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Sample records for est based phylogenomics

  1. Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

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    Hartmann Stefanie

    2008-03-01

    Full Text Available Abstract Background While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood and studied ways to improve the accuracy of trees obtained from such datasets. Results We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion These results demonstrate that partial gene

  2. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

    Science.gov (United States)

    Hartmann, Stefanie; Vision, Todd J

    2008-03-26

    While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a

  3. Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach.

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    Lugli, Gabriele Andrea; Milani, Christian; Duranti, Sabrina; Mancabelli, Leonardo; Mangifesta, Marta; Turroni, Francesca; Viappiani, Alice; van Sinderen, Douwe; Ventura, Marco

    2018-02-15

    For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genus Bifidobacterium by employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria. IMPORTANCE Nowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido)bacterial taxons should be validated with a phylogenomic assessment like the approach presented here. Copyright © 2018 American Society for Microbiology.

  4. Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data.

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    Panzera, Alejandra; Leaché, Adam D; D'Elía, Guillermo; Victoriano, Pedro F

    2017-01-01

    The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto ), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus , L. monticola , L. nigroviridis and L. nitidus , and L. platei and L. velosoi . Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the

  5. Phylogenomic analyses data of the avian phylogenomics project

    DEFF Research Database (Denmark)

    Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J

    2015-01-01

    ML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. CONCLUSIONS: The Avian Phylogenomics Project is the largest......, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences...... filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based Exa...

  6. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

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    Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd

    2018-01-01

    Abstract The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs’ relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses. PMID:29177474

  7. Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence.

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    Nan, Fangru; Feng, Jia; Lv, Junping; Liu, Qi; Fang, Kunpeng; Gong, Chaoyan; Xie, Shulian

    2017-06-07

    Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415-484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.

  8. Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

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    Margarita Gomila

    2017-12-01

    Full Text Available The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.

  9. Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees.

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    Romiguier, Jonathan; Cameron, Sydney A; Woodard, S Hollis; Fischman, Brielle J; Keller, Laurent; Praz, Christophe J

    2016-03-01

    As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honey bees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here, we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a nonhomogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honey bees, bumble bees, and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic data sets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci.

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    Streicher, Jeffrey W; Miller, Elizabeth C; Guerrero, Pablo C; Correa, Claudio; Ortiz, Juan C; Crawford, Andrew J; Pie, Marcio R; Wiens, John J

    2018-02-01

    Phylogenomic approaches offer a wealth of data, but a bewildering diversity of methodological choices. These choices can strongly affect the resulting topologies. Here, we explore two controversial approaches (binning genes into "supergenes" and inclusion of only rapidly evolving sites), using new data from hyloid frogs. Hyloid frogs encompass ∼53% of frog species, including true toads (Bufonidae), glassfrogs (Centrolenidae), poison frogs (Dendrobatidae), and treefrogs (Hylidae). Many hyloid families are well-established, but relationships among these families have remained difficult to resolve. We generated a dataset of ultraconserved elements (UCEs) for 50 ingroup species, including 18 of 19 hyloid families and up to 2214 loci spanning >800,000 aligned base pairs. We evaluated these two general approaches (binning, rapid sites only) based primarily on their ability to recover and strongly support well-established clades. Data were analyzed using concatenated likelihood and coalescent species-tree methods (NJst, ASTRAL). Binning strongly affected inferred relationships, whereas use of only rapidly evolving sites did not (indicating ∼87% of the data contributed little information). The optimal approaches for maximizing recovery and support of well-established clades were concatenated likelihood analysis and the use of a limited number of naive bins (statistical binning gave more problematic results). These two optimal approaches converged on similar relationships among hyloid families, and resolved them with generally strong support. The relationships found were very different from most previous estimates of hyloid phylogeny, and a new classification is proposed. The new phylogeny also suggests an intriguing biogeographical scenario, in which hyloids originated in southern South America before radiating throughout the world. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. PCR-Based EST Mapping in Wheat (Triticum aestivum L.

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    J. PERRY GUSTAFSON

    2009-04-01

    Full Text Available Mapping expressed sequence tags (ESTs to hexaploid wheat is aimed to reveal the structure and function of the hexaploid wheat genome. Sixty eight ESTs representing 26 genes were mapped into all seven homologous chromosome groups of wheat (Triticum aestivum L using a polymerase chain reaction technique. The majority of the ESTs were mapped to homologous chromosome group 2, and the least were mapped to homologous chromosome group 6. Comparative analysis between the EST map from this study and the EST map based on RFLPs showed 14 genes that have been mapped by both approaches were mapped to the same arm of the same homologous chromosome, which indicated that using PCR-based ESTs was a reliable approach in mapping ESTs in hexaploid wheat.

  12. Phylogenomic grouping of Listeria monocytogenes.

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    Doijad, Swapnil; Weigel, Markus; Barbuddhe, Sukhadeo; Blom, Jochen; Goesmann, Alexander; Hain, Torsten; Chakraborty, Trinad

    2015-09-01

    The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.

  13. Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis.

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    Attigala, Lakshmi; Wysocki, William P; Duvall, Melvin R; Clark, Lynn G

    2016-08-01

    We explored phylogenetic relationships among the twelve lineages of the temperate woody bamboo clade (tribe Arundinarieae) based on plastid genome (plastome) sequence data. A representative sample of 28 taxa was used and maximum parsimony, maximum likelihood and Bayesian inference analyses were conducted to estimate the Arundinarieae phylogeny. All the previously recognized clades of Arundinarieae were supported, with Ampelocalamus calcareus (Clade XI) as sister to the rest of the temperate woody bamboos. Well supported sister relationships between Bergbambos tessellata (Clade I) and Thamnocalamus spathiflorus (Clade VII) and between Kuruna (Clade XII) and Chimonocalmus (Clade III) were revealed by the current study. The plastome topology was tested by taxon removal experiments and alternative hypothesis testing and the results supported the current plastome phylogeny as robust. Neighbor-net analyses showed few phylogenetic signal conflicts, but suggested some potentially complex relationships among these taxa. Analyses of morphological character evolution of rhizomes and reproductive structures revealed that pachymorph rhizomes were most likely the ancestral state in Arundinarieae. In contrast leptomorph rhizomes either evolved once with reversions to the pachymorph condition or multiple times in Arundinarieae. Further, pseudospikelets evolved independently at least twice in the Arundinarieae, but the ancestral state is ambiguous. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

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    Pardinas Jose R

    2008-04-01

    Full Text Available Abstract Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  15. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

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    Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

    2008-04-10

    Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  16. Phylogenomic relationship of feijoa (Acca sellowiana (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences.

    Science.gov (United States)

    Machado, Lilian de Oliveira; Vieira, Leila do Nascimento; Stefenon, Valdir Marcos; Oliveira Pedrosa, Fábio de; Souza, Emanuel Maltempi de; Guerra, Miguel Pedro; Nodari, Rubens Onofre

    2017-04-01

    Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance. In the present work, we reported the complete cp genome of feijoa. The feijoa cp genome is a circular molecule of 159,370 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC 88,028 bp) and a Small Single Copy region (SSC 18,598 bp) separated by Inverted Repeat regions (IRs 26,372 bp). The genome structure, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. When compared to other cp genome sequences of Myrtaceae, feijoa showed closest relationship with pitanga (Eugenia uniflora L.). Furthermore, a comparison of pitanga synonymous (Ks) and nonsynonymous (Ka) substitution rates revealed extremely low values. Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of three Myrtoideae clades.

  17. HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.

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    Bi, Guiqi; Mao, Yunxiang; Xing, Qikun; Cao, Min

    2018-01-01

    Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git, and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks. yxmao@ouc.edu.cn or fenghen360@126.com. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Phylogenomics provides strong evidence for relationships of butterflies and moths.

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    Kawahara, Akito Y; Breinholt, Jesse W

    2014-08-07

    Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly-moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  19. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.

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    Burki, Fabien; Kudryavtsev, Alexander; Matz, Mikhail V; Aglyamova, Galina V; Bulman, Simon; Fiers, Mark; Keeling, Patrick J; Pawlowski, Jan

    2010-12-02

    Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica). 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this

  20. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists

    Directory of Open Access Journals (Sweden)

    Bulman Simon

    2010-12-01

    Full Text Available Abstract Background Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp., Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae and Gromiida (Gromia sphaerica. Results 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin

  1. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists

    Science.gov (United States)

    2010-01-01

    Background Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica). Results 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea

  2. Crawling through time: Transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomics.

    Science.gov (United States)

    Medina, Mónica; Lal, Shruti; Vallès, Yvonne; Takaoka, Tori L; Dayrat, Benoît A; Boore, Jeffrey L; Gosliner, Terrence

    2011-03-01

    Sea slugs (Gastropoda: Opisthobranchia) are characterized by extensive morphological homoplasy. In particular, reduced or absent shells are predominant throughout the group. This trend towards shell loss has resulted in a poor fossil record. DNA-based phylogenies have been helpful in improving our understanding of the evolution of this group and major clades are emerging. We report 13 new complete opisthobranch mitochondrial genomes that provide robust support for some of these emerging nodes. We name three new clades within the Opisthobranchia, the Actopleura (Acteonoidea plus Nudipleura), Placoesophaga (Cephalaspidea plus Anaspidea), and Siphoglossa (Sacoglossa plus the Siphonaria). Finally we use molecular clock dating that suggests an earlier opisthobranch divergence than previously reported. The implications of this evolutionary scenario are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Insect phylogenomics: results, problems and the impact of matrix composition.

    Science.gov (United States)

    Letsch, Harald O; Meusemann, Karen; Wipfler, Benjamin; Schütte, Kai; Beutel, Rolf; Misof, Bernhard

    2012-08-22

    In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.

  4. ALPHA: A Toolkit for Automated Local Phylogenomic Analyses.

    Science.gov (United States)

    Elworth, R A Leo; Allen, Chabrielle; Benedict, Travis; Dulworth, Peter; Nakhleh, Luay

    2018-03-19

    The evolutionary histories of individual regions across a genomic alignment - called 'local genealogies' - can differ from each other, due to processes such as recombination. Elucidating and analyzing these local genealogies are important for a large number of inference tasks, including those pertaining to species phylogenies, evolutionary processes, and trait mapping. In this paper, we present a toolkit for automated local phylogenomic analyses, or ALPHA. The purpose of this toolkit is to provide a wide array of functionalities for automated inference of local genealogies as well as analyses based on these local genealogies. The toolkit uses sliding windows to construct local genealogies and can compute a wide array of local phylogeny based statistics, such as the D-statistic. The toolkit comes with a graphical user interface and several import/export functionalities. Over the last few decades, much emphasis in phylogenomics has been put on developing tools for inferring species phylogenies. This toolkit complements those efforts by emphasizing the "local" aspect of phylogenomics. ALPHA is freely available for installation and use, including source code, at https://github.com/chilleo/ALPHA. chilleo@gmail.com (RALE); nakhleh@rice.edu (LN). Supplementary data, including in-depth installation and example usage instructions are available online at https://github.com/chilleo/ALPHA.

  5. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    Quantitative trait locus (QTL) mapping is an important method in marker-assisted selection breeding. Many studies on the QTLs focus on cotton fibre yield and quality; however, most are conducted at the DNA level, which may reveal null QTLs. Hence, QTL mapping based on transcriptome maps at the cDNA level is often ...

  6. The impact of paralogy on phylogenomic studies - a case study on annelid relationships.

    Directory of Open Access Journals (Sweden)

    Torsten H Struck

    Full Text Available Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus including the robust bootstrap support could be attributed to the presence of paralogous sequences in two partitions. Excluding these sequences resulted in a different, weaker supported placement for these taxa. Moreover, the analyses revealed that paralogous sequences impacted the reconstruction when only a single taxon represented a previously supported higher taxon such as a polychaete family. One possibility of a priori detection of wrongly assigned paralogous sequences could combine 1 a screening of single-partition analyses based on criteria such as nodal support or internal branch length with 2 blast searches of suspicious cases as presented herein. Also possible are a posteriori approaches in which support for specific clades is investigated by comparing alternative hypotheses based on differences in per-site likelihoods. Increasing the sizes of EST libraries will also decrease the likelihood of wrongly assigned paralogous sequences, and in the case

  7. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    DPL. 21. 6 (28.6%). 0 (0). Gh. 8. 0 (0). 0 (0). MUSB. 6. 1 (16.7%). 0 (0). Total. 1270. 570 (44.9%). 303 (23.86%). Table 2. Basic information on the F2 transcriptome linkage map based on developing fibres at five DPA. Linkage group. Chromosome. Length (cM). Total loci. Average distance. Largest gap (cM). 1. Chr01. 78.53.

  8. Phylogenomics of the plant family Araceae.

    Science.gov (United States)

    Henriquez, Claudia L; Arias, Tatiana; Pires, J Chris; Croat, Thomas B; Schaal, Barbara A

    2014-06-01

    The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011, 2012; Nauheimer et al., 2012). However, phylogenetic ambiguity near the root of the tree precludes answering questions about the early evolution of the family. We use Illumina sequencing technology and reference based assembly to resolve the remaining questions in the deep phylogeny of Araceae. We sampled 32 genera and obtained 7 from GenBank (including an outgroup), representing 42 of 44 major clades described in Cusimano et al. (2011). A subsequent phylogenomic analysis based on mitochondrial data was performed to test congruence between plastid and mitochondrial data for phylogenetic inference. Plastid sequences produced strongly supported phylogenies. In contrast, mitochondrial phylogenies were weakly supported and incongruent with chloroplast data (Templeton test, p⩽0.0001), although several smaller clades were recovered. New strongly-supported clades seen here are: (1) Anubias and Montrichardia, excluding Calla, form a clade that is sister to the Zantedeschia clade; (2) the South African genus Zantedeschia is sister to the Old World Anchomanes clade; and (3) within the Zantedeschia clade, Philodendron is sister to the rest. Calla and Schismatoglottis form a clade at the base of one of two major clades in Aroideae based on complete chloroplast sequences. Although statistical support is weak, morphological and cytological features support this topology. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Phylogenomic analysis of marine Roseobacters.

    Directory of Open Access Journals (Sweden)

    Kai Tang

    2010-07-01

    Full Text Available Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution.In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML and neighbor joining (NJ. Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA, approximately unbiased (AU and Shimodaira-Hasegawa (SH tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes.Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes for dimethylsulfoniopropionate (DMSP degradation. These aquired genes are essential for the growth of Roseobacters and their eukaryotic partners.

  10. Excitatriz estática en base al microcontrolador Intel 8751

    OpenAIRE

    Rivera Gaibor, Juan Carlos; Ledesma Galindo, Bolívar

    1993-01-01

    Se presenta la descripción y características de una excitatriz estática de 4.8 KW realizada en base al microcontrolador Intel 8751, el diseño del conversor estático utilizado, los circuitos de medición, y el software desarrollado para el control del conversor con tiristores y para la regulación del voltaje generado.

  11. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

    Science.gov (United States)

    Pyron, R Alexander; Hendry, Catriona R; Chou, Vincent M; Lemmon, Emily M; Lemmon, Alan R; Burbrink, Frank T

    2014-12-01

    Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated their efficacy on a large-scale phylogenomic dataset, and compared them to previous concatenation strategies. Here, we generate such a dataset for Caenophidian snakes, a group with >2500 species that contains several rapid radiations that were poorly resolved with fewer loci. We generate sequence data for 333 single-copy nuclear loci with ∼100% coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies using neighbor joining, maximum parsimony, maximum likelihood, and three summary species-tree approaches (NJst, STAR, and MP-EST). All methods yield similar resolution and support for most nodes. However, not all methods support monophyly of Caenophidia, with Acrochordidae placed as the sister taxon to Pythonidae in some analyses. Thus, phylogenomic species-tree estimation may occasionally disagree with well-supported relationships from concatenated analyses of small numbers of nuclear or mitochondrial genes, a consideration for future studies. In contrast for at least two diverse, rapid radiations (Lamprophiidae and Colubridae), phylogenomic data and species-tree inference do little to improve resolution and support. Thus, certain nodes may lack strong signal, and larger datasets and more sophisticated analyses may still fail to resolve them. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Development of new candidate gene and EST-based molecular markers for Gossypium species

    Science.gov (United States)

    New source of molecular markers accelerates the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum expressed sequence tag (EST) sequences, and validated them through amplification, ge...

  13. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Wei, Chaochun; Brown, Randall H

    2006-01-01

    This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on trans alignments, in which expressed sequences are aligned to the genomic loci...... of putative homologs. Trans alignments contain a high proportion of mismatches, gaps, and/or apparently unspliceable introns, compared to alignments of cDNA sequences to their native loci. The Pairagon+N-SCAN_EST pipeline's first stage is Pairagon, a cDNA-to-genome alignment program based on a Pair......HMM probability model. This model relies on prior knowledge, such as the fact that introns must begin with GT, GC, or AT and end with AG or AC. It produces very precise alignments of high quality cDNA sequences. In the genomic regions between Pairagon's cDNA alignments, the pipeline combines EST alignments...

  14. Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing

    Directory of Open Access Journals (Sweden)

    Vingron Martin

    2004-09-01

    Full Text Available Abstract Background Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also allow to approximate the expression pattern of the related transcripts. However, the limited number of tissues represented in the EST data as well as the different cDNA construction protocols may influence the predictive capacity of ESTs to unravel tissue-specifically expressed transcripts. Methods We predict tissue and tumor specific splice isoforms based on the genomic mapping (SpliceNest of the EST consensus sequences and library annotation provided in the GeneNest database. We further ascertain the potentially rare tissue specific transcripts as the ones represented only by ESTs derived from normalized libraries. A subset of the predicted tissue and tumor specific isoforms are then validated via RT-PCR experiments over a spectrum of 40 tissue types. Results Our strategy revealed 427 genes with at least one tissue specific transcript as well as 1120 genes showing tumor specific isoforms. While our experimental evaluation of computationally predicted tissue-specific isoforms revealed a high success rate in confirming the expression of these isoforms in the respective tissue, the strategy frequently failed to detect the expected restricted expression pattern. The analysis of putative lowly expressed transcripts using normalized cDNA libraries suggests that our ability to detect tissue-specific isoforms strongly depends on the expression level of the respective transcript as well as on the sensitivity of the experimental methods. Especially splice isoforms predicted to be disease-specific tend to represent transcripts that are expressed in a set of healthy tissues rather than novel isoforms. Conclusions We propose to combine the computational prediction of alternative splice isoforms with experimental validation for

  15. Phylogenomics of ColombianHelicobacter pyloriisolates.

    Science.gov (United States)

    Gutiérrez-Escobar, Andrés Julián; Trujillo, Esperanza; Acevedo, Orlando; Bravo, María Mercedes

    2017-01-01

    During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori . Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H. pylori isolates. A total of 115 genomes of H. pylori were sequenced with Illumina technology from H. pylori isolates obtained in Colombia in a region of high risk for gastric cancer. The genomes were assembled, annotated and underwent phylogenomic analysis with 36 reference strains. Additionally, population differentiation analyses were performed for two bacterial genes. The phylogenetic tree revealed clustering of the Colombian strains with hspWestAfrica and hpEurope, along with three clades formed exclusively by Colombian strains, suggesting the presence of independent evolutionary lines for Colombia. Additionally, the nucleotide diversity of horB and vacA genes from Colombian isolates was lower than in the reference strains and showed a significant genetic differentiation supporting the hypothesis of independent clades with recent evolution. The presence of specific lineages suggest the existence of an hspColombia subtype that emerged from a small and relatively isolated ancestral population that accompanied crossbreeding of human population in Colombia.

  16. AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

    Directory of Open Access Journals (Sweden)

    Mevik Bjørn-Helge

    2009-10-01

    Full Text Available Abstract Background Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. Results Here we present a batch-oriented web-based program package, named AIR that allows 1 transformation of several single genes to one multigene alignment, 2 identification of evolutionary rates in multigene alignments and 3 removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR, which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal http://www.bioportal.uio.no, University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. Conclusion The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

  17. Spider phylogenomics: untangling the Spider Tree of Life

    Directory of Open Access Journals (Sweden)

    Nicole L. Garrison

    2016-02-01

    Full Text Available Spiders (Order Araneae are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results

  18. Phylogenomic re-assessment of the thermophilic genus Geobacillus.

    Science.gov (United States)

    Aliyu, Habibu; Lebre, Pedro; Blom, Jochen; Cowan, Don; De Maayer, Pieter

    2016-12-01

    Geobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA-DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness. We have applied whole genome approaches to estimate the phylogenetic relatedness among the sixty-three Geobacillus strains for which genome sequences are currently publicly available, including the type strains of eleven validly described species. The phylogenomic metrics AAI (Average Amino acid Identity), ANI (Average Nucleotide Identity) and dDDH (digital DNA-DNA hybridization) indicated that the current genus Geobacillus is comprised of sixteen distinct genomospecies, including several potentially novel species. Furthermore, a phylogeny constructed on the basis of the core genes identified from the whole genome analyses indicated that the genus clusters into two monophyletic clades that clearly differ in terms of nucleotide base composition. The G+C content ranges for clade I and II were 48.8-53.1% and 42.1-44.4%, respectively. We therefore suggest that the Geobacillus species currently residing within clade II be considered as a new genus. Copyright © 2016 Elsevier GmbH. All rights reserved.

  19. Defining the phylogenomics of Shigella species: a pathway to diagnostics.

    Science.gov (United States)

    Sahl, Jason W; Morris, Carolyn R; Emberger, Jennifer; Fraser, Claire M; Ochieng, John Benjamin; Juma, Jane; Fields, Barry; Breiman, Robert F; Gilmour, Matthew; Nataro, James P; Rasko, David A

    2015-03-01

    Shigellae cause significant diarrheal disease and mortality in humans, as there are approximately 163 million episodes of shigellosis and 1.1 million deaths annually. While significant strides have been made in the understanding of the pathogenesis, few studies on the genomic content of the Shigella species have been completed. The goal of this study was to characterize the genomic diversity of Shigella species through sequencing of 55 isolates representing members of each of the four Shigella species: S. flexneri, S. sonnei, S. boydii, and S. dysenteriae. Phylogeny inferred from 336 available Shigella and Escherichia coli genomes defined exclusive clades of Shigella; conserved genomic markers that can identify each clade were then identified. PCR assays were developed for each clade-specific marker, which was combined with an amplicon for the conserved Shigella invasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptive Shigella isolates, and sensitivity, by not identifying any of 151 diverse E. coli isolates incorrectly as Shigella. This new phylogenomics-based PCR assay represents a valuable tool for rapid typing of uncharacterized Shigella isolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  20. Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Daren W.; Butchko, Robert A.; Baker, Scott E.; Proctor, Robert H.

    2012-02-01

    Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, F. graminearum, F. oxysporum and Nectria haematococca (anamorph F. solani) identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted a phylogenomic and functional domain analysis. The resulting genealogy suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicate that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

  1. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships.

    Science.gov (United States)

    Pick, K S; Philippe, H; Schreiber, F; Erpenbeck, D; Jackson, D J; Wrede, P; Wiens, M; Alié, A; Morgenstern, B; Manuel, M; Wörheide, G

    2010-09-01

    Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.

  2. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Sraphet, Supajit; Boonchanawiwat, Athipong; Thanyasiriwat, Thanwanit; Boonseng, Opas; Tabata, Satoshi; Sasamoto, Shigemi; Shirasawa, Kenta; Isobe, Sachiko; Lightfoot, David A; Tangphatsornruang, Sithichoke; Triwitayakorn, Kanokporn

    2011-04-01

    Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.

  3. Nitrogen assimilation in Citrus based on CitEST data mining

    Directory of Open Access Journals (Sweden)

    Ester Wickert

    2007-01-01

    Full Text Available Assimilation of nitrate and ammonium are vital procedures for plant development and growth. From these primary paths of inorganic nitrogen assimilation, this metabolism integrates diverse paths for biosynthesis of macromolecules, such as amino acids and nucleotides, and the central intermediate metabolism, like carbon metabolism and photorespiration. This paper reports research performed in the CitEST (Citrus Expressed Sequence Tag database for the main genes involved in nitrogen metabolism and those previously described in other organisms. The results show that a complete cluster of genes involved in the assimilation of nitrogen and the metabolisms of glutamine, glutamate, aspartate and asparagine can be found in the CitEST data. The main enzymes found were nitrate reductase (NR, nitrite reductase (NiR, glutamine synthetase (GS, glutamate synthetase (GOGAT, glutamate dehydrogenase (GDH, aspartate aminotransferase (AspAT and asparagine synthetase (AS. The different enzymes involved in this metabolism have been shown to be highly conserved among the Citrus and Poncirus species. This work serves as a guide for future functional analysis of these enzymes in citrus.

  4. Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.

    Science.gov (United States)

    Julca, Irene; Marcet-Houben, Marina; Vargas, Pablo; Gabaldón, Toni

    2018-01-25

    Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of both mechanisms in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees. Our results depict a complex scenario involving at least three past polyploidization events, of which two-at the bases of the family Oleaceae and the tribe Oleeae, respectively-are likely to be the result of ancient allopolyploidization. A more recent polyploidization involves specifically the olive tree and relatives. Our results show the power of phylogenomics to distinguish between allo- and auto polyploidization events and clarify the contributions of duplications in the evolutionary history of the olive tree.

  5. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

    Science.gov (United States)

    Timme, Ruth E; Rand, Hugh; Shumway, Martin; Trees, Eija K; Simmons, Mustafa; Agarwala, Richa; Davis, Steven; Tillman, Glenn E; Defibaugh-Chavez, Stephanie; Carleton, Heather A; Klimke, William A; Katz, Lee S

    2017-01-01

    As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and "known" phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Our "outbreak" benchmark datasets represent the four major foodborne bacterial pathogens ( Listeria monocytogenes , Salmonella enterica , Escherichia coli , and Campylobacter jejuni ) and one simulated dataset where the "known tree" can be accurately called the "true tree". The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross

  6. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

    Directory of Open Access Journals (Sweden)

    Ruth E. Timme

    2017-10-01

    Full Text Available Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches. These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results Our “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion These five benchmark datasets will help standardize comparison of current and

  7. Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae

    Directory of Open Access Journals (Sweden)

    Yuan Huang

    2017-06-01

    Full Text Available Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in

  8. Genome Evolution and Phylogenomic Analysis of Candidatus Kinetoplastibacterium, the Betaproteobacterial Endosymbionts of Strigomonas and Angomonas

    Science.gov (United States)

    Alves, João M.P.; Serrano, Myrna G.; Maia da Silva, Flávia; Voegtly, Logan J.; Matveyev, Andrey V.; Teixeira, Marta M.G.; Camargo, Erney P.; Buck, Gregory A.

    2013-01-01

    It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus. PMID:23345457

  9. Phylogenomics resolves the timing and pattern of insect evolution.

    Science.gov (United States)

    Misof, Bernhard; Liu, Shanlin; Meusemann, Karen; Peters, Ralph S; Donath, Alexander; Mayer, Christoph; Frandsen, Paul B; Ware, Jessica; Flouri, Tomáš; Beutel, Rolf G; Niehuis, Oliver; Petersen, Malte; Izquierdo-Carrasco, Fernando; Wappler, Torsten; Rust, Jes; Aberer, Andre J; Aspöck, Ulrike; Aspöck, Horst; Bartel, Daniela; Blanke, Alexander; Berger, Simon; Böhm, Alexander; Buckley, Thomas R; Calcott, Brett; Chen, Junqing; Friedrich, Frank; Fukui, Makiko; Fujita, Mari; Greve, Carola; Grobe, Peter; Gu, Shengchang; Huang, Ying; Jermiin, Lars S; Kawahara, Akito Y; Krogmann, Lars; Kubiak, Martin; Lanfear, Robert; Letsch, Harald; Li, Yiyuan; Li, Zhenyu; Li, Jiguang; Lu, Haorong; Machida, Ryuichiro; Mashimo, Yuta; Kapli, Pashalia; McKenna, Duane D; Meng, Guanliang; Nakagaki, Yasutaka; Navarrete-Heredia, José Luis; Ott, Michael; Ou, Yanxiang; Pass, Günther; Podsiadlowski, Lars; Pohl, Hans; von Reumont, Björn M; Schütte, Kai; Sekiya, Kaoru; Shimizu, Shota; Slipinski, Adam; Stamatakis, Alexandros; Song, Wenhui; Su, Xu; Szucsich, Nikolaus U; Tan, Meihua; Tan, Xuemei; Tang, Min; Tang, Jingbo; Timelthaler, Gerald; Tomizuka, Shigekazu; Trautwein, Michelle; Tong, Xiaoli; Uchifune, Toshiki; Walzl, Manfred G; Wiegmann, Brian M; Wilbrandt, Jeanne; Wipfler, Benjamin; Wong, Thomas K F; Wu, Qiong; Wu, Gengxiong; Xie, Yinlong; Yang, Shenzhou; Yang, Qing; Yeates, David K; Yoshizawa, Kazunori; Zhang, Qing; Zhang, Rui; Zhang, Wenwei; Zhang, Yunhui; Zhao, Jing; Zhou, Chengran; Zhou, Lili; Ziesmann, Tanja; Zou, Shijie; Li, Yingrui; Xu, Xun; Zhang, Yong; Yang, Huanming; Wang, Jian; Wang, Jun; Kjer, Karl M; Zhou, Xin

    2014-11-07

    Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects. Copyright © 2014, American Association for the Advancement of Science.

  10. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.

    Science.gov (United States)

    Hackett, Jeremiah D; Yoon, Hwan Su; Li, Shenglan; Reyes-Prieto, Adrian; Rümmele, Susanne E; Bhattacharya, Debashish

    2007-08-01

    Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup Chromalveolata (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multigene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and, surprisingly, two members of the Rhizaria, Reticulomyxa filosa and Bigelowiella natans. The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.

  11. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi

    OpenAIRE

    Juan Li; Fei Gu; Runian Wu; JinKui Yang; Ke-Qin Zhang

    2017-01-01

    Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal king...

  12. A functional phylogenomic view of the seed plants.

    Science.gov (United States)

    Lee, Ernest K; Cibrian-Jaramillo, Angelica; Kolokotronis, Sergios-Orestis; Katari, Manpreet S; Stamatakis, Alexandros; Ott, Michael; Chiu, Joanna C; Little, Damon P; Stevenson, Dennis Wm; McCombie, W Richard; Martienssen, Robert A; Coruzzi, Gloria; Desalle, Rob

    2011-12-01

    A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.

  13. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  14. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  15. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda.

    Science.gov (United States)

    Komulainen, P; Brown, G R; Mikkonen, M; Karhu, A; García-Gil, M R; O'Malley, D; Lee, B; Neale, D B; Savolainen, O

    2003-08-01

    A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F(1) progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.

  16. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

    Directory of Open Access Journals (Sweden)

    Rita eSharma

    2013-08-01

    Full Text Available Glycoside hydrolases (GH catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/. This database integrates multiple data types including the structural features, orthologous relationships, mutant availability and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

  17. ReproPhylo: An Environment for Reproducible Phylogenomics.

    Directory of Open Access Journals (Sweden)

    Amir Szitenberg

    2015-09-01

    Full Text Available The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This 'single file' approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.

  18. Formação do audiodescritor: a estética cinematográfica como base para o aprendizado da estética da audiodescrição - materiais, métodos e produtos

    Directory of Open Access Journals (Sweden)

    Soraya Ferreira Alves

    2016-09-01

    Full Text Available http://dx.doi.org/10.5007/2175-7968.2016v36n3p34 A Audiodescrição (AD, recurso utilizado para tornar o teatro, o cinema, a TV, bem como obras de arte visuais, acessíveis a pessoas com deficiência visual, vem aos poucos sendo implantada no Brasil e demandando profissionais capacitados. Com base nessa constatação, este artigo traz o relato de um projeto desenvolvido durante estágio pós-doutoral que se dedicou ao confronto da estética cinematográfica com as técnicas de audiodescrição a fim de verificar como o conhecimento da primeira pode contribuir para a formação do audiodescritor. Por meio da pesquisa-ação, foi produzido um curta-metragem adaptado de um conto de Mário de Andrade intitulado O Peru de Natal. O filme homônimo, assim como sua audiodescrição, foram realizados pelos alunos e professores da disciplina Tradução Intersemiótica do curso de Letras da Universidade Estadual do Ceará (UECE. Assim, pretendeu-se sugerir procedimentos didáticos que partiram da experiência dos alunos ao avaliarem suas escolhas e as implicações destas.

  19. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

    Directory of Open Access Journals (Sweden)

    Colombo Carlos A

    2011-02-01

    Full Text Available Abstract Background Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results Assembling the expressed sequence tags (ESTs of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion We present the first comprehensive

  20. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics

    Czech Academy of Sciences Publication Activity Database

    Weitemier, K.; Straub, S. C. K.; Cronn, R. C.; Fishbein, M.; Schmickl, Roswitha; McDonnell, A.; Liston, A.

    2014-01-01

    Roč. 2, č. 9 (2014), s. 1-7, no.1400042 ISSN 2168-0450 Institutional support: RVO:67985939 Keywords : evolution * sequencing * phylogenomics Subject RIV: EF - Botanics Impact factor: 0.667, year: 2014

  1. A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification.

    Science.gov (United States)

    Leaché, Adam D; Wagner, Philipp; Linkem, Charles W; Böhme, Wolfgang; Papenfuss, Theodore J; Chong, Rebecca A; Lavin, Brian R; Bauer, Aaron M; Nielsen, Stuart V; Greenbaum, Eli; Rödel, Mark-Oliver; Schmitz, Andreas; LeBreton, Matthew; Ineich, Ivan; Chirio, Laurent; Ofori-Boateng, Caleb; Eniang, Edem A; Baha El Din, Sherif; Lemmon, Alan R; Burbrink, Frank T

    2014-10-01

    Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using (*)BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for >10Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. An expanded nuclear phylogenomic PCR toolkit for Sapindales1

    Science.gov (United States)

    Collins, Elizabeth S.; Gostel, Morgan R.; Weeks, Andrea

    2016-01-01

    Premise of the study: We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Methods and Results: Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16–90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Conclusions: Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation. PMID:28101434

  3. An expanded nuclear phylogenomic PCR toolkit for Sapindales.

    Science.gov (United States)

    Collins, Elizabeth S; Gostel, Morgan R; Weeks, Andrea

    2016-12-01

    We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba . On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16-90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation.

  4. Type III Polyketide Synthases: Functional Classification and Phylogenomics.

    Science.gov (United States)

    Shimizu, Yugo; Ogata, Hiroyuki; Goto, Susumu

    2017-01-03

    Polyketide synthases (PKSs) catalyze the sequential condensation of simple acetate units to produce a large class of natural products, including pharmacologically valuable compounds. PKSs are classified into three types on the basis of their domain structures; type III PKSs have the simplest domain structure, although their products have various structures and functions. The sequence-function relationship is fundamental for predicting enzyme functions, but it has not been well investigated in type III PKSs to date. Consequently, the current methods for predicting type III PKS functions are still immature in comparison with those that target type I/II PKSs. In this review we summarize the current functional and phylogenomic knowledge about type III PKSs and propose a new classification of their enzymatic reactions. We also discuss possible directions for the development of better computational tools for functional prediction of type III PKS homologues. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi.

    Science.gov (United States)

    Li, Juan; Gu, Fei; Wu, Runian; Yang, JinKui; Zhang, Ke-Qin

    2017-03-30

    Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.

  6. Information Dropout Patterns in RAD Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-rich Moth Genus.

    Science.gov (United States)

    Lee, Kyung Min; Kivelä, Sami M; Ivanov, Vladislav; Hausmann, Axel; Kaila, Lauri; Wahlberg, Niklas; Mutanen, Marko

    2018-04-14

    A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, RAD (Restriction site Associated DNA) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for non-model species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely un-investigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6,172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3,256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs and PIS on nodal bootstrap

  7. A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation.

    Science.gov (United States)

    Zhang, Yan; Lin, Kui

    2012-09-07

    The Escherichia coli species contains a variety of commensal and pathogenic strains, and its intraspecific diversity is extraordinarily high. With the availability of an increasing number of E. coli strain genomes, a more comprehensive concept of their evolutionary history and ecological adaptation can be developed using phylogenomic analyses. In this study, we constructed two types of whole-genome phylogenies based on 34 E. coli strains using collinear genomic segments. The first phylogeny was based on the concatenated collinear regions shared by all of the studied genomes, and the second phylogeny was based on the variable collinear regions that are absent from at least one genome. Intuitively, the first phylogeny is likely to reveal the lineal evolutionary history among these strains (i.e., an evolutionary phylogeny), whereas the latter phylogeny is likely to reflect the whole-genome similarities of extant strains (i.e., a similarity phylogeny). Within the evolutionary phylogeny, the strains were clustered in accordance with known phylogenetic groups and phenotypes. When comparing evolutionary and similarity phylogenies, a concept emerges that Shigella may have originated from at least three distinct ancestors and evolved into a single clade. By scrutinizing the properties that are shared amongst Shigella strains but missing in other E. coli genomes, we found that the common regions of the Shigella genomes were mainly influenced by mobile genetic elements, implying that they may have experienced convergent evolution via horizontal gene transfer. Based on an inspection of certain key branches of interest, we identified several collinear regions that may be associated with the pathogenicity of specific strains. Moreover, by examining the annotated genes within these regions, further detailed evidence associated with pathogenicity was revealed. Collinear regions are reliable genomic features used for phylogenomic analysis among closely related genomes while linking

  8. A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation

    Directory of Open Access Journals (Sweden)

    Zhang Yan

    2012-09-01

    Full Text Available Abstract Background The Escherichia coli species contains a variety of commensal and pathogenic strains, and its intraspecific diversity is extraordinarily high. With the availability of an increasing number of E. coli strain genomes, a more comprehensive concept of their evolutionary history and ecological adaptation can be developed using phylogenomic analyses. In this study, we constructed two types of whole-genome phylogenies based on 34 E. coli strains using collinear genomic segments. The first phylogeny was based on the concatenated collinear regions shared by all of the studied genomes, and the second phylogeny was based on the variable collinear regions that are absent from at least one genome. Intuitively, the first phylogeny is likely to reveal the lineal evolutionary history among these strains (i.e., an evolutionary phylogeny, whereas the latter phylogeny is likely to reflect the whole-genome similarities of extant strains (i.e., a similarity phylogeny. Results Within the evolutionary phylogeny, the strains were clustered in accordance with known phylogenetic groups and phenotypes. When comparing evolutionary and similarity phylogenies, a concept emerges that Shigella may have originated from at least three distinct ancestors and evolved into a single clade. By scrutinizing the properties that are shared amongst Shigella strains but missing in other E. coli genomes, we found that the common regions of the Shigella genomes were mainly influenced by mobile genetic elements, implying that they may have experienced convergent evolution via horizontal gene transfer. Based on an inspection of certain key branches of interest, we identified several collinear regions that may be associated with the pathogenicity of specific strains. Moreover, by examining the annotated genes within these regions, further detailed evidence associated with pathogenicity was revealed. Conclusions Collinear regions are reliable genomic features used for

  9. Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses.

    Science.gov (United States)

    Whelan, Nathan V; Halanych, Kenneth M

    2017-03-01

    As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too

  10. Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach.

    Science.gov (United States)

    Rodriguez, Juanita; Jones, Tappey H; Sierwald, Petra; Marek, Paul E; Shear, William A; Brewer, Michael S; Kocot, Kevin M; Bond, Jason E

    2018-02-16

    With fossil representatives from the Silurian capable of respiring atmospheric oxygen, millipedes are among the oldest terrestrial animals, and likely the first to acquire diverse and complex chemical defenses against predators. Exploring the origin of complex adaptive traits is critical for understanding the evolution of Earth's biological complexity, and chemical defense evolution serves as an ideal study system. The classic explanation for the evolution of complexity is by gradual increase from simple to complex, passing through intermediate "stepping stone" states. Here we present the first phylogenetic-based study of the evolution of complex chemical defenses in millipedes by generating the largest genomic-based phylogenetic dataset ever assembled for the group. Our phylogenomic results demonstrate that chemical complexity shows a clear pattern of escalation through time. New pathways are added in a stepwise pattern, leading to greater chemical complexity, independently in a number of derived lineages. This complexity gradually increased through time, leading to the advent of three distantly related chemically complex evolutionary lineages, each uniquely characteristic of each of the respective millipede groups.

  11. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    Science.gov (United States)

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-04

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. plantarum and 'Bacillus oryzicola' are later heterotypic synonyms of Bacillus velezensis based on phylogenomics.

    Science.gov (United States)

    Dunlap, Christopher A; Kim, Soo-Jin; Kwon, Soon-Wo; Rooney, Alejandro P

    2016-03-01

    Bacillus velezensis was previously reported to be a later heterotypic synonym of Bacillus amyloliquefaciens , based primarily on DNA-DNA relatedness values. We have sequenced a draft genome of B. velezensis NRRL B-41580 T . Comparative genomics and DNA-DNA relatedness calculations show that it is not a synonym of B. amyloliquefaciens. It was instead synonymous with Bacillus methylotrophicus. ' Bacillus oryzicola ' is a recently described species that was isolated as an endophyte of rice ( Oryza sativa ). The strain was demonstrated to have plant-pathogen antagonist activity in greenhouse assays, and the 16S rRNA gene was reported to have 99.7 % sequence similarity with Bacillus siamensis and B. methylotrophicus , which are both known for their plant pathogen antagonism. To better understand the phylogenetics of these closely related strains, we sequenced the genome of ' B . oryzicola ' KACC 18228. Comparative genomic analysis showed only minor differences between this strain and the genomes of B. velezensis NRRL B-41580 T , B. methylotrophicus KACC 13015 T and Bacillus amyloliquefaciens subsp. plantarum FZB42 T . The pairwise in silico DNA-DNA hybridization values calculated in comparisons between the strains were all greater than 84 %, which is well above the standard species threshold of 70 %. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the strains share phenotype and genotype coherence. Therefore, we propose that B. methylotrophicus KACC 13015 T , B. amyloliquefaciens subsp. plantarum FZB42 T , and ' B. oryzicola' KACC 18228 should be reclassified as later heterotypic synonyms of B. velezensis NRRL B-41580 T , since the valid publication date of B. velezensis precedes the other three strains.

  13. galaxieEST: addressing EST identity through automated phylogenetic analysis.

    Science.gov (United States)

    Nilsson, R Henrik; Rajashekar, Balaji; Larsson, Karl-Henrik; Ursing, Björn M

    2004-07-05

    Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download / local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and

  14. Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads

    Science.gov (United States)

    Wu, Chung-Shien; Chaw, Shu-Miaw; Huang, Ya-Yi

    2013-01-01

    Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo–cycad sister-group hypothesis. PMID:23315384

  15. Acoel flatworms are not platyhelminthes: evidence from phylogenomics.

    Directory of Open Access Journals (Sweden)

    Hervé Philippe

    Full Text Available Acoel flatworms are small marine worms traditionally considered to belong to the phylum Platyhelminthes. However, molecular phylogenetic analyses suggest that acoels are not members of Platyhelminthes, but are rather extant members of the earliest diverging Bilateria. This result has been called into question, under suspicions of a long branch attraction (LBA artefact. Here we re-examine this problem through a phylogenomic approach using 68 different protein-coding genes from the acoel Convoluta pulchra and 51 metazoan species belonging to 15 different phyla. We employ a mixture model, named CAT, previously found to overcome LBA artefacts where classical models fail. Our results unequivocally show that acoels are not part of the classically defined Platyhelminthes, making the latter polyphyletic. Moreover, they indicate a deuterostome affinity for acoels, potentially as a sister group to all deuterostomes, to Xenoturbellida, to Ambulacraria, or even to chordates. However, the weak support found for most deuterostome nodes, together with the very fast evolutionary rate of the acoel Convoluta pulchra, call for more data from slowly evolving acoels (or from its sister-group, the Nemertodermatida to solve this challenging phylogenetic problem.

  16. Pangenome and Phylogenomic Analysis of the Pathogenic Actinobacterium Rhodococcus equi

    Science.gov (United States)

    Anastasi, Elisa; MacArthur, Iain; Scortti, Mariela; Alvarez, Sonsiray; Giguère, Steeve; Vázquez-Boland, José A.

    2016-01-01

    We report a comparative study of 29 representative genomes of the animal pathogen Rhodococcus equi. The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for ≈80% of an isolates’ gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core–genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome. This included the lack of a phosphoenolpyruvate:carbohydrate transport system (PTS), unique among the rhodococci except for the closely related Rhodococcus defluvii, reflecting selective PTS gene loss in the R. equi–R. defluvii sublineage. Thought to be asaccharolytic, rbsCB and glcP non-PTS sugar permease homologues were identified in the core genome and, albeit inefficiently, R. equi utilized their putative substrates, ribose and (irregularly) glucose. There was no correlation between R. equi whole-genome phylogeny and host or geographical source, with evidence of global spread of genomovars. The distribution of host-associated virulence plasmid types was consistent with the exchange of the plasmids (and corresponding host shifts) across the R. equi population, and human infection being zoonotically acquired. Phylogenomic analyses demonstrated that R. equi occupies a central position in the Rhodococcus phylogeny, not supporting the recently proposed transfer of the species to a new genus. PMID:27638249

  17. Broad phylogenomic sampling and the sister lineage of land plants.

    Science.gov (United States)

    Timme, Ruth E; Bachvaroff, Tsvetan R; Delwiche, Charles F

    2012-01-01

    The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that 'stoneworts,' or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as "pond scum") as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1) the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2) the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.

  18. Architecture of a Species: Phylogenomics of Staphylococcus aureus.

    Science.gov (United States)

    Planet, Paul J; Narechania, Apurva; Chen, Liang; Mathema, Barun; Boundy, Sam; Archer, Gordon; Kreiswirth, Barry

    2017-02-01

    A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement. Copyright © 2016. Published by Elsevier Ltd.

  19. Broad phylogenomic sampling and the sister lineage of land plants.

    Directory of Open Access Journals (Sweden)

    Ruth E Timme

    Full Text Available The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that 'stoneworts,' or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as "pond scum" as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1 the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2 the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.

  20. Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

    Energy Technology Data Exchange (ETDEWEB)

    Sjolander, Kimmen [Univ. of California, Berkeley, CA (United States)

    2014-12-08

    The major advance during this last reporting period (8/15/12 to present) is our release of data on the PhyloFacts website: phylogenetic trees, multiple sequence alignments and other data for protein families are now available for download from http://phylogenomics.berkeley.edu/data/. This project as a whole aimed to develop high-throughput functional annotation systems that exploit information from protein 3D structure and evolution to provide highly precise inferences of various aspects of gene function, including molecular function, biological process, pathway association, Pfam domains, cellular localization and so on. We accomplished these aims by developing and testing different systems on a database of protein family trees: the PhyloFacts Phylogenomic Encyclopedia (at http://phylogenomics.berkeley.edu/phylofacts/ ).

