WorldWideScience

Sample records for genome size differentiates

  1. Genome size variation in Begonia.

    Science.gov (United States)

    Dewitte, Angelo; Leus, Leen; Eeckhaut, Tom; Vanstechelman, Ives; Van Huylenbroeck, Johan; Van Bockstaele, Erik

    2009-10-01

    The genome sizes of a Begonia collection comprising 37 species and 23 hybrids of African, Asiatic, Middle American, and South American origin were screened using flow cytometry. Within the collection, 1C values varied between 0.23 and 1.46 pg DNA. Genome sizes were, in most cases, not positively correlated with chromosome number, but with pollen size. A 12-fold difference in mean chromosome size was found between the genotypes with the largest and smallest chromosomes. In general, chromosomes from South American genotypes were smaller than chromosomes of African, Asian, or Middle American genotypes, except for B. boliviensis and B. pearcei. Cytological chromosome studies in different genotypes showed variable chromosome numbers, length, width, and total chromosome volume, which confirmed the diversity in genome size. Large secondary constrictions were present in several investigated genotypes. These data show that chromosome number and structure exhibit a great deal of variation within the genus Begonia, and likely help to explain the large number of taxa found within the genus.

  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 genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome 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.

  3. Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms.

    Science.gov (United States)

    Zenil-Ferguson, Rosana; Ponciano, José M; Burleigh, J Gordon

    2016-07-01

    Whole-genome duplications (WGDs) can rapidly increase genome size in angiosperms. Yet their mean genome size is not correlated with ploidy. We compared three hypotheses to explain the constancy of genome size means across ploidies. The genome downsizing hypothesis suggests that genome size will decrease by a given percentage after a WGD. The genome size threshold hypothesis assumes that taxa with large genomes or large monoploid numbers will fail to undergo or survive WGDs. Finally, the genome downsizing and threshold hypothesis suggests that both genome downsizing and thresholds affect the relationship between genome size means and ploidy. We performed nonparametric bootstrap simulations to compare observed angiosperm genome size means among species or genera against simulated genome sizes under the three different hypotheses. We evaluated the hypotheses using a decision theory approach and estimated the expected percentage of genome downsizing. The threshold hypothesis improves the approximations between mean genome size and simulated genome size. At the species level, the genome downsizing with thresholds hypothesis best explains the genome size means with a 15% genome downsizing percentage. In the genus level simulations, the monoploid number threshold hypothesis best explains the data. Thresholds of genome size and monoploid number added to genome downsizing at species level simulations explain the observed means of angiosperm genome sizes, and monoploid number is important for determining the genome size mean at the genus level. © 2016 Botanical Society of America.

  4. Unraveling the karyotype structure of the spurges Euphorbia hirta Linnaeus, 1753 and E. hyssopifolia Linnaeus, 1753 (Euphorbiaceae) using genome size estimation and heterochromatin differentiation

    Science.gov (United States)

    Santana, Karla C. B.; Pinangé, Diego S. B.; Vasconcelos, Santelmo; Oliveira, Ana R.; Brasileiro-Vidal, Ana C.; Alves, Marccus V.; Benko-Iseppon, Ana M.

    2016-01-01

    Abstract Euphorbia Linnaeus, 1753 (Euphorbiaceae) is one of the most diverse and complex genera among the angiosperms, showing a huge diversity in morphologic traits and ecologic patterns. In order to improve the knowledge of the karyotype organization of Euphorbia hirta (2n = 18) and Euphorbia hyssopifolia (2n = 12), cytogenetic studies were performed by means of conventional staining with Giemsa, genome size estimations with flow cytometry, heterochromatin differentiation with chromomycin A3 (CMA) and 4’,6-diamidino-2-phenylindole (DAPI) and Giemsa C-banding, fluorescent in situ hybridization (FISH) with 45S and 5S rDNA probes, and impregnation with silver nitrate (AgNO3). Our results revealed small metacentric chromosomes, CMA+/DAPI0 heterochromatin in the pericentromeric regions of all chromosomes and CMA+/DAPI− in the distal part of chromosome arms carriers of nucleolar organizing regions (NORs). The DNA content measurements revealed small genomes for both species: Euphorbia hirta with 2C = 0.77 pg and Euphorbia hyssopifolia with 2C = 1.41 pg. After FISH procedures, Euphorbia hirta, and Euphorbia hyssopifolia presented three and four pairs of terminal 45S rDNA sites, respectively, colocalizing with CMA+ heterochromatic blocks, besides only one interstitial pair of 5S rDNA signals. Additionally, the maximum number of active NORs agreed with the total number of observed 45S rDNA sites. This work represents the first analysis using FISH in the subfamily Euphorbioideae, revealing a significant number of chromosomal markers, which may be very helpful to understand evolutionary patterns among Euphorbia species. PMID:28123686

  5. 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.

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

    Science.gov (United States)

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

    2009-12-22

    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 dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77-2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97-2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05-5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.

  7. Genome size and longevity in fish.

    Science.gov (United States)

    Griffith, O L; Moodie, G E E; Civetta, A

    2003-03-01

    The wide variety of genome sizes (measured as C-value) observed across taxa is not related to organismal complexity or number of coding genes. Partial answers to this C-value enigma have been found by establishing associations between C-value and particular phenotypic characteristics. One such controversial association has been recently suggested between genome size and longevity in birds. In order to determine whether genome size is a general predictor of longevity, we have extended the analysis to the Actinoptergyian fish, a widely divergent group in terms of both longevity and genome size. We collected data on genome size, longevity and body mass for species covering fourteen orders of bony fish. Analysis of covariance using order as a cofactor shows a significant effect of genome size on longevity (corrected for body mass), with lifespan increasing as a function of genome size. Analysis of phylogenetically independent contrasts for orders with a large number of species with a well resolved phylogenetic relationship (Acipenseriformes, Cypriniformes, and Salmoniformes) found the same trend of longer lifespan with increases in genome size but the relationship was not significant. Our results consistently show an increase in lifespan for fish with larger genomes.

  8. 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.

  9. On the Relationship between Pollen Size and Genome Size

    Directory of Open Access Journals (Sweden)

    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.

  10. Dynamics of genome size evolution in birds and mammals

    Science.gov (United States)

    Feschotte, Cédric

    2017-01-01

    Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified “accordion” model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives. PMID:28179571

  11. The evolution of genome size in ants

    Directory of Open Access Journals (Sweden)

    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

  12. Cell size, genome size and the dominance of Angiosperms

    Science.gov (United States)

    Simonin, K. A.; Roddy, A. B.

    2016-12-01

    Angiosperms are capable of maintaining the highest rates of photosynthetic gas exchange of all land plants. High rates of photosynthesis depends mechanistically both on efficiently transporting water to the sites of evaporation in the leaf and on regulating the loss of that water to the atmosphere as CO2 diffuses into the leaf. Angiosperm leaves are unique in their ability to sustain high fluxes of liquid and vapor phase water transport due to high vein densities and numerous, small stomata. Despite the ubiquity of studies characterizing the anatomical and physiological adaptations that enable angiosperms to maintain high rates of photosynthesis, the underlying mechanism explaining why they have been able to develop such high leaf vein densities, and such small and abundant stomata, is still incomplete. Here we ask whether the scaling of genome size and cell size places a fundamental constraint on the photosynthetic metabolism of land plants, and whether genome downsizing among the angiosperms directly contributed to their greater potential and realized primary productivity relative to the other major groups of terrestrial plants. Using previously published data we show that a single relationship can predict guard cell size from genome size across the major groups of terrestrial land plants (e.g. angiosperms, conifers, cycads and ferns). Similarly, a strong positive correlation exists between genome size and both stomatal density and vein density that together ultimately constrains maximum potential (gs, max) and operational stomatal conductance (gs, op). Further the difference in the slopes describing the covariation between genome size and both gs, max and gs, op suggests that genome downsizing brings gs, op closer to gs, max. Taken together the data presented here suggests that the smaller genomes of angiosperms allow their final cell sizes to vary more widely and respond more directly to environmental conditions and in doing so bring operational photosynthetic

  13. Genome sizes for all genera of Cycadales.

    Science.gov (United States)

    Zonneveld, B J M

    2012-01-01

    Nuclear DNA content (2C) is reported for all genera of the Cycadales, using flow cytometry with propidium iodide. Nuclear DNA content ranges from 24 to 64 pg in cycads. This implies that the largest genome contains roughly 40 × 10(9) more base pairs than the smallest genome. The narrow range in nuclear DNA content within a genus is remarkable for such an old group. Furthermore, 42 of the 58 plants measured, covering five genera, have 18 chromosomes. They vary from 36.1 to 64.7 pg, covering the whole range of genome sizes (excluding the genome of Cycas). Hence, their does not seem to be a correlation between genome size and the number of chromosomes.

  14. Genome size is inversely correlated with relative brain size in parrots and cockatoos.

    Science.gov (United States)

    Andrews, Chandler B; Gregory, T Ryan

    2009-03-01

    Genome size (haploid nuclear DNA content) has been found to correlate positively with cell size and negatively with cell division rate in a variety of taxa. These cytological relationships manifest in various ways at the organism level, for example, in terms of body size, metabolic rate, or developmental rate, depending on the biology of the organisms. In birds, it has been suggested that high metabolic rate and strong flight ability are linked to small genome size. However, it was also hypothesized that the exceptional cognitive abilities of birds may impose additional constraints on genome size through effects on neuron size and differentiation, as has been observed in amphibians. To test this hypothesis, a comparative analysis was made between genome size, cell (erythrocyte) size, and brain size in 54 species of parrots and cockatoos (order Psittaciformes, family Psittacidae). Relative brain volume, which is taken as an indicator of investment in brain tissue and is widely correlated with behavioural and ecological traits, was found to correlate inversely with genome size. Several possible and mutually compatible explanations for this relationship are described.

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

    OpenAIRE

    Kang, Ming; Wang, Jing; Huang, Hongwen

    2015-01-01

    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 en...

  16. Genome size and genome evolution in diploid Triticeae species.

    Science.gov (United States)

    Eilam, T; Anikster, Y; Millet, E; Manisterski, J; Sagi-Assif, O; Feldman, M

    2007-11-01

    One of the intriguing issues concerning the dynamics of plant genomes is the occurrence of intraspecific variation in nuclear DNA amount. The aim of this work was to assess the ranges of intraspecific, interspecific, and intergeneric variation in nuclear DNA content of diploid species of the tribe Triticeae (Poaceae) and to examine the relation between life form or habitat and genome size. Altogether, 438 plants representing 272 lines that belong to 22 species were analyzed. Nuclear DNA content was estimated by flow cytometry. Very small intraspecific variation in DNA amount was found between lines of Triticeae diploid species collected from different habitats or between different morphs. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various diploid species. Within the genus Aegilops, the 1C DNA amount ranged from 4.84 pg in A. caudata to 7.52 pg in A. sharonensis; among genera, the 1C DNA amount ranged from 4.18 pg in Heteranthelium piliferum to 9.45 pg in Secale montanum. No evidence was found for a smaller genome size in annual, self-pollinating species relative to perennial, cross-pollinating ones. Diploids that grow in the southern part of the group's distribution have larger genomes than those growing in other parts of the distribution. The contrast between the low variation at the intraspecific level and the high variation at the interspecific one suggests that changes in genome size originated in close temporal proximity to the speciation event, i.e., before, during, or immediately after it. The possible effects of sudden changes in genome size on speciation processes are discussed.

  17. Patterns of genome size variation in snapping shrimp.

    Science.gov (United States)

    Jeffery, Nicholas W; Hultgren, Kristin; Chak, Solomon Tin Chi; Gregory, T Ryan; Rubenstein, Dustin R

    2016-06-01

    Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.

  18. 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 ...

  19. Comparative genomics of brain size evolution

    OpenAIRE

    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 ...

  20. Evolutionary forces shaping genomic islands of population differentiation in humans

    Directory of Open Access Journals (Sweden)

    Hofer Tamara

    2012-03-01

    Full Text Available Abstract Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM. A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i as much as 20% of islands are in non-genic regions ii these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii most loci are

  1. Comparative genomics of brain size evolution

    Directory of Open Access Journals (Sweden)

    Wolfgang eEnard

    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.

  2. Genome size estimation: a new methodology

    Science.gov (United States)

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

    2007-03-01

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

  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. Paleogenomic data suggest mammal-like genome size in the ancestral amniote and derived large genome size in amphibians.

    Science.gov (United States)

    Organ, C L; Canoville, A; Reisz, R R; Laurin, M

    2011-02-01

    An unsolved question in evolutionary genomics is whether amniote genomes have been expanding or contracting since the common ancestor of this diverse group. Here, we report on the polarity of amniote genome size evolution using genome size estimates for 14 extinct tetrapod genera from the Paleozoic and early Mesozoic Eras using osteocyte lacunae size as a correlate. We find substantial support for a phylogenetically controlled regression model relating genome size to osteocyte lacunae size (P of slopes amphibians, contractions along the diapsid lineage, and no directional change within the synapsid lineage leading to mammals.

  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

    2016-06-03

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

  6. A first exploration of genome size diversity in sponges.

    Science.gov (United States)

    Jeffery, Nicholas W; Jardine, Catherine B; Gregory, T Ryan

    2013-08-01

    The phyla known as early-branching lineages of animals have become the subject of increasing interest from the perspectives of genomics and evolutionary biology. Unfortunately, data on even the most fundamental properties of their genomes, such as genome size, remain very scarce. In this study, genome size estimates are reported for 75 species of sponges (phylum Porifera) representing 33 families and 12 orders, marking the first large survey of genome size diversity for an early-branching phylum. Sponge genome sizes averaged around 0.2 pg but exhibited a 17-fold range overall (0.04-0.63 pg). In addition, the results of comparisons of two methods of genome size quantification (flow cytometry and Feulgen image analysis densitometry) are presented, thereby facilitating future work on these animals. Some particularly promising avenues for future investigation are highlighted.

  7. Random distribution pattern and non-adaptivity of genome size in a highly variable population of Festuca pallens.

    Science.gov (United States)

    Smarda, Petr; Bures, Petr; Horová, Lucie

    2007-07-01

    The spatial and statistical distribution of genome sizes and the adaptivity of genome size to some types of habitat, vegetation or microclimatic conditions were investigated in a tetraploid population of Festuca pallens. The population was previously documented to vary highly in genome size and is assumed as a model for the study of the initial stages of genome size differentiation. Using DAPI flow cytometry, samples were measured repeatedly with diploid Festuca pallens as the internal standard. Altogether 172 plants from 57 plots (2.25 m(2)), distributed in contrasting habitats over the whole locality in South Moravia, Czech Republic, were sampled. The differences in DNA content were confirmed by the double peaks of simultaneously measured samples. At maximum, a 1.115-fold difference in genome size was observed. The statistical distribution of genome sizes was found to be continuous and best fits the extreme (Gumbel) distribution with rare occurrences of extremely large genomes (positive-skewed), as it is similar for the log-normal distribution of the whole Angiosperms. Even plants from the same plot frequently varied considerably in genome size and the spatial distribution of genome sizes was generally random and unautocorrelated (P > 0.05). The observed spatial pattern and the overall lack of correlations of genome size with recognized vegetation types or microclimatic conditions indicate the absence of ecological adaptivity of genome size in the studied population. These experimental data on intraspecific genome size variability in Festuca pallens argue for the absence of natural selection and the selective non-significance of genome size in the initial stages of genome size differentiation, and corroborate the current hypothetical model of genome size evolution in Angiosperms (Bennetzen et al., 2005, Annals of Botany 95: 127-132).

  8. 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.

  9. Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size

    Science.gov (United States)

    Hatfull, Graham F.; Jacobs-Sera, Deborah; Lawrence, Jeffrey G.; Pope, Welkin H.; Russell, Daniel A.; Ko, Ching-Chung; Weber, Rebecca J.; Patel, Manisha C.; Germane, Katherine L.; Edgar, Robert H.; Hoyte, Natasha N.; Bowman, Charles A.; Tantoco, Anthony T.; Paladin, Elizabeth C.; Myers, Marlana S.; Smith, Alexis L.; Grace, Molly S.; Pham, Thuy T.; O'Brien, Matthew B.; Vogelsberger, Amy M.; Hryckowian, Andrew J.; Wynalek, Jessica L.; Donis-Keller, Helen; Bogel, Matt W.; Peebles, Craig L.; Cresawn, Steve G.; Hendrix, Roger W.

    2010-01-01

    Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of sixty – all infecting a common bacterial host – provides further insight into their diversity and evolution. Of the sixty phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, five of which can be further divided into subclusters; five genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the six genomes in cluster D share more than 97.5% average nucleotide similarity with each other. In contrast, similarity between the two genomes in Cluster I is barely detectable by diagonal plot analysis. The total of 6,858 predicted ORFs have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit smaller average size than genes of their host (205 residues compared to 315), phage genes in higher flux average only ∼100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains. PMID:20064525

  10. Size-selected genomic libraries: the distribution and size-fractionation of restricted genomic DNA fragments by gel electrophoresis.

    Science.gov (United States)

    Gondo, Y

    1995-02-01

    By using one-dimensional genome scanning, it is possible to directly identify the restricted genomic DNA fragment that reflects the site of genetic change. The subsequent strategies to obtain the molecular clones of the corresponding restriction fragment are usually as follows: (i) the restriction of a mass quantity of an appropriate genomic DNA, (ii) the size-fractionation of the restricted DNA on a preparative electrophoresis gel in order to enrich the corresponding restriction fragment, (iii) the construction of the size-selected libraries from the fractionated genomic DNA, and (iv) the screening of the library to obtain an objective clone which is identified on the analytical genome scanning gel. A knowledge of the size distribution pattern of restriction fragments of the genomic DNA makes it possible to calculate the heterogeneity or complexity of the restriction fragment in each size-fraction. This manuscript first describes the distribution of the restriction fragments with respect to their length. Some examples of the practical application of this theory to genome scanning is then discussed using presumptive genome scanning gels. The way to calculate such DNA complexities in the prepared size-fractionated samples is also demonstrated. Such information should greatly facilitate the design of experimental strategies for the cloning of a certain size of genomic DNA after digestion with restriction enzyme(s) as is the case with genome scanning.

  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).

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

    Science.gov (United States)

    Randhir, R J; Hanau, R M

    1997-10-01

    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 x 10(7) bp, respectively. Genomic reconstruction experiments based on Southern blot hybridization between a cloned single-copy gene, PYR1 (orotate phosphoribosyl transferase), and maize-pathotype DNA confirmed the size of the nuclear genome. The single-copy component of the genomes of both pathotypes was estimated at about 90%. For both pathotypes, ca. 7% of the genome represented repetitive DNA, and 2 to 3% was foldback DNA.

  13. 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.

  14. Metabolic 'engines' of flight drive genome size reduction in birds.

    Science.gov (United States)

    Wright, Natalie A; Gregory, T Ryan; Witt, Christopher C

    2014-03-22

    The tendency for flying organisms to possess small genomes has been interpreted as evidence of natural selection acting on the physical size of the genome. Nonetheless, the flight-genome link and its mechanistic basis have yet to be well established by comparative studies within a volant clade. Is there a particular functional aspect of flight such as brisk metabolism, lift production or maneuverability that impinges on the physical genome? We measured genome sizes, wing dimensions and heart, flight muscle and body masses from a phylogenetically diverse set of bird species. In phylogenetically controlled analyses, we found that genome size was negatively correlated with relative flight muscle size and heart index (i.e. ratio of heart to body mass), but positively correlated with body mass and wing loading. The proportional masses of the flight muscles and heart were the most important parameters explaining variation in genome size in multivariate models. Hence, the metabolic intensity of powered flight appears to have driven genome size reduction in birds.

  15. Recent updates and developments to plant genome size databases

    Science.gov (United States)

    Garcia, Sònia; Leitch, Ilia J.; Anadon-Rosell, Alba; Canela, Miguel Á.; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Siljak-Yakovlev, Sonja; Vallès, Joan; Vitales, Daniel; Bennett, Michael D.

    2014-01-01

    Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols. PMID:24288377

  16. Genome size increases in recently diverged hornwort clades.

    Science.gov (United States)

    Bainard, Jillian D; Villarreal, Juan Carlos

    2013-08-01

    As our knowledge of plant genome size estimates continues to grow, one group has continually been neglected: the hornworts. Hornworts (Anthocerotophyta) have been traditionally grouped with liverworts and mosses because they share a haploid dominant life cycle; however, recent molecular studies place hornworts as the sister lineage to extant tracheophytes. Given the scarcity of information regarding the DNA content of hornworts, our objective was to estimate the 1C-value for a range of hornwort species within a phylogenetic context. Using flow cytometry, we estimated genome size for 36 samples representing 24 species. This accounts for roughly 10% of known hornwort species. Haploid genome sizes (1C-value) ranged from 160 Mbp or 0.16 pg (Leiosporoceros dussii) to 719 Mbp or 0.73 pg (Nothoceros endiviifolius). The average 1C-value was 261 ± 104 Mbp (0.27 ± 0.11 pg). Ancestral reconstruction of genome size on a hornwort phylogeny suggests a small ancestral genome size and revealed increases in genome size in the most recently divergent clades. Much more work is needed to understand DNA content variation in this phylogenetically important group, but this work has significantly increased our knowledge of genome size variation in hornworts.

  17. 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.

  18. Hawaiian Drosophila genomes: size variation and evolutionary expansions.

    Science.gov (United States)

    Craddock, Elysse M; Gall, Joseph G; Jonas, Mark

    2016-02-01

    This paper reports genome sizes of one Hawaiian Scaptomyza and 16 endemic Hawaiian Drosophila species that include five members of the antopocerus species group, one member of the modified mouthpart group, and ten members of the picture wing clade. Genome size expansions have occurred independently multiple times among Hawaiian Drosophila lineages, and have resulted in an over 2.3-fold range of genome sizes among species, with the largest observed in Drosophila cyrtoloma (1C = 0.41 pg). We find evidence that these repeated genome size expansions were likely driven by the addition of significant amounts of heterochromatin and satellite DNA. For example, our data reveal that the addition of seven heterochromatic chromosome arms to the ancestral haploid karyotype, and a remarkable proportion of ~70 % satellite DNA, account for the greatly expanded size of the D. cyrtoloma genome. Moreover, the genomes of 13/17 Hawaiian picture wing species are composed of substantial proportions (22-70 %) of detectable satellites (all but one of which are AT-rich). Our results suggest that in this tightly knit group of recently evolved species, genomes have expanded, in large part, via evolutionary amplifications of satellite DNA sequences in centric and pericentric domains (especially of the X and dot chromosomes), which have resulted in longer acrocentric chromosomes or metacentrics with an added heterochromatic chromosome arm. We discuss possible evolutionary mechanisms that may have shaped these patterns, including rapid fixation of novel expanded genomes during founder-effect speciation.

  19. Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae).

    Science.gov (United States)

    Veleba, Adam; Šmarda, Petr; Zedek, František; Horová, Lucie; Šmerda, Jakub; Bureš, Petr

    2017-02-01

    Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. 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. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  1. Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing.

    Science.gov (United States)

    Henry, Thomas A; Bainard, Jillian D; Newmaster, Steven G

    2014-10-01

    Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.

  2. Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

    Directory of Open Access Journals (Sweden)

    Gan Xiaoni

    2010-06-01

    Full Text Available Abstract Background Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. Results Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89% and that in the Te. nigroviridis genome (4.66%. In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp. Conclusion Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different

  3. Methodology significantly affects genome size estimates: quantitative evidence using bryophytes.

    Science.gov (United States)

    Bainard, Jillian D; Fazekas, Aron J; Newmaster, Steven G

    2010-08-01

    Flow cytometry (FCM) is commonly used to determine plant genome size estimates. Methodology has improved and changed during the past three decades, and researchers are encouraged to optimize protocols for their specific application. However, this step is typically omitted or undescribed in the current plant genome size literature, and this omission could have serious consequences for the genome size estimates obtained. Using four bryophyte species (Brachythecium velutinum, Fissidens taxifolius, Hedwigia ciliata, and Thuidium minutulum), three methodological approaches to the use of FCM in plant genome size estimation were tested. These included nine different buffers (Baranyi's, de Laat's, Galbraith's, General Purpose, LB01, MgSO(4), Otto's, Tris.MgCl(2), and Woody Plant), seven propidium iodide (PI) staining periods (5, 10, 15, 20, 45, 60, and 120 min), and six PI concentrations (10, 25, 50, 100, 150, and 200 microg ml(-1)). Buffer, staining period and staining concentration all had a statistically significant effect (P = 0.05) on the genome size estimates obtained for all four species. Buffer choice and PI concentration had the greatest effect, altering the 1C-values by as much as 8% and 14%, respectively. As well, the quality of the data varied with the different methodology used. Using the methodology determined to be the most accurate in this study (LB01 buffer and PI staining for 20 min at 150 microg ml(-1)), three new genome size estimates were obtained: B. velutinum: 0.46 pg, H. ciliata: 0.30 pg, and T. minutulum: 0.46 pg. While the peak quality of flow cytometry histograms is important, researchers must consider that changes in methodology can also affect the relative peak positions and therefore the genome size estimates obtained for plants using FCM.

  4. Total centromere size and genome size are strongly correlated in ten grass species.

    Science.gov (United States)

    Zhang, Han; Dawe, R Kelly

    2012-05-01

    It has been known for decades that centromere size varies across species, but the factors involved in setting centromere boundaries are unknown. As a means to address this question, we estimated centromere sizes in ten species of the grass family including rice, maize, and wheat, which diverged 60~80 million years ago and vary by 40-fold in genome size. Measurements were made using a broadly reactive antibody to rice centromeric histone H3 (CENH3). In species-wide comparisons, we found a clear linear relationship between total centromere size and genome size. Species with large genomes and few chromosomes tend to have the largest centromeres (e.g., rye) while species with small genomes and many chromosomes have the smallest centromeres (e.g., rice). However, within a species, centromere size is surprisingly uniform. We present evidence from three oat-maize addition lines that support this claim, indicating that each of three maize centromeres propagated in oat are not measurably different from each other. In the context of previously published data, our results suggest that the apparent correlation between chromosome and centromere size is incidental to a larger trend that reflects genome size. Centromere size may be determined by a limiting component mechanism similar to that described for Caenorhabditis elegans centrosomes.

  5. Determination of sample size in genome-scale RNAi screens.

    Science.gov (United States)

    Zhang, Xiaohua Douglas; Heyse, Joseph F

    2009-04-01

    For genome-scale RNAi research, it is critical to investigate sample size required for the achievement of reasonably low false negative rate (FNR) and false positive rate. The analysis in this article reveals that current design of sample size contributes to the occurrence of low signal-to-noise ratio in genome-scale RNAi projects. The analysis suggests that (i) an arrangement of 16 wells per plate is acceptable and an arrangement of 20-24 wells per plate is preferable for a negative control to be used for hit selection in a primary screen without replicates; (ii) in a confirmatory screen or a primary screen with replicates, a sample size of 3 is not large enough, and there is a large reduction in FNRs when sample size increases from 3 to 4. To search a tradeoff between benefit and cost, any sample size between 4 and 11 is a reasonable choice. If the main focus is the selection of siRNAs with strong effects, a sample size of 4 or 5 is a good choice. If we want to have enough power to detect siRNAs with moderate effects, sample size needs to be 8, 9, 10 or 11. These discoveries about sample size bring insight to the design of a genome-scale RNAi screen experiment.

  6. 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.

  7. Stomatal vs. genome size in angiosperms: the somatic tail wagging the genomic dog?

    Science.gov (United States)

    Hodgson, J G; Sharafi, M; Jalili, A; Díaz, S; Montserrat-Martí, G; Palmer, C; Cerabolini, B; Pierce, S; Hamzehee, B; Asri, Y; Jamzad, Z; Wilson, P; Raven, J A; Band, S R; Basconcelo, S; Bogard, A; Carter, G; Charles, M; Castro-Díez, P; Cornelissen, J H C; Funes, G; Jones, G; Khoshnevis, M; Pérez-Harguindeguy, N; Pérez-Rontomé, M C; Shirvany, F A; Vendramini, F; Yazdani, S; Abbas-Azimi, R; Boustani, S; Dehghan, M; Guerrero-Campo, J; Hynd, A; Kowsary, E; Kazemi-Saeed, F; Siavash, B; Villar-Salvador, P; Craigie, R; Naqinezhad, A; Romo-Díez, A; de Torres Espuny, L; Simmons, E

    2010-04-01

    Genome size is a function, and the product, of cell volume. As such it is contingent on ecological circumstance. The nature of 'this ecological circumstance' is, however, hotly debated. Here, we investigate for angiosperms whether stomatal size may be this 'missing link': the primary determinant of genome size. Stomata are crucial for photosynthesis and their size affects functional efficiency. Stomatal and leaf characteristics were measured for 1442 species from Argentina, Iran, Spain and the UK and, using PCA, some emergent ecological and taxonomic patterns identified. Subsequently, an assessment of the relationship between genome-size values obtained from the Plant DNA C-values database and measurements of stomatal size was carried out. Stomatal size is an ecologically important attribute. It varies with life-history (woody species angiosperms. Correlation is not, however, proof of causality and here our interpretation is hampered by unexpected deficiencies in the scientific literature. Firstly, there are discrepancies between our own observations and established ideas about the ecological significance of stomatal size; very large stomata, theoretically facilitating photosynthesis in deep shade, were, in this study (and in other studies), primarily associated with vernal geophytes of unshaded habitats. Secondly, the lower size limit at which stomata can function efficiently, and the ecological circumstances under which these minute stomata might occur, have not been satisfactorally resolved. Thus, our hypothesis, that the optimization of stomatal size for functional efficiency is a major ecological determinant of genome size, remains unproven.

  8. Patterns of genome size diversity in bats (order Chiroptera).

    Science.gov (United States)

    Smith, Jillian D L; Bickham, John W; Gregory, T Ryan

    2013-08-01

    Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 "microbat" species from 12 families and complements a previous study on members of the family Pteropodidae ("megabats"). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ("megabats") and nonpteropodids ("microbats").

  9. 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

  10. The bat genome: GC-biased small chromosomes associated with reduction in genome size.

    Science.gov (United States)

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

    2013-12-01

    Bats are distinct from other mammals in their small genome size as well as their high metabolic rate, possibly related to flight ability. Although the genome sequence has been published in two species, the data lack cytogenetic information. In this study, the size and GC content of each chromosome are measured from the flow karyotype of the mouse-eared bat, Myotis myotis (MMY). The smaller chromosomes are GC-rich compared to the larger chromosomes, and the relative proportions of homologous segments between MMY and human differ among the MMY chromosomes. The MMY genome size calculated from the sum of the chromosome sizes is 2.25 Gb, and the total GC content is 42.3%, compared to human and dog with 41.0 and 41.2%, respectively. The GC-rich small MMY genome is characterised by GC-biased smaller chromosomes resulting from preferential loss of AT-rich sequences. Although the association between GC-rich small chromosomes and small genome size has been reported only in birds so far, we show in this paper, for the first time, that the same phenomenon is observed in at least one group of mammals, implying that this may be a mechanism common to genome evolution in general.

  11. Genome size determination in peronosporales (Oomycota) by Feulgen image analysis.

    Science.gov (United States)

    Voglmayr, H; Greilhuber, J

    1998-12-01

    Genome size was determined, by nuclear Feulgen staining and image analysis, in 46 accessions of 31 species of Peronosporales (Oomycota), including important plant pathogens such as Bremia lactucae, Plasmopara viticola, Pseudoperonospora cubensis, and Pseudoperonospora humuli. The 1C DNA contents ranged from 0.046 (45. 6 Mb) to 0.163 pg (159.9 Mb). This is 0.041- to 0.144-fold that of Glycine max (soybean, 1C = 1.134 pg), which was used as an internal standard for genome size determination. The linearity of Feulgen absorbance photometry method over this range was demonstrated by calibration of Aspergillus species (1C = 31-38 Mb) against Glycine, which revealed differences of less than 6% compared to the published CHEF data. The low coefficients of variation (usually between 5 and 10%), repeatability of the results, and compatibility with CHEF data prove the resolution power of Feulgen image analysis. The applicability and limitations of Feulgen photometry are discussed in relation to other methods of genome size determination (CHEF gel electrophoresis, reassociation kinetics, genomic reconstruction) that have been previously applied to Oomycota. Copyright 1998 Academic Press.

  12. 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.

  13. 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...... 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...... marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how...

  14. 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.

  15. Genome Size in North American Fireflies: Substantial Variation Likely Driven by Neutral Processes

    Science.gov (United States)

    Johnston, J. Spencer; Stanger-Hall, Kathrin F.; Hjelmen, Carl E.; Hanrahan, Shawn J.; Korunes, Katharine; Hall, David

    2017-01-01

    Abstract Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies). The 23 species considered represent an excellent study system because of the greater than 5-fold range of genome sizes, documented here using flow cytometry, and the 3-fold range in body size, measured using pronotum width. We also identified common genomic repetitive elements using low-coverage sequencing. We found a positive relationship between genome size and repetitive DNA, particularly retrotransposons. Both genome size and these elements were evolving as expected given phylogenetic relatedness. We also tested whether genome size varied with body size and found no relationship. Together, our results suggest that genome size is evolving neutrally in fireflies. PMID:28541478

  16. Transcriptome and genome size analysis of the Venus flytrap.

    Science.gov (United States)

    Jensen, Michael Krogh; Vogt, Josef Korbinian; Bressendorff, Simon; Seguin-Orlando, Andaine; Petersen, Morten; Sicheritz-Pontén, Thomas; Mundy, John

    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. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.

  17. Transcriptome and genome size analysis of the Venus flytrap.

    Directory of Open Access Journals (Sweden)

    Michael Krogh Jensen

    Full Text Available 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. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.

  18. Developmental regulation of nucleolus size during Drosophila eye differentiation.

    Science.gov (United States)

    Baker, Nicholas E

    2013-01-01

    When cell cycle withdrawal accompanies terminal differentiation, biosynthesis and cellular growth are likely to change also. In this study, nucleolus size was monitored during cell fate specification in the Drosophila eye imaginal disc using fibrillarin antibody labeling. Nucleolus size is an indicator of ribosome biogenesis and can correlate with cellular growth rate. Nucleolar size was reduced significantly during cell fate specification and differentiation, predominantly as eye disc cells entered a cell cycle arrest that preceded cell fate specification. This reduction in nucleolus size required Dpp and Hh signaling. A transient enlargement of the nucleolus accompanied cell division in the Second Mitotic Wave. Nucleoli continued to diminish in postmitotic cells following fate specification. These results suggest that cellular growth is regulated early in the transition from proliferating progenitor cells to terminal cell fate specification, contemporary with regulation of the cell cycle, and requiring the same extracellular signals.

  19. Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms.

    Science.gov (United States)

    Puttick, Mark N; Clark, James; Donoghue, Philip C J

    2015-12-07

    Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity. © 2015 The Authors.

  20. Genome downsizing and karyotype constancy in diploid and polyploid congeners: a model of genome size variation.

    Science.gov (United States)

    Poggio, Lidia; Realini, María Florencia; Fourastié, María Florencia; García, Ana María; González, Graciela Esther

    2014-06-26

    Evolutionary chromosome change involves significant variation in DNA amount in diploids and genome downsizing in polyploids. Genome size and karyotype parameters of Hippeastrum species with different ploidy level were analysed. In Hippeastrum, polyploid species show less DNA content per basic genome than diploid species. The rate of variation is lower at higher ploidy levels. All the species have a basic number x = 11 and bimodal karyotypes. The basic karyotypes consist of four short metacentric chromosomes and seven large chromosomes (submetacentric and subtelocentric). The bimodal karyotype is preserved maintaining the relative proportions of members of the haploid chromosome set, even in the presence of genome downsizing. The constancy of the karyotype is maintained because changes in DNA amount are proportional to the length of the whole-chromosome complement and vary independently in the long and short sets of chromosomes. This karyotype constancy in taxa of Hippeastrum with different genome size and ploidy level indicates that the distribution of extra DNA within the complement is not at random and suggests the presence of mechanisms selecting for constancy, or against changes, in karyotype morphology.

  1. 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.

  2. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes

    Directory of Open Access Journals (Sweden)

    Reva Oleg N

    2005-10-01

    Full Text Available Abstract Background Complete sequencing of bacterial genomes has become a common technique of present day microbiology. Thereafter, data mining in the complete sequence is an essential step. New in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of ORFs. We tested the usefulness of local oligonucleotide usage (OU patterns to recognize and differentiate types of atypical oligonucleotide composition in DNA sequences of bacterial genomes. Results A total of 163 bacterial genomes of eubacteria and archaea published in the NCBI database were analyzed. Local OU patterns exhibit substantial intrachromosomal variation in bacteria. Loci with alternative OU patterns were parts of horizontally acquired gene islands or ancient regions such as genes for ribosomal proteins and RNAs. OU statistical parameters, such as local pattern deviation (D, pattern skew (PS and OU variance (OUV enabled the detection and visualization of gene islands of different functional classes. Conclusion A set of approaches has been designed for the statistical analysis of nucleotide sequences of bacterial genomes. These methods are useful for the visualization and differentiation of regions with atypical oligonucleotide composition prior to or accompanying gene annotation.

  3. The dynamic evolutionary history of genome size in North American woodland salamanders.

    Science.gov (United States)

    Newman, Catherine E; Gregory, T Ryan; Austin, Christopher C

    2017-04-01

    The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

  4. Meta-basic estimates the size of druggable human genome.

    Science.gov (United States)

    Plewczynski, Dariusz; Rychlewski, Leszek

    2009-06-01

    We present here the estimation of the upper limit of the number of molecular targets in the human genome that represent an opportunity for further therapeutic treatment. We select around approximately 6300 human proteins that are similar to sequences of known protein targets collected from DrugBank database. Our bioinformatics study estimates the size of 'druggable' human genome to be around 20% of human proteome, i.e. the number of the possible protein targets for small-molecule drug design in medicinal chemistry. We do not take into account any toxicity prediction, the three-dimensional characteristics of the active site in the predicted 'druggable' protein families, or detailed chemical analysis of known inhibitors/drugs. Instead we rely on remote homology detection method Meta-BASIC, which is based on sequence and structural similarity. The prepared dataset of all predicted protein targets from human genome presents the unique opportunity for developing and benchmarking various in silico chemo/bio-informatics methods in the context of the virtual high throughput screening.

  5. Interactions of photosynthesis with genome size and function.

    Science.gov (United States)

    Raven, John A; Beardall, John; Larkum, Anthony W D; Sánchez-Baracaldo, Patricia

    2013-07-19

    Photolithotrophs are divided between those that use water as their electron donor (Cyanobacteria and the photosynthetic eukaryotes) and those that use a different electron donor (the anoxygenic photolithotrophs, all of them Bacteria). Photolithotrophs with the most reduced genomes have more genes than do the corresponding chemoorganotrophs, and the fastest-growing photolithotrophs have significantly lower specific growth rates than the fastest-growing chemoorganotrophs. Slower growth results from diversion of resources into the photosynthetic apparatus, which accounts for about half of the cell protein. There are inherent dangers in (especially oxygenic) photosynthesis, including the formation of reactive oxygen species (ROS) and blue light sensitivity of the water spitting apparatus. The extent to which photolithotrophs incur greater DNA damage and repair, and faster protein turnover with increased rRNA requirement, needs further investigation. A related source of environmental damage is ultraviolet B (UVB) radiation (280-320 nm), whose flux at the Earth's surface decreased as oxygen (and ozone) increased in the atmosphere. This oxygenation led to the requirements of defence against ROS, and decreasing availability to organisms of combined (non-dinitrogen) nitrogen and ferrous iron, and (indirectly) phosphorus, in the oxygenated biosphere. Differential codon usage in the genome and, especially, the proteome can lead to economies in the use of potentially growth-limiting elements.

  6. Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable to the Genome Size of the Strain Ikeda.

    Science.gov (United States)

    Liao, Hsiao-Mei; Chao, Chien-Chung; Lei, Haiyan; Li, Bingjie; Tsai, Shien; Hung, Guo-Chiuan; Ching, Wei-Mei; Lo, Shyh-Ching

    2016-08-18

    Orientia tsutsugamushi, an intracellular bacterium, belongs to the family Rickettsiaceae This study presents the draft genome sequence of strain Karp, with 2.0 Mb as the size of the completed genome. This nearly finished draft genome sequence was annotated with the RAST server and the contents compared to those of the other strains.

  7. Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable to the Genome Size of the Strain Ikeda

    Science.gov (United States)

    Liao, Hsiao-Mei; Chao, Chien-Chung; Lei, Haiyan; Li, Bingjie; Tsai, Shien; Hung, Guo-Chiuan

    2016-01-01

    Orientia tsutsugamushi, an intracellular bacterium, belongs to the family Rickettsiaceae. This study presents the draft genome sequence of strain Karp, with 2.0 Mb as the size of the completed genome. This nearly finished draft genome sequence was annotated with the RAST server and the contents compared to those of the other strains. PMID:27540052

  8. Genome-wide screen for differential DNA methylation associated with neural cell differentiation in mouse.

    Directory of Open Access Journals (Sweden)

    Rene Cortese

    Full Text Available Cellular differentiation involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. Using Differential Methylation Hybridization (DMH in combination with a custom DMH array containing 51,243 features covering more than 16,000 murine genes, we carried out a genome-wide screen for cell- and tissue-specific differentially methylated regions (tDMRs in undifferentiated embryonic stem cells (ESCs, in in-vitro induced neural stem cells (NSCs and 8 differentiated embryonic and adult tissues. Unsupervised clustering of the generated data showed distinct cell- and tissue-specific DNA methylation profiles, revealing 202 significant tDMRs (p1.96 enrichment for genes involved in neural differentiation, including, for example, Jag1 and Tcf4. Our results provide robust evidence for the relevance of DNA methylation in early neural development and identify novel marker candidates for neural cell differentiation.

  9. First genome size estimations for some eudicot families and genera

    Directory of Open Access Journals (Sweden)

    Garcia, S.

    2010-12-01

    Full Text Available Genome size diversity in angiosperms varies roughly 2400-fold, although approximately 45% of angiosperm families lack a single genome size estimation, and therefore, this range could be enlarged. To contribute completing family and genera representation, DNA C-Values are here provided for 19 species from 16 eudicot families, including first values for 6 families, 14 genera and 17 species. The sample of species studied is very diverse, including herbs, weeds, vines, shrubs and trees. Data are discussed regarding previous genome size estimates of closely related species or genera, if any, their chromosome number, growth form or invasive behaviour. The present research contributes approximately 1.5% new values for previously unreported angiosperm families, being the current coverage around 55% of angiosperm families, according to the Plant DNA C-Values Database.

    La diversidad del tamaño del genoma en angiospermas es muy amplia, siendo el valor más elevado aproximadamente unas 2400 veces superior al más pequeño. Sin embargo, cerca del 45% de las familias no presentan ni una sola estimación, por lo que el rango real podría ser ampliado. Para contribuir a completar la representación de familias y géneros de angiospermas, este estudio contribuye con valores C para 19 especies de 16 familias de eudicoticotiledóneas, incluyendo los primeros valores para 6 familias, 14 géneros y 17 especies. La muestra estudiada es muy diversa, e incluye hierbas, malezas, enredaderas, arbustos y árboles. Se discuten los resultados en función de estimaciones previas del tamaño del genoma de especies o géneros estrechamente relacionados, del número de cromosomas, la forma de crecimiento o el comportamiento invasor de las especies analizadas. El presente estudio contribuye aproximadamente en un 1,5% de nuevos valores para familias de angiospermas no estudiadas previamente, de las que actualmente existe información para el 55%, según la base de datos

  10. Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity

    Science.gov (United States)

    Ellis, Lisa L.; Huang, Wen; Quinn, Andrew M.; Ahuja, Astha; Alfrejd, Ben; Gomez, Francisco E.; Hjelmen, Carl E.; Moore, Kristi L.; Mackay, Trudy F. C.; Johnston, J. Spencer; Tarone, Aaron M.

    2014-01-01

    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. PMID:25057905

  11. 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.

  12. Genome size as a key to evolutionary complex aquatic plants: polyploidy and hybridization in Callitriche (Plantaginaceae.

