allows us to determine the total number of mutations as well as the probability of advantageous mutations. Not surprisingly, this probability proves to be fairly small. A more precise estimate can be determined by accounting for the differences in the chromosomal structure and phenomena like horizontal gene transfer.

  5. Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

    Energy Technology Data Exchange (ETDEWEB)

    McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

    2005-08-26

    Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

  6. Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes.

    Science.gov (United States)

    Lu, Min; An, Huaming; Li, Liangliang

    2016-01-01

    Rosa roxburghii Tratt is an important commercial horticultural crop in China that is recognized for its nutritional and medicinal values. In spite of the economic significance, genomic information on this rose species is currently unavailable. In the present research, a genome survey of R. roxburghii was carried out using next-generation sequencing (NGS) technologies. Total 30.29 Gb sequence data was obtained by HiSeq 2500 sequencing and an estimated genome size of R. roxburghii was 480.97 Mb, in which the guanine plus cytosine (GC) content was calculated to be 38.63%. All of these reads were technically assembled and a total of 627,554 contigs with a N50 length of 1.484 kb and furthermore 335,902 scaffolds with a total length of 409.36 Mb were obtained. Transposable elements (TE) sequence of 90.84 Mb which comprised 29.20% of the genome, and 167,859 simple sequence repeats (SSRs) were identified from the scaffolds. Among these, the mono-(66.30%), di-(25.67%), and tri-(6.64%) nucleotide repeats contributed to nearly 99% of the SSRs, and sequence motifs AG/CT (28.81%) and GAA/TTC (14.76%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. Genome analysis predicted a total of 22,721 genes which have an average length of 2311.52 bp, an average exon length of 228.15 bp, and average intron length of 401.18 bp. Eleven genes putatively involved in ascorbate metabolism were identified and its expression in R. roxburghii leaves was validated by quantitative real-time PCR (qRT-PCR). This is the first report of genome-wide characterization of this rose species. PMID:26849133

  7. Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

    Science.gov (United States)

    Stukenbrock, Eva H.; Jørgensen, Frank G.; Zala, Marcello; Hansen, Troels T.; McDonald, Bruce A.; Schierup, Mikkel H.

    2010-01-01

    The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000–12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural

  8. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola.

    Directory of Open Access Journals (Sweden)

    Eva H Stukenbrock

    Full Text Available The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000-12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was

  9. Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes.

    Directory of Open Access Journals (Sweden)

    Min Lu

    Full Text Available Rosa roxburghii Tratt is an important commercial horticultural crop in China that is recognized for its nutritional and medicinal values. In spite of the economic significance, genomic information on this rose species is currently unavailable. In the present research, a genome survey of R. roxburghii was carried out using next-generation sequencing (NGS technologies. Total 30.29 Gb sequence data was obtained by HiSeq 2500 sequencing and an estimated genome size of R. roxburghii was 480.97 Mb, in which the guanine plus cytosine (GC content was calculated to be 38.63%. All of these reads were technically assembled and a total of 627,554 contigs with a N50 length of 1.484 kb and furthermore 335,902 scaffolds with a total length of 409.36 Mb were obtained. Transposable elements (TE sequence of 90.84 Mb which comprised 29.20% of the genome, and 167,859 simple sequence repeats (SSRs were identified from the scaffolds. Among these, the mono-(66.30%, di-(25.67%, and tri-(6.64% nucleotide repeats contributed to nearly 99% of the SSRs, and sequence motifs AG/CT (28.81% and GAA/TTC (14.76% were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. Genome analysis predicted a total of 22,721 genes which have an average length of 2311.52 bp, an average exon length of 228.15 bp, and average intron length of 401.18 bp. Eleven genes putatively involved in ascorbate metabolism were identified and its expression in R. roxburghii leaves was validated by quantitative real-time PCR (qRT-PCR. This is the first report of genome-wide characterization of this rose species.

  10. Trajectory averaging for stochastic approximation MCMC algorithms

    CERN Document Server

    Liang, Faming

    2010-01-01

    The subject of stochastic approximation was founded by Robbins and Monro [Ann. Math. Statist. 22 (1951) 400--407]. After five decades of continual development, it has developed into an important area in systems control and optimization, and it has also served as a prototype for the development of adaptive algorithms for on-line estimation and control of stochastic systems. Recently, it has been used in statistics with Markov chain Monte Carlo for solving maximum likelihood estimation problems and for general simulation and optimizations. In this paper, we first show that the trajectory averaging estimator is asymptotically efficient for the stochastic approximation MCMC (SAMCMC) algorithm under mild conditions, and then apply this result to the stochastic approximation Monte Carlo algorithm [Liang, Liu and Carroll J. Amer. Statist. Assoc. 102 (2007) 305--320]. The application of the trajectory averaging estimator to other stochastic approximation MCMC algorithms, for example, a stochastic approximation MLE al...