  1. Anonymous and EST-based microsatellite DNA markers that transfer broadly across the fig tree genus (Ficus, Moraceae).

    Science.gov (United States)

    Heer, Katrin; Machado, Carlos A; Himler, Anna G; Herre, Edward Allen; Kalko, Elisabeth K V; Dick, Christopher W

    2012-08-01

    We developed a set of microsatellite markers for broad utility across the species-rich pantropical tree genus Ficus (fig trees). The markers were developed to study population structure, hybridization, and gene flow in neotropical species. We developed seven novel primer sets from expressed sequence tag (EST) libraries of F. citrifolia and F. popenoei (subgen. Urostigma sect. Americana) and optimized five previously developed anonymous loci for cross-species amplification. The markers were successfully tested on four species from the basal subgenus Pharmacosycea sect. Pharmacosycea (F. insipida, F. maxima, F. tonduzii, and F. yoponensis) and seven species of the derived subgenus Urostigma (F. citrifolia, F. colubrinae, F. costaricana, F. nymphaeifolia, F. obtusifolia, F. pertusa, and F. popenoei). The 12 markers amplified consistently and displayed polymorphism in all the species. This set of microsatellite markers is transferable across the phylogenetic breadth of Ficus, and should therefore be useful for studies of population structure and gene flow in approximately 750 fig species worldwide.

  2. EST-based gene indices for the cattle fever tick, the horn fly, and the screwworm fly.

    Science.gov (United States)

    Guerrero, F D; Wang, M; Nene, V M; Dowd, S E; Saldivar, L

    2008-01-01

    The southern cattle tick, Rhip,cephalus (Boophilus) microplus, the horn fly, Haematobia irritans, and the New World screwworm, Cochl,omyia hominivorax, are economically important parasites of cattle throughout the world. Understanding the biology and genomics of these pests is critical to developing novel control methods. We developed EST sequence databases for these parasites and used bioinformatic analysis to identify conceptual open reading frames and assigned Gene Ontology (GO) terms to those database transcripts that had informative BlasIX hits. Bloinformatic analysis showed that a large fraction of the tick database entries have no clear matches in other sequenced genomes. Several putative tick G protein-coupled receptors (GPCRs) were identified that mightserve as starting points to develop novel control technologies.

  3. Phylogenomic analysis of ants, bees and stinging wasps: Improved taxon sampling enhances understanding of hymenopteran evolution

    Science.gov (United States)

    The importance of taxon sampling in phylogenetic accuracy is a topic of active debate. We investigated the role of taxon sampling in causing incongruent results between two recent phylogenomic studies of stinging wasps (Hymenoptera: Aculeata), a diverse lineage that includes ants, bees and the major...

  4. Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale.

    Science.gov (United States)

    Foster, Charles S P; Ho, Simon Y W

    2017-10-01

    Evolutionary timescales can be inferred from molecular sequence data using a Bayesian phylogenetic approach. In these methods, the molecular clock is often calibrated using fossil data. The uncertainty in these fossil calibrations is important because it determines the limiting posterior distribution for divergence-time estimates as the sequence length tends to infinity. Here, we investigate how the accuracy and precision of Bayesian divergence-time estimates improve with the increased clock-partitioning of genome-scale data into clock-subsets. We focus on a data set comprising plastome-scale sequences of 52 angiosperm taxa. There was little difference among the Bayesian date estimates whether we chose clock-subsets based on patterns of among-lineage rate heterogeneity or relative rates across genes, or by random assignment. Increasing the degree of clock-partitioning usually led to an improvement in the precision of divergence-time estimates, but this increase was asymptotic to a limit presumably imposed by fossil calibrations. Our clock-partitioning approaches yielded highly precise age estimates for several key nodes in the angiosperm phylogeny. For example, when partitioning the data into 20 clock-subsets based on patterns of among-lineage rate heterogeneity, we inferred crown angiosperms to have arisen 198-178 Ma. This demonstrates that judicious clock-partitioning can improve the precision of molecular dating based on phylogenomic data, but the meaning of this increased precision should be considered critically. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Phylogenomics and barcoding of Panax: toward the identification of ginseng species.

    Science.gov (United States)

    Manzanilla, V; Kool, A; Nguyen Nhat, L; Nong Van, H; Le Thi Thu, H; de Boer, H J

    2018-04-03

    The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.

  6. EST-SSRs

    African Journals Online (AJOL)

    user1

    2012-09-04

    Sep 4, 2012 ... sequence repeats (EST-SSRs) for Musa and their applicability in authentication of a Musa ... understanding of Musa genetics, in marker-trait associations, thereby enhancing the effectiveness of breeding programs. Key words: EST ...... antioxidant, in cavendish banana. J. Agric. Food Chem. 48(3):844-. 848.

  7. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

    Directory of Open Access Journals (Sweden)

    Jose Eduardo de la Torre-Bárcena

    2009-06-01

    Full Text Available Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales, which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group.We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice, well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations.We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support

  8. Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation.

    Science.gov (United States)

    Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward; Roger, Andrew J

    2018-03-01

    Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.

  9. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

    Science.gov (United States)

    Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca

    2010-12-01

    Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect

  10. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria

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    Chiari Ylenia

    2012-07-01

    Full Text Available Abstract Background The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes, to archosaurs (birds and crocodiles, or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. Results In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation

  11. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).

    Science.gov (United States)

    Chiari, Ylenia; Cahais, Vincent; Galtier, Nicolas; Delsuc, Frédéric

    2012-07-27

    The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. These results provide a phylogenetic framework

  12. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

    Science.gov (United States)

    2012-01-01

    Background The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. Results In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. Conclusions These results

  13. Annotation of novel neuropeptide precursors in the migratory locust based on transcript screening of a public EST database and mass spectrometry

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    De Loof Arnold

    2006-08-01

    Full Text Available Abstract Background For holometabolous insects there has been an explosion of proteomic and peptidomic information thanks to large genome sequencing projects. Heterometabolous insects, although comprising many important species, have been far less studied. The migratory locust Locusta migratoria, a heterometabolous insect, is one of the most infamous agricultural pests. They undergo a well-known and profound phase transition from the relatively harmless solitary form to a ferocious gregarious form. The underlying regulatory mechanisms of this phase transition are not fully understood, but it is undoubtedly that neuropeptides are involved. However, neuropeptide research in locusts is hampered by the absence of genomic information. Results Recently, EST (Expressed Sequence Tag databases from Locusta migratoria were constructed. Using bioinformatical tools, we searched these EST databases specifically for neuropeptide precursors. Based on known locust neuropeptide sequences, we confirmed the sequence of several previously identified neuropeptide precursors (i.e. pacifastin-related peptides, which consolidated our method. In addition, we found two novel neuroparsin precursors and annotated the hitherto unknown tachykinin precursor. Besides one of the known tachykinin peptides, this EST contained an additional tachykinin-like sequence. Using neuropeptide precursors from Drosophila melanogaster as a query, we succeeded in annotating the Locusta neuropeptide F, allatostatin-C and ecdysis-triggering hormone precursor, which until now had not been identified in locusts or in any other heterometabolous insect. For the tachykinin precursor, the ecdysis-triggering hormone precursor and the allatostatin-C precursor, translation of the predicted neuropeptides in neural tissues was confirmed with mass spectrometric techniques. Conclusion In this study we describe the annotation of 6 novel neuropeptide precursors and the neuropeptides they encode from the

  14. EST Vocabulary Instruction

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    Célia D.S. Bell

    2012-05-01

    Full Text Available This study aims at contributing to the investigation on the instruction of EST (English for Science and Technology vocabulary, in terms of receptive use of the language. It evaluates the effectiveness of two teaching approaches to the acquisition of vocabulary. The first approach consisted of teaching vocabulary through the use of dictionaries, where the words were merely translated into the learners’ L1 or defined in the target language thus promoting superficial level of word processing. The second approach employed activities promoting deep level of word processing. Data were analysed quantitatively. Results indicated that the two approaches seem to have some equipotentiality, as far as EST vocabulary is concerned.

  15. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians.

    Science.gov (United States)

    Whelan, Nathan V; Kocot, Kevin M; Halanych, Kenneth M

    2015-12-01

    Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  16. Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping.

    Science.gov (United States)

    An, Chuanfu; Saha, Sukumar; Jenkins, Johnie N; Ma, Din-Pow; Scheffler, Brian E; Kohel, Russell J; Yu, John Z; Stelly, David M

    2008-05-01

    R2R3-MYB transcription factors of plants are involved in the regulation of trichome length and density. Several of them are differentially expressed during initiation and elongation of cotton fibers. We report sequence phylogenomic characterization of the six MYB genes, their chromosomal localization, and linkage mapping via SNP marker in AD-genome cotton (2n = 52). Phylogenetic grouping and comparison to At- and Dt-genome putative ancestral diploid species of allotetraploid cotton facilitated differentiation between genome-specific polymorphisms (GSPs) and marker-suitable locus-specific polymorphisms (LSPs). The SNP frequency averaged one per 77 bases overall, and one per 106 and 30 bases in coding and non-coding regions, respectively. SNP-based multivariate relationships conformed to independent evolution of the six MYB homoeologous loci in the four tetraploid species. Nucleotide diversity analysis indicated that the six MYB loci evolved more quickly in the Dt- than At-genome. The greater variation in the Dt-D genome comparisons than that in At-A genome comparisons showed no significant bias among synonymous substitution, non-synonymous substitution, and nucleotide change in non-coding regions. SNPs were concordantly mapped by deletion analysis and linkage mapping, which confirmed their value as candidate gene markers and indicated the reliability of the SNP discovery strategy in tetraploid cotton species. We consider that these SNPs may be useful for genetic dissection of economically important fiber and yield traits because of the role of these genes in fiber development.

  17. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction.

    Science.gov (United States)

    Fernández, Rosa; Edgecombe, Gregory D; Giribet, Gonzalo

    2016-09-01

    Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal

  18. Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups

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    Mok Amy

    2007-11-01

    Full Text Available Abstract Background Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales, very few or no distinctive molecular or biochemical characteristics are known. Results We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila endosymbiont. These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae. Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within α-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales. We also describe two conserved inserts in DNA

  19. Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups

    Science.gov (United States)

    Gupta, Radhey S; Mok, Amy

    2007-01-01

    Background Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. Results We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several α-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within α-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales)))))). We also describe two conserved inserts in DNA Gyrase B and RNA

  20. CitEST libraries

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    Maria Luísa P. Natividade Targon

    2007-01-01

    Full Text Available In order to obtain a better understanding of what is citrus, 33 cDNA libraries were constructed from different citrus species and genera. Total RNA was extracted from fruits, leaves, flowers, bark, seeds and roots, and subjected or not to different biotic and abiotic stresses (pathogens and drought and at several developmental stages. To identify putative promoter sequences, as well as molecular markers that could be useful for breeding programs, one shotgun library was prepared from sweet orange (Citrus sinensis var. Olimpia. In addition, EST libraries were also constructed for a citrus pathogen, the oomycete Phythophthora parasitica in either virulent or avirulent form. A total of 286,559 cDNA clones from citrus were sequenced from their 5’ end, generating 242,790 valid reads of citrus. A total of 9,504 sequences were produced in the shotgun library and the valid reads were assembled using CAP3. In this procedure, we obtained 1,131 contigs and 4,083 singletons. A total of 19,200 cDNA clones from P. parasitica were sequenced, resulting in 16,400 valid reads. The number of ESTs generated in this project is, to our knowledge, the largest citrus sequence database in the world.

  1. Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of microtus voles.

    Science.gov (United States)

    Lischer, Heidi E L; Excoffier, Laurent; Heckel, Gerald

    2014-04-01

    Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole (Microtus arvalis) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis. We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.

  2. Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes.

    Science.gov (United States)

    Ruane, Sara; Raxworthy, Christopher J; Lemmon, Alan R; Lemmon, Emily Moriarty; Burbrink, Frank T

    2015-10-12

    Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar's serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species

  3. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

    Science.gov (United States)

    Rota-Stabelli, Omar; Campbell, Lahcen; Brinkmann, Henner; Edgecombe, Gregory D.; Longhorn, Stuart J.; Peterson, Kevin J.; Pisani, Davide; Philippe, Hervé; Telford, Maximilian J.

    2011-01-01

    While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes—chelicerates, myriapods, crustaceans and hexapods—are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the close relationship of euarthropods to tardigrades and onychophorans. Morphology predicts that myriapods, insects and crustaceans form a monophyletic group, the Mandibulata, which has been contradicted by many molecular studies that support an alternative Myriochelata hypothesis (Myriapoda plus Chelicerata). Because of the conflicting insights from published molecular datasets, evidence from nuclear-coding genes needs corroboration from independent data to define the relationships among major nodes in the euarthropod tree. Here, we address this issue by analysing two independent molecular datasets: a phylogenomic dataset of 198 protein-coding genes including new sequences for myriapods, and novel microRNA complements sampled from all major arthropod lineages. Our phylogenomic analyses strongly support Mandibulata, and show that Myriochelata is a tree-reconstruction artefact caused by saturation and long-branch attraction. The analysis of the microRNA dataset corroborates the Mandibulata, showing that the microRNAs miR-965 and miR-282 are present and expressed in all mandibulate species sampled, but not in the chelicerates. Mandibulata is further supported by the phylogenetic analysis of a comprehensive morphological dataset covering living and fossil arthropods, and including recently proposed, putative apomorphies of Myriochelata. Our phylogenomic analyses also provide strong support for the inclusion of pycnogonids in a monophyletic Chelicerata, a paraphyletic Cycloneuralia, and a common origin of Arthropoda (tardigrades, onychophorans and arthropods), suggesting that previous phylogenies grouping tardigrades and nematodes may also have been subject to tree

  4. The Chloroplast Genome ofPassiflora edulis(Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales.

    Science.gov (United States)

    Cauz-Santos, Luiz A; Munhoz, Carla F; Rodde, Nathalie; Cauet, Stephane; Santos, Anselmo A; Penha, Helen A; Dornelas, Marcelo C; Varani, Alessandro M; Oliveira, Giancarlo C X; Bergès, Hélène; Vieira, Maria Lucia C

    2017-01-01

    The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora . In Brazil, the yellow passion fruit ( Passiflora edulis ) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.

  5. Phylogenomic Analysis Reveals Extensive Phylogenetic Mosaicism in the Human GPCR Superfamily

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    Mathew Woodwark

    2007-01-01

    Full Text Available A novel high throughput phylogenomic analysis (HTP was applied to the rhodopsin G-protein coupled receptor (GPCR family. Instances of phylogenetic mosaicism between receptors were found to be frequent, often as instances of correlated mosaicism and repeated mosaicism. A null data set was constructed with the same phylogenetic topology as the rhodopsin GPCRs. Comparison of the two data sets revealed that mosaicism was found in GPCRs in a higher frequency than would be expected by homoplasy or the effects of topology alone. Various evolutionary models of differential conservation, recombination and homoplasy are explored which could result in the patterns observed in this analysis. We find that the results are most consistent with frequent recombination events. A complex evolutionary history is illustrated in which it is likely frequent recombination has endowed GPCRs with new functions. The pattern of mosaicism is shown to be informative for functional prediction for orphan receptors. HTP analysis is complementary to conventional phylogenomic analyses revealing mosaicism that would not otherwise have been detectable through conventional phylogenetics.

  6. Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

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    Kevin Weitemier

    2014-08-01

    Full Text Available Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.

  7. Phylogenomic detection and functional prediction of genes potentially important for plant meiosis.

    Science.gov (United States)

    Zhang, Luoyan; Kong, Hongzhi; Ma, Hong; Yang, Ji

    2018-02-15

    Meiosis is a specialized type of cell division necessary for sexual reproduction in eukaryotes. A better understanding of the cytological procedures of meiosis has been achieved by comprehensive cytogenetic studies in plants, while the genetic mechanisms regulating meiotic progression remain incompletely understood. The increasing accumulation of complete genome sequences and large-scale gene expression datasets has provided a powerful resource for phylogenomic inference and unsupervised identification of genes involved in plant meiosis. By integrating sequence homology and expression data, 164, 131, 124 and 162 genes potentially important for meiosis were identified in the genomes of Arabidopsis thaliana, Oryza sativa, Selaginella moellendorffii and Pogonatum aloides, respectively. The predicted genes were assigned to 45 meiotic GO terms, and their functions were related to different processes occurring during meiosis in various organisms. Most of the predicted meiotic genes underwent lineage-specific duplication events during plant evolution, with about 30% of the predicted genes retaining only a single copy in higher plant genomes. The results of this study provided clues to design experiments for better functional characterization of meiotic genes in plants, promoting the phylogenomic approach to the evolutionary dynamics of the plant meiotic machineries. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. EST2Prot: Mapping EST sequences to proteins

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    Lin David M

    2006-03-01

    Full Text Available Abstract Background EST libraries are used in various biological studies, from microarray experiments to proteomic and genetic screens. These libraries usually contain many uncharacterized ESTs that are typically ignored since they cannot be mapped to known genes. Consequently, new discoveries are possibly overlooked. Results We describe a system (EST2Prot that uses multiple elements to map EST sequences to their corresponding protein products. EST2Prot uses UniGene clusters, substring analysis, information about protein coding regions in existing DNA sequences and protein database searches to detect protein products related to a query EST sequence. Gene Ontology terms, Swiss-Prot keywords, and protein similarity data are used to map the ESTs to functional descriptors. Conclusion EST2Prot extends and significantly enriches the popular UniGene mapping by utilizing multiple relations between known biological entities. It produces a mapping between ESTs and proteins in real-time through a simple web-interface. The system is part of the Biozon database and is accessible at http://biozon.org/tools/est/.

  9. Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.

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    Minjun Yang

    Full Text Available Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC. Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

  10. Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae.

    Science.gov (United States)

    Ng, Poh-Kheng; Lin, Showe-Mei; Lim, Phaik-Eem; Liu, Li-Chia; Chen, Chien-Ming; Pai, Tun-Wen

    2017-01-06

    The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined. The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support. Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of

  11. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.

    Science.gov (United States)

    Heins, Richard A; Cheng, Xiaoliang; Nath, Sangeeta; Deng, Kai; Bowen, Benjamin P; Chivian, Dylan C; Datta, Supratim; Friedland, Gregory D; D'Haeseleer, Patrik; Wu, Dongying; Tran-Gyamfi, Mary; Scullin, Chessa S; Singh, Seema; Shi, Weibing; Hamilton, Matthew G; Bendall, Matthew L; Sczyrba, Alexander; Thompson, John; Feldman, Taya; Guenther, Joel M; Gladden, John M; Cheng, Jan-Fang; Adams, Paul D; Rubin, Edward M; Simmons, Blake A; Sale, Kenneth L; Northen, Trent R; Deutsch, Samuel

    2014-09-19

    Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 β-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different β-linked disaccharides. For some GH1s we also observed activity toward laminarin, a more complex oligosaccharide present as a major component of macroalgae. An area of particular interest was the identification of GH1 enzymes compatible with the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), a next-generation biomass pretreatment technology. We thus searched for GH1 enzymes active at 70 °C and 20% (v/v) [C2mim][OAc] over the course of a 24-h saccharification reaction. Using our unbiased approach, we identified multiple enzymes of different phylogentic origin with such activities. Our approach of characterizing sequence diversity through targeted gene synthesis coupled to high-throughput screening technologies is a broadly applicable paradigm for a wide range of biological problems.

  12. A phylogenomic analysis of the bacterial phylum Fibrobacteres

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    Nurdyana eAbdul Rahman

    2016-01-01

    Full Text Available The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were obtained isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, motility is is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.

  13. A phylogenomic study of human, dog, and mouse.

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    Gina Cannarozzi

    2007-01-01

    Full Text Available In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria-distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate-carnivore clade with the exclusion of rodents.

  14. PHYLOGENOMICS - GUIDED VALIDATION OF FUNCTION FOR CONSERVED UNKNOWN GENES

    Energy Technology Data Exchange (ETDEWEB)

    V, DE CRECY-LAGARD; D, HANSON A

    2012-01-03

    Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown function, or wrongly or vaguely annotated. Many of these 'unknown' proteins are common to prokaryotes and plants. We accordingly set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction is integrative, coupling the extensive post-genomic resources available for plants with comparative genomics based on hundreds of microbial genomes, and functional genomic datasets from model microorganisms. The early phase is computer-assisted; later phases incorporate intellectual input from expert plant and microbial biochemists. The approach thus bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is much more powerful than purely computational approaches to identifying gene-function associations. Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) are conserved between plants and prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology .. independent characteristics associated in the SEED database with the prokaryotic members of each family, specifically gene clustering and phyletic spread, as well as availability of functional genomics data, and publications that could link candidate families to general metabolic areas, or to specific functions. In-depth comparative genomic analysis was then performed for about 500 top candidate families, which connected ~55 of them to general areas of metabolism and led to specific functional predictions for a subset of ~25 more. Twenty predicted functions were experimentally tested in at least one prokaryotic organism

  15. A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir S.; Boore, Jeffrey L.

    2005-08-25

    We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

  16. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture.

    Science.gov (United States)

    Caetano-Anollés, Gustavo; Kim, Hee Shin; Mittenthal, Jay E

    2007-05-29

    Metabolism represents a complex collection of enzymatic reactions and transport processes that convert metabolites into molecules capable of supporting cellular life. Here we explore the origins and evolution of modern metabolism. Using phylogenomic information linked to the structure of metabolic enzymes, we sort out recruitment processes and discover that most enzymatic activities were associated with the nine most ancient and widely distributed protein fold architectures. An analysis of newly discovered functions showed enzymatic diversification occurred early, during the onset of the modern protein world. Most importantly, phylogenetic reconstruction exercises and other evidence suggest strongly that metabolism originated in enzymes with the P-loop hydrolase fold in nucleotide metabolism, probably in pathways linked to the purine metabolic subnetwork. Consequently, the first enzymatic takeover of an ancient biochemistry or prebiotic chemistry was related to the synthesis of nucleotides for the RNA world.

  17. Phylogenomics and coalescent analyses resolve extant seed plant relationships.

    Science.gov (United States)

    Xi, Zhenxiang; Rest, Joshua S; Davis, Charles C

    2013-01-01

    The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.

  18. Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi.

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    Wanping Chen

    Full Text Available Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH from the Carbohydrate-Active enZymes (CAZy Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α-amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions.

  19. Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.

    Science.gov (United States)

    Li, Zhen; De La Torre, Amanda R; Sterck, Lieven; Cánovas, Francisco M; Avila, Concepción; Merino, Irene; Cabezas, José Antonio; Cervera, María Teresa; Ingvarsson, Pär K; Van de Peer, Yves

    2017-05-01

    Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets.

    Science.gov (United States)

    Narechania, Apurva; Baker, Richard; DeSalle, Rob; Mathema, Barun; Kolokotronis, Sergios-Orestis; Kreiswirth, Barry; Planet, Paul J

    2016-10-24

    Collective animal behavior, such as the flocking of birds or the shoaling of fish, has inspired a class of algorithms designed to optimize distance-based clusters in various applications, including document analysis and DNA microarrays. In a flocking model, individual agents respond only to their immediate environment and move according to a few simple rules. After several iterations the agents self-organize, and clusters emerge without the need for partitional seeds. In addition to its unsupervised nature, flocking offers several computational advantages, including the potential to reduce the number of required comparisons. In the tool presented here, Clusterflock, we have implemented a flocking algorithm designed to locate groups (flocks) of orthologous gene families (OGFs) that share an evolutionary history. Pairwise distances that measure phylogenetic incongruence between OGFs guide flock formation. We tested this approach on several simulated datasets by varying the number of underlying topologies, the proportion of missing data, and evolutionary rates, and show that in datasets containing high levels of missing data and rate heterogeneity, Clusterflock outperforms other well-established clustering techniques. We also verified its utility on a known, large-scale recombination event in Staphylococcus aureus. By isolating sets of OGFs with divergent phylogenetic signals, we were able to pinpoint the recombined region without forcing a pre-determined number of groupings or defining a pre-determined incongruence threshold. Clusterflock is an open-source tool that can be used to discover horizontally transferred genes, recombined areas of chromosomes, and the phylogenetic 'core' of a genome. Although we used it here in an evolutionary context, it is generalizable to any clustering problem. Users can write extensions to calculate any distance metric on the unit interval, and can use these distances to 'flock' any type of data.

  1. Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

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    Koh Eunhee

    2007-07-01

    Full Text Available Abstract Background EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information. Results Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1. Conclusion Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.

  2. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss).

    Science.gov (United States)

    Jonathan Shaw, A; Devos, Nicolas; Liu, Yang; Cox, Cymon J; Goffinet, Bernard; Flatberg, Kjell Ivar; Shaw, Blanka

    2016-08-01

    Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided. We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made

  3. EST Reading Curriculum & Instruction: An Alignment Analysis

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    Lubna Ali Mohammed

    2015-02-01

    Full Text Available In order for a curriculum to achieve its goals, it is imperative that the curriculum is coherent at all levels. In order to determine the coherency of a curriculum, the alignment of its theoretical underpinning and the label of a curriculum is one of the aspects that can be examined. The purpose of the current study was to examine if the theoretical grounding of the Yemeni EST senior secondary curriculum is in alignment with its communicative-based curriculum label. In line with its label, the reading curriculum embedded in the EST curriculum should be developed and designed based on the Communicative Language Teaching (CLT, which should be reflected in the EST reading instructional practice. In analysing the alignment of the communicative language teaching approach in the EST senior secondary school reading curriculum, the primary focus of the analysis was on the major SLA theories and L2 reading theories and the related instructional approaches. The data for this study were collected via an ESP textbook review as well as from the observation of the EST reading classroom instruction. The findings show that the EST senior secondary reading curriculum was not developed based on the socio-cognitive and socio-cultural theories which are the grounding principles of the communicative approach. Instead, the findings show that the EST senior secondary reading curriculum was primarily developed based on the cognitive information processing theory, in which teaching instruction reflects the student as an individual information processor and the focus on teaching vocabulary and grammatical rules using reading texts in non-communicative manner. Keywords: Communicative Approach, SLA Theories, L2 Reading Theories

  4. The complete mitochondrial genome of the threatened Neotropical catfish Lophiosilurus alexandri (Silurifomes: Pseudopimelodidae and phylogenomic analysis indicate monophyly of Pimelodoidea

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    Daniel Cardoso Carvalho

    Full Text Available Abstract Lophiosilurus alexandri is an endemic catfish from the São Francisco River Basin (Brazil popularly known as pacamã, which has economic potential for aquaculture farming. The mitochondrial genome was sequenced for the threatened Neotropical catfish L. alexandri. Assembly into scaffolds using MIRA and MITObim software produced the whole, circularized mitochondrial genome, which comprises 16,445 bp and presents the typical gene arrangement of Teleostei mitochondria. A phylogenomic analysis was performed after the concatenation of all proteins obtained from whole mitogenomes of 20 Siluriformes and two outgroups. The results confirmed the monophyly of nine families of catfishes and also clustered L. alexandri as a sister group to the family Pimelodidae, thus confirming the monophyly of the superfamily Pimelodoidea. This is the first mitochondrial phylogenomics study for Pimelodoidea and the first mitogenome described for the Pseudopimelodidae family, representing an important resource for phylogeography, evolutionary biology, and conservation genetics studies in Neotropical fishes.

  5. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

    Science.gov (United States)

    Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2011-07-01

    Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

  6. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

    Science.gov (United States)

    Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2011-01-01

    Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing. PMID:21646336

  7. Phylogenomic insights into the cambrian explosion, the colonization of land and the evolution of flight in arthropoda.

    Science.gov (United States)

    Wheat, Christopher W; Wahlberg, Niklas

    2013-01-01

    The timing of the origin of arthropods in relation to the Cambrian explosion is still controversial, as are the timing of other arthropod macroevolutionary events such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a Bayesian-relaxed molecular clock, we simultaneously reconstructed the phylogenetic relationships and the absolute times of divergences among the arthropods. Simulations were used to test whether our analysis could distinguish between alternative Cambrian explosion scenarios with increasing levels of autocorrelated rate variation. Our analyses support previous phylogenomic hypotheses and simulations indicate a Precambrian origin of the arthropods. Our results provide insights into the 3 independent colonizations of land by arthropods and suggest that evolution of insect wings happened much earlier than the fossil record indicates, with flight evolving during a period of increasing oxygen levels and impressively large forests. These and other findings provide a foundation for macroevolutionary and comparative genomic study of Arthropoda.

  8. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.

    Directory of Open Access Journals (Sweden)

    Kalliopi Georgiades

    Full Text Available BACKGROUND: The evolution of the Alphaproteobacteria and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the Rickettsiales order. Ten years ago, the bacterium Odyssella thessalonicensis was isolated from Acanthamoeba spp., and the 16S rDNA phylogeny placed it within the Rickettsiales. Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins. METHODOLOGY/PRINCIPAL FINDINGS: The results suggested that the O. thessalonicensis emerged between the Rickettsiales and other Alphaproteobacteria. The mitochondrial proteins of the Reclinomonas americana have been used to locate the phylogenetic position of the mitochondrion ancestor within the Alphaproteobacteria tree. Using the K tree score method, nine mitochondrion-encoded proteins, whose phylogenies were congruent with the Alphaproteobacteria phylogenomic tree, have been selected and concatenated for Bayesian and Maximum Likelihood phylogenies. The Reclinomonas americana mitochondrion is a sister taxon to the free-living bacteria Candidatus Pelagibacter ubique, and together, they form a clade that is deeply rooted in the Rickettsiales clade. CONCLUSIONS/SIGNIFICANCE: The Reclinomonas americana mitochondrion phylogenomic study confirmed that mitochondria emerged deeply in the Rickettsiales clade and that they are closely related to Candidatus Pelagibacter ubique.

  9. Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

    Science.gov (United States)

    Gupta, Radhey S.; Lo, Brian; Son, Jeen

    2018-01-01

    The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the “Tuberculosis-Simiae,” “Terrae,” “Triviale,” “Fortuitum-Vaccae,” and “Abscessus-Chelonae” clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the “Abscessus-Chelonae” clade forms the deepest branching lineage and does not form a monophyletic grouping with the “Fortuitum-Vaccae” clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five

  10. Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.

    Science.gov (United States)

    Gupta, Radhey S; Lo, Brian; Son, Jeen

    2018-01-01

    The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium , 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the " Tuberculosis-Simiae ," " Terrae," " Triviale ," " Fortuitum-Vaccae ," and " Abscessus-Chelonae " clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the " Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the " Fortuitum-Vaccae " clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we

  11. EST databases and web tools for EST projects.

    Science.gov (United States)

    Shen, Yao-Qing; O'Brien, Emmet; Koski, Liisa; Lang, B Franz; Burger, Gertraud

    2009-01-01

    This chapter outlines key considerations for constructing and implementing an EST database. Instead of showing the technological details step by step, emphasis is put on the design of an EST database suited to the specific needs of EST projects and how to choose the most suitable tools. Using TBestDB as an example, we illustrate the essential factors to be considered for database construction and the steps for data population and annotation. This process employs technologies such as PostgreSQL, Perl, and PHP to build the database and interface, and tools such as AutoFACT for data processing and annotation. We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices.

  12. Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.

    Science.gov (United States)

    Rodríguez, Ariel; Burgon, James D; Lyra, Mariana; Irisarri, Iker; Baurain, Denis; Blaustein, Leon; Göçmen, Bayram; Künzel, Sven; Mable, Barbara K; Nolte, Arne W; Veith, Michael; Steinfartz, Sebastian; Elmer, Kathryn R; Philippe, Hervé; Vences, Miguel

    2017-10-01

    The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduces a risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra, a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity. For all six species of the genus Salamandra, and two outgroup species from its sister genus Lyciasalamandra, we used RNA sequencing (RNAseq) and restriction site associated DNA sequencing (RADseq) to obtain data for: (1) 3070 nuclear protein-coding genes from RNAseq; (2) 7440 loci obtained by RADseq; and (3) full mitochondrial genomes. The RNAseq and RADseq data sets retrieved fully congruent topologies when each of them was analyzed in a concatenation approach, with high support for: (1) S. infraimmaculata being sister group to all other Salamandra species; (2) S. algira being sister to S. salamandra; (3) these two species being the sister group to a clade containing S. atra, S. corsica and S. lanzai; and (4) the alpine species S. atra and S. lanzai being sister taxa. The phylogeny inferred from the mitochondrial genome sequences differed from these results, most notably by strongly supporting a clade containing S. atra and S. corsica as sister taxa. A different placement of S. corsica was also retrieved when analysing the RNAseq and RADseq data under species tree approaches. Closer examination of gene trees derived from RNAseq revealed that only a low number of them supported each of the alternative placements of S. atra. Furthermore, gene jackknife support for the S. atra - S. lanzai node stabilized only with very large concatenated data sets. The phylogeny of true salamanders thus provides a

  13. Repeats and EST analysis for new organisms

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    Jonassen Inge

    2008-01-01

    Full Text Available Abstract Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask against known repeats from other species (i.e., model organisms. There are few studies that investigate the effectiveness of this approach, or attempt to evaluate the different methods for identifying and masking repeats. Results Using zebrafish and medaka as example organisms, we show that accurate repeat masking is an important factor for obtaining a high quality clustering. Furthermore, we show that masking with standard repeat libraries based on curated genomic information from other species has little or no positive effect on the quality of the resulting EST clustering. Library based repeat masking which often constitutes a computational bottleneck in the EST analysis pipeline can therefore be reduced to species specific repeat libraries, or perhaps eliminated entirely. In contrast, substantially improved results can be achived by applying a repeat library derived from a partial reference clustering (e.g., from mapping sequences against a partially sequenced genome. Conclusion Of the methods explored, we find that the best EST clustering is achieved after masking with repeat libraries that are species specific. In the absence of such libraries, library-less masking gives results superior to the current practice of using cross-species, genome-based libraries.

  14. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

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    Gupta Radhey S

    2007-03-01

    that are uniquely shared by M. kandleri and Methanobacteriales suggest a close evolutionary relationship between them. In contrast to the phylogenomics studies, a monophyletic grouping of archaea is not supported by phylogenetic analyses based on protein sequences. Conclusion The identified archaea-specific proteins provide novel molecular markers or signature proteins that are distinctive characteristics of Archaea and all of its major subgroups. The species distributions of these proteins provide novel insights into the evolutionary relationships among different groups within Archaea, particularly regarding the origin of methanogenesis. Most of these proteins are of unknown function and further studies should lead to discovery of novel biochemical and physiological characteristics that are unique to either all archaea or its different subgroups.

  15. Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria.

    Science.gov (United States)

    Spero, Melanie A; Aylward, Frank O; Currie, Cameron R; Donohue, Timothy J

    2015-04-14

    The proton-translocating NADH:quinone oxidoreductase (complex I) is a multisubunit integral membrane enzyme found in the respiratory chains of both bacteria and eukaryotic organelles. Although much research has focused on the enzyme's central role in the mitochondrial respiratory chain, comparatively little is known about its role in the diverse energetic lifestyles of different bacteria. Here, we used a phylogenomic approach to better understand the distribution of complex I across bacteria, the evolution of this enzyme, and its potential roles in shaping the physiology of different bacterial groups. By surveying 970 representative bacterial genomes, we predict complex I to be present in ~50% of bacteria. While this includes bacteria with a wide range of energetic schemes, the presence of complex I is associated with specific lifestyles, including aerobic respiration and specific types of phototrophy (bacteria with only a type II reaction center). A phylogeny of bacterial complex I revealed five main clades of enzymes whose evolution is largely congruent with the evolution of the bacterial groups that encode complex I. A notable exception includes the gammaproteobacteria, whose members encode one of two distantly related complex I enzymes predicted to participate in different types of respiratory chains (aerobic versus anaerobic). Comparative genomic analyses suggest a broad role for complex I in reoxidizing NADH produced from various catabolic reactions, including the tricarboxylic acid (TCA) cycle and fatty acid beta-oxidation. Together, these findings suggest diverse roles for complex I across bacteria and highlight the importance of this enzyme in shaping diverse physiologies across the bacterial domain. Living systems use conserved energy currencies, including a proton motive force (PMF), NADH, and ATP. The respiratory chain enzyme, complex I, connects these energy currencies by using NADH produced during nutrient breakdown to generate a PMF, which is

  16. Terapia fotodinámica (PDT en piel y estética: procedimiento, materiales y método en base a nuestra experiencia Photodinamic therapy in skin and aesthetics: procedure, matherials and method based on our experience

    Directory of Open Access Journals (Sweden)

    S. Mordon

    2012-09-01

    Full Text Available La terapia fotodinámica (PTD es un procedimiento cada vez más utilizado para tratar diversas afecciones dermatológicas y dermatoestéticas. Su aplicación obtiene buenos resultados en casos de carcinoma basocelular, enfermedad de Bowen, queratosis actínica, acné, rosácea y fotoenvejecimiento cutáneo. Los fotosensibilizantes y las fuentes de luz que se pueden utilizar son cada vez más variados, pero aún existe poco consenso en su metodología de aplicación, sistemas de irradiación y dosificaciones. En este artículo describimos los materiales y métodos disponibles en la actualidad y discutimos algunos detalles que, en base a nuestra experiencia, permiten mejorar los resultados. Presentamos también 5 casos clínicos ilustrativos de diferentes patologías.Photo Dynamic Therapy (PTD is an increasingly used technique in Dermatology and Dermocosmetics. PDT has a wide range of medical applications for the treatment of extended cutaneous cancer, offering also very good results in the treatment of basal cell carcinoma, Bowen's disease, actinic keratosis, acne, rosacea and in cutaneous rejuvenation. The sensitizers and light sources used for photoactivation are also more and more varied but there is still no consensus regarding methods and energy dosage. This study describes material and methods which are currently available and discusses a few details, that based on our own experience, can improve results. Five illustrative cases of different conditions are presented.

  17. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

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    James B Pease

    2016-02-01

    Full Text Available Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon, we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

  18. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

    Science.gov (United States)

    Xi, Zhenxiang; Ruhfel, Brad R.; Schaefer, Hanno; Amorim, André M.; Sugumaran, M.; Wurdack, Kenneth J.; Endress, Peter K.; Matthews, Merran L.; Stevens, Peter F.; Mathews, Sarah; Davis, Charles C.

    2012-01-01

    The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. We also found better branch support in trees inferred from a taxon-rich, data-sparse matrix, which deeply sampled only the phylogenetically critical placeholders, than in trees inferred from a taxon-sparse matrix with little missing data. Although this matrix has more missing data, our a posteriori partitioning strategy reduced the possibility of producing multiple distinct but equally optimal topologies and increased phylogenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic resolution in other poorly resolved major clades of angiosperms and to be more broadly useful in studies across the Tree of Life. PMID:23045684

  19. The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.

    Science.gov (United States)

    Zhi, Xiao-Yang; Jiang, Zhao; Yang, Ling-Ling; Huang, Ying

    2017-02-01

    The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation.

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    Agatha Schlüter

    Full Text Available BACKGROUND: The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins. METHODOLOGY/PRINCIPAL FINDINGS: Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid β-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer. CONCLUSIONS/SIGNIFICANCE: Our results support a prokaryotic origin, different from α-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.

  1. Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

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    Steenkamp Emma

    2009-01-01

    Full Text Available Abstract Background Resolving the evolutionary relationships among Fungi remains challenging because of their highly variable evolutionary rates, and lack of a close phylogenetic outgroup. Nucleariida, an enigmatic group of amoeboids, have been proposed to emerge close to the fungal-metazoan divergence and might fulfill this role. Yet, published phylogenies with up to five genes are without compelling statistical support, and genome-level data should be used to resolve this question with confidence. Results Our analyses with nuclear (118 proteins and mitochondrial (13 proteins data now robustly associate Nucleariida and Fungi as neighbors, an assemblage that we term 'Holomycota'. With Nucleariida as an outgroup, we revisit unresolved deep fungal relationships. Conclusion Our phylogenomic analysis provides significant support for the paraphyly of the traditional taxon Zygomycota, and contradicts a recent proposal to include Mortierella in a phylum Mucoromycotina. We further question the introduction of separate phyla for Glomeromycota and Blastocladiomycota, whose phylogenetic positions relative to other phyla remain unresolved even with genome-level datasets. Our results motivate broad sampling of additional genome sequences from these phyla.

  2. Consensus definitions to promote an evidence-based approach to management of the pleural space. A collaborative proposal by ESTS, AATS, STS, and GTSC.

    Science.gov (United States)

    Brunelli, Alessandro; Beretta, Egidio; Cassivi, Stephen D; Cerfolio, Robert J; Detterbeck, Frank; Kiefer, Thomas; Miserocchi, Giuseppe; Shrager, Joseph; Singhal, Sunil; Van Raemdonck, Dirk; Varela, Gonzalo

    2011-08-01

    The present project involved a collective effort agreed by the European Society of Thoracic Surgeons, the American Association for Thoracic Surgery, the Society of Thoracic Surgeons, and the General Thoracic Surgery Club to assemble a joint panel of experts to review the available data and address ambiguous aspects of chest tube definitions and nomenclature. The task force was composed of 11 invited participants, identified for their expertise in the area of chest tube management. The subject was divided in different topics, which were in turn assigned to at least two experts. The draft reports written by the experts on each topic were distributed to the entire expert panel, and comments solicited in advance of the meetings. During the meetings, the drafts were reviewed, discussed, and agreed on by the entire panel. Standardized definitions and nomenclature were proposed for the following topics related to chest tube management: pleural and respiratory mechanics after pulmonary resection; external suction versus no external suction; fixed versus variable suction; objective air leak evaluation; objective fluid drainage evaluation; and chest drain: type, number, and size. A standardized set of definitions and nomenclature were proposed to set a scientifically based framework with which to evaluate existing studies and to more clearly formulate questions, parameters, and outcomes for future studies. Copyright © 2011 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.

  3. School version of ESTE EU

    International Nuclear Information System (INIS)

    Carny, P.; Suchon, D.; Chyly, M.; Smejkalova, E.; Fabova, V.

    2008-01-01

    ESTE EU is information system and software for radiological impacts assessment to the territory of the country in case of radiation accident inside/outside of the country .The program enables to model dispersion of radioactive clouds in small-scale and meso-scale. The system enables the user to estimate prediction of the source term (release to the atmosphere ) for any point of radiation/nuclear accident in Europe (for any point of the release, but especially for the sites of European power reactors ). The system enables to utilize results of real radiological monitoring in the process of source term estimation. Radiological impacts of release to the atmosphere are modelled and calculated across the Europe and displayed in the geographical information system (GIS). The school version of ESTE EU is intended for students of the universities which are interested in or could work in the field of emergency response, radiological and nuclear accidents, dispersion modelling, radiological impacts calculation and urgent or preventive protective measures implementation. The school version of ESTE EU is planned to be donated to specialized departments of faculties in Slovakia, Czech Republic, etc. System can be fully operated in Slovak, Czech or English language. (authors)

  4. School version of ESTE EU

    International Nuclear Information System (INIS)

    Carny, P.; Suchon, D.; Chyly, M.; Smejkalova, E.; Fabova, V.

    2009-01-01

    ESTE EU is information system and software for radiological impacts assessment to the territory of the country in case of radiation accident inside/outside of the country .The program enables to model dispersion of radioactive clouds in small-scale and meso-scale. The system enables the user to estimate prediction of the source term (release to the atmosphere ) for any point of radiation/nuclear accident in Europe (for any point of the release, but especially for the sites of European power reactors ). The system enables to utilize results of real radiological monitoring in the process of source term estimation. Radiological impacts of release to the atmosphere are modelled and calculated across the Europe and displayed in the geographical information system (GIS). The school version of ESTE EU is intended for students of the universities which are interested in or could work in the field of emergency response, radiological and nuclear accidents, dispersion modelling, radiological impacts calculation and urgent or preventive protective measures implementation. The school version of ESTE EU is planned to be donated to specialized departments of faculties in Slovakia, Czech Republic, etc. System can be fully operated in Slovak, Czech or English language. (authors)

  5. Estômago em melancia, pericardite hemorrágica, tumor de pequenas células do pulmão e carcinoma pavimentocelular síncrono da base da língua

    Directory of Open Access Journals (Sweden)

    A. Murinello

    2010-07-01

    Full Text Available Resumo: Baseados num caso de gastropatia antral com ectasia vascular (estômago em melancia associado a pericardite hemorrágica e a um carcinoma de pequenas células do pulmão com metástases ganglionares ao longo do mediastino e a um carcinoma pavimentocelular síncrono da base da língua, os autores fazem uma revisão dos aspectos clínicos, endoscópicos e histopatológicos deste tipo de gastropatia, da sua associação a outras doenças e das possibilidades terapêuticas actuais por via endoscópica. Referem-se igualmente as causas mais frequentes de pericardite hemorrágica, salientando-se a necessidade de esclarecer se o derrame é ou não de origem neoplásica. Não está referida na literatura a associação deste tipo de gastropatia ao carcinoma de pequenas células do pulmão nem ao carcinoma pavimento-celular da base da língua. A invasão extensa dos gânglios mediastínicos pelo carcinoma de pequenas células do pulmão é ocorrência frequente.Rev Port Pneumol 2010; XVI (4: 659-670 Abstract: Based on a case of gastric antral vascular ectasia (watermelon stomach that was associated with hemorrhagic pericarditis, small cell lung carcinoma with mediastinal lymph node metastases and a synchronous squamous cell carcinoma of the base of the tongue, the authors made a review of the clinical, endoscopic and histopathological aspects of this type of gastropathy, and its association with other diseases, and of the results of its endoscopic therapy. The causes of hemorrhagic pericarditis are considered, emphasizing the necessity to know if the effusion has a malignant etiology. To the best of our knowledge the association of watermelon stomach to small cell lung carcinoma and squamous cell carcinoma of the base of the tongue has not yet been described. Extensive metastases to mediastal lymph nodes are common to small cell lung carcinoma.Rev Port Pneumol 2010; XVI (4: 659-670 Palavras-chave: Gastropatia antral com ectasia vascular, est

  6. DST no âmbito da relação estável: análise cultural com base na perspectiva da mulher EST en el ámbito de la relación estable: análisis cultural con base en la perspectiva de la mujer STD in scope of long-term relationships: cultural analysis based on women's perspective

    Directory of Open Access Journals (Sweden)

    Leilane Barbosa de Sousa

    2009-03-01

    Full Text Available O trabalho teve como objetivo analisar as significações da contaminação por DST para a mulher em união estável. Trata-se de uma pesquisa etnográfica, baseada na Teoria do Cuidado Cultural. Desenvolveu-se o estudo no Centro de Desenvolvimento Familiar (CEDEFAM e no contexto familiar de sete mulheres, durante nove meses. Os resultados mostraram que o diagnóstico de DST influencia o comportamento sexual das mulheres. Em face disso, todavia, verificou-se que os homens parecem se comportar como coadjuvantes no processo e ainda consideram o problema como inerente apenas à parte feminina. Conclui-se que é imprescindível a abordagem da cultura nas ações de Educação em Saúde para a promoção da saúde sexual e reprodutiva do casal.El estudio tuvo la intención de analizar las significaciones de contaminación por EST para la mujer en unión estable. Se trata de una pesquisa etnográfica, basada en la Teoría Cultural. El estudio ocurrió en el Centro de Desarrollo Familiar (CEDEFAM y en el contexto familiar de siete mujeres durante nueve meses. Los resultados mostraran que el diagnóstico de EST influencia el comportamiento sexual de las mujeres. Todavía, se verificó que los hombres parecen se comportar como coadyuvantes en el proceso y aun consideran el problema como inherente solamente a la parte femenina. Se concluye que es imprescindible el abordaje de la cultura en las acciones de Educación en Salud para la promoción de la salud sexual y procreadora de la pareja. Se puede creer que, basados en estrategias de Educación en Salud culturalmente encaminadas, podrán ser alcanzados resultados de impacto positivo en la asimilación del riesgo y rotura de la cadena de transmisión de ESTs.This study aimed to analyze the meaning of STD contamination for the women with stable union. The present study is an ethnographical research, based on Theory of Cultural Care. The study was developed in the Center of Family Development (CEDEFAM and

  7. Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

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    Finnerty John R

    2009-01-01

    Full Text Available Abstract Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal, were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

  8. Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1 gene family.