    Directory of Open Access Journals (Sweden)

    Jan Prančl

    Full Text Available Despite their complex evolutionary histories, aquatic plants are highly underrepresented in contemporary biosystematic studies. Of them, the genus Callitriche is particularly interesting because of such evolutionary features as wide variation in chromosome numbers and pollination systems. However, taxonomic difficulties have prevented broader investigation of this genus. In this study we applied flow cytometry to Callitriche for the first time in order to gain an insight into evolutionary processes and genome size differentiation in the genus. Flow cytometry complemented by confirmation of chromosome counts was applied to an extensive dataset of 1077 Callitriche individuals from 495 localities in 11 European countries and the USA. Genome size was determined for 12 taxa. The results suggest that many important processes have interacted in the evolution of the genus, including polyploidization and hybridization. Incongruence between genome size and ploidy level, intraspecific variation in genome size, formation of autotriploid and hybridization between species with different pollination systems were also detected. Hybridization takes place particularly in the diploid-tetraploid complex C. cophocarpa-C. platycarpa, for which the triploid hybrids were frequently recorded in the area of co-occurrence of its parents. A hitherto unknown hybrid (probably C. hamulata × C. cophocarpa with a unique chromosome number was discovered in the Czech Republic. However, hybridization occurs very rarely among most of the studied species. The main ecological preferences were also compared among the taxa collected. Although Callitriche taxa often grow in mixed populations, the ecological preferences of individual species are distinctly different in some cases. Anyway, flow cytometry is a very efficient method for taxonomic delimitation, determination and investigation of Callitriche species, and is even able to distinguish homoploid taxa and identify introduced

  13. Genome size diversity in angiosperms and its influence on gene space.

    Science.gov (United States)

    Dodsworth, Steven; Leitch, Andrew R; Leitch, Ilia J

    2015-12-01

    Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Differential DNA Methylation Analysis without a Reference Genome

    Directory of Open Access Journals (Sweden)

    Johanna Klughammer

    2015-12-01

    Full Text Available Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS, which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish. Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org. The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.

  15. Differential DNA Methylation Analysis without a Reference Genome.

    Science.gov (United States)

    Klughammer, Johanna; Datlinger, Paul; Printz, Dieter; Sheffield, Nathan C; Farlik, Matthias; Hadler, Johanna; Fritsch, Gerhard; Bock, Christoph

    2015-12-22

    Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.

  16. Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k-mer Analysis

    Science.gov (United States)

    He, Kang; Lin, Kejian; Wang, Guirong; Li, Fei

    2016-01-01

    The flow cytometry method was used to estimate the genome sizes of nine agriculturally important insects, including two coleopterans, five Hemipterans, and two hymenopterans. Among which, the coleopteran Lissorhoptrus oryzophilus (Kuschel) had the largest genome of 981 Mb. The average genome size was 504 Mb, suggesting that insects have a moderate-size genome. Compared with the insects in other orders, hymenopterans had small genomes, which were averagely about ~200 Mb. We found that the genome sizes of four insect species were different between male and female, showing the organismal complexity of insects. The largest difference occurred in the coconut leaf beetle Brontispa longissima (Gestro). The male coconut leaf beetle had a 111 Mb larger genome than females, which might be due to the chromosome number difference between the sexes. The results indicated that insect invasiveness was not related to genome size. We also determined the genome sizes of the small brown planthopper Laodelphax striatellus (Fallén) and the parasitic wasp Macrocentrus cingulum (Brischke) using k-mer analysis with Illunima Solexa sequencing data. There were slight differences in the results from the two methods. k-mer analysis indicated that the genome size of L. striatellus was 500–700 Mb and that of M. cingulum was ~150 Mb. In all, the genome sizes information presented here should be helpful for designing the genome sequencing strategy when necessary. PMID:27932995

  17. 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

  18. Adaptive and nonadaptive genome size evolution in Karst endemic flora of China.

    Science.gov (United States)

    Kang, Ming; Tao, Junjie; Wang, Jing; Ren, Chen; Qi, Qingwen; Xiang, Qiu-Yun; Huang, Hongwen

    2014-06-01

    Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. Several hypotheses for genome size evolution including neutral, maladaptive, and adaptive models have been proposed, but the relative importance of these models remains controversial. Primulina is a genus that is highly diversified in the Karst region of southern China, where genome size variation and the underlying evolutionary mechanisms are poorly understood. We reconstructed the phylogeny of Primulina using DNA sequences for 104 species and determined the genome sizes of 101 species. We examined the phylogenetic signal in genome size variation, and tested the fit to different evolutionary models and for correlations with variation in latitude and specific leaf area (SLA). The results showed that genome size, SLA and latitudinal variation all displayed strong phylogenetic signals, but were best explained by different evolutionary models. Furthermore, significant positive relationships were detected between genome size and SLA and between genome size and latitude. Our study is the first to investigate genome size evolution on such a comprehensive scale and in the Karst region flora. We conclude that genome size in Primulina is phylogenetically conserved but its variation among species is a combined outcome of both neutral and adaptive evolution.

  19. Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number.

    Science.gov (United States)

    Sankaran, Vijay G; Ludwig, Leif S; Sicinska, Ewa; Xu, Jian; Bauer, Daniel E; Eng, Jennifer C; Patterson, Heide Christine; Metcalf, Ryan A; Natkunam, Yasodha; Orkin, Stuart H; Sicinski, Piotr; Lander, Eric S; Lodish, Harvey F

    2012-09-15

    Genome-wide association studies (GWASs) have identified a genetic variant of moderate effect size at 6p21.1 associated with erythrocyte traits in humans. We show that this variant affects an erythroid-specific enhancer of CCND3. A Ccnd3 knockout mouse phenocopies these erythroid phenotypes, with a dramatic increase in erythrocyte size and a concomitant decrease in erythrocyte number. By examining human and mouse primary erythroid cells, we demonstrate that the CCND3 gene product cyclin D3 regulates the number of cell divisions that erythroid precursors undergo during terminal differentiation, thereby controlling erythrocyte size and number. We illustrate how cell type-specific specialization can occur for general cell cycle components-a finding resulting from the biological follow-up of unbiased human genetic studies.

  20. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms.

    Science.gov (United States)

    Fleischmann, Andreas; Michael, Todd P; Rivadavia, Fernando; Sousa, Aretuza; Wang, Wenqin; Temsch, Eva M; Greilhuber, Johann; Müller, Kai F; Heubl, Günther

    2014-12-01

    Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported

  1. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae).

    Science.gov (United States)

    Weng, Mao-Lun; Ruhlman, Tracey A; Gibby, Mary; Jansen, Robert K

    2012-09-01

    The phylogeny of 58 Pelargonium species was estimated using five plastid markers (rbcL, matK, ndhF, rpoC1, trnL-F) and one mitochondrial gene (nad5). The results confirmed the monophyly of three major clades and four subclades within Pelargonium but also indicate the need to revise some sectional classifications. This phylogeny was used to examine karyotype evolution in the genus: plotting chromosome sizes, numbers and 2C-values indicates that genome size is significantly correlated with chromosome size but not number. Accelerated rates of nucleotide substitution have been previously detected in both plastid and mitochondrial genes in Pelargonium, but sparse taxon sampling did not enable identification of the phylogenetic distribution of these elevated rates. Using the multigene phylogeny as a constraint, we investigated lineage- and locus-specific heterogeneity of substitution rates in Pelargonium for an expanded number of taxa and demonstrated that both plastid and mitochondrial genes have had accelerated substitution rates but with markedly disparate patterns. In the plastid, the exons of rpoC1 have significantly accelerated substitution rates compared to its intron and the acceleration was mainly due to nonsynonymous substitutions. In contrast, the mitochondrial gene, nad5, experienced substantial acceleration of synonymous substitution rates in three internal branches of Pelargonium, but this acceleration ceased in all terminal branches. Several lineages also have dN/dS ratios significantly greater than one for rpoC1, indicating that positive selection is acting on this gene, whereas the accelerated synonymous substitutions in the mitochondrial gene are the result of elevated mutation rates.

  2. Reductive genome evolution at both ends of the bacterial population size spectrum.

    Science.gov (United States)

    Batut, Bérénice; Knibbe, Carole; Marais, Gabriel; Daubin, Vincent

    2014-12-01

    Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

  3. Genomic Differentiation Between Gossypium barbadense and G.hirsutum

    Institute of Scientific and Technical Information of China (English)

    ZHANG Tian-zhen

    2008-01-01

    @@ Sea Island cotton (Gossypium barbadense L.) has superior fiber quality properties,while Uplandcotton (G.hirsutum L.) is characterized by its high yield.Although these two species are easilycrossed,it is difficult to integrate their superior genes.It will be very helpful to molecular breedingand evolution study in Gossypium to reveal genomic differentiation between G.barbadense and G.hir-suture.An enhanced genetic map consisting of 2247 loci and covering 3514.6 cM,with an average in-ter-marker distance of 1.5 cM has been developed.

  4. Identification of differentially expressed genes associated with differential body size in mandarin fish (Siniperca chuatsi).

    Science.gov (United States)

    Tian, Changxu; Li, Ling; Liang, Xu-Fang; He, Shan; Guo, Wenjie; Lv, Liyuan; Wang, Qingchao; Song, Yi

    2016-08-01

    Body size is an obvious and important characteristic of fish. Mandarin fish Siniperca chuatsi (Basilewsky) is one of the most valuable perciform species widely cultured in China. Individual differences in body size are common in mandarin fish and significantly influence the aquaculture production. However, little is currently known about its genetic control. In this study, digital gene expression profiling and transcriptome sequencing were performed in mandarin fish with differential body size at 30 and 180 days post-hatch (dph), respectively. Body weight, total length and body length of fish with big-size were significantly higher than those with small-size at both 30 and 180 dph (P mandarin fish that went through the same training procedure. The genes were involved in the growth hormone-insulin-like growth factor axis, cell proliferation and differentiation, appetite control, glucose metabolism, reproduction and sexual size dimorphism pathways. This study will help toward a comprehensive understanding of the complexity of regulation of body size in mandarin fish individuals and provide valuable information for future research.

  5. Genome size correlates with reproductive fitness in seed beetles.

    Science.gov (United States)

    Arnqvist, Göran; Sayadi, Ahmed; Immonen, Elina; Hotzy, Cosima; Rankin, Daniel; Tuda, Midori; Hjelmen, Carl E; Johnston, J Spencer

    2015-09-22

    The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the 'C-value paradox'. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4-5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

  6. Genome size correlates with reproductive fitness in seed beetles

    Science.gov (United States)

    Arnqvist, Göran; Sayadi, Ahmed; Immonen, Elina; Hotzy, Cosima; Rankin, Daniel; Tuda, Midori; Hjelmen, Carl E.; Johnston, J. Spencer

    2015-01-01

    The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the ‘C-value paradox’. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4–5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution. PMID:26354938

  7. Differential metabolism of Mycoplasma species as revealed by their genomes

    Directory of Open Access Journals (Sweden)

    Fabricio B.M. Arraes

    2007-01-01

    Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

  8. An overview of differential mobility analyzers for size classification of nanometer-sized aerosol particles

    Directory of Open Access Journals (Sweden)

    Nakorn Tippayawong

    2008-03-01

    Full Text Available Size classification of nanoparticles is an important process in the electrical mobility particle size analyzer. The differential mobility analyzer (DMA is one of the most commonly used devices for classifying and measuring nanometersized aerosol particles between 1 nm to 1 μm in diameter, based on their electrical mobility. The DMA can be described as an assembly of two concentrically cylindrical electrodes with an air gap between the walls. In the DMA, air and aerosol flows enter from one end, pass through the annulus and exit the other end. An electric field is applied between the inner and outer electrodes. Particles having a specific mobility exit with the monodisperse air flow through a small slit located at the bottom of the inner electrode. These particles are transferred to a particle counter to determine the particle number concentration. In the past several decades, there have been numerous extensive studies and developments on the DMA. Nonetheless, they are different in terms of specific applications, construction, particle size range, as well as time response and resolution. The purpose of this article is to provide an overview of the state-of-the-art existing cylindrical DMAs for aerosol particle size classification as well as for the generation of monodisperse aerosol in nanometer size range. A description of the operating principles, detailed physical characteristics of these DMAs, including the single-channel and multi-channel DMAs, as well as some examples of applications to nanotechnology are given.

  9. An Effect Size Measure for Raju's Differential Functioning for Items and Tests

    Science.gov (United States)

    Wright, Keith D.; Oshima, T. C.

    2015-01-01

    This study established an effect size measure for differential functioning for items and tests' noncompensatory differential item functioning (NCDIF). The Mantel-Haenszel parameter served as the benchmark for developing NCDIF's effect size measure for reporting moderate and large differential item functioning in test items. The effect size of…

  10. Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans.

    Science.gov (United States)

    Alfsnes, Kristian; Leinaas, Hans Petter; Hessen, Dag Olav

    2017-08-01

    Despite the major role of genome size for physiology, ecology, and evolution, there is still mixed evidence with regard to proximate and ultimate drivers. The main causes of large genome size are proliferation of noncoding elements and/or duplication events. The relative role and interplay between these proximate causes and the evolutionary patterns shaped by phylogeny, life history traits or environment are largely unknown for the arthropods. Genome size shows a tremendous variability in this group, and it has a major impact on a range of fitness-related parameters such as growth, metabolism, life history traits, and for many species also body size. In this study, we compared genome size in two major arthropod groups, insects and crustaceans, and related this to phylogenetic patterns and parameters affecting ambient temperature (latitude, depth, or altitude), insect developmental mode, as well as crustacean body size and habitat, for species where data were available. For the insects, the genome size is clearly phylogeny-dependent, reflecting primarily their life history and mode of development, while for crustaceans there was a weaker association between genome size and phylogeny, suggesting life cycle strategies and habitat as more important determinants. Maximum observed latitude and depth, and their combined effect, showed positive, and possibly phylogenetic independent, correlations with genome size for crustaceans. This study illustrate the striking difference in genome sizes both between and within these two major groups of arthropods, and that while living in the cold with low developmental rates may promote large genomes in marine crustaceans, there is a multitude of proximate and ultimate drivers of genome size.

  11. The mode and tempo of genome size evolution in the subgenus Sophophora

    Science.gov (United States)

    Johnston, J. Spencer

    2017-01-01

    Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s Cmean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s Cmean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships. PMID:28267812

  12. Genome size and metabolic intensity in tetrapods: a tale of two lines.

    Science.gov (United States)

    Vinogradov, Alexander E; Anatskaya, Olga V

    2006-01-07

    We show the negative link between genome size and metabolic intensity in tetrapods, using the heart index (relative heart mass) as a unified indicator of metabolic intensity in poikilothermal and homeothermal animals. We found two separate regression lines of heart index on genome size for reptiles-birds and amphibians-mammals (the slope of regression is steeper in reptiles-birds). We also show a negative correlation between GC content and nucleosome formation potential in vertebrate DNA, and, consistent with this relationship, a positive correlation between genome GC content and nuclear size (independent of genome size). It is known that there are two separate regression lines of genome GC content on genome size for reptiles-birds and amphibians-mammals: reptiles-birds have the relatively higher GC content (for their genome sizes) compared to amphibians-mammals. Our results suggest uniting all these data into one concept. The slope of negative regression between GC content and nucleosome formation potential is steeper in exons than in non-coding DNA (where nucleosome formation potential is generally higher), which indicates a special role of non-coding DNA for orderly chromatin organization. The chromatin condensation and nuclear size are supposed to be key parameters that accommodate the effects of both genome size and GC content and connect them with metabolic intensity. Our data suggest that the reptilian-birds clade evolved special relationships among these parameters, whereas mammals preserved the amphibian-like relationships. Surprisingly, mammals, although acquiring a more complex general organization, seem to retain certain genome-related properties that are similar to amphibians. At the same time, the slope of regression between nucleosome formation potential and GC content is steeper in poikilothermal than in homeothermal genomes, which suggests that mammals and birds acquired certain common features of genomic organization.

  13. A genome-wide methylation study on obesity: differential variability and differential methylation.

    Science.gov (United States)

    Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Hidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

    2013-05-01

    Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common complex disease. We analyzed genome-wide methylation profiles of over 470,000 CpGs in peripheral blood samples from 48 obese and 48 lean African-American youth aged 14-20 y old. A substantial number of differentially variable CpG sites (DVCs), using statistics based on variances, as well as a substantial number of differentially methylated CpG sites (DMCs), using statistics based on means, were identified. Similar to the findings in cancers, DVCs generally exhibited an outlier structure and were more variable in cases than in controls. By randomly splitting the current sample into a discovery and validation set, we observed that both the DVCs and DMCs identified from the first set could independently predict obesity status in the second set. Furthermore, both the genes harboring DMCs and the genes harboring DVCs showed significant enrichment of genes identified by genome-wide association studies on obesity and related diseases, such as hypertension, dyslipidemia, type 2 diabetes and certain types of cancers, supporting their roles in the etiology and pathogenesis of obesity. We generalized the recent finding on methylation variability in cancer research to obesity and demonstrated that differential variability is also an important feature of obesity-related methylation changes. Future studies on the epigenetics of obesity will benefit from both statistics based on means and statistics based on variances.

  14. Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae).

    Science.gov (United States)

    Krahulcová, Anna; Trávnícek, Pavel; Krahulec, František; Rejmánek, Marcel

    2017-04-01

    Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra. The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages.

  15. A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions

    Directory of Open Access Journals (Sweden)

    Zhao Zhongming

    2006-12-01

    Full Text Available Abstract Background The local environment of single nucleotide polymorphisms (SNPs contains abundant genetic information for the study of mechanisms of mutation, genome evolution, and causes of diseases. Recent studies revealed that neighboring-nucleotide biases on SNPs were strong and the genome-wide bias patterns could be represented by a small subset of the total SNPs. It remains unsolved for the estimation of the effective SNP size, the number of SNPs that are sufficient to represent the bias patterns observed from the whole SNP data. Results To estimate the effective SNP size, we developed a novel statistical method, SNPKS, which considers both the statistical and biological significances. SNPKS consists of two major steps: to obtain an initial effective size by the Kolmogorov-Smirnov test (KS test and to find an intermediate effective size by interval evaluation. The SNPKS algorithm was implemented in computer programs and applied to the real SNP data. The effective SNP size was estimated to be 38,200, 39,300, 38,000, and 38,700 in the human, chimpanzee, dog, and mouse genomes, respectively, and 39,100, 39,600, 39,200, and 42,200 in human intergenic, genic, intronic, and CpG island regions, respectively. Conclusion SNPKS is the first statistical method to estimate the effective SNP size. It runs efficiently and greatly outperforms the algorithm implemented in SNPNB. The application of SNPKS to the real SNP data revealed the similar small effective SNP size (38,000 – 42,200 in the human, chimpanzee, dog, and mouse genomes as well as in human genomic regions. The findings suggest strong influence of genetic factors across vertebrate genomes.

  16. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.

    Directory of Open Access Journals (Sweden)

    Yubo Hou

    Full Text Available The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10-transformed protein-coding gene number (Y' versus log(10-transformed genome size (X', genome size in kbp were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91. Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1% compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%. The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6 kbp contains 38,188 protein-coding (40,086 total genes and the largest (245x10(6 kbp 87,688 protein-coding (92,013 total genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.

  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. 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.

  19. Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

    Science.gov (United States)

    Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

    2007-08-29

    The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

  20. Transposable element distribution, abundance and role in genome size variation in the genus Oryza

    Directory of Open Access Journals (Sweden)

    Collura Kristi

    2007-08-01

    Full Text Available Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]. Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys account for a significant portion of the genome size variations present in the Oryza genus.

  1. Placental Size Is Associated Differentially With Postnatal Bone Size and Density

    Science.gov (United States)

    Holroyd, Christopher R; Osmond, Clive; Barker, David JP; Ring, Sue M; Lawlor, Debbie A; Tobias, Jon H; Smith, George Davey; Harvey, Nicholas C

    2016-01-01

    offspring bone development persist into older childhood, even during puberty, and that placental size is differentially related to bone size and volumetric density. © 2016 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research (ASBMR). PMID:26999363

  2. Survey of genome size in 28 hydrothermal vent species covering 10 families.

    Science.gov (United States)

    Bonnivard, Eric; Catrice, Olivier; Ravaux, Juliette; Brown, Spencer C; Higuet, Dominique

    2009-06-01

    Knowledge of genome size is a useful and necessary prerequisite for the development of many genomic resources. To better understand the origins and effects of DNA gains and losses among species, it is important to collect data from a broad taxonomic base, but also from particular ecosystems. Oceanic thermal vents are an interesting model to investigate genome size in very unstable environments. Here we provide data estimated by flow cytometry for 28 vent-living species among the most representative from different hydrothermal vents. We also report the genome size of closely related coastal decapods. Haploid C-values were compared with those previously reported for species from corresponding orders or infraorders. This is the first broad survey of 2C values in vent organisms. Contrary to expectations, it shows that certain hydrothermal vent species have particularly large genomes. The vent squat lobster Munidopsis recta has the largest genome yet reported for any anomuran: 2C=31.1 pg=30.4x10(9) bp. In several groups, such as Brachyura, Phyllodocida, and Veneroida, vent species have genomes that clearly rank at the high end of published values for each group. We also describe the highest DNA content yet recorded for the Brachyura (coastal crabs Xantho pilipes and Necora puber). Finally, analysis of genome size variation across populations revealed unexpected intraspecific variation in the vent shrimp Mirocaris fortunata that could not be attributed simply to ploidy changes.

  3. Reptiles: a group of transition in the evolution of genome size and of the nucleotypic effect.

    Science.gov (United States)

    Olmo, E

    2003-01-01

    A comparison between genome size and some phenotypic parameters, such as developmental length and metabolic rate, showed in reptiles a nucleotypic correlation similar to the one observed in birds and mammals. Indeed, like homeotherms, reptiles exhibit a highly significant, inverse correlation of genome size with metabolic rate but unlike amphibians, no relationship with developmental length. Several lines of evidence suggest that these nucleotypic correlations are influenced by body temperature, which also affects the guanine + cytosine nuclear percentage, and that they play an important role in the adaptation of these amniotes. However, the reptilian suborders exhibit differences in the quantitative and compositional characters of the genome that do not completely correspond to differences in the phenotypic parameters commonly involved in the nucleotypic effect. Thus, additional factors could have influenced genome size in this class. These data could be explained with the model of Hartl and Petrov, who observed an inverse correlation between genome size, non-coding portion of the genome and rate of DNA loss and hypothesized a strong role for different spectra of spontaneous insertions and deletions (indels) in the variations of genome size. It is thus reasonable to surmise that variations in the reptilian genome were initially influenced by different indels spectra typical of the diverse lineages, possibly related to different chromosome compartmentalizations. The consequent size increases or decreases would have influenced various morphological and functional cell parameters, and through these some phenotypic characteristics of the whole organism, especially the metabolic rate, very important for environmental adaptation and thus subject to natural selection. Through this "nucleotypic" bond, natural selection would also have controlled genome size variations.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  5. Identification of differential translation in genome wide studies.

    Science.gov (United States)

    Larsson, Ola; Sonenberg, Nahum; Nadon, Robert

    2010-12-14

    Regulation of gene expression through translational control is a fundamental mechanism implicated in many biological processes ranging from memory formation to innate immunity and whose dysregulation contributes to human diseases. Genome wide analyses of translational control strive to identify differential translation independent of cytosolic mRNA levels. For this reason, most studies measure genes' translation levels as log ratios (translation levels divided by corresponding cytosolic mRNA levels obtained in parallel). Counterintuitively, arising from a mathematical necessity, these log ratios tend to be highly correlated with the cytosolic mRNA levels. Accordingly, they do not effectively correct for cytosolic mRNA level and generate substantial numbers of biological false positives and false negatives. We show that analysis of partial variance, which produces estimates of translational activity that are independent of cytosolic mRNA levels, is a superior alternative. When combined with a variance shrinkage method for estimating error variance, analysis of partial variance has the additional benefit of having greater statistical power and identifying fewer genes as translationally regulated resulting merely from unrealistically low variance estimates rather than from large changes in translational activity. In contrast to log ratios, this formal analytical approach estimates translation effects in a statistically rigorous manner, eliminates the need for inefficient and error-prone heuristics, and produces results that agree with biological function. The method is applicable to datasets obtained from both the commonly used polysome microarray method and the sequencing-based ribosome profiling method.

  6. Economy, Speed and Size Matter: Evolutionary Forces Driving Nuclear Genome Miniaturization and Expansion

    OpenAIRE

    CAVALIER-SMITH, THOMAS

    2005-01-01

    • Background Nuclear genome size varies 300 000-fold, whereas transcriptome size varies merely 17-fold. In the largest genomes nearly all DNA is non-genic secondary DNA, mostly intergenic but also within introns. There is now compelling evidence that secondary DNA is functional, i.e. positively selected by organismal selection, not the purely neutral or ‘selfish’ outcome of mutation pressure. The skeletal DNA theory argued that nuclear volumes are genetically determined primarily by nuclear D...

  7. Larger Daphnia at lower temperature: a role for cell size and genome configuration?

    Science.gov (United States)

    Jalal, Marwa; Wojewodzic, Marcin W; Laane, Carl Morten M; Hessen, Dag O

    2013-09-01

    Experiments with Daphnia magna and Daphnia pulex raised at 10 and 20 °C yielded larger adult size at the lower temperature. This must reflect increased cell size, increased cell numbers, or a combination of both. As it is difficult to achieve good estimates on cell size in crustaceans, we, therefore, measured nucleus and genome size using flow cytometry at 10 and 20 °C. DNA was stained with propidium iodide, ethidium bromide, and DAPI. Both nucleus and genome size estimates were elevated at 10 °C compared with 20 °C, suggesting that larger body size at low temperature could partly be accredited to an enlarged nucleus and thus cell size. Confocal microscopy observations confirmed the staining properties of fluorochromes. As differences in nucleotide numbers in response of growth temperature within a life span is unlikely, these results seem accredited to changed DNA-fluorochrome binding properties, presumably reflecting increased DNA condensation at low temperature. This implies that genome size comparisons may be impacted by ambient temperature in ectotherms. It also suggests that temperature-induced structural changes in the genome could affect cell size and for some species even body size.

  8. Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs

    DEFF Research Database (Denmark)

    Chen, Mubo; Baumbach, Jan; Vandin, Fabio

    2016-01-01

    twin pairs to find evidence for such “programming” effects, but no significant results emerged. We further investigated this issue using a new computational approach: Instead of probing single genomic sites for significant alterations in epigenetic marks, we scan for differentially methylated genomic...... regions. Whole genome DNA methylation levels were measured in whole blood from 150 pairs of adult identical twins discordant for birth-weight. Intrapair differential DNA methylation was associated with qualitative (large or small) and quantitative (percentage) birth-weight discordance at each genomic site...

  9. Size-isolation of ultrasound-mediated phase change perfluorocarbon droplets using differential centrifugation.

    Science.gov (United States)

    Mercado, Karla P; Radhakrishnan, Kirthi; Stewart, Kyle; Snider, Lindsay; Ryan, Devin; Haworth, Kevin J

    2016-05-01

    Perfluorocarbon droplets that are capable of an ultrasound-mediated phase transition have applications in diagnostic and therapeutic ultrasound. Techniques to modify the droplet size distribution are of interest because of the size-dependent acoustic response of the droplets. Differential centrifugation has been used to isolate specific sizes of microbubbles. In this work, differential centrifugation was employed to isolate droplets with diameters between 1 and 3 μm and 2 and 5 μm from an initially polydisperse distribution. Further, an empirical model was developed for predicting the droplet size distribution following differential centrifugation and to facilitate the selection of centrifugation parameters for obtaining desired size distributions.

  10. Genome Size Is a Strong Predictor of Root Meristem Growth Rate

    Directory of Open Access Journals (Sweden)

    Adam Gruner

    2010-01-01

    Full Text Available Variation in genome size (GS has been linked to several facets of the plant phenotype. Recently it was shown that GS is significantly correlated with cell size and the duration of the cell cycle. Here we test the hypothesis that GS might also be a predictor of apical root meristem growth rate (RMGR. We studied eight species of eudicots with varying GS using time-lapse microscopic image analysis. A significant negative exponential relationship was observed between GS and RMGR. Our results show significantly decreased RMGR for large genome species. This relationship represents a significant consequence of GS expansion in plants and may partly explain why genome sizes tend to be small in eudicots. Interestingly, parasitic plants, which do not rely on root growth as much, often have large genomes.

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

    Science.gov (United States)

    Li, Dirson Jian; Zhang, Shengli

    2010-02-05

    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.

  12. Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality

    Science.gov (United States)

    Pantrang, Madhulatha; Stahl, Buffy; Briska, Adam M.; Stemper, Mary E.; Wagner, Trevor K.; Zentz, Emily B.; Callister, Steven M.; Lovrich, Steven D.; Henkhaus, John K.; Dykes, Colin W.

    2012-01-01

    Despite being a clonal pathogen, Staphylococcus aureus continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette mec (SCCmec) by horizontal gene transfer from other staphylococci. The potential virulence of a S. aureus strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a high-resolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant S. aureus (MRSA) could be used to predict the presence of methicillin resistance, SCCmec type, and Panton-Valentine leukocidin (PVL)-producing genes on an S. aureus genome. We determined the WGMs of 47 diverse clinical isolates of S. aureus, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCCmec types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive S. aureus based on the presence or absence of the SCCmec motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of mecA, SCCmec types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype S. aureus but also to

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

    Science.gov (United States)

    Roth, Gerhard; Walkowiak, Wolfgang

    2015-08-10

    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.

  14. Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis.

    Science.gov (United States)

    Zedek, František; Smerda, Jakub; Smarda, Petr; Bureš, Petr

    2010-11-30

    Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis. Using flow cytometry, we measured the genome sizes of members of the genus Eleocharis (Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in Eleocharis. We analyzed PCR-amplified sequences of various reverse transcriptases of the LTR retrotransposons Ty1-copia and Ty3-gypsy (762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-copia and Ty3-gypsy within the genomes of the analyzed species. We detected an increasing density of Ty1-copia elements in evolutionarily younger Eleocharis species and found a positive correlation between Ty1-copia densities and C/n-values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-copia sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-copia. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later

  15. Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species.

    Science.gov (United States)

    Kanzi, Aquillah Mumo; Wingfield, Brenda Diana; Steenkamp, Emma Theodora; Naidoo, Sanushka; van der Merwe, Nicolaas Albertus

    2016-01-01

    In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.

  16. 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.

  17. 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.

  18. Genome Size and GC Content Evolution of Festuca: Ancestral Expansion and Subsequent Reduction

    Science.gov (United States)

    Šmarda, Petr; Bureš, Petr; Horová, Lucie; Foggi, Bruno; Rossi, Graziano

    2008-01-01

    Background and Aims Plant evolution is well known to be frequently associated with remarkable changes in genome size and composition; however, the knowledge of long-term evolutionary dynamics of these processes still remains very limited. Here a study is made of the fine dynamics of quantitative genome evolution in Festuca (fescue), the largest genus in Poaceae (grasses). Methods Using flow cytometry (PI, DAPI), measurements were made of DNA content (2C-value), monoploid genome size (Cx-value), average chromosome size (C/n-value) and cytosine + guanine (GC) content of 101 Festuca taxa and 14 of their close relatives. The results were compared with the existing phylogeny based on ITS and trnL-F sequences. Key Results The divergence of the fescue lineage from related Poeae was predated by about a 2-fold monoploid genome and chromosome size enlargement, and apparent GC content enrichment. The backward reduction of these parameters, running parallel in both main evolutionary lineages of fine-leaved and broad-leaved fescues, appears to diverge among the existing species groups. The most dramatic reductions are associated with the most recently and rapidly evolving groups which, in combination with recent intraspecific genome size variability, indicate that the reduction process is probably ongoing and evolutionarily young. This dynamics may be a consequence of GC-rich retrotransposon proliferation and removal. Polyploids derived from parents with a large genome size and high GC content (mostly allopolyploids) had smaller Cx- and C/n-values and only slightly deviated from parental GC content, whereas polyploids derived from parents with small genome and low GC content (mostly autopolyploids) generally had a markedly increased GC content and slightly higher Cx- and C/n-values. Conclusions The present study indicates the high potential of general quantitative characters of the genome for understanding the long-term processes of genome evolution, testing evolutionary

  19. Efficiency of genomic DNA extraction dependent on the size of magnetic nanoclusters

    Science.gov (United States)

    Cho, Hyun Ah; Hyun Min, Ji; Hua Wu, Jun; Woo Jang, Jin; Lim, Chae-Seung; Keun Kim, Young

    2014-05-01

    We report the efficiency of genomic DNA extraction as a function of particle size and quantity. For DNA extraction, we synthesized magnetic nanoclusters of various sizes and coated the surface of these magnetic nanoclusters with meso-2,3-dimercaptosuccinic acid. We showed that the nanoclusters had a tight particle size distribution and high crystallinity. Furthermore, we observed that the three types of magnetic nanoclusters studied exhibited ferrimagnetic behavior and that larger nanoclusters showed larger saturation magnetization values. The resultant efficiency of DNA extraction is inversely proportional to particle size in the range of nanoclusters tested, due to the fact that the surface-to-volume ratio decreases as particle size increases.

  20. GENOME SIZE DETERMINATION AND RAPD ANALYSIS OF FOUR EDIBLE AROIDS OF NORTH EAST INDIA

    Directory of Open Access Journals (Sweden)

    Jyoti P. Saikia1*, Bolin K. Konwar 2 and Susmita Singh3

    2010-10-01

    Full Text Available Four edible aroid species were selected for the study. The genomic DNA of the plants was isolated and estimated. A part of the genomic DNA was used for analysis using six different primers from Operon Technologies, USA. The genome size determined for the aroids is in the order of Colocasia esculenta> Xanthosoma caracu> Xanthosoma sagittifolium > Amorphophallus paeonifolius. Amorphophallus species was found to be 50% similar to both Xanthosoma caracu and Colocasia esculenta. The analysis will provide a ground for exploring the vast diversified aroid population of the region.

  1. 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.

  2. Chromosome Numbers and Genome Size Variation in Indian Species of Curcuma (Zingiberaceae)

    Science.gov (United States)

    Leong-Škorničková, Jana; Šída, Otakar; Jarolímová, Vlasta; Sabu, Mamyil; Fér, Tomáš; Trávníček, Pavel; Suda, Jan

    2007-01-01

    Background and Aims Genome size and chromosome numbers are important cytological characters that significantly influence various organismal traits. However, geographical representation of these data is seriously unbalanced, with tropical and subtropical regions being largely neglected. In the present study, an investigation was made of chromosomal and genome size variation in the majority of Curcuma species from the Indian subcontinent, and an assessment was made of the value of these data for taxonomic purposes. Methods Genome size of 161 homogeneously cultivated plant samples classified into 51 taxonomic entities was determined by propidium iodide flow cytometry. Chromosome numbers were counted in actively growing root tips using conventional rapid squash techniques. Key Results Six different chromosome counts (2n = 22, 42, 63, >70, 77 and 105) were found, the last two representing new generic records. The 2C-values varied from 1·66 pg in C. vamana to 4·76 pg in C. oligantha, representing a 2·87-fold range. Three groups of taxa with significantly different homoploid genome sizes (Cx-values) and distinct geographical distribution were identified. Five species exhibited intraspecific variation in nuclear DNA content, reaching up to 15·1 % in cultivated C. longa. Chromosome counts and genome sizes of three Curcuma-like species (Hitchenia caulina, Kaempferia scaposa and Paracautleya bhatii) corresponded well with typical hexaploid (2n = 6x = 42) Curcuma spp. Conclusions The basic chromosome number in the majority of Indian taxa (belonging to subgenus Curcuma) is x = 7; published counts correspond to 6x, 9x, 11x, 12x and 15x ploidy levels. Only a few species-specific C-values were found, but karyological and/or flow cytometric data may support taxonomic decisions in some species alliances with morphological similarities. Close evolutionary relationships among some cytotypes are suggested based on the similarity in homoploid genome sizes and geographical grouping

  3. Intra-specific variation in genome size in maize: cytological and phenotypic correlates

    Science.gov (United States)

    Realini, María Florencia; Poggio, Lidia; Cámara-Hernández, Julián; González, Graciela Esther

    2016-01-01

    Genome size variation accompanies the diversification and evolution of many plant species. Relationships between DNA amount and phenotypic and cytological characteristics form the basis of most hypotheses that ascribe a biological role to genome size. The goal of the present research was to investigate the intra-specific variation in the DNA content in maize populations from Northeastern Argentina and further explore the relationship between genome size and the phenotypic traits seed weight and length of the vegetative cycle. Moreover, cytological parameters such as the percentage of heterochromatin as well as the number, position and sequence composition of knobs were analysed and their relationships with 2C DNA values were explored. The populations analysed presented significant differences in 2C DNA amount, from 4.62 to 6.29 pg, representing 36.15 % of the inter-populational variation. Moreover, intra-populational genome size variation was found, varying from 1.08 to 1.63-fold. The variation in the percentage of knob heterochromatin as well as in the number, chromosome position and sequence composition of the knobs was detected among and within the populations. Although a positive relationship between genome size and the percentage of heterochromatin was observed, a significant correlation was not found. This confirms that other non-coding repetitive DNA sequences are contributing to the genome size variation. A positive relationship between DNA amount and the seed weight has been reported in a large number of species, this relationship was not found in the populations studied here. The length of the vegetative cycle showed a positive correlation with the percentage of heterochromatin. This result allowed attributing an adaptive effect to heterochromatin since the length of this cycle would be optimized via selection for an appropriate percentage of heterochromatin. PMID:26644343

  4. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits.

    Science.gov (United States)

    Szulkin, M; Gagnaire, P-A; Bierne, N; Charmantier, A

    2016-01-01

    Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.

  5. Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

    Science.gov (United States)

    Carreras, Carlos; Ordóñez, Víctor; Zane, Lorenzo; Kruschel, Claudia; Nasto, Ina; Macpherson, Enrique; Pascual, Marta

    2017-01-01

    The assessment of the genetic structuring of biodiversity is crucial for management and conservation. For species with large effective population sizes a low number of markers may fail to identify population structure. A solution of this shortcoming can be high-throughput sequencing that allows genotyping thousands of markers on a genome-wide approach while facilitating the detection of genetic structuring shaped by selection. We used Genotyping-by-Sequencing (GBS) on 176 individuals of the endemic East Atlantic peacock wrasse (Symphodus tinca), from 6 locations in the Adriatic and Ionian seas. We obtained a total of 4,155 polymorphic SNPs and we observed two strong barriers to gene flow. The first one differentiated Tremiti Islands, in the northwest, from all the other locations while the second one separated east and south-west localities. Outlier SNPs potentially under positive selection and neutral SNPs both showed similar patterns of structuring, although finer scale differentiation was unveiled with outlier loci. Our results reflect the complexity of population genetic structure and demonstrate that both habitat fragmentation and positive selection are on play. This complexity should be considered in biodiversity assessments of different taxa, including non-model yet ecologically relevant organisms. PMID:28262802

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

    Science.gov (United States)

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

    2015-08-04

    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.

  7. Genome Size Is a Strong Predictor of Root Meristem Growth Rate

    OpenAIRE

    Adam Gruner; Nathan Hoverter; Tylia Smith; Charles A. Knight

    2010-01-01

    Variation in genome size (GS) has been linked to several facets of the plant phenotype. Recently it was shown that GS is significantly correlated with cell size and the duration of the cell cycle. Here we test the hypothesis that GS might also be a predictor of apical root meristem growth rate (RMGR). We studied eight species of eudicots with varying GS using time-lapse microscopic image analysis. A significant negative exponential relationship was observed between GS and RMGR. Our results sh...

  8. Optimizing human embryonic stem cells differentiation efficiency by screening size-tunable homogenous embryoid bodies.

    Science.gov (United States)

    Moon, Sung-Hwan; Ju, Jongil; Park, Soon-Jung; Bae, Daekyeong; Chung, Hyung-Min; Lee, Sang-Hoon

    2014-07-01

    Human embryonic stem cells (hESCs) are generally induced to differentiate by forming spherical structures termed embryoid bodies (EBs) in the presence of soluble growth factors. hEBs are generated by suspending small clumps of hESC colonies; however, the resulting hEBs are heterogeneous because this method lacks the ability to control the number of cells in individual EBs. This heterogeneity affects factors that influence differentiation such as cell-cell contact and the diffusion of soluble factors, and consequently, the differentiation capacity of each EB varies. Here, we fabricated size-tunable concave microwells to control the physical environment, thereby regulating the size of EBs formed from single hESCs. Defined numbers of single hESCs were forced to aggregate and generate uniformly sized EBs with high fidelity, and the size of the EBs was controlled using concave microwells of different diameters. Differentiation patterns in H9- and CHA15-hESCs were affected by EB size in both the absence and presence of growth factors. By screening EB size in the presence of various BMP4 concentrations, a two-fold increase in endothelial cell differentiation was achieved. Because each hESC line has unique characteristics, the findings of this study demonstrate that concave microwells could be used to screen different EB sizes and growth factor concentrations to optimize differentiation for each hESC line.

  9. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

    DEFF Research Database (Denmark)

    Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam;

    2013-01-01

    Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced...... metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (genomes were assembled into complete or near-complete chromosomes....... Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06–1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than...

  10. 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.

  11. Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.

    Science.gov (United States)

    Galán-Vásquez, Edgardo; Sánchez-Osorio, Ismael; Martínez-Antonio, Agustino

    2016-01-01

    The description of transcriptional regulatory networks has been pivotal in the understanding of operating principles under which organisms respond and adapt to varying conditions. While the study of the topology and dynamics of these networks has been the subject of considerable work, the investigation of the evolution of their topology, as a result of the adaptation of organisms to different environmental conditions, has received little attention. In this work, we study the evolution of transcriptional regulatory networks in bacteria from a genome reduction perspective, which manifests itself as the loss of genes at different degrees. We used the transcriptional regulatory network of Escherichia coli as a reference to compare 113 smaller, phylogenetically-related γ-proteobacteria, including 19 genomes of symbionts. We found that the type of regulatory action exerted by transcription factors, as genomes get progressively smaller, correlates well with their degree of conservation, with dual regulators being more conserved than repressors and activators in conditions of extreme reduction. In addition, we found that the preponderant conservation of dual regulators might be due to their role as both global regulators and nucleoid-associated proteins. We summarize our results in a conceptual model of how each TF type is gradually lost as genomes become smaller and give a rationale for the order in which this phenomenon occurs.

  12. Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.

    Directory of Open Access Journals (Sweden)

    Edgardo Galán-Vásquez

    Full Text Available The description of transcriptional regulatory networks has been pivotal in the understanding of operating principles under which organisms respond and adapt to varying conditions. While the study of the topology and dynamics of these networks has been the subject of considerable work, the investigation of the evolution of their topology, as a result of the adaptation of organisms to different environmental conditions, has received little attention. In this work, we study the evolution of transcriptional regulatory networks in bacteria from a genome reduction perspective, which manifests itself as the loss of genes at different degrees. We used the transcriptional regulatory network of Escherichia coli as a reference to compare 113 smaller, phylogenetically-related γ-proteobacteria, including 19 genomes of symbionts. We found that the type of regulatory action exerted by transcription factors, as genomes get progressively smaller, correlates well with their degree of conservation, with dual regulators being more conserved than repressors and activators in conditions of extreme reduction. In addition, we found that the preponderant conservation of dual regulators might be due to their role as both global regulators and nucleoid-associated proteins. We summarize our results in a conceptual model of how each TF type is gradually lost as genomes become smaller and give a rationale for the order in which this phenomenon occurs.

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

    Directory of Open Access Journals (Sweden)

    Yun-peng Du

    2017-07-01

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

  14. Wage differentials by firm size: the efficiency wage test in a developing country

    National Research Council Canada - National Science Library

    Menezes, Tatiane Almeida de; Raposo, Isabel Pessoa de Arruda

    2014-01-01

    Using data from the Brazilian Labor Monthly Survey (PME/ IBGE) for the years of 2006 and 2007, the paper investigates if the wage differential by firm size in Brazil can be explained by the predictions of the Efficiency Wage Theory...

  15. Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population.

    Directory of Open Access Journals (Sweden)

    Silvia Teresa Rodríguez-Ramilo

    Full Text Available Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry or runs of homozygosity (inbreeding. The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

  16. Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population.

