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

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

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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

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.

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Zhang, Shu-Dong; Jin, Jian-Jun; Chen, Si-Yun; Chase, Mark W; Soltis, Douglas E; Li, Hong-Tao; Yang, Jun-Bo; Li, De-Zhu; Yi, Ting-Shuang

2017-05-01

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae based on sequence capture data

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Alejandra Panzera

2017-10-01

Full Text Available 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

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

ReproPhylo: An Environment for Reproducible Phylogenomics.

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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.

Morphometrics of Daucus (Apiaceae): A counterpart to a phylogenomic study

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Molecular phylogenetics of genome-scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. A companion phylogenomics analysis of Daucus (carrots) using 94 conserved nuclear orthologs supported many of the traditional species but showed unexpected results that ...

Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae

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Tang, Xianghai; Xu, Kuipeng; Han, Xiaojuan; Mo, Zhaolan; Mao, Yunxiang

2018-03-01

Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022T using single molecule real-time sequencing technology (SMRT) and performed comparative genomics and phylogenomics analyses. The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 tRNA genes, and 21 rRNA genes. The C. marina JCM 21022T genome contained a set of crucial genes involved in surface colonization processes. The comparative genome analysis indicated the significant differences between C. marina JCM 21022T and Cobetia amphilecti KMM 296 (formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these differences, pan and core genome analysis showed similar gene functions between the two strains. The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.

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

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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

Phylogenomics of Colombian Helicobacter pylori isolates.

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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.

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.

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

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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.

Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

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Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

2016-01-01

Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

Phylogenetic and Phylogenomic Definition of Rhizopus Species

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Andrii P. Gryganskyi

2018-06-01

Full Text Available Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar. A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.

Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics1

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Weitemier, Kevin; Straub, Shannon C. K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron

2014-01-01

• 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. PMID:25225629

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae).

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Tucker, Derek B; Colli, Guarino R; Giugliano, Lilian G; Hedges, S Blair; Hendry, Catriona R; Lemmon, Emily Moriarty; Lemmon, Alan R; Sites, Jack W; Pyron, R Alexander

2016-10-01

A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena). Copyright © 2016 Elsevier Inc. All rights reserved.

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling.

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Reddy, Sushma; Kimball, Rebecca T; Pandey, Akanksha; Hosner, Peter A; Braun, Michael J; Hackett, Shannon J; Han, Kin-Lan; Harshman, John; Huddleston, Christopher J; Kingston, Sarah; Marks, Ben D; Miglia, Kathleen J; Moore, William S; Sheldon, Frederick H; Witt, Christopher C; Yuri, Tamaki; Braun, Edward L

2017-09-01

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which

Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.

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Ghatak, Sandeep; Blom, Jochen; Das, Samir; Sanjukta, Rajkumari; Puro, Kekungu; Mawlong, Michael; Shakuntala, Ingudam; Sen, Arnab; Goesmann, Alexander; Kumar, Ashok; Ngachan, S V

2016-07-01

Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.

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/ ).

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

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Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

2014-01-01

Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

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

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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.

Phylogenomics of the carrot genus (Daucus, Apiaceae)

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Molecular phylogenetics of genome-scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. We here explore the utility of multiple nuclear orthologs for the taxonomic resolution of a wide variety of Daucus species and outgroups. We studied the phylogeny of 89 ...

Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales.

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Luo, Yang; Ma, Peng-Fei; Li, Hong-Tao; Yang, Jun-Bo; Wang, Hong; Li, De-Zhu

2016-04-06

The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatales tree precludes answering questions about the early evolution of the order. Here, we sequenced the first complete plastid genomes from three key families in this order:Potamogeton perfoliatus(Potamogetonaceae),Sagittaria lichuanensis(Alismataceae), andTofieldia thibetica(Tofieldiaceae). Each family possesses the typical quadripartite structure, with plastid genome sizes of 156,226, 179,007, and 155,512 bp, respectively. Among them, the plastid genome ofS. lichuanensisis the largest in monocots and the second largest in angiosperms. Like other sequenced Alismatales plastid genomes, all three families generally encode the same 113 genes with similar structure and arrangement. However, we detected 2.4 and 6 kb inversions in the plastid genomes ofSagittariaandPotamogeton, respectively. Further, we assembled a 79 plastid protein-coding gene sequence data matrix of 22 taxa that included the three newly generated plastid genomes plus 19 previously reported ones, which together represent all primary lineages of monocots and outgroups. In plastid phylogenomic analyses using maximum likelihood and Bayesian inference, we show both strong support for Acorales as sister to the remaining monocots and monophyly of Alismatales. More importantly, Tofieldiaceae was resolved as the most basal lineage within Alismatales. These results provide new insights into the evolution of Alismatales as well as the early-diverging monocots as a whole. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.

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Edwards, Scott V; Cloutier, Alison; Baker, Allan J

2017-11-01

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis. © The Author(s) 2017. Published by Oxford University Press on behalf of the Systematic Biologists.

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

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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...

A functional phylogenomic view of the seed plants.

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Ernest K Lee

2011-12-01

Full Text Available 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.

Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta

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Karolina Fučíková

2016-06-01

Full Text Available The chloroplast genomes of green algae are highly variable in their architecture. In this article we summarize gene content across newly obtained and published chloroplast genomes in Chlorophyceae, including new data from nine of species in Sphaeropleales (Chlorophyceae, Chlorophyta. We present genome architecture information, including genome synteny analysis across two groups of species. Also, we provide a phylogenetic tree obtained from analysis of gene order data for species in Chlorophyceae with fully sequenced chloroplast genomes. Further analyses and interpretation of the data can be found in “Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta reveal complex patterns of sequence evolution” (Fučíková et al., In review [1].

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

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

2014-11-01

The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e.g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for more than 50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only eight chloroplast loci to the combined data set yielded almost identical

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

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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.

Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

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Leaché, Adam D; Banbury, Barbara L; Linkem, Charles W; de Oca, Adrián Nieto-Montes

2016-03-22

Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20-25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.

Spider phylogenomics: untangling the Spider Tree of Life

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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

Spider phylogenomics: untangling the Spider Tree of Life

Science.gov (United States)

Garrison, Nicole L.; Rodriguez, Juanita; Agnarsson, Ingi; Coddington, Jonathan A.; Griswold, Charles E.; Hamilton, Christopher A.; Hedin, Marshal; Kocot, Kevin M.; Ledford, Joel M.

2016-01-01

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 challenge the

Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family

Czech Academy of Sciences Publication Activity Database

Lugli, G. A.; Milani, C.; Turroni, F.; Duranti, S.; Mancabelli, L.; Mangifesta, M.; Ferrario, C.; Modesto, M.; Mattarelli, P.; Killer, Jiří; van Sinderen, D.

2017-01-01

Roč. 18, č. 1 (2017), č. článku 568. ISSN 1471-2164 Institutional support: RVO:67985904 Keywords : Bifidobacteriaceae * genomics * phlogenomics Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.729, year: 2016

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

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

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

Science.gov (United States)

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

Science.gov (United States)

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

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.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

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Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

2015-12-01

In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

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.

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.

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Simon, Meinhard; Scheuner, Carmen; Meier-Kolthoff, Jan P; Brinkhoff, Thorsten; Wagner-Döbler, Irene; Ulbrich, Marcus; Klenk, Hans-Peter; Schomburg, Dietmar; Petersen, Jörn; Göker, Markus

2017-06-01

Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.

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.

Contesting Citizenship: Comparative Analyses

DEFF Research Database (Denmark)

Siim, Birte; Squires, Judith

2007-01-01

importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

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Pieter De Maayer

2017-09-01

Full Text Available Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.

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De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Venter, Stephanus N; Coutinho, Teresa A

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes , has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis . While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Analysing and Comparing Encodability Criteria

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Kirstin Peters

2015-08-01

Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

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Vikas Kumar

Full Text Available Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides from all orders except Dermoptera (flying lemurs. Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.

Phylogenomic analysis of marine Roseobacters.

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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.

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae).