    Directory of Open Access Journals (Sweden)

    Mia T Levine

    Full Text Available Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin.

  9. Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria.

    Directory of Open Access Journals (Sweden)

    Sumit Mukherjee

    Full Text Available Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative genomics studies of riboswitches focusing on their gross distribution across different bacterial taxa have been carried out recently, systematic functional annotation and analysis of lysine riboswitches and the genes they regulate are still lacking. We analyzed 2785 complete bacterial genome sequences to systematically identify 468 lysine riboswitches (not counting hits from multiple strains of the same species and obtain a detailed phylogenomic map of gene-specific lysine riboswitch distribution across diverse prokaryotic phyla. We find that lysine riboswitches are most abundant in Firmicutes and Gammaproteobacteria where they are found upstream to both biosynthesis and/or transporter genes. They are relatively rare in all other prokaryotic phyla where if present they are primarily found upstream to operons containing many lysine biosynthesis genes. The genome-wide study of the genetic organisation of the lysine riboswitches show considerable variation both within and across different Firmicute orders. Correlating the location of a riboswitch with its genomic context and its phylogenetic relationship with other evolutionarily related riboswitch carrying species, enables identification and annotation of many lysine biosynthesis, transporter and catabolic genes. It also reveals previously unknown patterns of lysine riboswitch distribution and gene/operon regulation and allows us to draw inferences about the possible point of origin of lysine riboswitches. Additionally, evidence of horizontal transfer of riboswitches was found between Firmicutes and Actinobacteria. Our analysis provides a useful resource

  10. A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins

    Directory of Open Access Journals (Sweden)

    Mizuguchi Kenji

    2008-09-01

    Full Text Available Abstract Background Hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated. Results A search for putative Hrs in the genomes of 43 archaea, 444 bacteria and 135 eukaryotes, revealed their presence in 3 archaea, 118 bacteria, several fungi, one apicomplexan, a heterolobosan, a cnidarian and several annelids. About a fourth of the Hr sequences were identified as N- or C-terminal domains of chimeric, chemotactic gene regulators. The function of the remaining single domain bacterial Hrs remains to be determined. In addition to oxygen transport, the possible functions in annelids have been proposed to include cadmium-binding, antibacterial action and immunoprotection. A Bayesian phylogenetic tree revealed a split into two clades, one encompassing archaea, bacteria and fungi, and the other comprising the remaining eukaryotes. The annelid and sipunculan Hrs share the same intron-exon structure, different from that of the cnidarian Hr. Conclusion The phylogenomic profile of Hrs demonstrated a limited occurrence in bacteria and archaea and a marked absence in the vast majority of multicellular organisms. Among the metazoa, Hrs have survived in a cnidarian and in a few protostome groups; hence, it appears that in metazoans the Hr gene was lost in deuterostome ancestor(s after the radiata/bilateria split. Signal peptide sequences in several Hirudinea Hrs suggest for the first time, the possibility of extracellular localization. Since the α-helical bundle is likely to have been among the earliest protein folds, Hrs represent an ancient family of iron-binding proteins, whose primary function in bacteria may have been that of an oxygen sensor, enabling aerophilic or aerophobic responses. Although Hrs evolved to function as O2 transporters in brachiopods, priapulids and sipunculans, their function in

  11. Qui est Méduse?

    Directory of Open Access Journals (Sweden)

    Julia Kristeva

    2015-04-01

    Full Text Available Une belle histoire de têtes coupées traverse l'Antiquité grecque : celle des Gorgones, trois monstres ailés au corps de femme et à la chevelure de serpents, dont le regard changeait en pierre celui qui se risquait à les contempler – Méduse, Euryalé et Sthéno. Pour commencer, Méduse est une jeune fille qui se fait remarquer : séduite puis violée par Poséidon, elle se révèle fertile puisqu'elle accouche de faux jumeaux, le cheval Pégase et le géant Chrysaor. Une longue fable la transforme en terrible puissance. Pour simplifier, disons que le monstre est par deux fois tué : Persée assassine d'abord Méduse pour assurer la protection de sa mère, Danaé, importunée par le roi Polydectès. Ensuite, il délivre Andromède des liens méduséens qui la retiennent et, pour ce faire, tranche la tête de la Gorgone. La mer se teinte de sang, tandis que le vainqueur tient à l'écart l'épouvantail de Méduse, de peur que ne soient changés en statues de pierre ceux qui s'exposeraient à sa vue.

  12. A phylogenomic and molecular marker based proposal for the division of the genus Borrelia into two genera: the emended genus Borrelia containing only the members of the relapsing fever Borrelia, and the genus Borreliella gen. nov. containing the members of the Lyme disease Borrelia (Borrelia burgdorferi sensu lato complex).

    Science.gov (United States)

    Adeolu, Mobolaji; Gupta, Radhey S

    2014-06-01

    The genus Borrelia contains two groups of organisms: the causative agents of Lyme disease and their relatives and the causative agents of relapsing fever and their relatives. These two groups are morphologically indistinguishable and are difficult to distinguish biochemically. In this work, we have carried out detailed comparative genomic analyses on protein sequences from 38 Borrelia genomes to identify molecular markers in the forms of conserved signature inserts/deletions (CSIs) that are specifically found in the Borrelia homologues, and conserved signature proteins (CSPs) which are uniquely present in Borrelia species. Our analyses have identified 31 CSIs and 82 CSPs that are uniquely shared by all sequenced Borrelia species, providing molecular markers for this group of organisms. In addition, our work has identified 7 CSIs and 21 CSPs which are uniquely found in the Lyme disease Borrelia species and eight CSIs and four CSPs that are specific for members of the relapsing fever Borrelia group. Additionally, 38 other CSIs, in proteins which are uniquely found in Borrelia species, also distinguish these two groups of Borrelia. The identified CSIs and CSPs provide novel and highly specific molecular markers for identification and distinguishing between the Lyme disease Borrelia and the relapsing fever Borrelia species. We also report the results of average nucleotide identity (ANI) analysis on Borrelia genomes and phylogenetic analysis for these species based upon 16S rRNA sequences and concatenated sequences for 25 conserved proteins. These analyses also support the distinctness of the two Borrelia clades. On the basis of the identified molecular markers, the results from ANI and phylogenetic studies, and the distinct pathogenicity profiles and arthropod vectors used by different Borrelia spp. for their transmission, we are proposing a division of the genus Borrelia into two separate genera: an emended genus Borrelia, containing the causative agents of relapsing

  13. Population genetics, phylogenomics and hybrid speciation of Juglans in China determined from whole chloroplast genomes, transcriptomes, and genotyping-by-sequencing (GBS)

    Science.gov (United States)

    Peng Zhao; Hui-Juan Zhou; Daniel Potter; Yi-Heng Hu; Xiao-Jia Feng; Meng Dang; Li Feng; Saman Zulfiqar; Wen-Zhe Liu; Gui-Fang Zhao; Keith Woeste

    2018-01-01

    Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among Chinese Juglans remain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast...

  14. La parole est à vous

    CERN Multimedia

    Staff Association

    2015-01-01

    Nous avons identifié, ci-dessous, 3 grands chapitres pour lesquelles bon nombre d’entre vous se posent des questions et ont fréquemment sollicités leurs délégués, qui n’ont pas toujours pu donner de réponses : La retraite et sa préparation. L’affiliation aux régimes sécurité sociale de nos états hôtes et ses conséquences au moment de la retraite. La fiscalité en général. Le service juridique, que nous avons interrogé récemment, n’est pas toujours informé de vos interrogations et de ce fait, il n’a pas encore pu investiguer sur ces questions auprès des services compétents. Il nous a suggéré de vous interroger afin de collecter vos questions, de les synthétiser, afin de les transmettre...

  15. Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (poaceae).

    Science.gov (United States)

    Ma, Peng-Fei; Zhang, Yu-Xiao; Zeng, Chun-Xia; Guo, Zhen-Hua; Li, De-Zhu

    2014-11-01

    relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs database

    Directory of Open Access Journals (Sweden)

    Boore Jeffrey L

    2006-04-01

    Full Text Available Abstract Background We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community. Discussion The PhIGs database currently contains 23 completely sequenced genomes of fungi and metazoans, containing 409,653 genes that have been grouped into 42,645 gene clusters. Each gene cluster is built such that the gene sequence distances are consistent with the known organismal relationships and in so doing, maximizing the likelihood for the clusters to represent truly orthologous genes. The PhIGs website contains tools that allow the study of genes within their phylogenetic framework through keyword searches on annotations, such as GO and InterPro assignments, and sequence similarity searches by BLAST and HMM. In addition to displaying the evolutionary relationships of the genes in each cluster, the website also allows users to view the relative physical positions of homologous genes in specified sets of genomes. Summary Accurate analyses of genes and genomes can only be done within their full phylogenetic context. The PhIGs database and

  17. Population genetics, phylogenomics and hybrid speciation of Juglans in China determined from whole chloroplast genomes, transcriptomes, and genotyping-by-sequencing (GBS).

    Science.gov (United States)

    Zhao, Peng; Zhou, Hui-Juan; Potter, Daniel; Hu, Yi-Heng; Feng, Xiao-Jia; Dang, Meng; Feng, Li; Zulfiqar, Saman; Liu, Wen-Zhe; Zhao, Gui-Fang; Woeste, Keith

    2018-04-18

    Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among Chinese Juglans remain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast genomes (Cp genome) data to infer processes of lineage formation among the five native Chinese species of the walnut genus (Juglans, Juglandaceae), a widespread, economically important group. We found that the processes of isolation generated diversity during glaciations, but that the recent range expansion of J. regia, probably from multiple refugia, led to hybrid formation both within and between sections of the genus. In southern China, human dispersal of J. regia brought it into contact with J. sigillata, which we determined to be an ecotype of J. regia that is now maintained as a landrace. In northern China, walnut hybridized with a distinct lineage of J. mandshurica to form J. hopeiensis, a controversial taxon (considered threatened) that our data indicate is a horticultural variety. Comparisons among whole chloroplast genomes and nuclear transcriptome analyses provided conflicting evidence for the timing of the divergence of Chinese Juglans taxa. J. cathayensis and J. mandshurica are poorly differentiated based our genomic data. Reconstruction of Juglans evolutionary history indicate that episodes of climatic variation over the past 4.5 to 33.80 million years, associated with glacial advances and retreats and population isolation, have shaped Chinese walnut demography and evolution, even in the presence of gene flow and introgression. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. AcEST: BP918444 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU001_000113_E11 570 Adiantum capillus-veneris mRNA. clone: YMU001_000113_E11. BP918444 - Show BP9184...is mRNA. clone: YMU001_000113_E11. Accession BP918444 Tissue type prothallium Developmental stage - Contig I...tion of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= BP918444|Adiantum capillus...base search programs, Nucleic Acids Res. 25:3389-3402. Query= BP918444|Adiantum capillus-veneris mRNA, clone

  19. AcEST: BP918456 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU001_000113_F11 456 Adiantum capillus-veneris mRNA. clone: YMU001_000113_F11. BP9184...56 CL2911Contig1 Show BP918456 Clone id YMU001_000113_F11 Library YMU01 Length 456 Definition Adiantum ca...pillus-veneris mRNA. clone: YMU001_000113_F11. Accession BP918456 Tissue type prothallium Developmental stag...base search programs, Nucleic Acids Res. 25:3389-3402. Query= BP918456|Adiantum c...2 +EI+ ++DSDPRAAYFRQA+ G+YIRMA Sbjct: 2184 NEISREIDSDPRAAYFRQAEYGMYIRMA 2211 TrEMBL (release 39.9) Link to B

  20. AcEST: BP918459 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU001_000113_G02 467 Adiantum capillus-veneris mRNA. clone: YMU001_000113_G02. BP918459 - Show BP9184...is mRNA. clone: YMU001_000113_G02. Accession BP918459 Tissue type prothallium Developmental stage - Contig I...base search programs, Nucleic Acids Res. 25:3389-3402. Query= BP918459|Adiantum c..., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= BP9184

  1. AcEST: BP919765 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU001_000128_H07 531 Adiantum capillus-veneris mRNA. clone: YMU001_000128_H07. BP919765 - Show BP9197...is mRNA. clone: YMU001_000128_H07. Accession BP919765 Tissue type prothallium Developmental stage - Contig I... Res. 25:3389-3402. Query= BP919765|Adiantum capillus-veneris mRNA, clone: YMU001_000128_H07. (516 letters) ...base search programs, Nucleic Acids Res. 25:3389-3402. Query= BP919765|Adiantum capillus-veneris mRNA, clone

  2. SNP-finding in pig mitochondrial ESTs

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Cirera Salicio, Susanna; Gilchrist, M.J.

    2008-01-01

    The Sino-Danish pig genome project produced 685 851 ESTs (Gorodkin et al. 2007), of which 41 499 originated from the mitochondrial genome. In this study, the mitochondrial ESTs were assembled, and 374 putative SNPs were found. Chromatograms for the ESTs containing SNPs were manually inspected...

  3. Is pertussis actually reemerging? Insights from an individual-based model A coqueluche realmente está reermegindo? Reflexões a partir de um modelo baseado no indivíduo

    Directory of Open Access Journals (Sweden)

    Cláudia Torres Codeço

    2001-06-01

    Full Text Available In this paper, we introduce a spatially explicit, individual-based model developed to simulate the dynamics of pertussis in a small population. With this simulation approach, complex epidemic systems can be built using information on parasite population structure (strain diversity, virulence diversity, etc., human population structure (individual risk, age structure, interaction matrices, immune response, etc., as well as mechanisms of evolution and learning. We parameterized our model to describe pertussis in an age-structured community. Pertussis or whooping cough is an acute infection of the respiratory tract caused by Bordetella pertussis. Despite wide-scale vaccination in many countries, this disease is reemerging throughout the world in both adults and children. Emergence has been explained by many factors: wane of vaccine and natural immunity, increase of asymptomatic carriers, and/or natural selection of non-vaccine strains. Here, we model these hypotheses and analyze their potential impact on the observed increase of pertussis notification.Neste trabalho, nós apresentamos um modelo de indivíduos, cuja representação espacial é explícita, para simular a dinâmica da coqueluche numa pequena população. Utilizando esta abordagem de simulação, podemos construir modelos complexos utilizando informações sobre a estrutura populacional dos parasitas (diversidade fenotípica, de virulência, etc sobre a estrutura populacional humana (risco individual, estrutura etária, matrizes de interação, resposta imunológica, etc assim como processos evolutivos e de aprendizagem. Nós parametrizamos este modelo para representar a dinâmica da coqueluche numa população com estrutura etária. Coqueluche é uma infecção aguda do trato respiratório, causada por Bordetella pertussis. Apesar da vacinação em larga escala em vários países, esta infecção está reemergindo por todo o mundo, atacando adultos e crianças. Reemergência tem sido

  4. Diseño definitivo comparativo del puente de 60.0 m. de luz sobre el rio Toachi en base a las normas AASHTO estándar y LRFD. : Tomo I

    OpenAIRE

    Prieto Salazar, Juan Carlos; Tipán Aceveso, René Oswaldo

    2012-01-01

    Generalidades. Análisis de estudios preliminares. Diseño estructural (código AASHTO estándar). Aplicación de las normas AASHTO LRFD al diseño estructural de puentes. Diseño estructural (código AASHTO estándar).Presupuesto y programación de obra. Comparación técnico económica. Impacto ambiental. Conclusiones y recomendaciones. Bibliografía

  5. Villa d'Este i Tivoli

    DEFF Research Database (Denmark)

    Bach-Nielsen, Carsten

    2012-01-01

    Om Villa d'Este, en renæssancehave ved Rom, der tematiserer Herkules' valg mellem dydens og lastens vej......Om Villa d'Este, en renæssancehave ved Rom, der tematiserer Herkules' valg mellem dydens og lastens vej...

  6. Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I).

    Science.gov (United States)

    Gupta, Radhey S; Gao, Beile

    2009-02-01

    The species of Clostridium comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of Clostridium that form a distinct cluster in the 16S rRNA tree (cluster I) should be regarded as the true representatives of the genus Clostridium (i.e. Clostridium sensu stricto). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of Clostridium cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other Clostridium species that are not part of this cluster grouped reliably with other species of clostridia in a number of well-resolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of Clostridium cluster I and are not found in any other bacteria. blastp searches on various proteins in the genomes of Clostridium tetani E88 and Clostridium perfringens SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of Clostridium cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus Clostridium sensu stricto in more

  7. Ortodoncia estética invisible

    OpenAIRE

    Chávez Sevillano, Manuel Gustavo; Soldevilla Galarza, Luciano

    2014-01-01

    El adulto suele ofrecer resistencia a los convencionales tratamientos ortodóncicos, debido a la necesidad de llevar brackets visibles, tanto metálicos como estéticos de porcelana. El concepto de Ortodoncia Estética Invisible u Ortodoncia Lingual cubre las expectativas de este tipo de pacientes. La técnica multibrackets con aparatología lingual tiene aproximadamente 25 años de desarrollo y con la experiencia de los casos tratados, se ha llegado a la concepción de una técnica completamente prot...

  8. Phylogenomic resolution of paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data.

    Science.gov (United States)

    Hedin, Marshal; Starrett, James; Akhter, Sajia; Schönhofer, Axel L; Shultz, Jeffrey W

    2012-01-01

    Next-generation sequencing technologies are rapidly transforming molecular systematic studies of non-model animal taxa. The arachnid order Opiliones (commonly known as "harvestmen") includes more than 6,400 described species placed into four well-supported lineages (suborders). Fossil plus molecular clock evidence indicates that these lineages were diverging in the late Silurian to mid-Carboniferous, with some fossil harvestmen representing the earliest known land animals. Perhaps because of this ancient divergence, phylogenetic resolution of subordinal interrelationships within Opiliones has been difficult. We present the first phylogenomics analysis for harvestmen, derived from comparative RNA-Seq data for eight species representing all suborders. Over 30 gigabases of original Illumina short-read data were used in de novo assemblies, resulting in 50-80,000 transcripts per taxon. Transcripts were compared to published scorpion and tick genomics data, and a stringent filtering process was used to identify over 350 putatively single-copy, orthologous protein-coding genes shared among taxa. Phylogenetic analyses using various partitioning strategies, data coding schemes, and analytical methods overwhelmingly support the "classical" hypothesis of Opiliones relationships, including the higher-level clades Palpatores and Phalangida. Relaxed molecular clock analyses using multiple alternative fossil calibration strategies corroborate ancient divergences within Opiliones that are possibly deeper than the recorded fossil record indicates. The assembled data matrices, comprising genes that are conserved, highly expressed, and varying in length and phylogenetic informativeness, represent an important resource for future molecular systematic studies of Opiliones and other arachnid groups.

  9. In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus).

    Science.gov (United States)

    Domingos, Fabricius M C B; Colli, Guarino R; Lemmon, Alan; Lemmon, Emily Moriarty; Beheregaray, Luciano B

    2017-02-01

    The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups.

    Directory of Open Access Journals (Sweden)

    Joakim Agren

    Full Text Available The rapid development of Next Generation Sequencing technologies leads to the accumulation of huge amounts of sequencing data. The scientific community faces an enormous challenge in how to deal with this explosion. Here we present a software tool, 'Gegenees', that uses a fragmented alignment approach to facilitate the comparative analysis of hundreds of microbial genomes. The genomes are fragmented and compared, all against all, by a multithreaded BLAST control engine. Ready-made alignments can be complemented with new genomes without recalculating the existing data points. Gegenees gives a phylogenomic overview of the genomes and the alignment can then be mined for genomic regions with conservation patterns matching a defined target group and absent from a background group. The genomic regions are given biomarker scores forming a uniqueness signature that can be viewed and explored, graphically and in tabular form. A primer/probe alignment tool is also included for specificity verification of currently used or new primers. We exemplify the use of Gegenees on the Bacillus cereus group, on Foot and Mouth Disease Viruses, and on strains from the 2011 Escherichia coli O104:H4 outbreak. Gegenees contributes towards an increased capacity of fast and efficient data mining as more and more genomes become sequenced.

  11. The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis.

    Science.gov (United States)

    Jameson Kiesling, Natalie M; Yi, Soojin V; Xu, Ke; Gianluca Sperone, F; Wildman, Derek E

    2015-01-01

    The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. A caminho da estética

    Directory of Open Access Journals (Sweden)

    Amaral Filho, Fausto dos Santos

    2007-01-01

    Full Text Available O presente estudo tenta compreender, ainda que de maneira sumária, quais os caminhos que a Estética tomou; desde Hegel e a dedução filosófica dos conceitos, até a corrente, influenciada por Wittgenstein, da análise da liguagem comum, acabando por apontar, diante das dificuldades dos referidos caminhos, para a Estética da circularidade; tanto a de Heidegger quanto a de George Dickie

  13. Turismo y estética formativa

    Directory of Open Access Journals (Sweden)

    Clara Inés Sánchez Arciniegas

    2002-11-01

    Full Text Available ¿Existe alguna armonía entre el conocimiento y la estética? Sin duda alguna el hombre con conocimiento y sin virtud de la estética es un autómata; este necesita de las diferentes manifestaciones en las que se encuentra plasmada y necesita recordarlas continuamente. La estética como doctrina de conocimiento no es reciente, en el siglo xviii cuando por primera vez se define teóricamente hasta nuestros días en la Universidad actual. Esta última aparentemente menos evidente debido a las nuevas formas de aprendizaje con herramientas tecnológicas muy avanzadas y contraria a la imagen del universitario que hace dos siglos como complemento a su educación se distraía a través del Gran Tour, partida que tiene el turismo para fomentar el goce estético. ¿Cuál es entonces la relación entre distracción y formación? Se debe entonces reflexionar y comprender que el conocimiento interdisciplinario y la metodología debe procurar en los hombres actitudes adecuadas frente a la cultura y el arte a través del conocimiento.

  14. Construction, database integration, and application of an Oenothera EST library.

    Science.gov (United States)

    Mrácek, Jaroslav; Greiner, Stephan; Cho, Won Kyong; Rauwolf, Uwe; Braun, Martha; Umate, Pavan; Altstätter, Johannes; Stoppel, Rhea; Mlcochová, Lada; Silber, Martina V; Volz, Stefanie M; White, Sarah; Selmeier, Renate; Rudd, Stephen; Herrmann, Reinhold G; Meurer, Jörg

    2006-09-01

    Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.

  15. Estética en prótesis removibles

    Directory of Open Access Journals (Sweden)

    LVM Lucas

    2010-06-01

    Full Text Available La estética actualmente recibe una importante consideración en el contexto social. Una sonrisa atractiva es aspiración de la mayoría de los pacientes que precisan tratamiento protésico. Los implantes propiciaron una mejoría significativa, con relación a las prótesis removibles, debido a su funcionalidad. El objetivo de este estudio fue explorar en la literatura científica moderna, a fin de hallar aspectos relacionados con la estética en la rehabilitación mediante prótesis removibles. Fueron encontrados factores importantes como: la selección de los dientes artificiales, la disposición de los mismos, la caracterización de la base de resina acrílica, además de los tipos de retenedores para las prótesis parciales removibles. La planificación y aplicación apropiada de este procedimiento, con criterios estéticos correctos, debe ser responsabilidad del profesional.

  16. EST-PAC a web package for EST annotation and protein sequence prediction

    Directory of Open Access Journals (Sweden)

    Strahm Yvan

    2006-10-01

    Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

  17. Errare humanum est : sincronia, diacronia e erro

    OpenAIRE

    Teixeira, José

    1996-01-01

    O falante de uma língua natural, na maior parte dos casos, tem sempre à sua disposição mais que uma forma/fórmula. A sincronia não é um conjunto de processos unívocos (de comunicar) mas sim um sistema de identidades processuais. O que o falante faz é procurar, buscar, optar por um ou por outro. Este processo não é imóvel, fixo, estático, mas errante, sinónimo de dinâmico.

  18. Estética del rock

    OpenAIRE

    Rey, Sebastián

    2014-01-01

    El objetivo del presente artículo es el de analizar la estética del Rock en términos de la experiencia que ofrece este género musical. En primer lugar se construirá una relación entre el Nacimiento de la tragedia de Nietzsche y el surgimiento del Rock, bajo la premisa de que el origen del Rock es eminentemente dionisíaco; luego se mostrará una forma de la experiencia en la vida cotidiana de quien escucha Rock, en donde se da cuenta de la necesidad de expresar los sentimientos de placer y disp...

  19. Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

    Directory of Open Access Journals (Sweden)

    Adams Josephine C

    2006-04-01

    Full Text Available Abstract Background Thrombospondins (TSPs are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish. Results We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestral genomic context of vertebrate TSPs. Conclusion A new model for TSP evolution in vertebrates is presented. The TSP-5 protein sequence has evolved rapidly from a TSP-4-like sequence as an innovation in the tetrapod lineage. TSP biology in fish is complicated by the presence of additional lineage- and species-specific TSP paralogues. These novel results give deeper insight into the evolution of TSPs in vertebrates and open new directions for understanding the physiological and pathological roles of TSP-4 and TSP-5 in humans.

  20. Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids.

    Science.gov (United States)

    Grant, Jessica R; Katz, Laura A

    2014-09-01

    Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence--a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence--to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma.

    Science.gov (United States)

    Ješovnik, Ana; González, Vanessa L; Schultz, Ted R

    2016-01-01

    Fungus-farming ("attine") ants are model systems for studies of symbiosis, coevolution, and advanced eusociality. A New World clade of nearly 300 species in 15 genera, all attine ants cultivate fungal symbionts for food. In order to better understand the evolution of ant agriculture, we sequenced, assembled, and analyzed transcriptomes of four different attine ant species in two genera: three species in the higher-attine genus Sericomyrmex and a single lower-attine ant species, Apterostigma megacephala, representing the first genomic data for either genus. These data were combined with published genomes of nine other ant species and the honey bee Apis mellifera for phylogenomic and divergence-dating analyses. The resulting phylogeny confirms relationships inferred in previous studies of fungus-farming ants. Divergence-dating analyses recovered slightly older dates than most prior analyses, estimating that attine ants originated 53.6-66.7 million of years ago, and recovered a very long branch subtending a very recent, rapid radiation of the genus Sericomyrmex. This result is further confirmed by a separate analysis of the three Sericomyrmex species, which reveals that 92.71% of orthologs have 99% - 100% pairwise-identical nucleotide sequences. We searched the transcriptomes for genes of interest, most importantly argininosuccinate synthase and argininosuccinate lyase, which are functional in other ants but which are known to have been lost in seven previously studied attine ant species. Loss of the ability to produce the amino acid arginine has been hypothesized to contribute to the obligate dependence of attine ants upon their cultivated fungi, but the point in fungus-farming ant evolution at which these losses occurred has remained unknown. We did not find these genes in any of the sequenced transcriptomes. Although expected for Sericomyrmex species, the absence of arginine anabolic genes in the lower-attine ant Apterostigma megacephala strongly suggests that the

  2. Expressed sequence tags (ESTs) and single nucleotide ...

    African Journals Online (AJOL)

    Expressed Sequence Tags (ESTs) and Single Nucleotide Polymorphisms (SNPs) are providing in depth knowledge in plant biology, breeding and biotechnology. The emergence of many novel molecular marker techniques are changing and accelerating the process of producing mutations in plant molecular biology ...

  3. An EST database from saffron stigmas

    Directory of Open Access Journals (Sweden)

    Chiusano Maria Luisa

    2007-10-01

    Full Text Available Abstract Background Saffron (Crocus sativus L., Iridaceae flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part – the stigmas – are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron. Results We produced 6,603 high quality Expressed Sequence Tags (ESTs from a saffron stigma cDNA library. This collection is accessible and searchable through the Saffron Genes database http://www.saffrongenes.org. The ESTs have been grouped into 1,893 Clusters, each corresponding to a different expressed gene, and annotated. The complete set of raw EST sequences, as well as of their electopherograms, are maintained in the database, allowing users to investigate sequence qualities and EST structural features (vector contamination, repeat regions. The saffron stigma transcriptome contains a series of interesting sequences (putative sex determination genes, lipid and carotenoid metabolism enzymes, transcription factors. Conclusion The Saffron Genes database represents the first reference collection for the genomics of Iridaceae, for the molecular biology of stigma biogenesis, as well as for the metabolic pathways underlying saffron secondary metabolism.

  4. An EST database from saffron stigmas.

    Science.gov (United States)

    D'Agostino, Nunzio; Pizzichini, Daniele; Chiusano, Maria Luisa; Giuliano, Giovanni

    2007-10-09

    Saffron (Crocus sativus L., Iridaceae) flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part - the stigmas - are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron. We produced 6,603 high quality Expressed Sequence Tags (ESTs) from a saffron stigma cDNA library. This collection is accessible and searchable through the Saffron Genes database http://www.saffrongenes.org. The ESTs have been grouped into 1,893 Clusters, each corresponding to a different expressed gene, and annotated. The complete set of raw EST sequences, as well as of their electopherograms, are maintained in the database, allowing users to investigate sequence qualities and EST structural features (vector contamination, repeat regions). The saffron stigma transcriptome contains a series of interesting sequences (putative sex determination genes, lipid and carotenoid metabolism enzymes, transcription factors). The Saffron Genes database represents the first reference collection for the genomics of Iridaceae, for the molecular biology of stigma biogenesis, as well as for the metabolic pathways underlying saffron secondary metabolism.

  5. An optimized procedure greatly improves EST vector contamination removal

    Directory of Open Access Journals (Sweden)

    Wu Huan-Bin

    2007-11-01

    Full Text Available Abstract Background The enormous amount of sequence data available in the public domain database has been a gold mine for researchers exploring various themes in life sciences, and hence the quality of such data is of serious concern to researchers. Removal of vector contamination is one of the most significant operations to obtain accurate sequence data containing only a cDNA insert from the basecalls output by an automatic DNA sequencer. Popular bioinformatics programs to accomplish vector trimming include LUCY, cross_match and SeqClean. Results In a recent study, where the program SeqClean was used to remove vector contamination from our test set of EST data compiled through various library construction systems, however, a significant number of errors remained after preliminary trimming. These errors were later almost completely corrected by simply using a re-linearized form of the cloning vector to compare against the target ESTs. The modified trimming procedure for SeqClean was also compared with the trimming efficiency of the other two popular programs, LUCY2, and cross_match. Using SeqClean with a re-linearized form of the cloning vector significantly surpassed the other two programs in all tested conditions, while the performance of the other two programs was not influenced by the modified procedure. Vector contamination in dbEST was also investigated in this study: 2203 out of the 48212 ESTs sampled from dbEST (2007-04-18 freeze were found to match sequences in UNIVEC. Conclusion Vector contamination remains a serious concern to the data quality in the public sequence database nowadays. Based on the results presented here, we feel that our modified procedure with SeqClean should be recommended to all researchers for the task of vector removal from EST or genomic sequences.

  6. Ensinando subtração para pessoas com deficiência mental com base em relações de equivalência de estímulos

    Directory of Open Access Journals (Sweden)

    Priscila Mara de Araújo

    Full Text Available Foi avaliado um procedimento para o ensino de subtração a indivíduos deficientes mentais, por meio de relações ambientadas em tarefas de MTS. O primeiro passo consistiu nos testes das relações da classe ABC (relações quantitativas de 1 a 9 e FGH (operadores menos e igual. O segundo consistiu nos testes/treinos das relações entre as sentenças da classe IJK - falada (I, com conjuntos (J e com algarismos (K - para os valores de um a cinco. O terceiro passo consistiu nos treinos/testes, com valores de um a nove, das relações entre a sentença (classe IJK e o resultado (classe ABC. Ao final, verificou-se a emergência de algumas relações em sessões de teste, sugerindo potencialidade para a aquisição de responder adequado a novas combinações de estímulos numéricos. Contudo, testes em outras populações e com outras operações aritméticas são necessários para analisar a aplicabilidade do programa no ensino de operações matemáticas.

  7. FRIEDMAN Thomas, La terre est plate

    OpenAIRE

    Kociemba, Valérie

    2008-01-01

    « L’Église dit que la terre est plate, mais j’ai vu l’ombre sur la lune et j’ai plus foi en l’ombre qu’en l’église. » (Ferdinand Magellan) Bien des siècles plus tard, Thomas Friedman réitère l’affirmation en titre de son dernier ouvrage : La terre est plate, Une brève histoire du xxie siècle. À quelle Église appartient donc ce brillant éditorialiste du « New York Times » ? À l’Église de la toute puissance des nouvelles technologies de l’information, et il n’en fait pas mystère puisqu’il décla...

  8. Bessines – Le Grand Champ Est

    OpenAIRE

    Lemaître, Séverine; Landreau, Guilhem; Ferrié, Jean-Georges; Maguer, Patrick

    2013-01-01

    Identifiant de l'opération archéologique : 204625 Date de l'opération : 2008 (SP) Plusieurs opérations de diagnostics et de fouilles ont été entreprises depuis 2003 au sud-est de la Communauté d’Agglomérations de Niort. Elles montrent une occupation protohistorique particulièrement dense de l’âge du Bronze à l’âge du Fer, au sud-est de l’ancien golfe des Pictons, notamment sur les communes adjacentes de Niort, à Aiffres et à Bessines. Suite au dépôt d’un projet de ZAC, une opération de diagno...

  9. Comparaison n'est pas raison…

    Directory of Open Access Journals (Sweden)

    Yves Guermond

    2004-11-01

    Full Text Available Dans le contexte très politisé de la question palestinienne il est difficile de séparer l’analyse scientifique des réactions passionnelles, et l’utilisation de l’apartheid comme repoussoir peut donner l’impression de dédouaner le gouvernement israélien. C’est d’ailleurs un peu semble-t-il l’intention de Frédéric Giraut quand il écrit que « l’usage radical et systématique de l’analogie vise à condamner l’Etat d’Israël et le sionisme dans leur nature même ». « Cette approche infondée » serait ,...

  10. La actualidad estética

    Directory of Open Access Journals (Sweden)

    Alfonso Hanssen

    1966-07-01

    Full Text Available "La gente que se interesa por la filosofía del arte pertenece más o menos a dos tipos: artistas con inclinación filosófica o filósofos con gusto artístico". En mayor o menor grado, la peculiaridad y limitación de la estética han tenido que ver con esta disyuntiva.

  11. Estética, Subjetividad y Conocimiento

    Directory of Open Access Journals (Sweden)

    López Avendaño, Olimpia

    2002-12-01

    Full Text Available Este artículo trata de la tradicional dicotomía conocimiento objetivo-subjetivo. En él se analiza la posición de diferentes autores en búsqueda de los elementos que conducen al nacimiento de un nuevo paradigma, integrador, que supere la antinomia y permita visualizar al conocimiento pero sobre todo al individuo que lo produce, integralmente.

  12. Amar por cartas - este inferno de amara

    Directory of Open Access Journals (Sweden)

    Matildes Demetrio dos Santos

    1999-10-01

    Full Text Available Este trabalho tem por objetivo estudar o amor nas Folhas caídas e nas Cartas de amor à Viscondessa da Luz, de Almeida Garrett.Seus poemas cheios de erotismo e sensua lidade, inspirados numa mulher casada, Rosa Montúrar Infante, escandalizaram a sociedade portuguesado sécu lo XIX. Suas cartas de amor, em segredo, criavam uma ficção de características místicas.

  13. Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus).

    Science.gov (United States)

    Carr, Steven M; Duggan, Ana T; Stenson, Garry B; Marshall, H Dawn

    2015-01-01

    Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on "fast ice" attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40~60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping

  14. Phylogenomic Analysis Reveals an Asian Origin for African Burkholderia pseudomallei and Further Supports Melioidosis Endemicity in Africa.

    Science.gov (United States)

    Sarovich, Derek S; Garin, Benoit; De Smet, Birgit; Kaestli, Mirjam; Mayo, Mark; Vandamme, Peter; Jacobs, Jan; Lompo, Palpouguini; Tahita, Marc C; Tinto, Halidou; Djaomalaza, Innocente; Currie, Bart J; Price, Erin P

    2016-01-01

    Burkholderia pseudomallei, an environmental bacterium that causes the deadly disease melioidosis, is endemic in northern Australia and Southeast Asia. An increasing number of melioidosis cases are being reported in other tropical regions, including Africa and the Indian Ocean islands. B. pseudomallei first emerged in Australia, with subsequent rare dissemination event(s) to Southeast Asia; however, its dispersal to other regions is not yet well understood. We used large-scale comparative genomics to investigate the origins of three B. pseudomallei isolates from Madagascar and two from Burkina Faso. Phylogenomic reconstruction demonstrates that these African B. pseudomallei isolates group into a single novel clade that resides within the more ancestral Asian clade. Intriguingly, South American strains reside within the African clade, suggesting more recent dissemination from West Africa to the Americas. Anthropogenic factors likely assisted in B. pseudomallei dissemination to Africa, possibly during migration of the Austronesian peoples from Indonesian Borneo to Madagascar ~2,000 years ago, with subsequent genetic diversity driven by mutation and recombination. Our study provides new insights into global patterns of B. pseudomallei dissemination and adds to the growing body of evidence of melioidosis endemicity in Africa. Our findings have important implications for melioidosis diagnosis and management in Africa. IMPORTANCE Sporadic melioidosis cases have been reported in the African mainland and Indian Ocean islands, but until recently, these regions were not considered areas where B. pseudomallei is endemic. Given the high mortality rate of melioidosis, it is crucial that this disease be recognized and suspected in all regions of endemicity. Previous work has shown that B. pseudomallei originated in Australia, with subsequent introduction into Asia; however, the precise origin of B. pseudomallei in other tropical regions remains poorly understood. Using

  15. Phylogenomic and functional analyses of salmon lice aquaporins uncover the molecular diversity of the superfamily in Arthropoda.

    Science.gov (United States)

    Stavang, Jon Anders; Chauvigné, Francois; Kongshaug, Heidi; Cerdà, Joan; Nilsen, Frank; Finn, Roderick Nigel

    2015-08-19

    An emerging field in biomedical research is focusing on the roles of aquaporin water channels in parasites that cause debilitating or lethal diseases to their vertebrate hosts. The primary vectorial agents are hematophagous arthropods, including mosquitoes, flies, ticks and lice, however very little is known concerning the functional diversity of aquaporins in non-insect members of the Arthropoda. Here we conducted phylogenomic and functional analyses of aquaporins in the salmon louse, a marine ectoparasitic copepod that feeds on the skin and body fluids of salmonids, and used the primary structures of the isolated channels to uncover the genomic repertoires in Arthropoda. Genomic screening identified 7 aquaporin paralogs in the louse in contrast to 42 in its host the Atlantic salmon. Phylogenetic inference of the louse nucleotides and proteins in relation to orthologs identified in Chelicerata, Myriapoda, Crustacea and Hexapoda revealed that the arthropod aquaporin superfamily can be classified into three major grades (1) classical aquaporins including Big brain (Bib) and Prip-like (PripL) channels (2) aquaglyceroporins (Glp) and (3) unorthodox aquaporins (Aqp12-like). In Hexapoda, two additional subfamilies exist as Drip and a recently classified entomoglyceroporin (Eglp) group. Cloning and remapping the louse cDNAs to the genomic DNA revealed that they are encoded by 1-7 exons, with two of the Glps being expressed as N-terminal splice variants (Glp1_v1, -1_v2, -3_v1, -3_v2). Heterologous expression of the cRNAs in amphibian oocytes demonstrated that PripL transports water and urea, while Bib does not. Glp1_v1, -2, -3_v1 and -3_v2 each transport water, glycerol and urea, while Glp1_v2 and the Aqp12-like channels were retained intracellularly. Transcript abundance analyses revealed expression of each louse paralog at all developmental stages, except for glp1_v1, which is specific to preadult and adult males. Our data suggest that the aquaporin repertoires of

  16. Evaluación de la gestión técnica administrativa de enfermería en base a estándares de calidad y seguridad de atención a pacientes del hospital de atención integral del adulto mayor

    OpenAIRE

    Guaytarilla Salas, Sandra Monica

    2015-01-01

    La gestión de la calidad de enfermería exige el permanente monitoreo de estructuras, procesos y resultados de su gestión, con el propósito de brindar atención de salud con calidad y seguridad a los usuarios. Con éste antecedente el objetivo de este trabajo de investigación fue evaluar la gestión técnica administrativa de enfermería en base a los estándares de calidad y seguridad del paciente y proponer un plan de mejoramiento, que permita elevar la calidad de atención de una manera estandariz...

  17. Beleza e cirurgia estética

    OpenAIRE

    Vilas Bôas, Luana Michele da Silva

    2012-01-01

    Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas. Programa de Pós-Graduação em Psicologia O objetivo desse estudo foi identificar as representações sociais de homens e mulheres com diferentes formações acadêmicas a respeito de beleza e da cirurgia estética. Trata-se de um estudo de natureza descritiva e comparativa, com delineamento transversal, com a participação de 120 universitários dos cursos de Educação Física, Artes e Exatas, dis...

  18. Phylogenomic resolution of the class Ophiuroidea unlocks a global microfossil record.

    Science.gov (United States)

    O'Hara, Timothy D; Hugall, Andrew F; Thuy, Ben; Moussalli, Adnan

    2014-08-18

    Our understanding of the origin, evolution, and biogeography of seafloor fauna is limited because we have insufficient spatial and temporal data to resolve underlying processes. The abundance and wide distribution of modern and disarticulated fossil Ophiuroidea, including brittle stars and basket stars, make them an ideal model system for global marine biogeography if we have the phylogenetic framework necessary to link extant and fossil morphology in an evolutionary context. Here we construct a phylogeny from a highly complete 425-gene, 61-taxa transcriptome-based data set covering 15 of the 18 ophiuroid families and representatives of all extant echinoderm classes. We calibrate our phylogeny with a series of novel fossil discoveries from the early Mesozoic. We confirm the traditional paleontological view that ophiuroids are sister to the asteroids and date the crown group Ophiuroidea to the mid-Permian (270 ± 30 mega-annum). We refute all historical classification schemes of the Ophiuroidea based on gross structural characters but find strong congruence with schemes based on lateral arm plate microstructure and the temporal appearance of various plate morphologies in the fossil record. The verification that these microfossils contain phylogenetically informative characters unlocks their potential to advance our understanding of marine biogeographical processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Signaling pathways in a Citrus EST database

    Directory of Open Access Journals (Sweden)

    Angela Mehta

    2007-01-01

    Full Text Available Citrus spp. are economically important crops, which in Brazil are grown mainly in the State of São Paulo. Citrus cultures are attacked by several pathogens, causing severe yield losses. In order to better understand this culture, the Millenium Project (IAC Cordeirópolis was launched in order to sequence Citrus ESTs (expressed sequence tags from different tissues, including leaf, bark, fruit, root and flower. Plants were submitted to biotic and abiotic stresses and investigated under different development stages (adult vs. juvenile. Several cDNA libraries were constructed and the sequences obtained formed the Citrus ESTs database with almost 200,000 sequences. Searches were performed in the Citrus database to investigate the presence of different signaling pathway components. Several of the genes involved in the signaling of sugar, calcium, cytokinin, plant hormones, inositol phosphate, MAPKinase and COP9 were found in the citrus genome and are discussed in this paper. The results obtained may indicate that similar mechanisms described in other plants, such as Arabidopsis, occur in citrus. Further experimental studies must be conducted in order to understand the different signaling pathways present.

  20. AcEST(EST sequences of Adiantum capillus-veneris and their annotation) - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us AcEST AcEST(EST sequences of Adiantum capillus-veneris and their annotation) Data detail Dat...a name AcEST(EST sequences of Adiantum capillus-veneris and their annotation) DOI 10.18908/lsdba.nbdc00839-0...01 Description of data contents EST sequence of Adiantum capillus-veneris and its annotation (clone ID, libr...le search URL http://togodb.biosciencedbc.jp/togodb/view/archive_acest#en Data acquisition method Capillary ...ainst UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases) Number of data entries Adiantum capillus-veneris

  1. Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution

    Science.gov (United States)

    László G. Nagy; Robert Riley; Philip J. Bergmann; Krisztina Krizsán; Francis M. Martin; Igor V. Grigoriev; Dan Cullen; David S. Hibbett

    2016-01-01

    Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR...

  2. Marketing! Onde está o Paradigma?

    Directory of Open Access Journals (Sweden)

    Deosir Flávio Lobo de Castro Júnior

    2015-09-01

    Full Text Available O debate quantitativo-qualitativo, não é uma discussão recente. O objetivo desse trabalho, portanto, é verificar por meio do conceito de paradigma, novas perspectivas de compreender as pesquisas acadêmicas em marketing, a evolução do pensamento de marketing e as metodologias utilizadas nos estudos da qualidade de serviço. Sem a pretensão de esgotar este assunto e apresentar uma conclusão final, são apresentadas pesquisas que apontam para a necessidade e a importância da pesquisa qualitativa, uma vez que auxilia ao pesquisador uma melhor compreensão da natureza complexa do mundo social em que vivemos. Segundo Santana e Gomes (2007, após análise da discussão de Hegel e Kant, concluem que a razão e a própria epistemologia são construções históricas e evoluem a partir de contradições. O presente artigo está dividido em cinco momentos. Na primeira parte apresenta-se além da introdução a constituição dos objetivos desse ensaio teórico. Na segunda parte apresenta-se uma breve discussão a respeito do conceito de paradigma e o marketing. Na terceira parte apresenta-se uma retrospectiva histórica do marketing e sua evolução de suas escolas a partir dos estudos de Miranda e Arruda (2004. Na quarta parte, são apresentadas as metodologias dos estudos sobre qualidade de serviços e finalmente na quinta parte apresenta-se as considerações finais.

  3. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

    Science.gov (United States)

    Chang, Ying; Wang, Sishuo; Sekimoto, Satoshi; Aerts, Andrea L.; Choi, Cindy; Clum, Alicia; LaButti, Kurt M.; Lindquist, Erika A.; Yee Ngan, Chew; Ohm, Robin A.; Salamov, Asaf A.; Grigoriev, Igor V.; Spatafora, Joseph W.; Berbee, Mary L.

    2015-01-01

    As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant–fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya. PMID:25977457

  4. Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB

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    Papaj Grzegorz

    2003-12-01

    Full Text Available Abstract Background Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe2+ oxygenase superfamily. Results In this article, we report identification and sequence analysis of five human members of the (2OG-Fe2+ oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3 rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. Conclusions We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes.

  5. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae.

    Science.gov (United States)

    Medina, Rafael; Johnson, Matthew; Liu, Yang; Wilding, Nicholas; Hedderson, Terry A; Wickett, Norman; Goffinet, Bernard

    2018-03-01

    Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families.

    Science.gov (United States)

    Streicher, Jeffrey W; Wiens, John J

    2017-09-01

    Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates. © 2017 The Author(s).

  7. Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.

    Science.gov (United States)

    Chang, Ying; Wang, Sishuo; Sekimoto, Satoshi; Aerts, Andrea L; Choi, Cindy; Clum, Alicia; LaButti, Kurt M; Lindquist, Erika A; Yee Ngan, Chew; Ohm, Robin A; Salamov, Asaf A; Grigoriev, Igor V; Spatafora, Joseph W; Berbee, Mary L

    2015-05-14

    As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant-fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae

    Science.gov (United States)

    2013-01-01

    Background Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes. Results Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species. Conclusion This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy

  9. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae.