  11. From cellular doses to average lung dose

    International Nuclear Information System (INIS)

    Sensitive basal and secretory cells receive a wide range of doses in human bronchial and bronchiolar airways. Variations of cellular doses arise from the location of target cells in the bronchial epithelium of a given airway and the asymmetry and variability of airway dimensions of the lung among airways in a given airway generation and among bronchial and bronchiolar airway generations. To derive a single value for the average lung dose which can be related to epidemiologically observed lung cancer risk, appropriate weighting scenarios have to be applied. Potential biological weighting parameters are the relative frequency of target cells, the number of progenitor cells, the contribution of dose enhancement at airway bifurcations, the promotional effect of cigarette smoking and, finally, the application of appropriate regional apportionment factors. Depending on the choice of weighting parameters, detriment-weighted average lung doses can vary by a factor of up to 4 for given radon progeny exposure conditions. (authors)

  12. ANALYSIS OF THE FACTORS AFFECTING THE AVERAGE

    Directory of Open Access Journals (Sweden)

    Carmen BOGHEAN

    2013-12-01

    Full Text Available Productivity in agriculture most relevantly and concisely expresses the economic efficiency of using the factors of production. Labour productivity is affected by a considerable number of variables (including the relationship system and interdependence between factors, which differ in each economic sector and influence it, giving rise to a series of technical, economic and organizational idiosyncrasies. The purpose of this paper is to analyse the underlying factors of the average work productivity in agriculture, forestry and fishing. The analysis will take into account the data concerning the economically active population and the gross added value in agriculture, forestry and fishing in Romania during 2008-2011. The distribution of the average work productivity per factors affecting it is conducted by means of the u-substitution method.

  13. Statistics on exponential averaging of periodograms

    International Nuclear Information System (INIS)

    The algorithm of exponential averaging applied to subsequent periodograms of a stochastic process is used to estimate the power spectral density (PSD). For an independent process, assuming the periodogram estimates to be distributed according to a χ2 distribution with 2 degrees of freedom, the probability density function (PDF) of the PSD estimate is derived. A closed expression is obtained for the moments of the distribution. Surprisingly, the proof of this expression features some new insights into the partitions and Eulers infinite product. For large values of the time constant of the averaging process, examination of the cumulant generating function shows that the PDF approximates the Gaussian distribution. Although restrictions for the statistics are seemingly tight, simulation of a real process indicates a wider applicability of the theory. (orig.)

  14. Endogenous average cost based access pricing

    OpenAIRE

    Fjell, Kenneth; Foros, Øystein; Pal, Debashis

    2006-01-01

    We consider an industry where a downstream competitor requires access to an upstream facility controlled by a vertically integrated and regulated incumbent. The literature on access pricing assumes the access price to be exogenously fixed ex-ante. We analyze an endogenous average cost based access pricing rule, where both firms realize the interdependence among their quantities and the regulated access price. Endogenous access pricing neutralizes the artificial cost advantag...

  15. Extended Bidirectional Texture Function Moving Average Model

    Czech Academy of Sciences Publication Activity Database

    Havlíček, Michal

    Praha: České vysoké učení technické v Praze, 2015 - (Ambrož, P.; Masáková, Z.), s. 1-7 [Doktorandské dny 2015. Praha (CZ), 20.11.2015,27.11.2015] Institutional support: RVO:67985556 Keywords : Bidirectional texture function * moving average random field model Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2016/RO/havlicek-0455325.pdf

  16. Average Regression-Adjusted Controlled Regenerative Estimates

    OpenAIRE

    Lewis, Peter A.W.; Ressler, Richard

    1991-01-01

    Proceedings of the 1991 Winter Simulation Conference Barry L. Nelson, W. David Kelton, Gordon M. Clark (eds.) One often uses computer simulations of queueing systems to generate estimates of system characteristics along with estimates of their precision. Obtaining precise estimates, espescially for high traffic intensities, can require large amounts of computer time. Average regression-adjusted controlled regenerative estimates result from combining the two techniques ...

  17. Time-dependent angularly averaged inverse transport

    OpenAIRE

    Bal, Guillaume; Jollivet, Alexandre

    2009-01-01

    This paper concerns the reconstruction of the absorption and scattering parameters in a time-dependent linear transport equation from knowledge of angularly averaged measurements performed at the boundary of a domain of interest. We show that the absorption coefficient and the spatial component of the scattering coefficient are uniquely determined by such measurements. We obtain stability results on the reconstruction of the absorption and scattering parameters with respect to the measured al...

  18. Average Light Intensity Inside a Photobioreactor

    Directory of Open Access Journals (Sweden)

    Herby Jean

    2011-01-01

    Full Text Available For energy production, microalgae are one of the few alternatives with high potential. Similar to plants, algae require energy acquired from light sources to grow. This project uses calculus to determine the light intensity inside of a photobioreactor filled with algae. Under preset conditions along with estimated values, we applied Lambert-Beer's law to formulate an equation to calculate how much light intensity escapes a photobioreactor and determine the average light intensity that was present inside the reactor.