    Science.gov (United States)

    Rodríguez-Ramilo, Silvia Teresa; Fernández, Jesús; Toro, Miguel Angel; Hernández, Delfino; Villanueva, Beatriz

    2015-01-01

    Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

  17. Genome wide molecular analysis of minimally differentiated acute myeloid leukemia

    NARCIS (Netherlands)

    Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline

    2009-01-01

    Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other

  18. Genome wide molecular analysis of minimally differentiated acute myeloid leukemia

    NARCIS (Netherlands)

    Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline

    2009-01-01

    Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other criteri

  19. Aggregate Size Optimization in Microwells for Suspension-based Cardiac Differentiation of Human Pluripotent Stem Cells

    OpenAIRE

    Bauwens, Celine L.; Toms, Derek; Ungrin, Mark

    2016-01-01

    Cardiac differentiation of human pluripotent stems cells (hPSCs) is typically carried out in suspension cell aggregates. Conventional aggregate formation of hPSCs involves dissociating cell colonies into smaller clumps, with size control of the clumps crudely controlled by pipetting the cell suspension until the desired clump size is achieved. One of the main challenges of conventional aggregate-based cardiac differentiation of hPSCs is that culture heterogeneity and spatial disorganization l...

  20. Differential foraging preferences on seed size by rodents result in higher dispersal success of medium-sized seeds.

    Science.gov (United States)

    Cao, Lin; Wang, Zhenyu; Yan, Chuan; Chen, Jin; Guo, Cong; Zhang, Zhibin

    2016-11-01

    Rodent preference for scatter-hoarding large seeds has been widely considered to favor the evolution of large seeds. Previous studies supporting this conclusion were primarily based on observations at earlier stages of seed dispersal, or on a limited sample of successfully established seedlings. Because seed dispersal comprises multiple dispersal stages, we hypothesized that differential foraging preference on seed size by animal dispersers at different dispersal stages would ultimately result in medium-sized seeds having the highest dispersal success rates. In this study, by tracking a large number of seeds for 5 yr, we investigated the effects of seed size on seed fates from seed removal to seedling establishment of a dominant plant Pittosporopsis kerrii (Icacinaceae) dispersed by scatter-hoarding rodents in tropical forest in southwest China. We found that small seeds had a lower survival rate at the early dispersal stage where more small seeds were predated at seed stations and after removal; large seeds had a lower survival rate at the late dispersal stage, more large seeds were recovered, predated after being cached, or larder-hoarded. Medium-sized seeds experienced the highest dispersal success. Our study suggests that differential foraging preferences by scatter-hoarding rodents at different stages of seed dispersal could result in conflicting selective pressures on seed size and higher dispersal success of medium-sized seeds.

  1. Derivation of stochastic partial differential equations for size- and age-structured populations.

    Science.gov (United States)

    Allen, Edward J

    2009-01-01

    Stochastic partial differential equations (SPDEs) for size-structured and age- and size-structured populations are derived from basic principles, i.e. from the changes that occur in a small time interval. Discrete stochastic models of size-structured and age-structured populations are constructed, carefully taking into account the inherent randomness in births, deaths, and size changes. As the time interval decreases, the discrete stochastic models lead to systems of Itô stochastic differential equations. As the size and age intervals decrease, SPDEs are derived for size-structured and age- and size-structured populations. Comparisons between numerical solutions of the SPDEs and independently formulated Monte Carlo calculations support the accuracy of the derivations.

  2. Coconut genome size determined by flow cytometry: Tall versus Dwarf types.

    Science.gov (United States)

    Freitas Neto, M; Pereira, T N S; Geronimo, I G C; Azevedo, A O N; Ramos, S R R; Pereira, M G

    2016-02-11

    Coconuts (Cocos nucifera L.) are tropical palm trees that are classified into Tall and Dwarf types based on height, and both types are diploid (2n = 2x = 32 chromosomes). The reproduction mode is autogamous for Dwarf types and allogamous for Tall types. One hypothesis for the origin of the Dwarf coconut suggests that it is a Tall variant that resulted from either mutation or inbreeding, and differences in genome size between the two types would support this hypothesis. In this study, we estimated the genome sizes of 14 coconut accessions (eight Tall and six Dwarf types) using flow cytometry. Nuclei were extracted from leaf discs and stained with propidium iodide, and Pisum sativum (2C = 9.07 pg DNA) was used as an internal standard. Histograms with good resolution and low coefficients of variation (2.5 to 3.2%) were obtained. The 2C DNA content ranged from 5.72 to 5.48 pg for Tall accessions and from 5.58 to 5.52 pg for Dwarf accessions. The mean genome sizes for Tall and Dwarf specimens were 5.59 and 5.55 pg, respectively. Among all accessions, Rennel Island Tall had the highest mean DNA content (5.72 pg), whereas West African Tall had the lowest (5.48 pg). The mean coconut genome size (2C = 5.57 pg, corresponding to 2723.73 Mbp/haploid set) was classified as small. Only small differences in genome size existed among the coconut accessions, suggesting that the Dwarf type did not evolve from the Tall type.

  3. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.].

    Science.gov (United States)

    Scotti-Saintagne, Caroline; Mariette, Stéphanie; Porth, Ilga; Goicoechea, Pablo G; Barreneche, Teresa; Bodénès, Catherine; Burg, Kornel; Kremer, Antoine

    2004-11-01

    Interspecific differentiation values (G(ST)) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution of G(ST) values followed an L-shaped curve with most markers exhibiting low species differentiation (G(ST) 10% levels. Twelve percent of the loci exhibited significant G(ST) deviations to neutral expectations, suggesting that selection contributed to species divergence. Coding regions expressed higher differentiation than noncoding regions. Among the 389 markers, 158 could be mapped on the 12 linkage groups of the existing Q. robur genetic map. Outlier loci with large G(ST) values were distributed over 9 linkage groups. One cluster of three outlier loci was found within 0.51 cM; but significant autocorrelation of G(ST) was observed at distances <2 cM. The size and distribution of genomic regions involved in species divergence are discussed in reference to hitchhiking effects and disruptive selection.

  4. 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

    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...... of variance explained by genotyped SNPs, CD and SZ have a broadly dissimilar genetic architecture, due to differing mean effect size and proportion of non-null loci....

  5. Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis.

    Science.gov (United States)

    Makapedua, Daisy Monica; Barucca, Marco; Forconi, Mariko; Antonucci, Niki; Bizzaro, Davide; Amici, Adolfo; Carradori, Maria Rita; Olmo, Ettore; Canapa, Adriana

    2011-09-01

    The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.

  6. Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.

    Science.gov (United States)

    Sheehan, Sara; Harris, Kelley; Song, Yun S

    2013-07-01

    Throughout history, the population size of modern humans has varied considerably due to changes in environment, culture, and technology. More accurate estimates of population size changes, and when they occurred, should provide a clearer picture of human colonization history and help remove confounding effects from natural selection inference. Demography influences the pattern of genetic variation in a population, and thus genomic data of multiple individuals sampled from one or more present-day populations contain valuable information about the past demographic history. Recently, Li and Durbin developed a coalescent-based hidden Markov model, called the pairwise sequentially Markovian coalescent (PSMC), for a pair of chromosomes (or one diploid individual) to estimate past population sizes. This is an efficient, useful approach, but its accuracy in the very recent past is hampered by the fact that, because of the small sample size, only few coalescence events occur in that period. Multiple genomes from the same population contain more information about the recent past, but are also more computationally challenging to study jointly in a coalescent framework. Here, we present a new coalescent-based method that can efficiently infer population size changes from multiple genomes, providing access to a new store of information about the recent past. Our work generalizes the recently developed sequentially Markov conditional sampling distribution framework, which provides an accurate approximation of the probability of observing a newly sampled haplotype given a set of previously sampled haplotypes. Simulation results demonstrate that we can accurately reconstruct the true population histories, with a significant improvement over the PSMC in the recent past. We apply our method, called diCal, to the genomes of multiple human individuals of European and African ancestry to obtain a detailed population size change history during recent times.

  7. 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.

  8. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

    DEFF Research Database (Denmark)

    Petersen, Gitte; Cuenca, Argelia; Zervas, Athanasios

    2017-01-01

    The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes ...... mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus....

  9. Genomic insights into hybridization in a localized region of sympatr y between pewee sister species (Contopus sordidulus × C. virens) and their chromosomal patterns of differentiation

    Institute of Scientific and Technical Information of China (English)

    Joseph D Manthey; and Mark B Robbins

    2016-01-01

    Background: The Great Plains of the United States includes a large number of hybrid and contact zones between bird species. The amount of gene lfow between sister species in these zones ranges from very rare hybridization events to widespread and prevalent introgression. Some of these avian systems have been studied extensively, while others have been indeterminate of whether hybridization exists in areas of sympatry. Using genomic-level approaches allows investigation of genomic patterns of hybridization and gene lfow between species—or lack thereof. Methods: We investigated a narrow zone of sympatry in Nebraska, USA between pewee species (Contopus sordidu-lus and C. virens), for which no hybridization has been conifrmed. We used thousands of single nucleotide polymor-phisms to identify potential hybridization and investigate genomic patterns of differentiation between these two species. Results: We found evidence of multiple hybrid individuals in the contact zone. Little genomic variation was ifxed between species, but a large proportion had differentiated allele frequencies between species. There was a positive relationship between genetic differentiation and chromosome size. Conclusions: We provided the ifrst conclusive evidence of hybridization between C. sordidulus and C. virens, in a region where secondary contact likely occurred due to human disturbance and habitat modiifcation. The genomic patterns of differentiation affrm that these species split in the relatively recent past. Finally, the relationship of chro-mosome size and genetic differentiation may have resulted from differential rates of chromosomal recombination in songbirds and genetic differentiation between species largely due to genetic drift (possibly in concert with selection).

  10. Wage differentials by firm size: the efficiency wage test in a developing country

    Directory of Open Access Journals (Sweden)

    Tatiane Almeida de Menezes

    2014-03-01

    Full Text Available Using data from the Brazilian Labor Monthly Survey (PME/ IBGE for the years of 2006 and 2007, the paper investigates if the wage differential by firm size in Brazil can be explained by the predictions of the Efficiency Wage Theory. It is adopted a Switching Regression Model to estimate if large size companies pay a higher wage premium for dispended labor effort, as compared to smaller enterprises. The results prove the EW predictions since they evidence positive relationships between wages and labor effort, schooling and longer job duration. However, such findings are not sufficient to explain the existence of wage differentials by firm size in the Brazilian labor market.

  11. Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium

    Science.gov (United States)

    Iskandar, Christelle F.; Borges, Frédéric; Taminiau, Bernard; Daube, Georges; Zagorec, Monique; Remenant, Benoît; Leisner, Jørgen J.; Hansen, Martin A.; Sørensen, Søren J.; Mangavel, Cécile; Cailliez-Grimal, Catherine; Revol-Junelles, Anne-Marie

    2017-01-01

    Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium. PMID:28337181

  12. Genome-wide transcriptional profiling reveals molecular signatures of secondary xylem differentiation in Populus tomentosa.

    Science.gov (United States)

    Yang, X H; Li, X G; Li, B L; Zhang, D Q

    2014-11-11

    Wood formation occurs via cell division, primary cell wall and secondary wall formation, and programmed cell death in the vascular cambium. Transcriptional profiling of secondary xylem differentiation is essential for understanding the molecular mechanisms underlying wood formation. Differential gene expression in secondary xylem differentiation of Populus has been previously investigated using cDNA microarray analysis. However, little is known about the molecular mechanisms from a genome-wide perspective. In this study, the Affymetrix poplar genome chips containing 61,413 probes were used to investigate the changes in the transcriptome during secondary xylem differentiation in Chinese white poplar (Populus tomentosa). Two xylem tissues (newly formed and lignified) were sampled for genome-wide transcriptional profiling. In total, 6843 genes (~11%) were identified with differential expression in the two xylem tissues. Many genes involved in cell division, primary wall modification, and cellulose synthesis were preferentially expressed in the newly formed xylem. In contrast, many genes, including 4-coumarate:cinnamate-4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and caffeoyl CoA 3-O-methyltransferase (CCoAOMT), associated with lignin biosynthesis were more transcribed in the lignified xylem. The two xylem tissues also showed differential expression of genes related to various hormones; thus, the secondary xylem differentiation could be regulated by hormone signaling. Furthermore, many transcription factor genes were preferentially expressed in the lignified xylem, suggesting that wood lignification involves extensive transcription regulation. The genome-wide transcriptional profiling of secondary xylem differentiation could provide additional insights into the molecular basis of wood formation in poplar species.

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

    Directory of Open Access Journals (Sweden)

    Magdalena Anna Dąbrowska

    2015-07-01

    Full Text Available Despite long-term research, the aquatic genus Nymphaea still possesses major taxonomic challenges. High phenotypic plasticity and possible interspecific hybridization often make it impossible to identify individual specimens. The main aim of this study was to assess phenotypic variation in Nymphaea taxa sampled over a wide area of Eastern Europe and temperate Asia. Samples were identified based on species-specific genome sizes and diagnostic morphological characters for each taxon were then selected. A total of 353 specimens from 32 populations in Poland, Russia and Ukraine were studied, with nine biometric traits being examined. Although some specimens morphologically matched N. ×borealis (a hybrid between N. alba and N. candida according to published determination keys, only one hybrid individual was revealed based on genome size data. Other specimens with intermediate morphology possessed genome size corresponding to N. alba, N. candida or N. tetragona. This indicates that natural hybridization between N. alba and N. candida is not as frequent as previously suggested. Our results also revealed a considerably higher variation in the studied morphological traits (especially the quantitative ones in N. alba and N. candida than reported in the literature. A determination key for the investigated Nymphaea species is provided, based on taxonomically-informative morphological characters identified in our study.

  14. Flow cytometric analysis using SYBR Green I for genome size estimation in coffee.

    Science.gov (United States)

    Ronildo Clarindo, Wellington; Roberto Carvalho, Carlos

    2011-02-01

    Plant genome size has been measured by flow cytometry using propidium iodide as a dye for nuclear DNA staining. However, some authors have reported the occurrence of genome size estimation errors, especially in plants rich in secondary metabolites, such as the coffee tree. In this context, we tested an alternative cytometric protocol using the SYBR Green I as a fluorochrome for stoichiometrically staining nuclear double-stranded DNA in Coffea canephora (2x) and Coffea arabica (4x). The results showed that the respective mean genome size measured from nuclei stained with SYBR Green I and propidium iodide was statistically identical. However, the G(0)/G(1) peaks of nuclei stained with SYBR Green I exhibited lower coefficient variations (1.57-2.85%) compared to those stained with propidium iodide (2.75-4.80%). Coefficient variation statistical data suggest that SYBR Green I is adequate for stoichiometric nuclei staining using this methodology. Our results provide evidence that SYBR Green I can be used in flow cytometry measurements of plants, with the advantages of minimizing errors in nuclear DNA content quantification, staining relatively quicker, with high affinity, and being less mutagenic than propidium iodide.

  15. Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

    DEFF Research Database (Denmark)

    Nordlund, Jessica; Bäcklin, Christofer L; Wahlberg, Per

    2013-01-01

    BACKGROUND: Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic...

  16. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

    Science.gov (United States)

    Alverson, Andrew J; Wei, XiaoXin; Rice, Danny W; Stern, David B; Barry, Kerrie; Palmer, Jeffrey D

    2010-06-01

    The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.

  17. 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.

  18. A genome-wide methylation study on obesity Differential variability and differential methylation

    NARCIS (Netherlands)

    Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A.; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Huidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

    2013-01-01

    Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common

  19. A genome-wide methylation study on obesity Differential variability and differential methylation

    NARCIS (Netherlands)

    Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A.; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Huidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

    2013-01-01

    Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common

  20. 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.

  1. Plant regeneration through somatic embryogenesis and genome size analysis of Coriandrum sativum L.

    Science.gov (United States)

    Ali, Muzamil; Mujib, A; Tonk, Dipti; Zafar, Nadia

    2017-01-01

    In the present study, an improved plant regeneration protocol via primary and secondary somatic embryogenesis was established in two Co-1 and Rajendra Swathi (RS) varieties of Coriandrum sativum L. Callus was induced from root explants on 2, 4-D (0.5-2.0 mg/l) supplemented MS. The addition of BA (0.2 mg/l) improved callus induction and proliferation response significantly. The maximum callus induction frequency was on 1.0 mg/l 2, 4-D and 0.2 mg/l BA added MS medium (77.5 % in Co-1 and 72.3 % in RS). The callus transformed into embryogenic callus on 2, 4-D added MS with maximum embryogenic frequency was on 1.0 mg/l. The granular embryogenic callus differentiated into globular embryos on induction medium, which later progressed to heart-, torpedo- and cotyledonary embryos on medium amended with 0.5 mg/l NAA and 0.2 mg/l BA. On an average, 2-3 secondary somatic embryos (SEs) were developed on mature primary SEs, which increased the total embryo numbers in culture. Histology and scanning electron microscopy (SEM) studies are presented for the origin, development of primary and secondary embryos in coriander. Later, these induced embryos converted into plantlets on 1.0 mg/l BA and 0.2 mg/l NAA-amended medium. The regenerated plantlets were cultured on 0.5 mg/l IBA added ½ MS for promotion of roots. The well-rooted plantlets were acclimatized and transferred to soil. The genetic stability of embryo-regenerated plant was analyzed by flow cytometry with optimized Pongamia pinnata as standard. The 2C DNA content of RS coriander variety was estimated to 5.1 pg; the primary and secondary somatic embryo-derived plants had 5.26 and 5.44 pg 2C DNA content, respectively. The regenerated plants were genetically stable, genome size similar to seed-germinated coriander plants.

  2. Island selection on mammalian life-histories: genetic differentiation in offspring size

    Directory of Open Access Journals (Sweden)

    Saunanen Raimo

    2008-10-01

    Full Text Available Abstract Background Since Darwin's pioneering work, evolutionary changes in isolated island populations of vertebrates have continued to provide the strongest evidence for the theory of natural selection. Besides macro-evolutionary changes, micro-evolutionary changes and the relative importance of natural selection vs. genetic drift are under intense investigation. Our study focuses on the genetic differentiation in morphological and life-history traits in insular populations of a small mammal the bank vole Myodes glareolus. Results Our results do not support the earlier findings for larger adult size or lower reproductive effort in insular populations of small mammals. However, the individuals living on islands produced larger offspring than individuals living on the mainland. Genetic differentiation in offspring size was further confirmed by the analyses of quantitative genetics in lab. In insular populations, genetic differentiation in offspring size simultaneously decreases the additive genetic variation (VA for that trait. Furthermore, our analyses of differentiation in neutral marker loci (Fst indicate that VA is less than expected on the basis of genetic drift alone, and thus, a lower VA in insular populations could be caused by natural selection. Conclusion We believe that different selection pressures (e.g. higher intraspecific competition in an insular environment might favour larger offspring size in small mammals. Island selection for larger offspring could be the preliminary mechanism in a process which could eventually lead to a smaller litter size and lower reproductive effort frequently found in insular vertebrates.

  3. Application of high-resolution genomic profiling in the differential diagnosis of liposarcoma.

    Science.gov (United States)

    Koczkowska, Magdalena; Lipska-Ziętkiewicz, Beata Stefania; Iliszko, Mariola; Ryś, Janusz; Miettinen, Markku; Lasota, Jerzy; Biernat, Wojciech; Harazin-Lechowska, Agnieszka; Kruczak, Anna; Limon, Janusz

    2017-01-01

    Rarity and heterogeneity of liposarcomas (LPS) make their diagnosis difficult even for sarcoma-experts pathologists. The molecular mechanism underlying the development and progression of liposarcomas (LPS) remains only partially known. In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes. Copy number aberrations (CNAs) were identified in 98% of WDLPS and DDLPS and in 95% of MLPS cases. The minimal common region of amplification at 12q14.1q21.1 was observed in 96% of WDLPS and DDLPS cases. Four regions of CNAs, including losses of chromosome 6, 11 and 13 and gains of chromosome 14 were classified as recurrent in DDLPS; at least one was identified in 74% of DDLPS tumors. The DDLPS-associated losses were much more common in tumors with increased genomic complexity. In MLPS, the most frequent CNAs were losses of chromosome 6 (40%) and gains of chromosome 1 (30%), with the minimal overlapping regions 6q14.1q22.31 and 1q25.1q32.2, respectively. Our findings show that the application of array-CGH allows to delineate clearly the genomic profiles of WDLPS, DDLPS and MLPS that reflect biological differences between these tumors. Although CNAs varied widely, the subtypes of tumors have characteristic genomic profiles that could facilitate the differential diagnosis of LPS subtypes, especially between WDLPS and DDLPS.

  4. Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub

    Science.gov (United States)

    Mastretta-Yanes, Alicia; Zamudio, Sergio; Jorgensen, Tove H.; Arrigo, Nils; Alvarez, Nadir; Piñero, Daniel; Emerson, Brent C.

    2014-01-01

    Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species. PMID:25223767

  5. Power and Sample Size Calculations for Logistic Regression Tests for Differential Item Functioning

    Science.gov (United States)

    Li, Zhushan

    2014-01-01

    Logistic regression is a popular method for detecting uniform and nonuniform differential item functioning (DIF) effects. Theoretical formulas for the power and sample size calculations are derived for likelihood ratio tests and Wald tests based on the asymptotic distribution of the maximum likelihood estimators for the logistic regression model.…

  6. Differentiation of human embryonic stem cells into pancreatic endoderm in patterned size-controlled clusters.

    Science.gov (United States)

    Van Hoof, Dennis; Mendelsohn, Adam D; Seerke, Rina; Desai, Tejal A; German, Michael S

    2011-05-01

    Pancreatic β-cells function optimally when clustered in islet-like structures. However, nutrient and oxygen deprivation limits the viability of cells at the core of excessively large clusters. Hence, production of functional β-cells from human embryonic stem cells (hESCs) for patients with diabetes would benefit from the growth and differentiation of these cells in size-controlled aggregates. In this study, we controlled cluster size by seeding hESCs onto glass cover slips patterned by the covalent microcontact-printing of laminin in circular patches of 120 μm in diameter. These were used as substrates to grow and differentiate hESCs first into SOX17-positive/SOX7-negative definitive endoderm, after which many clusters released and formed uniformly sized three-dimensional clusters. Both released clusters and those that remained attached differentiated into HNF1β-positive primitive gut tube-like cells with high efficiency. Further differentiation yielded pancreatic endoderm-like cells that co-expressed PDX1 and NKX6.1. Controlling aggregate size allows efficient production of uniformly-clustered pancreatic endocrine precursors for in vivo engraftment or further in vitro maturation.

  7. Power and Sample Size Calculations for Logistic Regression Tests for Differential Item Functioning

    Science.gov (United States)

    Li, Zhushan

    2014-01-01

    Logistic regression is a popular method for detecting uniform and nonuniform differential item functioning (DIF) effects. Theoretical formulas for the power and sample size calculations are derived for likelihood ratio tests and Wald tests based on the asymptotic distribution of the maximum likelihood estimators for the logistic regression model.…

  8. Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes

    Science.gov (United States)

    Parker, Stephen C. J.; Gartner, Jared; Cardenas-Navia, Isabel; Wei, Xiaomu; Ozel Abaan, Hatice; Ajay, Subramanian S.; Hansen, Nancy F.; Song, Lingyun; Bhanot, Umesh K.; Killian, J. Keith; Gindin, Yevgeniy; Walker, Robert L.; Meltzer, Paul S.; Mullikin, James C.; Furey, Terrence S.; Crawford, Gregory E.; Rosenberg, Steven A.; Samuels, Yardena; Margulies, Elliott H.

    2012-01-01

    Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined. In order to establish a system to test the functional importance of non-coding somatic variants in cancer, we created a low-passage cell culture of a metastatic melanoma tumor sample. As a foundation for interpreting functional assays, we performed whole-genome sequencing and analysis of this cell culture, the metastatic tumor from which it was derived, and the patient-matched normal genomes. When comparing somatic mutations identified in the cell culture and tissue genomes, we observe concordance at the majority of single nucleotide variants, whereas copy number changes are more variable. To understand the functional impact of non-coding somatic variation, we leveraged functional data generated by the ENCODE Project Consortium. We analyzed regulatory regions derived from multiple different cell types and found that melanocyte-specific regions are among the most depleted for somatic mutation accumulation. Significant depletion in other cell types suggests the metastatic melanoma cells de-differentiated to a more basal regulatory state. Experimental identification of genome-wide regulatory sites in two different melanoma samples supports this observation. Together, these results show that mutation accumulation in metastatic melanoma is nonrandom across the genome and that a de-differentiated regulatory architecture is common among different samples. Our findings enable identification of the underlying genetic components of melanoma and define the differences between a tissue-derived tumor sample and the cell culture created from it. Such information helps establish a broader mechanistic understanding of the linkage between non-coding genomic variations and the cellular evolution of cancer

  9. Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.

    Directory of Open Access Journals (Sweden)

    Stephen C J Parker

    Full Text Available Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined. In order to establish a system to test the functional importance of non-coding somatic variants in cancer, we created a low-passage cell culture of a metastatic melanoma tumor sample. As a foundation for interpreting functional assays, we performed whole-genome sequencing and analysis of this cell culture, the metastatic tumor from which it was derived, and the patient-matched normal genomes. When comparing somatic mutations identified in the cell culture and tissue genomes, we observe concordance at the majority of single nucleotide variants, whereas copy number changes are more variable. To understand the functional impact of non-coding somatic variation, we leveraged functional data generated by the ENCODE Project Consortium. We analyzed regulatory regions derived from multiple different cell types and found that melanocyte-specific regions are among the most depleted for somatic mutation accumulation. Significant depletion in other cell types suggests the metastatic melanoma cells de-differentiated to a more basal regulatory state. Experimental identification of genome-wide regulatory sites in two different melanoma samples supports this observation. Together, these results show that mutation accumulation in metastatic melanoma is nonrandom across the genome and that a de-differentiated regulatory architecture is common among different samples. Our findings enable identification of the underlying genetic components of melanoma and define the differences between a tissue-derived tumor sample and the cell culture created from it. Such information helps establish a broader mechanistic understanding of the linkage between non-coding genomic variations and the cellular

  10. Cytogenetics of Aspidogaster limacoides (Trematoda, Aspidogastrea): karyotype, spermatocyte division, and genome size.

    Science.gov (United States)

    Bombarová, Marta; Špakulová, Marta; Kello, Martin; Nguyen, Petr; Bazsalovicsová, Eva; Králová-Hromadová, Ivica

    2015-04-01

    A detailed cytogenetic analysis of the aspidogastrean fluke Aspidogaster limacoides revealed a karyotype consisting of six medium-sized chromosome pairs. The first and the last pairs were two-armed while four remaining were one-armed; 2n = 12, n = 1 m + 1 m - sm + 4a. Fluorescence in situ hybridization with 18S ribosomal DNA (rDNA) probe detected a single cluster of ribosomal genes (NOR) located in pericentromeric regions of the long arms of the third chromosome pair in a site of secondary constriction apparent in meiotic prophase, especially in diplotene. The silver nitrate staining showed only a single active NOR site on one of homologous chromosomes in the majority of spermatogonia and spermatocyte divisions. A course of meiosis corresponded to standard schemes. The nucleolus was apparent in early meiotic spermatocytes and disintegrated by the end of pachytene. For the first time in Aspidogastrea, the genome size was determined. The flow cytometry showed 1.21 pg DNA per haploid nucleus in A. limacoides which is in accordance with relatively low genome sizes of other flukes and tapeworms (Neodermata). A comparison of cytogenetic data available to date in the fluke sister groups Aspidogastrea and Digenea suggests that the lower chromosome number of Aspidogastrea might represent an ancestral condition and their split might have been accompanied by an increase in chromosome number via either chromosome fissions or paleopolyploidy.

  11. Population genomics of eusocial insects: the costs of a vertebrate-like effective population size.

    Science.gov (United States)

    Romiguier, J; Lourenco, J; Gayral, P; Faivre, N; Weinert, L A; Ravel, S; Ballenghien, M; Cahais, V; Bernard, A; Loire, E; Keller, L; Galtier, N

    2014-03-01

    The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes – a marker of the effective population size – in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  12. Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones.

    Science.gov (United States)

    Harrison, Richard G; Larson, Erica L

    2016-06-01

    Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genomewide scale, and recent genome scans have focused on the presence of 'islands' of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the 'same' species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.

  13. Temperature and developmental responses of body and cell size in Drosophila; effects of polyploidy and genome configuration.

    Science.gov (United States)

    Jalal, Marwa; Andersen, Tom; Hessen, Dag O

    2015-07-01

    Increased adult body size in Drosophila raised at lower temperatures could be attributed both to an increase in the cell volume and cell number. It is not clear, however, whether increased cell size is related to (or even caused by) increased nuclear volume and genome size (or configuration). Experiments with Drosophila melanogaster stocks (Oregon-R and w1118) raised at 16, 22, 24, and 28°C resulted in larger adult body and wing size with lower temperature, while eye size was less affected. The increase in wing size reflected an increase in cell size in both males and females of both stocks. The nucleus size, genome size, and DNA condensation of adult flies, embryos, and Schneider 2 cells (S2 cells, of larval origin) were estimated by flow cytometry. In both adult flies and S2 cells, both nucleus size and DNA condensation varied with temperature, while DNA content appears to be constant. From 12% to 18% of the somatic cells were tetraploid (4C) and 2-5% were octoploid (8C), and for the Oregon strain we observed an increase in the fraction of polyploid cells with decreasing temperature. The observed increase in body size (and wing size) at low temperatures could partly be linked with the cell size and DNA condensation, while corresponding changes in the haploid genome size were not observed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Can adult and juvenile European rabbits be differentiated by their pellet sizes?

    Science.gov (United States)

    Delibes-Mateos, Miguel; Rouco, Carlos; Villafuerte, Rafael

    2009-03-01

    Recently, a new method for differentiating juvenile and adult rabbits based on faecal pellet size was published. According to this method, pellets >6 mm diameter are inferred to be deposited by adults, while those kittens. In this study, we designed a simple experiment to test the accuracy of this methodology. Twelve adult rabbits were housed in individual outdoor cages and their pellets were removed every day for 10 consecutive days. Pellets were separated using a sieve according to their size and counted. Results showed that adult rabbits produce pellets >6 mm diameter in the same proportion as those 6 mm, whereas others deposit mostly pellets <6 mm in size. Our findings demonstrate that pellet size is unsuitable for aging wild rabbits. Field biologists should therefore be cautious when employing the pellet size method of age determination in other wild animals in the absence of validating studies.

  15. 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

  16. 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.

  17. Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

    Directory of Open Access Journals (Sweden)

    Ahn Jong Hwa

    2011-01-01

    Full Text Available Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

  18. PPARgamma in adipocyte differentiation and metabolism--novel insights from genome-wide studies.

    Science.gov (United States)

    Siersbaek, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2010-08-04

    Adipocyte differentiation is controlled by a tightly regulated transcriptional cascade in which PPARgamma and members of the C/EBP family are key players. Here we review the roles of PPARgamma and C/EBPs in adipocyte differentiation with emphasis on the recently published genome-wide binding profiles for PPARgamma and C/EBPalpha. Interestingly, these analyses show that PPARgamma and C/EBPalpha binding sites are associated with most genes that are induced during adipogenesis suggesting direct activation of many more adipocyte genes than previously anticipated. Furthermore, an extensive overlap between the C/EBPalpha and PPARgamma cistromes indicate a hitherto unrecognized direct crosstalk between these transcription factors. As more genome-wide data emerge in the future, this crosstalk will likely be found to include several other adipogenic transcription factors. Copyright (c) 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  19. Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.

    Science.gov (United States)

    Uchino, Yoshihito; Miura, Takamasa; Hosoyama, Akira; Ohji, Shoko; Yamazoe, Atsushi; Ito, Masako; Takahata, Yoh; Suzuki, Ken-Ichiro; Fujita, Nobuyuki

    2015-01-01

    A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

  20. Cytogenetic evidences of genome rearrangement and differential epigenetic chromatin modification in the sea lamprey (Petromyzon marinus).

    Science.gov (United States)

    Covelo-Soto, Lara; Morán, Paloma; Pasantes, Juan J; Pérez-García, Concepción

    2014-12-01

    This work explores both the chromatin loss and the differential genome methylation in the sea lamprey (Petromyzon marinus) from a molecular cytogenetic point of view. Fluorescent in situ hybridization experiments on meiotic bivalents and mitotic chromosomes corroborate the chromatin loss previously observed during the development of the sea lamprey and demonstrate that the elimination affects not only to Germ1 sequences but also to the rpt200 satellite DNA and most part of the major ribosomal DNA present on the germinal line. 5-Methylcytosine immunolocation revealed that the GC-rich heterochromatin is highly methylated in the germ line but significantly less in somatic chromosomes. These findings not only support previous observations about genome rearrangements but also give new information about epigenetic changes in P. marinus. The key position of lampreys in the vertebrate phylogenetic tree makes them an interesting taxon to provide relevant information about genome evolution in vertebrates.

  1. Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage.

    Science.gov (United States)

    Vu, Giang T H; Cao, Hieu X; Reiss, Bernd; Schubert, Ingo

    2017-02-28

    In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate. We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution. Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome. Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.

  2. Molecular characterisation of the poorly differentiated and undifferentiated thyroid carcinomas using genome-wide approaches

    OpenAIRE

    Pita, Jaime Miguel Gomes, 1985-

    2013-01-01

    Tese de doutoramento, Bioquímica (Genética Molecular), Universidade de Lisboa, Faculdade de Ciências, 2013 Poorly differentiated (PDTC) and anaplastic thyroid carcinomas (ATC) are highly malignant tumours composed by dedifferentiated cells, for which current therapeutic options have been ineffective. In the present project, the molecular signatures and genetic alterations associated with these tumours were elucidated, by using genome-wide expression analysis as first assessment. The role ...

  3. One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome.

    Science.gov (United States)

    Jiménez-Mena, Belén; Tataru, Paula; Brøndum, Rasmus F; Sahana, Goutam; Guldbrandtsen, Bernt; Bataillon, Thomas

    2016-07-01

    Effective population size (Ne) is a central parameter in population and conservation genetics. It measures the magnitude of genetic drift, rates of accumulation of inbreeding in a population, and it conditions the efficacy of selection. It is often assumed that a single Ne can account for the evolution of genomes. However, recent work provides indirect evidence for heterogeneity in Ne throughout the genome. We study this by examining genome-wide diversity in the Danish Holstein cattle breed. Using the differences in allele frequencies over a single generation, we directly estimated Ne among autosomes and smaller windows within autosomes. We found statistically significant variation in Ne at both scales. However, no correlation was found between the detected regional variability in Ne, and proxies for the intensity of linked selection (local recombination rate, gene density), or the presence of either past strong selection or current artificial selection on traits of economic value. Our findings call for further caution regarding the wide applicability of the Ne concept for understanding quantitatively processes such as genetic drift and accumulation of consanguinity in both natural and managed populations.

  4. Optimizing k-mer size using a variant grid search to enhance de novo genome assembly

    Science.gov (United States)

    Cha, Soyeon; Bird, David McK

    2016-01-01

    Largely driven by huge reductions in per-base costs, sequencing nucleic acids has become a near-ubiquitous technique in laboratories performing biological and biomedical research. Most of the effort goes to re-sequencing, but assembly of de novogenerated, raw sequence reads into contigs that span as much of the genome as possible is central to many projects. Although truly complete coverage is not realistically attainable, maximizing the amount of sequence that can be correctly assembled into contigs contributes to coverage. Here we compare three commonly used assembly algorithms (ABySS, Velvet and SOAPdenovo2), and show that empirical optimization of k-mer values has a disproportionate influence on de novo assembly of a eukaryotic genome, the nematode parasite Meloidogynechitwoodi. Each assembler was challenged with about 40 million Iluumina II paired-end reads, and assemblies performed under a range of k-mer sizes. In each instance, the optimal k-mer was 127, although based on N50 values,ABySS was more efficient than the others. That the assembly was not spurious was established using the “Core Eukaryotic Gene Mapping Approach”, which indicated that 98.79% of the M. chitwoodi genome was accounted for by the assembly. Subsequent gene finding and annotation are consistent with this and suggest that k-mer optimization contributes to the robustness of assembly. PMID:28104957

  5. Size-dependent foraging gene expression and behavioral caste differentiation in Bombus ignitus

    Directory of Open Access Journals (Sweden)

    Yokoyama Jun

    2009-09-01

    Full Text Available Abstract Background In eusocial hymenopteran insects, foraging genes, members of the cGMP-dependent protein kinase family, are considered to contribute to division of labor through behavioral caste differentiation. However, the relationship between foraging gene expression and behavioral caste in honeybees is opposite to that observed in ants and wasps. In the previously examined eusocial Hymenoptera, workers behave as foragers or nurses depending on age. We reasoned that examination of a different system of behavioral caste determination might provide new insights into the relationship between foraging genes and division of labor, and accordingly focused on bumblebees, which exhibit size-dependent behavioral caste differentiation. We characterized a foraging gene (Bifor in bumblebees (Bombus ignitus and examined the relationship between Bifor expression and size-dependent behavioral caste differentiation. Findings A putative open reading frame of the Bifor gene was 2004 bp in length. It encoded 668 aa residues and showed high identity to orthologous genes in other hymenopterans (85.3-99.0%. As in ants and wasps, Bifor expression levels were higher in nurses than in foragers. Bifor expression was negatively correlated with individual body size even within the same behavioral castes (regression coefficient = -0.376, P P = 0.018, within foragers. Conclusion These findings indicate that Bifor expression is size dependent and support the idea that Bifor expression levels are related to behavioral caste differentiation in B. ignitus. Thus, the relationship between foraging gene expression and behavioral caste differentiation found in ants and wasps was identified in a different system of labor determination.

  6. 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.

  7. Convergent functional genomics of oligodendrocyte differentiation identifies multiple autoinhibitory signaling circuits.

    Science.gov (United States)

    Gobert, Rosanna Pescini; Joubert, Lara; Curchod, Marie-Laure; Salvat, Catherine; Foucault, Isabelle; Jorand-Lebrun, Catherine; Lamarine, Marc; Peixoto, Hélène; Vignaud, Chloé; Frémaux, Christèle; Jomotte, Thérèse; Françon, Bernard; Alliod, Chantal; Bernasconi, Lilia; Abderrahim, Hadi; Perrin, Dominique; Bombrun, Agnes; Zanoguera, Francisca; Rommel, Christian; Hooft van Huijsduijnen, Rob

    2009-03-01

    Inadequate remyelination of brain white matter lesions has been associated with a failure of oligodendrocyte precursors to differentiate into mature, myelin-producing cells. In order to better understand which genes play a critical role in oligodendrocyte differentiation, we performed time-dependent, genome-wide gene expression studies of mouse Oli-neu cells as they differentiate into process-forming and myelin basic protein-producing cells, following treatment with three different agents. Our data indicate that different inducers activate distinct pathways that ultimately converge into the completely differentiated state, where regulated gene sets overlap maximally. In order to also gain insight into the functional role of genes that are regulated in this process, we silenced 88 of these genes using small interfering RNA and identified multiple repressors of spontaneous differentiation of Oli-neu, most of which were confirmed in rat primary oligodendrocyte precursors cells. Among these repressors were CNP, a well-known myelin constituent, and three phosphatases, each known to negatively control mitogen-activated protein kinase cascades. We show that a novel inhibitor for one of the identified genes, dual-specificity phosphatase DUSP10/MKP5, was also capable of inducing oligodendrocyte differentiation in primary oligodendrocyte precursors. Oligodendrocytic differentiation feedback loops may therefore yield pharmacological targets to treat disease related to dysfunctional myelin deposition.

  8. Molecular phylogeny and genome size evolution of the genus Betula (Betulaceae).

    Science.gov (United States)

    Wang, Nian; McAllister, Hugh A; Bartlett, Paul R; Buggs, Richard J A

    2016-05-01

    Betula L. (birch) is a genus of approx. 60 species, subspecies or varieties with a wide distribution in the northern hemisphere, of ecological and economic importance. A new classification of Betula has recently been proposed based on morphological characters. This classification differs somewhat from previously published molecular phylogenies, which may be due to factors such as convergent evolution, hybridization, incomplete taxon sampling or misidentification of samples. While chromosome counts have been made for many species, few have had their genome size measured. The aim of this study is to produce a new phylogenetic and genome size analysis of the genus. Internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced for 76 Betula samples verified by taxonomic experts, representing approx. 60 taxa, of which approx. 24 taxa have not been included in previous phylogenetic analyses. A further 49 samples from other collections were also sequenced, and 108 ITS sequences were downloaded from GenBank. Phylogenetic trees were built for these sequences. The genome sizes of 103 accessions representing nearly all described species were estimated using flow cytometry. As expected for a gene tree of a genus where hybridization and allopolyploidy occur, the ITS tree shows clustering, but not resolved monophyly, for the morphological subgenera recently proposed. Most sections show some clustering, but species of the dwarf section Apterocaryon are unusually scattered. Betula corylifolia (subgenus Nipponobetula) unexpectedly clusters with species of subgenus Aspera Unexpected placements are also found for B. maximowicziana, B. bomiensis, B. nigra and B. grossa Biogeographical disjunctions were found within Betula between Europe and North America, and also disjunctions between North-east and South-west Asia. The 2C-values for Betula ranged from 0·88 to 5·33 pg, and polyploids are scattered widely throughout the ITS phylogeny. Species with large genomes

  9. Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in Angiosperms

    Directory of Open Access Journals (Sweden)

    Conchita eAlonso

    2015-01-01

    Full Text Available DNA cytosine methylation is a widespread epigenetic mechanism in eukaryotes, and plant genomes commonly are densely methylated. Genomic methylation can be associated with functional consequences such as mutational events, genomic instability or altered gene expression, but little is known on interspecific variation in global cytosine methylation in plants. In this paper, we compare global cytosine methylation estimates obtained by HPLC and use a phylogenetically-informed analytical approach to test for significance of evolutionary signatures of this trait across 54 angiosperm species in 25 families. We evaluate whether interspecific variation in global cytosine methylation is statistically related to phylogenetic distance and also whether it is evolutionarily correlated with genome size (C-value. Global cytosine methylation varied widely between species, ranging between 5.3% (Arabidopsis and 39.2% (Narcissus. Differences between species were related to their evolutionary trajectories, as denoted by the strong phylogenetic signal underlying interspecific variation. Global cytosine methylation and genome size were evolutionarily correlated, as revealed by the significant relationship between the corresponding phylogenetically independent contrasts. On average, a ten-fold increase in genome size entailed an increase of about 10% in global cytosine methylation. Results show that global cytosine methylation is an evolving trait in angiosperms whose evolutionary trajectory is significantly linked to changes in genome size, and suggest that the evolutionary implications of epigenetic mechanisms are likely to vary between plant lineages.

  10. Genome size variation in Corchorus olitorius (Malvaceae s.l.) and its correlation with elevation and phenotypic traits.

    Science.gov (United States)

    Benor, Solomon; Fuchs, Jörg; Blattner, Frank R

    2011-07-01

    In this study, we report genome size variations in Corchorus olitorius L. (Malvaceae s.l.), a crop species known for its morphological plasticity and broad geographical distribution, and Corchorus capsularis L., the second widely cultivated species in the genus. Flow cytometric analyses were conducted with several tissues and nuclei isolation buffers using 69 accessions of C. olitorius and 4 accessions of C. capsularis, representing different habitats and geographical origins. The mean 2C nuclear DNA content (± SD) of C. olitorius was estimated to be 0.918 ± 0.011 pg, with a minimum of 0.882 ± 0.004 pg, and a maximum of 0.942 ± 0.004 pg. All studied plant materials were found to be diploid with 2n = 14. The genome size is negatively correlated with days to flowering (r = -0.29, p genome size and growing elevation (r = 0.59, p genome sizes of C. olitorius and C. capsularis are much smaller, and therewith closer to that of rice. The relatively small genome sizes will be of general advantage for any efforts into genomics or sequencing approaches of these species.