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Qu, Xiao-Jian; Jin, Jian-Jun; Chaw, Shu-Miaw; Li, De-Zhu; Yi, Ting-Shuang

2017-01-25

Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA. We used multiple measures including data filtering and modifying, evolutionary model selection and coalescent phylogenetic reconstruction to alleviate the LBA artifact. Data filtering by strictly removing unreliable aligned regions and removing substitution saturation genes and rapidly evolving sites could significantly reduce branch lengths of subclades J and C and recovered a relationship of J (C, HCX). In addition, using coalescent phylogenetic reconstruction could elucidate the LBA artifact and recovered J (C, HCX). However, some valid methods for other taxa were inefficient in alleviating the LBA artifact in J-C-HCX. Different strategies should be carefully considered and justified to reduce LBA in phylogenetic reconstruction of different groups. Three subclades of J-C-HCX were estimated to have experienced ancient rapid divergence within a short period, which could be another major obstacle in resolving relationships. Furthermore, our plastid phylogenomic analyses fully resolved the intergeneric relationships of Cupressoideae.

Fast and accurate methods for phylogenomic analyses

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Warnow Tandy

2011-10-01

Full Text Available Abstract Background Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication and loss, so that no single gene tree is a reliable estimate of the species tree. Several methods have been developed to estimate species trees from estimated gene trees, differing according to the specific algorithmic technique used and the biological model used to explain differences between species and gene trees. Relatively little is known about the relative performance of these methods. Results We report on a study evaluating several different methods for estimating species trees from sequence datasets, simulating sequence evolution under a complex model including indels (insertions and deletions, substitutions, and incomplete lineage sorting. The most important finding of our study is that some fast and simple methods are nearly as accurate as the most accurate methods, which employ sophisticated statistical methods and are computationally quite intensive. We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct. Conclusions Our study shows that highly accurate estimations of species trees are achievable, even when gene trees differ from each other and from the species tree, and that these estimations can be obtained using fairly simple and computationally tractable methods.

Phylogenomic re-assessment of the thermophilic genus Geobacillus.

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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.

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

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Simon, Sabrina; Narechania, Apurva; DeSalle, Rob; Hadrys, Heike

2012-01-01

The evolution of the diverse insect lineages is one of the most fascinating issues in evolutionary biology. Despite extensive research in this area, the resolution of insect phylogeny especially of interordinal relationships has turned out to be still a great challenge. One of the challenges for insect systematics is the radiation of the polyneopteran lineages with several contradictory and/or unresolved relationships. Here, we provide the first transcriptomic data for three enigmatic polyneopteran orders (Dermaptera, Plecoptera, and Zoraptera) to clarify one of the most debated issues among higher insect systematics. We applied different approaches to generate 3 data sets comprising 78 species and 1,579 clusters of orthologous genes. Using these three matrices, we explored several key mechanistic problems of phylogenetic reconstruction including missing data, matrix selection, gene and taxa number/choice, and the biological function of the genes. Based on the first phylogenomic approach including these three ambiguous polyneopteran orders, we provide here conclusive support for monophyletic Polyneoptera, contesting the hypothesis of Zoraptera + Paraneoptera and Plecoptera + remaining Neoptera. In addition, we employ various approaches to evaluate data quality and highlight problematic nodes within the Insect Tree that still exist despite our phylogenomic approach. We further show how the support for these nodes or alternative hypotheses might depend on the taxon- and/or gene-sampling. PMID:23175716

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

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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.

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

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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

Phylogenomic reconstruction of lactic acid bacteria: an update

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Yu Li

2011-01-01

Full Text Available Abstract Background Lactic acid bacteria (LAB are important in the food industry for the production of fermented food products and in human health as commensals in the gut. However, the phylogenetic relationships among LAB species remain under intensive debate owing to disagreements among different data sets. Results We performed a phylogenetic analysis of LAB species based on 232 genes from 28 LAB genome sequences. Regardless of the tree-building methods used, combined analyses yielded an identical, well-resolved tree topology with strong supports for all nodes. The LAB species examined were divided into two groups. Group 1 included families Enterococcaceae and Streptococcaceae. Group 2 included families Lactobacillaceae and Leuconostocaceae. Within Group 2, the LAB species were divided into two clades. One clade comprised of the acidophilus complex of genus Lactobacillus and two other species, Lb. sakei and Lb. casei. In the acidophilus complex, Lb. delbrueckii separated first, while Lb. acidophilus/Lb. helveticus and Lb. gasseri/Lb. johnsonii were clustered into a sister group. The other clade within Group 2 consisted of the salivarius subgroup, including five species, Lb. salivarius, Lb. plantarum, Lb. brevis, Lb. reuteri, Lb. fermentum, and the genera Pediococcus, Oenococcus, and Leuconostoc. In this clade, Lb. salivarius was positioned most basally, followed by two clusters, one corresponding to Lb. plantarum/Lb. brevis pair and Pediococcus, and the other including Oenococcus/Leuconostoc pair and Lb. reuteri/Lb. fermentum pair. In addition, phylogenetic utility of the 232 genes was analyzed to identify those that may be more useful than others. The genes identified as useful were related to translation and ribosomal structure and biogenesis (TRSB, and a three-gene set comprising genes encoding ultra-violet resistance protein B (uvrB, DNA polymerase III (polC and penicillin binding protein 2B (pbpB. Conclusions Our phylogenomic analyses

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

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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.

Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.

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Jarvis, Erich D

2016-01-01

The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate the large-scale Avian Phylogenomics Project, which collected and sequenced genomes of 48 bird species representing most currently classified orders to address a range of questions in phylogenomics and comparative genomics. The consortium was able to answer questions not previously possible with just a few genomes. This success spurred on the creation of a project to sequence the genomes of at least one individual of all extant ∼10,500 bird species. The initiation of this project has led us to consider what questions now impossible to answer could be answered with all genomes, and could drive new questions now unimaginable. These include the generation of a highly resolved family tree of extant species, genome-wide association studies across species to identify genetic substrates of many complex traits, redefinition of species and the species concept, reconstruction of the genomes of common ancestors, and generation of new computational tools to address these questions. Here I present visions for the future by posing and answering questions regarding what scientists could potentially do with available genomes of an entire vertebrate class.

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

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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.

Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution.

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Fu, Chao-Nan; Li, Hong-Tao; Milne, Richard; Zhang, Ting; Ma, Peng-Fei; Yang, Jing; Li, De-Zhu; Gao, Lian-Ming

2017-12-08

The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified. Phylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.

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.

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

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Bukhari, Syed Abbas; Caetano-Anollés, Gustavo

2013-01-01

The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable. PMID:23555236

A Phylogenomic Solution to the Origin of Insects by Resolving Crustacean-Hexapod Relationships.

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Schwentner, Martin; Combosch, David J; Pakes Nelson, Joey; Giribet, Gonzalo

2017-06-19

Insects, the most diverse group of organisms, are nested within crustaceans, arguably the most abundant group of marine animals. However, to date, no consensus has been reached as to which crustacean taxon is the closest relative of hexapods. A majority of studies have proposed that Branchiopoda (e.g., fairy shrimps) is the sister group of Hexapoda [1-7]. However, these investigations largely excluded two equally important taxa, Remipedia and Cephalocarida. Other studies suggested Remipedia [8-11] or Remipedia + Cephalocarida [12, 13] as potential sister groups of hexapods, but they either did not include Cephalocarida or used only Sanger sequence data and morphology [9, 12]. Here we present the first phylogenomic study specifically addressing the origins of hexapods, including transcriptomes for two species each of Cephalocarida and Remipedia. Phylogenetic analyses of selected matrices, ranging from 81 to 1,675 orthogroups and up to 510,982 amino acid positions, clearly reject a sister-group relationship between Hexapoda and Branchiopoda [1-7]. Nonetheless, support for a hexapod sister-group relationship to Remipedia or to Cephalocarida-Remipedia was highly dependent on the employed analytical methodology. Further analyses assessing the effects of gene evolutionary rate and targeted taxon exclusion support Remipedia as the sole sister taxon of Hexapoda and suggest that the prior grouping of Remipedia + Cephalocarida is an artifact, possibly due to long branch attraction and compositional heterogeneity. We further conclude that terrestrialization of Hexapoda probably occurred in the late Cambrian to early Ordovician, an estimate that is independent of their proposed sister group [4, 8, 12, 14]. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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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

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

KAUST Repository

Wang, Xin; Drillon, Gué nola; Ryu, Taewoo; Voolstra, Christian R.; Aranda, Manuel

2017-01-01

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.