    Science.gov (United States)

    Wei, Li; Xin, Yi; Wang, Dongmei; Jing, Xiaoyan; Zhou, Qian; Su, Xiaoquan; Jia, Jing; Ning, Kang; Chen, Feng; Hu, Qiang; Xu, Jian

    2013-08-05

    Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes. Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species. This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of

  10. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni

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    Kuehl Jennifer V

    2007-09-01

    Full Text Available Abstract Background Teleost fish have seven paralogous clusters of Hox genes stemming from two complete genome duplications early in vertebrate evolution, and an additional genome duplication during the evolution of ray-finned fish, followed by the secondary loss of one cluster. Gene duplications on the one hand, and the evolution of regulatory sequences on the other, are thought to be among the most important mechanisms for the evolution of new gene functions. Cichlid fish, the largest family of vertebrates with about 2500 species, are famous examples of speciation and morphological diversity. Since this diversity could be based on regulatory changes, we chose to study the coding as well as putative regulatory regions of their Hox clusters within a comparative genomic framework. Results We sequenced and characterized all seven Hox clusters of Astatotilapia burtoni, a haplochromine cichlid fish. Comparative analyses with data from other teleost fish such as zebrafish, two species of pufferfish, stickleback and medaka were performed. We traced losses of genes and microRNAs of Hox clusters, the medaka lineage seems to have lost more microRNAs than the other fish lineages. We found that each teleost genome studied so far has a unique set of Hox genes. The hoxb7a gene was lost independently several times during teleost evolution, the most recent event being within the radiation of East African cichlid fish. The conserved non-coding sequences (CNS encompass a surprisingly large part of the clusters, especially in the HoxAa, HoxCa, and HoxDa clusters. Across all clusters, we observe a trend towards an increased content of CNS towards the anterior end. Conclusion The gene content of Hox clusters in teleost fishes is more variable than expected, with each species studied so far having a different set. Although the highest loss rate of Hox genes occurred immediately after whole genome duplications, our analyses showed that gene loss continued and is

  11. Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales.

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    Hafiz Sohail Naushad

    Full Text Available The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1-3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as

  12. A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens.

    Science.gov (United States)

    Katz, Lee S; Griswold, Taylor; Williams-Newkirk, Amanda J; Wagner, Darlene; Petkau, Aaron; Sieffert, Cameron; Van Domselaar, Gary; Deng, Xiangyu; Carleton, Heather A

    2017-01-01

    Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States agencies responsible for food safety including the CDC, FDA, and USDA, have been performing whole-genome sequencing (WGS) on all Listeria monocytogenes found in clinical, food, and environmental samples. Each year, more genomes of other foodborne pathogens such as Escherichia coli, Campylobacter jejuni , and Salmonella enterica are being sequenced. Comparing thousands of genomes across an entire species requires a fast method with coarse resolution; however, capturing the fine details of highly related isolates requires a computationally heavy and sophisticated algorithm. Most L. monocytogenes investigations employing WGS depend on being able to identify an outbreak clade whose inter-genomic distances are less than an empirically determined threshold. When the difference between a few single nucleotide polymorphisms (SNPs) can help distinguish between genomes that are likely outbreak-associated and those that are less likely to be associated, we require a fine-resolution method. To achieve this level of resolution, we have developed Lyve-SET, a high-quality SNP pipeline. We evaluated Lyve-SET by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios. To compare these pipelines, several distance and phylogeny-based comparison methods were applied, which collectively showed that multiple pipelines were able to identify most outbreak clusters and strains. Currently in the US PulseNet system, whole genome multi-locus sequence typing (wgMLST) is the preferred primary method for foodborne WGS cluster detection and outbreak investigation due to its ability to name standardized

  13. Base documentaire sur les artisanats gallo-romains en Lyonnaise et dans les cités du nord et de l’est de l’Aquitaine : Corpus de données. Présentation Documentary base on the Gallo-Roman craft industries in the Lyonnaise region and the cities of North and East Aquitaine: Data base – presentation

    Directory of Open Access Journals (Sweden)

    Alain Ferdière

    2009-05-01

    Full Text Available Un important corpus de tout type d’artisanat pour la période romaine a été constitué et est ici accessible en lien : il concerne l’ensemble de la province romaine de Lyonnaise (du Finistère au Lyonnais, ainsi que les cités du nord et de l’est de la grande Aquitaine, des Pictons à l’ouest au Gabales au sud-est. Ce corpus examine, par type d’artisanat, essentiellement les contextes (types de sites, chronologie, et non les aspects techniques ou typologiques concernant ces artisanats.An important body of all types of craft industries has been built up for the Roman period and is accessible here in context: it concerns the whole of the Lyonnaise Roman province (from Finistère to Lyonnais as well as the cities of the north and of greater Aquitaine, from the Pictons to the west to the Gabales to the south-east. This body essentially examines for each type of craft industry the contexts (type of site, chronology and not the technical aspects or typologies concerning the craft industries.

  14. La estética figural en la última escritura y trabajos visuales de Enrique Lihn

    OpenAIRE

    Juan Zapata Gacitúa; Mariela Fuentes Leal

    2015-01-01

    En este artículo analizo la última producción creativa de Enrique Lihn; por una parte, la que está vinculada con su poesía y, por otra parte, la relacionada con sus trabajos visuales. Ambas variantes de su trabajo están en una estrecha relación hacia el final de su vida, lo cual es posible demostrar desde la estética figural de Jean-Francois Lyotard y sobre la base de la crítica que ha estudiado la etapa final de la vida y de la obra del creador chileno.

  15. MELOGEN: an EST database for melon functional genomics.

    Science.gov (United States)

    Gonzalez-Ibeas, Daniel; Blanca, José; Roig, Cristina; González-To, Mireia; Picó, Belén; Truniger, Verónica; Gómez, Pedro; Deleu, Wim; Caño-Delgado, Ana; Arús, Pere; Nuez, Fernando; Garcia-Mas, Jordi; Puigdomènech, Pere; Aranda, Miguel A

    2007-09-03

    Melon (Cucumis melo L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions. We determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs) and 10,614 unclustered sequences (singletons). Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs) and 356 single nucleotide polymorphisms (SNPs) were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs) in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes. The collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN) which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of sequences constitutes also the basis for an oligo-based

  16. MELOGEN: an EST database for melon functional genomics

    Directory of Open Access Journals (Sweden)

    Puigdomènech Pere

    2007-09-01

    Full Text Available Abstract Background Melon (Cucumis melo L. is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs from eight normalized cDNA libraries from different tissues in different physiological conditions. Results We determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs and 10,614 unclustered sequences (singletons. Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs and 356 single nucleotide polymorphisms (SNPs were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes. Conclusion The collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of

  17. Umidade de equilíbrio de café cereja descascado baseadas em métodos estático e dinâmico Equilibrium moisture contents for peeled coffee cherry based on static and dynamic methods

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    José D. Henao

    2009-08-01

    Full Text Available Construíram-se as isotermas de dessorção de grãos da espécie Café Arábica (Coffea arábica L., da cultivar Novo Mundo-Acaiá, para as temperaturas de 50 e 73 °C e teores de mucilagem residual de 16,1 e 52,7%; posteriormente, oito modelos matemáticos de sorção de produtos higroscópicos foram ajustados aos dados experimentais (BET, BET Linear, GAB, Halsey, Halsey Modificado, Langmuir, Oswin e Peleg, com a finalidade de se obter seus coeficientes. A escolha do melhor ajuste se deu em função da avaliação do coeficiente de determinação (R², do desvio relativo médio (DRM, da tendência de distribuição dos resíduos provenientes dos ajustes dos modelos e do desvio padrão da estimativa. As isotermas de dessorção para temperatura de 50°C e teores de mucilagem residual de 16,1 e 52,7% podem ser representadas pelos modelos Peleg, Halsey Modificado, GAB e Oswin. Para a temperatura de 73°C, o modelo GAB não representa bem os dados experimentais, sendo que os modelos Peleg e Halsey Modificado indicam o melhor desempenho. Com vistas à estimativa das umidades de equilíbrio dinâmicas, a equação proposta por Fioreze mostrou-se altamente satisfatória.The desorption isotherms for 50 and 73 °C and residual mucilage content of 16.1 and 52.7% in Arabica Coffee (Coffea arábica L., cv Novo Mundo-Acaiá, were built. After this, eight mathematical models (BET, BET Linear, GAB, Halsey, Halsey Modified, Langmuir, Oswin e Peleg for desorption for hygroscopic products were adjusted to the experimental data for obtaining the coefficients of the models. The choice of the best adjustment was based on the analysis of the following parameters: determination coefficient (R², relative average deviation, residual distribution tendency and standard deviation of the estimation. The desorption isotherms at 50 °C for cherry coffee with 16.1 and 52.7% residual mucilage contents could be represented by Peleg, Modified Halsey, GAB e Oswin models. At 73

  18. Punta del Este terrane : a better knowledge

    International Nuclear Information System (INIS)

    Preciozzi, F.; Sanchez Bettucci, L; Basei, M.

    2002-01-01

    Field Punta del Este (TPE) is constituted by a series of gneisses and migmatites formed in the range of 1000 and 900 Ma, and have been intensely reworked during Rio Doce orogeny (ca. 600-500 Ma). This cortical segment represents high-grade metamorphic terrain, correlatable with complex gneiss Southwest Africa, particularly with Kibariáno Belt - Namaqualanos recognized in the southwestern portion of Africa (Namibia). U-Pb zircon ages in tonalite granitoids indicate values ​​between 1000 and 900 Ma and were interpreted as indicating the time of generation of these rocks. This should also be the age of high-grade metamorphism that affected a large part of the gneissic rocks of the region. Moreover, the anatectic related mobilized leucosomes ages of migmatites gave ca. 520-540 Ma, indicating that the metamorphic conditions (overlapping) during the Rio Doce orogeny reached at least the amphibolite facies. The metasedimentary cover TPE occurs in the vicinity of the towns of La Paloma Rocha. These are represented by a siliciclastic metasedimentary sequence represented by Rocha Formation. Despite the poly phase deformation and low grade metamorphism affecting this training, primary structures are common such as stratification plano-parallel, cross-bedding, hummock y and massive levels with gradational stratification

  19. APOSENTADORIA: como professores vivenciam este momento?

    Directory of Open Access Journals (Sweden)

    Cristiane Nervis Conrado Machado

    2017-05-01

    Full Text Available O presente artigo buscou compreender as implicações que a aposentadoria causa na vida de professores, levando em conta o significado que a aposentadoria representa à estes, considerando os pontos de maior mudança após a aposentadoria, bem como os aspectos positivos e negativos causados pela aposentadoria na percepção dos sujeitos da pesquisa. Para tanto, foi realizada uma pesquisa qualitativa caracterizada como exploratória e descritiva com professores aposentados por mais de dois anos, com idade entre 58 e 66 anos, através de entrevistas individuais, com roteiros semiestruturados. A análise dos dados foi por meio da análise de conteúdo de Bardin (2011. Entre os principais resultados, destaca-se o significado de “liberdade” que a aposentadoria representa, a rotina como maior mudança e flexibilidade de horários dentre os pontos positivos e a falta dos alunos como aspecto negativo, contudo, pode-se perceber que a aposentadoria possibilitou e contribuiu para que os professores pudessem desfrutar de momentos de lazer, dedicando cuidado à família e realizando seus anseios e vontades.

  20. Distribution of DNA repair-related ESTs in sugarcane

    Directory of Open Access Journals (Sweden)

    W.C. Lima

    2001-12-01

    Full Text Available DNA repair pathways are necessary to maintain the proper genomic stability and ensure the survival of the organism, protecting it against the damaging effects of endogenous and exogenous agents. In this work, we made an analysis of the expression patterns of DNA repair-related genes in sugarcane, by determining the EST (expressed sequence tags distribution in the different cDNA libraries of the SUCEST transcriptome project. Three different pathways - photoreactivation, base excision repair and nucleotide excision repair - were investigated by employing known DNA repair proteins as probes to identify homologous ESTs in sugarcane, by means of computer similarity search. The results showed that DNA repair genes may have differential expressions in tissues, depending on the pathway studied. These in silico data provide important clues on the potential variation of gene expression, to be confirmed by direct biochemical analysis.As vias de reparo de DNA são requeridas para manter a necessária estabilidade genômica e garantir a sobrevivência do organismo, frente aos efeitos deletérios causados por fatores endógenos e exógenos. Neste trabalho, realizamos a análise dos padrões de expressão dos genes de reparo de DNA encontrados na cana-de-açúcar, pela determinação da distribuição de ESTs nas diferentes bibliotecas de cDNA no projeto de transcriptoma SUCEST. Três vias de reparo - fotorreativação, reparo por excisão de bases e reparo por excisão de nucleotídeos - foram estudadas através do uso de proteínas de reparo como sondas para identificação de ESTs homólogos em cana-de-açúcar, com base na procura computacional de similaridade. Os resultados indicam que os genes de reparo de DNA possuem uma expressão diferencial nos tecidos, dependendo da via de reparo analisada. Esses dados in silico fornecem importantes indícios da expressão diferencial, a qual deve ser confirmada por análises bioquímicas diretas.

  1. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    age groups, with 37 remaining loci unmapped. The total length of the transcriptome linkage map was 1938.72cM. (table 2; figure 1). The longest linkage group was 132.74 cM with 15 loci (LG05/Chr05), while the shortest linkage group was 2.33cM with two loci (LG31/Chr25); generally, the average length of a linkage group ...

  2. Kohvik-restoran C'est La Vie = Cafe-restaurant C'est La Vie

    Index Scriptorium Estoniae

    2008-01-01

    Kohvik-restorani C'est La Vie (Suur-Karja 5, Tallinn) sisekujundusest. Sisearhitekt: Maile Grünberg, kes kavandas ka valdavalt mööbli. Laevalgusti disainis Tõnis Vellama. Skulptuuride (koopiad) autor on keraamik Ülle Rajasalu. Maile Grünbergist, tema viimased tööd. Keldrikorruse ja I korruse plaan, 8 värv. vaadet, foto M. Grünbergist

  3. El nuevo regionalismo en el Este de Asia El nuevo regionalismo en el Este de Asia

    Directory of Open Access Journals (Sweden)

    Adriana Roldán Pérez

    2008-12-01

    Full Text Available Las ideas de un nuevo regionalismo surgen en el Este de Asia a finales de losaños noventa como respuesta al cambiante entorno económico mundial; estorepresenta un quiebre en la fuerte tendencia multilateralista que ha predominadohistóricamente en la región. El siguiente trabajo pretende analizar cuáles son losprincipales impedimentos para la creación de un regionalismo en el Este de Asia,qué factores están motivando un nuevo regionalismo allí y cuáles son las iniciativasregionalistas de mayor relevancia.The ideas of a new regionalism arose in East Asia in the late 90s as a response to the world’s new economic scenario. This situation sets up a framework that contrasts with the strong multilateral tendencies which have historically prevailed in the region. This work aims to analyze the obstacles for the creation of a new regionalism in East Asia, the factors motivating it, and the most relevant regionalist initiatives.

  4. Construction of full-length cDNA library and development of EST-derived simple sequence repeat (EST-SSR) markers in Senecio scandens.

    Science.gov (United States)

    Qian, Gang; Ping, Junjiao; Lu, Jian; Zhang, Zhen; Wang, Lei; Xu, Delin

    2014-12-01

    Senecio scandens Buch.-Ham. ex D. Don (Compositae) is a crucial source of Chinese traditional medicine with antibacterial properties. We constructed a cDNA library and obtained expressed sequence tags (ESTs) to show the distribution of gene ontology annotations for mRNAs, using an individual plant with superior antibacterial characteristics. Analysis of comparative genomics indicates that the putative uncharacterized proteins (21.07%) might be derived from "molecular function unknown" clones or rare transcripts. Furthermore, the Compositae had high cross-species transferability of EST-derived simple sequence repeats (EST-SSR), based on valid amplifications of 206 primer pairs developed from the newly assembled expressed sequence tag sequences in Artemisia annua L. Among those EST-SSR markers, 52 primers showed polymorphic amplifications between individuals with contrasting diverse antibacterial traits. Our sequence data and molecular markers will be cost-effective tools for further studies such as genome annotation, molecular breeding, and novel transcript profiles within Compositae species.

  5. Analysis of expressed sequence tags (ESTs) from a normalized cDNA library and isolation of EST simple sequence repeats from the invasive cotton mealybug Phenacoccus solenopsis.

    Science.gov (United States)

    Li, Hui; Lang, Kun-Ling; Fu, Hai-Bin; Shen, Chang-Peng; Wan, Fang-Hao; Chu, Dong

    2015-12-01

    The cotton mealybug, Phenacoccus solenopsis Tinsley, is a serious and invasive pest. At present, genetic resources for studying P. solenopsis are limited, and this negatively affects genetic research on the organism and, consequently, translational work to improve management of this pest. In the present study, expressed sequence tags (ESTs) were analyzed from a normalized complementary DNA library of P. solenopsis. In addition, EST-derived microsatellite loci (also known as simple sequence repeats or SSRs) were isolated and characterized. A total of 1107 high-quality ESTs were acquired from the library. Clustering and assembly analysis resulted in 785 unigenes, which were classified functionally into 23 categories according to the Gene Ontology database. Seven EST-based SSR markers were developed in this study and are expected to be useful in characterizing how this invasive species was introduced, as well as providing insights into its genetic microevolution. © 2014 Institute of Zoology, Chinese Academy of Sciences.

  6. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

  7. Algunas observaciones sobre el "control del estímulo"

    OpenAIRE

    Ribes Iñesta,Emilio

    2011-01-01

    Se reflexiona sobre el concepto de control del estímulo en la teoría del condicionamiento operante y, en especial, sobre el concepto de estímulo discriminativo. Para ello se señalan los problemas lógicos y definicionales que reviste el uso del concepto de estímulo en general y el de estímulo discriminativo en particular. Se reseñan diversos experimentos del autor para mostrar la incapacidad del concepto de estímulo discriminativo para dar cuenta de una serie de datos que muestran las insufici...

  8. MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda.

    Science.gov (United States)

    Campbell, Lahcen I; Rota-Stabelli, Omar; Edgecombe, Gregory D; Marchioro, Trevor; Longhorn, Stuart J; Telford, Maximilian J; Philippe, Hervé; Rebecchi, Lorena; Peterson, Kevin J; Pisani, Davide

    2011-09-20

    Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations--comparisons of model fit, signal dissection, and taxonomic pruning--we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.

  9. Le développement durable : est-il possible? est-il mesurable?

    Directory of Open Access Journals (Sweden)

    Belmokaddem MOSTEFA

    2011-04-01

    Full Text Available A la première question, nous répondrons bien sûr, par l’affirmative puisque tous les pays sont engagés dans une nouvelle approche du développement qui ne consiste pas seulement à produire le plus de biens et au moindre coût, afin de vendre beaucoup et réaliser de grands profits. C’était la vision en vigueur dans toutes les techniques de gestion mais on s’est rendu compte que cette production, supposée au moindre coût, était en fait, souvent d’un coût exorbitant, relativement aux dégâts occasionnés dans l’environnement et dans les nuisances occasionnées à la santé de l’homme et à sa tranquillité. Il est temps d’inclure d’autres variables dans le calcul du prix de revient tout en revoyant certaines techniques de production trop salissantes, dangereuses ou grosses consommatrices d’énergie. Nous répondrons aussi par la négative quand on pense qu’au niveau micro économique, les comportements sont édictés par les satisfactions immédiates et les maximisations des profits. Ces comportements qui ne s’intéressent qu’aux résultats à court terme, ne s’intègrent pas facilement dans les plans de développement visant les équilibres macro économiques à long terme.A la deuxième question, nous dirons qu’il y a effectivement des indicateurs pour tester les niveaux de qualité dans l’éducation, la santé, les ressources naturelles... et les gains tirés au niveau social mais les calculs économiques qui déterminent la rentabilité des projets, les profits espérés, les risques financiers encourus ne sont pas toujours en rapport avec les efforts pour réaliser le développement durable qui, eux dépassent la simple notion d’efficacité et de satisfaction. Quand on pense aux générations futures, ce n’est pas seulement en termes de durée dans le temps mais aussi dans la manière d’apprécier les gains espérés.Notre recherche repose sur ces questions qui minent bien des efforts alors qu

  10. EVER-EST: a virtual research environment for Earth Sciences

    Science.gov (United States)

    Marelli, Fulvio; Albani, Mirko; Glaves, Helen

    2016-04-01

    scientific workflows. The EVER-EST data processing infrastructure will be based on a Cloud Computing approach, in which new applications can be integrated using "virtual machines" that have their own specifications (disk size, processor speed, operating system etc.) and run on shared private (physical deployment over local hardware) or commercial Cloud infrastructures. The EVER-EST e-infrastructure will be validated by four virtual research communities (VRC) covering different multidisciplinary Earth Science domains including: ocean monitoring, natural hazards, land monitoring and risk management (volcanoes and seismicity). Each VRC will use the virtual research environment according to its own specific requirements for data, software, best practice and community engagement. This user-centric approach will allow an assessment to be made of the capability for the proposed solution to satisfy the heterogeneous needs of a variety of Earth Science communities for more effective collaboration, and higher efficiency and creativity in research. EVER-EST is funded by the European Commission's H2020 for three years starting in October 2015. The project is led by the European Space Agency (ESA), involves some of the major European Earth Science data providers/users including NERC, DLR, INGV, CNR and SatCEN.

  11. Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour.

    Science.gov (United States)

    Romiguier, Jonathan; Rolland, Jonathan; Morandin, Claire; Keller, Laurent

    2018-03-28

    The ants of the Formica genus are classical model species in evolutionary biology. In particular, Darwin used Formica as model species to better understand the evolution of slave-making, a parasitic behaviour where workers of another species are stolen to exploit their workforce. In his book "On the Origin of Species" (1859), Darwin first hypothesized that slave-making behaviour in Formica evolved in incremental steps from a free-living ancestor. The absence of a well-resolved phylogenetic tree of the genus prevent an assessment of whether relationships among Formica subgenera are compatible with this scenario. In this study, we resolve the relationships among the 4 palearctic Formica subgenera (Formica str. s., Coptoformica, Raptiformica and Serviformica) using a phylogenomic dataset of 945 genes for 16 species. We provide a reference tree resolving the relationships among the main Formica subgenera with high bootstrap supports. The branching order of our tree suggests that the free-living lifestyle is ancestral in the Formica genus and that parasitic colony founding could have evolved a single time, probably acting as a pre-adaptation to slave-making behaviour. This phylogenetic tree provides a solid backbone for future evolutionary studies in the Formica genus and slave-making behaviour.

  12. Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis

    Directory of Open Access Journals (Sweden)

    Deleury Emeline

    2009-07-01

    Full Text Available Abstract Background Coral reef ecosystems are renowned for their diversity and beauty. Their immense ecological success is due to a symbiotic association between cnidarian hosts and unicellular dinoflagellate algae, known as zooxanthellae. These algae are photosynthetic and the cnidarian-zooxanthellae association is based on nutritional exchanges. Maintenance of such an intimate cellular partnership involves many crosstalks between the partners. To better characterize symbiotic relationships between a cnidarian host and its dinoflagellate symbionts, we conducted a large-scale EST study on a symbiotic sea anemone, Anemonia viridis, in which the two tissue layers (epiderm and gastroderm can be easily separated. Results A single cDNA library was constructed from symbiotic tissue of sea anemones A. viridis in various environmental conditions (both normal and stressed. We generated 39,939 high quality ESTs, which were assembled into 14,504 unique sequences (UniSeqs. Sequences were analysed and sorted according to their putative origin (animal, algal or bacterial. We identified many new repeated elements in the 3'UTR of most animal genes, suggesting that these elements potentially have a biological role, especially with respect to gene expression regulation. We identified genes of animal origin that have no homolog in the non-symbiotic starlet sea anemone Nematostella vectensis genome, but in other symbiotic cnidarians, and may therefore be involved in the symbiosis relationship in A. viridis. Comparison of protein domain occurrence in A. viridis with that in N. vectensis demonstrated an increase in abundance of some molecular functions, such as protein binding or antioxidant activity, suggesting that these functions are essential for the symbiotic state and may be specific adaptations. Conclusion This large dataset of sequences provides a valuable resource for future studies on symbiotic interactions in Cnidaria. The comparison with the closest

  13. ESTIMA, a tool for EST management in a multi-project environment.

    Science.gov (United States)

    Kumar, Charu G; LeDuc, Richard; Gong, George; Roinishivili, Levan; Lewin, Harris A; Liu, Lei

    2004-11-04

    Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http

  14. ESTIMA, a tool for EST management in a multi-project environment

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2004-11-01

    Full Text Available Abstract Background Single-pass, partial sequencing of complementary DNA (cDNA libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs, and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. Results A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA, has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera, cattle (Bos taurus, songbird (Taeniopygia guttata, corn rootworm (Diabrotica vergifera, catfish (Ictalurus punctatus, Ictalurus furcatus, and apple (Malus x domestica. The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. Conclusions The scripts used to create the ESTIMA interface are freely available to academic users in

  15. Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages

    Directory of Open Access Journals (Sweden)

    Zhao Xuechun

    2008-03-01

    Full Text Available Abstract Background Tall fescue (Festuca arundinacea Schreb is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence tag (EST database developed from nine cDNA libraries representing tissues from different plant organs, developmental stages, and abiotic stress factors. The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported. Results A total of 41,516 ESTs were generated from nine cDNA libraries of tall fescue representing tissues from different plant organs, developmental stages, and abiotic stress conditions. The Festuca Gene Index (FaGI has been established. To date, this represents the first publicly available tall fescue EST database. In silico gene expression studies using these ESTs were performed to understand stress responses in tall fescue. A large number of ESTs of known stress response gene were identified from stressed tissue libraries. These ESTs represent gene homologues of heat-shock and oxidative stress proteins, and various transcription factor protein families. Highly expressed ESTs representing genes of unknown functions were also identified in the stressed tissue libraries. Conclusion FaGI provides a useful resource for genomics studies of tall fescue and other closely related forage and turf grass species. Comparative genomic analyses between tall fescue and other grass species, including ryegrasses (Lolium sp., meadow fescue (F. pratensis and tetraploid fescue (F. arundinacea var glaucescens will benefit from this database. These ESTs are an excellent resource for the development of simple sequence repeat (SSR and single nucleotide polymorphism (SNP PCR-based molecular markers.

  16. [Development of new SSR markers from EST of SSH cDNA libraries on rose fragrance].

    Science.gov (United States)

    Yan, Hui-Jun; Zhang, Hao; Xie, Ji-Rong; Li, Shu-Fa; Jian, Hong-Ying; Qiu, Xian-Qin; Wang, Qi-Gang; Wang, Ji-Hua; Tang, Kai-Xue

    2009-09-01

    The new SSR markers of rose related fragrance were developed based on the SSH cDNA libraries of rose floral scent mutant. In this study, 10 EST-SSRs (2.6%) from 391 ESTs in the libraries were identified. Six EST-SSRs primers were designed to sequence flanking SSRs. The primer pairs designed were screened on the wild-type Jinyindao, which has flowers full of pleasant scent, and the mutant-type Wangriqinghuai without perceivable floral scent. Five primer pairs were amplified effectively in Jinyindao and Wangriqinghuai, and 3 were polymorphic between Jinyindao and Wangriqinghuai. Eighteen rose cultivars including fragrant roses and nonfragrant roses were identified by the five prime pairs. These results proved that EST-SSR markers are effective markers to identify the polymorphism of the rose.

  17. EST data - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...st.zip File URL: ftp://ftp.biosciencedbc.jp/archive/red/LATEST/red_est.zip File size: 629 KB Simple search U...ase Database Description Download License Update History of This Database Site Policy | Contact Us EST data - RED | LSDB Archive ...

  18. Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus.

    Science.gov (United States)

    Teng, Jade L L; Huang, Yi; Tse, Herman; Chen, Jonathan H K; Tang, Ying; Lau, Susanna K P; Woo, Patrick C Y

    2014-10-20

    Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the "sanguinis group." As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the "mitis group." On the basis of the findings, we propose a novel group, named "sinensis group," to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Two EST-derived marker systems for cultivar identification in tree peony.

    Science.gov (United States)

    Zhang, J J; Shu, Q Y; Liu, Z A; Ren, H X; Wang, L S; De Keyser, E

    2012-02-01

    Tree peony (Paeonia suffruticosa Andrews), a woody deciduous shrub, belongs to the section Moutan DC. in the genus of Paeonia of the Paeoniaceae family. To increase the efficiency of breeding, two EST-derived marker systems were developed based on a tree peony expressed sequence tag (EST) database. Using target region amplification polymorphism (TRAP), 19 of 39 primer pairs showed good amplification for 56 accessions with amplicons ranging from 120 to 3,000 bp long, among which 99.3% were polymorphic. In contrast, 7 of 21 primer pairs demonstrated adequate amplification with clear bands for simple sequence repeats (SSRs) developed from ESTs, and a total of 33 alleles were found in 56 accessions. The similarity matrices generated by TRAP and EST-SSR markers were compared, and the Mantel test (r = 0.57778, P = 0.0020) showed a moderate correlation between the two types of molecular markers. TRAP markers were suitable for DNA fingerprinting and EST-SSR markers were more appropriate for discriminating synonyms (the same cultivars with different names due to limited information exchanged among different geographic areas). The two sets of EST-derived markers will be used further for genetic linkage map construction and quantitative trait locus detection in tree peony.

  20. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis for Crossbreeding

    Directory of Open Access Journals (Sweden)

    Yueting Dai

    2017-11-01

    Full Text Available Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu. However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotus eryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.

  1. Estética en prótesis removibles

    OpenAIRE

    LVM Lucas; FH Gennari; Marcello Cohello Goiato; DM Dos Santos; A Moreno; RM Falcón-Antenucci

    2010-01-01

    La estética actualmente recibe una importante consideración en el contexto social. Una sonrisa atractiva es aspiración de la mayoría de los pacientes que precisan tratamiento protésico. Los implantes propiciaron una mejoría significativa, con relación a las prótesis removibles, debido a su funcionalidad. El objetivo de este estudio fue explorar en la literatura científica moderna, a fin de hallar aspectos relacionados con la estética en la rehabilitación mediante prótesis removibles. Fueron e...

  2. Esferas estáticas en relatividad general

    Directory of Open Access Journals (Sweden)

    J. Ospino

    2007-01-01

    Full Text Available Recientemente K. Lake ha presentado un algoritmo que permit e obtener todas las soluciones estáticas de las ecuaciones de Einstein, para el caso de un fluido perfecto con simetría esférica, a partir de u na sola función dada. Este algoritmo se extiende al caso de un fluido localmen te anisótropo. Como era de esperar, este nuevo formalismo requiere del cono cimiento de dos funciones en lugar de una. Para ilustrar el método se dedu cen de nuevo algunas soluciones conocidas.

  3. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes.

    Science.gov (United States)

    Brenner, Eric D; Katari, Manpreet S; Stevenson, Dennis W; Rudd, Stephen A; Douglas, Andrew W; Moss, Walter N; Twigg, Richard W; Runko, Suzan J; Stellari, Giulia M; McCombie, W R; Coruzzi, Gloria M

    2005-10-15

    Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters found in the early, extinct seed plants and extant cycads. To establish a molecular base to understand the evolution of seeds and pollen, we created a cDNA library and EST dataset from the reproductive structures of male (microsporangiate), female (megasporangiate), and vegetative organs (leaves) of Ginkgo biloba. RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6,434 ESTs were generated. These 6,434 ESTs from Ginkgo biloba were clustered into 3,830 unigenes. A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis, and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants--many with multiple matches to genes in non-angiosperm plants. Conversely, another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development, including MADS box genes as well as post-transcriptional regulators. Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes. We also note here the presence of ESTs in G. biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads. Our analysis of an EST dataset from G. biloba revealed genes potentially unique to gymnosperms. Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms. Other Ginkgo ESTs are similar to developmental regulators in higher plants. This work sets the stage for future studies on Ginkgo to better understand seed and pollen evolution, and to resolve the ambiguous phylogenetic

  4. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia.

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    Jonathan J Fong

    Full Text Available In resolving the vertebrate tree of life, two fundamental questions remain: 1 what is the phylogenetic position of turtles within amniotes, and 2 what are the relationships between the three major lissamphibian (extant amphibian groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.

  5. Characterization and development of EST-SSR markers in sweet potato (Ipomoea batatas (L.) Lam).

    Science.gov (United States)

    Kim, Jin-Hee; Kim, Jun-Hoi; Jo, Won-Sam; Ham, Jeong-Gwan; Chung, Il Kyung; Kim, Kyung-Min

    2016-12-01

    In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.

  6. Rapid EST isolation from chromosome 1R of rye

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    Chen Yu-Hong

    2008-03-01

    Full Text Available Abstract Background To obtain important expressed sequence tags (ESTs located on specific chromosomes is currently difficult. Construction of single-chromosome EST library could be an efficient strategy to isolate important ESTs located on specific chromosomes. In this research we developed a method to rapidly isolate ESTs from chromosome 1R of rye by combining the techniques of chromosome microdissection with hybrid specific amplification (HSA. Results Chromosome 1R was isolated by a glass needle and digested with proteinase K (PK. The DNA of chromosome 1R was amplified by two rounds of PCR using a degenerated oligonucleotide 6-MW sequence with a Sau3AI digestion site as the primer. The PCR product was digested with Sau3AI and linked with adaptor HSA1, then hybridized with the Sau3AI digested cDNA with adaptor HSA2 of rye leaves with and without salicylic acid (SA treatment, respectively. The hybridized DNA fragments were recovered by the HSA method and cloned into pMD18-T vector. The cloned inserts were released by PCR using the partial sequences in HSA1 and HSA2 as the primers and then sequenced. Of the 94 ESTs obtained and analyzed, 6 were known sequences located on rye chromosome 1R or on homologous group 1 chromosomes of wheat; all of them were highly homologous with ESTs of wheat, barley and/or other plants in Gramineae, some of which were induced by abiotic or biotic stresses. Isolated in this research were 22 ESTs with unknown functions, probably representing some new genes on rye chromosome 1R. Conclusion We developed a new method to rapidly clone chromosome-specific ESTs from chromosome 1R of rye. The information reported here should be useful for cloning and investigating the new genes found on chromosome 1R.

  7. Aproximaciones a una estética de lo americano

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    María del Milagro Casalla

    2010-01-01

    Full Text Available El legado filosófico que nos ha dejado Rodolfo Kusch tiene cada vez más presencia y valor en este largo itinerario de descubrirnos como americanos. La pasión de este pensador por la América profunda es una fuente de ins- piración para quienes creemos que vivir en América no es simplemente un episodio geográfico sino un horizonte desde y a partir del cual construimos nuestra identidad. En este trabajo se pretende recrear sus consideracio - nes estéticas recogidas en su ensayo “Anotaciones para una estética de lo americano”, escrito en el año 1955. Aunque se trata de uno de los primeros escritos de Rodolfo Kusch, en el mismo se encuentran presentes numerosos conceptos que luego serán tematizados extensamente a lo largo de toda su obra. Considero que el abordaje a sus consideraciones estéticas no ha sido tan frecuentado como sí otros aspectos de su pensamiento (ser-estar, geocultura, símbolo y religión, etc.. Por ello, creo que este trabajo puede constituir una orientación preeliminar para futuras interpretaciones y, a la vez, ser un humilde homenaje a su filosofía, que, a lo largo de los años, sigue estimulando a antiguas y nuevas generaciones de pensadores dedicados a la filosofía latinoamericana.

  8. Wheat EST resources for functional genomics of abiotic stress

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    Links Matthew G

    2006-06-01

    Full Text Available Abstract Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets. Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in

  9. activismo y estéticas en experimento

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    Omar Rincón

    2005-01-01

    Full Text Available Podemos comunicarlo todo: tenemos las tecnologías de la comunicación cada vez más cerca; pero no podemos contar nada, porque no tenemos nada qué decir, ni sabemos cómo decirlo. Hay que inventarlo todo, intervenir de nuevo la sociedad desde la comunicación. Es necesario convertir los medios en experiencia estética, social y política. ¿Cómo? Usando a las tecnologías para el activismo y el experimento; recurriendo a los llamado retro, porque no es lo más actual, lo más mercado, como experiencia de inspiración y emoción. Hay que volver a las estéticas, a los modos de narrar y a las historias que están inscritas en nuestras identidades locales; en nuestras sensibilidades femeninas, juveniles o sexuales; en nuestras tradiciones étnicas, o en nuestros modos urbanos. Sólo basta una minicámara para inventar el universo. En este ensayo se realiza un alegato contra los universos estético-narrativopolíticos construidos por la máquina televisiva y la homogeneidad del mercado. En este texto se argumenta a favor del activismo comunicativo, de la exploración tecnológica y de la inspiración étnica como estrategias para generar una mayor conciencia sobre el valor social de la comunicación, la intervención estético-narrativa de la sociedad y la importancia política de los medios de la gente.

  10. SEffEst: Effort estimation in software projects using fuzzy logic and neural networks

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    Israel

    2012-08-01

    Full Text Available Academia and practitioners confirm that software project effort prediction is crucial for an accurate software project management. However, software development effort estimation is uncertain by nature. Literature has developed methods to improve estimation correctness, using artificial intelligence techniques in many cases. Following this path, this paper presents SEffEst, a framework based on fuzzy logic and neural networks designed to increase effort estimation accuracy on software development projects. Trained using ISBSG data, SEffEst presents remarkable results in terms of prediction accuracy.

  11. El leviatán estético

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    Jorge Peñuela

    2011-05-01

    Full Text Available En este ensayo exploro algunos argumentos de Hannah Arendt, con el fin de mostrar las razones que explican el odio que se manifestaba en las discusiones artísticas de comienzos del siglo XX, odio que persiste aún en muchos escenarios artísticos actuales. Con Arendt sostengo que este fenómeno no está superado, porque el odio es la herramienta que despliega el Capital, para amalgamar a todos los desheredados que ha creado. Contextualizo en la práctica artística colombiana el siguiente argumento de Arendt: el capitalismo creó una amalgama de frustrados sociales, políticos y estéticos que destruye la esfera pública como lugar para el acontecer de la política, amalgama que denominó populacho. Introduzco la categoría de populacho estético, para hablar del odio que ha animado las prácticas artísticas en Colombia desde 1940.

  12. Construction of EST Database for Comparative Gene Studies of Acanthamoeba

    Science.gov (United States)

    Moon, Eun-Kyung; Kim, Joung-Ok; Xuan, Ying-Hua; Yun, Young-Sun; Kang, Se Won; Lee, Yong Seok; Ahn, Tae-In; Hong, Yeon-Chul; Chung, Dong-Il

    2009-01-01

    The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and amebic keratitis in humans. However, little genomic information of Acanthamoeba has been reported. Here, we constructed Acanthamoeba expressed sequence tags (EST) database (Acanthamoeba EST DB) derived from our 4 kinds of Acanthamoeba cDNA library. The Acanthamoeba EST DB contains 3,897 EST generated from amebae under various conditions of long term in vitro culture, mouse brain passage, or encystation, and downloaded data of Acanthamoeba from National Center for Biotechnology Information (NCBI) and Taxonomically Broad EST Database (TBestDB). The almost reported cDNA/genomic sequences of Acanthamoeba provide stand alone BLAST system with nucleotide (BLAST NT) and amino acid (BLAST AA) sequence database. In BLAST results, each gene links for the significant information including sequence data, gene orthology annotations, relevant references, and a BlastX result. This is the first attempt for construction of Acanthamoeba database with genes expressed in diverse conditions. These data were integrated into a database (http://www.amoeba.or.kr). PMID:19488415

  13. Identification and Characterization of MicroRNAs in Macaca fascicularis by EST Analysis

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    Hao Yang

    2012-01-01

    Full Text Available MicroRNAs (miRNAs are small noncoding RNAs which repress gene expression at the posttranscriptional level. In this study, an expressed sequence tag (EST-based combined method was applied for the detection of miRNAs in Macaca fascicularis which is used as a model animal extensively in medical experiments, particularly those involved with neuroscience and disease. Initially, previously known miRNA sequences from metazoans were used to blast with the EST databases of Macaca fascicularis, and then a range of filtering criteria was conducted to remove some pseudo ones. At last a total of 8 novel conserved miRNAs were identified; their functions were further predicted and analyzed. Together, our study provides insight into miRNAs and their functions in Macaca fascicularis, indicating that the EST analysis is an efficient and affordable alternative approach for identifying novel miRNA candidates.

  14. Los saberes del arte. LA experiencia estética en Nietzsche

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    Luis Eduardo Gama

    2008-01-01

    sobre el arte pueda tener al interior de la esfera estética misma: ¿qué es lo específico del arte frente a otras esferas de la acción humana? ¿En qué consiste propiamente la experiencia estética? ¿Qué resulta para el individuo y para la cultura del encuentro con el fenómeno del arte? El presente artículo constituye un primer intento de responder estas cuestiones. Su base de análisis se concentra en El nacimiento de la tragedia, y en menor medida en la fisiología del arte del Crepúsculo de los ídolos. La tesis central que se defiende es que la experiencia estética para Nietzsche es esencialmente una experiencia de conocimiento, de un tipo de saber que da acceso a la verdad.

  15. Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases.

    Science.gov (United States)

    Mata-Montero, Manrique; Shalaby, Nabil; Sheppard, Bradley

    2013-01-01

    Obtaining unique oligos from an EST database is a problem of great importance in bioinformatics, particularly in the discovery of new genes and the mapping of the human genome. Many algorithms have been developed to find unique oligos, many of which are much less time consuming than the traditional brute force approach. An algorithm was presented by Zheng et al. (2004) which finds the solution of the unique oligos search problem efficiently. We implement this algorithm as well as several new algorithms based on some theorems included in this paper. We demonstrate how, with these new algorithms, we can obtain unique oligos much faster than with previous ones. We parallelize these new algorithms to further improve the time of finding unique oligos. All algorithms are run on ESTs obtained from a Barley EST database.

  16. Le travail social est-il de gauche ?

    OpenAIRE

    Girault, Eloïse

    2011-01-01

    Le sociographe est une revue de recherches en travail social, publiée par différents instituts de formation en travail social et qui entend proposer « un cadre de travail, d'écritures, de lectures et d'échanges pour développer une réflexion sur les méthodes et les pratiques d'intervention ». Dans ce numéro, Le sociographe s'efforce d'apporter des éléments de réponse à la question suivante : « Le travail social est-il de gauche ? ». Cette interrogation est fort légitime dans la mesure où, comm...

  17. Estética afirmativa em Arthur Schopenhauer.

    OpenAIRE

    Bastos, Eduardo Reina

    2012-01-01

    A tradição filosófica caracteriza a filosofia de Arhur Schopenhauer como pessimista como dado acabado e incontornável. Esta dissertação tem como principal objetivo demonstrar que sua parte estética se insere como uma alternativa a esta constatação e demonstrar que existe um grande contraste entre criação e negação. Através de uma reconstrução de sua teoria do conhecimento, a chamada pré-estética, e reconstrução de sua estética, nos alçamos àquela que serve como força apaziguadora da Vontade, ...

  18. Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data.

    Science.gov (United States)

    Zhou, Sun; Ji, Guoli; Liu, Xiaolin; Li, Pei; Moler, James; Karro, John E; Liang, Chun

    2012-05-03

    implemented in the AFST software tool, can be utilized to reveal wet-lab errors such as restriction enzyme cutting abnormities and chimeric EST sequences, detect various data abnormalities embedded in existing Sanger EST datasets, improve the accuracy of identifying and extracting bona fide cDNA inserts from raw ESTs, and therefore greatly benefit downstream EST-based applications.

  19. Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data

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    Zhou Sun

    2012-05-01

    or filtered by AFST. Conclusions cDNA terminal pattern analysis, as implemented in the AFST software tool, can be utilized to reveal wet-lab errors such as restriction enzyme cutting abnormities and chimeric EST sequences, detect various data abnormalities embedded in existing Sanger EST datasets, improve the accuracy of identifying and extracting bona fide cDNA inserts from raw ESTs, and therefore greatly benefit downstream EST-based applications.

  20. SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera

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    Sabourault Cécile

    2006-06-01

    Full Text Available Abstract Background The Lepidoptera Spodoptera frugiperda is a pest which causes widespread economic damage on a variety of crop plants. It is also well known through its famous Sf9 cell line which is used for numerous heterologous protein productions. Species of the Spodoptera genus are used as model for pesticide resistance and to study virus host interactions. A genomic approach is now a critical step for further new developments in biology and pathology of these insects, and the results of ESTs sequencing efforts need to be structured into databases providing an integrated set of tools and informations. Description The ESTs from five independent cDNA libraries, prepared from three different S. frugiperda tissues (hemocytes, midgut and fat body and from the Sf9 cell line, are deposited in the database. These tissues were chosen because of their importance in biological processes such as immune response, development and plant/insect interaction. So far, the SPODOBASE contains 29,325 ESTs, which are cleaned and clustered into non-redundant sets (2294 clusters and 6103 singletons. The SPODOBASE is constructed in such a way that other ESTs from S. frugiperda or other species may be added. User can retrieve information using text searches, pre-formatted queries, query assistant or blast searches. Annotation is provided against NCBI, UNIPROT or Bombyx mori ESTs databases, and with GO-Slim vocabulary. Conclusion The SPODOBASE database provides integrated access to expressed sequence tags (EST from the lepidopteran insect Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of gene families of interest for scientific community. SPODOBASE is available from URL: http://bioweb.ensam.inra.fr/spodobase

  1. Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes

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    Brendel Volker

    2008-02-01

    Full Text Available Abstract Background Although originally thought to be less frequent in plants than in animals, alternative splicing (AS is now known to be widespread in plants. Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt and Lotus japonicus (Lj. Results Based on cognate EST alignments alone, the observed frequency of alternatively spliced genes is lower in Mt (~10%, 1,107 genes and Lj (~3%, 92 genes than in Arabidopsis and rice (both around 20%. However, AS frequencies are comparable in all four species if EST levels are normalized. Intron retention is the most common form of AS in all four plant species (~50%, with slightly lower frequency in legumes compared to Arabidopsis and rice. This differs notably from vertebrates, where exon skipping is most common. To uncover additional AS events, we aligned ESTs from other legume species against the Mt genome sequence. In this way, 248 additional Mt genes were predicted to be alternatively spliced. We also identified 22 AS events completely conserved in two or more plant species. Conclusion This study extends the range of plant taxa shown to have high levels of AS, confirms the importance of intron retention in plants, and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events. The results also indicate that the frequency of AS in plants is comparable to that observed in mammals. Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

  2. Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413

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    Gutiérrez Santiago

    2006-07-01

    Full Text Available Abstract Background The filamentous fungus Trichoderma harzianum is used as biological control agent of several plant-pathogenic fungi. In order to study the genome of this fungus, a functional genomics project called "TrichoEST" was developed to give insights into genes involved in biological control activities using an approach based on the generation of expressed sequence tags (ESTs. Results Eight different cDNA libraries from T. harzianum strain CECT 2413 were constructed. Different growth conditions involving mainly different nutrient conditions and/or stresses were used. We here present the analysis of the 8,710 ESTs generated. A total of 3,478 unique sequences were identified of which 81.4% had sequence similarity with GenBank entries, using the BLASTX algorithm. Using the Gene Ontology hierarchy, we performed the annotation of 51.1% of the unique sequences and compared its distribution among the gene libraries. Additionally, the InterProScan algorithm was used in order to further characterize the sequences. The identification of the putatively secreted proteins was also carried out. Later, based on the EST abundance, we examined the highly expressed genes and a hydrophobin was identified as the gene expressed at the highest level. We compared our collection of ESTs with the previous collections obtained from Trichoderma species and we also compared our sequence set with different complete eukaryotic genomes from several animals, plants and fungi. Accordingly, the presence of similar sequences in different kingdoms was also studied. Conclusion This EST collection and its annotation provide a significant resource for basic and applied research on T. harzianum, a fungus with a high biotechnological interest.