  11. Phylogenetics and differentiation of Salmonella Newport lineages by whole genome sequencing.

    Directory of Open Access Journals (Sweden)

    Guojie Cao

    Full Text Available Salmonella Newport has ranked in the top three Salmonella serotypes associated with foodborne outbreaks from 1995 to 2011 in the United States. In the current study, we selected 26 S. Newport strains isolated from diverse sources and geographic locations and then conducted 454 shotgun pyrosequencing procedures to obtain 16-24 × coverage of high quality draft genomes for each strain. Comparative genomic analysis of 28 S. Newport strains (including 2 reference genomes and 15 outgroup genomes identified more than 140,000 informative SNPs. A resulting phylogenetic tree consisted of four sublineages and indicated that S. Newport had a clear geographic structure. Strains from Asia were divergent from those from the Americas. Our findings demonstrated that analysis using whole genome sequencing data resulted in a more accurate picture of phylogeny compared to that using single genes or small sets of genes. We selected loci around the mutS gene of S. Newport to differentiate distinct lineages, including those between invH and mutS genes at the 3' end of Salmonella Pathogenicity Island 1 (SPI-1, ste fimbrial operon, and Clustered, Regularly Interspaced, Short Palindromic Repeats (CRISPR associated-proteins (cas. These genes in the outgroup genomes held high similarity with either S. Newport Lineage II or III at the same loci. S. Newport Lineages II and III have different evolutionary histories in this region and our data demonstrated genetic flow and homologous recombination events around mutS. The findings suggested that S. Newport Lineages II and III diverged early in the serotype evolution and have evolved largely independently. Moreover, we identified genes that could delineate sublineages within the phylogenetic tree and that could be used as potential biomarkers for trace-back investigations during outbreaks. Thus, whole genome sequencing data enabled us to better understand the genetic background of pathogenicity and evolutionary history of S

  12. Genome-wide gene amplification during differentiation of neural progenitor cells in vitro.

    Science.gov (United States)

    Fischer, Ulrike; Keller, Andreas; Voss, Meike; Backes, Christina; Welter, Cornelius; Meese, Eckart

    2012-01-01

    DNA sequence amplification is a phenomenon that occurs predictably at defined stages during normal development in some organisms. Developmental gene amplification was first described in amphibians during gametogenesis and has not yet been described in humans. To date gene amplification in humans is a hallmark of many tumors. We used array-CGH (comparative genomic hybridization) and FISH (fluorescence in situ hybridization) to discover gene amplifications during in vitro differentiation of human neural progenitor cells. Here we report a complex gene amplification pattern two and five days after induction of differentiation of human neural progenitor cells. We identified several amplified genes in neural progenitor cells that are known to be amplified in malignant tumors. There is also a striking overlap of amplified chromosomal regions between differentiating neural progenitor cells and malignant tumor cells derived from astrocytes. Gene amplifications in normal human cells as physiological process has not been reported yet and may bear resemblance to developmental gene amplifications in amphibians and insects.

  13. Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae).

    Science.gov (United States)

    Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

    2015-01-01

    The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.

  14. A genome-wide screen indicates correlation between differentiation and expression of metabolism related genes.

    Science.gov (United States)

    Roy, Priti; Kumar, Brijesh; Shende, Akhilesh; Singh, Anupama; Meena, Anil; Ghosal, Ritika; Ranganathan, Madhav; Bandyopadhyay, Amitabha

    2013-01-01

    Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus) embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation.

  15. A genome-wide screen indicates correlation between differentiation and expression of metabolism related genes.

    Directory of Open Access Journals (Sweden)

    Priti Roy

    Full Text Available Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation.

  16. Tumor size interpretation for predicting cervical lymph node metastasis using a differentiated thyroid cancer risk model

    Science.gov (United States)

    Shi, Rong-liang; Qu, Ning; Yang, Shu-wen; Ma, Ben; Lu, Zhong-wu; Wen, Duo; Sun, Guo-hua; Wang, Yu; Ji, Qing-hai

    2016-01-01

    Lymph node metastasis (LNM) is common in differentiated thyroid cancer (DTC), but management of clinically negative DTC is controversial. This study evaluated primary tumor size as a predictor of LNM. Multivariate logistic regression analysis was used for DTC patients who were treated with surgery between 2002 and 2012 in the Surveillance, Epidemiology, and End Results (SEER) database, to determine the association of tumor size at 10 mm increments with LNM. A predictive model was then developed to estimate the risk of LNM in DTC, using tumor size and other clinicopathological characteristics identified from the multivariate analysis. We identified 80,565 eligible patients with DTC in the SEER database. Final histology confirmed 9,896 (12.3%) cases affected with N1a disease and 8,194 (10.2%) cases with N1b disease. After the patients were classified into subgroups by tumor size, we found that the percentages of male sex, white race, follicular histology, gross extrathyroidal extension, lateral lymph node metastasis, and distant metastasis gradually increased with size. In multivariate analysis, tumor size was a significant independent prognostic factor for LNM; in particular, the odds ratio for lateral lymph node metastasis continued to increase by size relative to a 1–10 mm baseline. The coefficient for tumor size in the LNM predictive model waŝ0.20, indicating extra change in log(odds ratio) for LNM as 0.2 per unit increment in size relative to baseline. In conclusion, larger tumors are likely to have aggressive features and metastasize to a cervical compartment. Multistratification by size could provide more precise estimates of the likelihood of LNM before surgery. PMID:27574443

  17. Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

    Directory of Open Access Journals (Sweden)

    Guojun Wu

    2017-02-01

    Full Text Available The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95 of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups, including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized.

  18. T-cell-specific deletion of Mof blocks their differentiation and results in genomic instability in mice.

    Science.gov (United States)

    Gupta, Arun; Hunt, Clayton R; Pandita, Raj K; Pae, Juhee; Komal, K; Singh, Mayank; Shay, Jerry W; Kumar, Rakesh; Ariizumi, Kiyoshi; Horikoshi, Nobuo; Hittelman, Walter N; Guha, Chandan; Ludwig, Thomas; Pandita, Tej K

    2013-05-01

    Ataxia telangiectasia patients develop lymphoid malignancies of both B- and T-cell origin. Similarly, ataxia telangiectasia mutated (Atm)-deficient mice exhibit severe defects in T-cell maturation and eventually develop thymomas. The function of ATM is known to be influenced by the mammalian orthologue of the Drosophila MOF (males absent on the first) gene. Here, we report the effect of T-cell-specific ablation of the mouse Mof (Mof) gene on leucocyte trafficking and survival. Conditional Mof(Flox/Flox) (Mof (F/F)) mice expressing Cre recombinase under control of the T-cell-specific Lck proximal promoter (Mof(F/F)/Lck-Cre(+)) display a marked reduction in thymus size compared with Mof(F/F)/Lck-Cre(-) mice. In contrast, the spleen size of Mof(F/F)/Lck-Cre(+) mice was increased compared with control Mof(F/F)/Lck-Cre(-) mice. The thymus of Mof(F/F)/Lck-Cre(+) mice contained significantly reduced T cells, whereas thymic B cells were elevated. Within the T-cell population, CD4(+)CD8(+) double-positive T-cell levels were reduced, whereas the immature CD4(-)CD8(-) double-negative (DN) population was elevated. Defective T-cell differentiation is also evident as an increased DN3 (CD44(-)CD25(+)) population, the cell stage during which T-cell receptor rearrangement takes place. The differentiation defect in T cells and reduced thymus size were not rescued in a p53-deficient background. Splenic B-cell distributions were similar between Mof(F/F)/Lck-Cre(+) and Mof(F/F)/Lck-Cre(-) mice except for an elevation of the κ light-chain population, suggestive of an abnormal clonal expansion. T cells from Mof(F/F)/Lck-Cre(+) mice did not respond to phytohaemagglutinin (PHA) stimulation, whereas LPS-stimulated B cells from Mof(F/F)/Lck-Cre(+) mice demonstrated spontaneous genomic instability. Mice with T-cell-specific loss of MOF had shorter lifespans and decreased survival following irradiation than did Mof(F/F)/Lck-Cre(-) mice. These observations suggest that Mof plays a critical

  19. Phenotypic consequences of polyploidy and genome size at the microevolutionary scale: a multivariate morphological approach.

    Science.gov (United States)

    Balao, Francisco; Herrera, Javier; Talavera, Salvador

    2011-10-01

    • Chromosomal duplications and increases in DNA amount have the potential to alter quantitative plant traits like flower number, plant stature or stomata size. This has been documented often across species, but information on whether such effects also occur within species (i.e. at the microevolutionary or population scale) is scarce. • We studied trait covariation associated with polyploidy and genome size (both monoploid and total) in 22 populations of Dianthus broteri s.l., a perennial herb with several cytotypes (2x, 4x, 6x and 12x) that do not coexist spatially. Principal component scores of organ size/number variations were assessed as correlates of polyploidy, and phylogenetic relatedness among populations was controlled using phylogenetic generalized least squares. • Polyploidy covaried with organ dimensions, causing multivariate characters to increase, remain unchanged, or decrease with DNA amount. Variations in monoploid DNA amount had detectable consequences on some phenotypic traits. According to the analyses, some traits would experience phenotypic selection, while others would not. • We show that polyploidy contributes to decouple variation among traits in D. broteri, and hypothesize that polyploids may experience an evolutionary advantage in this plant lineage, for example, if it helps to overcome the constraints imposed by trait integration.

  20. Incipient Genome Differentiation in Gossypium. III. Comparison of Chromosomes of G. HIRSUTUM and Asiatic Diploids Using Heterozygous Translocations.

    Science.gov (United States)

    Menzel, M Y; Hasenkampf, C A; Stewart, J M

    1982-01-01

    Hybrids between upland cotton (G. hirsutum, genome constitution 2A(h)D(h)) and either A-genome or D-genome diploid species exhibit 26 paired and 13 unpaired chromosomes at metaphase I. The A(h) and D(h) genomes are therefore considered homoeologous with those of the respective diploids. Previous studies, nevertheless, revealed a low level of ("incipient") differentiation between D(h) and various diploid D genomes. The diploid A genomes have been regarded as more closely homologous to A(h) on the basis of low preferential pairing and autotetraploid segregation ratios in allohexaploids.-The present study addressed the following questions: Are the diploid A genomes differentiated from A(h) in meiotic homology? If so, is the differentiation manifested equally by all 13 chromosomes or is it localized in certain chromosomes?-Three diploid A-genome lines representing G. herbaceum and G. arboreum were hybridized by in ovulo culture of embryos (1) with a standard line of G. hirsutum, which differs from G. herbaceum by two and from G. arboreum by three naturally occurring reciprocal translocations involving chromosomes 1-5, and (2) with six lines homozygous for experimental translocations involving chromosomes 6, 7, 10, 11, 12 and 13. Chiasma frequencies in hybrids were compared with those in appropriate G. hirsutum controls. In every comparison overall chiasma frequencies were slightly lower in the hybrids. Therefore A(h) appears to be differentiated from the diploid A genomes. No localized differentiation was detected in chromosomes marked by experimental translocations. The differentiation may be localized mainly in chromosomes 4 and 5.

  1. Differential wolf-pack-size persistence and the role of risk when hunting dangerous prey

    Science.gov (United States)

    Barber-Meyer, Shannon M.; Mech, L. David; Newton, Wesley E.; Borg, Bridget

    2016-01-01

    Risk to predators hunting dangerous prey is an emerging area of research and could account for possible persistent differences in gray wolf (Canis lupus) pack sizes. We documented significant differences in long-term wolf-pack-size averages and variation in the Superior National Forest (SNF), Denali National Park and Preserve, Yellowstone National Park, and Yukon, Canada (paccount for possible persistent differences in gray wolf (Canis lupus) pack sizes. We documented significant differences in long-term wolf-pack-size averages and variation in the Superior National Forest (SNF), Denali National Park and Preserve, Yellowstone National Park, and Yukon, Canada (p<0.01). The SNF differences could be related to the wolves’ risk when hunting primary prey, for those packs (N=3) hunting moose (Alces americanus) were significantly larger than those (N=10) hunting white-tailed deer (Odocoileus virginianus) (F1,8=16.50, p=0.004). Our data support the hypothesis that differential pack-size persistence may be perpetuated by differences in primary prey riskiness to wolves, and we highlight two important extensions of this idea: (1) the potential for wolves to provision and defend injured packmates from other wolves and (2) the importance of less-risky, buffer prey to pack-size persistence and year-to-year variation.

  2. Genome-size Variation in Switchgrass (Panicum virgatum: Flow Cytometry and Cytology Reveal Rampant Aneuploidy

    Directory of Open Access Journals (Sweden)

    Denise E. Costich

    2010-11-01

    Full Text Available Switchgrass ( L., a native perennial dominant of the prairies of North America, has been targeted as a model herbaceous species for biofeedstock development. A flow-cytometric survey of a core set of 11 primarily upland polyploid switchgrass accessions indicated that there was considerable variation in genome size within each accession, particularly at the octoploid (2 = 8 = 72 chromosome ploidy level. Highly variable chromosome counts in mitotic cell preparations indicated that aneuploidy was more common in octoploids (86.3% than tetraploids (23.2%. Furthermore, the incidence of hyper- versus hypoaneuploidy is equivalent in tetraploids. This is clearly not the case in octoploids, where close to 90% of the aneuploid counts are lower than the euploid number. Cytogenetic investigation using fluorescent in situ hybridization (FISH revealed an unexpected degree of variation in chromosome structure underlying the apparent genomic instability of this species. These results indicate that rapid advances in the breeding of polyploid biofuel feedstocks, based on the molecular-genetic dissection of biomass characteristics and yield, will be predicated on the continual improvement of our understanding of the cytogenetics of these species.

  3. The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.

    Science.gov (United States)

    Schulz, Herbert; Kolde, Raivo; Adler, Priit; Aksoy, Irène; Anastassiadis, Konstantinos; Bader, Michael; Billon, Nathalie; Boeuf, Hélène; Bourillot, Pierre-Yves; Buchholz, Frank; Dani, Christian; Doss, Michael Xavier; Forrester, Lesley; Gitton, Murielle; Henrique, Domingos; Hescheler, Jürgen; Himmelbauer, Heinz; Hübner, Norbert; Karantzali, Efthimia; Kretsovali, Androniki; Lubitz, Sandra; Pradier, Laurent; Rai, Meena; Reimand, Jüri; Rolletschek, Alexandra; Sachinidis, Agapios; Savatier, Pierre; Stewart, Francis; Storm, Mike P; Trouillas, Marina; Vilo, Jaak; Welham, Melanie J; Winkler, Johannes; Wobus, Anna M; Hatzopoulos, Antonis K

    2009-09-03

    Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the "Functional Genomics in Embryonic Stem Cells" consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in "Expression Waves" and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells.

  4. The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.

    Directory of Open Access Journals (Sweden)

    Herbert Schulz

    Full Text Available Embryonic stem (ES cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the "Functional Genomics in Embryonic Stem Cells" consortium (FunGenES has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in "Expression Waves" and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells.

  5. DNA Lossless Differential Compression Algorithm based on Similarity of Genomic Sequence Database

    CERN Document Server

    Afify, Heba; Wahed, Manal Abdel

    2011-01-01

    Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information theory are often perceived as being of interest for data communication and storage. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison of genomic databases. This paper presents a differential compression algorithm that is based on production of difference sequences according to op-code table in order to optimize the compression of homologous sequences in dataset. Therefore, the stored data are composed of reference sequence, the set of differences, and differences locations, instead of storing each sequence individually. This algorithm does not require a priori knowledge about the statistics of the sequence set. The...

  6. Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop.

    Science.gov (United States)

    Stetter, Markus G; Schmid, Karl J

    2017-04-01

    The genus Amaranthus consists of 50-70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joining tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages

  7. Genome size, chromosome number, and rDNA organisation in Algerian populations of Artemisia herba-alba (Asteraceae, a basic plant for animal feeding facing overgrazing erosion

    Directory of Open Access Journals (Sweden)

    Youcef Bougoutaia

    2016-11-01

    Full Text Available Artemisia herba-alba is a largely-distributed and often landscape-dominating taxon in arid areas of the Mediterranean and Irano-Turanian regions. In Algeria, in 2010 its communities covered 10% of the steppe territory, but its populations have been subjected to overgrazing. A karyological study based on 22 populations together with a cytogenetic characterisation of this species has been performed for the first time in Algerian materials, through genome size and chromosome number determination. Fluorescence in situ hybridisation (FISH was also used to assess the rDNA loci number and distribution in the two ploidy levels detected. The studied accessions are diploid (2n = 2x = 18 chromosomes, 6 populations or tetraploid (2n = 4x = 36 chromosomes, 15 populations. One population, occupying a more or less central geographic position among the studied area, presented both cytotypes. Genome size reflects well the two ploidy levels, with no evidence of downsizing with polyploidy. The karyotypes are rather symmetric (2A Stebbins’ class. FISH analyses detected four signals (2 loci in diploid and eight signals (4 loci in tetraploid cytotypes for both ribosomal DNA genes, which present an L-type (linked organisation, i.e. with loci from both rDNA genes colocalised. The presence of two ploidy levels suggest a genomic dynamism and even a possible differentiation underlying the morphological uniformity and despite the dramatic decrease experienced by this plant in Algeria in terms of surface coverage.

  8. Variable step size and order strategy for delay differential equations in PIE(CIE)s mode

    Science.gov (United States)

    Aziz, Nurul Huda Abdul; Majid, Zanariah Abdul

    2014-12-01

    This article deals with the strategy of variable step size and variable order implementation that has been formulated for solving first order of delay differential equations. This strategy is adapted in PIE(CIE)s mode which is generally based on predictor-corrector scheme in multistep block method of order 4 to 9 with s is for convergence test. The purpose here is to enhance the efficiency of the developed predictor-corrector algorithm in the capability to vary automatically not only for the step size, but the order of the method employed as well. All order and coefficients are stored in the code in order to avoid an expensive computational work. The delay argument would be evaluated using Newton divided-difference interpolation at which the points involved would be similar to the current order of the method. Illustrative examples are included to demonstrate the validity and applicability of the presented strategy and comparison is made with the existing results.

  9. Whole-genome fingerprint of the DNA methylome during human B-cell differentiation

    Science.gov (United States)

    Kulis, Marta; Merkel, Angelika; Heath, Simon; Queirós, Ana C.; Schuyler, Ronald P.; Castellano, Giancarlo; Beekman, Renée; Raineri, Emanuele; Esteve, Anna; Clot, Guillem; Verdaguer-Dot, Nuria; Duran-Ferrer, Martí; Russiñol, Nuria; Vilarrasa-Blasi, Roser; Ecker, Simone; Pancaldi, Vera; Rico, Daniel; Agueda, Lidia; Blanc, Julie; Richardson, David; Clarke, Laura; Datta, Avik; Pascual, Marien; Agirre, Xabier; Prosper, Felipe; Alignani, Diego; Paiva, Bruno; Caron, Gersende; Fest, Thierry; Muench, Marcus O.; Fomin, Marina E.; Lee, Seung-Tae; Wiemels, Joseph L.; Valencia, Alfonso; Gut, Marta; Flicek, Paul; Stunnenberg, Hendrik G.; Siebert, Reiner; Küppers, Ralf; Gut, Ivo G.; Campo, Elías; Martín-Subero, José I.

    2017-01-01

    We analyzed the DNA methylome of ten subpopulations spanning the entire B-cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays. We observed that non-CpG methylation disappeared upon B-cell commitment whereas CpG methylation changed extensively during B-cell maturation, showing an accumulative pattern and affecting around 30% of all measured CpGs. Early differentiation stages mainly displayed enhancer demethylation, which was associated with upregulation of key B-cell transcription factors and affected multiple genes involved in B-cell biology. Late differentiation stages, in contrast, showed extensive demethylation of heterochromatin and methylation gain of polycomb-repressed areas, and did not affect genes with apparent functional impact in B cells. This signature, which has been previously linked to aging and cancer, was particularly widespread in mature cells with extended life span. Comparing B-cell neoplasms with their normal counterparts, we identified that they frequently acquire methylation changes in regions undergoing dynamic methylation already during normal B-cell differentiation. PMID:26053498

  10. Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    Full Text Available Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low CaratioMg ratio in A. lyrata.

  11. Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS.

    Directory of Open Access Journals (Sweden)

    Rosa C Baños

    2009-06-01

    Full Text Available Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

  12. Cassava (Manihot esculenta Krantz) genome harbors KNOX genes differentially expressed during storage root development.

    Science.gov (United States)

    Guo, D; Li, H L; Tang, X; Peng, S Q

    2014-12-18

    In plants, homeodomain proteins play a critical role in regulating various aspects of plant growth and development. KNOX proteins are members of the homeodomain protein family. The KNOX transcription factors have been reported from Arabidopsis, rice, and other higher plants. The recent publication of the draft genome sequence of cassava (Manihot esculenta Krantz) has allowed a genome-wide search for M. esculenta KNOX (MeKNOX) transcription factors and the comparison of these positively identified proteins with their homologs in model plants. In the present study, we identified 12 MeKNOX genes in the cassava genome and grouped them into two distinct subfamilies based on their domain composition and phylogenetic analysis. Furthermore, semi-quantitative reverse transcription polymerase chain reaction analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of root development. The analysis of MeKNOX expression profiles of indicated that 12 MeKNOX genes display differential expressions either in their transcript abundance or expression patterns.

  13. Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

    Science.gov (United States)

    Egan, Jan B; Barrett, Michael T; Champion, Mia D; Middha, Sumit; Lenkiewicz, Elizabeth; Evers, Lisa; Francis, Princy; Schmidt, Jessica; Shi, Chang-Xin; Van Wier, Scott; Badar, Sandra; Ahmann, Gregory; Kortuem, K Martin; Boczek, Nicole J; Fonseca, Rafael; Craig, David W; Carpten, John D; Borad, Mitesh J; Stewart, A Keith

    2014-01-01

    Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR) where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

  14. Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

    Directory of Open Access Journals (Sweden)

    Jan B Egan

    Full Text Available Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

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

    OpenAIRE

    Wang, Jing; Liu, Juan; Kang, Ming

    2015-01-01

    Flow cytometry (FCM) is a commonly used method for estimating genome size in many organisms. The use of FCM 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 r...

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

    OpenAIRE

    Jing eWang; Juan eLiu; Ming eKang

    2015-01-01

    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...

  17. Quantitative PCR-based genome size estimation of the astigmatid mites Sarcoptes scabiei, Psoroptes ovis and Dermatophagoides pteronyssinus

    Directory of Open Access Journals (Sweden)

    Mounsey Kate E

    2012-01-01

    Full Text Available Abstract Background The lack of genomic data available for mites limits our understanding of their biology. Evolving high-throughput sequencing technologies promise to deliver rapid advances in this area, however, estimates of genome size are initially required to ensure sufficient coverage. Methods Quantitative real-time PCR was used to estimate the genome sizes of the burrowing ectoparasitic mite Sarcoptes scabiei, the non-burrowing ectoparasitic mite Psoroptes ovis, and the free-living house dust mite Dermatophagoides pteronyssinus. Additionally, the chromosome number of S. scabiei was determined by chromosomal spreads of embryonic cells derived from single eggs. Results S. scabiei cells were shown to contain 17 or 18 small (S. scabiei and P. ovis were 96 (± 7 Mb and 86 (± 2 Mb respectively, among the smallest arthropod genomes reported to date. The D. pteronyssinus genome was estimated to be larger than its parasitic counterparts, at 151 Mb in female mites and 218 Mb in male mites. Conclusions This data provides a starting point for understanding the genetic organisation and evolution of these astigmatid mites, informing future sequencing projects. A comparitive genomic approach including these three closely related mites is likely to reveal key insights on mite biology, parasitic adaptations and immune evasion.

  18. 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.

  19. Computational analysis of whole-genome differential allelic expression data in human.

    Science.gov (United States)

    Wagner, James R; Ge, Bing; Pokholok, Dmitry; Gunderson, Kevin L; Pastinen, Tomi; Blanchette, Mathieu

    2010-07-08

    Allelic imbalance (AI) is a phenomenon where the two alleles of a given gene are expressed at different levels in a given cell, either because of epigenetic inactivation of one of the two alleles, or because of genetic variation in regulatory regions. Recently, Bing et al. have described the use of genotyping arrays to assay AI at a high resolution (approximately 750,000 SNPs across the autosomes). In this paper, we investigate computational approaches to analyze this data and identify genomic regions with AI in an unbiased and robust statistical manner. We propose two families of approaches: (i) a statistical approach based on z-score computations, and (ii) a family of machine learning approaches based on Hidden Markov Models. Each method is evaluated using previously published experimental data sets as well as with permutation testing. When applied to whole genome data from 53 HapMap samples, our approaches reveal that allelic imbalance is widespread (most expressed genes show evidence of AI in at least one of our 53 samples) and that most AI regions in a given individual are also found in at least a few other individuals. While many AI regions identified in the genome correspond to known protein-coding transcripts, others overlap with recently discovered long non-coding RNAs. We also observe that genomic regions with AI not only include complete transcripts with consistent differential expression levels, but also more complex patterns of allelic expression such as alternative promoters and alternative 3' end. The approaches developed not only shed light on the incidence and mechanisms of allelic expression, but will also help towards mapping the genetic causes of allelic expression and identify cases where this variation may be linked to diseases.

  20. Differential differences in methylation status of putative imprinted genes among cloned swine genomes.

    Directory of Open Access Journals (Sweden)

    Chih-Jie Shen

    Full Text Available DNA methylation is a major epigenetic modification in the mammalian genome that regulates crucial aspects of gene function. Mammalian cloning by somatic cell nuclear transfer (SCNT often results in gestational or neonatal failure with only a small proportion of manipulated embryos producing live births. Many of the embryos that survive to term later succumb to a variety of abnormalities that are likely due to inappropriate epigenetic reprogramming. Aberrant methylation patterns of imprinted genes in cloned cattle and mice have been elucidated, but few reports have analyzed the cloned pig genome. Four surviving cloned sows that were created by ear fibroblast nuclear transfer, each with a different life span and multiple organ defects, such as heart defects and bone growth delay, were used as epigenetic study materials. First, we identified four putative differential methylation regions (DMR of imprinted genes in the wild-type pig genome, including two maternally imprinted loci (INS and IGF2 and two paternally imprinted loci (H19 and IGF2R. Aberrant DNA methylation, either hypermethylation or hypomethylation, commonly appeared in H19 (45% of imprinted loci hypermethylated vs. 30% hypomethylated, IGF2 (40% vs. 0%, INS (50% vs. 5%, and IGF2R (15% vs. 45% in multiple tissues from these four cloned sows compared with wild-type pigs. Our data suggest that aberrant epigenetic modifications occur frequently in the genome of cloned swine. Even with successful production of cloned swine that avoid prenatal or postnatal death, the perturbation of methylation in imprinted genes still exists, which may be one of reason for their adult pathologies and short life. Understanding the aberrant pattern of gene imprinting would permit improvements in future cloning techniques.

  1. Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation

    Science.gov (United States)

    Zektser, Yulia; Mahajan, Shivani; Bachtrog, Doris

    2013-01-01

    Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes

  2. Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation.

    Directory of Open Access Journals (Sweden)

    Beatriz Vicoso

    Full Text Available Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females. Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae, but completely heteromorphic sex chromosomes in both garter snakes (Colubridae and pygmy rattlesnake (Viperidae. Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases. This demonstrates that mutation rates are male-biased in snakes (male-driven evolution, but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex

  3. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability

    Directory of Open Access Journals (Sweden)

    Joardar Vinita

    2012-12-01

    Full Text Available Abstract Background The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Results Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus, A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum. The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus, contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. Conclusions The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent

  4. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians.

    Science.gov (United States)

    Tenaillon, Maud I; Hufford, Matthew B; Gaut, Brandon S; Ross-Ibarra, Jeffrey

    2011-01-01

    The genome of maize (Zea mays ssp. mays) consists mostly of transposable elements (TEs) and varies in size among lines. This variation extends to other species in the genus Zea: although maize and Zea luxurians diverged only ∼140,000 years ago, their genomes differ in size by ∼50%. We used paired-end Illumina sequencing to evaluate the potential contribution of TEs to the genome size difference between these two species. We aligned the reads both to a filtered gene set and to an exemplar database of unique repeats representing 1,514 TE families; ∼85% of reads mapped against TE repeats in both species. The relative contribution of TE families to the B73 genome was highly correlated with previous estimates, suggesting that reliable estimates of TE content can be obtained from short high-throughput sequencing reads, even at low coverage. Because we used paired-end reads, we could assess whether a TE was near a gene by determining if one paired read mapped to a TE and the second read mapped to a gene. Using this method, Class 2 DNA elements were found significantly more often in genic regions than Class 1 RNA elements, but Class 1 elements were found more often near other TEs. Overall, we found that both Class 1 and 2 TE families account for ∼70% of the genome size difference between B73 and luxurians. Interestingly, the relative abundance of TE families was conserved between species (r = 0.97), suggesting genome-wide control of TE content rather than family-specific effects.

  5. Genome Sequence of Staphylococcus aureus PX03, an Acetoin-Producing Strain with a Small-Sized Genome.

    Science.gov (United States)

    Zhang, Ge; Wang, Qian; Su, Yulong; Li, Shugui; Liu, Haobao

    2017-09-14

    Staphylococcus aureus PX03 can produce acetoin efficiently. Here, we present a 2.38-Mb assembly of its genome sequence, which might provide further insights into the molecular mechanism of its acetoin biosynthesis to further improve its biotechnological applications. Copyright © 2017 Zhang et al.

  6. Genome size and base composition of five Pinus species from the Balkan region.

    Science.gov (United States)

    Bogunic, F; Muratovic, E; Brown, S C; Siljak-Yakovlev, S

    2003-08-01

    The 2C DNA content and base composition of five Pinus (2 n=24) species and two Pinus subspecies from the Balkan region have been estimated by flow cytometry. P. heldreichii (five populations) and P. peuce (one population) were assessed for the first time, as also were subspecies of P. nigra (three populations-two of subspecies nigra and one of subspecies dalmatica) along with P. sylvestris, and P. mugo from the same region. The 2C DNA values of these Pinus ranged from 42.5 pg to 54.9 pg (41.7-53.8 x 10(9)bp), and the base composition was quite stable (about 39.5% GC). Significant differences were observed between two subspecies of P. nigra and even between two populations of subsp. nigra. The two other species (P. sylvestris and P. mugo) had 2C values of 42.5 pg and 42.8 pg, respectively, while that of P. peuce was 54.9 pg. These genome sizes are in accordance with published values except for P. sylvestris, which was 20% below estimates made by other authors.

  7. Testing the link between genome size and growth rate in maize

    Directory of Open Access Journals (Sweden)

    Maud I. Tenaillon

    2016-09-01

    Full Text Available Little is known about the factors driving within species Genome Size (GS variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27. However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.

  8. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

    Science.gov (United States)

    Kalinka, Anna; Poter, Paulina

    2017-01-01

    Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue. PMID:28149679

  9. Platelet activation patterns in platelet size sub-populations: differential responses to aspirin in vitro.

    Science.gov (United States)

    Mangalpally, Kiran Kumar R; Siqueiros-Garcia, Alan; Vaduganathan, Muthiah; Dong, Jing-Fei; Kleiman, Neal S; Guthikonda, Sasidhar

    2010-10-01

    Circulating platelets are heterogeneous in size and structure. Whether this translates into differences in platelet function and efficacy of antiplatelet therapy is unclear. Hence, we decided to investigate the activation patterns among different platelet populations differentiated by size, and to compare the inhibitory effects of aspirin in these populations. Circulating platelets from 9 healthy volunteers were separated by size and stratified into the largest and smallest quintiles. Platelets were stimulated with 75 μM arachidonic acid (AA), 10 μM ADP or 25 μM TRAP. Alpha-granule protein secretion and expression (P-selectin, VWF, fibrinogen), surface-protein activation (activated integrin αIIbβ3) were assessed. Platelet thromboxane B(2) (TxB(2)) synthesis following AA stimulation was measured in vitro before and after incubation with 265 μM aspirin. Reticulated (juvenile) platelets were assessed using thiazole orange staining. A greater number of large platelets in the largest quintile were reticulated compared with the smallest quintile (6.1 ± 2.8% vs. 1.2 ± 1.5% respectively, p aspirin (1029 ± 190 pg/mL vs. 851 ± 159 pg/mL, respectively, p = 0.03). After stimulation with each agonist, a greater proportion of large platelets bound fibrinogen, VWF, P-selectin and activated integrin αIIbβ3 than small platelets both in the presence and in the absence of in vitro aspirin. In an in vitro setting, large platelets appear to be more active than small platelets and continue to be more active even after in vitro aspirin. Platelets exhibit heterogeneity in size and structure. Whether this translates into platelet function and efficacy of antiplatelet therapy is unclear. We evaluated platelet functional properties and the effects of aspirin on separated platelet subpopulations in an in vitro setting. Platelets were sorted into the largest and smallest size quintiles using flow cytometry forward scatter. Alpha-granule protein release, dense granule content

  10. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

    Directory of Open Access Journals (Sweden)

    Hu Shunling

    2011-03-01

    Full Text Available Abstract Background Six nucleotide (nt insertion in the 5'-noncoding region (NCR of the nucleoprotein (NP gene of Newcaslte disease virus (NDV is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX. Results In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates. Conclusions The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

  11. When problem size matters: differential effects of brain stimulation on arithmetic problem solving and neural oscillations.

    Directory of Open Access Journals (Sweden)

    Bruno Rütsche

    Full Text Available The problem size effect is a well-established finding in arithmetic problem solving and is characterized by worse performance in problems with larger compared to smaller operand size. Solving small and large arithmetic problems has also been shown to involve different cognitive processes and distinct electroencephalography (EEG oscillations over the left posterior parietal cortex (LPPC. In this study, we aimed to provide further evidence for these dissociations by using transcranial direct current stimulation (tDCS. Participants underwent anodal (30min, 1.5 mA, LPPC and sham tDCS. After the stimulation, we recorded their neural activity using EEG while the participants solved small and large arithmetic problems. We found that the tDCS effects on performance and oscillatory activity critically depended on the problem size. While anodal tDCS improved response latencies in large arithmetic problems, it decreased solution rates in small arithmetic problems. Likewise, the lower-alpha desynchronization in large problems increased, whereas the theta synchronization in small problems decreased. These findings reveal that the LPPC is differentially involved in solving small and large arithmetic problems and demonstrate that the effects of brain stimulation strikingly differ depending on the involved neuro-cognitive processes.

  12. Size-differential feeding in Pinna nobilis L. (Mollusca: Bivalvia): Exploitation of detritus, phytoplankton and zooplankton

    Science.gov (United States)

    Davenport, John; Ezgeta-Balić, Daria; Peharda, Melita; Skejić, Sanda; Ninčević-Gladan, Živana; Matijević, Slavica

    2011-04-01

    The endangered fan shell Pinna nobilis is a large bivalve mollusc (<120 cm shell length) endemic to the Mediterranean that lives one-third buried in soft substrata, generally in shallow coastal waters. We hypothesised that P. nobilis of different sizes would ingest different food sources, because small fan shells will inhale material from closer to the substratum than do large fan shells. We studied stomach contents and faeces of 18 fan shells, 6 small (mean 23.0 cm length), 6 medium-sized (mean 41.5 cm length) and 6 large (mean 62.7 cm length) living in a small area of a low-energy coastal detritic bottom characterised by mud, sand and macroalgae at Mali Ston Bay, Croatia. We found that all P. nobilis ingested copious quantities of undetermined detritus (probably at least 95% of ingested material), phytoplankton, micro and mesozooplankton and pollen grains. Large P. nobilis stomach contents showed a preponderance of water column calanoid copepods, while small fan shells had higher numbers of bivalve larvae. All fan shells took in high numbers of harpacticoid copepods that are benthonic, feeding on microbial communities of detritus and benthic vegetation. There was also a significant selection of phytoplankton species, some apparently occurring between inhalation and ingestion. The stomach contents of small P. nobilis had a higher organic matter content than either medium-sized or large fan shells; this indicated that small fan shells ingested detritus of higher organic content than did larger P. nobilis. As the faeces of all P. nobilis had similar organic matter content, this also indicates higher assimilation efficiencies in small fan shells. The demonstration of differential dietary selectivity by different sized animals has implications for future trophic studies of this endangered species. This study also provides the first demonstration of predation on zooplankton by P. nobilis.

  13. 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.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    traits such as mammary disease traits in dairy cattle. METHODS: Data on progeny means of six traits related to mastitis resistance in dairy cattle (general mastitis resistance and five pathogen-specific mastitis resistance traits) were analyzed using a bivariate Bayesian SNP-based genomic model......)variances of mastitis resistance traits in dairy cattle using multivariate genomic models......., per chromosome, and in regions of 100 SNP on a chromosome. RESULTS: Genomic proportions of the total variance differed between traits. Genomic correlations were lower than pedigree-based genetic correlations and they were highest between general mastitis and pathogen-specific traits because...

  15. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

    Science.gov (United States)

    Angly, Florent E; Willner, Dana; Prieto-Davó, Alejandra; Edwards, Robert A; Schmieder, Robert; Vega-Thurber, Rebecca; Antonopoulos, Dionysios A; Barott, Katie; Cottrell, Matthew T; Desnues, Christelle; Dinsdale, Elizabeth A; Furlan, Mike; Haynes, Matthew; Henn, Matthew R; Hu, Yongfei; Kirchman, David L; McDole, Tracey; McPherson, John D; Meyer, Folker; Miller, R Michael; Mundt, Egbert; Naviaux, Robert K; Rodriguez-Mueller, Beltran; Stevens, Rick; Wegley, Linda; Zhang, Lixin; Zhu, Baoli; Rohwer, Forest

    2009-12-01

    Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.

  16. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

    Directory of Open Access Journals (Sweden)

    Florent E Angly

    2009-12-01

    Full Text Available Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS, a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and

  17. Differential DNA methylation regions in cytokine and transcription factor genomic loci associate with childhood physical aggression.

    Directory of Open Access Journals (Sweden)

    Nadine Provençal

    Full Text Available BACKGROUND: Animal and human studies suggest that inflammation is associated with behavioral disorders including aggression. We have recently shown that physical aggression of boys during childhood is strongly associated with reduced plasma levels of cytokines IL-1α, IL-4, IL-6, IL-8 and IL-10, later in early adulthood. This study tests the hypothesis that there is an association between differential DNA methylation regions in cytokine genes in T cells and monocytes DNA in adult subjects and a trajectory of physical aggression from childhood to adolescence. METHODOLOGY/PRINCIPAL FINDINGS: We compared the methylation profiles of the entire genomic loci encompassing the IL-1α, IL-6, IL-4, IL-10 and IL-8 and three of their regulatory transcription factors (TF NFkB1, NFAT5 and STAT6 genes in adult males on a chronic physical aggression trajectory (CPA and males with the same background who followed a normal physical aggression trajectory (control group from childhood to adolescence. We used the method of methylated DNA immunoprecipitation with comprehensive cytokine gene loci and TF loci microarray hybridization, statistical analysis and false discovery rate correction. We found differentially methylated regions to associate with CPA in both the cytokine loci as well as in their transcription factors loci analyzed. Some of these differentially methylated regions were located in known regulatory regions whereas others, to our knowledge, were previously unknown as regulatory areas. However, using the ENCODE database, we were able to identify key regulatory elements in many of these regions that indicate that they might be involved in the regulation of cytokine expression. CONCLUSIONS: We provide here the first evidence for an association between differential DNA methylation in cytokines and their regulators in T cells and monocytes and male physical aggression.

  18. The battle of the sexes over seed size: support for both kinship genomic imprinting and interlocus contest evolution.

    Science.gov (United States)

    Willi, Yvonne

    2013-06-01

    Outcrossing creates a venue for parental conflict. When one sex provides parental care to offspring fertilized by several partners, the nonproviding sex is under selection to maximally exploit the caring sex. The caring sex may counteradapt, and a coevolutionary arms race ensues. Genetic models of this conflict include the kinship theory of genomic imprinting (parent-of-origin-specific expression of maternal-care effectors) and interlocus conflict evolution (interaction between male selfish signals and female abatement). Predictions were tested by measuring the sizes of seeds produced by within-population crosses (diallel design) and between-population crosses in outcrossing and selfing populations of Arabidopsis lyrata. Within-population diallel crosses revealed substantial maternal variance in seed size in most populations. The comparison of between- and within-population crosses showed that seeds were larger when pollen came from another outcrossing population than when pollen came from a selfing or the same population, supporting interlocus contest evolution between male selfish genes and female recognition genes. Evidence for kinship genomic imprinting came from complementary trait means of seed size in reciprocal between-population crosses independent of whether populations were predominantly selfing or outcrossing. Hence, both kinship genomic imprinting and interlocus contest are supported in outcrossing Arabidopsis, whereas only kinship genomic imprinting is important in selfing populations.

  19. Optimal Location and Sizing of UPQC in Distribution Networks Using Differential Evolution Algorithm

    Directory of Open Access Journals (Sweden)

    Seyed Abbas Taher

    2012-01-01

    Full Text Available Differential evolution (DE algorithm is used to determine optimal location of unified power quality conditioner (UPQC considering its size in the radial distribution systems. The problem is formulated to find the optimum location of UPQC based on an objective function (OF defined for improving of voltage and current profiles, reducing power loss and minimizing the investment costs considering the OF's weighting factors. Hence, a steady-state model of UPQC is derived to set in forward/backward sweep load flow. Studies are performed on two IEEE 33-bus and 69-bus standard distribution networks. Accuracy was evaluated by reapplying the procedures using both genetic (GA and immune algorithms (IA. Comparative results indicate that DE is capable of offering a nearer global optimal in minimizing the OF and reaching all the desired conditions than GA and IA.

  20. Genomic diversity and differentiation of a managed island wild boar population

    DEFF Research Database (Denmark)

    Iacolina, Laura; Scandura, Massimo; J. Goedbloed, Daniel;

    2016-01-01

    The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed...... since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number...... of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (FST=0.126–0.138), and from DP (FST=0...

  1. Genome differentiation in Magonoliaceae as revealed from meiotic pairing in interspecific and intergeneric hybrids

    Institute of Scientific and Technical Information of China (English)

    Shou-Zhou ZHANG; Ya-Ling WANG; Zi-Can HE; Erland EJDER

    2011-01-01

    The cross compatibility within and between Yulania Spach and Michelia L.(Magnoliaceae) is relatively good and various such hybrids,obtained by conventional artificial hybridization,are available.The aim of the present study was to determine the extent of genome differentiation between the species involved in these crosses through the observation of chromosome pairing during meiosis in pollen mother cells (PMCs) of the hybrids.Chromosome pairing behavior was studied in five species (2n =38) and two interspecific hybrids of Michelia,eight species (2n =38,76 and 114) and 10 interspecific hybrids of Yulania,and three intergeneric hybrids between Michelia and Yulania.The results showed that chromosome pairing was normal with bivalent formation in diploid parental species and in interspecific hybrids.In addition to bivalents,multivalents were encountered in polyploid parental species and polyploid interspecific hybrids.In the intergeneric hybrids between a tetraploid Yulania and two diploid Michelia,19 chromosomes,most likely originating from Michelia,were unable to synapse from zygotene to metaphase I.Meiotic chromosome pairing indicated a high degree of homology between species within Michelia and Yulania and less homology between the genomes of these two genera.The differentiation of morphological characters and the distinctness of natural distribution also support the conclusion that these two genera are likely independent monophyletic groups.This suggests that the two genera were split at early evolution of Magnoliaceae and the overlapping characteristics in external morphology and internal structures of the two genera may be the result of parallel evolution or ancient common ancestry.

  2. Environmentally selected aphid variants in clonality context display differential patterns of methylation in the genome.

    Directory of Open Access Journals (Sweden)

    Claude Pasquier

    Full Text Available Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature because their asexual phase generates a stochastic and/or environment-oriented repertoire of variants. The a priori unchanged genome in clonal individuals prompts us to hypothesize whether covalent methyl DNA marks might be associated to the phenotypic variability and fitness selection. The full differential transcriptome between two environmentally selected clonal variants that originated from the same founder mother was mapped on the entire genomic scaffolds, in parallel with the methyl cytosine distribution. Data suggest that the assortments of heavily methylated DNA sites are distinct in these two clonal phenotypes. This might constitute an epigenetic mechanism that confers the robust adaptation of insect species to various environments involving clonal reproduction.