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.

Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits.

Science.gov (United States)

Cruz-Morales, Pablo; Ramos-Aboites, Hilda E; Licona-Cassani, Cuauhtémoc; Selem-Mójica, Nelly; Mejía-Ponce, Paulina M; Souza-Saldívar, Valeria; Barona-Gómez, Francisco

2017-09-01

Desferrioxamines are hydroxamate siderophores widely conserved in both aquatic and soil-dwelling Actinobacteria. While the genetic and enzymatic bases of siderophore biosynthesis and their transport in model families of this phylum are well understood, evolutionary studies are lacking. Here, we perform a comprehensive desferrioxamine-centric (des genes) phylogenomic analysis, which includes the genomes of six novel strains isolated from an iron and phosphorous depleted oasis in the Chihuahuan desert of Mexico. Our analyses reveal previously unnoticed desferrioxamine evolutionary patterns, involving both biosynthetic and transport genes, likely to be related to desferrioxamines chemical diversity. The identified patterns were used to postulate experimentally testable hypotheses after phenotypic characterization, including profiling of siderophores production and growth stimulation of co-cultures under iron deficiency. Based in our results, we propose a novel des gene, which we term desG, as responsible for incorporation of phenylacetyl moieties during biosynthesis of previously reported arylated desferrioxamines. Moreover, a genomic-based classification of the siderophore-binding proteins responsible for specific and generalist siderophore assimilation is postulated. This report provides a much-needed evolutionary framework, with specific insights supported by experimental data, to direct the future ecological and functional analysis of desferrioxamines in the environment. © FEMS 2017.

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae

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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

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.

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

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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.

Comparative biochemical analyses of venous blood and peritoneal fluid from horses with colic using a portable analyser and an in-house analyser.

Science.gov (United States)

Saulez, M N; Cebra, C K; Dailey, M

2005-08-20

Fifty-six horses with colic were examined over a period of three months. The concentrations of glucose, lactate, sodium, potassium and chloride, and the pH of samples of blood and peritoneal fluid, were determined with a portable clinical analyser and with an in-house analyser and the results were compared. Compared with the in-house analyser, the portable analyser gave higher pH values for blood and peritoneal fluid with greater variability in the alkaline range, and lower pH values in the acidic range, lower concentrations of glucose in the range below 8.3 mmol/l, and lower concentrations of lactate in venous blood in the range below 5 mmol/l and in peritoneal fluid in the range below 2 mmol/l, with less variability. On average, the portable analyser underestimated the concentrations of lactate and glucose in peritoneal fluid in comparison with the in-house analyser. Its measurements of the concentrations of sodium and chloride in peritoneal fluid had a higher bias and were more variable than the measurements in venous blood, and its measurements of potassium in venous blood and peritoneal fluid had a smaller bias and less variability than the measurements made with the in-house analyser.

When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii.

Science.gov (United States)

Pearson, Talima; Hornstra, Heidie M; Sahl, Jason W; Schaack, Sarah; Schupp, James M; Beckstrom-Sternberg, Stephen M; O'Neill, Matthew W; Priestley, Rachael A; Champion, Mia D; Beckstrom-Sternberg, James S; Kersh, Gilbert J; Samuel, James E; Massung, Robert F; Keim, Paul

2013-09-01

Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.].

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

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Ana Ješovnik

Full Text Available 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

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

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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.

Accounting for rate variation among lineages in comparative demographic analyses

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Hope, Andrew G.; Ho, Simon Y. W.; Malaney, Jason L.; Cook, Joseph A.; Talbot, Sandra L.

2014-01-01

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.

Analyses of karyotypes and comparative physical locations of the ...

African Journals Online (AJOL)

The frequencies of signal detection of the marker, RG556 and the BAC clone, 44B4, were 8.0 and 41.3% in O. sativa, while 9.0 and 42.3% in O. officinalis, respectively. Based on a comparative RFLP map of a wild rice, O. officinalis and O. sativa, comparative analyses of karyotypes of O. officinalis were demonstrated firstly ...

Broad phylogenomic sampling and the sister lineage of land plants.

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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.

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.

The phylogenomic position of the grey nurse shark Carcharias taurus Rafinesque, 1810 (Lamniformes, Odontaspididae) inferred from the mitochondrial genome.

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Bowden, Deborah L; Vargas-Caro, Carolina; Ovenden, Jennifer R; Bennett, Michael B; Bustamante, Carlos

2016-11-01

The complete mitochondrial genome of the grey nurse shark Carcharias taurus is described from 25 963 828 sequences obtained using Illumina NGS technology. Total length of the mitogenome is 16 715 bp, consisting of 2 rRNAs, 13 protein-coding regions, 22 tRNA and 2 non-coding regions thus updating the previously published mitogenome for this species. The phylogenomic reconstruction inferred from the mitogenome of 15 species of Lamniform and Carcharhiniform sharks supports the inclusion of C. taurus in a clade with the Lamnidae and Cetorhinidae. This complete mitogenome contributes to ongoing investigation into the monophyly of the Family Odontaspididae.

Comparison of BEACON and COMPARE reactor cavity subcompartment analyses

International Nuclear Information System (INIS)

Burkett, M.W.; Idar, E.S.; Gido, R.G.; Lime, J.F.; Koestel, A.

1984-04-01

In this study, a more advanced best-estimate containment code, BEACON-MOD3A, was ued to calculate force and moment loads resulting from a high-energy blowdown for two reactor cavity geometries previously analyzed with the licensing computer code COMPARE-MOD1A. The BEACON force and moment loads were compared with the COMPARE results to determine the safety margins provided by the COMPARE code. The forces and moments calculated by the codes were found to be different, although not in any consistent manner, for the two reactor cavity geometries studied. Therefore, generic summary statements regarding margins cannot be made because of the effects of the detailed physical configuration. However, differences in the BEACON and COMPARE calculated forces and moments can be attributed to differences in the modeling assumptions used in the codes and the analyses

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes.

Science.gov (United States)

Chen, Xiao; Wang, Yurui; Sheng, Yalan; Warren, Alan; Gao, Shan

2018-05-01

Microeukaryotes are among the most important components of the microbial food web in almost all aquatic and terrestrial ecosystems worldwide. In order to gain a better understanding their roles and functions in ecosystems, sequencing coupled with phylogenomic analyses of entire genomes or transcriptomes is increasingly used to reconstruct the evolutionary history and classification of these microeukaryotes and thus provide a more robust framework for determining their systematics and diversity. More importantly, phylogenomic research usually requires high levels of hands-on bioinformatics experience. Here, we propose an efficient automated method, "Guided Phylogenomic Search in trees" (GPSit), which starts from predicted protein sequences of newly sequenced species and a well-defined customized orthologous database. Compared with previous protocols, our method streamlines the entire workflow by integrating all essential and other optional operations. In so doing, the manual operation time for reconstructing phylogenetic relationships is reduced from days to several hours, compared to other methods. Furthermore, GPSit supports user-defined parameters in most steps and thus allows users to adapt it to their studies. The effectiveness of GPSit is demonstrated by incorporating available online data and new single-cell data of three nonculturable marine ciliates (Anteholosticha monilata, Deviata sp. and Diophrys scutum) under moderate sequencing coverage (~5×). Our results indicate that the former could reconstruct robust "deep" phylogenetic relationships while the latter reveals the presence of intermediate taxa in shallow relationships. Based on empirical phylogenomic data, we also used GPSit to evaluate the impact of different levels of missing data on two commonly used methods of phylogenetic analyses, maximum likelihood (ML) and Bayesian inference (BI) methods. We found that BI is less sensitive to missing data when fast-evolving sites are removed. © 2018 John

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.

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.

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Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A

2016-07-01

Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.