  3. Análisis estático de programas

    OpenAIRE

    Arroyo, Marcelo; Bavera, Francisco; Regis, Germán

    2010-01-01

    En el presente trabajo se describen las líneas de investigación en desarrollo por el grupo de investigación en análisis estático de propiedades de programas. Los integrantes del grupo atacan el problema del análisis de propiedades de programas mediante diferentes enfoques. Algunos trabajan a nivel de modelos mientras que otros lo hacen directamente a nivel de código fuente. Se utilizan técnicas tanto de análisis estático liviano como pesados (basados en demostradores de teoremas o model-ch...

  4. Estéticas de las culturas de ocio

    OpenAIRE

    Sañudo Vélez, Luis Guillermo

    2009-01-01

    El presente trabajo tiene como propósito explorar el significado estético del ocio en la cultura contemporánea. Para cumplir este objetivo ha sido necesario hacer un breve balance de la manera como el concepto de ocio se ha entendido tanto en los escritos de algunos destacados filósofos (Aristóteles, Séneca y Kant) como en los escritos de algunos pensadores sociales modernos (Thorstein Veblen) y contemporáneos (Jean Baudrillard, Erich Weber, Joffre Dumazedier, Gilles Lipovetsky, Vicente Verdú...

  5. Dia mundial da espirometria na ESTeSL

    OpenAIRE

    Dias, Hermínia Brites; Carolino, Elisabete

    2011-01-01

    Objectivos do estudo: associar a ESTeSL e a AC de CPL às comemorações do Dia Mundial da Espirometria promovidas pela Fundação Europeia do Pulmão; realizar o maior número possível de espirometrias; consciencializar a comunidade para o papel da espirometria no diagnóstico precoce da patologia respiratória; colocar a ESTeSL, enquanto entidade formadora de Técnicos de Cardiopneumologia, na primeira linha das iniciativas relacionadas com o estudo espirométrico; identificar possíveis alter...

  6. Evidencias visuales de las nuevas estéticas mestizas

    OpenAIRE

    Andrade Polo, Pedro Gustavo

    2017-01-01

    El presente trabajo, pretende reflexionar y evidenciar, la visualidad que ha tenido la estética de la imagen latinoamericana en su proceso de mestizaje, concentrándose en aquella identidad fragmentaria y poco codificada que se da en los espacios locales y populares .Planteo entonces una actitud que se presenta emancipada de una estética formal. Despojada de la carga que históricamente ha impuesto la “identidad” latinoamericana, se instala libre e irresponsable para crear sus íconos y definici...

  7. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.

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    Yang Jun-Bo

    2010-12-01

    Full Text Available Abstract Background The castor bean (Ricinus communis L., a monotypic species in the spurge family (Euphorbiaceae, 2n = 20, is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85% in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs provide valuable resources to develop gene-associated SSR markers. Results In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly

  8. Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes.

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    Wenjing Tao

    Full Text Available Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (∼ 71132 base pairs for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9-7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.

  9. A estética como factor promotor da aprendizagem

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    Fátima Maria BEZERRA BARBOSA

    2012-02-01

    Full Text Available La reflexión filosófica sobre el arte, lo hermoso, lo bueno, lo verdadero y su capacidad de promover el desarrollo humano es un tema que remonta a Platón en la cultura occidental. Considerando que la educación debe ser entendida como un fenómeno integral, que abarca no sólo las dimensiones intelectuales sino también las dimensiones sensibles, la intuición y el raciocinio, las capacidades imaginativas y creativas, el «saber ser» y el «saber estar» parejas del «conocer» y del «saber hacer», pensamos que es incuestionable la importancia de la estética en el fenómeno educativo. El objetivo de este trabajo es demostrar la importancia de la educación estética como motor fundamental de desarrollo humano y, en este sentido, como catalizador de la motivación y del aprendizaje, para que, a través de la imaginación y de la creatividad, sea posible la innovación en la construcción de vías alternativas para un mundo más humano y placentero.

  10. Releyendo Frankfurt: la Experiencia Estética en Adorno

    Directory of Open Access Journals (Sweden)

    Stra, Sebastián Matías

    2013-01-01

    Full Text Available [es]Intentaremos en este trabajo explorar la noción de Experiencia Estética en la obra de Theodor Adorno, entendiéndola como una compleja mediación conceptual que nos puede permitir dar cuenta de las oscuras configuraciones de la relación entre arte, cultura y conocimiento en la producción del pensador de Frankfurt. En este marco, cruzaremos las reflexiones estéticas adornianas con lecturas más cercanas a nuestro campo disciplinar, como la noción de Industria Cultural y la interpretación del mito y su derivación en la conformación de la racionalidad moderna. [en] In this work, we will try to explore the notion of Aesthetic Experience in Theodor Adorno`s work, understanding it as a complex conceptual mediation that can allow us getting in the dark settings of the relationship between art, culture and knowledge in the production of Frankfurt`s thinker. Like this, we are going to cross adornians aesthetic reflections with readings that are going to be closer to our disciplinary field, as the notion of cultural industry and the interpretation of myth and its derivation in the configuration of modern rationality.

  11. Estética y espiritualidad. [RESEÑA

    OpenAIRE

    Caballero, J.L. (Juan Luis)

    2014-01-01

    Francisco Javier SANCHO FERMÍN (coord.), Estética y espiritualidad. «Via pulchritudinis». La belleza en el arte sagrado, la educación, la música, la arquitectura, el cine, la pintura, Burgos: Monte Carmelo – Ávila: CITeSUniversidad de la Mística, 2012, 31

  12. “Quem Está Falando?”

    Directory of Open Access Journals (Sweden)

    Rôssi Alves Gonçalves

    2016-07-01

    comunitários, a princípio apadrinhados por ilustres nomes da cultura brasileira, vêm pontuando o meio cultural com obras, no mínimo, provocativas e que desnudam questões que já pareciam esgotadas. Com isso, estão conseguindo movimentar o tradicional cânone literário brasileiro.

  13. Ambientes virtuais e redes: estética e socialidade

    Directory of Open Access Journals (Sweden)

    Daniela Stevanin Hoffmann

    2011-12-01

    Full Text Available Este artigo propõe-se a apresentar dois ambientes virtuais, o AMADIS e o Orkut, a fim de estabelecer relações entre eles, tendo como apoio teórico os conceitos de estética e socialidade. O primeiro é um ambiente virtual de aprendizagem desenvolvido para fins pedagógicos; o segundo é um ambiente virtual que tem alcance mundial e agrega indivíduos por suas redes de interesses e amizades. O objetivo deste artigo é analisar o entrelaçamento entre teoria e algumas das características dos ambientes, suas semelhanças e distinções, a partir do estudo da formação de redes digitais suscitadas por influências estéticas. Foi realizado um estudo qualitativo comparativo estrutural entre os ambientes, colocando-os em paralelo, traçando analogias entre suas áreas, funcionalidades e possibilidades de ações dos usuários. Ao final do estudo e da argumentação, conclui-se que as redes de relações entre os conceitos-chave do estudo da correlação estética-socialidade (neotribalismo, corpo coletivo, ator-persona, espacialidade e pertença, de acordo com Maffesoli, estruturadas a partir do confronto entre as subdivisões dos ambientes, são rearranjáveis e recriáveis.

  14. GrowInclusive : la plateforme tant attendue est en construction ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    4 janv. 2018 ... La croissance inclusive est devenue une idée centrale dans la plupart des plans de développement nationaux, mais pour beaucoup, elle reste avant tout une aspiration. Les gouvernements, les bailleurs de fonds internationaux et les organisations de la société civile manquent de mécanismes éprouvés ...

  15. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  16. EST Table: DN236912 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DN236912 EST00037 10/09/29 79 %/179 aa ref|NP_001119732.1| lebocin-3 precursor [Bom...byx mori] sp|P55796.2|LEB3_BOMMO RecName: Full=Lebocin-3; Short=LEB 3; Flags: Precursor dbj|BAA22883.1| leboc

  17. Las afecciones estéticas: un problema para prevenir

    Directory of Open Access Journals (Sweden)

    Yulisa Otero Baxter

    2001-08-01

    Full Text Available La estética facial asociada con los dientes ha preocupado a la sociedad desde la antigüedad. El temor al rechazo social por cambios de forma, color o posiciones dentales, puede producir un gran impacto psicológico en los pacientes. Con el objetivo de valorar la repercusión psicosocial de las alteraciones estéticas faciales, de determinar el nivel de prioridad que ocupan los tratamientos estéticos dentales y demostrar así la necesidad de intensificar nuestra labor educativa encaminada a evitar aquellas afecciones estéticas que más inciden en nuestra población, procedimos a la aplicación de una encuesta anónima en 110 pacientes que acudieron al Servicio de Estomatología Integral de la Facultad de Estomatología entre noviembre de 1999 y abril del 2000. Se recogió información sobre: actitud asumida por pacientes afectados, prioridades de tratamientos, etcétera. Dicha información fue procesada en tablas estadísticas. Los resultados del trabajo nos permiten concluir que las afecciones estéticas dentales tienen gran repercusión psicosocial, lo que unido al haber encontrado las lesiones traumáticas como las afecciones estéticas de mayor prevalencia, nos evidencia la necesidad de enfatizar nuestra labor educativa en este aspecto.Society has worried about facial esthetics associated with teeth since ancient times. Being afraid of social rejection due to changes of dental form, color or positions may produce a great psychological impact on patients. In order to assess the psychosocial repercussion of the facial esthetic alterations, to determine the priorty level of the esthetic dental treatments and to show the need of intensifying our educative work directed to prevent the most common esthetic affections in our population, we did an anonimous survey among 110 patients that received attention at the Service of Comprehensive Stomatology of the Faculty of Stomatology between November, 1999, and April, 2000. Information was gathered

  18. Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus

    Directory of Open Access Journals (Sweden)

    Eshwar K

    2005-08-01

    Full Text Available Abstract Background Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. Results An EST library was constructed after subtractive suppressive hybridization (SSH of root tissue from two very closely related chickpea genotypes (Cicer arietinum. A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen. Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum, secondary (C. pinnatifidum, C. bijugum and C. judaicum, and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum gene-pools. A large proportion of EST alleles (45% were only

  19. annot8r: GO, EC and KEGG annotation of EST datasets.

    Science.gov (United States)

    Schmid, Ralf; Blaxter, Mark L

    2008-04-09

    The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non-model species EST-sequencing projects.

  20. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae).

    Science.gov (United States)

    Bruun-Lund, Sam; Clement, Wendy L; Kjellberg, Finn; Rønsted, Nina

    2017-04-01

    Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75million years. However, despite significant taxon sampling, combinations of low copy nuclear, nuclear ribosomal and chloroplast regions have not been able to confidently resolve relationships among major groups of figs. Using a high throughput sequencing approach we attempted to resolve the major lineages of Ficus based on plastome data. In this study, we show that the use of a de novo assembled plastome from within the genus provides less ambiguity and higher coverage across the 59 Ficus and 6 outgroup plastome assemblies compared to using the nearest available reference plastome outside the genus resulting in improved resolution and higher support of the phylogenetic relationships within Ficus inferred from plastome data. Chloroplast genome data confidently resolved relationships among major groups of figs and largely support current understanding based on nuclear sequence data including passively pollinated Neotropical section Pharmacosycea as sister lineage to all other Ficus. However, conflicts between the new plastome topology and previous nuclear studies are observed for both individual species as well as relationships among some sections at deeper levels. Conflicts could be caused by lack of resolution in the nuclear data or may indicate potential cyto-nuclear discordance as previously observed in an African lineage of Ficus. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era.

    Science.gov (United States)

    Teng, Jade L L; Tang, Ying; Huang, Yi; Guo, Feng-Biao; Wei, Wen; Chen, Jonathan H K; Wong, Samson S Y; Lau, Susanna K P; Woo, Patrick C Y

    2016-01-01

    Owing to the highly similar phenotypic profiles, protein spectra and 16S rRNA gene sequences observed between three pairs of Tsukamurella species (Tsukamurella pulmonis/Tsukamurella spongiae, Tsukamurella tyrosinosolvens/Tsukamurella carboxy-divorans, and Tsukamurella pseudospumae/Tsukamurella sunchonensis), we hypothesize that and the six Tsukamurella species may have been misclassified and that there may only be three Tsukamurella species. In this study, we characterized the type strains of these six Tsukamurella species by tradition DNA-DNA hybridization (DDH) and "digital DDH" after genome sequencing to determine their exact taxonomic positions. Traditional DDH showed 81.2 ± 0.6% to 99.7 ± 1.0% DNA-DNA relatedness between the two Tsukamurella species in each of the three pairs, which was above the threshold for same species designation. "Digital DDH" based on Genome-To-Genome Distance Calculator and Average Nucleotide Identity for the three pairs also showed similarity results in the range of 82.3-92.9 and 98.1-99.1%, respectively, in line with results of traditional DDH. Based on these evidence and according to Rules 23a and 42 of the Bacteriological Code, we propose that T. spongiae Olson et al. 2007, should be reclassified as a later heterotypic synonym of T. pulmonis Yassin et al. 1996, T. carboxydivorans Park et al. 2009, as a later heterotypic synonym of T. tyrosinosolvens Yassin et al. 1997, and T. sunchonensis Seong et al. 2008 as a later heterotypic synonym of T. pseudospumae Nam et al. 2004. With the advancement of genome sequencing technologies, classification of bacterial species can be readily achieved by "digital DDH" than traditional DDH.

  2. The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis

    Science.gov (United States)

    Koczyk, Grzegorz; Dawidziuk, Adam; Popiel, Delfina

    2015-01-01

    Abstract In recent years, the influx of newly sequenced fungal genomes has enabled sampling of secondary metabolite biosynthesis on an unprecedented scale. However, explanations of extant diversity which take into account both large-scale phylogeny reconstructions and knowledge gained from multiple genome projects are still lacking. We analyzed the evolutionary sources of genetic diversity in aromatic polyketide biosynthesis in over 100 model fungal genomes. By reconciling the history of over 400 nonreducing polyketide synthases (NR-PKSs) with corresponding species history, we demonstrate that extant fungal NR-PKSs are clades of distant siblings, originating from a burst of duplications in early Pezizomycotina and thinned by extensive losses. The capability of higher fungi to biosynthesize the simplest precursor molecule (orsellinic acid) is highlighted as an ancestral trait underlying biosynthesis of aromatic compounds. This base activity was modified during early evolution of filamentous fungi, toward divergent reaction schemes associated with biosynthesis of, for example, aflatoxins and fusarubins (C4–C9 cyclization) or various anthraquinone derivatives (C6–C11 cyclization). The functional plasticity is further shown to have been supplemented by modularization of domain architecture into discrete pieces (conserved splice junctions within product template domain), as well as tight linkage of key accessory enzyme families and divergence in employed transcriptional factors. Although the majority of discord between species and gene history is explained by ancient duplications, this landscape has been altered by more recent duplications, as well as multiple horizontal gene transfers. The 25 detected transfers include previously undescribed events leading to emergence of, for example, fusarubin biosynthesis in Fusarium genus. Both the underlying data and the results of present analysis (including alternative scenarios revealed by sampling multiple reconciliation

  3. A set of EST-SNPs for map saturation and cultivar identification in melon

    Directory of Open Access Journals (Sweden)

    Monforte Antonio J

    2009-07-01

    Full Text Available Abstract Background There are few genomic tools available in melon (Cucumis melo L., a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR, restriction fragment length polymorphisms (RFLP and amplified fragment length polymorphisms (AFLP in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP, more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. Results EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC × 'Piel de sapo' (PS genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. Conclusion This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 × 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR. This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty

  4. A set of EST-SNPs for map saturation and cultivar identification in melon.

    Science.gov (United States)

    Deleu, Wim; Esteras, Cristina; Roig, Cristina; González-To, Mireia; Fernández-Silva, Iria; Gonzalez-Ibeas, Daniel; Blanca, José; Aranda, Miguel A; Arús, Pere; Nuez, Fernando; Monforte, Antonio J; Picó, Maria Belén; Garcia-Mas, Jordi

    2009-07-15

    There are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) x 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 x 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR

  5. The complete chloroplast genome sequence of Helwingia himalaica (Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae.

    Science.gov (United States)

    Yao, Xin; Liu, Ying-Ying; Tan, Yun-Hong; Song, Yu; Corlett, Richard T

    2016-01-01

    Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica , the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. The Helwingia genome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

  6. The complete chloroplast genome sequence of Helwingia himalaica (Helwingiaceae, Aquifoliales and a chloroplast phylogenomic analysis of the Campanulidae

    Directory of Open Access Journals (Sweden)

    Xin Yao

    2016-11-01

    Full Text Available Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species subclass Campanulidae in order to investigate relationships at the order and family levels. The Helwingia genome consists of 158,362 bp containing a pair of inverted repeat (IR regions of 25,996 bp separated by a large single-copy (LSC region and a small single-copy (SSC region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

  7. Plastome Evolution in the Sole Hemiparasitic Genus Laurel Dodder (Cassytha) and Insights into the Plastid Phylogenomics of Lauraceae.

    Science.gov (United States)

    Wu, Chung-Shien; Wang, Ting-Jen; Wu, Chia-Wen; Wang, Ya-Nan; Chaw, Shu-Miaw

    2017-10-01

    To date, little is known about the evolution of plastid genomes (plastomes) in Lauraceae. As one of the top five largest families in tropical forests, the Lauraceae contain many species that are important ecologically and economically. Lauraceous species also provide wonderful materials to study the evolutionary trajectory in response to parasitism because they contain both nonparasitic and parasitic species. This study compared the plastomes of nine Lauraceous species, including the sole hemiparasitic and herbaceous genus Cassytha (laurel dodder; here represented by Cassytha filiformis). We found differential contractions of the canonical inverted repeat (IR), resulting in two IR types present in Lauraceae. These two IR types reinforce Cryptocaryeae and Neocinnamomum-Perseeae-Laureae as two separate clades. Our data reveal several traits unique to Cas. filiformis, including loss of IRs, loss or pseudogenization of 11 ndh and rpl23 genes, richness of repeats, and accelerated rates of nucleotide substitutions in protein-coding genes. Although Cas. filiformis is low in chlorophyll content, our analysis based on dN/dS ratios suggests that both its plastid house-keeping and photosynthetic genes are under strong selective constraints. Hence, we propose that short generation time and herbaceous lifestyle rather than reduced photosynthetic ability drive the accelerated rates of nucleotide substitutions in Cas. filiformis. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Taxonomic status of the three color variants in sea cucumber (Apostichopus japonicus): evidence from mitochondrial phylogenomic analyses.

    Science.gov (United States)

    Zhang, Wei; Cao, Zhengfei; Li, Yuchun; Zhao, Hong; Huang, Jianjun; Liang, Zhenlin; Huang, Luqi

    2016-07-01

    Color variation in sea cucumber is one of the most crucial traits affecting price and taste in East Asian countries. However, the relationship and taxonomic status of the three color variants are still unclear. We used 14 samples that covered all three color variants and their geographic distributions, to construct the first phylogeny for the color variants based on the complete mitochondrial genome sequence and a number of tree-building methods (maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI)). The divergence times within color variants were estimated by the Bayesian molecular clock approach using the BEAST program. Our results showed that the color variants were not monophyletic in the well-resolved phylogenetic tree, which strongly refuted their separate species status. The molecular dating estimate revealed that the sea cucumber was a young group, which originated in the early Miocene period (22.03 mya) and rapidly diverged after the late Miocene period. It is interesting that individuals within each variant or geographic distribution were not always closely related and thus did not share a common origin. We propose that although they differ in body color, the three color morphs all belong to a single species of Apostichopus japonicus and the historical marine climate and the hydrographic complexity of the ocean currents could be responsible for their present distribution patterns.

  9. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes

    Directory of Open Access Journals (Sweden)

    Runko Suzan J

    2005-10-01

    Full Text Available Abstract Background Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters found in the early, extinct seed plants and extant cycads. To establish a molecular base to understand the evolution of seeds and pollen, we created a cDNA library and EST dataset from the reproductive structures of male (microsporangiate, female (megasporangiate, and vegetative organs (leaves of Ginkgo biloba. Results RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6,434 ESTs were generated. These 6,434 ESTs from Ginkgo biloba were clustered into 3,830 unigenes. A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis, and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants – many with multiple matches to genes in non-angiosperm plants. Conversely, another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development, including MADS box genes as well as post-transcriptional regulators. Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes. We also note here the presence of ESTs in G. biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads. Conclusion Our analysis of an EST dataset from G. biloba revealed genes potentially unique to gymnosperms. Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms. Other Ginkgo ESTs are similar to developmental regulators in higher plants. This work sets the stage for future studies on Ginkgo to better understand seed and

  10. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes

    Science.gov (United States)

    Brenner, Eric D; Katari, Manpreet S; Stevenson, Dennis W; Rudd, Stephen A; Douglas, Andrew W; Moss, Walter N; Twigg, Richard W; Runko, Suzan J; Stellari, Giulia M; McCombie, WR; Coruzzi, Gloria M

    2005-01-01

    Background Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters found in the early, extinct seed plants and extant cycads. To establish a molecular base to understand the evolution of seeds and pollen, we created a cDNA library and EST dataset from the reproductive structures of male (microsporangiate), female (megasporangiate), and vegetative organs (leaves) of Ginkgo biloba. Results RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6,434 ESTs were generated. These 6,434 ESTs from Ginkgo biloba were clustered into 3,830 unigenes. A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis, and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants – many with multiple matches to genes in non-angiosperm plants. Conversely, another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development, including MADS box genes as well as post-transcriptional regulators. Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes. We also note here the presence of ESTs in G. biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads. Conclusion Our analysis of an EST dataset from G. biloba revealed genes potentially unique to gymnosperms. Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms. Other Ginkgo ESTs are similar to developmental regulators in higher plants. This work sets the stage for future studies on Ginkgo to better understand seed and pollen evolution, and to

  11. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

    Science.gov (United States)

    Feng, Yan-Jie; Liang, Dan; Hillis, David M.; Cannatella, David C.; Zhang, Peng

    2017-01-01

    Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. PMID:28673970

  12. Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors.

    Directory of Open Access Journals (Sweden)

    Gabriel Castrillo

    Full Text Available Transcriptional regulation is an important mechanism underlying gene expression and has played a crucial role in evolution. The number, position and interactions between cis-elements and transcription factors (TFs determine the expression pattern of a gene. To identify functionally relevant cis-elements in gene promoters, a phylogenetic shadowing approach with a lipase gene (LIP1 was used. As a proof of concept, in silico analyses of several Brassicaceae LIP1 promoters identified a highly conserved sequence (LIP1 element that is sufficient to drive strong expression of a reporter gene in planta. A collection of ca. 1,200 Arabidopsis thaliana TF open reading frames (ORFs was arrayed in a 96-well format (RR library and a convenient mating based yeast one hybrid (Y1H screening procedure was established. We constructed an episomal plasmid (pTUY1H to clone the LIP1 element and used it as bait for Y1H screenings. A novel interaction with an HD-ZIP (AtML1 TF was identified and abolished by a 2 bp mutation in the LIP1 element. A role of this interaction in transcriptional regulation was confirmed in planta. In addition, we validated our strategy by reproducing the previously reported interaction between a MYB-CC (PHR1 TF, a central regulator of phosphate starvation responses, with a conserved promoter fragment (IPS1 element containing its cognate binding sequence. Finally, we established that the LIP1 and IPS1 elements were differentially bound by HD-ZIP and MYB-CC family members in agreement with their genetic redundancy in planta. In conclusion, combining in silico analyses of orthologous gene promoters with Y1H screening of the RR library represents a powerful approach to decipher cis- and trans-regulatory codes.

  13. ¿Está en peligro el periodismo?

    Directory of Open Access Journals (Sweden)

    José Rodríguez Elizondo

    2012-07-01

    Full Text Available Debatir sobre este tema tiene una historia propia. En un artículo publicado el año 2000 me referí al futuro de la prensa, las nuevas tecnologías de la comunicación y la hiper y auto-información como eventuales amenazas. El tema, de apariencia imponente y con hipótesis ominosas, tuvo de mi parte una decodificación optimista. Dado que aquel futuro lleva ya más de una década de desarrollo, este nuevo artículo servirá para contrastar las percepciones y los pronósticos de entonces. Lo haré en el disfrute de la mayor libertad crítica que es posible concebir, que es la que se expresa como autocrítica.

  14. Sobre a estética platônica

    Directory of Open Access Journals (Sweden)

    Luis Felipe Bellintani Ribeiro

    2007-04-01

    Full Text Available O texto começa pela consideração da aparente posição desfavorável da estética, entendida tanto como o domínio da arte, quanto como o relativo à sensação, perante a metafísica platônica. A consideração posterior, porém, do caráter ontológico do critério metafísico, que, em tese, poria a arte e a sensação a seu reboque, ensejou, mais que uma reabilitação, uma inversão: a metafísica platônica é que seria fundada numa estética.

  15. Pedro Almodovara filmu stils un estētika

    OpenAIRE

    Majorenkova, Madara

    2013-01-01

    Šī darba nosaukums ir „Pedro Almodovara filmu stils un estētika”. Darba galvenais mērķis ir pierādīt, ka P.Almodovaram piemīt savs stils un estētika. Almodovara karjeras uzplaukums sākās “La Movida Madrileña” laikā. “La Movida Madrileña” ir sociokulturāla kustība, kura parādījās pirmajos pārejas gados pēc Franko režīma Spānijā. Šī laikmeta kino atainoja visu to, kas bija aizliegts Franko režīma laikā, piemēram, homoseksualitāte, narkotiku lietošana, prostitūtica, transseksualitāte. Dar...

  16. DEVELOPMENT OF EST-SSR MARKERS TO ASSESS GENETIC DIVERSITY OF BROCCOLI AND ITS RELATED SPECIES

    Directory of Open Access Journals (Sweden)

    Nur Kholilatul Izzah

    2017-01-01

    Full Text Available Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.

  17. Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example

    Directory of Open Access Journals (Sweden)

    Benner Steven A

    2005-03-01

    Full Text Available Abstract Background Blocks of duplicated genomic DNA sequence longer than 1000 base pairs are known as low copy repeats (LCRs. Identified by their sequence similarity, LCRs are abundant in the human genome, and are interesting because they may represent recent adaptive events, or potential future adaptive opportunities within the human lineage. Sequence analysis tools are needed, however, to decide whether these interpretations are likely, whether a particular set of LCRs represents nearly neutral drift creating junk DNA, or whether the appearance of LCRs reflects assembly error. Here we investigate an LCR family containing the sulfotransferase (SULT 1A genes involved in drug metabolism, cancer, hormone regulation, and neurotransmitter biology as a first step for defining the problems that those tools must manage. Results Sequence analysis here identified a fourth sulfotransferase gene, which may be transcriptionally active, located on human chromosome 16. Four regions of genomic sequence containing the four human SULT1A paralogs defined a new LCR family. The stem hominoid SULT1A progenitor locus was identified by comparative genomics involving complete human and rodent genomes, and a draft chimpanzee genome. SULT1A expansion in hominoid genomes was followed by positive selection acting on specific protein sites. This episode of adaptive evolution appears to be responsible for the dopamine sulfonation function of some SULT enzymes. Each of the conclusions that this bioinformatic analysis generated using data that has uncertain reliability (such as that from the chimpanzee genome sequencing project has been confirmed experimentally or by a "finished" chromosome 16 assembly, both of which were published after the submission of this manuscript. Conclusion SULT1A genes expanded from one to four copies in hominoids during intra-chromosomal LCR duplications, including (apparently one after the divergence of chimpanzees and humans. Thus, LCRs may

  18. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii as a case study

    Directory of Open Access Journals (Sweden)

    Zhang Gong

    2007-03-01

    Full Text Available Abstract Background Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the ray-finned fishes – the largest vertebrate clade in need of phylogenetic resolution. Results A total of 154 candidate molecular markers – relatively well conserved, putatively single-copy gene fragments with long, uninterrupted exons – were obtained by comparing whole genome sequences of two model organisms, Danio rerio and Takifugu rubripes. Experimental tests of 15 of these (randomly picked markers on 36 taxa (representing two-thirds of the ray-finned fish orders demonstrate the feasibility of amplifying by PCR and directly sequencing most of these candidates from whole genomic DNA in a vast diversity of fish species. Preliminary phylogenetic analyses of sequence data obtained for 14 taxa and 10 markers (total of 7,872 bp for each species are encouraging, suggesting that the markers obtained will make significant contributions to future fish phylogenetic studies. Conclusion We present a practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny. Our method is an improvement over traditional approaches (e.g., manually picking genes for testing because it uses genomic information and automates the process to identify large numbers of candidate makers. This approach is shown here to be successful for fishes

  19. ¿Está escuchando? ASP (:60)

    Centers for Disease Control (CDC) Podcasts

    2015-09-08

    Este anuncio de servicio público de radio motivan a las mujeres a aprender los síntomas del cáncer ginecológico y a prestar atención a lo que les dice su cuerpo.  Created: 9/8/2015 by National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP).   Date Released: 9/8/2015.

  20. ¿Está escuchando? ASP (:30)

    Centers for Disease Control (CDC) Podcasts

    2015-09-08

    Este anuncio de servicio público de radio motivan a las mujeres a aprender los síntomas del cáncer ginecológico y a prestar atención a lo que les dice su cuerpo.  Created: 9/8/2015 by National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP).   Date Released: 9/8/2015.

  1. Extra heavy crudes and bitumens in the new EST technology

    International Nuclear Information System (INIS)

    Montanari, R.

    2001-01-01

    Strategic and market reasons dictate for the diversification of the supply sources. The huge reserves of extra heavy crudes and oil sands bitumen will provide the answer in this direction, but it is mandatory the availability of a suitable technology to process these poor quality feedstocks. EST Technology, developed by Snamprogetti and EniTecnologie, allows to get full conversion to produce high quality distillates [it

  2. « Le Paradis, c’est les autres »

    Directory of Open Access Journals (Sweden)

    Rachid Amirou

    2008-11-01

    Full Text Available L’engouement pour des sites ou des lieux est souvent dû à des « Nous » (des communautés éphémères, qui se constituent et qui consacrent ainsi l’espace de visite. La consécration collective est souvent un préalable au succès de certaines destinations (Ibiza, Saint-Tropez, Marrakech, etc.. Le succès des formules de villages de vacances hermétiquement fermés à l’extérieur et indifférents au pays de séjour atteste de l’existence d’un état d’esprit qu’on a classé sous le terme générique de « bulle touristique ». Cependant, la constitution de ces « bulles » – c’est-à-dire la rencontre d’un imaginaire, d’un « nous » et d���un espace touristiques – ne se fait pas uniquement par l’exclusion de l’autre. Elle repose aussi sur un principe interne positif : le rêve d’une sociabilité parfaite, une sorte de paradis relationnel. Le « paradis » touristique, c’est d’abord une rencontre de plain-pied avec les autres (« l’ambiance », souvent d’ailleurs avec les mêmes – rencontre synonyme de relations différentes et moins stressantes, basées sur une connivence réelle ou fantasmée. La généalogie de ce paradis touristique relationnel, qui peut être aussi un enfer pour les autres, reste à décrire et à expliciter, en montrant comment il compose le noyau central de l’imaginaire touristique.

  3. CONQuEST - Menu-selectable database system

    Energy Technology Data Exchange (ETDEWEB)

    Yeko, J.D. (Illinois State Geological Survey, Champaign (USA))

    1989-08-01

    The well database unit of the Illinois State Geological Survey Oil and Gas section began to design and develop a technically advanced oil and gas database system in 1988. The CONQuEST system integrates and replaces the existing oil and gas, water, coal, and geotechnical database systems. CONQuEST uses a distributed relational data model that allows integrated storage and retrieval of different data and well types in an almost unlimited variety of report forms. The software, written in C, consists of five menu-selectable modules that allow a novice computer user to enter, edit, retrieve, and report data. The GeoDES module is used to enter data from paper records and consists of numerous fill-in-the-blank screens. The TIDE module is used to edit or delete any existing data. There are two modules for data retrieval. QuARTz is used for quick, preplanned retrievals and ToPAz is used for self-designed retrievals. ToPAz retrieval designs may be saved and added to the menu systems and then accessed through the QuARTz module. The COReS module consists of numerous predesigned report options. Standard Query Language (SQL) is also available as an option. CONQuEST is currently run on a Digital Equipment Corporation VAX, that is interfaced to a series of PCs; however, all software can be run on a PC only. Benefits of the CONQuEST system over the previous system are increased speed, greater flexibility, the ability to run on a PC, and the menu system that allows for successful access and use of the data by novice computer users. Data system use is available to the general public for a fee.

  4. Multinaturalismo y estéticas de alteridad

    Directory of Open Access Journals (Sweden)

    Mario Madroñero Morillo

    2012-09-01

    Full Text Available La propuesta de una estética de alteridad problematiza la concepción de representación y su historia. Los conceptos de mimesis, formación y figuración serán aquí removidos del lugar habitual que ocupan en la teoría estética y la práctica artística, buscando una etno-grafía y estética de alteridad que permita una aproximación y ahondamiento de una relación vital con la alteridad de la tierra. Tal relación se aborda desde las márgenes que permiten los conceptos de la antropología pos-estructural propuestos por Eduardo Viveiros de Castro,multinaturalismo y perspectivismo, referidos a experiencias chamánicas y del pensar amerindio, como trazo y rasgo de modos de ser diferentes, de “procesos de alteración diferencial”, que tendrán en algunas acciones artísticas su exposición y donación de sentido.

  5. Professor-psicopedagogo: o que este profissional faz na escola

    Directory of Open Access Journals (Sweden)

    Caroline Andrea Pottker

    Full Text Available Este estudo teve como objetivo identificar o porquê da presença do professor-psicopedagogo nas escolas e qual a função que este desempenha dentro delas, bem como, suas implicações no processo ensino-aprendizagem. Para tanto, foram entrevistados dez professores-psicopedagogos, pertencentes a cinco escolas localizadas no Estado do Paraná. Os resultados apontaram que o cargo de professor-psicopedagogo foi ocupado por professores que tinham o título de especialista em Psicopedagogia, os quais passaram a realizar avaliações psicopedagógicas dos alunos com dificuldades de aprendizagem. Segundo a maioria desses profissionais, uma de suas funções constitui-se em auxiliar o professor que apresenta em sala de aula alunos com dificuldades de aprendizagem, assim como tentar compreender o porquê de estes alunos não estarem aprendendo, sobretudo, ajudá-los na reversão desta problemática. Concluímos que a atuação deste profissional nestas escolas pouco tem contribuído para resolução das dificuldades de aprendizagem, pois centram-se no indivíduo e não no processo ensino-aprendizagem.

  6. Gene expression profiling of chicken primordial germ cell ESTs

    Directory of Open Access Journals (Sweden)

    Lim Dajeong

    2006-08-01

    Full Text Available Abstract Background Germ cells are the only cell type that can penetrate from one generation to next generation. At the early embryonic developmental stages, germ cells originally stem from primordial germ cells, and finally differentiate into functional gametes, sperm in male or oocyte in female, after sexual maturity. This study was conducted to investigate a large-scale expressed sequence tag (EST analysis in chicken PGCs and compare the expression of the PGC ESTs with that of embryonic gonad. Results We constructed 10,851 ESTs from a chicken cDNA library of a collection of highly separated embryonic PGCs. After chimeric and problematic sequences were filtered out using the chicken genomic sequences, there were 5,093 resulting unique sequences consisting of 156 contigs and 4,937 singlets. Pearson chi-square tests of gene ontology terms in the 2nd level between PGC and embryonic gonad set showed no significance. However, digital gene expression profiling using the Audic's test showed that there were 2 genes expressed significantly with higher number of transcripts in PGCs compared with the embryonic gonads set. On the other hand, 17 genes in embryonic gonads were up-regulated higher than those in the PGC set. Conclusion Our results in this study contribute to knowledge of mining novel transcripts and genes involved in germline cell proliferation and differentiation at the early embryonic stages.

  7. Genome-wide analysis of immune system genes by EST profiling

    Science.gov (United States)

    Giallourakis, Cosmas; Benita, Yair; Molinie, Benoit; Cao, Zhifang; Despo, Orion; Pratt, Henry E.; Zukerberg, Lawrence R.; Daly, Mark J.; Rioux, John D.; Xavier, Ramnik J.

    2013-01-01

    Profiling studies of mRNA and miRNA, particularly microarray-based studies, have been extensively used to create compendia of genes that are preferentially expressed in the immune system. In some instances, functional studies have been subsequently pursued. Recent efforts such as ENCODE have demonstrated the benefit of coupling RNA-Seq analysis with information from expressed sequence tags (ESTs) for transcriptomic analysis. However, the full characterization and identification of transcripts that function as modulators of human immune responses remains incomplete. In this study, we demonstrate that an integrated analysis of human ESTs provides a robust platform to identify the immune transcriptome. Beyond recovering a reference set of immune-enriched genes and providing large-scale cross-validation of previous microarray studies, we discovered hundreds of novel genes preferentially expressed in the immune system, including non-coding RNAs. As a result, we have established the Immunogene database, representing an integrated EST “road map” of gene expression in human immune cells, which can be used to further investigate the function of coding and non-coding genes in the immune system. Using this approach, we have uncovered a unique metabolic gene signature of human macrophages and identified PRDM15 as a novel overexpressed gene in human lymphomas. Thus we demonstrate the utility of EST profiling as a basis for further deconstruction of physiologic and pathologic immune processes. PMID:23616578

  8. Hora do jogo: os professores estão prontos?

    Directory of Open Access Journals (Sweden)

    Eliana Maria Magnani

    2018-04-01

      Hora del juego: ¿los profesores están preparados? RESUMEN Las ideas discutidas en este texto están relacionadas con las actividades de enseñanza, investigación y extensión desarrolladas desde 2012 a través de la Universidad Estadual de Oeste de Paraná – UNIOESTE. El artículo señala la importancia de la clasificación y catalogación de juegos educativos, explicitando qué es un importante conocimiento propuesto a los Centros Municipales de Educación Infantil (CMEIs, localizados en una ciudad del Suroeste de Paraná, CMEIs que, en función de una ley local, empezaron la (re implementación de ludotecas en 2007. La metodología se efectuó en fases, dos de dichas fases fueron significativas para la revisión de la implementación, a saber: diagnóstico de cómo se organizaban los materiales existentes en las ludotecas, curso sobre la importancia de la clasificación y catalogación de diferentes tipos de juegos. Para ello, toda revisión se apoyó en las ideas de Jean Piaget (2010/1946, 1994/1932, quien elaboró una teoría sobre el juego. Dichos conocimientos sirvieron para la comprensión de que los maestros no están preparados para este tipo de actividad didáctico-pedagógica, pues dicha educación es un proceso que demanda toma de conciencia de propia praxis, la cual requiere el (re aprendizaje a respecto de los objetivos de diferentes tipos de juegos y del desarrollo infantil, siendo que ello necesita ocurrir en la formación inicial y en la formación continua de profesores. Por consiguiente, es necesaria la involucración de los (futuros profesores en actividades lúdicas de enseñanza, investigación y extensión realizadas en universidades. Palabras clave: Clasificación de Juegos. Educación Infantil. Formación docente.

  9. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

    Directory of Open Access Journals (Sweden)

    Brahmbhatt Sonal

    2008-11-01

    Full Text Available Abstract Background Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. Results 298,304 expressed sequence tags (ESTs from Atlantic salmon (69% of the total, 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species. Conclusion An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is

  10. Free Access Does Not Necessarily Encourage Practitioners to Use Online Evidence Based Information Tools. A Review of: Buchan, H., Lourey, E., D’Este, C., & Sanson-Fisher, R. (2009. Effectiveness of strategies to encourage general practitioners to accept an offer of free access to online evidence-based information: A randomised controlled trial. Implementation Science, 4, article 68.

    Directory of Open Access Journals (Sweden)

    Heather Ganshorn

    2010-12-01

    Full Text Available Objectives – To determine which strategies were most effective for encouraging general practitioners (GPs to sign up for free access to an online evidence based information resource; and to determine whether those who accepted the offer differed in their sociodemographic characteristics from those who did not.Design – Descriptive marketing research study.Setting – Australia’s public healthcare system.Subjects – 14,000 general practitioners (GPs from all regions of Australia.Methods – Subjects were randomly selected by Medicare Australia from its list of GPs that bill it for services. Medicare Australia had 18,262 doctors it deemed eligible; 14,000 of these were selected for a stratified random sample. Subjects were randomized to one of 7 groups of 2,000 each. Each group received a different letter offering two years of free access to BMJ Clinical Evidence, an evidence based online information tool. Randomization was done electronically, and the seven groups were stratified by age group, gender, and location. The interventions given to each group differed as follows:• Group 1: Received a letter offering 2 years of free access, with no further demands on the recipient.• Group 2: Received a letter offering 2 years of free access, but on the condition that they complete an initial questionnaire and another one at 12 months, as well as allowing the publisher to provide de-personalized usage data to the researchers.• Group 3: Same as Group 2, but with the additional offer of an online tutorial to assist them with using the resource.• Group 4: Same as Group 2, but with an additional pamphlet with positive testimonials about the resource from Australian medical opinion leaders.• Group 5: Same as Group 2, but with an additional offer of professional development credits towards their required annual totals.• Group 6: Same as Group 2, but with an additional offer to be entered to win a prize of $500 towards registration at a

  11. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  12. Ocio estético valioso en la Poética de Aristóteles

    Directory of Open Access Journals (Sweden)

    Mª Luisa Amigo Fernández De Arroyabe

    2015-01-01

    Full Text Available Este artículo se centra en el ocio estético valioso en Aristóteles, partiendo del análisis de la Poética y, específicamente, de la comprensión de la experiencia estética como actividad mental. Se destaca su dimensión ética, realzando su valor en el desarrollo del ser humano, así como el de la propia obra de arte, en la medida en que el poeta ha sabido construirla, encarnando en la trama los hechos y universalizándolos, al modo que le es propio. Aristóteles se refiere a la tragedia, pero por extensión esta valoración proporciona una pauta de lectura de la experiencia de ocio estético. El marco autónomo para el ámbito estético, que inaugura Aristóteles, y su valoración vinculada a la dimensión ética, a la comprensión intelectual y al placer estético proporcionan la base para sostener que el ocio estético se confirma como un horizonte enmarcado en la senda de lo valioso y adecuado para realizar la vida que le es propia al ser humano.

  13. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas).

    Science.gov (United States)

    Wang, Zhangying; Li, Jun; Luo, Zhongxia; Huang, Lifei; Chen, Xinliang; Fang, Boping; Li, Yujun; Chen, Jingyi; Zhang, Xiongjian

    2011-10-20

    Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative

  14. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas

    Directory of Open Access Journals (Sweden)

    Li Yujun

    2011-10-01

    Full Text Available Abstract Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas, which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9% being the most abundant followed by di- (41.2%, tetra- (9.2%, penta- (3.7% and hexa-nucleotide (3.1% repeat types. The top five motifs included AG/CT (26.9%, AAG/CTT (13.5%, AT/TA (10.6%, CCG/CGG (5.8% and AAT/ATT (4.5%. After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30 and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9% and 342 (41.9% primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would

  15. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)

    Science.gov (United States)

    2011-01-01

    Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for

  16. EVER-EST: European Virtual Environment for Research in Earth Science Themes

    Science.gov (United States)

    Glaves, H.; Albani, M.

    2016-12-01

    EVER-EST is an EC Horizon 2020 project having the goal to develop a Virtual Research Environment (VRE) providing a state-of-the-art solution to allow Earth Scientists to preserve their work and publications for reference and future reuse, and to share with others. The availability of such a solution, based on an innovative concept and state of art technology infrastructure, will considerably enhance the quality of how Earth Scientists work together within their own institution and also across other organizations, regions and countries. The concept of Research Objects (ROs), used in the Earth Sciences for the first time, will form the backbone of the EVER-EST VRE infrastructure. ROs will enhance the ability to preserve, re-use and share entire or individual parts of scientific workflows and all the resources related to a specific scientific investigation. These ROs will also potentially be used as part of the scholarly publication process. EVER-EST is building on technologies developed during almost 15 years of research on Earth Science data management infrastructures. The EVER-EST VRE Service Oriented Architecture is being meticulously designed to accommodate at best the requirements of a wide range of Earth Science communities and use cases: focus is put on common requirements and on minimising the level of complexity in the EVER-EST VRE to ensure future sustainability within the user communities beyond the end of the project. The EVER-EST VRE will be validated through its customisation and deployment by four Virtual Research Communities (VRCs) from different Earth Science disciplines and will support enhanced interaction between data providers and scientists in the Earth Science domain. User community will range from bio-marine researchers (Sea Monitoring use case), to common foreign and security policy institutions and stakeholders (Land Monitoring for Security use case), natural hazards forecasting systems (Natural Hazards use case), and disaster and risk

  17. Esplenectomía incidental: ¿Está justificada?

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    Eddy Sierra Enrique

    1997-12-01

    Full Text Available Se revisaron 77 historias clínicas de pacientes que presentaban lesiones incidentales del bazo ocurridas entre 1985 y 1994, durante operaciones intraabdominales y por examen laparoscópico. Las funciones inmunológicas del bazo y su papel contra las infecciones están bien definidas, por lo cual al ser suprimido este órgano a consecuencia de lesiones incidentales, favorecen las infecciones en dichos pacientes de por vida. De las 77 lesiones incidentales se realizaron 47(61 % esplenectomías incidentales y 30(39 % cirugías conservadoras. La úlcera duodenal y la hernia hiatal son las causas principales de esplenectomía incidental. Se presentaron 11 infecciones (23,4 % y 1 fallecido (2,1 % en la esplenectomía incidental contra 1 infección (3,3 % y ningún fallecido en la cirugía conservadora. Se llega a la conclusión de que la esplenectomía no está justificada dadas las desventajas que presenta77 medical histories of patients who presented incidental injuries of the spleen occurred between 1985 and 1994, during intraabdominal operations and by laparoscopic examination, were reviewed. The immunological functions of the spleen and its role against infections are well defined, so the removal of this organ due to incidental injuries favors the appearance of infections in these patients for the rest of their lives. Of the 77 incidental injuries 47 (61 % incidental splenectomies and 30 (39 % conservative surgeries were performed. Duodenal ulcer and hiatal hernia proved to be the main causes of incidental splenectomy. There were 11 infections (23.4 % and 1 death (2.1 % in the incidental splenectomy compared with 1 infection (3.3 % and no death in the conservative surgery. It is concluded that splenectomy is not justified because of its disadvantages

  18. Qu’est-ce que le naturalisme ?

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    Olivier Morin

    2012-01-01

    Full Text Available Cet article répond aux critiques récemment adressées aux tenants du « naturalisme social » dans les pages de la revue SociologieS. Il le fait en défendant un naturalisme minimal, bâti sur trois idées : l’interdisciplinarité est permise ; la pensée est un processus causal qui a lieu dans un monde matériel ; l’humanité est une espèce animale. Ces idées pourront sembler triviales ; le débat auquel nous assistons montre qu’il n’en est rien. Je passerai en revue les arguments les plus fréquemment opposés à ce naturalisme. Le dialogue entre sciences cognitives et sciences sociales ne prélude pas à une O.P.A. de la neurobiologie sur les autres disciplines. Aucun chercheur sérieux ne voit la cognition humaine comme un assemblage de modules à l’architecture entièrement fixée dès la naissance et incapables d’interagir avec leur environnement. Le fait que les processus mentaux n’aient pas lieu uniquement dans nos têtes est aujourd’hui un lieu commun des sciences cognitives. Enfin, l’étude de l’évolution de l’humanité, vue comme une espèce biologique, est porteuse de conclusions qui pour être très générales, n’en sont pas moins pertinentes pour les sciences sociales.What is Naturalism?This article responds to recent critics addressed to the advocates of « social naturalism » in the journal SociologieS. It does so by defending a minimal naturalism structured around three ideas: interdisciplinarity is allowed; thought is a causal process that occurs in a material world; humanity is a species. These ideas may seem trivial; the debate we’re assisting to shows us otherwise. I will go through the arguments that most frequently oppose naturalism. The dialogue between cognitive and social sciences is not a prelude to the takeover of neurobiology on other disciplines. No serious researcher sees human cognition as an assembly of architectural modules entirely fixed from birth and incapable of

  19. Development and Characterization of 37 Novel EST-SSR Markers in Pisum sativum (Fabaceae

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    Xiaofeng Zhuang

    2013-01-01

    Full Text Available Premise of the study: Simple sequence repeat markers were developed based on expressed sequence tags (EST-SSR and screened for polymorphism among 23 Pisum sativum individuals to assist development and refinement of pea linkage maps. In particular, the SSR markers were developed to assist in mapping of white mold disease resistance quantitative trait loci. Methods and Results: Primer pairs were designed for 46 SSRs identified in EST contiguous sequences assembled from a 454 pyrosequenced transcriptome of the pea cultivar, ‘LIFTER’. Thirty-seven SSR markers amplified PCR products, of which 11 (30% SSR markers produced polymorphism in 23 individuals, including parents of recombinant inbred lines, with two to four alleles. The observed and expected heterozygosities ranged from 0 to 0.43 and from 0.31 to 0.83, respectively. Conclusions: These EST-SSR markers for pea will be useful for refinement of pea linkage maps, and will likely be useful for comparative mapping of pea and as tools for marker-based pea breeding.