  3. Differentiation of mouse iPS cells is dependent on embryoid body size in microwell chip culture.

    Science.gov (United States)

    Miyamoto, Daisuke; Nakazawa, Kohji

    2016-10-01

    A microwell chip possessing microwells of several hundred micrometers is a promising platform for generating embryoid bodies (EBs) of stem cells. Here, we investigated the effects of initial EB size on the growth and differentiation of mouse iPS cells in microwell chip culture. We fabricated a chip that contained 195 microwells in a triangular arrangement at a diameter of 600 μm. To evaluate the effect of EB size, four similar conditions were designed with different seeding cell densities of 100, 500, 1000, and 2000 cells/EB. The cells in each microwell gradually aggregated and then spontaneously formed a single EB within 1 d of culture, and EB size increased with further cell proliferation. EB growth was regulated by the initial EB size, and the growth ability of smaller EBs was higher than that of larger EBs. Furthermore, stem cell differentiation also depended on the initial EB size, and the EBs at more than 500 cells/EB promoted hepatic and cardiac differentiations, but the EBs at 100 cells/EB preferred vascular differentiation. These results indicated that the initial EB size was one of the important factors controlling the proliferation and differentiation of stem cells in the microwell chip culture.

  4. Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers.

    Directory of Open Access Journals (Sweden)

    Christin Habig

    Full Text Available The Lohmann Selected Leghorn (LSL and Lohmann Brown (LB layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05 among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.

  5. Characterization of size-differentiated inorganic composition of aerosols in Mexico City

    Science.gov (United States)

    Moya, Mireya; Castro, Telma; Zepeda, Monica; Baez, Armando

    Size-differentiated atmospheric aerosol particles were collected during December 2000-October 2001 in Mexico City (19°N, 99°W) using a micro-orifice uniform deposit impactor. Sulfate and ammonium, which were correlated, were major features of the size distributions. The more predominant mode was at 0.32±0.1 μm, aerodynamic diameter. This peak of concentration is likely the result of condensation of secondary aerosol components from the gas phase. During part of the rainy season (April and June), a larger mode was found at 0.56±0.2 μm, aerodynamic diameter. This peak of concentration, identified as a droplet mode, is probably the result of aqueous-phase reactions (i.e., oxidation of sulfur dioxide in liquid droplets). During August, the peak of concentration was observed at both size ranges of the accumulation mode. Overall, ion balances were achieved with a small deficit of cations, except for the April and June samples, where a significant amount of excess sulfate was present as a result of moderate-high activity of the neighboring volcano Popocatepetl, as well as ambient conditions that favored production of sulfate (moderate-high relative humidity values). Based on the analysis of the ammonia/sulfate molar ratios, the ammonia concentrations were sufficient to fully neutralize sulfate concentrations, except for the April and June samples. During these months, ammonium bisulfate, letovicite and H 2SO 4(aq) (or a solution of the corresponding ions) were the dominant form of sulfate present in both fine and coarse modes. The acidic nature of these particles (with NH 3/H 2SO 4 molar ratio less than 2) is potentially important in assessing health effects of inhaled particles.

  6. Differentiation of strains from the Bacillus cereus group by RFLP-PFGE genomic fingerprinting.

    Science.gov (United States)

    Otlewska, Anna; Oltuszak-Walczak, Elzbieta; Walczak, Piotr

    2013-11-01

    Bacillus mycoides, Bacillus pseudomycoides, Bacillus weihenstephanensis, Bacillus anthracis, Bacillus thuringiensis, and Bacillus cereus belong to the B. cereus group. The last three species are characterized by different phenotype features and pathogenicity spectrum, but it has been shown that these species are genetically closely related. The macrorestriction analysis of the genomic DNA with the NotI enzyme was used to generate polymorphism of restriction profiles for 39 food-borne isolates (B. cereus, B. mycoides) and seven reference strains (B. mycoides, B. thuringiensis, B. weihenstephanensis, and B. cereus). The PFGE method was applied to differentiate the examined strains of the B. cereus group. On the basis of the unweighted pair group method with the arithmetic mean method and Dice coefficient, the strains were divided into five clusters (types A-E), and the most numerous group was group A (25 strains). A total of 21 distinct pulsotypes were observed. The RFLP-PFGE analysis was successfully used for the differentiation and characterization of B. cereus and B. mycoides strains isolated from different food products.

  7. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

    Directory of Open Access Journals (Sweden)

    Sugnet Charles

    2006-12-01

    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  8. Spiral Structure and Differential Dust Size Distribution in the LKHα 330 Disk

    Science.gov (United States)

    Akiyama, Eiji; Hashimoto, Jun; baobabu Liu, Hauyu; i-hsiu Li, Jennifer; Bonnefoy, Michael; Dong, Ruobing; Hasegawa, Yasuhiro; Henning, Thomas; Sitko, Michael L.; Janson, Markus; Feldt, Markus; Wisniewski, John; Kudo, Tomoyuki; Kusakabe, Nobuhiko; Tsukagoshi, Takashi; Momose, Munetake; Muto, Takayuki; Taki, Tetsuo; Kuzuhara, Masayuki; Satoshi, Mayama; Takami, Michihiro; Ohashi, Nagayoshi; Grady, Carol A.; Kwon, Jungmi; Thalmann, Christian; Abe, Lyu; Brandner, Wolfgang; Brandt, Timothy D.; Carson, Joseph C.; Egner, Sebastian; Goto, Miwa; Guyon, Olivier; Hayano, Yutaka; Hayashi, Masahiko; Hayashi, Saeko S.; Hodapp, Klaus W.; Ishii, Miki; Iye, Masanori; Knapp, Gillian R.; Kandori, Ryo; Matsuo, Taro; Mcelwain, Michael W.; Miyama, Shoken; Morino, Jun-Ichi; Moro-Martin, Amaya; Nishimura, Tetsuo; Pyo, Tae-Soo; Serabyn, Eugene; Suenaga, Takuya; Suto, Hiroshi; Suzuki, Ryuji; Takahashi, Yasuhiro H.; Takato, Naruhisa; Terada, Hiroshi; Tomono, Daigo; Turner, Edwin L.; Watanabe, Makoto; Yamada, Toru; Takami, Hideki; Usuda, Tomonori; Tamura, Motohide

    2016-12-01

    Dust trapping accelerates the coagulation of dust particles, and, thus, it represents an initial step toward the formation of planetesimals. We report H-band (1.6 μm) linear polarimetric observations and 0.87 mm interferometric continuum observations toward a transitional disk around LkHα 330. As a result, a pair of spiral arms were detected in the H-band emission, and an asymmetric (potentially arm-like) structure was detected in the 0.87 mm continuum emission. We discuss the origin of the spiral arm and the asymmetric structure and suggest that a massive unseen planet is the most plausible explanation. The possibility of dust trapping and grain growth causing the asymmetric structure was also investigated through the opacity index (β) by plotting the observed spectral energy distribution slope between 0.87 mm from our Submillimeter Array observation and 1.3 mm from literature. The results imply that grains are indistinguishable from interstellar medium-like dust in the east side (β =2.0+/- 0.5) but are much smaller in the west side β ={0.7}-0.4+0.5, indicating differential dust size distribution between the two sides of the disk. Combining the results of near-infrared and submillimeter observations, we conjecture that the spiral arms exist at the upper surface and an asymmetric structure resides in the disk interior. Future observations at centimeter wavelengths and differential polarization imaging in other bands (Y-K) with extreme AO imagers are required to understand how large dust grains form and to further explore the dust distribution in the disk.

  9. Morphological and genome size variations within populations of Edraianthus graminifolius “Jugoslavicus” (Campanulaceae from the central Balkan peninsula

    Directory of Open Access Journals (Sweden)

    Rakić Tamara

    2014-01-01

    Full Text Available The E. graminifolius complex is widely distributed in the continental part of the central and western Balkan Peninsula and is characterized by pronounced morphological variability. Plants grow on different geological substrates, span a wide altitudinal range and inhabit heterogeneous microclimatic conditions. The aim of this study was to compare morpho-anatomical and genome size variations among 31 populations of E. graminifolius, and to correlate morphoanatomical characteristics of plants with the geomorphologic and bioclimatic characteristics of their habitats. For these purposes, multivariate statistical analyses were performed. Results showed that most of morphological variability could be explained as the adaptive responses of plants to diverse environmental conditions that accompany life at different altitudes. Populations from SE Serbia had larger genome size in respect to other investigated populations. Genome size was bigger in sympatric populations of Edraianthus then in allopatric ones. Apart from the general morphological variability, plants from the Ovčar-Kablar Gorge are particularly morphologically specific. [Projekat Ministarstva nauke Republike Srbije, br. 173030

  10. Genomic targets of Brachyury (T in differentiating mouse embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Amanda L Evans

    Full Text Available The T-box transcription factor Brachyury (T is essential for formation of the posterior mesoderm and the notochord in vertebrate embryos. Work in the frog and the zebrafish has identified some direct genomic targets of Brachyury, but little is known about Brachyury targets in the mouse.Here we use chromatin immunoprecipitation and mouse promoter microarrays to identify targets of Brachyury in embryoid bodies formed from differentiating mouse ES cells. The targets we identify are enriched for sequence-specific DNA binding proteins and include components of signal transduction pathways that direct cell fate in the primitive streak and tailbud of the early embryo. Expression of some of these targets, such as Axin2, Fgf8 and Wnt3a, is down regulated in Brachyury mutant embryos and we demonstrate that they are also Brachyury targets in the human. Surprisingly, we do not observe enrichment of the canonical T-domain DNA binding sequence 5'-TCACACCT-3' in the vicinity of most Brachyury target genes. Rather, we have identified an (AC(n repeat sequence, which is conserved in the rat but not in human, zebrafish or Xenopus. We do not understand the significance of this sequence, but speculate that it enhances transcription factor binding in the regulatory regions of Brachyury target genes in rodents.Our work identifies the genomic targets of a key regulator of mesoderm formation in the early mouse embryo, thereby providing insights into the Brachyury-driven genetic regulatory network and allowing us to compare the function of Brachyury in different species.

  11. Digital IIR filters design using differential evolution algorithm with a controllable probabilistic population size.

    Science.gov (United States)

    Zhu, Wu; Fang, Jian-an; Tang, Yang; Zhang, Wenbing; Du, Wei

    2012-01-01

    Design of a digital infinite-impulse-response (IIR) filter is the process of synthesizing and implementing a recursive filter network so that a set of prescribed excitations results a set of desired responses. However, the error surface of IIR filters is usually non-linear and multi-modal. In order to find the global minimum indeed, an improved differential evolution (DE) is proposed for digital IIR filter design in this paper. The suggested algorithm is a kind of DE variants with a controllable probabilistic (CPDE) population size. It considers the convergence speed and the computational cost simultaneously by nonperiodic partial increasing or declining individuals according to fitness diversities. In addition, we discuss as well some important aspects for IIR filter design, such as the cost function value, the influence of (noise) perturbations, the convergence rate and successful percentage, the parameter measurement, etc. As to the simulation result, it shows that the presented algorithm is viable and comparable. Compared with six existing State-of-the-Art algorithms-based digital IIR filter design methods obtained by numerical experiments, CPDE is relatively more promising and competitive.

  12. Novel nuclei isolation buffer for flow cytometric genome size estimation of Zingiberaceae: a comparison with common isolation buffers.

    Science.gov (United States)

    Sadhu, Abhishek; Bhadra, Sreetama; Bandyopadhyay, Maumita

    2016-11-01

    Cytological parameters such as chromosome numbers and genome sizes of plants are used routinely for studying evolutionary aspects of polyploid plants. Members of Zingiberaceae show a wide range of inter- and intrageneric variation in their reproductive habits and ploidy levels. Conventional cytological study in this group of plants is severely hampered by the presence of diverse secondary metabolites, which also affect their genome size estimation using flow cytometry. None of the several nuclei isolation buffers used in flow cytometry could be used very successfully for members of Zingiberaceae to isolate good quality nuclei from both shoot and root tissues. The competency of eight nuclei isolation buffers was compared with a newly formulated buffer, MB01, in six different genera of Zingiberaceae based on the fluorescence intensity of propidium iodide-stained nuclei using flow cytometric parameters, namely coefficient of variation of the G0/G1 peak, debris factor and nuclei yield factor. Isolated nuclei were studied using fluorescence microscopy and bio-scanning electron microscopy to analyse stain-nuclei interaction and nuclei topology, respectively. Genome contents of 21 species belonging to these six genera were determined using MB01. Flow cytometric parameters showed significant differences among the analysed buffers. MB01 exhibited the best combination of analysed parameters; photomicrographs obtained from fluorescence and electron microscopy supported the superiority of MB01 buffer over other buffers. Among the 21 species studied, nuclear DNA contents of 14 species are reported for the first time. Results of the present study substantiate the enhanced efficacy of MB01, compared to other buffers tested, in the generation of acceptable cytograms from all species of Zingiberaceae studied. Our study facilitates new ways of sample preparation for further flow cytometric analysis of genome size of other members belonging to this highly complex polyploid family.

  13. Functional genomic and radiosensitivity of human keratinocytes: from differentiated to stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Lamartine, J.; Rachidi, W.; Franco, N.; Lemaitre, G.; Vaigot, P.; Le Minter, P.; Waksman, G.; Martin, M.T. [Evry Univ. Lab. of Genomic and Radiobiology of Keratinocytes, Service de Genomique Fonctionnelle, CEA, 91 (France)

    2006-07-01

    Despite improvements in radiation techniques, patients can still experience radiation toxicity on the skin. Keratinocytes from the basal layer of the epidermis have been long proposed by ICRP as the main target of ionizing radiation in human skin, both for early and late effects of radiation. But the exact roles of these cells in radiation skin damage are still largely unknown., This is why a new program was started to define the radiosensitivity of human keratinocytes according to their differentiation. In a first study was characterized the response of differentiated keratinocytes to low and high doses of gamma radiation (1). To examine whether the response to low doses was different from that induced by high doses, cultured primary keratinocytes isolated from adult normal skin were irradiated with single doses of 1 c Gray or 2 c Gy. A major finding of this study was the identification of an important number of low dose specific genes (140), most of which were modulated at 48 h. Clustering analysis also revealed low dose specific profiles. These results show for the first time that low dose ionizing irradiation is able to induce specific transcriptional responses in human keratinocytes. Then came the part to characterize the radiosensitivity of human basal keratinocytes. The results show for the first time that keratinocytes stem cells from human epidermis are more resistant than proliferative basal keratinocytes. In summary, using cellular biology and functional genomics, we are improving the knowledge on the effects of ionizing radiation on human epidermis, one of the main target tissue of radiation in the human body. (N.C.)

  14. Genome-wide study of gene variants associated with differential cardiovascular event reduction by pravastatin therapy.

    Directory of Open Access Journals (Sweden)

    Dov Shiffman

    Full Text Available Statin therapy reduces the risk of coronary heart disease (CHD, however, the person-to-person variability in response to statin therapy is not well understood. We have investigated the effect of genetic variation on the reduction of CHD events by pravastatin. First, we conducted a genome-wide association study of 682 CHD cases from the Cholesterol and Recurrent Events (CARE trial and 383 CHD cases from the West of Scotland Coronary Prevention Study (WOSCOPS, two randomized, placebo-controlled studies of pravastatin. In a combined case-only analysis, 79 single nucleotide polymorphisms (SNPs were associated with differential CHD event reduction by pravastatin according to genotype (P<0.0001, and these SNPs were analyzed in a second stage that included cases as well as non-cases from CARE and WOSCOPS and patients from the PROspective Study of Pravastatin in the Elderly at Risk/PHArmacogenomic study of Statins in the Elderly at risk for cardiovascular disease (PROSPER/PHASE, a randomized placebo controlled study of pravastatin in the elderly. We found that one of these SNPs (rs13279522 was associated with differential CHD event reduction by pravastatin therapy in all 3 studies: P = 0.002 in CARE, P = 0.01 in WOSCOPS, P = 0.002 in PROSPER/PHASE. In a combined analysis of CARE, WOSCOPS, and PROSPER/PHASE, the hazard ratio for CHD when comparing pravastatin with placebo decreased by a factor of 0.63 (95% CI: 0.52 to 0.75 for each extra copy of the minor allele (P = 4.8 × 10(-7. This SNP is located in DnaJ homolog subfamily C member 5B (DNAJC5B and merits investigation in additional randomized studies of pravastatin and other statins.

  15. 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.

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

    Science.gov (United States)

    Wang, Jing; Liu, Juan; Kang, Ming

    2015-01-01

    Flow cytometry (FCM) is a commonly used method for estimating genome size in many organisms. The use of FCM 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 min at a PI concentration of 100 μg ml(-1). The quality of the estimates was not improved by 1-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 min. 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.

  17. A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica.

    Science.gov (United States)

    Papa, R; Acosta, J; Delgado-Salinas, A; Gepts, P

    2005-10-01

    Lack of introgression or divergent selection may be responsible for the maintenance of phenotypic differences between sympatric populations of crops and their wild progenitors. To distinguish between these hypotheses, amplified fragment length polymorphism markers were located on a molecular linkage map of Phaseolus vulgaris relative to genes for the domestication syndrome and other traits. Diversity for these same markers was then analyzed in two samples of wild and domesticated populations from Mesoamerica. Differentiation between wild and domesticated populations was significantly higher in parapatric and allopatric populations compared to sympatric populations. It was also significantly higher near genes for domestication compared to those away from these genes. Concurrently, the differences in genetic diversity between wild and domesticated populations were strongest around such genes. These data suggest that selection in the presence of introgression appears to be a major evolutionary factor maintaining the identity of wild and domesticated populations in sympatric situations. Furthermore, alleles from domesticated populations appear to have displaced alleles in sympatric wild populations, thus leading to a reduction in genetic diversity in such populations. These results also provide a possible experimental framework for assessing the long-term risk of transgene escape and the targeting of transgenes inside the genome to minimize the survival of these transgenes into wild populations following introduction by gene flow.

  18. rRNA operons and genome size of 'Candidatus Liberibacter americanus', a bacterium associated with citrus huanglongbing in Brazil.

    Science.gov (United States)

    Wulff, N A; Eveillard, S; Foissac, X; Ayres, A J; Bové, J-M

    2009-08-01

    Huanglongbing is one of the most severe diseases of citrus worldwide and is associated with 'Candidatus (Ca.) Liberibacter africanus' in Africa, 'Ca. Liberibacter asiaticus' in Asia and the Americas (Brazil, USA and Cuba) and 'Ca. Liberibacter americanus' (Lam) in Brazil. In the absence of axenic cultures, genetic information on liberibacters is scarce. The sequences of the entire 23S rRNA and 5S rRNA genes from Lam have now been obtained, using a consensus primer designed on known tRNAMet sequences of rhizobia. The size of the Lam genome was determined by PFGE, using Lam-infected periwinkle plants for bacterial enrichment, and was found to be close to 1.31 Mbp. In order to determine the number of ribosomal operons on the Lam genome, probes designed to detect the 16S rRNA gene and the 3' end of the 23S rRNA gene were developed and used for Southern hybridization with I-CeuI-treated genomic DNA. Our results suggest that there are three ribosomal operons in a circular genome. Lam is the first liberibacter species for which such data are available.

  19. gyrB Multiplex PCR To Differentiate between Acinetobacter calcoaceticus and Acinetobacter Genomic Species 3 ▿

    OpenAIRE

    Higgins, Paul G.; Lehmann, Marlene; Wisplinghoff, Hilmar; Seifert, Harald

    2010-01-01

    A previously established multiplex PCR that identifies to the species level Acinetobacter baumannii and Acinetobacter genomic species 13TU (GS13TU) was expanded to include Acinetobacter calcoaceticus and Acinetobacter genomic species 3.

  20. 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.

  1. Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells

    Science.gov (United States)

    To investigate genomic effects, human liver hepatocellular carcinoma (HepG2) cells were exposed for three days to two different forms of nanoparticles both composed of Ce02 (0.3, 3 and 30 µg/mL). The two Ce02 nanopartices had dry primary particle sizes of 8 nanometers {(M) ...

  2. Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells

    Science.gov (United States)

    To investigate genomic effects, human liver hepatocellular carcinoma (HepG2) cells were exposed for three days to two different forms of nanoparticles both composed of Ce02 (0.3, 3 and 30 µg/mL). The two Ce02 nanopartices had dry primary particle sizes of 8 nanometers {(M) ...

  3. 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.

  4. Porcine growth differentiation factor 9 gene polymorphisms and their associations with litter size

    Institute of Scientific and Technical Information of China (English)

    Yushan Zhang; Hongli Du; Jing Chen; Guanfu Yang; Xiquan Zhang

    2008-01-01

    Growth differentiation factor 9 (GDF9) is expressed in oocytes and is thought to be required for ovarian folliculogenesis.Given this function,GDF9 may be considered as a candidate gene controlling pig ovulate rate.In this study,the complete coding sequence was cloned (encoding a 444 amino acid),intron sequence and partial 5'-UTR of pig GDF9.RT-PCR results showed that GDF9 mRNA is expressed in a wide range of tissues of the ruttish Erhualian pig.The expression levels of GDF9 mRNA in pituitary,ovary,uterus and oviduct are higher in the Erhualian pigs than those in Duroc pigs,especially in pituitary with a significant difference (P<0.05).Comparative sequencing revealed 12 polymorphisms,including 8 single nucleotide polymorphisms (SNPS) and one 314 bp indel in noncoding regions,and the other 3 SNPS in coding regions.Four polymorphisms,G359C,C1801T,T1806C and 314 bp indel,were developed as markers for further use in population variation and association studies.The G359C polymorphism segregates only in Chinese native pigs,Erhualian and Dahuabai,on the contrary,314 bp indel segregates only in Duroc and Landrace.C1801T and T1806C sites seem to be completely linked and segregate in Erhualian,Dahuabai and Landrace.In a word,GDF9 may be not associated with pig litter size in extensive populations as per the studies of allele distributions of the four polymorphisms and pilot association in four breeds.

  5. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

    Directory of Open Access Journals (Sweden)

    Shuiquan eTang

    2016-02-01

    Full Text Available The genomes of two closely related Dehalobacter strains (strain CF and strain DCA were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF, 1,1,1-trichloroethane (1,1,1-TCA and 1,1-dichloroethane (1,1-DCA. The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA and strain DCA (that dechlorinates 1,1-DCA each contain 17 putative reductive dehalogenase homologous (rdh genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB, and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and greater than 99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1 and corrinoid biosynthesis pathways (strains E1 and PER-K23. The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to Dehalococcoides mccartyi

  6. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates.

    Science.gov (United States)

    Tang, Shuiquan; Wang, Po Hsiang; Higgins, Steven A; Löffler, Frank E; Edwards, Elizabeth A

    2016-01-01

    The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis

  7. Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

    Directory of Open Access Journals (Sweden)

    Julien Chaillot

    2017-02-01

    Full Text Available One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host.

  8. Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

    Science.gov (United States)

    Chaillot, Julien; Cook, Michael A.; Corbeil, Jacques; Sellam, Adnane

    2016-01-01

    One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host. PMID:28040776

  9. Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria.

    Science.gov (United States)

    Alavi, Peyman; Starcher, Margaret R; Thallinger, Gerhard G; Zachow, Christin; Müller, Henry; Berg, Gabriele

    2014-06-18

    In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. However, understanding the natural variation and possible differences between pathogens and beneficials is the main challenge in furthering these possibilities. The genus Stenotrophomonas contains representatives found to be associated with human and plant host. We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405T (both are biocontrol agents). We found an overall high degree of sequence similarity between the genomes of all three strains. Despite the notable similarity in potential factors responsible for host invasion and antibiotic resistance, other factors including several crucial virulence factors and heat shock proteins were absent in the plant-associated DSM14405T. Instead, S. rhizophila DSM14405T possessed unique genes for the synthesis and transport of the plant-protective spermidine, plant cell-wall degrading enzymes, and high salinity tolerance. Moreover, the presence or absence of bacterial growth at 37°C was identified as a very simple method in differentiating between pathogenic and non-pathogenic isolates. DSM14405T is not able to grow at this human-relevant temperature, most likely in great part due to the absence of heat shock genes and perhaps also because of the up-regulation at increased temperatures of several genes involved in a suicide mechanism. While this study is important for understanding the mechanisms behind the emerging pattern of infectious diseases, it is, to our knowledge, the first of its kind to

  10. DNA modifications and genome rearrangements during the development and sex differentiation of the bumble bee Bombus terrestris.

    Science.gov (United States)

    Bigot, Y; Jegot, G; Casteret, S; Aupinel, P; Tasei, J-N

    2011-04-01

    Bombus terrestris is a bumble bee that, like most hymenopteran species, exhibits ploidy-specific sex determination controlled by a single sex gene. Depending on their ploidy and the queen pheromone repression, the imagoes differentiate into three castes: males, workers and queens. Here, we focus on the differences of genome organization that occur during development and sex differentiation. We found that cytosine methylation is a significant epigenetic factor with profiles that can be correlated with both processes. We also showed that two kinds of genomic rearrangement occur. The first consists of important DNA amplifications that have sequence profiles that differ in the different developmental instars and sexes. In the second kind, DNA losses also occur, at least involving the mosaic transposable element B. terrestris mosaic repeat 1 (BTMR1).

  11. 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.

  12. Draft Genome Sequences of Two Novel Pseudomonas Strains Exhibiting Differential Hypersensitivity Reactions on Tobacco and Corn Seedlings

    Science.gov (United States)

    Tchagang, Caetanie Fometeu; Xu, Renlin; Mehrtash, Shima; Rahimi, Shabnam; Sidibé, Aïssata; Li, Xiang; Bromfield, Eden S. P.

    2016-01-01

    Two novel Pseudomonas strains (S1E40 and S3E12) isolated from corn roots are antagonistic to Rhizoctonia solani and exhibit differential hypersensitivity reactions on tobacco and corn seedlings. We report here the draft genome sequences of strains S1E40 and S3E12, consisting of 6.98 and 7.06 Mb with 6,150 and 6,129 predicted protein-coding sequences, respectively.

  13. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep.

    Directory of Open Access Journals (Sweden)

    Lifan Zhang

    Full Text Available Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms, we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome × for analysis. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. Based on pair-wise estimates of F(ST, significant genetic differentiation appeared between Suffolk and Rambouillet (F(ST = 0.1621, while Rambouillet and Targhee had the closest relationship (F(ST = 0.0681. A scan of the genome revealed 45 and 41 differentially selected regions (DSRs between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Our data indicated that regions 13 and 24 between Suffolk and Rambouillet might be good candidates for evaluating breed differences. Furthermore, ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.

  14. Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep.

    Science.gov (United States)

    Zhang, Lifan; Mousel, Michelle R; Wu, Xiaolin; Michal, Jennifer J; Zhou, Xiang; Ding, Bo; Dodson, Michael V; El-Halawany, Nermin K; Lewis, Gregory S; Jiang, Zhihua

    2013-01-01

    Sheep are among the major economically important livestock species worldwide because the animals produce milk, wool, skin, and meat. In the present study, the Illumina OvineSNP50 BeadChip was used to investigate genetic diversity and genome selection among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds from the United States. After quality-control filtering of SNPs (single nucleotide polymorphisms), we used 48,026 SNPs, including 46,850 SNPs on autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome × for analysis. Phylogenetic analysis based on all 46,850 SNPs clearly separated Suffolk from Rambouillet, Columbia, Polypay, and Targhee, which was not surprising as Rambouillet contributed to the synthesis of the later three breeds. Based on pair-wise estimates of F(ST), significant genetic differentiation appeared between Suffolk and Rambouillet (F(ST) = 0.1621), while Rambouillet and Targhee had the closest relationship (F(ST) = 0.0681). A scan of the genome revealed 45 and 41 differentially selected regions (DSRs) between Suffolk and Rambouillet and among Rambouillet-related breed populations, respectively. Our data indicated that regions 13 and 24 between Suffolk and Rambouillet might be good candidates for evaluating breed differences. Furthermore, ovine genome v3.1 assembly was used as reference to link functionally known homologous genes to economically important traits covered by these differentially selected regions. In brief, our present study provides a comprehensive genome-wide view on within- and between-breed genetic differentiation, biodiversity, and evolution among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds. These results may provide new guidance for the synthesis of new breeds with different breeding objectives.

  15. A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing.

    Science.gov (United States)

    Sangal, Vartul; Burkovski, Andreas; Hunt, Alison C; Edwards, Becky; Blom, Jochen; Hoskisson, Paul A

    2014-01-01

    The differentiation of clinically important Corynebacterium diphtheriae into specific biovars is complex and phylogenetically unclear. Comparative genomic analyses of 17 strains indicate that the division of C. diphtheriae into different biovars does not correlate with the variation in the gene content in the relevant metabolic categories that are potentially involved in the biovar discrimination. The biochemical separation is also not supported by phylogenetic analyses, suggesting molecular methods of typing C. diphtheriae strains should be adopted much more widely.

  16. Genome-wide differential expression reveals candidate genes involved in the pathogenesis of lupus and lupus nephritis.

    Science.gov (United States)

    AlFadhli, Suad; Ghanem, Aqeel A M; Nizam, Rasheeba

    2016-01-01

    Systemic lupus erythematosus (lupus) is an autoimmune disease characterized by multiorgan pathology, accelerated apoptosis and hyper-autoantibody production against self-components. The root cause of lupus remains unknown, although multiple susceptibility factors have been reported in different ethnic group. We aimed to explore the genome-wide differential expression spectrum of lupus and its severe form lupus nephritis (LN) in Arab females. A total of 98 subjects: 40 lupus, 18 LN and 40 age/gender/ethnically matched healthy controls (HC) were recruited. Carefully chosen subjects (n = 11) were employed for whole human-genome expression profiling using high-density Human Exon 1.0.ST arrays (Affymetrix) and statistical analysis was carried out using appropriate software. Validation cohorts (n = 98) were investigated to quantify the expression of the nine selected candidate genes relative to GAPDH as endogenous control. Genome-wide differential analysis revealed seven candidate genes in lupus and 36 in LN, when individually compared to HC (anova Welch t-test, P ≤ 0.005, Tukey's honestly post hoc analysis). Analysis of differentially expressed genes with a fold change of 2, revealed 16 Gene Ontology terms satisfying a P ≤ 0.05. We further detected five distinct inflammatory and metabolic pathways such as TWEAK, osteopontin, endochondral ossification, fluropyrimidine activity and urea cycle and metabolism of amino groups that significantly contribute to the pathogenesis of lupus (P Rheumatology and Wiley Publishing Asia Pty Ltd.

  17. Integrated functions of Pax3 and Pax7 in the regulation of proliferation, cell size and myogenic differentiation.

    Directory of Open Access Journals (Sweden)

    Charlotte A Collins

    Full Text Available Pax3 and Pax7 are paired-box transcription factors with roles in developmental and adult regenerative myogenesis. Pax3 and Pax7 are expressed by postnatal satellite cells or their progeny but are down regulated during myogenic differentiation. We now show that constitutive expression of Pax3 or Pax7 in either satellite cells or C2C12 myoblasts results in an increased proliferative rate and decreased cell size. Conversely, expression of dominant-negative constructs leads to slowing of cell division, a dramatic increase in cell size and altered morphology. Similarly to the effects of Pax7, retroviral expression of Pax3 increases levels of Myf5 mRNA and MyoD protein, but does not result in sustained inhibition of myogenic differentiation. However, expression of Pax3 or Pax7 dominant-negative constructs inhibits expression of Myf5, MyoD and myogenin, and prevents differentiation from proceeding. In fibroblasts, expression of Pax3 or Pax7, or dominant-negative inhibition of these factors, reproduce the effects on cell size, morphology and proliferation seen in myoblasts. Our results show that in muscle progenitor cells, Pax3 and Pax7 function to maintain expression of myogenic regulatory factors, and promote population expansion, but are also required for myogenic differentiation to proceed.

  18. Genome-wide scan for quantitative trait loci influencing LDL size and plasma triglyceride in familial hypertriglyceridemia.

    Science.gov (United States)

    Austin, Melissa A; Edwards, Karen L; Monks, Stephanie A; Koprowicz, Kent M; Brunzell, John D; Motulsky, Arno G; Mahaney, Michael C; Hixson, James E

    2003-11-01

    Small, dense LDLs and hypertriglyceridemia, two highly correlated and genetically influenced risk factors, are known to predict for risk of coronary heart disease. The objective of this study was to perform a whole-genome scan for linkage to LDL size and triglyceride (TG) levels in 26 kindreds with familial hypertriglyceridemia (FHTG). LDL size was estimated using gradient gel electrophoresis, and genotyping was performed for 355 autosomal markers with an average heterozygosity of 76% and an average spacing of 10.2 centimorgans (cMs). Using variance components linkage analysis, one possible linkage was found for LDL size [logarithm of odds (LOD) = 2.1] on chromosome 6, peak at 140 cM distal to marker F13A1 (closest marker D6S2436). With adjustment for TG and/or HDL cholesterol, the LOD scores were reduced, but remained in exactly the same location. For TG, LOD scores of 2.56 and 2.44 were observed at two locations on chromosome 15, with peaks at 29 and 61 cM distal to marker D15S822 (closest markers D15S643 and D15S211, respectively). These peaks were retained with adjustment for LDL size and/or HDL cholesterol. These findings, if confirmed, suggest that LDL particle size and plasma TG levels could be caused by two different genetic loci in FHTG.

  19. Balanced gene losses, duplications and intensive rearrangements led to an unusual regularly sized genome in Arbutus unedo chloroplasts.

    Directory of Open Access Journals (Sweden)

    Fernando Martínez-Alberola

    Full Text Available Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. Moreover, they can also be useful for exploiting chloroplast genetic engineering technology. Ericales account for approximately six per cent of eudicot diversity with 11,545 species from which only three complete plastome sequences are currently available. With the aim of increasing the number of ericalean complete plastome sequences, and to open new perspectives in understanding Mediterranean plant adaptations, a genomic study on the basis of the complete chloroplast genome sequencing of Arbutus unedo and an updated phylogenomic analysis of Asteridae was implemented. The chloroplast genome of A. unedo shows extensive rearrangements but a medium size (150,897 nt in comparison to most of angiosperms. A number of remarkable distinct features characterize the plastome of A. unedo: five-fold dismissing of the SSC region in relation to most angiosperms; complete loss or pseudogenization of a number of essential genes; duplication of the ndhH-D operon and its location within the two IRs; presence of large tandem repeats located near highly re-arranged regions and pseudogenes. All these features outline the primary evolutionary split between Ericaceae and other ericalean families. The newly sequenced plastome of A. unedo with the available asterid sequences allowed the resolution of some uncertainties in previous phylogenies of Asteridae.

  20. Geographical distribution of cytotypes in the Chrysanthemum indicum complex as evidenced by ploidy level and genome-size variation

    Institute of Scientific and Technical Information of China (English)

    Jing LI; Qian WAN; Richard J.ABBOTT; Guang-Yuan RAO

    2013-01-01

    A detailed knowledge of the geographical distribution ofcytotypes within and between species comprising a polyploid complex is critical to our understanding of the history and evolution of such complexes.In the present study we examined the geographical distributions ofcytotypes within six tentatively delimited species comprising the Chrysanthemum indicum complex in China.We determined the ploidy of 188 individuals sampled from 47 populations,based on DNA content using flow cytometry.In addition,chromosome counts were made on samples of each taxon.We confirmed that all samples of C.rhombifolium and C.lavandulifolium were diploid (2n =18),those of C.hypargyrum and C.potentilloides were tetraploid (2n--36),and those of C.vestitum were hexaploid (2n =54).In contrast,we confirmed that C.indicum contained both diploid and tetraploid cytotypes.We found that in addition to marked differences in genome size between ploidy levels,there was a variation in genome size between species of the same ploidy level.Although the diploid,tetraploid,and hexaploid taxa of the complex,as well as the diploid form of C.indicum,occurred only in central and northem China,the tetraploid form of C.indicum was widespread both north and south of the Yangtze River.We suggest that the tetraploid form of C.indicum may have expanded its range southward during recent Quatemary glacial periods when forests retreated in south China as conditions became drier.

  1. Chondrogenically differentiated mesenchymal stromal cell pellets stimulate endochondral bone regeneration in critical-sized bone defects

    NARCIS (Netherlands)

    J. van der Stok (Johan); M.K.E. Koolen; H. Jahr (Holger); N. Kops (Nicole); J.H. Waarsing (Jan); H.H. Weinans (Harrie); O.P. van der Jagt (Olav)

    2014-01-01

    markdownabstractAbstract: Grafting bone defects or atrophic non-unions with mesenchymal stromal cells (MSCs)-based grafts is not yet successful. MSC-based grafts typically use undifferentiated or osteogenically differentiated MSCs and regenerate bone through intramembranous ossification.

  2. Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.

    Directory of Open Access Journals (Sweden)

    Elijah R Behr

    Full Text Available Marked prolongation of the QT interval on the electrocardiogram associated with the polymorphic ventricular tachycardia Torsades de Pointes is a serious adverse event during treatment with antiarrhythmic drugs and other culprit medications, and is a common cause for drug relabeling and withdrawal. Although clinical risk factors have been identified, the syndrome remains unpredictable in an individual patient. Here we used genome-wide association analysis to search for common predisposing genetic variants. Cases of drug-induced Torsades de Pointes (diTdP, treatment tolerant controls, and general population controls were ascertained across multiple sites using common definitions, and genotyped on the Illumina 610k or 1M-Duo BeadChips. Principal Components Analysis was used to select 216 Northwestern European diTdP cases and 771 ancestry-matched controls, including treatment-tolerant and general population subjects. With these sample sizes, there is 80% power to detect a variant at genome-wide significance with minor allele frequency of 10% and conferring an odds ratio of ≥2.7. Tests of association were carried out for each single nucleotide polymorphism (SNP by logistic regression adjusting for gender and population structure. No SNP reached genome wide-significance; the variant with the lowest P value was rs2276314, a non-synonymous coding variant in C18orf21 (p  =  3×10(-7, odds ratio = 2, 95% confidence intervals: 1.5-2.6. The haplotype formed by rs2276314 and a second SNP, rs767531, was significantly more frequent in controls than cases (p  =  3×10(-9. Expanding the number of controls and a gene-based analysis did not yield significant associations. This study argues that common genomic variants do not contribute importantly to risk for drug-induced Torsades de Pointes across multiple drugs.

  3. Genome Wide Analysis of Drug-Induced Torsades de Pointes: Lack of Common Variants with Large Effect Sizes

    Science.gov (United States)

    Behr, Elijah R.; Ritchie, Marylyn D.; Tanaka, Toshihiro; Kääb, Stefan; Crawford, Dana C.; Nicoletti, Paola; Floratos, Aris; Sinner, Moritz F.; Kannankeril, Prince J.; Wilde, Arthur A. M.; Bezzina, Connie R.; Schulze-Bahr, Eric; Zumhagen, Sven; Guicheney, Pascale; Bishopric, Nanette H.; Marshall, Vanessa; Shakir, Saad; Dalageorgou, Chrysoula; Bevan, Steve; Jamshidi, Yalda; Bastiaenen, Rachel; Myerburg, Robert J.; Schott, Jean-Jacques; Camm, A. John; Steinbeck, Gerhard; Norris, Kris; Altman, Russ B.; Tatonetti, Nicholas P.; Jeffery, Steve; Kubo, Michiaki; Nakamura, Yusuke; Shen, Yufeng; George, Alfred L.; Roden, Dan M.

    2013-01-01

    Marked prolongation of the QT interval on the electrocardiogram associated with the polymorphic ventricular tachycardia Torsades de Pointes is a serious adverse event during treatment with antiarrhythmic drugs and other culprit medications, and is a common cause for drug relabeling and withdrawal. Although clinical risk factors have been identified, the syndrome remains unpredictable in an individual patient. Here we used genome-wide association analysis to search for common predisposing genetic variants. Cases of drug-induced Torsades de Pointes (diTdP), treatment tolerant controls, and general population controls were ascertained across multiple sites using common definitions, and genotyped on the Illumina 610k or 1M-Duo BeadChips. Principal Components Analysis was used to select 216 Northwestern European diTdP cases and 771 ancestry-matched controls, including treatment-tolerant and general population subjects. With these sample sizes, there is 80% power to detect a variant at genome-wide significance with minor allele frequency of 10% and conferring an odds ratio of ≥2.7. Tests of association were carried out for each single nucleotide polymorphism (SNP) by logistic regression adjusting for gender and population structure. No SNP reached genome wide-significance; the variant with the lowest P value was rs2276314, a non-synonymous coding variant in C18orf21 (p  =  3×10−7, odds ratio = 2, 95% confidence intervals: 1.5–2.6). The haplotype formed by rs2276314 and a second SNP, rs767531, was significantly more frequent in controls than cases (p  =  3×10−9). Expanding the number of controls and a gene-based analysis did not yield significant associations. This study argues that common genomic variants do not contribute importantly to risk for drug-induced Torsades de Pointes across multiple drugs. PMID:24223155

  4. Transcriptome-wide mining of the differentially expressed transcripts for natural variation of floral organ size in Physalis philadelphica.

    Science.gov (United States)

    Wang, Li; Li, Zhichao; He, Chaoying

    2012-11-01

    Natural phenotypic variation, a result of genetic variation, developed during evolution in response to environmental selections. Physalis philadelphica, known as tomatillo in the Solanaceae, is rich in floral and post-floral organ size diversity. However, its genetic variation is unknown. Here P. philadelphica was classified into three groups with large, intermediate, and small reproductive organ size, and a positive correlation was observed between floral organ and berry sizes. Through cDNA-amplified fragment length polymorphism (AFLP) analyses, 263 differentially expressed transcript-derived fragments (TDFs) were isolated from two accessions with different floral organ sizes. The genes encode various transcription factors, protein kinases, and enzymes, and they displayed multiple expression patterns during floral development, indicating a complexity in the genetic basis of phenotypic variation. Detailed expression analyses revealed that they were differentially expressed during floral and post-floral development, implying that they have roles in the development of flowers and fruits. Expression of three genes was further monitored in 26 accessions, and in particular the expression variation of Pp30, encoding an AP2-like transcription factor, correlates well with the observed phenotypic variations, which strongly supports an essential role for the gene in the natural variation of floral and post-floral organ size in Physalis. The results suggest that alteration in the expression pattern of a few key regulatory genes in the developmental process may be an important source of genetic variations that lead to natural variation in morphological traits.

  5. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes

    DEFF Research Database (Denmark)

    Langkjær, Rikke Breinhold; Cliften, P.F.; Johnston, M.

    2003-01-01

    Gene redundancy has been observed in yeast, plant and human genomes, and is thought to be a consequence of whole-genome duplications(1-3). Baker's yeast, Saccharomyces cerevisiae, contains several hundred duplicated genes(1). Duplication(s) could have occurred before or after a given speciation. ...

  6. Whole genome sequencing of sugarbeet and identification of differentially expressed genes regulating beet curly top resistance

    Science.gov (United States)

    The genome of KDH13 doubled haploid line has been sequenced using Illumina HiSeq2000 NGS platform. This line (PI663862) was released by USDA-ARS as a genetic stock resistant to beet curly top. Sequencing of a standard paired end and a 2kb-insert mate-pair genomic libraries, constructed from a leaf ...

  7. A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size.

    Science.gov (United States)

    Vasiliu, Daniel; Clamons, Samuel; McDonough, Molly; Rabe, Brian; Saha, Margaret

    2015-01-01

    Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED). Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.

  8. A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size.

    Directory of Open Access Journals (Sweden)

    Daniel Vasiliu

    Full Text Available Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED. Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.

  9. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.

    Science.gov (United States)

    Mao, Hailiang; Sun, Shengyuan; Yao, Jialing; Wang, Chongrong; Yu, Sibin; Xu, Caiguo; Li, Xianghua; Zhang, Qifa

    2010-11-09

    Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size. The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show an inhibitory effect on the OSR function; loss-of-function mutations of these domains produced very short grain. This study linked the functional domains of the GS3 protein to natural variation of grain size in rice.

  10. 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.; Justice, A.E.; Graff, M.; Barata, L.; Feitosa, M.F.; Groot, de C.P.G.M.