Science.gov (United States)

Martino, Maria Elena; Bayjanov, Jumamurat R; Caffrey, Brian E; Wels, Michiel; Joncour, Pauline; Hughes, Sandrine; Gillet, Benjamin; Kleerebezem, Michiel; van Hijum, Sacha A F T; Leulier, François

2016-12-01

The ability of bacteria to adapt to diverse environmental conditions is well-known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene-trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Phylogenomics provides strong evidence for relationships of butterflies and moths.

Science.gov (United States)

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.

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.

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

Science.gov (United States)

2013-01-01

Background Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts. Results The overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species. Conclusions The comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences

Comparative Transcriptional Analyses of Francisella tularensis and Francisella novicida.

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Siva T Sarva

Full Text Available Francisella tularensis is composed of a number of subspecies with varied geographic distribution, host ranges, and virulence. In view of these marked differences, comparative functional genomics may elucidate some of the molecular mechanism(s behind these differences. In this study a shared probe microarray was designed that could be used to compare the transcriptomes of Francisella tularensis subsp. tularensis Schu S4 (Ftt, Francisella tularensis subsp. holarctica OR960246 (Fth, Francisella tularensis subsp. holarctica LVS (LVS, and Francisella novicida U112 (Fn. To gain insight into expression differences that may be related to the differences in virulence of these subspecies, transcriptomes were measured from each strain grown in vitro under identical conditions, utilizing a shared probe microarray. The human avirulent Fn strain exhibited high levels of transcription of genes involved in general metabolism, which are pseudogenes in the human virulent Ftt and Fth strains, consistent with the process of genome decay in the virulent strains. Genes encoding an efflux system (emrA2 cluster of genes, siderophore (fsl operon, acid phosphatase, LPS synthesis, polyamine synthesis, and citrulline ureidase were all highly expressed in Ftt when compared to Fn, suggesting that some of these may contribute to the relative high virulence of Ftt. Genes expressed at a higher level in Ftt when compared to the relatively less virulent Fth included genes encoding isochorismatases, cholylglycine hydrolase, polyamine synthesis, citrulline ureidase, Type IV pilus subunit, and the Francisella Pathogenicity Island protein PdpD. Fth and LVS had very few expression differences, consistent with the derivation of LVS from Fth. This study demonstrated that a shared probe microarray designed to detect transcripts in multiple species/subspecies of Francisella enabled comparative transcriptional analyses that may highlight critical differences that underlie the relative

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

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Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-01-01

Abstract Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. PMID:29186447

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

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Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-02-01

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. © The Authors 2017. Published by Oxford University Press.

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

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Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

2015-07-01

The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

Phylogenomics of African guenons.

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Moulin, Sibyle; Gerbault-Seureau, Michèle; Dutrillaux, Bernard; Richard, Florence Anne

2008-01-01

The karyotypes of 28 specimens belonging to 26 species of Cercopithecinae have been compared with each other and with human karyotype by chromosome banding and, for some of them, by Zoo-FISH (human painting probes) techniques. The study includes the first description of the karyotypes of four species and a synonym of Cercopithecus nictitans. The chromosomal homologies obtained provide us with new data on a large number of rearrangements. This allows us to code chromosomal characters to draw Cercopithecini phylogenetic trees, which are compared to phylogenetic data based on DNA sequences. Our findings show that some of the superspecies proposed by Kingdon (1997 The Kingdon Field Guide to African Mammals, Academic Press.) and Groves (2001 Primates Taxonomy, Smithsonian Institution Press) do not form homogeneous groups and that the genus Cercopithecus is paraphyletic, in agreement with previous molecular analyses. The evolution of Cercopithecini karyotypes is mainly due to non-centromeric chromosome fissions and centromeric shifts or inversions. Non-Robertsonian translocations occurred in C. hamlyni and C. neglectus. The position of chromosomal rearrangements in the phylogenetic tree leads us to propose that the Cercopithecini evolution proceeded by either repeated fission events facilitated by peculiar genomic structures or successive reticulate phases, in which heterozygous populations for few rearranged chromosomes were present, allowing the spreading of chromosomal forms in various combinations, before the speciation process.

Comparative survey of dynamic analyses of free-piston Stirling engines

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Kankam, M. D.; Rauch, J. S.

1991-01-01

Reported dynamics analyses for evaluating the steady-state response and stability of free-piston Stirling engine (FPSE) systems are compared. Various analytical approaches are discussed to provide guidance on their salient features. Recommendations are made in the recommendations remarks for an approach which captures most of the inherent properties of the engine. Such an approach has the potential for yielding results which will closely match practical FPSE-load systems.

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.

Phylogenomics of 2,4-Diacetylphloroglucinol-Producing Pseudomonas and Novel Antiglycation Endophytes from Piper auritum.

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Gutiérrez-García, Karina; Neira-González, Adriana; Pérez-Gutiérrez, Rosa Martha; Granados-Ramírez, Giovana; Zarraga, Ramon; Wrobel, Kazimierz; Barona-Gómez, Francisco; Flores-Cotera, Luis B

2017-07-28

2,4-Diacetylphloroglucinol (DAPG) (1) is a phenolic polyketide produced by some plant-associated Pseudomonas species, with many biological activities and ecological functions. Here, we aimed at reconstructing the natural history of DAPG using phylogenomics focused at its biosynthetic gene cluster or phl genes. In addition to around 1500 publically available genomes, we obtained and analyzed the sequences of nine novel Pseudomonas endophytes isolated from the antidiabetic medicinal plant Piper auritum. We found that 29 organisms belonging to six Pseudomonas species contain the phl genes at different frequencies depending on the species. The evolution of the phl genes was then reconstructed, leading to at least two clades postulated to correlate with the known chemical diversity surrounding DAPG biosynthesis. Moreover, two of the newly obtained Pseudomonas endophytes with high antiglycation activity were shown to exert their inhibitory activity against the formation of advanced glycation end-products via DAPG and related congeners. Its isomer, 5-hydroxyferulic acid (2), detected during bioactivity-guided fractionation, together with other DAPG congeners, were found to enhance the detected inhibitory activity. This report provides evidence of a link between the evolution and chemical diversity of DAPG and congeners.

Missed, Not Missing: Phylogenomic Evidence for the Existence of Avian FoxP3.

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Michael P Denyer

Full Text Available The Forkhead box transcription factor FoxP3 is pivotal to the development and function of regulatory T cells (Tregs, which make a major contribution to peripheral tolerance. FoxP3 is believed to perform a regulatory role in all the vertebrate species in which it has been detected. The prevailing view is that FoxP3 is absent in birds and that avian Tregs rely on alternative developmental and suppressive pathways. Prompted by the automated annotation of foxp3 in the ground tit (Parus humilis genome, we have questioned this assumption. Our analysis of all available avian genomes has revealed that the foxp3 locus is missing, incomplete or of poor quality in the relevant genomic assemblies for nearly all avian species. Nevertheless, in two species, the peregrine falcon (Falco peregrinus and the saker falcon (F. cherrug, there is compelling evidence for the existence of exons showing synteny with foxp3 in the ground tit. A broader phylogenomic analysis has shown that FoxP3 sequences from these three species are similar to crocodilian sequences, the closest living relatives of birds. In both birds and crocodilians, we have also identified a highly proline-enriched region at the N terminus of FoxP3, a region previously identified only in mammals.

Comparative analyses of basal rate of metabolism in mammals: data selection does matter.

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Genoud, Michel; Isler, Karin; Martin, Robert D

2018-02-01

Basal rate of metabolism (BMR) is a physiological parameter that should be measured under strictly defined experimental conditions. In comparative analyses among mammals BMR is widely used as an index of the intensity of the metabolic machinery or as a proxy for energy expenditure. Many databases with BMR values for mammals are available, but the criteria used to select metabolic data as BMR estimates have often varied and the potential effect of this variability has rarely been questioned. We provide a new, expanded BMR database reflecting compliance with standard criteria (resting, postabsorptive state; thermal neutrality; adult, non-reproductive status for females) and examine potential effects of differential selectivity on the results of comparative analyses. The database includes 1739 different entries for 817 species of mammals, compiled from the original sources. It provides information permitting assessment of the validity of each estimate and presents the value closest to a proper BMR for each entry. Using different selection criteria, several alternative data sets were extracted and used in comparative analyses of (i) the scaling of BMR to body mass and (ii) the relationship between brain mass and BMR. It was expected that results would be especially dependent on selection criteria with small sample sizes and with relatively weak relationships. Phylogenetically informed regression (phylogenetic generalized least squares, PGLS) was applied to the alternative data sets for several different clades (Mammalia, Eutheria, Metatheria, or individual orders). For Mammalia, a 'subsampling procedure' was also applied, in which random subsamples of different sample sizes were taken from each original data set and successively analysed. In each case, two data sets with identical sample size and species, but comprising BMR data with different degrees of reliability, were compared. Selection criteria had minor effects on scaling equations computed for large clades

The necessity for comparative risk analyses as seen from the political point of view

International Nuclear Information System (INIS)

Steger, U.