  20. The pier and building of the European Solar Telescope (EST)

    Science.gov (United States)

    Bettonvil, F. C. M.; Codina, R.; Gómez Merchán, A.; Hammerschlag, R. H.; Hartman, J. J. M.; Hernández Suárez, E.; Jägers, A. P. L.; Murga Llano, G.; Pelser, J. W.; Sliepen, G.

    2010-07-01

    EST (European Solar Telescope) is a 4-m class solar telescope, which is currently in the conceptual design phase. EST will be located in the Canary Islands and will aim at high spectral, spatial and temporal resolution observations in the photosphere and chromosphere, using a suite of instruments that can produce efficiently two-dimensional spectropolarimetric information of the thermal, dynamic and magnetic properties of the plasma over many scale heights. The pier is defined as the construction that supports the telescope and the enclosure. It needs a certain height to minimize daytime ground turbulence. At the bottom of the pier a large instrument lab is located, 16 m in diameter and 10 m high. To the pier is attached a service building that accommodates all auxiliary services, possibly together with a separate building. Solid concrete- and open framework piers are compared, in terms of stability, thermal properties and flow characteristics and building structures in terms of construction issues. FE and CFD analysis are used to give qualitative insight in the differences between the alternatives. The preferred alternative is a cone shaped pier surrounded by an open framework.

  1. La seducción como estética

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    Claudia Barrera

    2012-09-01

    Full Text Available La seducción es tratada desde la literatura, la sociología, la psicología y la política como una estrategia de manipulación. Sin embargo, si se la estudia desde el campo filosófico y su tradición estética vemos sus poderes constructores de una sensibilidad poética por las fuerzas atractivas y repulsivas que contiene. La seducción, como fuerza e impulso, se inscribe en un movimiento en que el aparecer de la realidad, la imaginación y, desde luego, el arte —fuente de emotividad y sensaciones— permiten valorarla. La estética de la seducción se despliega desde la subjetividad y no desde los contenidos de la filosofía del arte. Su capacidad relacional y sus poderes condensados en el espíritu del hombre no pueden pertenecer al aparato instrumental de la sociedad de consumo o las estrategias de manipulación donde ha sido estigmatizada. Por esto la seducción es presentada como fuente de deseo y potencia vital.

  2. Arquitectura corporal: pasiones deportivas e identificaciones estéticas

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    Barreto Vargas, Carmen Marina

    2006-12-01

    Full Text Available In present-day societies, prevailing discourses on health, body and aesthetics regard the practice of sports as both a lifestyle and a way to constructing the body —a body increasingly constrained within certain standards of beauty in which the gender factor plays a clearly important role. The author analyzes this and other factors in the relationship between the body as a social construct and the sporting physical activity as a means that makes it possible.

    En nuestras sociedades actuales, los discursos predominantes sobre la salud, el cuerpo y la estética se vuelven hacia el deporte como un estilo de vida y como una vía de construcción del cuerpo; un cuerpo que debe, cada vez más, situarse dentro de unos estándares de belleza y, en cuya lectura, la clave de género tiene un papel ciertamente importante. El presente artículo analiza algunas de estas claves en la relación entre la construcción social del cuerpo y la práctica físico-deportiva en tanto que medio para hacerla posible.

  3. Upgrading Unconventional Oil Resources with the EST Process

    Energy Technology Data Exchange (ETDEWEB)

    Delbianco, Alberto; Meli, Salvatori; Panariti, Nicolleta; Rispoli, Giacomo

    2007-07-01

    We strongly believe that unconventional oils will play a much larger role in the growth of supply than is currently recognized. As a matter of fact, whereas the earth's conventional proven world oil reserves are 1.3 trillion barrels, extra-heavy plus bitumen resources amount to about 4 trillion barrels. The unconventional oils are characterized by low API gravity (<10), high viscosity and high concentration of poisons such as sulphur, nitrogen, metals, and asphaltenes. For this reason, a key role for the full exploitation of these hydrocarbon resources is played by the downstream processes that are required to upgrade and convert them into valuable products. In this scenario, Eni has developed a novel hydrocracking process (EST: Eni Slurry Technology) which is particularly well-suited for the conversion and upgrading of heavy feedstocks (conventional vacuum residues, extra-heavy oils and bitumen). EST employs nano-sized hydrogenation catalysts and an original process scheme that allow complete feedstock conversion to an upgraded synthetic crude oil (SCO) with an API gravity gain greater than 20 and avoid the production of residual by-products, such as pet-coke or heavy fuel oil. A Commercial Demonstration Unit (CDP) of 1200 bbl/d capacity is successfully operating in the Eni's Taranto refinery since November 2005. (auth)

  4. Fotomontajes feministas: dispositivos estético-políticos

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    Miguel Alfonso Bouhaben

    2017-12-01

    Full Text Available El presente artículo tiene el objetivo de estudiar los dispositivos estéticos y políticos que ponen en práctica los fotomontajes feministas de Martha Rosler y Barbara Kruger. Para ello, es necesario identificar cómo reaccionan estas obras contra el sistema impuesto por el patriarcado a través de la cultura mediática dominante. En los fotomontajes de Martha Rosler vamos a analizar los modos de cosificación de la mujer y las formas de control domopolítico que se establecen en el hogar. Además, nos adentraremos en los dispositivos de montaje y remontaje de imágenes, y de estructuración diferencial y deconstructiva, que la artista pone en práctica con fines emancipatorios. En el caso de Barbara Kruger nos centraremos en su crítica a los modos de representación de la mujer en los medios de comunicación. Asimismo, levantaremos acta de sus dispositivos de apropiación y de interrelación imagen-texto. Finalmente, haremos un balance de las implicaciones éticas y ontológicas que subyacen a estos dispositivos estético-políticos, en relación con las tesis defendidas por el feminismo.

  5. Desarrollo de la metodología de diseño de interfaces al usuario del estándar ISDB-Tb utilizando Ginga en base a las metodologías de diseño de interfaces al usuario para PC

    OpenAIRE

    Jaramillo Yánez, Andrés Gabriel; Mayorga Ortiz, Nelson Fernando; Egas Acosta, Carlos Roberto

    2012-01-01

    El presente trabajo se basa en diferentes metodologías de diseño de interfaz de usuario para PC para generar una metodología de diseño de interfaces de usuario de Televisión Digital Terrestre (TDT). Se inicia analizando las características de la televisión analógica actual y su alcance como un medio de comunicación masivo. A continuación se presenta el estándar de TDT adoptado por el país (ISDB-Tb) haciendo énfasis en el middleware GINGA que permite la implementación de aplicaciones d...

  6. Plan de Punta del Este, 1935: modelo de ciudad balnearia

    Directory of Open Access Journals (Sweden)

    Juan Alberto Articardi

    2013-07-01

    Full Text Available There are a few relatively known examples that show how modern town planning in South America developed. One of the few examples is Carlos Gómez Gavazzo’s Punta del Este Town Plan that was developed between 1934 and 1935 on his return to Uruguay after having worked with Le Corbusier. The town plan was presented to the National Tourist Board as a resort city for the east coast. The concept that was applied to Punta del Este’s resort can be interpreted as a defence of modern town planning that adapted its spatial design to topographical, geographical, and climatic considerations, and transformed the urban structure as well as the peninsula’s profile.

  7. Relatório de estágio

    OpenAIRE

    Santos, Filipa R. Bolota Velho Dinis dos

    2011-01-01

    Descrevemos, no presente relatório, o percurso realizado ao longo de três meses de estágio que decorreu numa empresa de turismo com sede na Covilhã (Turistrela). O produto final nunca é um facto isolado, mas um somatório de vários factores que para ele contribuem. Neste contexto, embora o resultado global, em termos objectivos, tenha sido a realização do Website Polistrade, muito aconteceu, até à construção do mesmo. Foi uma tarefa que implicou investigação, planificação e reflexão diár...

  8. La radio no está amenazada por internet

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    Bruce Girard

    2015-01-01

    Full Text Available La radio es mucho más penetrante y asequible, el uso de los servicios de Internet puede contribuir a informar mejor a sus clientes y establecer interactividad. En vista que por ahora la accesibilidad del Internet es accesible solo a unos pocos, para la radio no es una amenaza el Internet. Enuncia los roles de la radio y señala que está considerada como un vínculo comunitario. Trata además sobre las radio-cadenas satelitales, la radio e Internet: convergencia para la democracia y el crecimiento de la brecha de los que acceden a la información.

  9. Inferindo personalidade por meio de estórias

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    Guilherme Gomes Cardoso

    2014-11-01

    Full Text Available Recentemente aspectos sutis do ser humano começaram a ser estudados e utilizados por computadores, um desses é a personalidade. Existem vários estudos que analisam como estruturá-la e extraí-la computacionalmente. No entanto, um dos gargalos no seu estado da arte atual é a forma não sutil para inferir personalidade do usuário. Este trabalho tem como objetivo mostrar o relato de uma experiência que demonstra os passos iniciais e os resultados parciais de uma pesquisa em andamento sobre um método alternativo e mais sutil para inferir a personalidade do usuário. Os resultados apresentam o uso de histórias como uma abordagem promissora, entretanto demanda novos testes baseados em metodologias estatisticamente mais consistentes.

  10. annot8r: GO, EC and KEGG annotation of EST datasets

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    Schmid Ralf

    2008-04-01

    Full Text Available Abstract Background The expressed sequence tag (EST methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. Results annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO, Enzyme Commission (EC and Kyoto Encyclopaedia of Genes and Genomes (KEGG annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. Conclusion annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non

  11. Use of EST database markers from M. truncatula in the transferability to other forage legumes.

    Science.gov (United States)

    Chandra, Amaresh

    2011-05-01

    In general tropical forage legumes lack microsatellites or simple sequence repeat (SSR) markers. Development of genic SSR markers from expressed sequence tagged (EST) database is an alternate and efficient approach to generate the standard DNA markers for genome analysis of such crop species. In the present paper a total of 816 EST-SSRs containing perfect repeats of mono (33.5%), di (14.7%), tri (39.3%), tetra (2.7%), penta (0.7%) and hexa (0.4%) nucleotides were identified from 1,87,763 ESTs of Medicago truncatula. Along with, 70 (8.5%) SSRs of a compound type were also observed. Seven primer pairs of tri repeats were tested for cross transferability in 19 accessions of forage legumes comprising 11 genera. At two different annealing temperatures (55 and 60 degreesC) all primer pairs except AJ410087 reacted with many accessions of forage legumes. Atotal of 51 alleles were detected with six M. truncatula EST-SSRs primer-pairs against DNAfrom 19 accessions representing 11 genera where number of alleles ranged from 2 to 13. The cross-transferability of these EST-SSRs was 40.6% at 55 degreesC and 32.3% at 60 degreesC annealing temperature. 24 alleles of the total 50 (48%) at 55 degreesC and 27 of 51 (53%) at 60 degreesC were polymorphic among the accessions. These 27 polymorphic amplicons identified could be used as DNA markers. This study demonstrates the developed SSR markers from M. truncatula ESTs as a valuable genetic markers and also proposes the possibility of transferring these markers between species of different genera of the legumes of forage importance. It was evident from the results obtained with a set of Desmanthus virgatus accessions where SequentialAgglomerative Hierarchical and Nested (SAHN) cluster analysis based on Dice similarity and Unweighted Pair Group Method with Arithmetic mean Algorithm (UPGMA) revealed significant variability (24 to 74%) among the accessions. High bootstrap values (>30) supported the nodes generated by dendrogram analysis of

  12. A Consistent Phylogenetic Backbone for the Fungi

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  13. A consistent phylogenetic backbone for the fungi.

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-05-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.

  14. Avaliação físico-química de bolo de chocolate com coberturas comestíveis à base de gelatina, ácido esteárico, amido modificado ou cera de carnaúba Physical and chemical evaluation of chocolate cake covered with gelatin, stearic acid, modified starch or "carnaúba" wax edible icing

    Directory of Open Access Journals (Sweden)

    Cibele Cristina Osawa

    2009-03-01

    Full Text Available Coberturas comestíveis biodegradáveis são uma alternativa às embalagens sintéticas, que causam preocupações ambientais. Este trabalho avaliou o efeito de diferentes tipos de coberturas sobre propriedades físico-químicas de bolo de chocolate durante a estocagem, em comparação com bolo sem cobertura (CO e bolo sem cobertura embalado em polipropileno (EMB. As seguintes coberturas foram aplicadas sobre os bolos: 10% gelatina (GE, 10% gelatina com 10% ácido esteárico (GE + AE, 18% cera de carnaúba (CE, 10% amido modificado (AM e fondant (FO. Os bolos foram avaliados durante 10 dias de estocagem. FO e EMB apresentaram menor perda de massa, enquanto todos os demais tratamentos apresentaram valores superiores a CO. GE, GE + AE e EMB apresentaram a menor redução da atividade de água, enquanto CE e CO apresentaram a maior redução. As superfícies dos bolos recobertos estavam mais duras que as de CO e EMB. Os maiores valores para dureza e mastigabilidade foram encontrados para CE e CO e os menores, para EMB, GE e GE + AE. Em relação à cor, GE + AE foi diferente dos demais tratamentos, devido à presença do ácido esteárico. Os resultados indicam que a perda de massa dos bolos pode ser atribuída também à perda de água das coberturas.Biodegradable edible icing or frosting is an alternative to synthetic packaging that causes environmental concerns. This work evaluated the effect of different types of frosting on the physical-chemical properties of chocolate cake during storage in comparison to cakes without icing or frosting (C and cakes without frosting packed in polypropylene (CP. The following frostings were applied to the cakes: 10% gelatin (GE, 10% gelatin with 10% stearic acid (GE+SA, 18% "carnaúba" wax (CW, 10% modified starch (MS, and fondant (FO. The cakes were analyzed during 10 days of storage. FO and CP presented the lowest mass loss while all other treatments presented higher values than C. GE, GE+SA, and CP presented

  15. A Experiência Estética na Perspectiva Naturalista

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    Alberto Marinho Ribas Semeler

    2017-02-01

    Full Text Available Este artigo analisa algumas questões da neuroestética e suas relações com as reflexões históricas sobre a base biológica da experiência estética. A constatação dos vínculos entre biologia e estética não é novidade do mundo tecnológico, pois os gregos já pensavam a esse respeito, como é o caso da teoria naturalista de Aristóteles. O sentido da visão é compreendido enquanto meio produtor de conhecimento e intelecto visual. A neuroestética estabelece um diálogo entre tradição e inovação ao compreender as artes visuais como um subproduto da função evolutiva cerebral revalorizando-a no contexto da pesquisa científica.

  16. Restos de vida en Bajo este sol tremendo de Carlos Busqued

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    Marcos Seifert

    2017-07-01

    Full Text Available Este trabajo se propone analizar cómo la novela de Carlos Busqued Bajo este sol tremendo (2009 se apoya en la representación de vidas desechadas, basura y todo tipo de restos para instalarse en una tensión entre orden y exceso. La narración plantea una lógica en la que la basura, en lugar de constituirse en un indicio que posibilite la reconstrucción del paisaje social, exhibe lo desbordante, lo inasimilable y los vacíos de sentido. En el mundo que nos presenta Busqued lo viviente se vuelve resto en la medida en que encarna una heterogeneidad irreductible a cualquier estructura social y productiva. This paper analyzes the way in which Carlos Busqued's novel Bajo este sol tremendo (2009 is based on the representation of discarded lives, garbage, and all kinds of remains and thus proposes a tension between order and excess. The narration raises a logic in which garbage, instead of constituting an indicator that allows for the reconstruction of the social landscape, exhibits the overflowing, the unassimilable, and the voids of meaning. In the world that Busqued presents, the living becomes a remainder because it embodies an irreducible heterogeneity with regards to any social and productive structure.

  17. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao

    Science.gov (United States)

    Ferraz dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches’ broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. PMID:26949967

  18. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    Directory of Open Access Journals (Sweden)

    Lucas Ferraz Dos Santos

    Full Text Available The cupuassu tree (Theobroma grandiflorum (Willd. ex Spreng. Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified. The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values. Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

  19. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    Science.gov (United States)

    Ferraz Dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses; Micheli, Fabienne; Marcellino, Lucilia Helena

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

  20. Regional characterization of suspected land Punta del Este ( east of the Republica Oriental del Uruguay )

    International Nuclear Information System (INIS)

    Preciozzi, F.; Sanchez Bettucci, L.; Oyhantcabal, P.; Pecoits, E.; Aubet, N.; Peel, E.; Basei, M.

    2003-01-01

    Field Suspect Punta del Este (TSPE) is located in the easternmost portion of Uruguay (Figure 1). This is bounded to the west by Shear Zone Punta del Este-Cordillera (Masquelin, 1990; Preciozzi et al., 1999; 2002), while the east with Rocha makes Formation (Hasui et al, 1975;.. Sanchez-Bettucci and Mezzano, 1993). The TSPE is represented by gneisses and Migmatites formed in the range of 1100 and 630 Ma (Preciozzi et al, in prep.) and have been intensively reworked during Rio Doce orogeny (ca. 600 Ma). Field Suspect Punta del Este (TSPE) is separated from the Neoproterozoic granitoids or granitoids by central Shear Zone Punta del Este-Cordillera represented by a thin strip of mylonite s and gneisses mylonitic able to anatexis. Granitoids are sub alkaline trend throughout of this guideline. The mylonitic foliation has a general direction between N15ºE and N40ºE with sub vertical slope where development ductile quartz and muscovite bands observed (Figure 2). The base of TSPE consists essentially of porphyritic granitoids deformed with biotite and muscovite, and ortho gneisses oftalmíticos granitoids, showing an attenuation of that reaching isotropic deformation terms. From studies in zircons from a sample of ortho gneisses (UCUR 03) by U / Pb conventional and SHRIMP ages of 753 ± 14 Ma for the edge obtained (consistent with the conventional age) and 1000 Ma for zircon center. This has allowed us to recognize in the protoliths one Grenvillian heritage in this area, preserved during crustal melting processes. Also, new U / Pb (Preciozzi et al., In prep.) Data show a orogénesis penicontemporánea to the Brasiliano cycle would be responsible for most of the generation of the rocks that make up the TSPE

  1. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    Directory of Open Access Journals (Sweden)

    Cherubini Marcello

    2010-10-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs are a source of simple sequence repeats (SSRs that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut. Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283 were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak

  2. Characterization of simple sequence repeats (SSRs from Phlebotomus papatasi (Diptera: Psychodidae expressed sequence tags (ESTs

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    Hamarsheh Omar

    2011-09-01

    Full Text Available Abstract Background Phlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs, or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers. Results Simple sequence repeats (SSRs were characterized in P. papatasi expressed sequence tags (ESTs derived from a public database, National Center for Biotechnology Information (NCBI. A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AXn repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation. Conclusion The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

  3. Genetic diversity of Phytophthora sojae isolates in Heilongjiang Province in China assessed by RAPD and EST-SSR

    Science.gov (United States)

    Wu, J. J.; Xu, P. F.; Liu, L. J.; Wang, J. S.; Lin, W. G.; Zhang, S. Z.; Wei, L.

    Random-amplified polymorphic DNA (RAPD) and EST-SSR markers were used to estimate the genetic relationship among thirty-nine P.sojae isolates from three locations in Heilongjiang Province, and nine isolates from Ohio in America were made as reference strains. 10 of 50 RAPD primers and 5 of 33 EST-SSR were polymorphic across 48 P.sojae isolates. Similarity values among P.sojae isolates were from 49% to 82% based on the RAPD data. The similarities based on EST-SSR markers ranged from 47% to 85%. The genetic diversity revealed by EST-SSR marker analysis was higher than that obtained from RAPD. The similarity matrices for the SSR data and the RAPD data were moderately correlated (r = 0.47). Genetic similarity coefficients were also relatively lower, which demonstrated complicated genetic background within each location. The high similarity values range revealed the ability of RAPD/EST-SSR markers to distinguish even among morphological similar phytophthora.

  4. Mundus Totus Exilium Est: Reflections on the Critic in Exile

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    Robert T. Tally Jr.

    2011-05-01

    Full Text Available In his reflections on the project of literary criticism, Erich Auerbach cites the wisdom of a twelfth-century monk, who understood that while the ‘tender beginner’ cleaves to nationality, in the well-developed human being, ‘the whole world is a foreign country [mundus totus exilium est].’ What Auerbach means by quoting this is that a critic must work through his or her attachments to native soil, detach oneself from the local prejudices and comforts, and engage with one’s place as a foreigner or exile, who can thereby map such spaces critically without the distortions caused by undue familiarity. The exiles, émigrés, nomads, renegades, and refugees who create our literary maps also call for a criticism attuned to the spatial peculiarities of the conditions of exile. In an era of globalization, in which the project of literature is fundamentally transnational, the critic who can view the entire world as a foreign land is best suited to making sense of these postnational ensembles.

  5. Orden de no reanimar, consideraciones sobre este problema

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    Dr. G. Luis Cereceda

    2011-05-01

    Se analizan los principales problemas, comenzando por las dificultades según los diferentes escenarios (servicio de urgencia, pabellón de maternidad, sala de hospitalizados, unidad de intensivo, pabellones quirúrgicos; se analiza la incertidumbre sobre el pronóstico de cada pacientes y sobre quién(es deben tomar las decisiones sobre el fin de la vida. Idealmente debe ser el paciente autónomo quien tome la decisión, pero en otros casos se requieren alternativas, una de ellas es la Orden Unilateral. Otros problemas son la Validez de las órdenes de no-RCP en los diferentes tiempos evolutivos, el problema de la Futilidad y la Validez de las “Directivas Anticipadas”, en este grupo resalta el enfoque POLST (Physician’s Order for Life Sustaining Treatment como más comprehensivo; como complemento ha surgido también el concepto AND (Allow Natural Death, que podría estar destinado a remplazar la orden de no-RCP (DNR.

  6. Qu'est que Lila dit? Construyendo Europa

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    Susana Torrado Morales

    2008-01-01

    Full Text Available En este momento, Europa se encuentra inmersa en el proceso de construcción de lo que algunos llaman “alma europea”, otros “sueño europeo”, y que podemos identificar, de forma más directa, con una “identidad europea”. Una “identidad europea” definida como “…aquellos valores que los europeos comparten y que otras partes del mundo admiran”. Pero, ¿realmente existen esos valores comunes?, ¿se muestran en el cine europeo?, ¿se aprecian en películas como Lila dit ça, Monsieur Ibrahim et les fleurs du Coran o Solino? In this moment, Europe is involved in the process of making up a “European soul”, also called “European identity”. The definition of European identity is: “... those Values than European People share and other countries admire”. But, really this values exist? And, if it was the case, we can find it in the European Cinema? In films as Lila dit ça, Monsieur Ibrahim et les fleurs du Coran or Solino?

  7. Putative resistance genes in the CitEST database

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    Simone Guidetti-Gonzalez

    2007-01-01

    Full Text Available Disease resistance in plants is usually associated with the activation of a wide variety of defense responses to prevent pathogen replication and/or movement. The ability of the host plant to recognize the pathogen and to activate defense responses is regulated by direct or indirect interaction between the products of plant resistance (R and pathogen avirulence (Avr genes. Attempted infection of plants by avirulent pathogens elicits a battery of defenses often followed by the collapse of the challenged host cells. Localized host cell death may help to prevent the pathogen from spreading to uninfected tissues, known as hypersensitive response (HR. When either the plant or the pathogen lacks its cognate gene, activation of the plant’s defense responses fails to occur or is delayed and does not prevent pathogen colonization. In the CitEST database, we identified 1,300 reads related to R genes in Citrus which have been reported in other plant species. These reads were translated in silico, and alignments of their amino acid sequences revealed the presence of characteristic domains and motifs that are specific to R gene classes. The description of the reads identified suggests that they function as resistance genes in citrus.

  8. Estética como fisiologia aplicada em Nietzsche

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    Renato Bittencourt

    2010-07-01

    Full Text Available A proposta deste artigo consiste em pensarmos a relação intrínseca que Nietzsche estabelece entre a estética e a compreensão orgânica da vida humana, associada diretamente a uma perspectiva fisiológica. Cabe ressaltar que a noção de fisiologia em Nietzsche não se fundamenta em parâmetros puramente biológicos ou materiais, mas envolve todos os atos criativos do indivíduo. Por conseguinte, para compreendermos de forma precisa a realização da criatividade artística é de suma importância que se faça valer a importância da fisiologia do artista no processo de elaboração da obra de arte. Onde os instintos vitais se encontram em declínio existencial, haverá uma obra de arte decadente; onde os instintos vitais manifestam exuberância, capacidade de assimilação e saúde, haverá uma glorificação da existência através da arte.

  9. Comparing two versions of a non-linear model for simulating leaf number and developmental stages in maize based on air temperature Comparativo de duas versões de modelo não-linear para a simulação do número de folhas e dos estágios de desenvolvimento do milho, baseado na temperatura do ar

    Directory of Open Access Journals (Sweden)

    Nereu Augusto Streck

    2009-06-01

    para a simulação do número de folhas e dos estágios de desenvolvimento em milho, considerando dois métodos de entrada da temperatura diária do ar (temperatura média diária do ar e temperatura mínima/máxima diária do ar. Um experimento de campo com a variedade de milho BRS Missões, semeado em várias datas de semeadura, foi conduzido em Santa Maria, Rio Grande do Sul, Brasil, durante os anos agrícolas 2005-2006 e 2006-2007. A f(T no modelo WE foi calculada usando-se a temperatura média diária do ar calculada pela média aritmética das temperaturas mínima (TN e máxima (TX diárias do ar (WE Tmean e pela média de f(T usando TN e pela de f(T usando TX (WE Tmm. O número de folhas expandidas e totais e os estágios de desenvolvimento (embonecamento e maturidade fisiológica coletados no ano agrícola 2005-2006 foram usados para estimarem-se os coeficientes dos modelos; por sua vez, os estágios coletados no ano agrícola 2006-2007 foram usados como dados independentes para avaliar os modelos. A simulação do número de folhas expandidas e totais, do embonecamento e da maturidade fisiológica da variedade de milho BRS Missões foi melhor com o modelo WE Tmm do que com o modelo WE Tmean.

  10. Estética en prótesis removibles The aesthetics in removable prostheses

    Directory of Open Access Journals (Sweden)

    LVM Lucas

    2010-06-01

    Full Text Available La estética actualmente recibe una importante consideración en el contexto social. Una sonrisa atractiva es aspiración de la mayoría de los pacientes que precisan tratamiento protésico. Los implantes propiciaron una mejoría significativa, con relación a las prótesis removibles, debido a su funcionalidad. El objetivo de este estudio fue explorar en la literatura científica moderna, a fin de hallar aspectos relacionados con la estética en la rehabilitación mediante prótesis removibles. Fueron encontrados factores importantes como: la selección de los dientes artificiales, la disposición de los mismos, la caracterización de la base de resina acrílica, además de los tipos de retenedores para las prótesis parciales removibles. La planificación y aplicación apropiada de este procedimiento, con criterios estéticos correctos, debe ser responsabilidad del profesional.Nowadays, aesthetics is very appreciated in the social context and a attractive smile is the object of desire in most of patients requiring prosthesis treatment. In case of removable prosthesis, total or partial, this feature is more significant since some or all teeth may be absents. Implants leading to a significant improvement in relation to function and comfort of removable prosthesis users, but the aesthetics of these prostheses had little attention in the current scientific literature. Thus, the aim of present article was to make a review of the literature on the aesthetic features related to rehabilitation with removable prostheses. In present study we found as significant factors for the aesthetics in removable partial and total prostheses: selection of artificial teeth and their arrangement, characterization of acrylic resin basis and also the types and location of retainers for the removable partial prostheses. We conclude that the involvement and the aesthetic knowledge during the appropriate planning of this process is responsibility of the professional.

  11. EST and microarray analysis of horn development in Onthophagus beetles

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    Tang Zuojian

    2009-10-01

    Full Text Available Abstract Background The origin of novel traits and their subsequent diversification represent central themes in evo-devo and evolutionary ecology. Here we explore the genetic and genomic basis of a class of traits that is both novel and highly diverse, in a group of organisms that is ecologically complex and experimentally tractable: horned beetles. Results We developed two high quality, normalized cDNA libraries for larval and pupal Onthophagus taurus and sequenced 3,488 ESTs that assembled into 451 contigs and 2,330 singletons. We present the annotation and a comparative analysis of the conservation of the sequences. Microarrays developed from the combined libraries were then used to contrast the transcriptome of developing primordia of head horns, prothoracic horns, and legs. Our experiments identify a first comprehensive list of candidate genes for the evolution and diversification of beetle horns. We find that developing horns and legs show many similarities as well as important differences in their transcription profiles, suggesting that the origin of horns was mediated partly, but not entirely, by the recruitment of genes involved in the formation of more traditional appendages such as legs. Furthermore, we find that horns developing from the head and prothorax differ in their transcription profiles to a degree that suggests that head and prothoracic horns are not serial homologs, but instead may have evolved independently from each other. Conclusion We have laid the foundation for a systematic analysis of the genetic basis of horned beetle development and diversification with the potential to contribute significantly to several major frontiers in evolutionary developmental biology.

  12. Duchamp e a anestesia estética na publicidade

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    João Anzanello Carrascoza

    2008-09-01

    Full Text Available A criação publicitária resulta de uma prática de bricolagem levada a termo pelo redator e pelo diretor de arte – profissionais que atuam em dupla nas agências de propaganda e são os responsáveis pela elaboração das mensagens. Nesse processo, lançam mão de todo tipo de material cultural para criar as peças solicitadas. Ambos se valem sistematicamente, como matéria-prima, de citações de imagens e enunciados fundadores, interferindo em seu significado, o que nos faz pensar nos ready-mades de Duchamp. Este artigo traz uma reflexão sobre o ready-made como método de criação na propaganda e suas implicações no mundo dos signos. Palavras-chave: Publicidade; processo criativo; bricolagem, dialogismo; ready-made. ABSTRACT The creation of advertising is the result of a bricolage process between a writer and an art director leading to an end result. These professional people work as partnership teams in advertising agencies and are responsible for the development of advertising messages. In this process, they use all forms of cultural material to stimulate them in creating the requested pieces. Both individuals systematically draw from the raw material of existing images and phrases to create meaning in the advertising in a way that makes us think of Duchamp’s ready-mades. This article is a reflection on the ready-made as a method of advertisement creation and the implications of it in the world of signs. Keywords: Advertisement; creative process; bricolage, dialogism; ready-made.

  13. Comme c'est curieux, comme c'est bizarre et quelle coïncidence ! concours de nouvelles

    CERN Document Server

    2015-01-01

    Elles sont partout : dans la nature, nichées au coeur des tournesols, des cristaux de quartz et des coquilles d'escargot sous la forme du nombre d'or ; dans nos vies ponctuées de rencontres, d'événements qui se font écho. Coïncidences : simples fruits du hasard, vraiment, ou signes d'une causalité cachée ? Un pigeon aux intestins facétieux rencontre un Président de la République malchanceux... Un obus rencontre une chambre à coucher – mais ses occupants ont rendez-vous avec un gâteau… Un dictateur qui abuse son peuple à coups de coïncidences truquées sera démasqué grâce à la rencontre inopinée d'un officier et d'un poisson… Jonglant avec les probabilités, l'Histoire et l'actualité, les lauréats de cette 6e édition ont montré, cette fois encore, que la rigueur scientifique est la meilleure amie de la fantaisie et de l'imagination. Quant à la table ronde qui ouvre ce recueil, elle croise étymologie, chaînes de causalités et lignes d'univers pour arriver à ce constat, partag�...

  14. Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis.

    Science.gov (United States)

    Low, Eng-Ti L; Alias, Halimah; Boon, Soo-Heong; Shariff, Elyana M; Tan, Chi-Yee A; Ooi, Leslie Cl; Cheah, Suan-Choo; Raha, Abdul-Rahim; Wan, Kiew-Lian; Singh, Rajinder

    2008-05-29

    Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as

  15. Oil palm (Elaeis guineensis Jacq. tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis

    Directory of Open Access Journals (Sweden)

    Ooi Leslie CL

    2008-05-01

    Full Text Available Abstract Background Oil palm (Elaeis guineensis Jacq. is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. Results A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs. The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. Conclusion This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However

  16. Le bonheur n’est pas l’essentiel ?

    Directory of Open Access Journals (Sweden)

    Salome Berthon

    2007-01-01

    Full Text Available Si nos recherches ethnologiques portent en creux la marque du bonheur et du plaisir, à notre connaissance, ces notions ont rarement sinon jamais été exploitées systématiquement. Des émotions positives que l’on nous narre, en des termes souvent valorisants, aux formes du plaisir que les corps, expressifs ou silencieux, traduisent, c’est au croisement de nos terrains respectifs, pointant différents indicateurs, que nous avons tenté de définir ces notions. Visant à dépasser l’anecdotique et le liminaire au moyen d’une méthodologie « prospective », cette écriture commune fait place libre à une réflexion sur le bonheur et les plaisirs en anthropologie. Distinguant l’immédiateté du plaisir, de l’aspect différé, construit, négocié du bonheur, nous tâchons de voir en quoi, selon les situations et les relations, ils relèvent tantôt du « choisi », tantôt du « subi ». Nous portons ensuite un regard réflexif sur la position du chercheur, dont la subjectivité et les affects n’ont de cesse de mettre son ethnographie et son objectivité à l’épreuve. Si son autorité le conduit à dénier cette part émotionnelle, il devra pourtant s’engager, donner de sa personne pour gagner la confiance de ses interlocuteurs, ouvrir au discours et dévoiler quelques traces, faire surgir le non-dit des émotions, observer tant l’intime que le collectif et, in fine, comprendre ce qui du bonheur fait sens. Amorçant notre conclusion, nous nous interrogeons sur les causes et les effets de ces émotions positives, croisant pratiques et représentations, paroles et silences, automatisme et évidence, naturalité et construction, stabilité et mouvement, etc.

  17. A plausibilidade da pós-história no sentido estético

    Directory of Open Access Journals (Sweden)

    Rodrigo Duarte

    2011-01-01

    Full Text Available A ideia do "fim da história", subentendida no capítulo final da Fenomenologia do espírito, serviu de base para o início de uma discussão, feita a partir das posições assumidas por Alexandre Kojève nos seus cursos sobre Hegel em Paris, na década de 1930, e em sua publicação no final dos anos 1940 (com reedição em 1968, voltou à baila com o artigo de Francis Fukuyama, de 1989, sobre o "fim da história", no qual ele comemorava o fim do "socialismo real" e a hegemonia mundial completa dos Estados Unidos da América. Passada a euforia sobre a "nova ordem mundial", inclusive em virtude de sucessivas crises econômicas, é interessante recolocar a questão sobre as condições sob as quais são aceitáveis conceitos associados a esse tema, especialmente o substantivo "pós-história" e o adjetivo "pós-histórico". A tese a ser defendida nesse artigo é a de que o campo da estética é um âmbito em que esses conceitos são defensáveis. Como exemplos de reflexões estéticas frutíferas que deles se valem, são consideradas a noção de "arte pós-histórica", de Arthur Danto, e os desdobramentos estéticos do conceito de "pós-história", tal como sustentado por Vilém Flusser.

  18. MuSICa at GRIS: a prototype image slicer for EST at GREGOR

    Science.gov (United States)

    Calcines, A.; Collados, M.; López, R. L.

    2013-05-01

    This communication presents a prototype image slicer for the 4-m European Solar Telescope (EST) designed for the spectrograph of the 1.5-m GREGOR solar telescope (GRIS). The design of this integral field unit has been called MuSICa (Multi-Slit Image slicer based on collimator-Camera). It is a telecentric system developed specifically for the integral field, high resolution spectrograph of EST and presents multi-slit capability, reorganizing a bidimensional field of view of 80 arcsec^{2} into 8 slits, each one of them with 200 arcsec length × 0.05 arcsec width. It minimizes the number of optical components needed to fulfil this multi-slit capability, three arrays of mirrors: slicer, collimator and camera mirror arrays (the first one flat and the other two spherical). The symmetry of the layout makes it possible to overlap the pupil images associated to each part of the sliced entrance field of view. A mask with only one circular aperture is placed at the pupil position. This symmetric characteristic offers some advantages: facilitates the manufacturing process, the alignment and reduces the costs. In addition, it is compatible with two modes of operation: spectroscopic and spectro-polarimetric, offering a great versatility. The optical quality of the system is diffraction-limited. The prototype will improve the performances of GRIS at GREGOR and is part of the feasibility study of the integral field unit for the spectrographs of EST. Although MuSICa has been designed as a solar image slicer, its concept can also be applied to night-time astronomical instruments (Collados et al. 2010, Proc. SPIE, Vol. 7733, 77330H; Collados et al. 2012, AN, 333, 901; Calcines et al. 2010, Proc. SPIE, Vol. 7735, 77351X)

  19. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

    Directory of Open Access Journals (Sweden)

    Charneau Sébastien

    2009-05-01

    Full Text Available Abstract Background The Plasmodium falciparum genome (3D7 strain published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of P. falciparum genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a P. falciparum FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH to study genes expressed during merozoite morphogenesis, with the aim of: 1 obtaining an exhaustive collection of schizont specific ESTs, 2 experimentally validating or correcting P. falciparum gene models and 3 pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains. Results A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the P. falciparum genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7 and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8, TARE subtelomeric regions (several chromosomes and the recently described telomerase RNA gene (chromosome 9. Conclusion This FcB1-schizont-EST analysis confirmed the actual expression of 243

  20. All 5' EST - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...n of data contents 5' EST sequences Data file File name: CSV: kome_est_5end_all.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...fasta.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_est_5end_...se Description Download License Update History of This Database Site Policy | Contact Us All 5' EST - KOME | LSDB Archive ...

  1. All 3' EST - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...n of data contents 3' EST sequences Data file File name: CSV: kome_est_3end_all.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...fasta.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_est_3end_...se Description Download License Update History of This Database Site Policy | Contact Us All 3' EST - KOME | LSDB Archive ...

  2. Alicyclobacillus acidocaldarius Thermophilic Esterase EST2's Activity in Milk and Cheese Models

    NARCIS (Netherlands)

    Mandrich, L.; Manco, M.; Rossie, M.; Floris, E.; Jansen-van den Bosch, T.; Smit, G.; Wouters, J.A.

    2006-01-01

    The aim of this work was to investigate the behavior of thermophilic esterase EST2 from Alicyclobacillus acidocaldarius in milk and cheese models. The pure enzyme was used to compare the EST2 hydrolytic activity to the activity of endogenous esterase EstA from Lactococcus lactis. The results

  3. Overexpressed Genes/ESTs and Characterization of Distinct Amplicons on 17823 in Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Ayse E. Erson

    2001-01-01

    Full Text Available 17823 is a frequent site of gene amplification in breast cancer. Several lines of evidence suggest the presence of multiple amplicons on 17823. To characterize distinct amplicons on 17823 and localize putative oncogenes, we screened genes and expressed sequence tags (ESTs in existing physical and radiation hybrid maps for amplification and overexpression in breast cancer cell lines by semiquantitative duplex PCR, semiquantitative duplex RT-PCR, Southern blot, Northern blot analyses. We identified two distinct amplicons on 17823, one including TBX2 and another proximal region including RPS6KB1 (PS6K and MUL. In addition to these previously reported overexpressed genes, we also identified amplification and overexpression of additional uncharacterized genes and ESTs, some of which suggest potential oncogenic activity. In conclusion, we have further defined two distinct regions of gene amplification and overexpression on 17823 with identification of new potential oncogene candidates. Based on the amplification and overexpression patterns of known and as of yet unrecognized genes on 17823, it is likely that some of these genes mapping to the discrete amplicons function as oncogenes and contribute to tumor progression in breast cancer cells.

  4. Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids

    Science.gov (United States)

    2011-01-01

    Background Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economically important floriculture industry worldwide. We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome. Results To maximize sequence diversity, we pooled RNA from 10 samples of different tissues, various developmental stages, and biotic- or abiotic-stressed plants. We obtained 206,960 expressed sequence tags (ESTs) with an average read length of 228 bp. These reads were assembled into 8,233 contigs and 34,630 singletons. The unigenes were searched against the NCBI non-redundant (NR) protein database. Based on sequence similarity with known proteins, these analyses identified 22,234 different genes (E-value cutoff, e-7). Assembled sequences were annotated with Gene Ontology, Gene Family and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these annotations, over 780 unigenes encoding putative transcription factors were identified. Conclusion Pyrosequencing was effective in identifying a large set of unigenes from Phalaenopsis. The informative EST dataset we developed constitutes a much-needed resource for discovery of genes involved in various biological processes in Phalaenopsis and other orchid species. These transcribed sequences will narrow the gap between study of model organisms with many genomic resources and species that are important for ecological and evolutionary studies. PMID:21749684

  5. Enhanced rhamnolipid production by Pseudomonas aeruginosa overexpressing estA in a simple medium.

    Directory of Open Access Journals (Sweden)

    Leticia Dobler

    Full Text Available A modified Pseudomonas aeruginosa strain capable of overexpressing the estA gene, an encoding gene for a membrane-bound esterase, was constructed and its rhamnolipid (RML production was studied. Fermentations using wild-type (WT and modified P. aeruginosa strains were conducted until exhaustion of glycerol in Medium Salt Production, using two different C/N ratios. At a C/N of 83.2, the modified strain produced up to 3.9 times more RMLs than the WT, yielding a maximum concentration of 14.62 g/L RML when measured by HPLC and 22 g/L by the orcinol assay. Cell-free supernatant from the modified strain reduced surface tension to 29.4 mN/m and had a CMC of 240 mg/L and CMD of 56.05. This is the first report on the construction of an estA-based recombinant strain for RML production.

  6. Estímulo ao desenvolvimento infantil: produção do conhecimento em enfermagem

    Directory of Open Access Journals (Sweden)

    Bruna Cristine Peres Falbo

    2012-02-01

    Full Text Available Este estudo teve como objetivo identificar as ações de enfermagem para estímulo ao desenvolvimento infantil, em periódicos nacionais e internacionais, no período de 2000 a 2009. Revisão integrativa da literatura, nas bases de dados Medline e Lilacs, com análise de quinze artigos. Os resultados apontam o lúdico como essencial ao desenvolvimento infantil, devendo ser explorado pela enfermagem por meio da arte, música, brinquedos e teatro. Amenizar o estresse da hospitalização com adequação ambiental reduz o seu impacto sobre o desenvolvimento infantil. Orientar e intervir nos inter-relacionamentos são ações de enfermagem para o desenvolvimento social e comportamental infantil. Os temas abordados na literatura são fundamentais para uma prática de enfermagem no cuidado integral à saúde da criança.

  7. Relatório de estágio II de Paula Cristina Paiva da Rocha

    OpenAIRE

    Rocha, Paula Cristina Paiva da

    2017-01-01

    Este relatório de estágio encontra-se inserido na unidade curricular Estágio II, no âmbito do curso, Mestrado Integrado em Ciências Farmacêuticas. Este estágio apresenta a duração total de cinco meses, sendo que 3 meses decorrem em Farmácia Hospitalar, e os restantes 2 meses decorrem em Farmácia Comunitária. Este relatório de estágio consiste na descrição de todas as atividades desenvolvidas no seu decorrer, tanto nos Serviços Farmacêuticos do Hospital General Universitário de Castellón, ...

  8. ESSE versus ESTE in Brazilian movies: substitution or specialization?

    Directory of Open Access Journals (Sweden)

    Hélcius Batista Pereira

    2013-02-01

    Full Text Available This study aims at contributing to the discussion on the uses of demonstrative pronouns in Brazilian Portuguese. For this end, samples of Brazilian films were analyzed. It was found that in the endophoric uses and in the spatial exophoric uses there is a tendency to substitute “este” with “esse”. Based on these results, it was found that Marine thesis (2004 which defends that “Brazilian Portuguese” has a binary paradigm, in which “esse” has become specialized in endophoric uses and “este” has become specialized in exophoric uses is not correct.

  9. Genome based analyses of six hexacorallian species reject the “naked coral” hypothesis

    KAUST Repository

    Wang, Xin

    2017-09-23

    Scleractinian corals are the foundation species of the coral-reef ecosystem. Their calcium carbonate skeletons form extensive structures that are home to millions of species, making coral reefs one of the most diverse ecosystems of our planet. However, our understanding of how reef-building corals have evolved the ability to calcify and become the ecosystem builders they are today is hampered by uncertain relationships within their subclass Hexacorallia. Corallimorpharians have been proposed to originate from a complex scleractinian ancestor that lost the ability to calcify in response to increasing ocean acidification, suggesting the possibility for corals to lose and gain the ability to calcify in response to increasing ocean acidification. Here we employed a phylogenomic approach using whole-genome data from six hexacorallian species to resolve the evolutionary relationship between reef-building corals and their non-calcifying relatives. Phylogenetic analysis based on 1,421 single-copy orthologs, as well as gene presence/absence and synteny information, converged on the same topologies, showing strong support for scleractinian monophyly and a corallimorpharian sister clade. Our broad phylogenomic approach using sequence-based and sequence-independent analyses provides unambiguous evidence for the monophyly of scleractinian corals and the rejection of corallimorpharians as descendants of a complex coral ancestor.