    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

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

    NARCIS (Netherlands)

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

    2015-01-01

    textabstractGenome-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

  12. 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

  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, 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 betw

  14. Role of Endothelial Differentiated Adipose-derived Stem Cells in Repairing Calvarial Critical Size Defects in the Laboratory Rat (Rattus norvegicus)

    Science.gov (United States)

    2014-07-16

    Differentiated Adipose-derived Stem Cells in Repairing Calvarial Critical Size Defects in the Laboratory Rat (Rattus norvegicus) PRINCIPAL INVESTIGATOR...SUBTITLE FDG20110033A "Role of Endothelial Differentiated Adipose-derived Stem Cells in Repairing Calvarial Critical Size Defects in the Laboratory Rat (Rattus

  15. Genomic islands as a marker to differentiate between clinical and environmental Burkholderia pseudomallei.

    Directory of Open Access Journals (Sweden)

    Thanatchaporn Bartpho

    Full Text Available Burkholderia pseudomallei, as a saprophytic bacterium that can cause a severe sepsis disease named melioidosis, has preserved several extra genes in its genome for survival. The sequenced genome of the organism showed high diversity contributed mainly from genomic islands (GIs. Comparative genome hybridization (CGH of 3 clinical and 2 environmental isolates, using whole genome microarrays based on B. pseudomallei K96243 genes, revealed a difference in the presence of genomic islands between clinical and environmental isolates. The largest GI, GI8, of B. pseudomallei was observed as a 2 sub-GI named GIs8.1 and 8.2 with distinguishable %GC content and unequal presence in the genome. GIs8.1, 8.2 and 15 were found to be more common in clinical isolates. A new GI, GI16c, was detected on chromosome 2. Presences of GIs8.1, 8.2, 15 and 16c were evaluated in 70 environmental and 64 clinical isolates using PCR assays. A combination of GIs8.1 and 16c (positivity of either GI was detected in 70% of clinical isolates and 11.4% of environmental isolates (P0.05. Some virulence genes located in the absent GIs and the difference of GIs seems to contribute less to bacterial virulence. The PCR detection of 2 GIs could be used as a cost effective and rapid tool to detect potentially virulent isolates that were contaminated in soil.

  16. Differential Gender Selection on Floral Size: An Experimental Approach Using Cistus salvifolius

    National Research Council Canada - National Science Library

    Montserrat Arista; Pedro Luis Ortiz

    2007-01-01

    ...-specific selection is scarce. 2. We experimentally altered flower size of the hermaphrodite Cistus salvifolius in three sites differing in physical characteristics, and measured the effect of this manipulation on both male and female success. 3...

  17. Size Differentiation Of A Continuous Stream Of Particles Using Acoustic Emissions

    Science.gov (United States)

    Nsugbe, E.; Starr, A.; Foote, P.; Ruiz-Carcel, C.; Jennions, I.

    2016-11-01

    Procter and Gamble (P&G) require an online system that can monitor the particle size distribution of their washing powder mixing process. This would enable the process to take a closed loop form which would enable process optimisation to take place in real time. Acoustic Emission (AE) was selected as the sensing method due to its non-invasive nature and primary sensitivity to frequencies which particle events emanate. This work details the results of the first experiment carried out in this research project. This experiment involved the use of AE to distinguish between the sizes of sieved polyethylene particle (53-250microns) and glass beads (150-600microns) which were dispensed on a target plate using a funnel. By conducting a threshold analysis of the impact peaks in the signal, the sizes of the particles could be distinguished and a signal feature was found which could be directly linked to the sizes of the particles.

  18. A Monte Carlo Study Investigating Missing Data, Differential Item Functioning, and Effect Size

    Science.gov (United States)

    Garrett, Phyllis

    2009-01-01

    The use of polytomous items in assessments has increased over the years, and as a result, the validity of these assessments has been a concern. Differential item functioning (DIF) and missing data are two factors that may adversely affect assessment validity. Both factors have been studied separately, but DIF and missing data are likely to occur…

  19. A simulation study provided sample size guidance for differential item functioning (DIF) studies using short scales

    DEFF Research Database (Denmark)

    Scott, Neil W; Fayers, Peter M; Aaronson, Neil K;

    2009-01-01

    Differential item functioning (DIF) analyses are increasingly used to evaluate health-related quality of life (HRQoL) instruments, which often include relatively short subscales. Computer simulations were used to explore how various factors including scale length affect analysis of DIF by ordinal...

  20. VARIABLE STEP-SIZE IMPLICIT-EXPLICIT LINEAR MULTISTEP METHODS FOR TIME-DEPENDENT PARTIAL DIFFERENTIAL EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    Dong Wang; Steven J. Ruuth

    2008-01-01

    Implicit-explicit (IMEX) linear multistep methods are popular techniques for solving partial differential equations (PDEs) with terms of different types. While fixed time-step versions of such schemes have been developed and studied, implicit-explicit schemes also naturally arise in general situations where the temporal smoothness of the solution changes. In this paper we consider easily implementable variable step-size implicit-explicit (VSIMEX) linear multistep methods for time-dependent PDEs. Families of order-p, p-step VSIMEX schemes are constructed and analyzed, where p ranges from 1 to 4. The corresponding schemes are simple to implement and have the property that they reduce to the classical IMEX schemes whenever constant time step-sizes are imposed. The methods are validated on the Burgers' equation. These results demonstrate that by varying the time step-size, VSIMEX methods can outperform their fixed time step counterparts while still maintaining good numerical behavior.

  1. Diversification and genetic differentiation of cultivated melon inferred from sequence polymorphism in the chloroplast genome

    OpenAIRE

    Tanaka, Katsunori; Akashi, Yukari; FUKUNAGA, Kenji; Yamamoto, Tatsuya; Aierken, Yasheng; Nishida, Hidetaka; Long, Chun Lin; Yoshino, Hiromichi; Sato, Yo-Ichiro; KATO, Kenji

    2013-01-01

    Molecular analysis encouraged discovery of genetic diversity and relationships of cultivated melon (Cucumis melo L.). We sequenced nine inter- and intra-genic regions of the chloroplast genome, about 5500 bp, using 60 melon accessions and six reference accessions of wild species of Cucumis to show intra-specific variation of the chloroplast genome. Sequence polymorphisms were detected among melon accessions and other Cucumis species, indicating intra-specific diversification of the chloroplas...

  2. Flow cytometric determination of genome size in European sunbleak Leucaspius delineatus (Heckel, 1843).

    Science.gov (United States)

    Filipiak, Marta; Tylko, Grzegorz; Kilarski, Wincenty

    2012-04-01

    The aim of this study was to compare DNA content in hepatocyte and erythrocyte nuclei of the European sunbleak, Leucaspius delineatus, in relation to nuclear and cell size by means of flow cytometry and fluorescence microscopy. The DNA standards, chicken and rainbow trout erythrocytes, were prepared in parallel with both cell types, with initial separation of liver cells in pepsin solution followed by cell filtering. Standards and investigated cells were stained with a mixture of propidium iodide, citric acid, and Nonidet P40 in the presence of RNAse, and fluorescence of at least 50,000 nuclei was analyzed by flow cytometry. Average cell size was determined by flow cytometry, using fresh cell suspension in relation to latex beads of known diameter. The size of nuclei was examined on the basis of digital micrographs obtained by fluorescence microscopy after nuclei staining with DAPI. The sunbleak's erythrocyte nuclei contain 2.25 ± 0.06 pg of DNA, whereas the hepatocyte nuclei contain 2.46 ± 0.06 pg of DNA. This difference in DNA content was determined spectroscopically using isolated DNA from the two cell types. The modal diameters of the erythrocytes and hepatocytes were estimated to be 5.1 ± 0.2 and 22.3 ± 5.0 μm, respectively, and the corresponding modal dimensions of their nuclei (measured as surface area) were 15.2 and 21.4 μm(2), respectively. The nucleoplasmic index, as calculated from diameters estimated from surface area of nuclear profiles, was 2.51 for the erythrocytes compared with 0.08 for hepatocytes.

  3. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats

    KAUST Repository

    Jimenez Infante, Francy M.

    2014-05-22

    Using dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated from the East (Japan) Sea. The PS1 clade is a sister group to the OCS116 clade, together forming a putatively novel order closely related to Rhizobiales. While most genomic features and most of the genetic content are conserved between RS24 and IMCC14465, their average nucleotide identity (ANI) is < 81%, suggesting two distinct species of the PS1 clade. Next to encoding two different variants of proteorhodopsin genes, they also harbor several unique genomic islands that contain genes related to degradation of aromatic compounds in IMCC14465 and in polymer degradation in RS24, possibly reflecting the physicochemical differences in the environment they were isolated from. No clear differences in abundance of the genomic content of either strain could be found in fragment recruitment analyses using different metagenomic datasets, in which both genomes were detectable albeit as minor part of the communities. The comparative genomic analysis of both isolates of the PS1 clade and the fragment recruitment analysis provide first insights into the ecology of this group. © 2014 Federation of European Microbiological Societies.

  4. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases.

    Directory of Open Access Journals (Sweden)

    Roberto Amato

    Full Text Available Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or F(ST. We performed a genome-wide estimation of F(ST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of F(ST values between autosomes and heterochromosomes. When we compared the F(ST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of F(ST, while several pathways related to cell signalling, growth and morphogenesis showed high F(ST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.

  5. Genome-wide copy number profiling of mouse neural stem cells during differentiation

    Directory of Open Access Journals (Sweden)

    U. Fischer

    2015-09-01

    Full Text Available There is growing evidence that gene amplifications were present in neural stem and progenitor cells during differentiation. We used array-CGH to discover copy number changes including gene amplifications and deletions during differentiation of mouse neural stem cells using TGF-ß and FCS for differentiation induction. Array data were deposited in GEO (Gene Expression Omnibus, NCBI under accession number GSE35523. Here, we describe in detail the cell culture features and our TaqMan qPCR-experiments to validate the array-CGH analysis. Interpretation of array-CGH experiments regarding gene amplifications in mouse and further detailed analysis of amplified chromosome regions associated with these experiments were published by Fischer and colleagues in Oncotarget (Fischer et al., 2015. We provide additional information on deleted chromosome regions during differentiation and give an impressive overview on copy number changes during differentiation induction at a time line.

  6. 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.

  7. Whole-Genome Analysis Revealed the Positively Selected Genes during the Differentiation of indica and Temperate japonica Rice

    Science.gov (United States)

    Sun, Xinli; Jia, Qi; Guo, Yuchun; Zheng, Xiujuan; Liang, Kangjing

    2015-01-01

    To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93–11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I. PMID:25774680

  8. Activities of E7 promoters in the human papillomavirus type 16 genome during cell differentiation

    DEFF Research Database (Denmark)

    Hansen, Christina Neigaard; Nielsen, Lone; Norrild, Bodil

    2010-01-01

    to deregulation of the cell cycle control. HPV-16 preferably infects the proliferating cells that will differentiate when they move upwards in the epithelium. The viral gene-expression is tightly coupled to the cellular differentiation program with early gene-expression being initiated in non- or low-differentiated...... cells and late gene-expression in more differentiated cells. We induced epithelial cells to differentiate by growth in medium with a high calcium concentration and measured the activity of different promoters thought to initiate E6 and/or E7 transcripts. The overall activity of the main promoter, P97......, situated in the long control region as well as the two promoters, P441 and P542, in the E6 ORF upstream of the E7 ORF, were decreased during differentiation. However, P441 and P542 were not down-regulated as much as P97. Therefore, we suggest that P441 and P542 regulate gene-expression in differentiated...

  9. “One-size-fits-all”? Differentiation in destinations’ marketing goals and strategies to achieve them

    OpenAIRE

    Avraham, Eli; Ketter, Eran

    2015-01-01

    While tourism marketing literature tends to present marketing as a ‘one-size-fits-all’ process, the current study suggests various destination marketing goals. Until today, the literature mainly concentrated on analyzing marketing strategies, tactics, tools and initiatives for enhancing and perceiving tourism, while other marketing goals were neglected, such as marketing unfamiliar destinations or promoting tourism during and after tourism crises. The purpose of this study is to propose the m...

  10. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders.

    Science.gov (United States)

    Keers, Robert; Coleman, Jonathan R I; Lester, Kathryn J; Roberts, Susanna; Breen, Gerome; Thastum, Mikael; Bögels, Susan; Schneider, Silvia; Heiervang, Einar; Meiser-Stedman, Richard; Nauta, Maaike; Creswell, Cathy; Thirlwall, Kerstin; Rapee, Ronald M; Hudson, Jennifer L; Lewis, Cathryn; Plomin, Robert; Eley, Thalia C

    2016-01-01

    The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such variants has so far been limited to preselected candidate genes. In this study we extended the differential susceptibility hypothesis from a candidate gene to a genome-wide approach to test whether a polygenic score of environmental sensitivity predicted response to cognitive behavioural therapy (CBT) in children with anxiety disorders. We identified variants associated with environmental sensitivity using a novel method in which within-pair variability in emotional problems in 1,026 monozygotic twin pairs was examined as a function of the pairs' genotype. We created a polygenic score of environmental sensitivity based on the whole-genome findings and tested the score as a moderator of parenting on emotional problems in 1,406 children and response to individual, group and brief parent-led CBT in 973 children with anxiety disorders. The polygenic score significantly moderated the effects of parenting on emotional problems and the effects of treatment. Individuals with a high score responded significantly better to individual CBT than group CBT or brief parent-led CBT (remission rates: 70.9, 55.5 and 41.6%, respectively). Pending successful replication, our results should be considered exploratory. Nevertheless, if replicated, they suggest that individuals with the greatest environmental sensitivity may be more likely to develop emotional problems in adverse environments but also benefit more from the most intensive types of treatment. © 2016 S. Karger AG, Basel.

  11. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders

    Science.gov (United States)

    Keers, Robert; Coleman, Jonathan R.I.; Lester, Kathryn J.; Roberts, Susanna; Breen, Gerome; Thastum, Mikael; Bögels, Susan; Schneider, Silvia; Heiervang, Einar; Meiser-Stedman, Richard; Nauta, Maaike; Creswell, Cathy; Thirlwall, Kerstin; Rapee, Ronald M.; Hudson, Jennifer L.; Lewis, Cathryn; Plomin, Robert; Eley, Thalia C.

    2016-01-01

    Background The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such variants has so far been limited to preselected candidate genes. In this study we extended the differential susceptibility hypothesis from a candidate gene to a genome-wide approach to test whether a polygenic score of environmental sensitivity predicted response to cognitive behavioural therapy (CBT) in children with anxiety disorders. Methods We identified variants associated with environmental sensitivity using a novel method in which within-pair variability in emotional problems in 1,026 monozygotic twin pairs was examined as a function of the pairs' genotype. We created a polygenic score of environmental sensitivity based on the whole-genome findings and tested the score as a moderator of parenting on emotional problems in 1,406 children and response to individual, group and brief parent-led CBT in 973 children with anxiety disorders. Results The polygenic score significantly moderated the effects of parenting on emotional problems and the effects of treatment. Individuals with a high score responded significantly better to individual CBT than group CBT or brief parent-led CBT (remission rates: 70.9, 55.5 and 41.6%, respectively). Conclusions Pending successful replication, our results should be considered exploratory. Nevertheless, if replicated, they suggest that individuals with the greatest environmental sensitivity may be more likely to develop emotional problems in adverse environments but also benefit more from the most intensive types of treatment. PMID:27043157

  12. swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing.

    Directory of Open Access Journals (Sweden)

    Zhen Wang

    Full Text Available DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs is fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swDMR/ for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach. It is an integrated tool designed for WGBS data, which not only implements accessible statistical methods to perform hypothesis test adapted to two or more samples without replicates, but false discovery rate was also controlled by multiple test correction. Downstream analysis tools were also provided, including cluster, annotation and visualization modules. In summary, based on WGBS data, swDMR can produce abundant information of differential methylated regions. As a convenient and flexible tool, we believe swDMR will bring us closer to unveil the potential functional regions involved in epigenetic regulation.

  13. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.

    Science.gov (United States)

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-03-03

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

  14. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    Science.gov (United States)

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level. PMID:28256554

  15. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

    Science.gov (United States)

    2013-01-01

    Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that

  16. Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis.

    Science.gov (United States)

    Volkov, Petr; Bacos, Karl; Ofori, Jones K; Esguerra, Jonathan Lou S; Eliasson, Lena; Rönn, Tina; Ling, Charlotte

    2017-04-01

    Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology. Here, we performed whole-genome bisulfite sequencing, which is a comprehensive and unbiased method to study DNA methylation throughout the genome at a single nucleotide resolution, in pancreatic islets from donors with T2D and control subjects without diabetes. We identified 25,820 DMRs in islets from individuals with T2D. These DMRs cover loci with known islet function, e.g., PDX1, TCF7L2, and ADCY5 Importantly, binding sites previously identified by ChIP-seq for islet-specific transcription factors, enhancer regions, and different histone marks were enriched in the T2D-associated DMRs. We also identified 457 genes, including NR4A3, PARK2, PID1, SLC2A2, and SOCS2, that had both DMRs and significant expression changes in T2D islets. To mimic the situation in T2D islets, candidate genes were overexpressed or silenced in cultured β-cells. This resulted in impaired insulin secretion, thereby connecting differential methylation to islet dysfunction. We further explored the islet methylome and found a strong link between methylation levels and histone marks. Additionally, DNA methylation in different genomic regions and of different transcript types (i.e., protein coding, noncoding, and pseudogenes) was associated with islet expression levels. Our study provides a comprehensive picture of the islet DNA methylome in individuals with and without diabetes and highlights the importance of epigenetic dysregulation in pancreatic islets and T2D

  17. Identification and analysis of genomic regions with large between-population differentiation in humans.

    Science.gov (United States)

    Myles, S; Tang, K; Somel, M; Green, R E; Kelso, J; Stoneking, M

    2008-01-01

    The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that show large differences between populations are expected to be associated with genomic regions exhibiting large allele frequency differences between populations. Thus, from genome-wide polymorphism data genomic regions with large allele frequency differences between populations can be identified, and evaluated as candidates for large between-population phenotypic differences. Here we use allele frequency data from approximately 1.5 million SNPs from three human populations, and present an algorithm that identifies genomic regions containing SNPs with extreme Fst. We demonstrate that our candidate regions have reduced heterozygosity in Europeans and Chinese relative to African-Americans, and are likely enriched with genes that have experienced positive natural selection. We identify genes that are likely responsible for phenotypes known to differ dramatically between human populations and present several candidates worthy of future investigation. Our list of high Fst genomic regions is a first step in identifying the genetic variants that contribute to large phenotypic differences between populations, many of which have likely experienced positive natural selection. Our approach based on between population differences can compliment traditional within population linkage and association studies to uncover novel genotype-phenotype relationships.

  18. Follistatin N terminus differentially regulates muscle size and fat in vivo.

    Science.gov (United States)

    Zheng, Hui; Qiao, Chunping; Tang, Ruhang; Li, Jianbin; Bulaklak, Karen; Huang, Zhenhua; Zhao, Chunxia; Dai, Yi; Li, Juan; Xiao, Xiao

    2017-09-15

    Delivery of follistatin (FST) represents a promising strategy for both muscular dystrophies and diabetes, as FST is a robust antagonist of myostatin and activin, which are critical regulators of skeletal muscle and adipose tissues. FST is a multi-domain protein, and deciphering the function of different domains will facilitate novel designs for FST-based therapy. Our study aims to investigate the role of the N-terminal domain (ND) of FST in regulating muscle and fat mass in vivo. Different FST constructs were created and packaged into the adeno-associated viral vector (AAV). Overexpression of wild-type FST in normal mice greatly increased muscle mass while decreasing fat accumulation, whereas overexpression of an N terminus mutant or N terminus-deleted FST had no effect on muscle mass but moderately decreased fat mass. In contrast, FST-I-I containing the complete N terminus and double domain I without domain II and III had no effect on fat but increased skeletal muscle mass. The effects of different constructs on differentiated C2C12 myotubes were consistent with the in vivo finding. We hypothesized that ND was critical for myostatin blockade, mediating the increase in muscle mass, and was less pivotal for activin binding, which accounts for the decrease in the fat tissue. An in vitro TGF-beta1-responsive reporter assay revealed that FST-I-I and N terminus-mutated or -deleted FST showed differential responses to blockade of activin and myostatin. Our study provided direct in vivo evidence for a role of the ND of FST, shedding light on future potential molecular designs for FST-based gene therapy.

  19. The evolutionary consequences of habitat fragmentation: Body morphology and coloration differentiation among brook trout populations of varying size.

    Science.gov (United States)

    Zastavniouk, Carol; Weir, Laura K; Fraser, Dylan J

    2017-09-01

    A reduction in population size due to habitat fragmentation can alter the relative roles of different evolutionary mechanisms in phenotypic trait differentiation. While deterministic (selection) and stochastic (genetic drift) mechanisms are expected to affect trait evolution, genetic drift may be more important than selection in small populations. We examined relationships between mature adult traits and ecological (abiotic and biotic) variables among 14 populations of brook trout. These naturally fragmented populations have shared ancestry but currently exhibit considerable variability in habitat characteristics and population size (49 habitat variation or operational sex ratio than to population size, suggesting that selection may overcome genetic drift at small population size. Phenotype-environment associations were also stronger in females than males, suggesting that natural selection due to abiotic conditions may act more strongly on females than males. Our results suggest that natural and sexual-selective pressures on phenotypic traits change during the process of habitat fragmentation, and that these changes are largely contingent upon existing habitat conditions within isolated fragments. Our study provides an improved understanding of the ecological and evolutionary consequences of habitat fragmentation and lends insight into the ability of some small populations to respond to selection and environmental change.

  20. Host size-dependent anisakid infection in Baltic cod Gadus morhua associated with differential food preferences

    DEFF Research Database (Denmark)

    Zuo, Shaozhi; Huwer, Bastian; Bahlool, Qusay

    2016-01-01

    sarsi) are preferred food items by small cod, the isopod Saduria entomon is taken by all size classes, and sprat Sprattus sprattus are common prey items for cod larger than 30 cm. Parasitological investigations (microscopic and molecular analyses) of H. sarsi (100 specimens) and S. entomon (40 specimens......) did not reveal infection in these invertebrates, but 11.6% of sprat (265 specimens examined) was shown to be infected with 1-8 C. osculatum third stage larvae per fish. Analyses of sprat stomach contents confirmed that copepods and cladocerans are the main food items of sprat. These observations...

  1. 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

  2. Differential methylation of E2 binding sites in episomal and integrated HPV 16 genomes in preinvasive and invasive cervical lesions.

    Science.gov (United States)

    Chaiwongkot, Arkom; Vinokurova, Svetlana; Pientong, Chamsai; Ekalaksananan, Tipaya; Kongyingyoes, Bunkerd; Kleebkaow, Pilaiwan; Chumworathayi, Bandit; Patarapadungkit, Natcha; Reuschenbach, Miriam; von Knebel Doeberitz, Magnus

    2013-05-01

    Enhanced expression of the HPV 16 E6-E7 oncogenes may trigger neoplastic transformation of the squamous epithelial cells at the uterine cervix. The HPV E2 protein is a key transcriptional regulator of the E6-E7 genes. It binds to four E2 binding sites (E2BSs 1-4) in the viral upstream regulatory region (URR). Modification of E2 functions, for example, by methylation of E2BSs is hypothesized to trigger enhanced expression of the viral E6-E7 oncogenes. In the majority of HPV-transformed premalignant lesions and about half of cervical carcinomas HPV genomes persist in an extra-chromosomal, episomal state, whereas they are integrated into host cells chromosomes in the remaining lesions. Here we compared the methylation profile of E2BSs 1-4 of the HPV 16 URR in a series of 18 HPV16-positive premalignant lesions and 33 invasive cervical cancers. CpGs within the E2BSs 1, 3, and 4 were higher methylated in all lesions with only episomal HPV16 genomes compared with lesions displaying single integrated copies. Samples with multiple HPV16 integrated copies displayed high methylation levels for all CpGs suggesting that the majority of multiple copies were silenced by extensive methylation. These data support the hypothesis that differential methylation of the E2BSs 1, 3 and 4 is related to the activation of viral oncogene expression in cervical lesions as long as the viral genome remains in the episomal state. Once the virus becomes integrated into host cell chromosomes these methylation patterns may be substantially altered due to complex epigenetic changes of integrated HPV genomes.

  3. Immune-Modulatory Genomic Properties Differentiate Gut Microbiotas of Infants with and without Eczema

    KAUST Repository

    Yap, Gaik Chin

    2015-10-14

    Background: The gastrointestinal tract is the primary site of interaction between the host immune system and microorganisms. Studies have suggested that selective microbial targets may influence the development of the allergic diseases. But the difference in functional gene composition remains unknown. We aim to assess the structural and functional gene composition of stool microbiota of infants with eczema and their matched (for age, gender, mode of delivery, feeding) controls at the age of 1 month. Methods: Twelve children with eczema and their controls were selected from the placebo arm of a birth cohort of at-risk infants participating in a randomized double-blind trial on the protective effects of supplemental probiotics in early life on allergic outcomes. The four were caesarean delivery followed by formula feeding (eczema = 2 and healthy control = 2) and the eight were vaginal delivery followed by partial breast feeding mixed with formula feeding (eczema = 4 and healthy control = 4). Bacterial genomic DNA were extracted from fecal samples and prepared for Illumina Miseq and Hiseq sequencing. Data analysis such as sequence quality check, contigs assembly and gene annotation were carried out for the DNA sequences obtained from Miseq and Hiseq sequencing. Results: Phylogenetic analysis of metagenomic sequences revealed that four phyla dominated both microbial communities: Proteobacteria (54% and 63% for healthy and eczema communities, respectively), Firmicutes (26% and 18%), Actinobacteria (13% and 8%), Bacteroidetes (7% and 8%). Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in healthy communities, many of which were encoded by Bifidobacterium (38% of the total motifs in the healthy communities). Draft genomes of five Bifidobacterium species (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum ) were recovered from metagenomic datasets. The B. longum BFN-121- 2 genome encoded more

  4. Gradients in pore size enhance the osteogenic differentiation of human mesenchymal stromal cells in three-dimensional scaffolds

    Science.gov (United States)

    di Luca, Andrea; Ostrowska, Barbara; Lorenzo-Moldero, Ivan; Lepedda, Antonio; Swieszkowski, Wojcech; van Blitterswijk, Clemens; Moroni, Lorenzo

    2016-03-01

    Small fractures in bone tissue can heal by themselves, but in case of larger defects current therapies are not completely successful due to several drawbacks. A possible strategy relies on the combination of additive manufactured polymeric scaffolds and human mesenchymal stromal cells (hMSCs). The architecture of bone tissue is characterized by a structural gradient. Long bones display a structural gradient in the radial direction, while flat bones in the axial direction. Such gradient presents a variation in bone density from the cancellous bone to the cortical bone. Therefore, scaffolds presenting a gradient in porosity could be ideal candidates to improve bone tissue regeneration. In this study, we present a construct with a discrete gradient in pore size and characterize its ability to further support the osteogenic differentiation of hMSCs. Furthermore, we studied the behaviour of hMSCs within the different compartments of the gradient scaffolds, showing a correlation between osteogenic differentiation and ECM mineralization, and pore dimensions. Alkaline phosphatase activity and calcium content increased with increasing pore dimensions. Our results indicate that designing structural porosity gradients may be an appealing strategy to support gradual osteogenic differentiation of adult stem cells.

  5. Developmentally coordinated extrinsic signals drive human pluripotent stem cell differentiation toward authentic DARPP-32+ medium-sized spiny neurons.

    Science.gov (United States)

    Delli Carri, Alessia; Onorati, Marco; Lelos, Mariah J; Castiglioni, Valentina; Faedo, Andrea; Menon, Ramesh; Camnasio, Stefano; Vuono, Romina; Spaiardi, Paolo; Talpo, Francesca; Toselli, Mauro; Martino, Gianvito; Barker, Roger A; Dunnett, Stephen B; Biella, Gerardo; Cattaneo, Elena

    2013-01-15

    Medium-sized spiny neurons (MSNs) are the only neostriatum projection neurons, and their degeneration underlies some of the clinical features of Huntington's disease. Using knowledge of human developmental biology and exposure to key neurodevelopmental molecules, human pluripotent stem (hPS) cells were induced to differentiate into MSNs. In a feeder-free adherent culture, ventral telencephalic specification is induced by BMP/TGFβ inhibition and subsequent SHH/DKK1 treatment. The emerging FOXG1(+)/GSX2(+) telencephalic progenitors are then terminally differentiated, resulting in the systematic line-independent generation of FOXP1(+)/FOXP2(+)/CTIP2(+)/calbindin(+)/DARPP-32(+) MSNs. Similar to mature MSNs, these neurons carry dopamine and A2a receptors, elicit a typical firing pattern and show inhibitory postsynaptic currents, as well as dopamine neuromodulation and synaptic integration ability in vivo. When transplanted into the striatum of quinolinic acid-lesioned rats, hPS-derived neurons survive and differentiate into DARPP-32(+) neurons, leading to a restoration of apomorphine-induced rotation behavior. In summary, hPS cells can be efficiently driven to acquire a functional striatal fate using an ontogeny-recapitulating stepwise method that represents a platform for in vitro human developmental neurobiology studies and drug screening approaches.

  6. Genome-wide differential gene expression in children exposed to air pollution in the Czech Republic

    DEFF Research Database (Denmark)

    van Leeuwen, D M; van Herwijnen, M H M; Pedersen, Marie

    2006-01-01

    The Teplice area in the Czech Republic is a mining district where elevated levels of air pollution including airborne carcinogens, have been demonstrated, especially during winter time. This environmental exposure can impact human health; in particular children may be more vulnerable. To study....... This suggests an effect of air pollution on the primary structural unit of the condensed DNA. In addition, several other pathways were modulated. Based on the results of this study, we suggest that transcriptomic analysis represents a promising biomarker for environmental carcinogenesis....... the impact of air pollution in children at the transcriptional level, peripheral blood cells were subjected to whole genome response analysis, in order to identify significantly modulated biological pathways and processes as a result of exposure. Using genome-wide oligonucleotide microarrays, we investigated...

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

    Science.gov (United States)

    Multi-partite 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). We provide the first report of a multi-partite mitochondrial genome architecture...

  8. Synthesis and size differentiation of Ge nanocrystals in amorphous SiO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Agan, S. [University of Illinois, Department of Materials Science and Engineering, Urbana, IL (United States); Kirikale University, Physics Department, Kirikale (Turkey); Celik-Aktas, A. [University of Illinois, Department of Nuclear, Plasma and Radiological Engineering, Urbana, IL (United States); Zuo, J.M. [University of Illinois, Department of Materials Science and Engineering, Urbana, IL (United States); Dana, A.; Aydinli, A. [Bilkent University, Physics Department, Ankara (Turkey)

    2006-04-15

    Germanosilicate layers were grown on Si substrates by plasma enhanced chemical vapor deposition (PECVD) and annealed at different temperatures ranging from 700-1010 C for durations of 5 to 60 min. Transmission electron microscopy (TEM) was used to investigate Ge nanocrystal formation in SiO{sub 2}:Ge films. High-resolution cross section TEM images, electron energy-loss spectroscopy and energy dispersive X-ray analysis (EDX) data indicate that Ge nanocrystals are present in the amorphous silicon dioxide films. These nanocrystals are formed in two spatially separated layers with average sizes of 15 and 50 nm, respectively. EDX analysis indicates that Ge also diffuses into the Si substrate. (orig.)

  9. Effects of apatite particle size in two apatite/collagen composites on the osteogenic differentiation profile of osteoblastic cells.

    Science.gov (United States)

    Hatakeyama, Wataru; Taira, Masayuki; Chosa, Naoyuki; Kihara, Hidemichi; Ishisaki, Akira; Kondo, Hisatomo

    2013-12-01

    The development of new osteoconductive bone substitute materials is expected in medicine. In this study, we attempted to produce new hydroxylapatite (HAP)/collagen (Col) composites using two HAP particles of different sizes and porcine type I collagen. The two HAP particles were either nano-sized (40 nm in average diameter; n-HAP) or had macro-pore sizes of 0.5‑1.0 mm in length with fully interconnected pores (m-HAP). The aim of this study was to investigate the effects of apatite particle size in two HAP/Col composites on the osteogenic differentiation profile in osteoblast-like cells (SaOS-2). We created a collagen control sponge (Col) and two HAP/Col composite sponges (n-HAP/Col and m-HAP/Col) using freeze-drying and dehydrothermal cross-linking techniques, and then punched out samples of 6 mm in diameter and 1 mm in height. The SaOS-2 cells were cultured on three test materials for 1, 2, 3 and 4 weeks. Total RNA was extracted from the cultured cells and the expression of osteogenic differentiation-related genes was evaluated by reverse transcription PCR (RT-PCR) using primer sets of alkaline phosphatase (ALP), type 1 collagen (COL1), bone sialoprotein (BSP) and osteocalcin precursor [bone gamma-carboxyglutamate (gla) protein (BGLAP)] genes, as well as the β-actin gene. The cells were also cultured on Col, n-HAP/Col and m-HAP/Col specimens for 1 and 4 weeks, and were then observed under a scanning electron microscope (SEM). The experimental results were as follows: RT-PCR indicated that osteogenic differentiation, particularly the gene expression of BSP, was most accelerated when the cells were cultured on n-HAP/Col specimens, followed by m-HAP/Col, whilst the weakest accelaeration was observed when the cells were cultured on Col specimens. As shown by the SEM images, the SaOS-2 cells were fibroblastic when cultured on Col specimens for up to 4 weeks; they were fibroblastic when cultured on n-HAP/Col specimens for 1 week, but appeared as spheroids

  10. Hospital morbidity in a medium-sized city: differentials between men and women

    Directory of Open Access Journals (Sweden)

    Guilherme Oliveira de Arruda

    2014-01-01

    Full Text Available OBJECTIVE: characterize the hospital morbidity of adults living in the city of Maringá, PR, Brazil, between 2000 and 2011, focusing on the differential between men and women. METHOD: this descriptive study was developed based on data from the Hospital Information System of the Unified Health System in order to investigate the association between groups of hospitalization causes and the average length of hospitalization per gender, in three-year periods. RESULTS: the main groups of hospitalization causes for men were: mental disorders, lesions and circulatory diseases; and, among women: tumors, circulatory and genitourinary diseases. Mental disorders and lesions, tumors, circulatory and genitourinary diseases were significantly associated with the female and male genders across the study period. Although not significant, the mean length of hospitalization dropped across the four three-year periods, and only showed a significant difference between men and women in the second triennium. CONCLUSION: differences in the hospital morbidity profile between men and women underline the need for specific health and nursing actions, especially in primary health care, with a view to reducing hospitalizations due to the main groups of causes in the city.

  11. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation.

    Directory of Open Access Journals (Sweden)

    Shen-Hsi Yang

    Full Text Available Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of pluripotency or differentiation. In this study we have focused on how mouse embryonic stem cells begin to differentiate and lose pluripotency and, in particular, the role that the ERK MAP kinase and GSK3 signaling pathways play in this process. Through a genome-wide siRNA screen we have identified more than 400 genes involved in loss of pluripotency and promoting the onset of differentiation. These genes were functionally associated with the ERK and/or GSK3 pathways, providing an important resource for studying the roles of these pathways in controlling escape from the pluripotent ground state. More detailed analysis identified MAP kinase phosphatases as a focal point of regulation and demonstrated an important role for these enzymes in controlling ERK activation kinetics and subsequently determining early embryonic stem cell fate decisions.

  12. Differential patterns of whole-genome DNA methylation in institutionalized children and children raised by their biological parents.

    Science.gov (United States)

    Naumova, Oksana Yu; Lee, Maria; Koposov, Roman; Szyf, Moshe; Dozier, Mary; Grigorenko, Elena L

    2012-02-01

    Previous studies with nonhuman species have shown that animals exposed to early adversity show differential DNA methylation relative to comparison animals. The current study examined differential methylation among 14 children raised since birth in institutional care and 14 comparison children raised by their biological parents. Blood samples were taken from children in middle childhood. Analysis of whole-genome methylation patterns was performed using the Infinium HumanMethylation27 BeadChip assay (Illumina), which contains 27,578 CpG sites, covering approximately 14,000 gene promoters. Group differences were registered, which were characterized primarily by greater methylation in the institutionalized group relative to the comparison group, with most of these differences in genes involved in the control of immune response and cellular signaling systems, including a number of crucial players important for neural communication and brain development and functioning. The findings suggest that patterns of differential methylation seen in nonhuman species with altered maternal care are also characteristic of children who experience early maternal separation.

  13. [Particle Size and Number Density Online Analysis for Particle Suspension with Polarization-Differentiation Elastic Light Scattering Spectroscopy].

    Science.gov (United States)

    Chen, Wei-kang; Fang, Hui

    2016-03-01

    The basic principle of polarization-differentiation elastic light scattering spectroscopy based techniques is that under the linear polarized light incidence, the singlely scattered light from the superficial biological tissue and diffusively scattered light from the deep tissue can be separated according to the difference of polarization characteristics. The novel point of the paper is to apply this method to the detection of particle suspension and, to realize the simultaneous measurement of its particle size and number density in its natural status. We design and build a coaxial cage optical system, and measure the backscatter signal at a specified angle from a polystyrene microsphere suspension. By controlling the polarization direction of incident light with a linear polarizer and adjusting the polarization direction of collected light with another linear polarizer, we obtain the parallel polarized elastic light scattering spectrum and cross polarized elastic light scattering spectrum. The difference between the two is the differential polarized elastic light scattering spectrum which include only the single scattering information of the particles. We thus compare this spectrum to the Mie scattering calculation and extract the particle size. We then also analyze the cross polarized elastic light scattering spectrum by applying the particle size already extracted. The analysis is based on the approximate expressions taking account of light diffusing, from which we are able to obtain the number density of the particle suspension. We compare our experimental outcomes with the manufacturer-provided values and further analyze the influence of the particle diameter standard deviation on the number density extraction, by which we finally verify the experimental method. The potential applications of the method include the on-line particle quality monitoring for particle manufacture as well as the fat and protein density detection of milk products.

  14. 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.

    Directory of Open Access Journals (Sweden)

    Yvette A Halley

    Full Text Available 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.

  15. 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.

  16. A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits.

    Science.gov (United States)

    Bainard, Jillian D; Bainard, Luke D; Henry, Thomas A; Fazekas, Aron J; Newmaster, Steven G

    2012-12-01

    Genome size (C-value) and endopolyploidy (endoreduplication index, EI) are known to correlate with various morphological and ecological traits, in addition to phylogenetic placement. A phylogenetically controlled multivariate analysis was used to explore the relationships between DNA content and phenotype in angiosperms. Seeds from 41 angiosperm species (17 families) were grown in a common glasshouse experiment. Genome size (2C-value and 1Cx-value) and EI (in four tissues: leaf, stem, root, petal) were determined using flow cytometry. The phylogenetic signal was calculated for each measure of DNA content, and phylogenetic canonical correlation analysis (PCCA) explored how the variation in genome size and EI was correlated with 18 morphological and ecological traits. Phylogenetic signal (λ) was strongest for EI in all tissues, and λ was stronger for the 2C-value than the 1Cx-value. PCCA revealed that EI was correlated with pollen length, stem height, seed mass, dispersal mechanism, arbuscular mycorrhizal association, life history and flowering time, and EI and genome size were both correlated with stem height and life history. PCCA provided an effective way to explore multiple factors of DNA content variation and phenotypic traits in a phylogenetic context. Traits that were correlated significantly with DNA content were linked to plant competitive ability. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  17. Dividing the pie: differential dung pat size utilization by sympatric Haematobia irritans and Musca autumnalis.

    Science.gov (United States)

    Fowler, F E; Mullens, B A

    2016-06-01

    Horn flies [Haematobia irritans (Diptera: Muscidae) (L.)] and face flies [Musca autumnalis (Diptera: Muscidae) De Geer] use the same larval resource, but their interactions are poorly studied. Dung pats (n = 350) were core sampled in the summers of 2012 and 2013 from irrigated pastures in Pomona, California, U.S.A. (34°03'N, 117°48'W) and held for face fly and horn fly emergence. Surface areas and estimated weights were recorded for each whole pat. Almost half (42.0%) of the pat cores yielded neither fly, 29.7% yielded horn flies only, 12.9% yielded face flies only and 15.4% yielded both flies. Of the fly-positive pats, surface area and mass were larger for face fly-occupied pats, whereas horn fly-occupied pats were smaller. Pats shared by the two species were intermediate. Horn flies per positive core were unaffected by the absence/presence of face flies, but half as many face flies emerged when pats were co-inhabited by horn flies. Face flies inhabited larger pats, which might better resist heating and drying, to which they are susceptible; horn flies inhabited a broad pat size range. Horn fly tolerance of lower dung moisture probably allows horn flies to colonize and survive in a wide range of pats in dry areas like southern California.

  18. Rice starch granule amylolysis--differentiating effects of particle size, morphology, thermal properties and crystalline polymorph.

    Science.gov (United States)

    Dhital, Sushil; Butardo, Vito M; Jobling, Stephen A; Gidley, Michael J

    2015-01-22

    The underlying mechanism of amylolysis of rice starch granules was investigated using isolated starch granules from wild-type, as well as SBEIIb mutant and down-regulated lines. Fused granule agglomerates isolated from mutant and transgenic lines were hydrolysed at similar rates by amylases, and had similar crystalline patterns and thermal properties as individual granules. Surface pores, a feature previously only reported for A-polymorphic starch granules, were also observed in B- and C-polymorphic rice starch granules. Although the microscopic patterns of hydrolysis among granules with different crystalline polymorphs were qualitatively similar, the extent and the rate of amylolysis were different, suggesting that B-type crystalline polymorphs are intrinsically more resistant to enzymatic hydrolysis than A-type in rice starch granules. It is proposed that the slightly longer branch lengths of amylopectin which leads to the formation of more stable B-type double helical structures compared to their A-type counterparts is the major parameter, with other factors such as granule size, surface pores and interior channels having secondary roles, in determining the rate of enzymatic hydrolysis of rice starch granules.

  19. E-business inom fastighetsbranschen : En undersökning av fastighetsbyrån Fantastic Franks differentiering genom E-business

    OpenAIRE

    2015-01-01

    Utifrån Canvas analysmodell, hur ser Fantastic Franks E-business ut? Hur är synen på E-business hos en liten nischad fastighetsbyrå? Syftet med denna studie är att analysera Fantastic Franks E-business genom Canvas analysmodell och analysera hur differentiering genom E-business påverkar företagets framgång. Genom intervju med ledningsgruppsrepresentant från Fantastic Frank samt med fastighetsmäklare på Fantastic Frank applicerades företagets affärsmodell på modellen Källor till värdeskapande ...

  20. Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin.

    Science.gov (United States)

    Acosta, M J; Marchal, J A; Fernández-Espartero, C H; Bullejos, M; Sánchez, A

    2008-01-01

    The chromosomal distribution of mobile genetic elements is scarcely known in Arvicolinae species, but could be of relevance to understand the origin and complex evolution of the sex chromosome heterochromatin. In this work we cloned two retrotransposon sequences, L1 and SINE-B1, from the genome of Chionomys nivalis and investigated their chromosomal distribution on several arvicoline species. Our results demonstrate first that both retroelements are the most abundant repeated DNA sequences in the genome of these species. L1 elements, in most species, are highly accumulated in the sex chromosomes compared to the autosomes. This favoured L1 insertion could have played an important role in the origin of the enlarged heterochromatic blocks existing in the sex chromosomes of some Microtus species. Also, we propose that L1 accumulation on the X heterochromatin could have been the consequence of different, independent and rapid amplification processes acting in each species. SINE elements, however, were completely lacking from the constitutive heterochromatin, either in autosomes or in the heterochromatic blocks of sex chromosomes. These data could indicate that some SINE elements are incompatible with the formation of heterochromatic complexes and hence are necessarily missing from the constitutive heterochromatin.

  1. Differentiating sibling species of Zeugodacus caudatus (Insecta: Tephritidae) by complete mitochondrial genome.

    Science.gov (United States)

    Yong, Hoi-Sen; Song, Sze-Looi; Lim, Phaik-Eem; Eamsobhana, Praphathip; Suana, I Wayan

    2016-10-01

    Zeugodacus caudatus is a pest of pumpkin flowers. It has a Palearctic and Oriental distribution. We report here the complete mitochondrial genome of the Malaysian and Indonesian samples of Z. caudatus determined by next-generation sequencing of genomic DNA and determine their taxonomic status as sibling species and phylogeny with other taxa of the genus Zeugodacus. The whole mitogenome of both samples possessed 37 genes (13 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region. The mitogenome of the Indonesian sample (15,885 bp) was longer than that of the Malaysian sample (15,866 bp). In both samples, TΨC-loop was absent in trnF and DHU-loop was absent in trnS1. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes), with the two samples of Z. caudatus forming a sister group and the genus Zeugodacus was monophyletic. The Malaysian and Indonesian samples of Z. caudatus have a genetic distance of p = 7.8 % based on 13 PCGs and p = 7.0 % based on 15 mitochondrial genes, indicating status of sibling species. They are proposed to be accorded specific status as members of a species complex.