  19. A Visibility Graph Averaging Aggregation Operator

    OpenAIRE

    Chen, Shiyu; Hu, Yong; Mahadevan, Sankaran; Deng, Yong

    2013-01-01

    The problem of aggregation is considerable importance in many disciplines. In this paper, a new type of operator called visibility graph averaging (VGA) aggregation operator is proposed. This proposed operator is based on the visibility graph which can convert a time series into a graph. The weights are obtained according to the importance of the data in the visibility graph. Finally, the VGA operator is used in the analysis of the TAIEX database to illustrate that it is practical and compare...

  20. On Heroes and Average Moral Human Beings

    OpenAIRE

    Kirchgässner, Gebhard

    2001-01-01

    After discussing various approaches about heroic behaviour in the literature, we first give a definition and classification of moral behaviour, in distinction to intrinsically motivated and ‘prudent' behaviour. Then, we present some arguments on the function of moral behaviour according to ‘minimal' standards of the average individual in a modern democratic society, before we turn to heroic behaviour. We conclude with some remarks on methodological as well as social problems which arise or ma...

  1. Dollar-Cost Averaging: An Investigation

    OpenAIRE

    Fang, Wei

    2007-01-01

    Dollar-cost Averaging (DCA) is a common and useful systematic investment strategy for mutual fund managers, private investors, financial analysts and retirement planners. The issue of performance effectiveness of DCA is greatly controversial among academics and professionals. As a popularly recommended investment strategy, DCA is recognized as a risk reduction strategy; however, the advantage was claimed as the expense of generating higher returns. The dissertation is to intensively inves...

  2. Spatial averaging infiltration model for layered soil

    Institute of Scientific and Technical Information of China (English)

    HU HePing; YANG ZhiYong; TIAN FuQiang

    2009-01-01

    To quantify the influences of soil heterogeneity on infiltration, a spatial averaging infiltration model for layered soil (SAI model) is developed by coupling the spatial averaging approach proposed by Chen et al. and the Generalized Green-Ampt model proposed by Jia et al. In the SAI model, the spatial heterogeneity along the horizontal direction is described by a probability distribution function, while that along the vertical direction is represented by the layered soils. The SAI model is tested on a typical soil using Monte Carlo simulations as the base model. The results show that the SAI model can directly incorporate the influence of spatial heterogeneity on infiltration on the macro scale. It is also found that the homogeneous assumption of soil hydraulic conductivity along the horizontal direction will overestimate the infiltration rate, while that along the vertical direction will underestimate the infiltration rate significantly during rainstorm periods. The SAI model is adopted in the spatial averaging hydrological model developed by the authors, and the results prove that it can be applied in the macro-scale hydrological and land surface process modeling in a promising way.

  3. Average neutron detection efficiency for DEMON detectors

    International Nuclear Information System (INIS)

    The neutron detection efficiency of a DEMON detector, averaged over the whole volume, was calculated using GEANT and applied to determine neutron multiplicities in an intermediate heavy ion reaction. When a neutron source is set at a distance of about 1 m from the front surface of the detector, the average efficiency, ϵav, is found to be significantly lower (20–30%) than the efficiency measured at the center of the detector, ϵ0. In the GEANT simulation the ratio R=ϵav/ϵ0 was calculated as a function of neutron energy. The experimental central efficiency multiplied by R was then used to determine the average efficiency. The results were applied to a study of the 64Zn+112Sn reaction at 40 A MeV which employed 16 DEMON detectors. The neutron multiplicity was extracted using a moving source fit. The derived multiplicities are compared well with those determined using the neutron ball in the NIMROD detector array in a separate experiment. Both are in good agreement with multiplicities predicted by a transport model calculation using an antisymmetric molecular dynamics (AMD) model code

  4. Modern average global sea-surface temperature

    Science.gov (United States)

    Schweitzer, Peter N.

    1993-01-01

    The data contained in this data set are derived from the NOAA Advanced Very High Resolution Radiometer Multichannel Sea Surface Temperature data (AVHRR MCSST), which are obtainable from the Distributed Active Archive Center at the Jet Propulsion Laboratory (JPL) in Pasadena, Calif. The JPL tapes contain weekly images of SST from October 1981 through December 1990 in nine regions of the world ocean: North Atlantic, Eastern North Atlantic, South Atlantic, Agulhas, Indian, Southeast Pacific, Southwest Pacific, Northeast Pacific, and Northwest Pacific. This data set represents the results of calculations carried out on the NOAA data and also contains the source code of the programs that made the calculations. The objective was to derive the average sea-surface temperature of each month and week throughout the whole 10-year series, meaning, for example, that data from January of each year would be averaged together. The result is 12 monthly and 52 weekly images for each of the oceanic regions. Averaging the images in this way tends to reduce the number of grid cells that lack valid data and to suppress interannual variability.

  5. Unscrambling The "Average User" Of Habbo Hotel

    Directory of Open Access Journals (Sweden)

    Mikael Johnson

    2007-01-01

    Full Text Available The “user” is an ambiguous concept in human-computer interaction and information systems. Analyses of users as social actors, participants, or configured users delineate approaches to studying design-use relationships. Here, a developer’s reference to a figure of speech, termed the “average user,” is contrasted with design guidelines. The aim is to create an understanding about categorization practices in design through a case study about the virtual community, Habbo Hotel. A qualitative analysis highlighted not only the meaning of the “average user,” but also the work that both the developer and the category contribute to this meaning. The average user a represents the unknown, b influences the boundaries of the target user groups, c legitimizes the designer to disregard marginal user feedback, and d keeps the design space open, thus allowing for creativity. The analysis shows how design and use are intertwined and highlights the developers’ role in governing different users’ interests.