1981-01-01

The author describes the current insufficient utilization of risk analyses in the political decision process and investigates if other technologies encounter the same difficulties of acceptance as in the nuclear energy field. This being likely he is trying to find out which contribution comparative risk analyses could make to the process of democratic will-formation so that new technologies are accepted. Firstly the author establishes theses criticizing the recent scientific efforts made in the field of risk analyses and their usability for the political decision process. He then defines the criteria risk analyses have to meet in order to serve as scientific elements for consultative political discussions. (orig./HP) [de

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.

EST based phylogenomics of Syndermata questions monophyly of Eurotatoria

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Bucher Gregor

2008-12-01

Full Text Available Abstract Background The metazoan taxon Syndermata comprising Rotifera (in the classical sense of Monogononta+Bdelloidea+Seisonidea and Acanthocephala has raised several hypotheses connected to the phylogeny of these animal groups and the included subtaxa. While the monophyletic origin of Syndermata and Acanthocephala is well established based on morphological and molecular data, the phylogenetic position of Syndermata within Spiralia, the monophyletic origin of Monogononta, Bdelloidea, and Seisonidea and the acanthocephalan sister group are still a matter of debate. The comparison of the alternative hypotheses suggests that testing the phylogenetic validity of Eurotatoria (Monogononta+Bdelloidea is the key to unravel the phylogenetic relations within Syndermata. The syndermatan phylogeny in turn is a prerequisite for reconstructing the evolution of the acanthocephalan endoparasitism. Results Here we present our results from a phylogenomic approach studying i the phylogenetic position of Syndermata within Spiralia, ii the monophyletic origin of monogononts and bdelloids and iii the phylogenetic relations of the latter two taxa to acanthocephalans. For this analysis we have generated EST libraries of Pomphorhynchus laevis, Echinorhynchus truttae (Acanthocephala and Brachionus plicatilis (Monogononta. By extending these data with database entries of B. plicatilis, Philodina roseola (Bdelloidea and 25 additional metazoan species, we conducted phylogenetic reconstructions based on 79 ribosomal proteins using maximum likelihood and bayesian approaches. Our findings suggest that the phylogenetic position of Syndermata within Spiralia is close to Platyhelminthes, that Eurotatoria are not monophyletic and that bdelloids are more closely related to acanthocephalans than monogononts. Conclusion Mapping morphological character evolution onto molecular phylogeny suggests the (partial or complete reduction of the corona and the emergence of a retractable

Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.

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Melissa Dsouza

Full Text Available Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR. However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs, primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

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Stata, Matt; Wang, Wei; White, Merlin M.; Moncalvo, Jean-Marc

2018-01-01

ABSTRACT Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects. PMID:29764946

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

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Bombarely Aureliano

2012-08-01

Full Text Available Abstract Background Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco and parental genome donors, N. sylvesteris (S-Genome and N. tomentosiformis (T-Genome, a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant. Results A comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters expressed above background level (more than 5 reads showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks and non-synonymous nucleotide substitution (Kn provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place. Conclusions Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD events, polyploid genomes usually maintain a high percentage of

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

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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.

Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes.

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Chen, Xin; Lemmon, Alan R; Lemmon, Emily Moriarty; Pyron, R Alexander; Burbrink, Frank T

2017-06-01

Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeographic origins and rates of diversification. We explore processes leading to the diversity of global ratsnakes and test several important hypotheses related to areas of origin and enhanced diversification upon colonizing new continents. We estimate species trees inferred from phylogenomic scale data (304 loci) while exploring several strategies that consider topological error from each individual gene tree. With a dated species tree, we examine taxonomy and test previous hypotheses that suggest the ratsnakes originated in the Old World (OW) and dispersed to New World (NW). Furthermore, we determine if dispersal to the NW represented a source of ecological opportunity, which should show elevated rates of species diversification. We show that ratsnakes originated in the OW during the mid-Oligocene and subsequently dispersed to the NW by the mid-Miocene; diversification was also elevated in a subclade of NW taxa. Finally, the optimal biogeographic region-dependent speciation model shows that the uptick in ratsnake diversification was associated with colonization of the NW. We consider several alternative explanations that account for regionally distinct diversification rates. Copyright © 2017 Elsevier Inc. All rights reserved.

Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis.

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Xu, Lin; Wu, Yue-Hong; Zhou, Peng; Cheng, Hong; Liu, Qian; Xu, Xue-Wei

2018-05-23

Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079 T and P. tepidarius DSM 10594 T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins. Comparative genomic studies have revealed that different thermal types exist in different taxa, and few studies have been focused on the class Alphaproteobacteria, especially the family Erythrobacteraceae. In this study, eight genomes of Porphyrobacter strains were compared to elucidate how Porphyrobacter thermophiles developed mechanisms to adapt to thermal environments. P. cryptus DSM 12079 T grew optimally at 50 °C, which was higher than the optimal growth temperature of other Porphyrobacter type strains. Phylogenomic analysis of the genus Porphyrobacter revealed that P. cryptus DSM 12079 T formed a distinct and independent clade. Comparative genomic studies uncovered that 1405 single-copy genes were shared by Porphyrobacter type strains. Alignments of single-copy proteins showed that various types of amino acid substitutions existed between P. cryptus DSM 12079 T and the other Porphyrobacter strains. The primary substitution types were changes from glycine/serine to alanine. P. cryptus DSM 12079 T was the sole thermophile within the genus Porphyrobacter. Phylogenomic analysis and amino acid frequencies indicated that amino acid substitutions might play an important role in the thermophily of P. cryptus DSM 12079 T . Bioinformatic analysis revealed that major amino acid substitutional types

Comparative Phenotypical and Molecular Analyses of Arabidopsis Grown under Fluorescent and LED Light

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Franka Seiler

2017-06-01

Full Text Available Comparative analyses of phenotypic and molecular traits of Arabidopsis thaliana grown under standardised conditions is still a challenge using climatic devices supplied with common light sources. These are in most cases fluorescent lights, which have several disadvantages such as heat production at higher light intensities, an invariable spectral output, and relatively rapid “ageing”. This results in non-desired variations of growth conditions and lowers the comparability of data acquired over extended time periods. In this study, we investigated the growth behaviour of Arabidopsis Col0 under different light conditions, applying fluorescent compared to LED lamps, and we conducted physiological as well as gene expression analyses. By changing the spectral composition and/or light intensity of LEDs we can clearly influence the growth behaviour of Arabidopsis and thereby study phenotypic attributes under very specific light conditions that are stable and reproducible, which is not necessarily given for fluorescent lamps. By using LED lights, we can also roughly mimic the sun light emission spectrum, enabling us to study plant growth in a more natural-like light set-up. We observed distinct growth behaviour under the different light regimes which was reflected by physiological properties of the plants. In conclusion, LEDs provide variable emission spectra for studying plant growth under defined, stable light conditions.

Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

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Mei Jiang

2018-05-01

Full Text Available To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

Genome sequencing and comparative genomics analysis revealed pathogenic potential in Penicillium capsulatum as a novel fungal pathogen belonging to Eurotiales

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Ying Yang

2016-10-01

Full Text Available Penicillium capsulatum is a rare Penicillium species used in paper manufacturing, but recently it has been reported to cause invasive infection. To research the pathogenicity of the clinical Penicillium strain, we sequenced the genomes and transcriptome of the clinical and environmental strains of P. capsulatum. Comparative analyses of these two P. capsulatum strains and close related strains belonging to Eurotiales were performed. The assembled genome sizes of P. capsulatum are approximately 34.4 Mbp in length and encode 11,080 predicted genes. The different isolates of P. capsulatum are highly similar, with the exception of several unique genes, INDELs or SNP in the genes coding for glycosyl hydrolases, amino acid transporters and circumsporozoite protein. A phylogenomic analysis was performed based on the whole genome data of 38 strains belonging to Eurotiales. By comparing the whole genome sequences and the virulence-related genes from 20 important related species, including fungal pathogens and non-human pathogens belonging to Eurotiales, we found meaningful pathogenicity characteristics between P. capsulatum and its closely related species. Our research indicated that P. capsulatum may be a neglected opportunistic pathogen. This study is beneficial for mycologists, geneticists and epidemiologists to achieve a deeper understanding of the genetic basis of the role of P. capsulatum as a newly reported fungal pathogen.

Comparative Genomic and Transcriptional Analyses of CRISPR Systems Across the Genus Pyrobaculum

Directory of Open Access Journals (Sweden)

David L Bernick

2012-07-01

Full Text Available Within the domain Archaea, the CRISPR immune system appears to be nearly ubiquitous based on computational genome analyses. Initial studies in bacteria demonstrated that the CRISPR system targets invading plasmid and viral DNA. Recent experiments in the model archaeon Pyrococcus furiosus uncovered a novel RNA-targeting variant of the CRISPR system potentially unique to archaea. Because our understanding of CRISPR system evolution in other archaea is limited, we have taken a comparative genomic and transcriptomic view of the CRISPR arrays across six diverse species within the crenarchaeal genus Pyrobaculum. We present transcriptional data from each of four species in the genus (P. aerophilum, P. islandicum, P. calidifontis, P. arsenaticum, analyzing mature CRISPR-associated small RNA abundance from over 20 arrays. Within the genus, there is remarkable conservation of CRISPR array structure, as well as unique features that are have not been studied in other archaeal systems. These unique features include: a nearly invariant CRISPR promoter, conservation of direct repeat families, the 5' polarity of CRISPR-associated small RNA abundance, and a novel CRISPR-specific association with homologues of nurA and herA. These analyses provide a genus-level evolutionary perspective on archaeal CRISPR systems, broadening our understanding beyond existing non-comparative model systems.

CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species.

Science.gov (United States)

Chen, Hao; Wang, Xiangfeng

2013-09-01

In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.

Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

Science.gov (United States)

Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

2015-01-01

S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

Science.gov (United States)

Li, Pengpeng; Kwok, Amy H Y; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C

2015-01-01

S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae

Czech Academy of Sciences Publication Activity Database

Ševčíková, T.; Klimeš, V.; Zbránková, V.; Strnad, Hynek; Hroudová, Miluše; Vlček, Čestmír; Eliáš, M.

2016-01-01

Roč. 8, č. 3 (2016), s. 705-722 ISSN 1759-6653 R&D Projects: GA ČR GA13-33039S Grant - others:GA MŠk(CZ) LO1208; GA MŠk(CZ) ED2.1.00/03.0100 Institutional support: RVO:68378050 Keywords : Eustigmatophyceae * evolution * phylogenomics * split genes * Stramenopiles * suppressor tRNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.979, year: 2016

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).

Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung.

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Weiling Zheng

Full Text Available The fish swimbladder is a unique organ in vertebrate evolution and it functions for regulating buoyancy in most teleost species. It has long been postulated as a homolog of the tetrapod lung, but the molecular evidence is scarce. In order to understand the molecular function of swimbladder as well as its relationship with lungs in tetrapods, transcriptomic analyses of zebrafish swimbladder were carried out by RNA-seq. Gene ontology classification showed that genes in cytoskeleton and endoplasmic reticulum were enriched in the swimbladder. Further analyses depicted gene sets and pathways closely related to cytoskeleton constitution and regulation, cell adhesion, and extracellular matrix. Several prominent transcription factor genes in the swimbladder including hoxc4a, hoxc6a, hoxc8a and foxf1 were identified and their expressions in developing swimbladder during embryogenesis were confirmed. By comparison of enriched transcripts in the swimbladder with those in human and mouse lungs, we established the resemblance of transcriptome of the zebrafish swimbladder and mammalian lungs. Based on the transcriptomic data of zebrafish swimbladder, the predominant functions of swimbladder are in its epithelial and muscular tissues. Our comparative analyses also provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung.

Comparative genomic data of the Avian Phylogenomics Project

DEFF Research Database (Denmark)

Zhang, Guojie; Li, Bo; Li, Cai

2014-01-01

species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting...

A Consistent Phylogenetic Backbone for the Fungi

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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

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.

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.

Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

Directory of Open Access Journals (Sweden)

Pengpeng Li

Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

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

Directory of Open Access Journals (Sweden)

Hartmann Stefanie

2008-03-01

sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.

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

major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.

CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN

Science.gov (United States)

Chen, Hao; Wang, Xiangfeng

2013-01-01

In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/. PMID:23898041

Identification of a new family of putative PD-(D/EXK nucleases with unusual phylogenomic distribution and a new type of the active site

Directory of Open Access Journals (Sweden)

Bujnicki Janusz M

2005-02-01

Full Text Available Abstract Background Prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. Theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. Here, we predict the three-dimensional fold and study the phylogenomic distribution of members of a large family of uncharacterized proteins classified in the Clusters of Orthologous Groups database as COG4636. Results Using protein fold-recognition we found that members of COG4636 are remotely related to Holliday junction resolvases and other nucleases from the PD-(D/EXK superfamily. Structure modeling and sequence analyses suggest that most members of COG4636 exhibit a new, unusual variant of the putative active site, in which the catalytic Lys residue migrated in the sequence, but retained similar spatial position with respect to other functionally important residues. Sequence analyses revealed that members of COG4636 and their homologs are found mainly in Cyanobacteria, but also in other bacterial phyla. They undergo horizontal transfer and extensive proliferation in the colonized genomes; for instance in Gloeobacter violaceus PCC 7421 they comprise over 2% of all protein-encoding genes. Thus, members of COG4636 appear to be a new type of selfish genetic elements, which may fulfill an important role in the genome dynamics of Cyanobacteria and other species they invaded. Our analyses provide a platform for experimental determination of the molecular and cellular function of members of this large protein family. Conclusion After submission of this manuscript, a crystal structure of one of the COG4636 members was released in the Protein Data Bank (code 1wdj

Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

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Janke Axel

2008-05-01

Full Text Available Abstract Background A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew, probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method. Results The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95–100 million years ago. Many of the following divergences occurred only a few (2–4 million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses. Conclusion The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in

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

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

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

Science.gov (United States)

Sun, Zhihong; Harris, Hugh M. B.; McCann, Angela; Guo, Chenyi; Argimón, Silvia; Zhang, Wenyi; Yang, Xianwei; Jeffery, Ian B; Cooney, Jakki C.; Kagawa, Todd F.; Liu, Wenjun; Song, Yuqin; Salvetti, Elisa; Wrobel, Agnieszka; Rasinkangas, Pia; Parkhill, Julian; Rea, Mary C.; O'Sullivan, Orla; Ritari, Jarmo; Douillard, François P.; Paul Ross, R.; Yang, Ruifu; Briner, Alexandra E.; Felis, Giovanna E.; de Vos, Willem M.; Barrangou, Rodolphe; Klaenhammer, Todd R.; Caufield, Page W.; Cui, Yujun; Zhang, Heping; O'Toole, Paul W.

2015-01-01

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species. PMID:26415554

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Science.gov (United States)

Sun, Zhihong; Harris, Hugh M B; McCann, Angela; Guo, Chenyi; Argimón, Silvia; Zhang, Wenyi; Yang, Xianwei; Jeffery, Ian B; Cooney, Jakki C; Kagawa, Todd F; Liu, Wenjun; Song, Yuqin; Salvetti, Elisa; Wrobel, Agnieszka; Rasinkangas, Pia; Parkhill, Julian; Rea, Mary C; O'Sullivan, Orla; Ritari, Jarmo; Douillard, François P; Paul Ross, R; Yang, Ruifu; Briner, Alexandra E; Felis, Giovanna E; de Vos, Willem M; Barrangou, Rodolphe; Klaenhammer, Todd R; Caufield, Page W; Cui, Yujun; Zhang, Heping; O'Toole, Paul W

2015-09-29

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.