  2. Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing

    Science.gov (United States)

    Jain, Mukesh; Chevala, VVS Narayana; Garg, Rohini

    2014-01-01

    MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that orchestrate plant development. Although several genomic resources have been developed for the legume crop chickpea, miRNAs have not been discovered until now. For genome-wide discovery of miRNAs in chickpea (Cicer arietinum), we sequenced the small RNA content from seven major tissues/organs employing Illumina technology. About 154 million reads were generated, which represented more than 20 million distinct small RNA sequences. We identified a total of 440 conserved miRNAs in chickpea based on sequence similarity with known miRNAs in other plants. In addition, 178 novel miRNAs were identified using a miRDeep pipeline with plant-specific scoring. Some of the conserved and novel miRNAs with significant sequence similarity were grouped into families. The chickpea miRNAs targeted a wide range of mRNAs involved in diverse cellular processes, including transcriptional regulation (transcription factors), protein modification and turnover, signal transduction, and metabolism. Our analysis revealed several miRNAs with differential spatial expression. Many of the chickpea miRNAs were expressed in a tissue-specific manner. The conserved and differential expression of members of the same miRNA family in different tissues was also observed. Some of the same family members were predicted to target different chickpea mRNAs, which suggested the specificity and complexity of miRNA-mediated developmental regulation. This study, for the first time, reveals a comprehensive set of conserved and novel miRNAs along with their expression patterns and putative targets in chickpea, and provides a framework for understanding regulation of developmental processes in legumes. PMID:25151616

  3. Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques.

    Directory of Open Access Journals (Sweden)

    Anna de Lang

    2007-08-01

    Full Text Available The pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity. Using functional genomics, we analyzed early host responses to SARS-CoV infection in the lungs of adolescent cynomolgus macaques (Macaca fascicularis that show lung pathology similar to that observed in human adults with SARS. Analysis of gene signatures revealed induction of a strong innate immune response characterized by the stimulation of various cytokine and chemokine genes, including interleukin (IL-6, IL-8, and IP-10, which corresponds to the host response seen in acute respiratory distress syndrome. As opposed to many in vitro experiments, SARS-CoV induced a wide range of type I interferons (IFNs and nuclear translocation of phosphorylated signal transducer and activator of transcription 1 in the lungs of macaques. Using immunohistochemistry, we revealed that these antiviral signaling pathways were differentially regulated in distinctive subsets of cells. Our studies emphasize that the induction of early IFN signaling may be critical to confer protection against SARS-CoV infection and highlight the strength of combining functional genomics with immunohistochemistry to further unravel the pathogenesis of SARS.

  4. Differential pathway dependency discovery associated with drug response across cancer cell lines. | Office of Cancer Genomics

    Science.gov (United States)

    The effort to personalize treatment plans for cancer patients involves the identification of drug treatments that can effectively target the disease while minimizing the likelihood of adverse reactions. In this study, the gene-expression profile of 810 cancer cell lines and their response data to 368 small molecules from the Cancer Therapeutics Research Portal (CTRP) are analyzed to identify pathways with significant rewiring between genes, or differential gene dependency, between sensitive and non-sensitive cell lines.

  5. Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study.

    Directory of Open Access Journals (Sweden)

    Yao-Zhong Liu

    Full Text Available Osteoporosis, the most prevalent metabolic bone disease among older people, increases risk for low trauma hip fractures (HF that are associated with high morbidity and mortality. Hip bone size (BS has been identified as one of the key measurable risk factors for HF. Although hip BS is highly genetically determined, genetic factors underlying the trait are still poorly defined. Here, we performed the first genome-wide association study (GWAS of hip BS interrogating approximately 380,000 SNPs on the Affymetrix platform in 1,000 homogeneous unrelated Caucasian subjects, including 501 females and 499 males. We identified a gene, PLCL1 (phospholipase c-like 1, that had four SNPs associated with hip BS at, or approaching, a genome-wide significance level in our female subjects; the most significant SNP, rs7595412, achieved a p value of 3.72x10(-7. The gene's importance to hip BS was replicated using the Illumina genotyping platform in an independent UK cohort containing 1,216 Caucasian females. Two SNPs of the PLCL1 gene, rs892515 and rs9789480, surrounded by the four SNPs identified in our GWAS, achieved p values of 8.62x10(-3 and 2.44x10(-3, respectively, for association with hip BS. Imputation analyses on our GWAS and the UK samples further confirmed the replication signals; eight SNPs of the gene achieved combined imputed p values<10(-5 in the two samples. The PLCL1 gene's relevance to HF was also observed in a Chinese sample containing 403 females, including 266 with HF and 177 control subjects. A SNP of the PLCL1 gene, rs3771362 that is only approximately 0.6 kb apart from the most significant SNP detected in our GWAS (rs7595412, achieved a p value of 7.66x10(-3 (odds ratio = 0.26 for association with HF. Additional biological support for the role of PLCL1 in BS comes from previous demonstrations that the PLCL1 protein inhibits IP3 (inositol 1,4,5-trisphosphate-mediated calcium signaling, an important pathway regulating mechanical sensing of

  6. Genome-wide assessment of differential effector gene use in embryogenesis.

    Science.gov (United States)

    Barsi, Julius C; Tu, Qiang; Calestani, Cristina; Davidson, Eric H

    2015-11-15

    Six different populations of cells were isolated by fluorescence-activated cell sorting from disaggregated late blastula- and gastrula-stage sea urchin embryos according to the regulatory states expressed in these cells, as reported by recombineered bacterial artificial chromosomes producing fluorochromes. Transcriptomes recovered from these embryonic cell populations revealed striking, early differential expression of large cohorts of effector genes. The six cell populations were presumptive pigment cells, presumptive neurogenic cells, presumptive skeletogenic cells, cells from the stomodeal region of the oral ectoderm, ciliated band cells and cells from the endoderm/ectoderm boundary that will give rise both to hindgut and to border ectoderm. Transcriptome analysis revealed that each of these domains specifically expressed several hundred effector genes at significant levels. Annotation indicated the qualitative individuality of the functional nature of each cell population, even though they were isolated from embryos only 1-2 days old. In no case was more than a tiny fraction of the transcripts enriched in one population also enriched in any other of the six populations studied. As was particularly clear in the cases of the presumptive pigment, neurogenic and skeletogenic cells, all three of which represent precociously differentiating cell types of this embryo, most specifically expressed genes of given cell types are not significantly expressed at all in the other cell types. Thus, at the effector gene level, a dramatic, cell type-specific pattern of differential gene regulation is established well before any significant embryonic morphogenesis has occurred.

  7. Generalised Anxiety Disorder--A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression.

    Directory of Open Access Journals (Sweden)

    Matthew N Davies

    Full Text Available Generalised Anxiety Disorder (GAD is a common anxiety-related diagnosis, affecting approximately 5% of the adult population. One characteristic of GAD is a high degree of anxiety sensitivity (AS, a personality trait which describes the fear of arousal-related sensations. Here we present a genome-wide association study of AS using a cohort of 730 MZ and DZ female twins. The GWAS showed a significant association for a variant within the RBFOX1 gene. A heritability analysis of the same cohort also confirmed a significant genetic component with h2 of 0.42. Additionally, a subset of the cohort (25 MZ twins discordant for AS was studied for evidence of differential expression using RNA-seq data. Significant differential expression of two exons with the ITM2B gene within the discordant MZ subset was observed, a finding that was replicated in an independent cohort. While previous research has shown that anxiety has a high comorbidity with a variety of psychiatric and neurodegenerative disorders, our analysis suggests a novel etiology specific to AS.

  8. Generalised Anxiety Disorder--A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression.

    Science.gov (United States)

    Davies, Matthew N; Verdi, Serena; Burri, Andrea; Trzaskowski, Maciej; Lee, Minyoung; Hettema, John M; Jansen, Rick; Boomsma, Dorret I; Spector, Tim D

    2015-01-01

    Generalised Anxiety Disorder (GAD) is a common anxiety-related diagnosis, affecting approximately 5% of the adult population. One characteristic of GAD is a high degree of anxiety sensitivity (AS), a personality trait which describes the fear of arousal-related sensations. Here we present a genome-wide association study of AS using a cohort of 730 MZ and DZ female twins. The GWAS showed a significant association for a variant within the RBFOX1 gene. A heritability analysis of the same cohort also confirmed a significant genetic component with h2 of 0.42. Additionally, a subset of the cohort (25 MZ twins discordant for AS) was studied for evidence of differential expression using RNA-seq data. Significant differential expression of two exons with the ITM2B gene within the discordant MZ subset was observed, a finding that was replicated in an independent cohort. While previous research has shown that anxiety has a high comorbidity with a variety of psychiatric and neurodegenerative disorders, our analysis suggests a novel etiology specific to AS.

  9. Rheological Behavior, Granule Size Distribution and Differential Scanning Calorimetry of Cross-Linked Banana (Musa paradisiaca) Starch.

    Science.gov (United States)

    Núñez-Santiago, María C.; Maristany-Cáceres, Amira J.; Suárez, Francisco J. García; Bello-Pérez, Arturo

    2008-07-01

    Rheological behavior at 60 °C, granule size distribution and Differential Scanning Calorimetry (DSC) tests were employed to study the effect of diverse reaction conditions: adipic acid concentration, pH and temperature during cross-linking of banana (Musa paradisiaca) starch. These properties were determined in native banana starch pastes for the purpose of comparison. Rheological behavior from pastes of cross-linked starch at 60 °C did not show hysteresis, probably due the cross-linkage of starch that avoided disruption of granules, elsewhere, native starch showed hysteresis in a thixotropic loop. All pastes exhibited non-Newtonian shear thinning behavior. In all cases, size distribution showed a decrease in the median diameter in cross-linked starches. This condition produces a decrease in swelling capacity of cross-linked starch. The median diameter decreased with an increase of acid adipic concentration; however, an increase of pH and Temperature produced an increase in this variable. Finally, an increase in gelatinization temperature and entalphy (ΔH) were observed as an effect of cross-linkage. An increase in acid adipic concentration produced an increase in Tonset and a decrease in ΔH. pH and temperature. The cross-linked of banana starch produced granules more resistant during the pasting procedure.

  10. Differential genomic effects on canonical signaling pathways by two different CeO2 nanoparticles in HepG2 cells

    Science.gov (United States)

    Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells. Sheau-Fung Thai1, Kathleen A. Wallace1, Carlton P. Jones1, Hongzu Ren2, Benjamin T. Castellon1, James Crooks2, Kirk T. Kitchin1. 1Integrated Systems Toxicology Divison, 2Resea...

  11. Differential genomic effects on canonical signaling pathways by two different CeO2 nanoparticles in HepG2 cells

    Science.gov (United States)

    Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells. Sheau-Fung Thai1, Kathleen A. Wallace1, Carlton P. Jones1, Hongzu Ren2, Benjamin T. Castellon1, James Crooks2, Kirk T. Kitchin1. 1Integrated Systems Toxicology Divison, 2Resea...

  12. The Langerhans islet cells of female rabbits are differentially affected by hypothyroidism depending on the islet size.

    Science.gov (United States)

    Rodríguez-Castelán, J; Nicolás, L; Morimoto, S; Cuevas, E

    2015-04-01

    Effects of hypothyroidism on the glucose and insulin levels are controversial, and its impact on the Langerhans islet morphology of adult subjects has been poorly addressed. In spite of hypothyroidism and diabetes mellitus are more frequent in females than in males, most studies using animal models have been done in males. The effect of hypothyroidism on the immunolabeling of thyroid hormone receptors (TRs) and thyrotropin receptor (TSHR) of islet cells is unknown. The aim of this study was to determine the effect of hypothyroidism on the glucose and insulin concentrations, morphometry of islets, and immunostaining of TRs α1-2 and β1 and TSHR of islet cells in female rabbits. Control and hypothyroid (0.02% of methimazole for 30 days) animals were used to quantify blood levels of glucose and insulin, density of islets, cross-sectional area (CSA) of islets, number of cells per islet, cell proliferation, and the immunolabeling of TRs α1-2, TRβ1, and TSHR. Student's t or Mann-Whitney-U tests, two-way ANOVAs, and Fischer's tests were applied. Concentrations of glucose and insulin, as well as the insulin resistance were similar between groups. Hypothyroidism did not affect the density or the CSA of islets. The analysis of islets by size showed that hypothyroidism reduced the cell number in large and medium islets, but not in small ones. In small islets, cell proliferation was increased. The immunoreactivity of TRα1-2, TRβ1, and TSHR was increased by hypothyroidism in all islet sizes. Our results show that hypothyroidism affects differentially the islet cells depending on the size of islets.

  13. Differential clustering of sperm subpopulations in infertile males with clinical varicocele and carriers of rearranged genomes.

    Science.gov (United States)

    García-Peiró, Agustín; Oliver-Bonet, María; Navarro, Joaquima; Abad, Carlos; Amengual, María José; López-Fernández, Carmen; Gosálvez, Jaime; Benet, Jordi

    2012-01-01

    Some methods for determining sperm DNA fragmentation, such as the sperm chromatin structure assay (SCSA) and the sperm chromatin dispersion test (SCD), provide additional information about particular subgroups of spermatozoa with specific irregularities. Thus, SCSA recognizes a specific sperm subpopulation, the high-DNA stainability sperm subpopulation (HDS), and SCD recognizes the so-called DNA-degraded sperm (DDS) subpopulation. Although some studies associate the presence of these subpopulations with specific aspects related to infertility, the relationship between both sperm subpopulations and their preponderance in specific clinical groups of infertile males has not been extensively investigated. In this study, HDS and DDS subpopulations were determined in a total of 37 human males: 8 males with proven fertility, 9 infertile males with asthenoteratozoospermia, 10 carriers of chromosomal reorganizations, and 10 infertile males with clinical varicocele. Results showed a significant increase of the DDS subpopulation (P HDS subpopulation (P = .542), but the highest values were found in the varicocele and rearranged-genome groups. However, no correlation between the HDS and DDS subpopulations were found (r = 0.196; P = .244), suggesting that both represent a different class of sperm subpopulation in the ejaculate. A significant increase in HDS, and especially DDS, can be associated with the presence of varicocele or the rearrangement of chromosomes. Specific diagnostic tests to confirm the diagnosis must be performed in patients with increased DDS and HDS values.

  14. Differential interactions of plasmid DNA, RNA and genomic DNA with amino acid-based affinity matrices.

    Science.gov (United States)

    Sousa, Angela; Sousa, Fani; Queiroz, João A

    2010-09-01

    The development of a strategy to plasmid DNA (pDNA) purification has become necessary for the development of gene therapy and DNA vaccine production processes in recent years, since this nucleic acid and most of contaminants, such as RNA, genomic DNA and endotoxins, are negatively charged. An ideal separation methodology may be achieved with the use of affinity interactions between immobilized amino acids and nucleic acids. In this study, the binding behaviour of nucleic acids under the influence of different environmental conditions, such as the composition and ionic strength of elution buffer, and the temperature, is compared with various amino acids immobilized on chromatography resins. Supercoiled (sc) plasmid isoform was isolated with all matrices used, but in some cases preferential interactions with other nucleic acids were found. Particularly, lysine chromatography showed to be an ideal technology mainly on RNA purification using low salt concentration. On the other hand, arginine ligands have shown a greater ability to retain the sc isoform comparatively to the other nucleic acids retention, becoming this support more adequate to sc pDNA purification. The temperature variation, competitive elution and oligonucleotides affinity studies also allowed to recognize the dominant interactions inherent to biorecognition of pDNA molecule and the affinity matrices.

  15. Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines

    Directory of Open Access Journals (Sweden)

    Cornish Katrina

    2009-11-01

    Full Text Available Abstract Background Parthenium argentatum (guayule is an industrial crop that produces latex, which was recently commercialized as a source of latex rubber safe for people with Type I latex allergy. The complete plastid genome of P. argentatum was sequenced. The sequence provides important information useful for genetic engineering strategies. Comparison to the sequences of plastid genomes from three other members of the Asteraceae, Lactuca sativa, Guitozia abyssinica and Helianthus annuus revealed details of the evolution of the four genomes. Chloroplast-specific DNA barcodes were developed for identification of Parthenium species and lines. Results The complete plastid genome of P. argentatum is 152,803 bp. Based on the overall comparison of individual protein coding genes with those in L. sativa, G. abyssinica and H. annuus, we demonstrate that the P. argentatum chloroplast genome sequence is most closely related to that of H. annuus. Similar to chloroplast genomes in G. abyssinica, L. sativa and H. annuus, the plastid genome of P. argentatum has a large 23 kb inversion with a smaller 3.4 kb inversion, within the large inversion. Using the matK and psbA-trnH spacer chloroplast DNA barcodes, three of the four Parthenium species tested, P. tomentosum, P. hysterophorus and P. schottii, can be differentiated from P. argentatum. In addition, we identified lines within P. argentatum. Conclusion The genome sequence of the P. argentatum chloroplast will enrich the sequence resources of plastid genomes in commercial crops. The availability of the complete plastid genome sequence may facilitate transformation efficiency by using the precise sequence of endogenous flanking sequences and regulatory elements in chloroplast transformation vectors. The DNA barcoding study forms the foundation for genetic identification of commercially significant lines of P. argentatum that are important for producing latex.

  16. [Genomic noncoding sequences and the size of eukaryotic cell nucleus as important factors of gene protection from chemical mutagens].

    Science.gov (United States)

    Minkevich, I G; Patrushev, L I

    2007-01-01

    An improved quantitative model describing a protective function of eukaryotic genomic noncoding sequences was developed. In this new model, two factors affecting gene protection from chemical mutagens are considered: (1) the ratio of the total lengths of coding and noncoding genomic sequences and (2) the volume of the cell nucleus. An increase in the noncoding DNA in the genome reduces the number of mutagen-damaged nucleotides in the coding region, whereas an increase in the volume of the nucleus decreases the flow of mutagens per unit of nuclear volume that attacks its surface.

  17. Calcium-release channels in paramecium. Genomic expansion, differential positioning and partial transcriptional elimination.

    Directory of Open Access Journals (Sweden)

    Eva-Maria Ladenburger

    Full Text Available The release of Ca²⁺ from internal stores is a major source of signal Ca²⁺ in almost all cell types. The internal Ca²⁺ pools are activated via two main families of intracellular Ca²⁺-release channels, the ryanodine and the inositol 1,4,5-trisphosphate (InsP₃ receptors. Among multicellular organisms these channel types are ubiquitous, whereas in most unicellular eukaryotes the identification of orthologs is impaired probably due to evolutionary sequence divergence. However, the ciliated protozoan Paramecium allowed us to prognosticate six groups, with a total of 34 genes, encoding proteins with characteristics typical of InsP₃ and ryanodine receptors by BLAST search of the Paramecium database. We here report that these Ca²⁺-release channels may display all or only some of the characteristics of canonical InsP₃ and ryanodine receptors. In all cases, prediction methods indicate the presence of six trans-membrane regions in the C-terminal domains, thus corresponding to canonical InsP₃ receptors, while a sequence homologous to the InsP₃-binding domain is present only in some types. Only two types have been analyzed in detail previously. We now show, by using antibodies and eventually by green fluorescent protein labeling, that the members of all six groups localize to distinct organelles known to participate in vesicle trafficking and, thus, may provide Ca²⁺ for local membrane-membrane interactions. Whole genome duplication can explain radiation within the six groups. Comparative and evolutionary evaluation suggests derivation from a common ancestor of canonical InsP₃ and ryanodine receptors. With one group we could ascertain, to our knowledge for the first time, aberrant splicing in one thoroughly analyzed Paramecium gene. This yields truncated forms and, thus, may indicate a way to pseudogene formation. No comparable analysis is available for any other, free-living or parasitic/pathogenic protozoan.

  18. Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

    Directory of Open Access Journals (Sweden)

    Ozand Pinar T

    2010-06-01

    Full Text Available Abstract Background Hepatocellular carcinoma (HCC is the third-leading cause of cancer-related deaths worldwide. It is often diagnosed at an advanced stage, and hence typically has a poor prognosis. To identify distinct molecular mechanisms for early HCC we developed a rat model of liver regeneration post-hepatectomy, as well as liver cells undergoing malignant transformation and compared them to normal liver using a microarray approach. Subsequently, we performed cross-species comparative analysis coupled with copy number alterations (CNA of independent early human HCC microarray studies to facilitate the identification of critical regulatory modules conserved across species. Results We identified 35 signature genes conserved across species, and shared among different types of early human HCCs. Over 70% of signature genes were cancer-related, and more than 50% of the conserved genes were mapped to human genomic CNA regions. Functional annotation revealed genes already implicated in HCC, as well as novel genes which were not previously reported in liver tumors. A subset of differentially expressed genes was validated using quantitative RT-PCR. Concordance was also confirmed for a significant number of genes and pathways in five independent validation microarray datasets. Our results indicated alterations in a number of cancer related pathways, including p53, p38 MAPK, ERK/MAPK, PI3K/AKT, and TGF-β signaling pathways, and potential critical regulatory role of MYC, ERBB2, HNF4A, and SMAD3 for early HCC transformation. Conclusions The integrative analysis of transcriptional deregulation, genomic CNA and comparative cross species analysis brings new insights into the molecular profile of early hepatoma formation. This approach may lead to robust biomarkers for the detection of early human HCC.

  19. Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes

    Directory of Open Access Journals (Sweden)

    Santiviago Carlos A

    2009-08-01

    Full Text Available Abstract Background The recently described Type VI Secretion System (T6SS represents a new paradigm of protein secretion in bacteria. A number of bioinformatic studies have been conducted to identify T6SS gene clusters in the available bacterial genome sequences. According to these studies, Salmonella harbors a unique T6SS encoded in the Salmonella Pathogenicity Island 6 (SPI-6. Since these studies only considered few Salmonella genomes, the present work aimed to identify novel T6SS loci by in silico analysis of every genome sequence of Salmonella available. Results The analysis of sequencing data from 44 completed or in progress Salmonella genome projects allowed the identification of 3 novel T6SS loci. These clusters are located in differentially-distributed genomic islands we designated SPI-19, SPI-20 and SPI-21, respectively. SPI-19 was identified in a subset of S. enterica serotypes including Dublin, Weltevreden, Agona, Gallinarum and Enteritidis. In the later, an internal deletion eliminated most of the island. On the other hand, SPI-20 and SPI-21 were restricted to S. enterica subspecies arizonae (IIIa serotype 62:z4,z23:-. Remarkably, SPI-21 encodes a VgrG protein containing a C-terminal extension similar to S-type pyocins of Pseudomonas aeruginosa. This is not only the first evolved VgrG described in Salmonella, but also the first evolved VgrG including a pyocin domain described so far in the literature. In addition, the data indicate that SPI-6 T6SS is widely distributed in S. enterica and absent in serotypes Enteritidis, Gallinarum, Agona, Javiana, Paratyphi B, Virchow, IIIa 62:z4,z23:- and IIIb 61:1,v:1,5,(7. Interestingly, while some serotypes harbor multiple T6SS (Dublin, Weltvreden and IIIa 62:z4,z23:- others do not encode for any (Enteritidis, Paratyphi B, Javiana, Virchow and IIIb 61:1,v:1,5,(7. Comparative and phylogenetic analyses indicate that the 4 T6SS loci in Salmonella have a distinct evolutionary history. Finally, we

  20. Immunohistochemical study of hepatocyte, cholangiocyte and stem cell markers of hepatocellular carcinoma: the second report: relationship with tumor size and cell differentiation.

    Science.gov (United States)

    Kumagai, Arisa; Kondo, Fukuo; Sano, Keiji; Inoue, Masafumi; Fujii, Takeshi; Hashimoto, Masaji; Watanabe, Masato; Soejima, Yurie; Ishida, Tsuyoshi; Tokairin, Takuo; Saito, Koji; Sasajima, Yuko; Takahashi, Yoshihisa; Uozaki, Hiroshi; Fukusato, Toshio

    2016-07-01

    The purpose of this study is to investigate whether ordinary hepatocellular carcinomas (HCCs) show positivity of stem/progenitor cell markers and cholangiocyte markers during the process of tumor progression. Ninety-four HCC lesions no larger than 8 cm from 94 patients were immuno-histochemically studied using two hepatocyte markers (Hep par 1 and α-fetoprotein), five cholangiocyte markers (cytokeratin CK7, CK19, Muc1, epithelial membrane antigen and carcinoembryonic antigen) and three hepatic stem/progenitor cell markers (CD56, c-Kit and EpCAM). The tumors were classified into three groups by tumor size: S1, tumors were also classified according to tumor differentiation: well, moderately and poorly differentiated. The relationship between the positive ratios of these markers, tumor size and tumor differentiation was examined. The positive ratios of cholangiocyte markers tended to be higher in larger sized and more poorly differentiated tumors (except for CK7). The positive ratios of stem/progenitor cell markers tended to be higher in larger sized and more poorly differentiated tumors (except for c-Kit). Ordinary HCC can acquire the characteristic of positivity of cholangiocyte and stem/progenitor cell markers during the process of tumor progression. © 2016 The Authors. Journal of Hepato-Biliary-Pancreatic Sciences published by John Wiley & Sons Australia, Ltd on behalf of Japanese Society of Hepato-Biliary-Pancreatic Surgery.

  1. Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses

    Science.gov (United States)

    Li, Jianfang; Yang, Yuchen; Chen, Qipian; Fang, Lu; He, Ziwen; Guo, Wuxia; Qiao, Sitan; Wang, Zhengzhen; Guo, Miaomiao; Zhong, Cairong; Zhou, Renchao; Shi, Suhua

    2016-01-01

    Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia. PMID:27380895

  2. Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae)

    Science.gov (United States)

    da Silva, Rangeline Azevedo; Souza, Gustavo; Lemos, Lívia Santos Lima; Lopes, Uilson Vanderlei; Patrocínio, Nara Geórgia Ribeiro Braz; Alves, Rafael Moysés; Marcellino, Lucília Helena; Clement, Didier; Micheli, Fabienne

    2017-01-01

    The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI− bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted. PMID:28187131

  3. Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae).

    Science.gov (United States)

    da Silva, Rangeline Azevedo; Souza, Gustavo; Lemos, Lívia Santos Lima; Lopes, Uilson Vanderlei; Patrocínio, Nara Geórgia Ribeiro Braz; Alves, Rafael Moysés; Marcellino, Lucília Helena; Clement, Didier; Micheli, Fabienne; Gramacho, Karina Peres

    2017-01-01

    The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI- bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.

  4. Binary Logistic Regression Analysis for Detecting Differential Item Functioning: Effectiveness of R[superscript 2] and Delta Log Odds Ratio Effect Size Measures

    Science.gov (United States)

    Hidalgo, Mª Dolores; Gómez-Benito, Juana; Zumbo, Bruno D.

    2014-01-01

    The authors analyze the effectiveness of the R[superscript 2] and delta log odds ratio effect size measures when using logistic regression analysis to detect differential item functioning (DIF) in dichotomous items. A simulation study was carried out, and the Type I error rate and power estimates under conditions in which only statistical testing…

  5. Binary Logistic Regression Analysis for Detecting Differential Item Functioning: Effectiveness of R[superscript 2] and Delta Log Odds Ratio Effect Size Measures

    Science.gov (United States)

    Hidalgo, Mª Dolores; Gómez-Benito, Juana; Zumbo, Bruno D.

    2014-01-01

    The authors analyze the effectiveness of the R[superscript 2] and delta log odds ratio effect size measures when using logistic regression analysis to detect differential item functioning (DIF) in dichotomous items. A simulation study was carried out, and the Type I error rate and power estimates under conditions in which only statistical testing…

  6. Relationship between hierarchic - spatial differentiation of social structure and population size of municipalities in turkey: Evidence from the election case of local administration in 2004

    Directory of Open Access Journals (Sweden)

    Murat Çiftçi

    2011-07-01

    Full Text Available Turkey, whose population is young and dynamic, is a country where social change has a high acceleration. This circumstance has led to a spatial heterogeneity of social structure in the scale of campuses. Almost all the municipalities differ significantly from each other. In results of statistical applications, it was possible to conclude that there is a relationship between spatial differentiation of social structure indicators (PDI, PIDI and population sizes in municipalities. This relationship also supports that there was a differentiation of graded spatial social structure among municipalities in the Turkey of 2004. It is possible to make contact with this to the spatial differentiation that moves in parallel with population size and is in transition degree from a community to a society.

  7. Genome-wide distribution of histone H3 acetylation in all-trans retinoic acid induced neuronal differentiation of SH-SY5Y cells

    Institute of Scientific and Technical Information of China (English)

    FANG HongBo; MI Yang; WU NingHua; ZHANG Ye; SHEN YuFei

    2009-01-01

    With chromatin immunoprecipitation (CHIP) and promoter DNA microarray analyses (ChiP-on-chip), we analyzed the variations of acetylation on histone H3 in all-trans retinoic acid (RA) induced neuronal cell differentiation. Neuroblastoma SH-SY5Y cells were treated with RA for 24 h and the acetylation on histone H3 in the promoter region of the genes was detected. Results showed that, after treatment, the level of acetylation on histone H3 elevated in 597 genes in the genome, and reduced in the other 647 genes compared with those of the control. In summary, we have successfully adopted a high throughput technique to detect and analyze variations of acetylation of histone H3 in human genome at the early phage of RA induced neuronal differentiation of the SH-SY5Y cells.

  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. Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

    OpenAIRE

    Nylander Johan AA; Larsson John; Bergman Birgitta

    2011-01-01

    Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique o...

  10. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

    Science.gov (United States)

    2011-01-01

    Background The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES) and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it is responsible for transposon silencing in this mosquito. Results Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Conclusions Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome, suggest that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster. PMID:22171608

  11. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

    Directory of Open Access Journals (Sweden)

    Arensburger Peter

    2011-12-01

    Full Text Available Abstract Background The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it is responsible for transposon silencing in this mosquito. Results Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Conclusions Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome, suggest that some aspects of the piRNA system differ between Ae. aegypti and D

  12. Genomic Organization of Repetitive DNA in Woodpeckers (Aves, Piciformes): Implications for Karyotype and ZW Sex Chromosome Differentiation.

    Science.gov (United States)

    de Oliveira, Thays Duarte; Kretschmer, Rafael; Bertocchi, Natasha Avila; Degrandi, Tiago Marafiga; de Oliveira, Edivaldo Herculano Corrêa; Cioffi, Marcelo de Bello; Garnero, Analía Del Valle; Gunski, Ricardo José

    2017-01-01

    Birds are characterized by a low proportion of repetitive DNA in their genome when compared to other vertebrates. Among birds, species belonging to Piciformes order, such as woodpeckers, show a relatively higher amount of these sequences. The aim of this study was to analyze the distribution of different classes of repetitive DNA-including microsatellites, telomere sequences and 18S rDNA-in the karyotype of three Picidae species (Aves, Piciformes)-Colaptes melanochloros (2n = 84), Colaptes campestris (2n = 84) and Melanerpes candidus (2n = 64)-by means of fluorescence in situ hybridization. Clusters of 18S rDNA were found in one microchromosome pair in each of the three species, coinciding to a region of (CGG)10 sequence accumulation. Interstitial telomeric sequences were found in some macrochromosomes pairs, indicating possible regions of fusions, which can be related to variation of diploid number in the family. Only one, from the 11 different microsatellite sequences used, did not produce any signals. Both species of genus Colaptes showed a similar distribution of microsatellite sequences, with some difference when compared to M. candidus. Microsatellites were found preferentially in the centromeric and telomeric regions of micro and macrochromosomes. However, some sequences produced patterns of interstitial bands in the Z chromosome, which corresponds to the largest element of the karyotype in all three species. This was not observed in the W chromosome of Colaptes melanochloros, which is heterochromatic in most of its length, but was not hybridized by any of the sequences used. These results highlight the importance of microsatellite sequences in differentiation of sex chromosomes, and the accumulation of these sequences is probably responsible for the enlargement of the Z chromosome.

  13. Genome-wide DNA methylation pattern in visceral adipose tissue differentiates insulin-resistant from insulin-sensitive obese subjects.

    Science.gov (United States)

    Crujeiras, A B; Diaz-Lagares, A; Moreno-Navarrete, J M; Sandoval, J; Hervas, D; Gomez, A; Ricart, W; Casanueva, F F; Esteller, M; Fernandez-Real, J M

    2016-12-01

    Elucidating the potential mechanisms involved in the detrimental effect of excess body weight on insulin action is an important priority in counteracting obesity-associated diseases. The present study aimed to disentangle the epigenetic basis of insulin resistance by performing a genome-wide epigenetic analysis in visceral adipose tissue (VAT) from morbidly obese patients depending on the insulin sensitivity evaluated by the clamp technique. The global human methylome screening performed in VAT from 7 insulin-resistant (IR) and 5 insulin-sensitive (IS) morbidly obese patients (discovery cohort) analyzed using the Infinium HumanMethylation450 BeadChip array identified 982 CpG sites able to perfectly separate the IR and IS samples. The identified sites represented 538 unique genes, 10% of which were diabetes-associated genes. The current work identified novel IR-related genes epigenetically regulated in VAT, such as COL9A1, COL11A2, CD44, MUC4, ADAM2, IGF2BP1, GATA4, TET1, ZNF714, ADCY9, TBX5, and HDACM. The gene with the largest methylation fold-change and mapped by 5 differentially methylated CpG sites located in island/shore and promoter region was ZNF714. This gene presented lower methylation levels in IR than in IS patients in association with increased transcription levels, as further reflected in a validation cohort (n = 24; 11 IR and 13 IS). This study reveals, for the first time, a potential epigenetic regulation involved in the dysregulation of VAT that could predispose patients to insulin resistance and future type 2 diabetes in morbid obesity, providing a potential therapeutic target and biomarkers for counteracting this process. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Genomic Organization of Repetitive DNA in Woodpeckers (Aves, Piciformes): Implications for Karyotype and ZW Sex Chromosome Differentiation

    Science.gov (United States)

    Kretschmer, Rafael; Bertocchi, Natasha Avila; Degrandi, Tiago Marafiga; de Oliveira, Edivaldo Herculano Corrêa; Cioffi, Marcelo de Bello; Garnero, Analía del Valle; Gunski, Ricardo José

    2017-01-01

    Birds are characterized by a low proportion of repetitive DNA in their genome when compared to other vertebrates. Among birds, species belonging to Piciformes order, such as woodpeckers, show a relatively higher amount of these sequences. The aim of this study was to analyze the distribution of different classes of repetitive DNA—including microsatellites, telomere sequences and 18S rDNA—in the karyotype of three Picidae species (Aves, Piciformes)—Colaptes melanochloros (2n = 84), Colaptes campestris (2n = 84) and Melanerpes candidus (2n = 64)–by means of fluorescence in situ hybridization. Clusters of 18S rDNA were found in one microchromosome pair in each of the three species, coinciding to a region of (CGG)10 sequence accumulation. Interstitial telomeric sequences were found in some macrochromosomes pairs, indicating possible regions of fusions, which can be related to variation of diploid number in the family. Only one, from the 11 different microsatellite sequences used, did not produce any signals. Both species of genus Colaptes showed a similar distribution of microsatellite sequences, with some difference when compared to M. candidus. Microsatellites were found preferentially in the centromeric and telomeric regions of micro and macrochromosomes. However, some sequences produced patterns of interstitial bands in the Z chromosome, which corresponds to the largest element of the karyotype in all three species. This was not observed in the W chromosome of Colaptes melanochloros, which is heterochromatic in most of its length, but was not hybridized by any of the sequences used. These results highlight the importance of microsatellite sequences in differentiation of sex chromosomes, and the accumulation of these sequences is probably responsible for the enlargement of the Z chromosome. PMID:28081238

  15. Genome-Wide Analysis of Differentially Expressed Genes Relevant to Rhizome Formation in Lotus Root (Nelumbo nucifera Gaertn.

    Directory of Open Access Journals (Sweden)

    Libao Cheng

    Full Text Available Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root.

  16. Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant model Arabidopsis arenosa.

    Science.gov (United States)

    Kolář, Filip; Fuxová, Gabriela; Záveská, Eliška; Nagano, Atsushi J; Hyklová, Lucie; Lučanová, Magdalena; Kudoh, Hiroshi; Marhold, Karol

    2016-08-01

    Quaternary climatic oscillations profoundly impacted temperate biodiversity. For many diverse yet undersampled areas, however, the consequences of this impact are still poorly known. In Europe, particular uncertainty surrounds the role of Balkans, a major hotspot of European diversity, in postglacial recolonization of more northerly areas, and the Carpathians, a debatable candidate for a northern 'cryptic' glacial refugium. Using genome-wide SNPs and microsatellites, we examined how the interplay of historical processes and niche shifts structured genetic diversity of diploid Arabidopsis arenosa, a little-known member of the plant model genus that occupies a wide niche range from sea level to alpine peaks across eastern temperate Europe. While the northern Balkans hosted one isolated endemic lineage, most of the genetic diversity was concentrated further north in the Pannonian Basin and the Carpathians, where it likely survived the last glaciation in northern refugia. Finally, a distinct postglacial environment in northern Europe was colonized by populations of admixed origin from the two Carpathian lineages. Niche differentiation along altitude-related bioclimatic gradients was the main trend in the phylogeny of A. arenosa. The most prominent niche shifts, however, characterized genetically only slightly divergent populations that expanded into narrowly defined alpine and northern coastal postglacial environments. Our study highlights the role of eastern central European mountains not only as refugia for unique temperate diversity but also sources for postglacial expansion into novel high-altitude and high-latitude niches. Knowledge of distinct genetic substructure of diploid A. arenosa also opens new opportunities for follow-up studies of this emerging model of evolutionary biology.

  17. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice

    OpenAIRE

    Mao, Hailiang; Sun, Shengyuan; Yao, Jialing; Wang, Chongrong; Yu, Sibin; Xu, Caiguo; Li, Xianghua; Zhang, Qifa

    2010-01-01

    Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size. The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-...

  18. Comparison of genome size and synthesis of structural proteins of Hirame Rhabdovirus, infectious hematopoietic necrosis virus, and viral hemorrhagic Septicemia virus

    Science.gov (United States)

    Nishizawa, Toyohiko; Yoshimizu, Mamoru; Winton, James R.; Kimura, Takahisa

    1991-01-01

    Genomic RNA was extracted from purified virions of hirame rhabdovirus (HRV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV). The full-length RNA was analyzed using formaldehyde agarose gel electrophoresis followed by ethidium bromide staining. Compared with an internal RNA size standard, all three viral genomic RNAs appeared to have identical relative mobilities and were estimated to be approximately 10.7 kilobases in length or about 3.7 megadaltons in molecular mass. Structural protein synthesis of HRV, IHNV, and VHSV was studied using cell cultures treated with actinomycin D. At 2 h intervals, proteins were labeled with 35S-methionine, extracted, and analyzed by SDS-polyacrylamide gel electrophoresis and autoradiography. The five structural proteins of each of the three viruses appeared in the following order : nucleoprotein (N), matrix protein 1 (M1), matrix protein 2 (M2), glycoprotein (G), and polymerase (L) reflecting both the approximate relative abundance of each protein within infected cells and the gene order within the viral genome.

  19. An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation

    Science.gov (United States)

    Mandal, Kamal; Bader, Samuel L.; Kumar, Pankaj; Malakar, Dipankar; Campbell, David S.; Pradhan, Bhola Shankar; Sarkar, Rajesh K.; Wadhwa, Neerja; Sensharma, Souvik; Jain, Vaibhav; Moritz, Robert L.

    2017-01-01

    Abstract Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database. Proteomic SWATH-MS analysis provided extensive quantification of nuclear and cytoplasmic protein fractions revealing 1,670 proteins differentially located between the nucleus and cytoplasm of infant Sc and 890 proteins differentially located within those of pubertal Sc. Based on our multi-omics approach, the transcription factor YY1 was identified as one of the lead candidates regulating differentiation of Sc.YY1 was found to have abundant binding sites on promoters of genes upregulated during puberty. To determine its significance, we generated transgenic rats with Sc specific knockdown of YY1 that led to compromised spermatogenesis. PMID:28065881

  20. Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines

    Science.gov (United States)

    Jahoor, Ahmed; Orabi, Jihad; Andersen, Jeppe R.; Janss, Luc L.; Jensen, Just

    2017-01-01

    Wheat breeding programs generate a large amount of variation which cannot be completely explored because of limited phenotyping throughput. Genomic prediction (GP) has been proposed as a new tool which provides breeding values estimations without the need of phenotyping all the material produced but only a subset of it named training population (TP). However, genotyping of all the accessions under analysis is needed and, therefore, optimizing TP dimension and genotyping strategy is pivotal to implement GP in commercial breeding schemes. Here, we explored the optimum TP size and we integrated pedigree records and genome wide association studies (GWAS) results to optimize the genotyping strategy. A total of 988 advanced wheat breeding lines were genotyped with the Illumina 15K SNPs wheat chip and phenotyped across several years and locations for yield, lodging, and starch content. Cross-validation using the largest possible TP size and all the SNPs available after editing (~11k), yielded predictive abilities (rGP) ranging between 0.5–0.6. In order to explore the Training population size, rGP were computed using progressively smaller TP. These exercises showed that TP of around 700 lines were enough to yield the highest observed rGP. Moreover, rGP were calculated by randomly reducing the SNPs number. This showed that around 1K markers were enough to reach the highest observed rGP. GWAS was used to identify markers associated with the traits analyzed. A GWAS-based selection of SNPs resulted in increased rGP when compared with random selection and few hundreds SNPs were sufficient to obtain the highest observed rGP. For each of these scenarios, advantages of adding the pedigree information were shown. Our results indicate that moderate TP sizes were enough to yield high rGP and that pedigree information and GWAS results can be used to greatly optimize the genotyping strategy. PMID:28081208

  1. Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution.

    Science.gov (United States)

    El Baidouri, Moaine; Panaud, Olivier

    2013-01-01

    Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants.

  2. Primary tumour size is a prognostic parameter in patients suffering from differentiated thyroid carcinoma with extrathyroidal growth: results of the MSDS trial.

    Science.gov (United States)

    Krämer, Jan Alexander; Schmid, Kurt Werner; Dralle, Henning; Dietlein, Markus; Schicha, Harald; Lerch, Hartmut; Gerss, Joachim; Frankewitsch, Thomas; Schober, Otmar; Riemann, Burkhard

    2010-10-01

    The Multicentre Study Differentiated Thyroid Cancer (MSDS) collective represents a well-defined group of patients with thyroid carcinomas with extrathyroidal extension. The aim of the present study was to evaluate the relationship of the primary tumour size with clinicopathological features as well as the outcome of patients with minimum and extensive extrathyroidal growth (pT3b- and pT4a-tumours; UICC 2002/2003, 6th ed). The tumour diameter was available in 324 out of 351 MSDS patients (244 females, 80 males). Mean age of patients was 47.7±12.0 years (range, 20.1-69.8 years), and the median follow-up was 6.2 years. The relationship between primary tumour size and the following clinicopathological data was investigated: age, gender, histological tumour type (papillary thyroid carcinomas (PTC) versus follicular thyroid carcinomas (FTC)) and UICC/AJCC TNM classification. In addition, the correlation between primary tumour size and event-free and overall survival was assessed. The FTC of our series were significantly larger than PTC (3.46 vs 1.84 cm; P2 cm. Furthermore, event-free and overall survival were significantly correlated with increasing tumour size (P2 cm remained independent predictors of survival. In patients suffering from differentiated thyroid carcinoma with extrathyroidal growth (pT3b and pT4a), the tumour size is an independent predictor of event-free and overall survival.

  3. Genome-Wide Scan Reveals LEMD3 and WIF1 on SSC5 as the Candidates for Porcine Ear Size

    Science.gov (United States)

    Luo, Weizhen; Liu, Xin; Yan, Hua; Zhao, Kebin; Shi, Huibi; Zhang, Yuebo; Wang, Ligang; Wang, Lixian

    2014-01-01

    The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14–40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia. PMID:25006967

  4. Genome-wide scan reveals LEMD3 and WIF1 on SSC5 as the candidates for porcine ear size.

    Science.gov (United States)

    Zhang, Longchao; Liang, Jing; Luo, Weizhen; Liu, Xin; Yan, Hua; Zhao, Kebin; Shi, Huibi; Zhang, Yuebo; Wang, Ligang; Wang, Lixian

    2014-01-01

    The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14-40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia.