  6. On Backus average for generally anisotropic layers

    CERN Document Server

    Bos, Len; Slawinski, Michael A; Stanoev, Theodore

    2016-01-01

    In this paper, following the Backus (1962) approach, we examine expressions for elasticity parameters of a homogeneous generally anisotropic medium that is long-wave-equivalent to a stack of thin generally anisotropic layers. These expressions reduce to the results of Backus (1962) for the case of isotropic and transversely isotropic layers. In over half-a-century since the publications of Backus (1962) there have been numerous publications applying and extending that formulation. However, neither George Backus nor the authors of the present paper are aware of further examinations of mathematical underpinnings of the original formulation; hence, this paper. We prove that---within the long-wave approximation---if the thin layers obey stability conditions then so does the equivalent medium. We examine---within the Backus-average context---the approximation of the average of a product as the product of averages, and express it as a proposition in terms of an upper bound. In the presented examination we use the e...

  7. Average fidelity between random quantum states

    CERN Document Server

    Zyczkowski, K; Zyczkowski, Karol; Sommers, Hans-Jurgen

    2003-01-01

    We analyze mean fidelity between random density matrices of size N, generated with respect to various probability measures in the space of mixed quantum states: Hilbert-Schmidt measure, Bures (statistical) measure, the measures induced by partial trace and the natural measure on the space of pure states. In certain cases explicit probability distributions for fidelity are derived.

  8. Draft genome sequences of two closely-related aflatoxigenic Aspergillus species obtained from the Ivory Coast

    Science.gov (United States)

    The genomes of the A. ochraceoroseus and A. rambellii type strains were sequenced using a personal genome machine, followed by annotation of their genes. The genome size for A. ochraceoroseus was found to be approximately 23 Mb and contained 7,837 genes, while the A. rambellii genome was found to be...

  9. Genome sequence surveyws of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities.

    Science.gov (United States)

    Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but with a size range of 2.3 Mb to 19.5 Mb the nature of the larger genomes remains unknown. Here we have undertaken genome sequence surveys ...

  10. Complete genome sequence of a virulent Streptococcus agalactiae strain 138P isolated from disease Nile tilapia

    Science.gov (United States)

    The complete genome of a virulent Streptococcus agalactiae strain 138P is 1838701 bp in size, containing 1831 genes. The genome has 1593 coding sequences, 152 pseudo genes, 16 rRNAs, 69 tRNAs, and 1 non-coding RNA. The annotation of the genome is added by the NCBI Prokaryotic Genome Annotation Pipel...

  11. Genome structure of cottontail rabbit herpesvirus.

    OpenAIRE

    Cebrian, J; Berthelot, N; Laithier, M

    1989-01-01

    The genome structure of a herpesvirus isolated from primary cultures of kidney cells from the cottontail rabbit Sylvilagus floridanus was elucidated by using electron microscopy and restriction enzyme analysis. The genome, which was about 150 kilobase pairs long and which had an average G + C composition of 45%, consisted of two regions with unique base sequences (54 and 47 kilobase pairs) enclosed by reiterations of a 925-base-pair sequence with a variable copy number. The internal repeats w...

  12. Whole genome analysis of a Vietnamese trio

    Indian Academy of Sciences (India)

    Dang Thanh Hai; Nguyen Dai Thanh; Pham Thi Minh Trang; Le Si Quang; Phan Thi Thu Hang; Dang Cao Cuong; Hoang Kim Phuc; Nguyen Huu Duc; Do Duc Dong; Bui Quang Minh; Pham Bao Son; Le Sy Vinh

    2015-03-01

    We here present the first whole genome analysis of an anonymous Kinh Vietnamese (KHV) trio whose genomes were deeply sequenced to 30-fold average coverage. The resulting short reads covered 99.91% of the human reference genome (GRCh37d5). We identified 4,719,412 SNPs and 827,385 short indels that satisfied the Mendelian inheritance law. Among them, 109,914 (2.3%) SNPs and 59,119 (7.1%) short indels were novel. We also detected 30,171 structural variants of which 27,604 (91.5%) were large indels. There were 6,681 large indels in the range 0.1–100 kbp occurring in the child genome that were also confirmed in either the father or mother genome.We compared these large indels against the DGV database and found that 1,499 (22.44%) were KHV specific. De novo assembly of high-quality unmapped reads yielded 789 contigs with the length ≥ 300 bp. There were 235 contigs from the child genome of which 199 (84.7%) were significantly matched with at least one contig from the father or mother genome. Blasting these 199 contigs against other alternative human genomes revealed 4 novel contigs. The novel variants identified from our study demonstrated the necessity of conducting more genome-wide studies not only for Kinh but also for other ethnic groups in Vietnam.