Comparative Analyses of Zebrafish Anxiety-Like Behavior Using Conflict-Based Novelty Tests.

Science.gov (United States)

Kysil, Elana V; Meshalkina, Darya A; Frick, Erin E; Echevarria, David J; Rosemberg, Denis B; Maximino, Caio; Lima, Monica Gomes; Abreu, Murilo S; Giacomini, Ana C; Barcellos, Leonardo J G; Song, Cai; Kalueff, Allan V

2017-06-01

Modeling of stress and anxiety in adult zebrafish (Danio rerio) is increasingly utilized in neuroscience research and central nervous system (CNS) drug discovery. Representing the most commonly used zebrafish anxiety models, the novel tank test (NTT) focuses on zebrafish diving in response to potentially threatening stimuli, whereas the light-dark test (LDT) is based on fish scototaxis (innate preference for dark vs. bright areas). Here, we systematically evaluate the utility of these two tests, combining meta-analyses of published literature with comparative in vivo behavioral and whole-body endocrine (cortisol) testing. Overall, the NTT and LDT behaviors demonstrate a generally good cross-test correlation in vivo, whereas meta-analyses of published literature show that both tests have similar sensitivity to zebrafish anxiety-like states. Finally, NTT evokes higher levels of cortisol, likely representing a more stressful procedure than LDT. Collectively, our study reappraises NTT and LDT for studying anxiety-like states in zebrafish, and emphasizes their developing utility for neurobehavioral research. These findings can help optimize drug screening procedures by choosing more appropriate models for testing anxiolytic or anxiogenic drugs.

THE GOAL OF VALUE-BASED MEDICINE ANALYSES: COMPARABILITY. THE CASE FOR NEOVASCULAR MACULAR DEGENERATION

Science.gov (United States)

Brown, Gary C.; Brown, Melissa M.; Brown, Heidi C.; Kindermann, Sylvia; Sharma, Sanjay

2007-01-01

Purpose To evaluate the comparability of articles in the peer-reviewed literature assessing the (1) patient value and (2) cost-utility (cost-effectiveness) associated with interventions for neovascular age-related macular degeneration (ARMD). Methods A search was performed in the National Library of Medicine database of 16 million peer-reviewed articles using the key words cost-utility, cost-effectiveness, value, verteporfin, pegaptanib, laser photocoagulation, ranibizumab, and therapy. All articles that used an outcome of quality-adjusted life-years (QALYs) were studied in regard to (1) percent improvement in quality of life, (2) utility methodology, (3) utility respondents, (4) types of costs included (eg, direct healthcare, direct nonhealthcare, indirect), (5) cost bases (eg, Medicare, National Health Service in the United Kingdom), and (6) study cost perspective (eg, government, societal, third-party insurer). To qualify as a value-based medicine analysis, the patient value had to be measured using the outcome of the QALYs conferred by respective interventions. As with value-based medicine analyses, patient-based time tradeoff utility analysis had to be utilized, patient utility respondents were necessary, and direct medical costs were used. Results Among 21 cost-utility analyses performed on interventions for neovascular macular degeneration, 15 (71%) met value-based medicine criteria. The 6 others (29%) were not comparable owing to (1) varying utility methodology, (2) varying utility respondents, (3) differing costs utilized, (4) differing cost bases, and (5) varying study perspectives. Among value-based medicine studies, laser photocoagulation confers a 4.4% value gain (improvement in quality of life) for the treatment of classic subfoveal choroidal neovascularization. Intravitreal pegaptanib confers a 5.9% value gain (improvement in quality of life) for classic, minimally classic, and occult subfoveal choroidal neovascularization, and photodynamic therapy

The goal of value-based medicine analyses: comparability. The case for neovascular macular degeneration.

Science.gov (United States)

Brown, Gary C; Brown, Melissa M; Brown, Heidi C; Kindermann, Sylvia; Sharma, Sanjay

2007-01-01

To evaluate the comparability of articles in the peer-reviewed literature assessing the (1) patient value and (2) cost-utility (cost-effectiveness) associated with interventions for neovascular age-related macular degeneration (ARMD). A search was performed in the National Library of Medicine database of 16 million peer-reviewed articles using the key words cost-utility, cost-effectiveness, value, verteporfin, pegaptanib, laser photocoagulation, ranibizumab, and therapy. All articles that used an outcome of quality-adjusted life-years (QALYs) were studied in regard to (1) percent improvement in quality of life, (2) utility methodology, (3) utility respondents, (4) types of costs included (eg, direct healthcare, direct nonhealthcare, indirect), (5) cost bases (eg, Medicare, National Health Service in the United Kingdom), and (6) study cost perspective (eg, government, societal, third-party insurer). To qualify as a value-based medicine analysis, the patient value had to be measured using the outcome of the QALYs conferred by respective interventions. As with value-based medicine analyses, patient-based time tradeoff utility analysis had to be utilized, patient utility respondents were necessary, and direct medical costs were used. Among 21 cost-utility analyses performed on interventions for neovascular macular degeneration, 15 (71%) met value-based medicine criteria. The 6 others (29%) were not comparable owing to (1) varying utility methodology, (2) varying utility respondents, (3) differing costs utilized, (4) differing cost bases, and (5) varying study perspectives. Among value-based medicine studies, laser photocoagulation confers a 4.4% value gain (improvement in quality of life) for the treatment of classic subfoveal choroidal neovascularization. Intravitreal pegaptanib confers a 5.9% value gain (improvement in quality of life) for classic, minimally classic, and occult subfoveal choroidal neovascularization, and photodynamic therapy with verteporfin confers

CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

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Proost, Sebastian; Mutwil, Marek

2018-05-01

The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.

A modeling approach to compare ΣPCB concentrations between congener-specific analyses

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Gibson, Polly P.; Mills, Marc A.; Kraus, Johanna M.; Walters, David M.

2017-01-01

Changes in analytical methods over time pose problems for assessing long-term trends in environmental contamination by polychlorinated biphenyls (PCBs). Congener-specific analyses vary widely in the number and identity of the 209 distinct PCB chemical configurations (congeners) that are quantified, leading to inconsistencies among summed PCB concentrations (ΣPCB) reported by different studies. Here we present a modeling approach using linear regression to compare ΣPCB concentrations derived from different congener-specific analyses measuring different co-eluting groups. The approach can be used to develop a specific conversion model between any two sets of congener-specific analytical data from similar samples (similar matrix and geographic origin). We demonstrate the method by developing a conversion model for an example data set that includes data from two different analytical methods, a low resolution method quantifying 119 congeners and a high resolution method quantifying all 209 congeners. We used the model to show that the 119-congener set captured most (93%) of the total PCB concentration (i.e., Σ209PCB) in sediment and biological samples. ΣPCB concentrations estimated using the model closely matched measured values (mean relative percent difference = 9.6). General applications of the modeling approach include (a) generating comparable ΣPCB concentrations for samples that were analyzed for different congener sets; and (b) estimating the proportional contribution of different congener sets to ΣPCB. This approach may be especially valuable for enabling comparison of long-term remediation monitoring results even as analytical methods change over time. 

Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.

Science.gov (United States)

Yonezawa, Takahiro; Segawa, Takahiro; Mori, Hiroshi; Campos, Paula F; Hongoh, Yuichi; Endo, Hideki; Akiyoshi, Ayumi; Kohno, Naoki; Nishida, Shin; Wu, Jiaqi; Jin, Haofei; Adachi, Jun; Kishino, Hirohisa; Kurokawa, Ken; Nogi, Yoshifumi; Tanabe, Hideyuki; Mukoyama, Harutaka; Yoshida, Kunio; Rasoamiaramanana, Armand; Yamagishi, Satoshi; Hayashi, Yoshihiro; Yoshida, Akira; Koike, Hiroko; Akishinonomiya, Fumihito; Willerslev, Eske; Hasegawa, Masami

2017-01-09

The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative chloroplast genomics: Analyses including new sequencesfrom the angiosperms Nuphar advena and Ranunculus macranthus

Energy Technology Data Exchange (ETDEWEB)

Raubeso, Linda A.; Peery, Rhiannon; Chumley, Timothy W.; Dziubek,Chris; Fourcade, H. Matthew; Boore, Jeffrey L.; Jansen, Robert K.