  10. Phylogenomics characterization of a highly virulent Edwardsiella strain ET080813(T) encoding two distinct T3SS and three T6SS gene clusters: Propose a novel species as Edwardsiella anguillarum sp. nov.

    Science.gov (United States)

    Shao, Shuai; Lai, Qiliang; Liu, Qin; Wu, Haizhen; Xiao, Jingfan; Shao, Zongze; Wang, Qiyao; Zhang, Yuanxing

    2015-02-01

    As important zoonotic organisms causing infections in humans, Edwardsiella bacteria are also notorious leading fish pathogens haunting worldwide aquaculture industries. However, the taxa are now widely recognized to be misclassified, which hurdled the understanding of the epidemiology and development of effective diagnostics and vaccines. Currently the genus Edwardsiella consists of three species Edwardsiella tarda, E. ictaluri, and E. hoshinae. Previous phylogenomic analysis revealed that E. tarda strains display two major highly divergent genomic types (genotypes), EdwGI and EdwGII, and the former represents a genotype of fish-pathogenic isolates and being recently proposed as a novel species E. piscicida, sp. nov. Here multiple phylogenetic analyses and the genome-level comparisons of EdwGI strains disclose that the phylogroup strains from diseased eel formed an obviously distinct cluster that could be equated with a new species status. The phylogenetic evidence for the new species assignment was also supported by corresponding DNA-DNA hybridization estimation values and by phenotypic characteristics. Interestingly, further comparative genomics reveals that these strains have acquired the locus of enterocyte effacement (LEE) genes and as a result these bacteria contain at least 2 sets of distinct T3SS and 3 sets of T6SS gene clusters, respectively. It is therefore proposed that the phylogroup strains from diseased eel should be classified as Edwardisella anguillarum sp. nov., and the type strain is ET080813(T) (=DSM27202(T)=CCUG 64215(T)=CCTCC AB2013118(T)=MCCC 1K00238(T)). These findings will contribute to development of species-specific control measures against Edwardsiella bacterium in aquatic animals, while also shedding light on the pathogenesis evolution in Edwardsiella bacterium. Copyright © 2014 Elsevier GmbH. All rights reserved.

  11. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik

    2007-01-01

    MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data...... in public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non...

  12. De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers.

    Directory of Open Access Journals (Sweden)

    Yan Long

    Full Text Available Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp. The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%, suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.

  13. Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues

    Directory of Open Access Journals (Sweden)

    Mouchiroud Dominique

    2006-04-01

    Full Text Available Abstract Background Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this study was to scan for such genes by whole-genome in silico subtraction using Expressed Sequence Tag (EST data. Methods Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis. Results Our genome-wide expression analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined. Conclusion Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers, our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer.

  14. EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.

    Science.gov (United States)

    Forment, Javier; Gilabert, Francisco; Robles, Antonio; Conejero, Vicente; Nuez, Fernando; Blanca, Jose M

    2008-01-07

    Expressed sequence tag (EST) collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation. We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval. The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http://bioinf.comav.upv.es/est2uni. This site also provides detailed instructions

  15. EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration

    Directory of Open Access Journals (Sweden)

    Nuez Fernando

    2008-01-01

    Full Text Available Abstract Background Expressed sequence tag (EST collections are composed of a high number of single-pass, redundant, partial sequences, which need to be processed, clustered, and annotated to remove low-quality and vector regions, eliminate redundancy and sequencing errors, and provide biologically relevant information. In order to provide a suitable way of performing the different steps in the analysis of the ESTs, flexible computation pipelines adapted to the local needs of specific EST projects have to be developed. Furthermore, EST collections must be stored in highly structured relational databases available to researchers through user-friendly interfaces which allow efficient and complex data mining, thus offering maximum capabilities for their full exploitation. Results We have created EST2uni, an integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections. The pipeline uses standard EST analysis tools and the software has a modular design to facilitate the addition of new analytical methods and their configuration. Currently implemented analyses include functional and structural annotation, SNP and microsatellite discovery, integration of previously known genetic marker data and gene expression results, and assistance in cDNA microarray design. It can be run in parallel in a PC cluster in order to reduce the time necessary for the analysis. It also creates a web site linked to the database, showing collection statistics, with complex query capabilities and tools for data mining and retrieval. Conclusion The software package presented here provides an efficient and complete bioinformatics tool for the management of EST collections which is very easy to adapt to the local needs of different EST projects. The code is freely available under the GPL license and can be obtained at http://bioinf.comav.upv.es/est

  16. A experiência estética sob um olhar fenomenológico

    Directory of Open Access Journals (Sweden)

    Alice Casanova Reis

    2011-01-01

    Full Text Available Este artículo describe la experiencia estética como un fenómeno centrado en la percepción sensorial. El trabajo se desarrolla a partir de una investigación de la psicología social basado en la fenomenología, sobre todo en los planteamientos de Merleau-Ponty y Dufrenne. Concibe la experiencia estética como un modo de relación mediada por la percepción sensorial de un objeto estético. Se analizan diversos aspectos de la experiencia estética: la dimensión relacional y sensible; ¿cómo se constituye el sujeto y el objeto estético; la dimensión corporal de la experiencia estética; la intencionalidad en la estética; la experiencia estética de la naturaleza. Llegamos a la conclusión de que hay un significado ontológico de la experiencia estética, ya que proporciona una apertura a la diferencia por el contacto con la alteridad, y una nueva mirada a la realidad. Se destaca al final la relevancia de esta experiencia a la Psicología Social.

  17. Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs

    Directory of Open Access Journals (Sweden)

    Lanfranchi Gerolamo

    2002-10-01

    Full Text Available Abstract Background We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 EST clusters from a non-normalized subtracted muscle EST sequencing project (28,074 EST sequences. This set included 369 novel EST clusters showing no match to previously characterized proteins in any database. Each probe set was designed to contain 20–32 25 mer oligonucleotides (10–16 paired perfect match and mismatch probe pairs per gene, with each probe evaluated for hybridization kinetics (Tm and similarity to other sequences. The 120,000 oligonucleotides were synthesized by photolithography and light-activated chemistry on each microarray. Results Hybridization of human muscle cRNAs to this MuscleChip (33 samples showed a correlation of 0.6 between the number of ESTs sequenced in each cluster and hybridization intensity. Out of 369 novel EST clusters not showing any similarity to previously characterized proteins, we focused on 250 EST clusters that were represented by robust probe sets on the MuscleChip fulfilling all stringent rules. 102 (41% were found to be consistently "present" by analysis of hybridization to human muscle RNA, of which 40 ESTs (39% could be genome anchored to potential transcription units in the human genome sequence. 19 ESTs of the 40 ESTs were furthermore computer-predicted as exons by one or more than three gene identification algorithms. Conclusion Our analysis found 40 transcriptionally validated, genome-anchored novel EST clusters to be expressed in human muscle. As most of these ESTs were low copy clusters (duplex and triplex in the original 28,000 EST project, the identification of these as significantly expressed is a robust validation of the transcript units that permits subsequent focus on the novel proteins encoded by these genes.

  18. O estágio supervisionado: fios, desafios, movimentos e possibilidades de formação

    Directory of Open Access Journals (Sweden)

    Luis Távora Furtado Ribeiro

    2017-09-01

    Full Text Available Discute-se aqui o estágio supervisionado como um processo que deve possibilitar aos estagiários fazer uso constante do diálogo, da indagação e da reflexão sobre as experiências, as habilidades, as atitudes e os conhecimentos construídos e em construção, buscando sempre dar significado às aprendizagens apreendidas a partir deste processo. Com base em pesquisas e ensaios relevantes sobre o tema, busca-se aqui sublinhar a experiência do estágio como um processo contínuo e dinâmico de aprendizagens acerca da profissão docente, assim como suas relações com os variados territórios e tempos e, ainda, os modos de ser, de fazer e de estar na profissão. Conclui-se sublinhando a importância de se vivenciar uma experiência do estágio ancorando-se em uma perspectiva crítica-reflexiva, assim como a relevância da participação, do interesse e do estagiário manter uma postura ativa nas atividades realizadas no estágio.

  19. Est16, a New Esterase Isolated from a Metagenomic Library of a Microbial Consortium Specializing in Diesel Oil Degradation.

    Science.gov (United States)

    Pereira, Mariana Rangel; Mercaldi, Gustavo Fernando; Maester, Thaís Carvalho; Balan, Andrea; Lemos, Eliana Gertrudes de Macedo

    2015-01-01

    Lipolytic enzymes have attracted attention from a global market because they show enormous biotechnological potential for applications such as detergent production, leather processing, cosmetics production, and use in perfumes and biodiesel. Due to the intense demand for biocatalysts, a metagenomic approach provides methods of identifying new enzymes. In this study, an esterase designated as Est16 was selected from 4224 clones of a fosmid metagenomic library, revealing an 87% amino acid identity with an esterase/lipase (accession number ADM63076.1) from an uncultured bacterium. Phylogenetic studies showed that the enzyme belongs to family V of bacterial lipolytic enzymes and has sequence and structural similarities with an aryl-esterase from Pseudomonas fluorescens and a patented Anti-Kazlauskas lipase (patent number US20050153404). The protein was expressed and purified as a highly soluble, thermally stable enzyme that showed a preference for basic pH. Est16 exhibited activity toward a wide range of substrates and the highest catalytic efficiency against p-nitrophenyl butyrate and p-nitrophenyl valerate. Est16 also showed tolerance to the presence of organic solvents, detergents and metals. Based on molecular modeling, we showed that the large alpha-beta domain is conserved in the patented enzymes but not the substrate pocket. Here, it was demonstrated that a metagenomic approach is suitable for discovering the lipolytic enzyme diversity and that Est16 has the biotechnological potential for use in industrial processes.

  20. Est16, a New Esterase Isolated from a Metagenomic Library of a Microbial Consortium Specializing in Diesel Oil Degradation.

    Directory of Open Access Journals (Sweden)

    Mariana Rangel Pereira

    Full Text Available Lipolytic enzymes have attracted attention from a global market because they show enormous biotechnological potential for applications such as detergent production, leather processing, cosmetics production, and use in perfumes and biodiesel. Due to the intense demand for biocatalysts, a metagenomic approach provides methods of identifying new enzymes. In this study, an esterase designated as Est16 was selected from 4224 clones of a fosmid metagenomic library, revealing an 87% amino acid identity with an esterase/lipase (accession number ADM63076.1 from an uncultured bacterium. Phylogenetic studies showed that the enzyme belongs to family V of bacterial lipolytic enzymes and has sequence and structural similarities with an aryl-esterase from Pseudomonas fluorescens and a patented Anti-Kazlauskas lipase (patent number US20050153404. The protein was expressed and purified as a highly soluble, thermally stable enzyme that showed a preference for basic pH. Est16 exhibited activity toward a wide range of substrates and the highest catalytic efficiency against p-nitrophenyl butyrate and p-nitrophenyl valerate. Est16 also showed tolerance to the presence of organic solvents, detergents and metals. Based on molecular modeling, we showed that the large alpha-beta domain is conserved in the patented enzymes but not the substrate pocket. Here, it was demonstrated that a metagenomic approach is suitable for discovering the lipolytic enzyme diversity and that Est16 has the biotechnological potential for use in industrial processes.

  1. As estratégias da microempresa varejista e seus estágios de informatização.

    Directory of Open Access Journals (Sweden)

    Roberto Antônio Hoffmann

    2009-04-01

    Full Text Available Usualmente, os estudos relacionados à estratégia organizacional verificam comoos comportamentos estratégicos (MILES; SNOW, 1978 são abordados pelas organizações.Este trabalho contrapõe tais comportamentos aos estágios de informatizaçãodetectados, visando à possibilidade de o comportamento estratégico daempresa influenciar ou não sua percepção da tecnologia da informação (TI. Adeterminação do estágio de informatização em que as empresas desta pesquisase encontravam foi embasada nos processos de absorção da TI, elaborados porNolan (1979, nos quais se detectou predominância de abstenções (não uso eestágios mais avançados (controle, desmistificando a fase de iniciação como proeminente.O comportamento estratégico predominante detectado foi o defensivo.Com base nos elementos diagnosticados (estágio e comportamento, verificousea correlação entre eles por meio de um teste ANOVA, que indicou, de formaconclusiva, a existência dessa dependência nas variáveis envolvidas, resultandoque as empresas pesquisadas podem estar utilizando a informatização como umaferramenta estratégica.

  2. The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics.

    Science.gov (United States)

    Linchangco, Gregorio V; Foltz, David W; Reid, Rob; Williams, John; Nodzak, Conor; Kerr, Alexander M; Miller, Allison K; Hunter, Rebecca; Wilson, Nerida G; Nielsen, William J; Mah, Christopher L; Rouse, Greg W; Wray, Gregory A; Janies, Daniel A

    2017-10-01

    Multi-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century. Open questions include relationships within asteroids and the status of the enigmatic taxon Xyloplax. Xyloplax is thought by some to represent a newly discovered sixth class of echinoderms - and by others to be an asteroid. To address these questions, we applied a novel workflow to a large RNA-seq dataset that encompassed a broad taxonomic and genomic sample. This study included 15 species sampled from all extant orders and 13 families, plus four ophiuroid species as an outgroup. To expand the taxonomic coverage, the study also incorporated five previously published transcriptomes and one previously published expressed sequence tags (EST) dataset. We developed and applied methods that used a range of alignment parameters with increasing permissiveness in terms of gap characters present within an alignment. This procedure facilitated the selection of phylogenomic data subsets from large amounts of transcriptome data. The results included 19 nested data subsets that ranged from 37 to 4,281loci. Tree searches on all data subsets reconstructed Xyloplax as a velatid asteroid rather than a new class. This result implies that asteroid morphology remains labile well beyond the establishment of the body plan of the group. In the phylogenetic tree with the highest average asteroid nodal support several monophyletic groups were recovered. In this tree, Forcipulatida and Velatida are monophyletic and form a clade that includes Brisingida as sister to

  3. Rapid in silico cloning of genes using expressed sequence tags (ESTs).

    Science.gov (United States)

    Gill, R W; Sanseau, P

    2000-01-01

    Expressed sequence tags (ESTs) are short single-pass DNA sequences obtained from either end of cDNA clones. These ESTs are derived from a vast number of cDNA libraries obtained from different species. Human ESTs are the bulk of the data and have been widely used to identify new members of gene families, as markers on the human chromosomes, to discover polymorphism sites and to compare expression patterns in different tissues or pathologies states. Information strategies have been devised to query EST databases. Since most of the analysis is performed with a computer, the term "in silico" strategy has been coined. In this chapter we will review the current status of EST databases, the pros and cons of EST-type data and describe possible strategies to retrieve meaningful information.

  4. Lecture actentielle dans Trop c'est trop de Protais Asseng | IKANGA ...

    African Journals Online (AJOL)

    La naissance de cet enfant lui conférait le titre de "Papa national" Bakony symbolise la recherche de bonheur sur le dos d'un humain. C'est de l'exploitation de la femme par l'homme. Mais la multipare Bissabey, son épouse, n'est pas de son avis. Cette instrumentalisation est alors la pomme de discorde entre le couple et ...

  5. Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

    Directory of Open Access Journals (Sweden)

    Dunham Rex

    2007-06-01

    Full Text Available Abstract Background EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. Results A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus and 5 from blue catfish (I. furcatus. A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. Conclusion The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.

  6. An elm EST database for identifying leaf beetle egg-induced defense genes

    Directory of Open Access Journals (Sweden)

    Büchel Kerstin

    2012-06-01

    Full Text Available Abstract Background Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor, egg laying by the elm leaf beetle ( Xanthogaleruca luteola activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes. Results Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i untreated control elms, and elms treated with (ii egg laying and feeding by elm leaf beetles, (iii feeding, (iv artificial transfer of egg clutches, and (v methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs were identified which clustered into 52,823 unique transcripts (Unitrans and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction

  7. ¿Lo que este texto quiere [o no quiere] decir?

    Directory of Open Access Journals (Sweden)

    Daiane Lopes

    2014-07-01

    Full Text Available Sabemos que la literatura suscita conocimiento. El proceso de aprendizaje a través de la lectura literaria acompaña todas las fases de la vida. Sin embargo, una definición para ese tipo de conocimiento es compleja, ya que él es subjetivo y se manifiesta de modo muy individual. Eso ocurre debido al diálogo que pasa entre texto, autor y lector. Se cada individuo carga consigo un texto, al leer, nuestra producción de sentidos irá diferir de la producción de los demás lectores. De esa forma, expondremos, en el presente estudio, algunas reflexiones sobre el conocimiento propiciado por la lectura literaria. Primeramente, presentaremos una síntesis del cuento “En Casa”, de Anton Pavlovitch Tchekhov, texto que motivó la realización del artículo y que servirá de ejemplo para todas las ponderaciones presentadas. Enseguida, realizaremos algunas consideraciones sobre la literatura infantil, considerándola como el inicio del contacto con el texto literario. Argumentaremos sobre los efectos de la literatura tanto en adultos como en niños, así como sobre las maneras de presentación de tal arte al lector. Finalmente, intentaremos caracterizar el conocimiento provocado por la literatura, teniendo como base, entre otros, autores como Vigotsky y Umberto Eco. El texto es compuesto de cuestionamientos y de posibles respuestas, ya que no posee la intención de exhibir convicciones, pero de promover reflexiones sobre la temática. En nuestra investigación teórica, percibimos, entonces, que no es posible contestar a la indagación sobre “lo que un texto quiere decir”, cuestionamiento que intitula el artigo. Tal respuesta irá sufrir variaciones todas las veces que la lectura fuere hecha por lectores diferentes o hasta mismo cuando el mismo lector leer el mismo texto otra vez. Las posibles respuestas, en realidad, estarán respondiendo a una otra cuestión: ¿cómo es el conocimiento propiciado por la literatura? Para este, presentaremos

  8. An elm EST database for identifying leaf beetle egg-induced defense genes.

    Science.gov (United States)

    Büchel, Kerstin; McDowell, Eric; Nelson, Will; Descour, Anne; Gershenzon, Jonathan; Hilker, Monika; Soderlund, Carol; Gang, David R; Fenning, Trevor; Meiners, Torsten

    2012-06-15

    Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor), egg laying by the elm leaf beetle ( Xanthogaleruca luteola) activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes. Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i) untreated control elms, and elms treated with (ii) egg laying and feeding by elm leaf beetles, (iii) feeding, (iv) artificial transfer of egg clutches, and (v) methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs) were identified which clustered into 52,823 unique transcripts (Unitrans) and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant) database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism

  9. La estética del entorno y el cognitivismo científico

    OpenAIRE

    Rosa Martínez, María del Mar

    2014-01-01

    Abandonado el estudio de la naturaleza durante casi dos siglos, la estética del entorno entronca hoy con la estética de la naturaleza de Kant y debate sus presupuestos en dos posiciones fundamentales: cognitivismo y no-cognitivismo. En particular, el llamado cognitivismo científico reclama para el juicio estético la mediación imprescindible de conceptos científicos. En el artículo se discute la teoría de Allen Carlson, su principal representante, y se compara con la estética no cognitivista d...

  10. A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Srinivasan Ramamurthy

    2009-11-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L., an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs and gene-based markers. Results A total of 20,162 (18,435 high quality drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons. Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965 had significant similarity (≤1E-05 to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut and three model plant species (rice, Arabidopsis and poplar provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3% significant unigenes, only 2,071 (32.3% unigenes could be functionally categorised according to Gene Ontology (GO descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs in 742 contigs (with ≥ 5 ESTs were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive

  11. Genetic characterization of an elite coffee germplasm assessed by gSSR and EST-SSR markers.

    Science.gov (United States)

    Missio, R F; Caixeta, E T; Zambolim, E M; Pena, G F; Zambolim, L; Dias, L A S; Sakiyama, N S

    2011-10-06

    Coffee is one of the main agrifood commodities traded worldwide. In 2009, coffee accounted for 6.1% of the value of Brazilian agricultural production, generating a revenue of US$6 billion. Despite the importance of coffee production in Brazil, it is supported by a narrow genetic base, with few accessions. Molecular differentiation and diversity of a coffee breeding program were assessed with gSSR and EST-SSR markers. The study comprised 24 coffee accessions according to their genetic origin: arabica accessions (six traditional genotypes of C. arabica), resistant arabica (six leaf rust-resistant C. arabica genotypes with introgression of Híbrido de Timor), robusta (five C. canephora genotypes), Híbrido de Timor (three C. arabica x C. canephora), triploids (three C. arabica x C. racemosa), and racemosa (one C. racemosa). Allele and polymorphism analysis, AMOVA, the Student t-test, Jaccard's dissimilarity coefficient, cluster analysis, correlation of genetic distances, and discriminant analysis, were performed. EST-SSR markers gave 25 exclusive alleles per genetic group, while gSSR showed 47, which will be useful for differentiating accessions and for fingerprinting varieties. The gSSR markers detected a higher percentage of polymorphism among (35% higher on average) and within (42.9% higher on average) the genetic groups, compared to EST-SSR markers. The highest percentage of polymorphism within the genetic groups was found with gSSR markers for robusta (89.2%) and for resistant arabica (39.5%). It was possible to differentiate all genotypes including the arabica-related accessions. Nevertheless, combined use of gSSR and EST-SSR markers is recommended for coffee molecular characterization, because EST-SSRs can provide complementary information.

  12. Radiation-induced progressive decreasing in the expression of reverse transcriptase gene of hEST2 and telomerase activity

    International Nuclear Information System (INIS)

    Zhu Hanneng; Chen Wenying; Xiong Sidong

    2000-01-01

    Telomerase is a ribonucleoprotein complex that adds heximeric repeats called telomeres to the growing ends of chromosomal DNA. Telomerase activity is present in a vast majority of tumors but is repressed in most normal tissues. Human telomerase catalytic subunit gene (hEST2) reverse transcriptase (RT) segment was cloned by PCR according to the sequence published in GeneBank. PCR was used to investigate the expression of the hEST2 RT segment in diverse tumors as well as in various normal tissues. Results indicated that hEST2 RT segment was detectable in tumor cells lines but not in normal cells and tissues. In order to identify the relationship between telomerase and the biological effect of radiation injury, HeLa cells, KB cells and A431 cells were employed to measure the change in telomerase activity after 60 Co-ray irradiation at RNA level and protein level. Quantitative PCR determined that expression of hEST2 RT segment that encodes seven motifs of the human telomeras decreased with increasing dosage of radiation. In addition, a PCR-based telomeric repeat amplification protocol was used to assay telomerase activity after exposure to radiation. The results strongly support the experiments we had made: Telomerase activity decreases with increasing dosage of radiation. We conclude that detection of the hEST2 RT segment by Northern blotting is a new method for detecting telomerase activity. Furthermore, radiation can cause a dose-dependent decrease in telomerase activity. The effect of radiation on telomerase is one possible reason for the death of cancer cells after irradiation. (author)

  13. Este tiempo clausurado que no me pertenece: Los años falsos, de Josefina Vicens

    Directory of Open Access Journals (Sweden)

    Gerardo Bustamante Bermúdez

    2011-07-01

    Full Text Available En 1982, Josefina Vicens dio a conocer su segunda novela titulada Los años falsos. En este artículo se analiza el tema del patriarcado mexicano en las estructuras familiares en donde el poder, la violencia, la infidelidad, la corrupción, el machismo y la subordinación de las mujeres respecto a la autoridad del patriarca constituyen la base de un discurso incisivo en el que Vicens observa las relaciones de género dentro de la familia tradicional mexicana. A lo largo de este texto se habla sobre la identidad asignada al protagonista de la novela, así como la ambigüedad respecto a su construcción de género que, no obstante, queda al margen de sus deseos y posibles realizaciones. Se trata de una vida anulada por una especie de testamento de género por parte del patriarca ausente / presente. In 1982, Josefina Vicens published her second novel entitled The False Years. This article discusses the issue of Mexican patriarchy in family structures where power, violence, infidelity, corruption, machismo and the subordination of women with regard to the authority of the patriarch form the basis of an incisive discourse in which Vicens observes gender relations within the traditional Mexican family. The identity of the novel’s protagonist is discussed throughout the narrative, as is his ambivalence with respect to the construction of his gender, a feeling relegated to the margins of his wishes and possible acheivements. It is the portrait of a life nullified by a sort of testament of gender handed down by the absent/present figure of the patriarch.

  14. Estética del devenir adverso en la narrativa de Franz Kafka

    Directory of Open Access Journals (Sweden)

    Adriana De La Hoz

    2015-08-01

    Full Text Available En este ensayo se disertará sobre un problema que parece ser poco cuestionado en los trabajos precedentes que se han inspirado en la incomparable narrativa de Franz Kafka. Hablamos en particular de la “estética de lo adverso”, de la imposibilidad, del obstáculo, del fracaso; aspectos que se desvelan como un vector temático con desarrollo semántico y de constante aparición en la obra del escritor checo. Frente a tan intrincada semiosis, nuestra pretensión es responder parcialmente a algunas preguntas que buscan abrir espacios sígnicos que permitan hacer una lectura más amplia y, quizá, más edificante de la obra kafkiana, lo que necesariamente concluirá en el fracaso como una nueva alternativa hermenéutica, o una alternativa hermenéutica construida desde el fracaso. This essay deals with a problem that does not seem to be questioned in preceding works based on Franz Kafta’s incomparable narrative. We are specifically speaking of “the aesthetics of the adverse,” the impossibility, the obstacle, the failure; aspects that are revealed as a topic with semantic development and with permanent appearance in the work of this Czech writer. Before such a complicated semiosis, our intention is to partially respond to some questions intended to open sign spaces that allow having a wider and maybe more edifying reading of Kaffa’s work, which will necessarily result in the failure as a new hermeneutic alternative or a hermeneutic alternative built from failure.

  15. Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

    Directory of Open Access Journals (Sweden)

    Weis Patrick

    2010-01-01

    Full Text Available Abstract Background The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration. Results A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish. Conclusion We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

  16. Plastics and microplastics on recreational beaches in Punta del Este (Uruguay): Unseen critical residents?

    Science.gov (United States)

    Lozoya, J P; Teixeira de Mello, F; Carrizo, D; Weinstein, F; Olivera, Y; Cedrés, F; Pereira, M; Fossati, M

    2016-11-01

    Beaches are social-ecological systems that provide several services improving human well-being. However, as one of the major coastal interfaces they are subject to plastic pollution, one of the most significant global environmental threats at present. For the first time for Uruguayan beaches, this study assessed and quantified the accumulation of plastic and microplastic debris on sandy beaches of the major touristic destination Punta del Este during the austral spring of 2013. Aiming to provide valuable information for decision-making, we performed a detailed analysis of plastic debris, their eventual transport pathways to the coast (from land and sea), and the associated persistent pollutants. The results indicated that the smallest size fractions (plastic debris, and their levels did not differ from baseline values reported for similar locations. The abundance of plastic debris was significantly and positively correlated with both the presence of possible land-based sources (e.g. storm-water drains, beach bars, beach access, car parking, and roads), and dissipative beach conditions. The analysis of coastal currents suggested some potential deposition areas along Punta del Este, and particularly for resin pellets, although modeling was not conclusive. From a local management point of view, the development and use of indices that allow predicting trends in the accumulation of plastic debris would be critically useful. The time dimension (e.g. seasonal) should also be considered for this threat, being crucial for locations such as Uruguay, where the use of beaches increases significantly during the summer. This first diagnosis aims to generate scientific baseline, necessary for improved management of plastic litter on beaches and their watersheds. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. A linkage map of the Atlantic salmon (Salmo salar based on EST-derived SNP markers

    Directory of Open Access Journals (Sweden)

    Kjøglum Sissel

    2008-05-01

    Full Text Available Abstract Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers. Results The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r2 dropped to half its maximum value (above baseline within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD' at inter-marker distances less than 5 cM. Conclusion The linkage map presented here is an important resource for genetic, comparative, and physical mapping of the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the male map length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparently small physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.

  18. Characterization of EST-based SSR loci in the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae)

    Science.gov (United States)

    B.M.T. Brunet; D. Doucet; B.R. Sturtevant; F.A.H. Sperling

    2013-01-01

    After identifying 114 microsatellite loci from Choristoneura fumiferana expressed sequence tags, 87 loci were assayed in a panel of 11 wild-caught individuals, giving 29 polymorphic loci. Further analysis of 20 of these loci on 31 individuals collected from a single population in northern Minnesota identified 14 in Hardy-Weinberg equilibrium.

  19. pyParticleEst: A Python Framework for Particle-Based Estimation Methods

    Directory of Open Access Journals (Sweden)

    Jerker Nordh

    2017-06-01

    Full Text Available Particle methods such as the particle filter and particle smoothers have proven very useful for solving challenging nonlinear estimation problems in a wide variety of fields during the last decade. However, there are still very few existing tools available to support and assist researchers and engineers in applying the vast number of methods in this field to their own problems. This paper identifies the common operations between the methods and describes a software framework utilizing this information to provide a flexible and extensible foundation which can be used to solve a large variety of problems in this domain, thereby allowing code reuse to reduce the implementation burden and lowering the barrier of entry for applying this exciting field of methods. The software implementation presented in this paper is freely available and permissively licensed under the GNU Lesser General Public License, and runs on a large number of hardware and software platforms, making it usable for a large variety of scenarios.

  20. An EST-SSR based linkage map for Persea americana Mill. (avocado)

    Science.gov (United States)

    Recent enhancement of the pool of known molecular markers for avocado has allowed the construction of the first moderate density genetic map for this species. Over 300 microsatellite markers have been characterized and 163 of these were used to construct a map from the cross of two Florida cultivar...

  1. Comparative expression profiling in grape (Vitis vinifera berries derived from frequency analysis of ESTs and MPSS signatures

    Directory of Open Access Journals (Sweden)

    Cook Douglas R

    2008-05-01

    Full Text Available Abstract Background Vitis vinifera (V. vinifera is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS and combined it with available Expressed Sequence Tag (EST data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. Results The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS. A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was ~49 TPM (Transcripts Per Million. Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. Conclusion The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed

  2. Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

    Science.gov (United States)

    Iandolino, Alberto; Nobuta, Kan; da Silva, Francisco Goes; Cook, Douglas R; Meyers, Blake C

    2008-05-12

    Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not

  3. Hermon est

    OpenAIRE

    Aliquot, Julien

    2012-01-01

    105. Deir el-Aachaiyer Architecture : Krencker & Zschietzschmann 1938, p. 256-264, 292-293, pl. 110-115 et 118, 27 (état des lieux en 1905, compléments en 1933) ; Dentzer-Feydy 1999, p. 531-532 et 551 (notes et dessins de W.J. Bankes) ; Chéhab 1949-1950, p. 111 (tête tourelée de Tyché). Photos : Taylor 1971, p. 86-89 ; Blas de Roblès, Pieri & Yon 2004, p. 179-180 ; Nordiguian 2005, p. 104-105. Site revu. Épigraphie : IGLS 11, 4 (dédicace). Le village moderne de Deir el-Aachaiyer (1250 m d’alt...

  4. Análisis de ESTs de yuca (Manihot esculenta: una herramienta para el descubrimiento de genes.

    Directory of Open Access Journals (Sweden)

    Andres Zapata

    2011-01-01

    Full Text Available La yuca (Manihot esculenta constituye la base de la alimentación para más de 1.000 millones de personas en el mundo, consolidándose como el cuarto cultivo más importante en el mundo después del arroz, el maíz y el trigo. La yuca es considerada como un cultivo relativamente tolerante a condiciones de estrés abiótico y biótico, sin embargo estas características se encuentran principalmente en variedades no comerciales. Las estrategias de mejoramiento genético convencional o mediadas por transformación genética representan una alternativa para introducir las características deseadas dentro de las variedades comerciales. Un paso fundamental con miras a acelerar los procesos de mejoramiento genético en yuca requiere el descubrimiento de los respectivos genes relacionados con las características buscadas, para lo cual los ESTs (del inglés Expressed Sequence Tags son una vía rápida para este fin. En este estudio se realizó un análisis de la colección completa de ESTs disponibles en yuca, representada por 80.459 secuencias, los cuales fueron ensamblados en un conjunto de de 29.231 genes únicos (unigen, representado por 10.945 contigs y 18.286 singletones. Estos 29.231 genes únicos pueden representar cerca del 80% de los genes del genoma de yuca. Entre el 5 y 10% de los unigenes de yuca no presentaron similitud con las secuencias presentes en las bases de datos de NCBI y pueden constituir genes específicos de yuca. A un grupo de secuencias del set unigen (29% fue posible asignarles una categoría funcionales de acuerdo al vocabulario Gene Ontology. El componente función molecular es el mejor representado con 43% de las secuencias, seguido por el componente proceso biológico (38% y finalmente el componente celular (19%. Dentro de la colección de ESTs de yuca se identificaron 3.709 microsatélites que podrán ser empleados como marcadores moleculares. Este estudio representa una contribución importante al conocimiento de la

  5. Analysis of inheritance mode in chrysanthemum using EST-derived SSR markers

    NARCIS (Netherlands)

    Park, Sang Kun; Arens, Paul; Esselink, Danny; Lim, Jin Hee; Shin, Hak Ki

    2015-01-01

    To study the inheritance mode of hexaploid chrysanthemum (random or preferential chromosome pairing), a segregation analysis was carried out using SSR markers derived from chrysanthemum ESTs in the public domain. A total of 248 EST-SSR primer pairs were screened in chrysanthemum cultivars

  6. Bajo un azul dilatado : Ensayo para una estética musical sudamericana

    OpenAIRE

    Menacho, Luis

    2015-01-01

    Tesis doctoral acerca de lineamientos desde donde pensar una estética musical de tradición escrita en la música sudamericana compuesta después de 1960. El abordaje de análisis de obras y compositores, sus vinculaciones contextuales y propuestas estéticas a la luz de un pensar sudamericano. Facultad de Bellas Artes

  7. Development of genomic SSR and potential EST-SSR markers in ...

    African Journals Online (AJOL)

    In addition, forty four EST-SSRs which can be amplified with expected sizes were identified from a B. chinense root cDNA library. The genomic SSR markers and potential EST-SSR markers developed in the present study should be useful for genetic diversity and molecular marker assistant selection breeding research in ...

  8. In silico comparative analysis of EST-SSRs in three cotton genomes

    African Journals Online (AJOL)

    reading 6

    2012-08-28

    Aug 28, 2012 ... In this study, expressed sequence tags- simple sequence repeat (EST-SSRs) were surveyed in three cotton genomes (Gossypium arboreum, Ga; Gossypium raimondii, Gr and Gossypium hirsutum, Gh). The frequency of EST-SSRs was highest in Gr, and motif type for hexanucleotide was obviously.

  9. The Reality of Fiction and the Ethics of Storytelling in Eleanor Estes's "The Witch Family"

    Science.gov (United States)

    Heinecken, Dawn

    2010-01-01

    This essay examines Eleanor Estes's critically neglected 1960 novel "The Witch Family", arguing that the novel anticipates some of the major preoccupations of later children's literature in its early concern with issues of textuality. While Estes is largely known as a writer of simple family stories, "The Witch Family" is an innovative work of…

  10. A second essential function of the Est1-binding arm of yeast telomerase RNA.

    Science.gov (United States)

    Lebo, Kevin J; Niederer, Rachel O; Zappulla, David C

    2015-05-01

    The enzymatic ribonucleoprotein telomerase maintains telomeres in many eukaryotes, including humans, and plays a central role in aging and cancer. Saccharomyces cerevisiae telomerase RNA, TLC1, is a flexible scaffold that tethers telomerase holoenzyme protein subunits to the complex. Here we test the hypothesis that a lengthy conserved region of the Est1-binding TLC1 arm contributes more than simply Est1-binding function. We separated Est1 binding from potential other functions by tethering TLC1 to Est1 via a heterologous RNA-protein binding module. We find that Est1-tethering rescues in vivo function of telomerase RNA alleles missing nucleotides specifically required for Est1 binding, but not those missing the entire conserved region. Notably, however, telomerase function is restored for this condition by expressing the arm of TLC1 in trans. Mutational analysis shows that the Second Essential Est1-arm Domain (SEED) maps to an internal loop of the arm, which SHAPE chemical mapping and 3D modeling suggest could be regulated by conformational change. Finally, we find that the SEED has an essential, Est1-independent role in telomerase function after telomerase recruitment to the telomere. The SEED may be required for establishing telomere extendibility or promoting telomerase RNP holoenzyme activity. © 2015 Lebo et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  11. Fukushima - radiological impact on the Central Europe simulated by the system ESTE

    International Nuclear Information System (INIS)

    Carny, P.; Suchon, D.; Smejkalova, E.; Chyly, M.; Krpelanova, M.; Liptak, L.

    2011-01-01

    Radiological impact of the events at nuclear installations Fukushima Dai-ichi on the Central Europe were modelled by system ESTE. Events in Fukushima and their radiological impacts are modelled mainly due to verification of our approaches, algorithms and models of ESTE. (authors)

  12. Bin mapping of genomic and EST-derived SSRs in melon (Cucumis melo L.).

    Science.gov (United States)

    Fernandez-Silva, I; Eduardo, I; Blanca, J; Esteras, C; Picó, B; Nuez, F; Arús, P; Garcia-Mas, J; Monforte, Antonio José

    2008-12-01

    We report the development of 158 primer pairs flanking SSR motifs in genomic (gSSR) and EST (EST-SSR) melon sequences, all yielding polymorphic bands in melon germplasm, except one that was polymorphic only in Cucurbita species. A similar polymorphism level was found among EST-SSRs and gSSRs, between dimeric and trimeric EST-SSRs, and between EST-SSRs placed in the open reading frame or any of the 5'- or 3'-untranslated regions. Correlation between SSR length and polymorphism was only found for dinucleotide EST-SSRs located within the untranslated regions, but not for trinucleotide EST-SSRs. Transferability of EST-SSRs to Cucurbita species was assayed and 12.7% of the primer pairs amplified at least in one species, although only 5.4% were polymorphic. A set of 14 double haploid lines from the cross between the cultivar "Piel de Sapo" and the accession PI161375 were selected for the bin mapping approach in melon. One hundred and twenty-one SSR markers were newly mapped. The position of 46 SSR loci was also verified by genotyping the complete population. A final bin-map was constructed including 80 RFLPs, 212 SSRs, 3 SNPs and the Nsv locus, distributed in 122 bins with an average bin length of 10.2 cM and a maximum bin length of 33 cM. Map density was 4.2 cM/marker or 5.9 cM/SSR.

  13. O rorschach posto à prova : A adição de estímulos auditivos.

    OpenAIRE

    Nunes, Fausto Rodrigues

    2011-01-01

    Dissertação de Mestrado apresentada ao ISPA - Instituto Universitário O silêncio é uma das regras base da aplicação do teste de Rorschach. Isto permite que o sujeito se concentre somente no estímulo visual da mancha representada no cartão e que não haja distracções aquando do processo-resposta. Contudo, nós vivemos rodeados por música, desde o rádio, à televisão, ao assobiar e até ao toque dos nossos telemóveis e esta está intimamente ligada às emoções ou estados emocionais. O presente ...

  14. Ya no estás más a mi lado, corazón: estética Camp en América Latina

    OpenAIRE

    Hueso Fibla, Silvia

    2012-01-01

    Esta tesis doctoral consta de tres capítulos cuyo recorrido pretende ilustrar que la puerta de entrada a la Estética Camp pasa por una mirada diferente sobre los productos culturales de masas y que su puerta de salida en América Latina atraviesa la Estética Neobarroca; por tanto, el Camp resulta tanto física como conceptualmente central en el trabajo. Se inserta el análisis de tres novelas y una obra teatral para mostrar cuáles son los mecanismos que el Camp adopta en América Latina: Tengo mi...

  15. La música de Beethoven en el pensament estètic d'Adorno

    OpenAIRE

    Custodio de Alba, Josep

    2007-01-01

    Aquest treball té com a finalitat una reconstrucció interpretativa del pensament estètic d'Adorno sobre la música de Beethoven i una valoració de la pretensió adorniana de fer de la interpretació estètica de Beethoven el punt de partida de la seva filosofia de la música. Este trabajo tiene como finalidad una reconstrucción interpretativa del pensamiento estético de Adorno sobre la música de Beethoven y una valoración de la pretensión adorniana de hacer de la interpretación estética de Beet...

  16. A estética política das mídias locativas

    Directory of Open Access Journals (Sweden)

    Lucia Santaella

    2008-04-01

    Full Text Available Las prácticas de acceso propiciadas por los dispositivos móviles conectados al Sistema de Posicionamiento Global (GPS están haciendo surgir un nuevo espacio social de combinaciones inextricables entre lo virtual (el ciberespacio y los ambientes físicos en los que se mueve nuestro cuerpo biológico. Este trabajo busca presentar las nuevas modalidades de comunicación, conexión e interacción que están apareciendo bajo el nombre de “medios de comunicación locativos”. Éstos son procesos que están dando origen a una estética políticamente orientada, cuyas principales características se discutirán en el artículo.

  17. Cultural history and aesthetics of nursing care La historia cultural y la estética de los cuidados de enfermería A história cultural e a estética dos cuidados de enfermagem

    Directory of Open Access Journals (Sweden)

    José Siles González

    2011-10-01

    Full Text Available The aim of this study was to clarify the role of aesthetics in the organization and motivation of care through history. The guiding questions were: What values and aesthetic feelings have supported and motivated pre-professional and professional care? and Based on what structures has pre-professional and professional care been historically socialized? Primary and secondary sources were consulted, selected according to established criteria with a view to avoiding search and selection bias. Data analysis was guided by the categories: "habitus" and "logical conformism". It was found that the relation between social structures and pre-professionals (motherhood, religiosity and professional aesthetic standards (professionalism, technologism of care through history is evidenced in the caregiving activity of the functional unit, in the functional framework and the functional element. In conclusion, in social structures, through the socialization process, "logical conformism" and "habitus" constitute the aesthetic standards of care through feelings like motherhood, religiosity, professionalism, technologism and humanism.El objetivo de este artículo fue clarificar el papel de la estética en la organización y la motivación de los cuidados en la historia. La preguntas orientadoras fueron: ¿En qué valores y sentimientos estéticos se han fundamentado y motivado los cuidados preprofesionales y profesionales? y ¿En qué estructuras, los cuidados preprofesionales y profesionales, se han socializado históricamente? Se consultaron fuentes secundarias y primarias seleccionadas de acuerdo con criterios establecidos para evitar sesgos de búsqueda y selección. El análisis de los datos se guió con las categorías: "habitus" y "conformismo lógico". Se encontró que la relación entre las estructuras sociales y los patrones estéticos preprofesionales (maternidad, religiosidad y profesionales (profesionalismo, tecnologicismo de los cuidados a través de la

  18. Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers.

    Science.gov (United States)

    Zhang, Gu-wen; Xu, Sheng-chun; Mao, Wei-hua; Hu, Qi-zan; Gong, Ya-ming

    2013-04-01

    The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (Ho) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (He) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future.

  19. SolEST database: a "one-stop shop" approach to the study of Solanaceae transcriptomes.

    Science.gov (United States)

    D'Agostino, Nunzio; Traini, Alessandra; Frusciante, Luigi; Chiusano, Maria Luisa

    2009-11-30

    Since no genome sequences of solanaceous plants have yet been completed, expressed sequence tag (EST) collections represent a reliable tool for broad sampling of Solanaceae transcriptomes, an attractive route for understanding Solanaceae genome functionality and a powerful reference for the structural annotation of emerging Solanaceae genome sequences. We describe the SolEST database http://biosrv.cab.unina.it/solestdb which integrates different EST datasets from both cultivated and wild Solanaceae species and from two species of the genus Coffea. Background as well as processed data contained in the database, extensively linked to external related resources, represent an invaluable source of information for these plant families. Two novel features differentiate SolEST from other resources: i) the option of accessing and then visualizing Solanaceae EST/TC alignments along the emerging tomato and potato genome sequences; ii) the opportunity to compare different Solanaceae assemblies generated by diverse research groups in the attempt to address a common complaint in the SOL community. Different databases have been established worldwide for collecting Solanaceae ESTs and are related in concept, content and utility to the one presented herein. However, the SolEST database has several distinguishing features that make it appealing for the research community and facilitates a "one-stop shop" for the study of Solanaceae transcriptomes.

  20. Assessment of Functional EST-SSR Markers (Sugarcane in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

    Directory of Open Access Journals (Sweden)

    Shamshad Ul Haq

    2016-01-01

    Full Text Available Expressed sequence tags (ESTs are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74% were the most abundant followed by di- (26.10%, tetra- (4.67%, penta- (1.5%, and hexanucleotide (1.2% repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA. Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

  1. Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix.

    Science.gov (United States)

    Nie, Qing; Yue, Xin; Chai, Xueliang; Wang, Hongxia; Liu, Baozhong

    2013-08-01

    The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Sonhos no (degelo: a análise fílmica na perspectiva da estética lukacsiana

    Directory of Open Access Journals (Sweden)

    Carlos Henrique Ferreira Magalhães

    2014-06-01

    Full Text Available http://dx.doi.org/10.5007/2175-8042.2014v26n42p161 Este artigo visa discutir, a partir do projeto de pesquisa das fontes áudio imagéticas , a análise do filme “Sonhos no gelo”, do diretor americano Tim Fywell (2005, a partir da estética Marxista proposta por Georg Lukács (1978. Desta forma, o estudo é de caráter qualitativo, por meio de uma sinopse interpretativa, trazendo as categorias da universalidade, singularidade e particularidade proposta pelo autor como base de reflexão e interpretação. Neste filme, tratamos a universalidade mais especificamente em relação à sociedade capitalista. Como singular, delimitamos o “ser patinadora”, ou seja, este processo de formação de uma atleta em uma sociedade onde o esporte competitivo é regido pela ética capitalista. Por conseguinte, trabalhamos o aspecto particular do contexto do filme entendendo como o esporte competitivo regido pela ética capitalista determina a história da personagem principal do mesmo. Assim, nossa intenção com a analise deste filme é promover subsídios para o professor refletir, de forma contextualizada a questão do esporte, da escola, da relação professor/técnico/aluno/conhecimento em uma sociedade regida pelo capital.

  3. Construindo castelos & pontes: o estágio docência na disciplina escolar de História

    Directory of Open Access Journals (Sweden)

    Felipe Nobrega Ferreira

    2010-10-01

    Full Text Available Chegar na última etapa da graduação em história-licenciatura é alcançar o momento fundamental do estágio supervisionado. É nesse momento que toda a bagagem constituída através das disciplinas teóricas deve se concretizar no plano prático e objetivo da realidade escolar. Assim, o presente trabalho visa colaborar no entendimento desse momento como um ato de aliar as questões teóricas às práticas e procedimentos docentes, de testar possibilidades, de realizar um trabalho diferenciado dentro do processo do estágio-docência. Aliando uma base teórica que encontra na práxis um norte, evidenciamos o relato de um trabalho efetuado dentro do estágio-supervisionado que levou em consideração fontes e abordagens diversas junto ao ensino fundamental. Por fim, têm-se algumas considerações que possuem a intenção de forma profícua dentro desse debate emergente dentro das licenciaturas brasileiras.