  13. A 3.5 genome equivalent multi access YAC library: construction, characterisation, screening and storage.

    OpenAIRE

    Anand, R; Riley, J H; Butler, R; Smith, J C; Markham, A F

    1990-01-01

    The construction of a yeast artificial chromosome (YAC) primary gridded library of 35,000 clones from human lymphoblastoid (48,XXXX) cell line DNA is described. The average YAC size is approximately 350kb representing a greater than 3.5 times coverage of the genome. The library is stored at -70 degrees C as gridded clones on nylon filters impregnated with 20% glycerol and as glycerol suspensions of individual clones in microtitre plates providing a prolonged multi-user potential. To date we h...

  14. Parents' Reactions to Finding Out That Their Children Have Average or above Average IQ Scores.

    Science.gov (United States)

    Dirks, Jean; And Others

    1983-01-01

    Parents of 41 children who had been given an individually-administered intelligence test were contacted 19 months after testing. Parents of average IQ children were less accurate in their memory of test results. Children with above average IQ experienced extremely low frequencies of sibling rivalry, conceit or pressure. (Author/HLM)

  15. Microbial species delineation using whole genome sequences

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos; Mukherjee, Supratim; Ivanova, Natalia; Mavrommatics, Kostas; Pati, Amrita; Konstantinidis, Konstantinos

    2014-10-20

    Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both phenotypic traits and sequence information of phylogenetic marker genes. With thousands of genomes being sequenced every year, an automated, uniform and scalable approach exploiting the rich genomic information in whole genome sequences is desired, at least for the initial assignment of species to an organism. We have evaluated pairwise genome-wide Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 genomes using our fast implementation of the computation, identifying robust and widely applicable hard cut-offs for species assignments based on AF and gANI. Using these cutoffs, we generated stable species-level clusters of organisms, which enabled the identification of several species mis-assignments and facilitated the assignment of species for organisms without species definitions.

  16. The National Average is a D: Who is to Blame?

    Directory of Open Access Journals (Sweden)

    Collie-Patterson, Janet M.

    2008-01-01

    Full Text Available The publishing of the Bahamas General Certificate of Secondary Education (RGCSE 2005 examination results sparked much debate about the national average being a D. Much of the debate was focused on the teacher and the school whilst very little was said about the other contributors to achievement in education. In her 1999 study of 1,036 students and 52 teachers from public and private schools in New Providence, Collie-Patterson found the students' characteristics consisting of student's prior ability, attitude toward school, socioeconomic status and parental involvement make the largest contribution (60% to mathematics achievement. Taken individually, the effect size indicated that student's prior ability made the largest contribution (48% to mathematics achievement. The set of teaches' characteristics, including professional development, teaching experience, and educational background, were significantly related to mathematics achievement and contributed only 8% to students' mathematics achievement. The set of classroom characteristics contributed 35% to mathematics achievement and the set of schools' characteristics contributed 12% to mathematics achievement. The purpose of this paper is to analyze the factors that could potentially influence the student performances in mathematics which greatly affects the national average due to the large number of students taking the mathematics examination and the low grade point average of that examination.

  17. Estimation of the average correlation coefficient for stratified bivariate data.

    Science.gov (United States)

    Rubenstein, L M; Davis, C S

    1999-03-15

    If the relationship between two ordered categorical variables X and Y is influenced by a third categorical variable with K levels, the Cochran-Mantel-Haenszel (CMH) correlation statistic QC is a useful stratum-adjusted summary statistic for testing the null hypothesis of no association between X and Y. Although motivated by and developed for the case of K I x J contingency tables, the correlation statistic QC is also applicable when X and Y are continuous variables. In this paper we derive a corresponding estimator of the average correlation coefficient for K I x J tables. We also study two estimates of the variance of the average correlation coefficient. The first is a restricted variance based on the variances of the observed cell frequencies under the null hypothesis of no association. The second is an unrestricted variance based on an asymptotic variance derived by Brown and Benedetti. The estimator of the average correlation coefficient works well in tables with balanced and unbalanced margins, for equal and unequal stratum-specific sample sizes, when correlation coefficients are constant over strata, and when correlation coefficients vary across strata. When the correlation coefficients are zero, close to zero, or the cell frequencies are small, the confidence intervals based on the restricted variance are preferred. For larger correlations and larger cell frequencies, the unrestricted confidence intervals give superior performance. We also apply the CMH statistic and proposed estimators to continuous non-normal data sampled from bivariate gamma distributions. We compare our methods to statistics for data sampled from normal distributions. The size and power of the CMH and normal theory statistics are comparable. When the stratum-specific sample sizes are small and the distributions are skewed, the proposed estimator is superior to the normal theory estimator. When the correlation coefficient is zero or close to zero, the restricted confidence intervals

  18. Genome expansion and gene loss in powdery mildew fungi reveal functional tradeoffs in extreme parasitism

    Science.gov (United States)

    Eukaryotic genomes vary in size over five orders of magnitude ranging from microsporidia (~2.9Mb) to the lung-fish (~1.2Tb). This extraordinary variation is largely a result of the proliferation of mobile DNA elements also referred to as “genomic parasites.” The constraints on genome size may be imp...