  5. Amplified fragment length polymorphism: an adept technique for genome mapping, genetic differentiation, and intraspecific variation in protozoan parasites.

    Science.gov (United States)

    Kumar, Awanish; Misra, Pragya; Dube, Anuradha

    2013-02-01

    With the advent of polymerase chain reaction (PCR), genetic markers are now accessible for all organisms, including parasites. Amplified fragment length polymorphism (AFLP) is a PCR-based marker for the rapid screening of genetic diversity and intraspecific variation. It is a potent fingerprinting technique for genomic DNAs of any origin or complexity and rapidly generates a number of highly replicable markers that allow high-resolution genotyping. AFLPs are convenient and reliable in comparison to other markers like random amplified polymorphic DNA, restriction fragment length polymorphism, and simple sequence repeat in terms of time and cost efficiency, reproducibility, and resolution as it does not require template DNA sequencing. In addition, AFLP essentially probes the entire genome at random, without prior sequence knowledge. So, AFLP markers have emerged as an advance type of genetic marker with broad application in genomic mapping, population genetics, and DNA fingerprinting and are ideally suited as screening tool for molecular markers linked with biological and clinical traits. This review describes the AFLP procedure and its applications and overview in the fingerprinting of a genome, which has been currently used in parasite genome research. We outline the AFLP procedure adapted for Leishmania genome study and discuss the benefits of AFLPs for assessing genetic variation and genome mapping over other existing molecular techniques. We highlight the possible use of AFLPs as genetic markers with its broad application in parasitological research because it allows random screening of the entire genome for linkage with genetic and clinical properties of the parasite. In this review, we have taken a pragmatic approach on the study of AFLP for genome mapping and polymorphism in protozoan parasites and conclude that AFLP is a very useful tool.

  6. 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

  7. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders

    NARCIS (Netherlands)

    Keers, Robert; Coleman, Jonathan R. I.; Lester, Kathryn J.; Roberts, Susanna; Breen, Gerome; Thastum, Mikael; Bogels, Susan; Schneider, Silvia; Heiervang, Einar; Meiser-Stedman, Richard; Nauta, Maaike; Creswell, Cathy; Thirlwall, Kerstin; Rapee, Ronald M.; Hudson, Jennifer L.; Lewis, Cathryn; Plomin, Robert; Eley, Thalia C.

    2016-01-01

    Background: The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such

  8. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders

    NARCIS (Netherlands)

    Keers, Robert; Coleman, Jonathan R. I.; Lester, Kathryn J.; Roberts, Susanna; Breen, Gerome; Thastum, Mikael; Bogels, Susan; Schneider, Silvia; Heiervang, Einar; Meiser-Stedman, Richard; Nauta, Maaike; Creswell, Cathy; Thirlwall, Kerstin; Rapee, Ronald M.; Hudson, Jennifer L.; Lewis, Cathryn; Plomin, Robert; Eley, Thalia C.

    2016-01-01

    Background: The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such vari

  9. Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes.

    Science.gov (United States)

    Maza, Elie; Frasse, Pierre; Senin, Pavel; Bouzayen, Mondher; Zouine, Mohamed

    2013-11-01

    In recent years, RNA-Seq technologies became a powerful tool for transcriptome studies. However, computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. In particular, it is known that the choice of a normalization procedure leads to a great variability in results of differential gene expression analysis. The present study compares the most widespread normalization procedures and proposes a novel one aiming at removing an inherent bias of studied transcriptomes related to their relative size. Comparisons of the normalization procedures are performed on real and simulated data sets. Real RNA-Seq data sets analyses, performed with all the different normalization methods, show that only 50% of significantly differentially expressed genes are common. This result highlights the influence of the normalization step on the differential expression analysis. Real and simulated data sets analyses give similar results showing 3 different groups of procedures having the same behavior. The group including the novel method named "Median Ratio Normalization" (MRN) gives the lower number of false discoveries. Within this group the MRN method is less sensitive to the modification of parameters related to the relative size of transcriptomes such as the number of down- and upregulated genes and the gene expression levels. The newly proposed MRN method efficiently deals with intrinsic bias resulting from relative size of studied transcriptomes. Validation with real and simulated data sets confirmed that MRN is more consistent and robust than existing methods.

  10. 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

  11. Genome-Wide analysis of allelic imbalance in laser microdissected prostate cancer tissue using the Affymetrix 50K Mapping array identifies genomic patterns associated with metastasis and differentiation

    DEFF Research Database (Denmark)

    Tørring, Niels; Borre, Michael; Sørensen, Karina;

    2007-01-01

    to be developed for patient stratification based on risk of progression. We analysed laser-microdissected prostate tumour tissue from 43 patients with histologically verified PCa, using the new high-resolution Affymetrix Mapping 50K single-nucleotide polymorphism array. The results showed six major loss......, tumour progression towards a metastatic stage, as well as poor differentiation, was identified by specific patterns of copy number gains of genomic regions located at chromosomes 8q, 1q, 3q and 7q. Androgen ablation therapy was further characterised by copy gain at chromosomes 2p and 10q. In conclusion...

  12. Effects of apatite particle size in two apatite/collagen composites on the osteogenic differentiation profile of osteoblastic cells

    OpenAIRE

    HATAKEYAMA, WATARU; TAIRA, Masayuki; Chosa, Naoyuki; KIHARA, HIDEMICHI; ISHISAKI,Akira; KONDO, HISATOMO

    2013-01-01

    The development of new osteoconductive bone substitute materials is expected in medicine. In this study, we attempted to produce new hydroxylapatite (HAP)/collagen (Col) composites using two HAP particles of different sizes and porcine type I collagen. The two HAP particles were either nano-sized (40 nm in average diameter; n-HAP) or had macro-pore sizes of 0.5–1.0 mm in length with fully interconnected pores (m-HAP). The aim of this study was to investigate the effects of apatite particle si...

  13. Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability.

    Directory of Open Access Journals (Sweden)

    Kelsie L Thu

    Full Text Available Recent evidence suggests that the observed clinical distinctions between lung tumors in smokers and never smokers (NS extend beyond specific gene mutations, such as EGFR, EML4-ALK, and KRAS, some of which have been translated into targeted therapies. However, the molecular alterations identified thus far cannot explain all of the clinical and biological disparities observed in lung tumors of NS and smokers. To this end, we performed an unbiased genome-wide, comparative study to identify novel genomic aberrations that differ between smokers and NS. High resolution whole genome DNA copy number profiling of 69 lung adenocarcinomas from smokers (n = 39 and NS (n = 30 revealed both global and regional disparities in the tumor genomes of these two groups. We found that NS lung tumors had a greater proportion of their genomes altered than those of smokers. Moreover, copy number gains on chromosomes 5q, 7p, and 16p occurred more frequently in NS. We validated our findings in two independently generated public datasets. Our findings provide a novel line of evidence distinguishing genetic differences between smoker and NS lung tumors, namely, that the extent of segmental genomic alterations is greater in NS tumors. Collectively, our findings provide evidence that these lung tumors are globally and genetically different, which implies they are likely driven by distinct molecular mechanisms.

  14. Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: Role of the LINE-encoded endonuclease

    Directory of Open Access Journals (Sweden)

    Gupta Abhishek K

    2011-05-01

    Full Text Available Abstract Background Entamoeba histolytica and Entamoeba dispar are closely related protistan parasites but while E. histolytica can be invasive, E. dispar is completely non pathogenic. Transposable elements constitute a significant portion of the genome in these species; there being three families of LINEs and SINEs. These elements can profoundly influence the expression of neighboring genes. Thus their genomic location can have important phenotypic consequences. A genome-wide comparison of the location of these elements in the E. histolytica and E. dispar genomes has not been carried out. It is also not known whether the retrotransposition machinery works similarly in both species. The present study was undertaken to address these issues. Results Here we extracted all genomic occurrences of full-length copies of EhSINE1 in the E. histolytica genome and matched them with the homologous regions in E. dispar, and vice versa, wherever it was possible to establish synteny. We found that only about 20% of syntenic sites were occupied by SINE1 in both species. We checked whether the different genomic location in the two species was due to differences in the activity of the LINE-encoded endonuclease which is required for nicking the target site. We found that the endonucleases of both species were essentially very similar, both in their kinetic properties and in their substrate sequence specificity. Hence the differential distribution of SINEs in these species is not likely to be influenced by the endonuclease. Further we found that the physical properties of the DNA sequences adjoining the insertion sites were similar in both species. Conclusions Our data shows that the basic retrotransposition machinery is conserved in these sibling species. SINEs may indeed have occupied all of the insertion sites in the genome of the common ancestor of E. histolytica and E. dispar but these may have been subsequently lost from some locations. Alternatively, SINE

  15. THE SIZE AND SURFACE COATING OF NANOSILVER DIFFERENTIALLY AFFECTS BIOLOGICAL ACTIVITY IN BLOOD BRAIN BARRIER (RBEC4) CELLS.

    Science.gov (United States)

    Linking the physical properties of nanoparticles with differences in their biological activity is critical for understanding their potential toxicity and mode of action. The influence of aggregate size, surface coating, and surface charge on nanosilver's (nanoAg) movement through...

  16. A genomic island linked to ecotype divergence in Atlantic cod

    DEFF Research Database (Denmark)

    Hansen, Jakob Hemmer; Eg Nielsen, Einar; Therkildsen, Nina O.;

    2013-01-01

    gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two......The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced....... Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high...

  17. Microarray and synchronization of neuronal differentiation with pathway changes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) databank in nerve growth factor-treated PC12 cells.

    Science.gov (United States)

    Lin, Chih-Ming; Feng, Wayne

    2012-08-01

    The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database creates networks from interrelations between molecular biology and underlying chemical elements. This allows for analysis of biologic networks, genomic information, and higher-order functional information at a systems level. We performed microarray experiments and used the KEGG database, systems biology analysis, and annotation of pathway function to study nerve growth factor (NGF)-induced differentiation of PC12 cells. Cells were cultured to 70%-80% confluence, treated with NGF for 1 or 3 hours (h), and RNA was extracted. Stage 1 data analysis involved analysis of variance (ANOVA), and stage 2 involved cluster analysis and heat map generation. We identified 2020 NGF-induced PC12 genes (1038 at 1 h and 1554 at 3 h). Results showed changes in gene expression over time. We compared these genes with 6035 genes from the KEGG database. Cross-matching resulted in 830 genes. Among these, we identified 395 altered genes (155 at 1 h and 301 at 3 h; 2-fold increase from 1 h to 3 h). We identified 191 biologic pathways in the KEGG database; the top 15 showed correlations with neuronal differentiation (mitogen-activated protein kinase [MAPK] pathway: 35 genes at 1 h, 54 genes at 3 h; genes associated with axonal guidance: 12 at 1 h, 26 at 3 h; Wnt pathway: 16 at 1 h, 25 at 3 h; neurotrophin pathway: 4 at 1 h, 14 at 3 h). Thus, we identified changes in neuronal differentiation pathways with the KEGG database, which were synchronized with NGF-induced differentiation.

  18. Genomic structures of the kW1 loci on the Z and W chromosomes in ratite birds: structural changes at an early stage of W chromosome differentiation.

    Science.gov (United States)

    Ishijima, Junko; Uno, Yoshinobu; Nishida, Chizuko; Matsuda, Yoichi

    2014-01-01

    The W chromosome of ratite birds shows minimal morphological differentiation and retains homology of genetic linkage and gene order with a substantial stretch of the Z chromosome; however, the molecular structure in the differentiated region is still not well known. The kW1 sequence was isolated from the kiwi as a W-specific DNA marker for PCR-based molecular sexing of ratite birds. In ratite W chromosomes, this sequence commonly contains a ∼200-bp deletion. To characterize the very early event of avian sex chromosome differentiation, we performed molecular cytogenetic analyses of kW1 and its flanking sequences in paleognathous and neognathous birds and reptiles. Female-specific repeats were found in the kW1-flanking sequence of the cassowary (Casuarius casuarius), and the repeats have been amplified in the pericentromeric region of the W chromosomes of ratites, which may have resulted from the cessation of meiotic recombination between the Z and W chromosomes at an early stage of sex chromosome differentiation. The presence of the kW1 sequence in neognathous birds and a crocodilian species suggests that the kW1 sequence was present in the ancestral genome of Archosauria; however, it disappeared in other reptilian taxa and several lineages of neognathous birds.

  19. Variant size- and glycoforms of the scavenger receptor cysteine-rich protein gp-340 with differential bacterial aggregation

    DEFF Research Database (Denmark)

    Eriksson, Christer; Frängsmyr, Lars; Danielsson Niemi, Liza

    2007-01-01

    Glycoprotein gp-340 aggregates bacteria in saliva as part of innate defence at mucosal surfaces. We have detected size- and glycoforms of gp-340 between human saliva samples (n = 7) and lung gp-340 from a proteinosis patient using antibodies and lectins in Western blots and ELISA measurements...... bands. Purified I to IV proteins all revealed a N-terminal sequence TGGWIP upon Edman degradation. Moreover, purified gp-340 from the seven donors and lung gp-340 shared N-glycans, sialylated Galbeta1-3GalNAc and (poly)lactosamine structures. However, the larger size gp-340 grouping II/III (n = 4....... Western blots of saliva samples, and of gp-340 purified, from the seven donors using a gp-340 specific antibody distinguished four gp-340 size variants, designated I to IV (n = 2,2,2 and 1). While saliva gp-340 variants I to III had single bands of increasing sizes, variant IV and lung gp-340 had double...

  20. Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei

    Directory of Open Access Journals (Sweden)

    Ghazal Peter

    2009-09-01

    Full Text Available Abstract Background Trypanosomes undergo extensive developmental changes during their complex life cycle. Crucial among these is the transition between slender and stumpy bloodstream forms and, thereafter, the differentiation from stumpy to tsetse-midgut procyclic forms. These developmental events are highly regulated, temporally reproducible and accompanied by expression changes mediated almost exclusively at the post-transcriptional level. Results In this study we have examined, by whole-genome microarray analysis, the mRNA abundance of genes in slender and stumpy forms of T.brucei AnTat1.1 cells, and also during their synchronous differentiation to procyclic forms. In total, five biological replicates representing the differentiation of matched parasite populations derived from five individual mouse infections were assayed, with RNAs being derived at key biological time points during the time course of their synchronous differentiation to procyclic forms. Importantly, the biological context of these mRNA profiles was established by assaying the coincident cellular events in each population (surface antigen exchange, morphological restructuring, cell cycle re-entry, thereby linking the observed gene expression changes to the well-established framework of trypanosome differentiation. Conclusion Using stringent statistical analysis and validation of the derived profiles against experimentally-predicted gene expression and phenotypic changes, we have established the profile of regulated gene expression during these important life-cycle transitions. The highly synchronous nature of differentiation between stumpy and procyclic forms also means that these studies of mRNA profiles are directly relevant to the changes in mRNA abundance within individual cells during this well-characterised developmental transition.

  1. Effects of ERBB2 amplicon size and genomic alterations of chromosomes 1, 3, and 10 on patient response to trastuzumab in metastatic breast cancer.

    Science.gov (United States)

    Morrison, Larry E; Jewell, Susan S; Usha, Lydia; Blondin, Beth A; Rao, Ruta D; Tabesh, Bita; Kemper, Matthew; Batus, Marta; Coon, John S

    2007-04-01

    Trastuzumab is widely used for advanced breast cancer patients with ERBB2-amplified tumors. Nevertheless, over half of these patients do not have an objective response. One reason may be altered expression of genes that might compensate for ERBB2 inhibition. We previously mapped the gene-rich region of chromosome 17 telomeric to ERBB2, and reported considerable variability in the telomeric extent of the ERBB2 amplicon. Here we examined whether the variable amplicon size may be associated with patient response to trastuzumab. In addition, we looked at associations between response and several signaling pathway-related genes unrelated to the ERBB2 amplicon, including AKT3, PTEN, PIK3CA, and PTGS2. In 35 patients with ERBB2-amplified metastatic breast cancer, with 40% overall response to trastuzumab, fluorescence in situ hybridization identified the telomeric extent of the ERBB2 amplicon and the status of the several pathway-related genes. Objective response strongly correlated with the telomeric amplicon size, with 62% of patients with shorter amplicons responding, compared with only 7% of patients with longer amplicons (P = 0.0015). Abnormal copy number of PTGS2 was marginally associated with objective response (P = 0.066), while abnormal copy numbers of two reference loci, 1q25 and the chromosome 10 centromere, were significantly associated with response. Pairwise combinations of copy number status of these loci and ERBB2 amplicon size provided stronger associations and identified a group of patients without responders. These results suggest that patient selection for trastuzumab may be improved by considering ERBB2 amplicon size and genomic status of the 1q25, PTGS2, and centromere 10 loci.

  2. 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

  3. 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.

  4. Differential effect of the overexpression of Rad2/XPG family endonucleases on genome integrity in yeast and human cells.

    Science.gov (United States)

    Jimeno, Sonia; Herrera-Moyano, Emilia; Ortega, Pedro; Aguilera, Andrés

    2017-09-01

    Eukaryotic cells possess several DNA endonucleases that are necessary to complete different steps in DNA metabolism. Rad2/XPG and Rad27/FEN1 belong to a group of evolutionary conserved proteins that constitute the Rad2 family. Given the important roles carried out by these nucleases in DNA repair and their capacity to create DNA breaks, we have investigated the effect that in vivo imbalance of these nucleases and others of the family have on genome integrity and cell proliferation. We show that overexpression of these nucleases causes genetic instability in both yeast and human cells. Interestingly, the type of recombination event and DNA damage induced suggest specific modes and timing of action of each nuclease that are beyond their known DNA repair function and are critical to preserve genome integrity. In addition to identifying new sources of genome instability, a hallmark of cancer cells, this study provides new genetic tools for studies of genome dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers

    Science.gov (United States)

    The evolution of animal mitochondrial (mt) genomes has yielded a highly conserved structure: a single circular chromosome approximately 14 to 20 kb long. Within the last two decades, exceptions to this conserved structure have been reported in a diverse set of organisms. One such exception is the di...

  6. Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques.

    NARCIS (Netherlands)

    A. de Lang (Anna); T. Baas (Tracey); T.H. Teal (Thomas); L.M.E. Leijten (Lonneke); B. Rain (Brandon); A.D.M.E. Osterhaus (Albert); B.L. Haagmans (Bart); M.G. Katze (Michael)

    2007-01-01

    textabstractThe pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) is likely mediated by disproportional immune responses and the ability of the virus to circumvent innate immunity. Using functional genomics, we analyzed early host responses to SARS-CoV infection in the lungs o

  7. 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...

  8. Effect of decellularized adipose tissue particle size and cell density on adipose-derived stem cell proliferation and adipogenic differentiation in composite methacrylated chondroitin sulphate hydrogels.

    Science.gov (United States)

    Brown, Cody F C; Yan, Jing; Han, Tim Tian Y; Marecak, Dale M; Amsden, Brian G; Flynn, Lauren E

    2015-07-30

    An injectable composite scaffold incorporating decellularized adipose tissue (DAT) as a bioactive matrix within a hydrogel phase capable of in situ polymerization would be advantageous for adipose-derived stem cell (ASC) delivery in the filling of small or irregular soft tissue defects. Building on previous work, the current study investigates DAT milling methods and the effects of DAT particle size and cell seeding density on the response of human ASCs encapsulated in photo-cross-linkable methacrylated chondroitin sulphate (MCS)-DAT composite hydrogels. DAT particles were generated by milling lyophilized DAT and the particle size was controlled through the processing conditions with the goal of developing composite scaffolds with a tissue-specific 3D microenvironment tuned to enhance adipogenesis. ASC proliferation and adipogenic differentiation were assessed in vitro in scaffolds incorporating small (average diameter of 38   ±   6 μm) or large (average diameter of 278   ±   3 μm) DAT particles in comparison to MCS controls over a period of up to 21 d. Adipogenic differentiation was enhanced in the composites incorporating the smaller DAT particles and seeded at the higher density of 5   ×   10(5) ASCs/scaffold, as measured by glycerol-3-phosphate dehydrogenase (GPDH) enzyme activity, semi-quantitative analysis of perilipin expression and oil red O staining of intracellular lipid accumulation. Overall, this study demonstrates that decellularized tissue particle size can impact stem cell differentiation through cell-cell and cell-matrix interactions, providing relevant insight towards the rational design of composite biomaterial scaffolds for adipose tissue engineering.

  9. Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis.

    Science.gov (United States)

    Thakur, Jitendra Kumar; Agarwal, Pinky; Parida, Swarup; Bajaj, Deepak; Pasrija, Richa

    2013-08-01

    The KIX domain, which mediates protein-protein interactions, was first discovered as a motif in the large multidomain transcriptional activator histone acetyltransferase p300/CBP. Later, the domain was also found in Mediator subunit MED15, where it interacts with many transcription factors. In both proteins, the KIX domain is a target of activation domains of diverse transcription activators. It was found to be an essential component of several specific gene-activation pathways in fungi and metazoans. Not much is known about KIX domain proteins in plants. This study aims to characterize all the KIX domain proteins encoded by the genomes of Arabidopsis and rice. All identified KIX domain proteins are presented, together with their chromosomal locations, phylogenetic analysis, expression and SNP analyses. KIX domains were found not only in p300/CBP- and MED15-like plant proteins, but also in F-box proteins in rice and DNA helicase in Arabidopsis, suggesting roles of KIX domains in ubiquitin-mediated proteasomal degradation and genome stability. Expression analysis revealed overlapping expression of OsKIX_3, OsKIX_5 and OsKIX_7 in different stages of rice seeds development. Moreover, an association analysis of 136 in silico mined SNP loci in 23 different rice genotypes with grain-length information identified three non-synonymous SNP loci in these three rice genes showing strong association with long- and short-grain differentiation. Interestingly, these SNPs were located within KIX domain encoding sequences. Overall, this study lays a foundation for functional analysis of KIX domain proteins in plants.

  10. Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

    Science.gov (United States)

    Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

    2015-01-01

    Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other

  11. Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data.

    Science.gov (United States)

    Li, Chung-I; Shyr, Yu

    2016-12-01

    As RNA-seq rapidly develops and costs continually decrease, the quantity and frequency of samples being sequenced will grow exponentially. With proteomic investigations becoming more multivariate and quantitative, determining a study's optimal sample size is now a vital step in experimental design. Current methods for calculating a study's required sample size are mostly based on the hypothesis testing framework, which assumes each gene count can be modeled through Poisson or negative binomial distributions; however, these methods are limited when it comes to accommodating covariates. To address this limitation, we propose an estimating procedure based on the generalized linear model. This easy-to-use method constructs a representative exemplary dataset and estimates the conditional power, all without requiring complicated mathematical approximations or formulas. Even more attractive, the downstream analysis can be performed with current R/Bioconductor packages. To demonstrate the practicability and efficiency of this method, we apply it to three real-world studies, and introduce our on-line calculator developed to determine the optimal sample size for a RNA-seq study.

  12. Interfacial Tension-Driven Differentiation-(ITDD) may result in a low-density central region inside kilometer-sized bodies

    Science.gov (United States)

    Arias, Francisco J.

    2016-03-01

    Interfacial Tension-Driven Differentiation, (ITDD), and its possible significance with regards to the interior structures of kilometer-sized bodies is discussed. Using a simple physical and geometrical model, an analytical expression for the conditions in which ITDD can occur is derived. It is shown that ITDD coupled with internal convection can lead to a counterintuitive result: that central regions may be less dense than outer regions in km-sized, initially melted bodies. ITDD offers an alternative explanation to the formation of microporosity inside of small bodies, (e.g. Churyumov-Gerasimenko-like objects), as well as macroporosity, which is suggested to occur in the interior of Mars' larger satellite Phobos, without recourse to rubble-pile models. Depending on the development of the velocity boundary layer at the solidification front, ITDD allows not just the possibility of central porosity, but also more complex scenarios, such as the formation of internal porosity rings.

  13. Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model.

    Directory of Open Access Journals (Sweden)

    Shamim H Rahman

    2015-05-01

    Full Text Available In vitro disease modeling based on induced pluripotent stem cells (iPSCs provides a powerful system to study cellular pathophysiology, especially in combination with targeted genome editing and protocols to differentiate iPSCs into affected cell types. In this study, we established zinc-finger nuclease-mediated genome editing in primary fibroblasts and iPSCs generated from a mouse model for radiosensitive severe combined immunodeficiency (RS-SCID, a rare disorder characterized by cellular sensitivity to radiation and the absence of lymphocytes due to impaired DNA-dependent protein kinase (DNA-PK activity. Our results demonstrate that gene editing in RS-SCID fibroblasts rescued DNA-PK dependent signaling to overcome radiosensitivity. Furthermore, in vitro T-cell differentiation from iPSCs was employed to model the stage-specific T-cell maturation block induced by the disease causing mutation. Genetic correction of the RS-SCID iPSCs restored T-lymphocyte maturation, polyclonal V(DJ recombination of the T-cell receptor followed by successful beta-selection. In conclusion, we provide proof that iPSC-based in vitro T-cell differentiation is a valuable paradigm for SCID disease modeling, which can be utilized to investigate disorders of T-cell development and to validate gene therapy strategies for T-cell deficiencies. Moreover, this study emphasizes the significance of designer nucleases as a tool for generating isogenic disease models and their future role in producing autologous, genetically corrected transplants for various clinical applications.

  14. From glacial refugia to modern populations: new assemblages of organelle genomes generated by differential cytoplasmic gene flow in transcontinental black spruce.

    Science.gov (United States)

    Gérardi, Sébastien; Jaramillo-Correa, Juan P; Beaulieu, Jean; Bousquet, Jean

    2010-12-01

    Assessing species' range-wide cytoplasmic diversity provides valuable insights regarding their dispersal and adaptive potential in a changing environment. Transcontinental chloroplast (cpDNA) and mitochondrial DNA (mtDNA) population structures were compared to identify putative ancestral and new cytoplasmic genome assemblages in black spruce (Picea mariana), a North American boreal conifer. Mean within-population diversity and allelic richness for cpSSR markers were 0.80 and 4.21, respectively, and diminished westward. Population differentiation based on G(ST) was lower for cpDNA than for mtDNA (G(ST) =0.104 and 0.645, respectively) but appeared comparable when estimated using Jost differentiation index (D=0.459 and 0.537, respectively). Further analyses resulted in the delineation of at least three genetically distinct cpDNA lineages partially congruent with those inferred from mtDNA data, which roughly corresponded to western, central and eastern Canada. Additionally, the patterns of variation in Alaska for both cpDNA and mtDNA markers suggested that black spruce survived the last glacial maximum in this northern region. The range-wide comparison of the geographic extent of cytoplasmic DNA lineages revealed that extensive pollen gene flow between ancestral lineages occurred preferentially from west to east during the postglacial expansion of the species, while seed-mediated gene flow remained geographically restricted. This differential gene flow promoted intraspecific cytoplasmic capture that generated new assemblages of cpDNA and mtDNA genomes during the Holocene. Hence, black spruce postglacial colonization unexpectedly resulted in an increase in genetic diversity with possible adaptive consequences. © 2010 Blackwell Publishing Ltd.

  15. Early prenatal androgen exposure reduces testes size and sperm concentration in sheep without altering neuroendocrine differentiation and masculine sexual behavior.

    Science.gov (United States)

    Scully, C M; Estill, C T; Amodei, R; McKune, A; Gribbin, K P; Meaker, M; Stormshak, F; Roselli, C E

    2017-07-29

    Prenatal androgens are largely responsible for growth and differentiation of the genital tract and testis and for organization of the control mechanisms regulating male reproductive physiology and behavior. The aim of the present study was to evaluate the impact of inappropriate exposure to excess testosterone (T) during the first trimester of fetal development on the reproductive function, sexual behavior, and fertility potential of rams. We found that biweekly maternal T propionate (100 mg) treatment administered from Day 30-58 of gestation significantly decreased (P sexually attracted to estrous females. In summary, these results suggest that exposure to exogenous T during the first trimester of gestation can negatively impact spermatogenesis and compromise the reproductive fitness of rams. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

    Science.gov (United States)

    Gazave, Elodie; Tassone, Erica E; Ilut, Daniel C; Wingerson, Megan; Datema, Erwin; Witsenboer, Hanneke M A; Davis, James B; Grant, David; Dyer, John M; Jenks, Matthew A; Brown, Jack; Gore, Michael A

    2016-01-01

    The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

  17. Genome sequence comparison reveals a candidate gene involved in male-hermaphrodite differentiation in papaya (Carica papaya) trees.

    Science.gov (United States)

    Ueno, Hiroki; Urasaki, Naoya; Natsume, Satoshi; Yoshida, Kentaro; Tarora, Kazuhiko; Shudo, Ayano; Terauchi, Ryohei; Matsumura, Hideo

    2015-04-01

    The sex type of papaya (Carica papaya) is determined by the pair of sex chromosomes (XX, female; XY, male; and XY(h), hermaphrodite), in which there is a non-recombining genomic region in the Y and Y(h) chromosomes. This region is presumed to be involved in determination of males and hermaphrodites; it is designated as the male-specific region in the Y chromosome (MSY) and the hermaphrodite-specific region in the Y(h) chromosome (HSY). Here, we identified the genes determining male and hermaphrodite sex types by comparing MSY and HSY genomic sequences. In the MSY and HSY genomic regions, we identified 14,528 nucleotide substitutions and 965 short indels with a large gap and two highly diverged regions. In the predicted genes expressed in flower buds, we found no nucleotide differences leading to amino acid changes between the MSY and HSY. However, we found an HSY-specific transposon insertion in a gene (SVP like) showing a similarity to the Short Vegetative Phase (SVP) gene. Study of SVP-like transcripts revealed that the MSY allele encoded an intact protein, while the HSY allele encoded a truncated protein. Our findings demonstrated that the SVP-like gene is a candidate gene for male-hermaphrodite determination in papaya.

  18. Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells.

    Directory of Open Access Journals (Sweden)

    Saleh Tamim

    Full Text Available miR-137 plays critical roles in the nervous system and tumor development; an increase in its expression is required for neuronal differentiation while its reduction is implicated in gliomagenesis. To evaluate the potential of miR-137 in glioblastoma therapy, we conducted genome-wide target mapping in glioblastoma cells by measuring the level of association between PABP and mRNAs in cells transfected with miR-137 mimics vs. controls via RIPSeq. Impact on mRNA levels was also measured by RNASeq. By combining the results of both experimental approaches, 1468 genes were found to be negatively impacted by miR-137--among them, 595 (40% contain miR-137 predicted sites. The most relevant targets include oncogenic proteins and key players in neurogenesis like c-KIT, YBX1, AKT2, CDC42, CDK6 and TGFβ2. Interestingly, we observed that several identified miR-137 targets are also predicted to be regulated by miR-124, miR-128 and miR-7, which are equally implicated in neuronal differentiation and gliomagenesis. We suggest that the concomitant increase of these four miRNAs in neuronal stem cells or their repression in tumor cells could produce a robust regulatory effect with major consequences to neuronal differentiation and tumorigenesis.

  19. Genetic differentiation and estimation of effective population size and migration rates in two sympatric ecotypes of the marine snail Littorina saxatilis.

    Science.gov (United States)

    Fernández, J; Galindo, J; Fernández, B; Pérez-Figueroa, A; Caballero, A; Rolán-Alvarez, E

    2005-01-01

    On exposed rocky shores in Galicia (northwest Spain), a striking polymorphism exists between two ecotypes (RB and SU) of Littorina saxatilis that occupy different levels of the intertidal zone and exhibit an incomplete reproductive isolation. The setting has been suggested to represent ongoing sympatric speciation by ecological adaptation of the two ecotypes to their respective habitats. In this article we address whether or not the ecotypes have developed their own population structures in response to the rigors of their corresponding environments and life histories. We analyzed four to five allozymic loci from three surveys of the same sites, spanning a 14-year period. An experimental design including three localities with two transects per locality and three shore levels allowed studying temporal and spatial population structure and estimation of effective population sizes (N(e)), neighborhood sizes (N(n)), and migration rates (m). Genetic differentiation was significantly lower in RB populations (theta(ST) = 0.067) than in SU ones (theta(ST) = 0.124). Mean estimates of N(e), N(n), and m did not differ significantly between ecotypes, but local ecotype differences in migration between the two closest localities (larger migration rates in RB than in SU populations) could explain the pattern in population differentiation.

  20. Differential behavior of plasmids containing chromosomal DNA insertions of various sizes during transformation and conjugation in Haemophilus influenzae

    Energy Technology Data Exchange (ETDEWEB)

    Balganesh, M.; Setlow, J.K.

    1985-01-01

    Plasmids with chromosomal insertions were constructed by removal of a 1.1-kilobase-pair piece from the 9.8-kilobase-pair vector plasmid pDM2 by EcoRI digestion and inserting in its place various lengths of chromosomal DNA (1.7, 3.4, and 9.0 kilobase pairs) coding for resistance to novobiocin. A fourth plasmid was constructed by insertion of the largest piece of chromosomal DNA into the SmaI site of pDM2. The plasmids without inserts were taken up poorly by competent cells and thus were considered not to contain specific DNA uptake sites. The presence of even the smallest insert of chromosomal DNA caused a large increase in transformation of Rec/sup +/ and Rec/sup -/ strains. The frequency of plasmid establishment in Rec/sup +/ cells by transformation increased exponentially with increasing insert size, but in Rec/sup -/ cells there was less transformation by the larger plasmids. Conjugal transfer of these plasmids was carried out with the 35-kilobase-pair mobilizing plasmid pHD147. The frequency of establishment of plasmids by this method not only was not markedly affected by the presence of the insertions, but also decreased somewhat with increase in insert size and was independent of rec-1 and rec-2 genes. Recombination between plasmid and chromosome was readily detected after transformation, but could not be detected after transconjugation even when the recipient cells were Rec/sup +/ and made competent. These data suggested that there is a special processing of plasmid DNA that enters the competent cells in transformation that makes possible recombination of homologous regions of the plasmid with the chromosome and pairing with the chromosome that aids plasmid establishment.

  1. Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

    Science.gov (United States)

    Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2014-06-01

    To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

  2. A differential genome-wide transcriptome analysis: impact of cellular copper on complex biological processes like aging and development.

    Directory of Open Access Journals (Sweden)

    Jörg Servos

    Full Text Available The regulation of cellular copper homeostasis is crucial in biology. Impairments lead to severe dysfunctions and are known to affect aging and development. Previously, a loss-of-function mutation in the gene encoding the copper-sensing and copper-regulated transcription factor GRISEA of the filamentous fungus Podospora anserina was reported to lead to cellular copper depletion and a pleiotropic phenotype with hypopigmentation of the mycelium and the ascospores, affected fertility and increased lifespan by approximately 60% when compared to the wild type. This phenotype is linked to a switch from a copper-dependent standard to an alternative respiration leading to both a reduced generation of reactive oxygen species (ROS and of adenosine triphosphate (ATP. We performed a genome-wide comparative transcriptome analysis of a wild-type strain and the copper-depleted grisea mutant. We unambiguously assigned 9,700 sequences of the transcriptome in both strains to the more than 10,600 predicted and annotated open reading frames of the P. anserina genome indicating 90% coverage of the transcriptome. 4,752 of the transcripts differed significantly in abundance with 1,156 transcripts differing at least 3-fold. Selected genes were investigated by qRT-PCR analyses. Apart from this general characterization we analyzed the data with special emphasis on molecular pathways related to the grisea mutation taking advantage of the available complete genomic sequence of P. anserina. This analysis verified but also corrected conclusions from earlier data obtained by single gene analysis, identified new candidates of factors as part of the cellular copper homeostasis system including target genes of transcription factor GRISEA, and provides a rich reference source of quantitative data for further in detail investigations. Overall, the present study demonstrates the importance of systems biology approaches also in cases were mutations in single genes are analyzed to

  3. Utility of Genomic Analysis in Differentiating Synchronous and Metachronous Lung Adenocarcinomas from Primary Adenocarcinomas with Intrapulmonary Metastasis.

    Science.gov (United States)

    Saab, Jad; Zia, Hamid; Mathew, Susan; Kluk, Michael; Narula, Navneet; Fernandes, Helen

    2017-06-01

    Distinguishing synchronous and metachronous primary lung adenocarcinomas from adenocarcinomas with intrapulmonary metastasis is essential for optimal patient management. In this study, multiple lung adenocarcinomas occurring in the same patient were evaluated using comprehensive histopathologic evaluation supplemented with molecular analysis. The cohort included 18 patients with a total of 52 lung adenocarcinomas. Eleven patients had a new diagnosis of multiple adenocarcinomas in the same lobe (n=5) or different lobe (n=6). Seven patients had a history of lung cancer and developed multiple new tumors. The final diagnosis was made in resection specimens (n=49), fine needle aspiration (n=2), and biopsy (n=1). Adenocarcinomas were non-mucinous, and histopathologic comparison of tumors was performed. All tumors save for one were subjected to ALK gene rearrangement testing and targeted Next Generation Sequencing (NGS). Using clinical, radiologic, and morphologic features, a confident conclusion favoring synchronous/metachronous or metastatic disease was made in 65% of patients. Cases that proved challenging included ones with more than three tumors showing overlapping growth patterns and lacking a predominant lepidic component. Genomic signatures unique to each tumor were helpful in determining the relationship of multiple carcinomas in 72% of patients. Collectively, morphologic and genomic data proved to be of greater value and achieved a conclusive diagnosis in 94% of patients. Assessment of the genomic profiles of multiple lung adenocarcinomas complements the histological findings, enabling a more comprehensive assessment of synchronous, metachronous, and metastatic lesions in most patients, thereby improving staging accuracy. Targeted NGS can identify genetic alterations with therapeutic implications. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Differentiation of service offerings to corporate clients: theory and implications for a medium-sized Belarusian bank

    OpenAIRE

    Burakov, Vladimir

    2005-01-01

    Abstract In this dissertation, the problem of differentiation of service offerings to corporate clients is considered from the marketing perspective where the main focus put on understanding of customers������â����â� �¢â�¬â�¢�����¢â�¬� ���¢�¢â���¬�¢â���¢������â�����¢�¢â���¬��� �������¢���¢�¢â�¬�¡���¬���¢�¢â�¬�¾���¢������â����â� �¢â�¬â�¢�������¢��...

  5. Genome Array on Differentially Expressed Genes of Skin Tissue in Cashmere Goat at Early Anagen of Cashmere Growth Cycle Using DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    DI Jiang; Marzeya Yasen; XU Xin-ming; Lazate Ainiwaer; ZHANG Yan-hua; TIAN Ke-chuan; YU Li-juan; WU Wei-wei; Hanikezi Tulafu; FU Xue-feng

    2014-01-01

    In order to study the molecular mechanism involved in cashmere regeneration, this study investigated the gene expression proifle of skin tissue at various stages of the cashmere growth cycle and screen differentially expressed genes at proangen in 10 cashmere goats at 2 years of age using agilent sheep oligo microarray. Signiifcance analysis of microarray (SAM) methods was used to identify the differentially expressed genes, Hierarchical clustering was performed to clarify these genes in association with different cashmere growth stages, and GO (Gene ontology) and the pathway analyses were con-ducted by a free web-based Molecular Annotation System3.0 (MAS 3.0). Approximately 10 200 probe sets were detected in skin tissue of 2-yr-old cashmere goat. After SAM analysis of the microarray data, totally 417 genes were shown to be differentially expressed at different cashmere growth stages, and 24 genes are signiifcantly up-regulated (21) or down-regulated (3) at proangen concurrently compared to angen and telogen. Hierarchical clustering analysis clearly distinguished the differentially expressed genes of each stage. GO analysis indicated that these altered genes at proangen were predominantly involved in collagen ifbril organization, integrin-mediated signaling pathway, cell-matrix adhesion, cell adhesion, transforming growth factor-β (TGF-β) receptor signaling pathway, regulation of cell growth. Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that the signiifcant pathways involved mainly included focal adhesion and extracellular matrixc (ECM)-receptor interaction. Some important genes involved in these biological processes, such as COL1A1, COL1A2, COL3A1, SPARC, CYR61 and CTGF, were related to tissue remolding and repairing and detected by more than one probe with similar expression trends at different stages of cashmere growth cycle. The different expression of these genes may contribute to understanding the molecular mechanism of cashmere

  6. Differentiation of Plum pox virus isolates by single-strand conformation polymorphism and low-stringency single specific primer PCR analysis of HC-Pro genome region.

    Science.gov (United States)

    Gadiou, S; Safárová, D; Navrátil, M

    2009-01-01

    Single-strand conformation polymorphism (SSCP) and low-stringency single specific primer (LSSP)-PCR were assessed for suitability and reliability in genotyping of Plum pox virus (PPV) isolates. Examined PPV isolates included 16 PPV-D, 12 PPV-M, and 14 PPV-Rec isolates collected in Czech Republic. The analysis was performed on the helper component protease (HC-Pro) region of the PPV genome. SSCP and LSSP-PCR allowed the differentiation of PPV strain, but SSCP was not able to distinguish isolates within the same strain. The individual genotyping of each PPV isolate was obtained by LSSP-PCR. Nevertheless, both SSCP and LSSP-PCR techniques are suitable for preliminary screening of genetic variability of plant RNA viruses.

  7. Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

    Science.gov (United States)

    Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

    2016-05-01

    The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.

  8. Genome-wide Anaplasma phagocytophilum AnkA-DNA interactions are enriched in intergenic regions and gene promoters and correlate with infection-induced differential gene expression.

    Directory of Open Access Journals (Sweden)

    J Stephen Dumler

    2016-09-01

    Full Text Available Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains. We hypothesize that identification of additional AnkA binding sites will better delineate how A. phagocytophilum infection results in reprogramming of the neutrophil genome. Using AnkA-binding ChIP-seq, we showed that AnkA binds broadly throughout all chromosomes in a reproducible pattern, especially at: i intergenic regions predicted to be matrix attachment regions (MARs; ii within predicted lamina-associated domains; and iii at promoters ≤3,000 bp upstream of transcriptional start sites. These findings provide genome-wide support for AnkA as a regulator of cis-gene transcription. Moreover, the dominant mark of AnkA in distal intergenic regions known to be AT-enriched, coupled with frequent enrichment in the nuclear lamina, provides strong support for its role as a MAR-binding protein and genome re-organizer. AnkA must be considered a prime candidate to promote neutrophil reprogramming and subsequent functional changes that belie improved microbial fitness and pathogenicity.

  9. Genome-scale NAD(H/(+ availability patterns as a differentiating feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in relation to fermentative metabolism.

    Directory of Open Access Journals (Sweden)

    Alejandro Acevedo

    Full Text Available Scheffersomyces stipitis is a yeast able to ferment pentoses to ethanol, unlike Saccharomyces cerevisiae, it does not present the so-called overflow phenomenon. Metabolic features characterizing the presence or not of this phenomenon have not been fully elucidated. This work proposes that genome-scale metabolic response to variations in NAD(H/(+ availability characterizes fermentative behavior in both yeasts. Thus, differentiating features in S. stipitis and S. cerevisiae were determined analyzing growth sensitivity response to changes in available reducing capacity in relation to ethanol production capacity and overall metabolic flux span. Using genome-scale constraint-based metabolic models, phenotypic phase planes and shadow price analyses, an excess of available reducing capacity for growth was found in S. cerevisiae at every metabolic phenotype where growth is limited by oxygen uptake, while in S. stipitis this was observed only for a subset of those phenotypes. Moreover, by using flux variability analysis, an increased metabolic flux span was found in S. cerevisiae at growth limited by oxygen uptake, while in S. stipitis flux span was invariant. Therefore, each yeast can be characterized by a significantly different metabolic response and flux span when growth is limited by oxygen uptake, both features suggesting a higher metabolic flexibility in S. cerevisiae. By applying an optimization-based approach on the genome-scale models, three single reaction deletions were found to generate in S. stipitis the reducing capacity availability pattern found in S. cerevisiae, two of them correspond to reactions involved in the overflow phenomenon. These results show a close relationship between the growth sensitivity response given by the metabolic network and fermentative behavior.

  10. Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

    Science.gov (United States)

    Acevedo, Alejandro; Aroca, German; Conejeros, Raul

    2014-01-01

    Scheffersomyces stipitis is a yeast able to ferment pentoses to ethanol, unlike Saccharomyces cerevisiae, it does not present the so-called overflow phenomenon. Metabolic features characterizing the p