  4. A supervisão enquanto dispositivo: narrativa docente do estágio profissional em psicologia do trabalho

    Directory of Open Access Journals (Sweden)

    Daniele Almeida Duarte

    2015-03-01

    Full Text Available Este texto versa sobre a supervisão enquanto dispositivo, ao apresentar o quadro teórico-conceitual que norteou a atuação e sua metodologia. Ao se debruçar sobre três campos de estágio, explicita o desafio de promover não apenas a saúde do trabalhador de saúde, mas, também, construir uma práxis questionadora da relação universidade-sociedade e formação. A partir da narrativa docente do estágio profissional em Psicologia do Trabalho, dimensiona-se como se constituiu a pesquisa-intervenção em bases interdisciplinares capazes de deslocar o saber centrado no expert para tencionar ações de coletivos transformadores, que, mediante a aproximação e o diálogo, oportunizassem o forjar de solidariedades e cooperação. Elementos profícuos para a ressignificação dessas esferas foram: a construção do diagnóstico institucional vinculado à demanda e o dispositivo supervisão, capaz de produzir narrativas originais para construir experiências de protagonização – correspondentes aos princípios da Política de Humanização.

  5. A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data.

    Science.gov (United States)

    Kim, H; Schmidt, C J; Decker, K S; Emara, M G

    2003-08-01

    Discovery of non-synonymous single nucleotide polymorphisms (nsSNP), which cause amino acid substitutions, is important because they are more likely to alter protein function than synonymous SNPs (sSNP) or those SNPs that do not result in amino acid changes. By changing the coding sequences, nsSNP may play a role in heritable differences between individual organisms. In the chicken and many other vertebrates, the main obstacle for identifying nsSNP is that there is insufficient protein and mRNA sequence information for self-species referencing and thus, determination of the correct reading frame for expressed sequence tags (ESTs) is difficult. Therefore, in order to estimate the correct reading frame at nsSNP in chicken ESTs, a double-screening approach was designed using self- or cross-species protein referencing, in addition to the ESTScan coding region estimation programme. Starting with 23 427 chicken ESTs, 1210 potential SNPs were discovered using a phred/phrap/polyphred/consed pipeline process and among these, 108 candidate nsSNP were identified with the double screening method. A searchable SNP database (chicksnps) for the candidate chicken SNPs, including both nsSNPs and sSNPs is available at http://chicksnps.afs.udel.edu. The chicken SNP data described in this paper have been submitted to the data base SNP under National Center for Biotechnology Information assay ID ss4387050-ss4388259.

  6. Estándares de calidad de la información y democracia de calidad

    Directory of Open Access Journals (Sweden)

    José Villamarin Carrascal

    2013-06-01

    Full Text Available Este artículo propone seis estándares de calidad de la información, indicadores mínimos para el desarrollo de un periodismo ético, responsable y creador de ciudadanía. Se complementa con casos de la prensa nacional y mundial en los que la ausencia de esos estándares puede terminar en evidentes formas de manipulación. Propone que la recuperación de la credibilidad de un discurso público como el periodismo depende de la rigurosidad de sus prácticas informativas.

  7. La importancia de la experiencia estética y el arte actual

    OpenAIRE

    Tejada, Jesús

    2003-01-01

    Es imprescindible que la reflexión estética aborde el problema de la crisis del arte actual y que analice las distintas respuestas que en la práctica se le están dando. La renovación del diálogo con planteamientos estéticos tradicionales puede arrojar una nueva luz sobre la actividad de la creatividad artística, al destacar los conceptos de emoción y conocimiento entre otros.

  8. Literatura chilena en digital: mapas, estéticas y conceptualizaciones

    OpenAIRE

    Carolina Gaínza C.

    2017-01-01

    En el presente artículo se busca analizar una experiencia estética vinculada a lo digital, que tiene como principales componentes la posibilidad de interactuar, participar y manipular las obras creadas en este formato. Con tal fin, se presentará un mapa de la literatura digital en Chile, para luego profundizar en el análisis de dos aspectos que permiten caracterizar una estética de lo digital: la hipertextualidad y el hackeo cultural. A partir de estos elementos y tomando en cuenta que la lit...

  9. Restauraciones estéticas en el sector anterior con resina compuesta. reporte de un caso.

    OpenAIRE

    Perdomo Pacheco, Yecenia

    2011-01-01

    Las carillas directas se están convirtiendo en una solución para casi todos los problemas estéticos de la odontología actual. Los nuevos materiales de resina compuesta aparecidos en los últimos años han mejorado de forma importante sus propiedades mecánicas y estéticas, sobre todo la estabilidad del color, la textura y el pulido. Es por eso que cuando un paciente tiene una sonrisa con pequeñas alteraciones dentales, el uso de tratamientos conservadores tales como recontorneado gingival y/o gi...

  10. Relatório de estágio II de Catarina Sofia Fernandes da Costa

    OpenAIRE

    Nunes, Catarina Sofia Moreira

    2017-01-01

    O presente relatório de estágio, elaborado no âmbito na unidade curricular estágio II do Mestrado Integrado em Ciências Farmacêuticas do Instituto Universitário de Ciências da Saúde, aborda as atividades do farmacêutico hospitalar e do farmacêutico comunitário, dividindo-se, por isso, em duas partes. O estágio hospitalar decorreu entre março e abril, no Hospital Pedro Hispano, no qual houve oportunidade de objetivar todas as atividades inerentes ao farmacêutico hospitalar, e ao circuito d...

  11. El aporte literario y estético de the Beatles

    Directory of Open Access Journals (Sweden)

    Gustavo Hernández Castro

    2013-07-01

    Full Text Available Este artículo intenta dilucidar el aporte literario y estético de la banda de rock and roll The Beatles a partir del reacomodo económico e ideológico moderno de la segunda mitad del siglo veinte. El punto de partida, para este análisis, es el pensamiento existencialista, específicamente las categorías del “absurdo”, “ser” y la “nada”, como conceptos de una espiral histórica en contradicción para nuestro tiempo.

  12. Redes Inalámbricas 802.11n el Nuevo Estándar

    OpenAIRE

    Héctor de Jesús Carlos Pérez; Karla Rocío Galván Salazar

    2006-01-01

    Existen varias compañías que se encuentran trabajando juntas para poder desarrollar el nuevo estándar llamado 802.11n. El estándar 802.11n será compatible con los estándares anteriores y contará con una mayor velocidad que las redes inalámbricas existentes, en donde se podrá transmitir video de alta calidad. Se espera que esta tecnología salga para el 2007.

  13. Relatório de Estágio Curricular – Gesto Apreciativo, Lda (Guarda)

    OpenAIRE

    Lino, Cristina

    2012-01-01

    Este Relatório resulta do Estágio Curricular realizado na empresa de consultoria e formação profissional, Gesto Apreciativo, Lda, na Guarda, onde foram realizadas tarefas nos vários departamentos da empresa, e que se enquadram no âmbito da Licenciatura em Gestão de Recursos Humanos da Escola Superior de Tecnologia e Gestão do Instituto Politécnico da Guarda. Durante as 400 horas em que decorreu o Estágio, foram desenvolvidas diversas atividades, quer na área de Recursos Humanos, quer noutr...

  14. Database Description - ClEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us ClEST Database Description General information of database Database name ClEST Alternative n... Tsukuba, Ibaraki 305-8566 Japan Tel: +81-29-861-6812 (ext.222-36812) Fax: +81-29-861-6812 E-mail: Database ...classification Nucleotide Sequence Databases Organism Taxonomy Name: Cimex lectul...arius Taxonomy ID: 79782 Database description Expressed sequence tags (EST) database of unique organs and wh...ole bodies of the bedbug, Cimex lectularius Features and manner of utilization of database The bedbug Cimex

  15. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

    Directory of Open Access Journals (Sweden)

    Richardson Annette C

    2008-07-01

    Full Text Available Abstract Background Kiwifruit (Actinidia spp. are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs. Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons. Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases and pathways (terpenoid biosynthesis is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.

  16. Perda de pressão estática em uma coluna de grãos de quinoa

    Directory of Open Access Journals (Sweden)

    Poliana T. da S. Gratão

    2013-08-01

    Full Text Available Objetivou-se, neste trabalho, avaliar os efeitos do fluxo de ar sobre a queda da pressão estática em massa granular de quinoa, cultivar Real, com diferentes teores de impurezas; ajustar os modelos matemáticos aos dados experimentais obtidos e selecionar o modelo que melhor represente o fenômeno. Inicialmente, o produto estava isento de impurezas e com teor de água de 17% base seco. Foram feitas adições de impurezas nos percentuais de 1, 2, 3, 4 e 5. Utilizando-se um equipamento devidamente projetado e construído e fluxos de ar variando de 0,1 a 0,4 m³ s-1 m-2, foram determinadas as pressões estáticas da quinoa limpa e com impurezas. Os dados experimentais de perda de carga foram ajustados às equações comumente utilizadas para descrever o fenômeno. Os resultados permitiram concluir que: a a pressão estática em uma coluna com grãos de quinoa aumenta com o incremento de fluxo de ar; b O aumento do nível de impureza provocou redução da queda de pressão estática; c As equações que melhor representam os dados experimentais da queda de pressão no interior do leito com grãos de quinoa, sem e com impurezas, foram as equações de Shedd e de Guimarães, respectivamente.

  17. MuSICa: the Multi-Slit Image Slicer for the est Spectrograph

    Science.gov (United States)

    Calcines, A.; López, R. L.; Collados, M.

    2013-09-01

    Integral field spectroscopy (IFS) is a technique that allows one to obtain the spectra of all the points of a bidimensional field of view simultaneously. It is being applied to the new generation of the largest night-time telescopes but it is also an innovative technique for solar physics. This paper presents the design of a new image slicer, MuSICa (Multi-Slit Image slicer based on collimator-Camera), for the integral field spectrograph of the 4-m aperture European Solar Telescope (EST). MuSICa is a multi-slit image slicer that decomposes an 80 arcsec2 field of view into slices of 50 μm and reorganizes it into eight slits of 0.05 arcsec width × 200 arcsec length. It is a telecentric system with an optical quality at diffraction limit compatible with the two modes of operation of the spectrograph: spectroscopic and spectro-polarimetric. This paper shows the requirements, technical characteristics and layout of MuSICa, as well as other studied design options.

  18. ESTs Analysis of Putative Genes Engaged in Polyporus umbellatus Sclerotial Development

    Directory of Open Access Journals (Sweden)

    Chao Song

    2014-09-01

    Full Text Available Polyporus umbellatus is one of the most widely used and precious medicinal fungi and the underground sclerotia are known to be with great medicinal value. However, the molecular mechanisms involved in sclerotial development are poorly understood. In the present study, we constructed a forward suppression subtractive hybridization (SSH cDNA library of Polyporus umbellatus to identify genes expressing differently between mycelium and sclerotia. In this library, a total of 1202 clones were sequenced, assembled into 222 contigs and 524 singletons which were further searched against the NCBI nonredundant (NR protein database (E-value cutoff, 10−5. Based on sequence similarity with known proteins, 378 sequences between mycelium and sclerotial were identified and classified into different functional categories through Gene Ontology (GO, Clusters of orthologous Groups of proteins (COGs. We have finally identified a majority of differentially expressed genes (constituting 5.6% of the present library between the two different periods. An expression level of 32 selected expressed sequence tags (ESTs generated from the above SSH cDNA library was studied through RT-PCR. This study provides the first global overview of genes putatively involved in Polyporus umbellatus sclerotial development and provides a preliminary basis for further functional research in terms of regulated gene expression in sclerotial production.

  19. Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains.

    Science.gov (United States)

    Zhang, Ming-Ying; Fritsch, Peter W; Ma, Peng-Fei; Wang, Hong; Lu, Lu; Li, De-Zhu

    2017-05-01

    Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is

  20. Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

    Directory of Open Access Journals (Sweden)

    Paweł Mackiewicz

    2014-12-01

    Full Text Available One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly

  1. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)

    DEFF Research Database (Denmark)

    Bruun-Lund, Sam; Clement, Wendy; Kjellberg, Finn

    2017-01-01

    , combinations of low copy nuclear, nuclear ribosomal and chloroplast regions have not been able to confidently resolve relationships among major groups of figs. Using a high throughput sequencing approach we attempted to resolve the major lineages of Ficus based on plastome data. In this study, we show...... that the use of a de novo assembled plastome from within the genus provides less ambiguity and higher coverage across the 59 Ficus and 6 outgroup plastome assemblies compared to using the nearest available reference plastome outside the genus resulting in improved resolution and higher support...

  2. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

    Directory of Open Access Journals (Sweden)

    Siddiqui Asim

    2005-10-01

    Full Text Available Abstract Background The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss. Results We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84% of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins, Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. Conclusion This report illustrates specific

  3. Enhancing the health of women living with HIV: the SMART/EST Women's Project

    Directory of Open Access Journals (Sweden)

    Stephen M Weiss

    2011-02-01

    Full Text Available Stephen M Weiss1, Jonathan N Tobin2, Michael Antoni1, Gail Ironson1, Mary Ishii1, Anita Vaughn2, Andrea Cassells2, Deborah Jones1, Neil Schneiderman1, Elizabeth Brondolo3, Arthur LaPerriere1, Maria Lopez1, Olga Villar-Loubet1, Joanne Camille2, Mahendra Kumar1, J Bryan Page1, SMART/EST Women's Project Team*1University of Miami, Miami, FL, USA; 2Clinical Directors Network, New York, NY, USA; 3St Johns University, Queens, NY, USA; *The SMART/EST Womens' Project Team: DeVieux J, Jean-Gilles M, Gousse Y, Alexander K, Bustamonte V, Lopez E, Casani J, Stanley H, Asthana D, Van Splunteren F, Goldstein A, Nasajon R, Wiesner Y, Zukerman M, Segal-Isaacson CJ, Romanowsky A, Masheb R, Coma C, Ubiera M, D'Andrea SM, Ittai N.Abstract: The principal objective of these multisite studies (Florida, New York, New Jersey: epicenters for human immunodeficiency virus [HIV] among women was to develop and implement effective combinations of behavioral interventions to optimize the health status of the most neglected and understudied population affected by the acquired immunodeficiency syndrome (AIDS epidemic in the United States: poor women of color living with HIV. The two studies enrolled nearly 900 women randomly assigned to “high intensity” (cognitive–behavioral stress management training combined with expressive–supportive therapy [CBSM]+ group or “low intensity” (individual psychoeducational program treatment conditions over a period of 9 years. The initial study of the stress management and relaxation training/expressive–supportive therapy (SMART/EST Women's Project (SWP I focused on reducing depression and anxiety, as well as improving self-efficacy and overall quality of life for women with case-defined AIDS. Findings from this study demonstrated the utility of CBSM+ in reducing distress (depression, anxiety and denial, while improving social support, self-efficacy, coping skills, and quality of life. The second study (SWP II, which included all

  4. Algunas consideraciones analíticas sobre el estándar de vida

    Directory of Open Access Journals (Sweden)

    Luis Fernando Gamboa

    2010-05-01

    Full Text Available El presente documento muestra las dificultades teóricas de la identificación del bienestar individual y las ventajas de interpretar el Índice de Condiciones de Vida (ICV y el Índice del Sistema de Selección de Beneficiarios (I-sisben como indicadores de estándar de vida. Se discuten el concepto de bienestar individual, tal como se concibe en la teoría económica convencional y en la teoría de Sen, y el concepto de estándar de vida. Se presentan dos lecturas que ha recibido el ICV: como un indicador de utilidad y como un indicador de estándar de vida. como resultado se recomienda leer el ICV como un indicador de estándar de vida, puesto que es una visión menos simplista que la tradicional

  5. El arte en el umbral. Estética y cultura del mercado

    Directory of Open Access Journals (Sweden)

    CARLOS FAJARDO FAJARDO

    2009-01-01

    Full Text Available Esta conferencia se centra en algunos aspectos donde creemos observar ciertas transformaciones importantes e ineludibles en la estética contemporánea. De este modo nos interesa indagar sobre las condiciones del arte y de las sensibilidades bajo los macroproyectos del mercado y de los medios, como también la mutación en algunas categorías de la estética moderna, tales como el concepto de obra de arte, el gusto estético, lo sublime, las relaciones entre arte y diseño. No es su propósito el rastrear la densa y exhaustiva historia de dichas mutaciones, más bien hemos realizado una mirada general a sus características actuales, mostrando algunos aspectos que operan en su interior.

  6. Restauraciones Estéticas en el Sector Anterior con Resina Compuesta. Reporte de un Caso.

    Directory of Open Access Journals (Sweden)

    Yecenia Perdomo Pacheco

    2011-10-01

    Full Text Available Las carillas directas se están convirtiendo en una solución para casi todos los problemas estéticos de la odontología actual. Los nuevos materiales de resina compuesta aparecidos en los últimos años han mejorado de forma importante sus propiedades mecánicas y estéticas, sobre todo la estabilidad del color, la textura y el pulido. Es por eso que cuando un paciente tiene una sonrisa con pequeñas alteraciones dentales, el uso de tratamientos conservadores tales como recontorneado gingival y/o gingivoplastia, blanqueamiento dental y restauraciones en resina, proporcionan un tratamiento predecible, con un resultado estético duradero, a un costo moderado.

  7. L'etat, C'est Moi: Why provincial Intra-governmental disputes in ...

    African Journals Online (AJOL)

    L'etat, C'est Moi: Why provincial Intra-governmental disputes in Shout Africa remain ungoverned by the final constitution and the Intergovernmental Relations Framework Act - and how we can best resolve them.

  8. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

    Science.gov (United States)

    Shaffer, H Bradley; McCartney-Melstad, Evan; Near, Thomas J; Mount, Genevieve G; Spinks, Phillip Q

    2017-10-01

    Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5-157.3Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66mya. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Composição arquitetônica e qualidade estética

    Directory of Open Access Journals (Sweden)

    Antônio Tarcísio da Luz Reis

    Full Text Available Este artigo analisa a relação entre composição arquitetônica e qualidade estética, considerando os pressupostos da estética filosófica e da estética empírica, e o papel da estética formal e da estética simbólica em explicar tal relação. Edificações históricas e contemporâneas com distintos níveis de ordem e estímulo visual são avaliadas por pessoas com distintos níveis e tipos de formação acadêmica e são identificadas as razões para tais avaliações. A coleta de dados inclui levantamentos de arquivo, levantamentos físicos, questionários e entrevistas realizados com 60 arquitetos, 60 não arquitetos com curso universitário e 60 pessoas sem curso universitário, que avaliaram imagens de três edificações históricas e três edificações contemporâneas, categorizadas conforme segue: ordem e estímulo visual; ordem e pouco estímulo visual; e desordem. As respostas dos questionários foram analisadas através de testes estatísticos não paramétricos, tais como Kruskal-Wallis e Kendall W. As informações fornecidas através das entrevistas foram analisadas por meio de suas frequências e significados. Os resultados indicam, que, embora os arquitetos tendam a valorizar a existência de ordem na composição arquitetônica e os não arquitetos a valorizar a existência de estímulo visual, quando ambos estão presentes a composição arquitetônica tende a ser avaliada positivamente.

  10. José Antonio Ocampo : l'inclusion sociale et économique est ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    14 oct. 2015 ... Le développement rural est essentiel à la paix en Colombie, compte tenu du fait que le conflit qui perdure est principalement à caractère rural, a déclaré l'éminent économiste du développement, José Antonio Ocampo, lors d'une allocution qui a attiré un grand nombre de personnes, à Ottawa, le 25 ...

  11. Soutenir des politiques d'alimentation plus saine en Asie du Sud-Est ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Soutenir des politiques d'alimentation plus saine en Asie du Sud-Est. Près d'un quart des décès causés par des maladies non transmissibles dans le monde surviennent en Asie du Sud-Est. Ce projet tentera de résoudre le problème en menant des recherches sur la façon dont les politiques peuvent favoriser des ...

  12. En Asie du Sud-Est, la recherche en écosanté contribue à la ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    29 avr. 2016 ... C'est en Thaïlande que l'on observe la plus forte incidence de cholangiocarcinome, forme mortelle de cancer du foie notamment attribuable à une infection parasitaire par l'opisthorchiase (Opisthorchis viverrini). À certains endroits du nord-est de la Thaïlande, près de 85 % des habitants sont infectés par ...

  13. Fronteras imaginadas y estereotipos : la creación de un monstruo llamado Europa del Este

    Directory of Open Access Journals (Sweden)

    Daniel Esparza

    2009-01-01

    Full Text Available En este artículo se observa como se han formado en el «oeste», desde la Guerra Fría hasta hoy, algunos estereotipos negativos sobre la marca «Europa del Este», la cual está cargada de connotaciones negativas (ciudades grises, guerras, inmigración ilegal, pobreza o criminalidad. Al mismo tiempo, como si de un oasis se tratara, se observa parojicamente como la marca Praga o Budapest (capitales de países de «Europa del Este» no son percibidas negativamente, precisamente porque no están relacionadas directamente con el Este, sino con centroeuropa y con imágenes positivas asociadas a la herencia artístico-cultural de los imperios centrales: el sacro imperio germano-romano y el austrohúngaro.In this article it is observed how from the Cold War till today have been formed in the West significant stereotypes towards Eastern Europe, which are endowed with negative images, such as grey towns, illegal immigration, wars, poverty or criminality. At the same time it is observed, paradoxically, how the brand Prague or Budapest (capitals of «Eastern European» countries are not perceived negatively, precisely because they are not directly associated with the East, but with the cultural heritage form the old central empires: the Sacred Roman-German empire first, and the Habsburg empire later.

  14. Update of the Diatom EST Database: a new tool for digital transcriptomics

    Science.gov (United States)

    Maheswari, Uma; Mock, Thomas; Armbrust, E. Virginia; Bowler, Chris

    2009-01-01

    The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3. PMID:19029140

  15. New functions of the este system - new possibilities for emergency response

    International Nuclear Information System (INIS)

    Carny, P.

    2005-01-01

    The ESTE system (Emergency Source Term Evaluation) is support instrument for off-site emergency response and its main objective is to assist to the crisis staff: - to mitigate radiological consequences of significant releases; - to manage the protective measures; - to manage emergency monitoring. At national level the ESTE system are implemented at the Emergency Response Centre of the Czech Republic (SUJB) and Austrian versions are implemented at the Crisis Centre of the Austrian Republic (BMLFUW). ESTE system can now be utilized not only in close (40 km) vicinity of the point of the release (NPP), but radiological impacts are now calculated across the whole country or over the country border. Puff Trajectory Model (PTM) with the background of geographical information system (GIS) is included in este. Numerical weather prediction data (wind fields) predicted for the whole or the part of the country are online connected with este and utilized for the puffs movement simulation and impacts calculations. It means that not only meteorological data from the point of release (measured or predicted), but 'meteorological data wind field' predicted for larger region across the country are used by the este system. (author)

  16. L'état de l'environnement industriel français est-il objectivement mesurable ?

    OpenAIRE

    Gotteland, David; Boulé, Jean-Marie

    2004-01-01

    Working paper serie RMT (WPS 04-07); the environmental state is a frequently modelized variable in marketing research. This paper proposes updated scales and panorama of the objective state of 58 industrial branches defined by INSEE based on three characteristic dimensions: dynamism, complexity and capacity.; l'état de l'environnement est une variable fréquemment modélisée dans la recherche en marketing. A partir de ce constat, cet article propose une échelle de mesure et un panorama actualis...

  17. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

    Directory of Open Access Journals (Sweden)

    Ruiz Manuel

    2008-10-01

    Full Text Available Abstract Background Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. Results Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species. Gene Ontology (GO annotation was applied to distribute the ESTs among the main GO categories. A specific information system (ESTtik was constructed to process, store and manage this EST collection allowing the user to query a database. To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection. A large collection of new genetic markers was provided by this ESTs collection. Conclusion This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow

  18. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions.

    Science.gov (United States)

    Argout, Xavier; Fouet, Olivier; Wincker, Patrick; Gramacho, Karina; Legavre, Thierry; Sabau, Xavier; Risterucci, Ange Marie; Da Silva, Corinne; Cascardo, Julio; Allegre, Mathilde; Kuhn, David; Verica, Joseph; Courtois, Brigitte; Loor, Gaston; Babin, Regis; Sounigo, Olivier; Ducamp, Michel; Guiltinan, Mark J; Ruiz, Manuel; Alemanno, Laurence; Machado, Regina; Phillips, Wilberth; Schnell, Ray; Gilmour, Martin; Rosenquist, Eric; Butler, David; Maximova, Siela; Lanaud, Claire

    2008-10-30

    Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species.Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories.A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database.To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection.A large collection of new genetic markers was provided by this ESTs collection. This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao

  19. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

    Science.gov (United States)

    Argout, Xavier; Fouet, Olivier; Wincker, Patrick; Gramacho, Karina; Legavre, Thierry; Sabau, Xavier; Risterucci, Ange Marie; Da Silva, Corinne; Cascardo, Julio; Allegre, Mathilde; Kuhn, David; Verica, Joseph; Courtois, Brigitte; Loor, Gaston; Babin, Regis; Sounigo, Olivier; Ducamp, Michel; Guiltinan, Mark J; Ruiz, Manuel; Alemanno, Laurence; Machado, Regina; Phillips, Wilberth; Schnell, Ray; Gilmour, Martin; Rosenquist, Eric; Butler, David; Maximova, Siela; Lanaud, Claire

    2008-01-01

    Background Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. Results Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species. Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories. A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database. To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection. A large collection of new genetic markers was provided by this ESTs collection. Conclusion This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high

  20. Algumas considerações acerca da medicina estética Some considerations about aesthetic medicine

    Directory of Open Access Journals (Sweden)

    Francisco Romão Ferreira

    2010-01-01

    Full Text Available Neste artigo, abordaremos alguns aspectos da construção de sentidos acerca do corpo a partir do discurso científico que se moldou com o pensamento moderno e se transformou no pensamento hegemônico de alguns setores da área médica. Ressaltaremos que os sentidos atribuídos ao corpo incorporam questões oriundas de outras áreas da vida social e vão moldar os parâmetros estéticos que influenciam a construção da identidade, a relação com o próprio corpo, a subjetividade e os cuidados com a saúde. Descreveremos alguns momentos dessa construção do pensamento científico moderno, a forma como este pensamento se torna hegemônico, influencia o senso comum, naturaliza a construção da identidade e a forma de lidar com o corpo, interfere nos cuidados com a saúde, expõe uma divisão entre alguns setores da biomedicina, reforça um tipo específico de racionalidade médica e serve de base epistêmica e fundamentação (teórica e discursiva para alguns setores ligados à medicina estética e às cirurgias estéticas.In this article, we will discuss some aspects of the construction of the meanings concerning the body from the scientific speech which was modeled based on modern thinking and became the hegemonic thinking of some sectors of the medical field. Meanings attributed to the body bring questions that come from other areas of the social life and those questions will build the aesthetic parameters which will be part of the identity construction, in the relation with the body itself, subjectivity and healthcare. We will describe some moments of the construction of the modern scientific thought and how this thought became hegemonic, influences the common sense, naturalizes identity construction and how dealing with the body, interferes in the healthcare, show a division among some sectors of the biomedicine, reinforce an specific type of medical rationality and makes an epistemic base and principle (theoretical and discursive to some

  1. Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.)

    Science.gov (United States)

    2011-01-01

    Background Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310) and two resistant yam genotypes (TDa 87-01091, TDa 95-0328) challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species. PMID:21303556

  2. Generation and analysis of expressed sequence tags (ESTs for marker development in yam (Dioscorea alata L.

    Directory of Open Access Journals (Sweden)

    Robert Asiedu

    2011-02-01

    Full Text Available Abstract Background Anthracnose (Colletotrichum gloeosporioides is a major limiting factor in the production of yam (Dioscorea spp. worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310 and two resistant yam genotypes (TDa 87-01091, TDa 95-0328 challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species.

  3. The construction of a cDNA library enriched for immune genes and the analysis of 7535 ESTs from Chinese mitten crab Eriocheir sinensis.

    Science.gov (United States)

    Gai, Yunchao; Wang, Lingling; Zhao, Jianmin; Qiu, Limei; Song, Linsheng; Li, Ling; Mu, Changkao; Wang, Wan; Wang, Mengqiang; Zhang, Ying; Yao, Xuemei; Yang, Jialong

    2009-12-01

    Chinese mitten crab Eriocheir sinensis is one of the most important aquaculture crustacean species in China. A cDNA library was constructed from hemocytes of E. sinensis challenged with the mixture of Listonella anguillarum and Staphylococcus aureus, and randomly sequenced to collect genomic information and identify genes involved in immune defense response. Single-pass 5' sequencing of 10368 clones yielded 7535 high quality ESTs (Expressed Sequence Tags) and these ESTs were assembled into 2943 unigenes. BLAST analysis revealed that 1706 unigenes (58.0% of the total) or 4593 ESTs (61.0% of the total) were novel genes that had no significant matches to any protein sequences in the public databases. The rest 1237 unigenes (42.0% of the total) were closely matched to the known genes or sequences deposited in public databases, which could be classed into 20 or 23 classifications according to "molecular function" or "biological process" respectively based on the Gene Ontology (GO). And 221 unigenes (7.5% of all 2943 unigenes, 17.9% of matched unigenes) or 969 ESTs (12.9% of all 7535 ESTs, 32.9% of matched ESTs) were identified to be immune genes. The relative higher proportion of immune-related genes in the present cDNA library than that in the normal library of E. sinensis and other crustaceans libraries, and the differences and changes in percentage and quantity of some key immune-related genes especially the immune inducible genes between two E. sinensis cDNA libraries may derive from the bacteria challenge to the Chinese mitten crab. The results provided a well-characterized EST resource for the genomics community, gene discovery especially for the identification of host-defense genes and pathways in crabs as well as other crustaceans.

  4. Le fascisme, c’est du théâtre. Macchina scenica e meccanica narrativa

    Directory of Open Access Journals (Sweden)

    Emanuele Canzaniello

    2015-11-01

    Full Text Available «Le fascisme, c’est du théâtre», sostiene Jean Genet, e come tale i suoi legami con la natura e la prassi della messa in scena sono essenziali alla specificità del fenomeno. La resa spettacolare della nazionalizzazione delle masse è stata senz’altro tra i temi fondamentali della ricerca sui totalitarismi. Il mio proposito è qui quello di intarsiare alcuni nuclei consolidati della ricerca storica con le rese squisitamente letterarie di quello che fu poco più che un  decennio di immensi tableaux vivants, visioni di un nuovo ordine di massa. Un’opera d’arte collettiva, basata su una premessa  fondamentale: dare “figurabilità” ai detriti e alle rovine (rimosse? di alcuni miti delle origini propri della cultura romantica, e  consapevolmente avviare e mettere in luce un enorme processo più generale di disgregazione del logos e di tutta la civiltà europea nella sua prospettiva diremo cartesiana, geometrica e razionalista. Il mio discorso si fonda, anche se in breve, su un testo solo: la Gerbe des forces (1937 di A. de Châteaubriant, uno dei più singolari resoconti di pellegrinaggio politico verso il miraggio totalitario che si sia dato tre le due guerre mondiali. Soccorsi non secondari sono il saggio di Sontag Under the sign of Saturn (1980 e quello di Tame La Mystique du Fascisme dans l’oeuvre de Robert Brasillach (1986. According to Jean Genet: «Le fascisme, c’est du théâtre», and as such its relationship with the nature and praxis of staging are essential to the specificity of the phenomenon. The magnificent representation of mass nationalisation is beyond doubt one of the fundamental issues when investigating totalitarianisms. My aim here is to link some wellestablished nuclei of historical research to the literary outputs of what was little more than a decade of immense tableaux vivants, visions of a new mass order. A collective work of art, based on a fundamental premise: to give ‘figurality’ to the rubble

  5. ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale.

    Directory of Open Access Journals (Sweden)

    Ming-Ming Zhao

    Full Text Available Dendrobiumofficinale (Orchidaceae is one of the world's most endangered plants with great medicinal value. In nature, D. officinale seeds must establish symbiotic relationships with fungi to germinate. However, the molecular events involved in the interaction between fungus and plant during this process are poorly understood. To isolate the genes involved in symbiotic germination, a suppression subtractive hybridization (SSH cDNA library of symbiotically germinated D. officinale seeds was constructed. From this library, 1437 expressed sequence tags (ESTs were clustered to 1074 Unigenes (including 902 singletons and 172 contigs, which were searched against the NCBI non-redundant (NR protein database (E-value cutoff, e(-5. Based on sequence similarity with known proteins, 579 differentially expressed genes in D. officinale were identified and classified into different functional categories by Gene Ontology (GO, Clusters of orthologous Groups of proteins (COGs and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. The expression levels of 15 selected genes emblematic of symbiotic germination were confirmed via real-time quantitative PCR. These genes were classified into various categories, including defense and stress response, metabolism, transcriptional regulation, transport process and signal transduction pathways. All transcripts were upregulated in the symbiotically germinated seeds (SGS. The functions of these genes in symbiotic germination were predicted. Furthermore, two fungus-induced calcium-dependent protein kinases (CDPKs, which were upregulated 6.76- and 26.69-fold in SGS compared with un-germinated seeds (UGS, were cloned from D. officinale and characterized for the first time. This study provides the first global overview of genes putatively involved in D. officinale symbiotic seed germination and provides a foundation for further functional research regarding symbiotic relationships in orchids.

  6. Auditoria del proceso de producción de sal en la provincia de Guayas, con el objetivo de sugerir estándares de control

    OpenAIRE

    Pinos Ullauri, Nathalia; Fernandez Ronquillo, Jorge

    2009-01-01

    Este trabajo es una auditoria al proceso de producción de la sal en la provincia del Guayas, proceso que se comparará con un modelo mejorado obtenido a base de consultas con otras industrias en el mundo, para poder así sugerir mejoras y nuevos estándares de control. El Capítulo I presenta una serie de generalidades de la sal, de los principales productores en el mundo, el consumo a nivel mundial, las normativas de calidad para consumo humano, las formas de cultivo y la extracción, etc. ...

  7. Formação de classes funcionais de estímulos musicais

    Directory of Open Access Journals (Sweden)

    Alex Roberto Machado

    2009-04-01

    Full Text Available O objetivo deste experimento foi verificar o efeito do treino discriminativo sobre a formação de classes funcionais de melodias em andamentos e modos diferentes. Nove estudantes universitários do 2° período da graduação em Psicologia foram divididos em três grupos: Modo, Andamento ou Misto. O software SomPsi, produzido especialmente para este estudo, treinou os participantes e gerou relatórios com informações sobre os desempenhos, nas quatro fases do procedimento. O treino proposto mostrou-se eficiente para a formação das classes funcionais de estímulos sonoros musicais. Observou-se que agrupamentos de estímulos pela propriedade andamento foram mais facilmente discriminados que os agrupados pela melodia. A manipulação combinada das duas propriedades, em condição convergente, permitiu desempenho superior dos participantes. A rápida formação de classes funcionais e equivalentes de estímulos musicais, a partir de procedimentos de ensino automatizado de relações condicionais entre estímulos musicais, indica a possibilidade de uso desse procedimento na iniciação à música.

  8. Hacia una estética de las nuevas tecnologías como proyecto educativo

    Directory of Open Access Journals (Sweden)

    Juan Sebastián López

    2011-01-01

    Full Text Available Este artículo parte de la descripción de un cambio de época en curso, analiza - do en los niveles del orden social, la cultura, la comunicación y las tecnologías. De ahí se extraen una serie de retos a los que se enfrenta cualquier proyecto de educación contemporáneo. En este marco problémico, se examinarán algunos puntos fundamentales de la teoría estética de Theodor Adorno. Lo que se intenta proponer es una concepción de la estética asumida como mediación conceptual de la experiencia del sujeto con su entorno. Este será el primer paso para consolidar un proyecto educativo que resuelva uno de sus retos más urgentes: reducir la brecha entre el desarrollo tecnológico y sus correspondientes mediaciones culturales.

  9. Estética fenomenológica. La obra de arte arquitectónica

    Directory of Open Access Journals (Sweden)

    Pedragosa, Pau

    2009-04-01

    Full Text Available The purpose of this article is to discuss the possibility and task of aesthetics under the phenomenological point of view. I focus on architecture and analyse its stratified structure, according to Roman Ingarden’s analysis, and the specific character of the aesthetic attitude against other attitudes that architecture also demands, according to the observations of Paul Valéry. I finally raise the central question about the possibility of the understanding art in general and architecture in particular, comparing phenomenological aesthetics and aesthetics of negativity.El propósito de este artículo es discutir la posibilidad y tarea de la estética bajo un enfoque fenomenológico. Nos centramos en la arquitectura, de la cual analizamos su estructura estratificada, siguiendo los análisis de Roman Ingarden, y la especificidad de la actitud estética, frente a otras actitudes que también reclama la arquitectura, según las observaciones de Paul Valéry. Planteamos finalmente la cuestión central acerca de la posibilidad de la comprensión del arte en general y de la arquitectura en particular comparando la estética fenomenológica con la estética de la negatividad.

  10. Developing new SSR markers from ESTs of pea (Pisum sativum L.).

    Science.gov (United States)

    Gong, Ya-ming; Xu, Sheng-chun; Mao, Wei-hua; Hu, Qi-zan; Zhang, Gu-wen; Ding, Ju; Li, Ya-dan

    2010-09-01

    The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

  11. EST-SSR marker revealed effective over biochemical and morphological scepticism towards identification of specific turmeric (Curcuma longa L.) cultivars.

    Science.gov (United States)

    Sahoo, Ambika; Jena, Sudipta; Kar, Basudeba; Sahoo, Suprava; Ray, Asit; Singh, Subhashree; Joshi, Raj Kumar; Acharya, Laxmikanta; Nayak, Sanghamitra

    2017-05-01

    Turmeric (Curcuma longa L., family Zingiberaceae) is one of the most economically important plants for its use in food, medicine, and cosmetic industries. Cultivar identification is a major constraint in turmeric, owing to high degree of morphological similarity that in turn, affects its commercialization. The present study addresses this constraint, using EST-SSR marker based, molecular identification of 8 elite cultivars and 88 accessions in turmeric. Fifty EST-SSR primers were screened against eight cultivars of turmeric (Suroma, Roma, Lakadong, Megha, Alleppey Supreme, Kedaram, Pratibha, and Suvarna); out of which 11 primers showed polymorphic banding pattern. The polymorphic information content (PIC) of these primers ranged from 0.13 to 0.48. However, only three SSR loci (CSSR 14, CSSR 15, and CSSR 18) gave reproducible unique banding pattern clearly distinguishing the cultivars 'Lakadong' and 'Suvarna' from other cultivars tested. These three unique SSR markers also proved to be effective in identification of 'Lakadong' cultivars when analysed with 88 accessions of turmeric collected from different agro-climatic regions. Furthermore, two identified cultivars (Lakadong and Suvarna) could also be precisely differentiated when analysed and based on phylogenetic tree, with other 94 genotypes of turmeric. The novel SSR markers can be used for identification and authentication of two commercially important turmeric cultivars 'Lakadong' and 'Suvarna'.

  12. Los patrones estéticos en los albores del siglo XXI. Hacia una revisión de los estudios en torno a este tema

    Directory of Open Access Journals (Sweden)

    CARMEN BAÑUELOS

    1994-01-01

    Full Text Available El culto del cuerpo se ha convertido en nuestros días en un fenómeno social de gran significación. La presentación del yo físico adquiere una especial relevancia en los nuevos estilos de vida. Diversos grupos sociales (médicos, psicologos, sociólogos, modistos, publicistas, estilistas, esteticistas, periodistas... centran su interés en la definición social del "cuerpo". el objetivo es contribuir a la creación de un modelo ideal único y generalizable, legitimando determinadas prácticas sociales dirigidas hacia este fín. La definición de este modelo esta en manos de un grupo de "diseñadores de cuerpos" que asumen el papel de especificar los límites de la normalidad corporal en nuestra sociedad. La expresión corporal se ha convertido en un lenguaje que, en último extremo, manifiesta el status y la posición social. Por otra parte, en las últimas décadas se plantea la cuestión de conocer como las diferencias biológicas entre los individuos se transforman en factores de discriminación social. En este sentido, diversos problemas de salud actuales chocan con la definición de "cuerpo" ideal. La gordura es un buen ejemplo para comprender como las modas sociales utilizan la categorización de enfermedad "etiquetando" lo "normal" en un momento dado como "patológico" en otro. La exclusión social de las personas obesas, el rechazo a la obesidad y la construcción social de su figura marginal correspondiente, adquieren una relevancia merecedora de un análisis sociológico mas exhaustivo. Por este motivo, es necesario comprender como se han impuesto criterios sociales para estigmatizar a personas cuyo peso no es un riesgo para la salud ni un obstaculo para su vida social...

  13. Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES proteins in parasitic nematodes using expressed sequence tags (ESTs.

    Directory of Open Access Journals (Sweden)

    Shivashankar H Nagaraj

    2008-09-01

    Full Text Available Parasitic nematodes of humans, other animals and plants continue to impose a significant public health and economic burden worldwide, due to the diseases they cause. Promising antiparasitic drug and vaccine candidates have been discovered from excreted or secreted (ES proteins released from the parasite and exposed to the immune system of the host. Mining the entire expressed sequence tag (EST data available from parasitic nematodes represents an approach to discover such ES targets.In this study, we predicted, using EST2Secretome, a novel, high-throughput, computational workflow system, 4,710 ES proteins from 452,134 ESTs derived from 39 different species of nematodes, parasitic in animals (including humans or plants. In total, 2,632, 786, and 1,292 ES proteins were predicted for animal-, human-, and plant-parasitic nematodes. Subsequently, we systematically analysed ES proteins using computational methods. Of these 4,710 proteins, 2,490 (52.8% had orthologues in Caenorhabditis elegans, whereas 621 (13.8% appeared to be novel, currently having no significant match to any molecule available in public databases. Of the C. elegans homologues, 267 had strong "loss-of-function" phenotypes by RNA interference (RNAi in this nematode. We could functionally classify 1,948 (41.3% sequences using the Gene Ontology (GO terms, establish pathway associations for 573 (12.2% sequences using Kyoto Encyclopaedia of Genes and Genomes (KEGG, and identify protein interaction partners for 1,774 (37.6% molecules. We also mapped 758 (16.1% proteins to protein domains including the nematode-specific protein family "transthyretin-like" and "chromadorea ALT," considered as vaccine candidates against filariasis in humans.We report the large-scale analysis of ES proteins inferred from EST data for a range of parasitic nematodes. This set of ES proteins provides an inventory of known and novel members of ES proteins as a foundation for studies focused on understanding the

  14. Needles in the EST Haystack: Large-Scale Identification and Analysis of Excretory-Secretory (ES) Proteins in Parasitic Nematodes Using Expressed Sequence Tags (ESTs)

    Science.gov (United States)

    Nagaraj, Shivashankar H.; Gasser, Robin B.; Ranganathan, Shoba

    2008-01-01

    Background Parasitic nematodes of humans, other animals and plants continue to impose a significant public health and economic burden worldwide, due to the diseases they cause. Promising antiparasitic drug and vaccine candidates have been discovered from excreted or secreted (ES) proteins released from the parasite and exposed to the immune system of the host. Mining the entire expressed sequence tag (EST) data available from parasitic nematodes represents an approach to discover such ES targets. Methods and Findings In this study, we predicted, using EST2Secretome, a novel, high-throughput, computational workflow system, 4,710 ES proteins from 452,134 ESTs derived from 39 different species of nematodes, parasitic in animals (including humans) or plants. In total, 2,632, 786, and 1,292 ES proteins were predicted for animal-, human-, and plant-parasitic nematodes. Subsequently, we systematically analysed ES proteins using computational methods. Of these 4,710 proteins, 2,490 (52.8%) had orthologues in Caenorhabditis elegans, whereas 621 (13.8%) appeared to be novel, currently having no significant match to any molecule available in public databases. Of the C. elegans homologues, 267 had strong “loss-of-function” phenotypes by RNA interference (RNAi) in this nematode. We could functionally classify 1,948 (41.3%) sequences using the Gene Ontology (GO) terms, establish pathway associations for 573 (12.2%) sequences using Kyoto Encyclopaedia of Genes and Genomes (KEGG), and identify protein interaction partners for 1,774 (37.6%) molecules. We also mapped 758 (16.1%) proteins to protein domains including the nematode-specific protein family “transthyretin-like” and “chromadorea ALT,” considered as vaccine candidates against filariasis in humans. Conclusions We report the large-scale analysis of ES proteins inferred from EST data for a range of parasitic nematodes. This set of ES proteins provides an inventory of known and novel members of ES proteins as a

  15. In silico mining for simple sequence repeat loci in a pineapple expressed sequence tag database and cross-species amplification of EST-SSR markers across Bromeliaceae.

    Science.gov (United States)

    Wöhrmann, Tina; Weising, Kurt

    2011-08-01

    A collection of 5,659 expressed sequence tags (ESTs) from pineapple [Ananas comosus (L.) Merr.] was screened for simple sequence repeats (EST-SSRs) with motif lengths between 1 and 6 bp. Lower thresholds of 15, 7 and 5 repeat units were used to define microsatellites of the mono-, di-, and tri- to hexanucleotide repeat type, respectively. Based on these criteria, 696 SSRs were identified among 3,389 EST unigenes, together representing 2,840 kb. This corresponds to an average density of one SSR every 4.1 kb of non-redundant EST sequences. Dinucleotide repeats were most abundant (38.4% of all SSRs) followed by trinucleotide repeats (38.1%). Flanking primer pairs were designed for 537 EST-SSR loci, and 49 of these were screened for their functionality in 12 accessions of A. comosus, 14 accessions of 5 additional Ananas species and 1 species of Pseudananas. Distinct PCR products of the expected size range were obtained with 36 primer pairs. Eighteen loci analyzed in more detail were all polymorphic in pineapple, and primer pairs flanking these loci also generated PCR products from a wide range of genera and species from six subfamilies of the Bromeliaceae. The potential to reveal polymorphism in a heterologous target species was demonstrated in Deuterocohnia brevifolia (subfamily Pitcairnioideae).

  16. Desenvolvimento de competências gerais durante o estágio supervisionado

    OpenAIRE

    Gladys Amelia Vélez Benito; Kamila Medani Tristão; Ana Claúdia Schuab Faria de Paula; Mariana Andrade dos Santos; Lorena Jácome Ataide; Rita de Cássia Duarte Lima

    2012-01-01

    Este artigo descreve as competências gerais dos profissionais de saúde e aponta possíveis articulações com o estágio supervisionado. O objetivo é chamar a atenção dos enfermeiros e futuros profissionais da área, sobre a importância de se vivenciar o estágio supervisionado, durante a formação, para a aquisição e aprimoramento das competências gerais dos profissionais de saúde, além das competências e habilidades específicas da Enfermagem. Nos serviços de saúde, tanto na esfera pública quanto n...

  17. Dispositivos estéticos y formas sensibles de la emancipación

    Directory of Open Access Journals (Sweden)

    María Luciana Cadahia

    2016-08-01

    Full Text Available Se explora la noción de dispositivo desde una perspectiva estético-política. Se inquieren los motivos para distanciarnos de las lecturas de Agamben, Esposito y el Colectivo tiqqun,se examina la interpretación de Deleuze al respecto, en una dimensión poco conocida, y se amplía esta perspectiva hacia una concepción estética del dispositivo, atendiendo para ello a Martín-Barbero. Finalmente, se considera el vínculo problemático entre el dispositivo y la positividad estética, para acercarnos a Schiller, quien da las pautas para disolver el vínculo problemático.