  19. Did genetic drift drive increases in genome complexity?

    Directory of Open Access Journals (Sweden)

    Kenneth D Whitney

    2010-08-01

    Full Text Available Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (N(e has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small N(e. Strong support for this model was claimed from a comparative analysis of N(eu and genome size for ≈30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between N(eu and genomic attributes: there were no statistically significant associations between N(eu and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between N(e and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables.

  20. Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

    Directory of Open Access Journals (Sweden)

    Garcia-Mas Jordi

    2010-11-01

    allowed us to gain further insight into characteristics of the melon genome such as gene density, average protein length, or microsatellite and transposon content. The annotation of the BAC sequences revealed a high degree of collinearity and protein sequence identity between melon and its close relative Cucumis sativus (cucumber. Transposon content analysis of the syntenic regions suggests that transposition activity after the split of both cucurbit species has been low in cucumber but very high in melon. Conclusions The results presented here show that the strategy followed, which combines shotgun and BAC-end sequencing together with anchored marker information, is an excellent method for sequencing specific genomic regions, especially from relatively compact genomes such as that of melon. However, in agreement with other results, this map-based, BAC approach is confirmed to be an expensive way of sequencing a whole plant genome. Our results also provide a partial description of the melon genome's structure. Namely, our analysis shows that the melon genome is highly collinear with the smaller one of cucumber, the size difference being mainly due to the expansion of intergenic regions and proliferation of transposable elements.

  1. The average free volume model for liquids

    CERN Document Server

    Yu, Yang

    2014-01-01

    In this work, the molar volume thermal expansion coefficient of 59 room temperature ionic liquids is compared with their van der Waals volume Vw. Regular correlation can be discerned between the two quantities. An average free volume model, that considers the particles as hard core with attractive force, is proposed to explain the correlation in this study. A combination between free volume and Lennard-Jones potential is applied to explain the physical phenomena of liquids. Some typical simple liquids (inorganic, organic, metallic and salt) are introduced to verify this hypothesis. Good agreement from the theory prediction and experimental data can be obtained.

  2. Phase-averaged transport for quasiperiodic Hamiltonians

    CERN Document Server

    Bellissard, J; Schulz-Baldes, H

    2002-01-01

    For a class of discrete quasi-periodic Schroedinger operators defined by covariant re- presentations of the rotation algebra, a lower bound on phase-averaged transport in terms of the multifractal dimensions of the density of states is proven. This result is established under a Diophantine condition on the incommensuration parameter. The relevant class of operators is distinguished by invariance with respect to symmetry automorphisms of the rotation algebra. It includes the critical Harper (almost-Mathieu) operator. As a by-product, a new solution of the frame problem associated with Weyl-Heisenberg-Gabor lattices of coherent states is given.

  3. Sparsity averaging for radio-interferometric imaging

    CERN Document Server

    Carrillo, Rafael E; Wiaux, Yves

    2014-01-01

    We propose a novel regularization method for compressive imaging in the context of the compressed sensing (CS) theory with coherent and redundant dictionaries. Natural images are often complicated and several types of structures can be present at once. It is well known that piecewise smooth images exhibit gradient sparsity, and that images with extended structures are better encapsulated in wavelet frames. Therefore, we here conjecture that promoting average sparsity or compressibility over multiple frames rather than single frames is an extremely powerful regularization prior.

  4. PROFILE OF HIRED FARMWORKERS, 1998 ANNUAL AVERAGES

    OpenAIRE

    Runyan, Jack L.

    2000-01-01

    An average of 875,000 persons 15 years of age and older did hired farmwork each week as their primary job in 1998. An additional 63,000 people did hired farmwork each week as their secondary job. Hired farmworkers were more likely than the typical U.S. wage and salary worker to be male, Hispanic, younger, less educated, never married, and not U.S. citizens. The West (42 percent) and South (31.4 percent) census regions accounted for almost three-fourths of the hired farmworkers. The rate of un...

  5. Fluctuations of wavefunctions about their classical average

    International Nuclear Information System (INIS)

    Quantum-classical correspondence for the average shape of eigenfunctions and the local spectral density of states are well-known facts. In this paper, the fluctuations of the quantum wavefunctions around the classical value are discussed. A simple random matrix model leads to a Gaussian distribution of the amplitudes whose width is determined by the classical shape of the eigenfunction. To compare this prediction with numerical calculations in chaotic models of coupled quartic oscillators, we develop a rescaling method for the components. The expectations are broadly confirmed, but deviations due to scars are observed. This effect is much reduced when both Hamiltonians have chaotic dynamics

  6. Time-dependent angularly averaged inverse transport

    International Nuclear Information System (INIS)

    This paper concerns the reconstruction of the absorption and scattering parameters in a time-dependent linear transport equation from knowledge of angularly averaged measurements performed at the boundary of a domain of interest. Such measurement settings find applications in medical and geophysical imaging. We show that the absorption coefficient and the spatial component of the scattering coefficient are uniquely determined by such measurements. We obtain stability results on the reconstruction of the absorption and scattering parameters with respect to the measured albedo operator. The stability results are obtained by a precise decomposition of the measurements into components with different singular behavior in the time domain

  7. Time-dependent angularly averaged inverse transport

    CERN Document Server

    Bal, Guillaume

    2009-01-01

    This paper concerns the reconstruction of the absorption and scattering parameters in a time-dependent linear transport equation from knowledge of angularly averaged measurements performed at the boundary of a domain of interest. We show that the absorption coefficient and the spatial component of the scattering coefficient are uniquely determined by such measurements. We obtain stability results on the reconstruction of the absorption and scattering parameters with respect to the measured albedo operator. The stability results are obtained by a precise decomposition of the measurements into components with different singular behavior in the time domain.

  8. High average power laser for EUV lithography

    Energy Technology Data Exchange (ETDEWEB)

    Kania, D.R.; Gaines, D.P.; Hermann, M.; Honig, J.; Hostetler, R.; Levesque, R.; Sommargren, G.E.; Spitzer, R.C.; Vernon, S.P.

    1995-01-19

    We have demonstrated the operation of a high average power, all solid state laser and target system for EUV lithography. The laser operates at 1.06 {mu}m with a pulse repetition rate of 200 Hz. Each pulse contains up to 400 mJ of energy and is less than 10 ns in duration. The ELTV conversion efficiency measured with the laser is independent of the laser repetition rate. Operating at 200 Hz, the laser has been used for lithography using a 3 bounce Kohler illuminator.

  9. Some averaging functions in image reduction

    Czech Academy of Sciences Publication Activity Database

    Paternain, D.; Bustince, H.; Fernández, J.; Beliakov, G.; Mesiar, Radko

    Berlin: Springer, 2010 - (García-Pedrajas, N.; Herrera, F.; Benítez, J.), s. 399-408. (Lecture Notes in Artificial Intelligence . 6098). ISBN 978-3-642-13032-8. ISSN 0302-9743. [IEA/AIE 2010. Cordoba (ES), 01.06.2010-04.06.2010] Institutional research plan: CEZ:AV0Z10750506 Keywords : image reduction * local reduction operators * aggregation functions Subject RIV: BA - General Mathematics http://library.utia.cas.cz/separaty/2010/E/mesiar-some averaging functions in image reduction.pdf

  10. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  11. Genomes on ice.

    Science.gov (United States)

    Parkhill, Julian

    2016-03-01

    This month's Genome Watch discusses the analysis of a Helicobacter pylori genome from the preserved Copper-Age mummy known as the Iceman and how ancient genomes shed light on the history of bacterial pathogens. PMID:26853114

  12. Pricing the Fish Market- Does size matter?

    OpenAIRE

    Eric Sjöberg

    2014-01-01

    The importance of fish size for price per kilo is studied using an inverse demand approach. Prices per kilo in different size categories of the same species differ significantly. This means that the average price for a species may change due to e.g., high-grading, growth overfishing or a changing climate which all have the potential to change the size composition of the catch. The estimates show that quantity flexibilities differ substantially across size and species while scale flexibilities...

  13. A MODEL OF MINIMUM SIZE LIMIT REGULATIONS

    OpenAIRE

    Homans, Frances R.; Ruliffson, Jane A.

    1998-01-01

    Minimum size limits have become an increasingly popular management tool in recreational fisheries. This popularity stems from the potential of minimum size limits to accomplish the twin goals of limiting overfishing and improving fishing quality through increasing the average size of fish caught. The success of minimum size limits in achieving these objectives depends in a complicated way on both the behavior of anglers and the biological mechanisms that guide the growth of the fish populatio...

  14. A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence.

    Science.gov (United States)

    Grattapaglia, Dario; Mamani, Eva M C; Silva-Junior, Orzenil B; Faria, Danielle A

    2015-03-01

    Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus. PMID:25146326

  15. Rademacher averages on noncommutative symmetric spaces

    CERN Document Server

    Merdy, Christian Le

    2008-01-01

    Let E be a separable (or the dual of a separable) symmetric function space, let M be a semifinite von Neumann algebra and let E(M) be the associated noncommutative function space. Let $(\\epsilon_k)_k$ be a Rademacher sequence, on some probability space $\\Omega$. For finite sequences $(x_k)_k of E(M), we consider the Rademacher averages $\\sum_k \\epsilon_k\\otimes x_k$ as elements of the noncommutative function space $E(L^\\infty(\\Omega)\\otimes M)$ and study estimates for their norms $\\Vert \\sum_k \\epsilon_k \\otimes x_k\\Vert_E$ calculated in that space. We establish general Khintchine type inequalities in this context. Then we show that if E is 2-concave, the latter norm is equivalent to the infimum of $\\Vert (\\sum y_k^*y_k)^{{1/2}}\\Vert + \\Vert (\\sum z_k z_k^*)^{{1/2}}\\Vert$ over all $y_k,z_k$ in E(M) such that $x_k=y_k+z_k$ for any k. Dual estimates are given when E is 2-convex and has a non trivial upper Boyd index. We also study Rademacher averages for doubly indexed families of E(M).

  16. Averaging in the presence of sliding errors

    International Nuclear Information System (INIS)

    In many cases the precision with which an experiment can measure a physical quantity depends on the value of that quantity. Not having access to the true value, experimental groups are forced to assign their errors based on their own measured value. Procedures which attempt to derive an improved estimate of the true value by a suitable average of such measurements usually weight each experiment's measurement according to the reported variance. However, one is in a position to derive improved error estimates for each experiment from the average itself, provided an approximate idea of the functional dependence of the error on the central value is known. Failing to do so can lead to substantial biases. Techniques which avoid these biases without loss of precision are proposed and their performance is analyzed with examples. These techniques are quite general and can bring about an improvement even when the behavior of the errors is not well understood. Perhaps the most important application of the technique is in fitting curves to histograms

  17. Trajectory averaging for stochastic approximation MCMC algorithms

    KAUST Repository

    Liang, Faming

    2010-10-01

    The subject of stochastic approximation was founded by Robbins and Monro [Ann. Math. Statist. 22 (1951) 400-407]. After five decades of continual development, it has developed into an important area in systems control and optimization, and it has also served as a prototype for the development of adaptive algorithms for on-line estimation and control of stochastic systems. Recently, it has been used in statistics with Markov chain Monte Carlo for solving maximum likelihood estimation problems and for general simulation and optimizations. In this paper, we first show that the trajectory averaging estimator is asymptotically efficient for the stochastic approximation MCMC (SAMCMC) algorithm under mild conditions, and then apply this result to the stochastic approximation Monte Carlo algorithm [Liang, Liu and Carroll J. Amer. Statist. Assoc. 102 (2007) 305-320]. The application of the trajectory averaging estimator to other stochastic approximationMCMC algorithms, for example, a stochastic approximation MLE algorithm for missing data problems, is also considered in the paper. © Institute of Mathematical Statistics, 2010.

  18. Beta-energy averaging and beta spectra

    International Nuclear Information System (INIS)

    A simple yet highly accurate method for approximately calculating spectrum-averaged beta energies and beta spectra for radioactive nuclei is presented. This method should prove useful for users who wish to obtain accurate answers without complicated calculations of Fermi functions, complex gamma functions, and time-consuming numerical integrations as required by the more exact theoretical expressions. Therefore, this method should be a good time-saving alternative for investigators who need to make calculations involving large numbers of nuclei (e.g., fission products) as well as for occasional users interested in restricted number of nuclides. The average beta-energy values calculated by this method differ from those calculated by ''exact'' methods by no more than 1 percent for nuclides with atomic numbers in the 20 to 100 range and which emit betas of energies up to approximately 8 MeV. These include all fission products and the actinides. The beta-energy spectra calculated by the present method are also of the same quality

  19. Genomic prediction of crossbred performance based on purebred Landrace and Yorkshire data using a dominance model

    DEFF Research Database (Denmark)

    Esfandyari, Hadi; Bijma, Piter; Henryon, Mark;

    2016-01-01

    explicitly including dominance in the genomic selection model may be an advantage when selecting purebreds for crossbred performance. Our objectives were two-fold: (1) to compare the predictive ability of genomic prediction models with additive or additive plus dominance effects, when the validation...... criterion is crossbred performance; and (2) to compare the use of two pure line reference populations to a single combined reference population. METHODS: We used data on litter size in the first parity from two pure pig lines (Landrace and Yorkshire) and their reciprocal crosses. Training was performed (1...... corrected crossbred-progeny performance, divided by the average accuracy of mean-progeny performance. We evaluated a model with additive effects only (MA) and a model with both additive and dominance effects (MAD). Two types of GEBV were computed: GEBV for purebred performance (GEBV) based on either the MA...

  20. Genomic Biomarkers for Breast Cancer Risk.

    Science.gov (United States)

    Walsh, Michael F; Nathanson, Katherine L; Couch, Fergus J; Offit, Kenneth

    2016-01-01

    Clinical risk assessment for cancer predisposition includes a three-generation pedigree and physical examination to identify inherited syndromes. Additionally genetic and genomic biomarkers may identify individuals with a constitutional basis for their disease that may not be evident clinically. Genomic biomarker testing may detect molecular variations in single genes, panels of genes, or entire genomes. The strength of evidence for the association of a genomic biomarker with disease risk may be weak or strong. The factors contributing to clinical validity and utility of genomic biomarkers include functional laboratory analyses and genetic epidemiologic evidence. Genomic biomarkers may be further classified as low, moderate or highly penetrant based on the likelihood of disease. Genomic biomarkers for breast cancer are comprised of rare highly penetrant mutations of genes such as BRCA1 or BRCA2, moderately penetrant mutations of genes such as CHEK2, as well as more common genomic variants, including single nucleotide polymorphisms, associated with modest effect sizes. When applied in the context of appropriate counseling and interpretation, identification of genomic biomarkers of inherited risk for breast cancer may decrease morbidity and mortality, allow for definitive prevention through assisted reproduction, and serve as a guide to targeted therapy . PMID:26987529