2007-03-01

The number of completely sequenced plastid genomes available is growing rapidly. This new array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is most useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the new genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (from the basal group of eudicots). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

COMPARATIVE BIOMECHANICAL ANALYSES OF SQUAT JUMP WITHOUT AND WITH FLEXION IN KNEE JOINT

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Saša Bubanj

2009-11-01

Full Text Available In sports hall of Faculty of sports and physical education in Niš, student demon- strated technique of squat jump – without and with flexion in knee joint. Elements of technique were recorded by using one digital video camera in sagital plane. By using comparative kinematics analyses, there were establish differences in values of kinema- tics parametres of different body segments. Bigger elevation of body centre of gravity was ascertain at bounce without flexion in knee joint.

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

Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

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Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

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Tamara Smokvina

Full Text Available Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis

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

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

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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.

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

Science.gov (United States)

Parks, Matthew B; Wickett, Norman J; Alverson, Andrew J

2018-01-01

Abstract Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available. PMID:29040712

Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.

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Anderson, Frank E; Williams, Bronwyn W; Horn, Kevin M; Erséus, Christer; Halanych, Kenneth M; Santos, Scott R; James, Samuel W

2017-05-30

Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.

Mixed Approach Retrospective Analyses of Suicide and Suicidal Ideation for Brand Compared with Generic Central Nervous System Drugs.

Science.gov (United States)

Cheng, Ning; Rahman, Md Motiur; Alatawi, Yasser; Qian, Jingjing; Peissig, Peggy L; Berg, Richard L; Page, C David; Hansen, Richard A

2018-04-01

Several different types of drugs acting on the central nervous system (CNS) have previously been associated with an increased risk of suicide and suicidal ideation (broadly referred to as suicide). However, a differential association between brand and generic CNS drugs and suicide has not been reported. This study compares suicide adverse event rates for brand versus generic CNS drugs using multiple sources of data. Selected examples of CNS drugs (sertraline, gabapentin, zolpidem, and methylphenidate) were evaluated via the US FDA Adverse Event Reporting System (FAERS) for a hypothesis-generating study, and then via administrative claims and electronic health record (EHR) data for a more rigorous retrospective cohort study. Disproportionality analyses with reporting odds ratios and 95% confidence intervals (CIs) were used in the FAERS analyses to quantify the association between each drug and reported suicide. For the cohort studies, Cox proportional hazards models were used, controlling for demographic and clinical characteristics as well as the background risk of suicide in the insured population. The FAERS analyses found significantly lower suicide reporting rates for brands compared with generics for all four studied products (Breslow-Day P brand CNS drugs in FAERS and adjusted retrospective cohort analyses remained significant only for sertraline. However, even for sertraline, temporal confounding related to the close proximity of black box warnings and generic availability is possible. Additional analyses in larger data sources with additional drugs are needed.

Genomic Sequencing of Ranaviruses Isolated from Turbot (Scophthalmus maximus) and Atlantic Cod (Gadus morhua)

DEFF Research Database (Denmark)

Ariel, Ellen; Steckler, Natalie K.; Subramaniam, Kuttichantran

2016-01-01

Ranaviruses have been isolated from Atlantic cod (Gadus morhua) and turbot (Scophthalmus maximus) in Denmark. Phylogenomic analyses revealed that these two ranaviruses are nearly identical and form a distinct clade at the base of the ranavirus tree branching off near other fish ranaviruses....

Genomic Sequencing of Ranaviruses Isolated from Edible Frogs (Pelophylax esculentus)

DEFF Research Database (Denmark)

Ariel, Ellen; Subramaniam, Kuttichantran; Imnoi, Kamonchai

2017-01-01

Ranaviruses were isolated from wild edible frogs (Pelophylax esculentus) during epizootics in Denmark and Italy. Phylogenomic analyses revealed that these isolates are closely related and belong to a clade of ranaviruses that includes the Andrias davidianus ranavirus (ADRV), common midwife toad r...

Genomic Sequence of a Ranavirus Isolated from Short-Finned Eel (Anguilla australis)

DEFF Research Database (Denmark)

Subramaniam, Kuttichantran; Toffan, Anna; Cappellozza, Elisabetta

2016-01-01

The short-finned eel ranavirus (SERV) was isolated from short-finned eel imported to Italy from New Zealand. Phylogenomic analyses revealed that SERV is a unique member of the genus Ranavirus, family Iridoviridae, branching at the base of the tree near other fish ranaviruses....

The Nothoaspis amazoniensis Complete Mitogenome: A Comparative and Phylogenetic Analysis

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Paulo H. C. Lima

2018-03-01

Full Text Available The molecular biology era, together with morphology, molecular phylogenetics, bioinformatics, and high-throughput sequencing technologies, improved the taxonomic identification of Argasidae family members, especially when considering specimens at different development stages, which remains a great difficulty for acarologists. These tools could provide important data and insights on the history and evolutionary relationships of argasids. To better understand these relationships, we sequenced and assembled the first complete mitochondrial genome of Nothoaspis amazoniensis. We used phylogenomics to identify the evolutionary history of this species of tick, comparing the data obtained with 26 complete mitochondrial sequences available in biological databases. The results demonstrated the absence of genetic rearrangements, high similarity and identity, and a close organizational link between the mitogenomes of N. amazoniensis and other argasids analyzed. In addition, the mitogenome had a monophyletic cladistic taxonomic arrangement, encompassed by representatives of the Afrotropical and Neotropical regions, with specific parasitism in bats, which may be indicative of an evolutionary process of cospeciation between vectors and the host.

Comparative multielement analyses of airborne particulate samples collected in various areas

International Nuclear Information System (INIS)

Mamuro, Tetsuo; Matsuda, Yatsuka; Mizohata, Akira

1973-01-01

In order to grasp the characteristic features of the air pollution by particulates in various areas in Japan, multielement analyses by instrumental neutron activation analysis and radioisotope energy dispersive X-ray fluorescence analysis were applied to 31 airborne particulate samples collected in 15 different areas, and the analytical results obtained were compared with one another. All the samples were collected by so-called ''10 micron cut'' samplers, the collection efficiency of which is considered to be 50% at 8μ and nearly zero beyond 10μ. Among the areas in question there are clean seaside areas, heavily industrialized areas, small cities along the Inland Sea or the Pacific Ocean around which industrialization is progressing, a small city having only a big iron work, an area famous for its ceramic industry and so on. The atmospheres over them were found to be quite different not only in pollution extent but also in pollution pattern. (auth.)

Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island.

Science.gov (United States)

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

2017-05-01

The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Comparative multivariate analyses of transient otoacoustic emissions and distorsion products in normal and impaired hearing.

Science.gov (United States)

Stamate, Mirela Cristina; Todor, Nicolae; Cosgarea, Marcel

2015-01-01

The clinical utility of otoacoustic emissions as a noninvasive objective test of cochlear function has been long studied. Both transient otoacoustic emissions and distorsion products can be used to identify hearing loss, but to what extent they can be used as predictors for hearing loss is still debated. Most studies agree that multivariate analyses have better test performances than univariate analyses. The aim of the study was to determine transient otoacoustic emissions and distorsion products performance in identifying normal and impaired hearing loss, using the pure tone audiogram as a gold standard procedure and different multivariate statistical approaches. The study included 105 adult subjects with normal hearing and hearing loss who underwent the same test battery: pure-tone audiometry, tympanometry, otoacoustic emission tests. We chose to use the logistic regression as a multivariate statistical technique. Three logistic regression models were developed to characterize the relations between different risk factors (age, sex, tinnitus, demographic features, cochlear status defined by otoacoustic emissions) and hearing status defined by pure-tone audiometry. The multivariate analyses allow the calculation of the logistic score, which is a combination of the inputs, weighted by coefficients, calculated within the analyses. The accuracy of each model was assessed using receiver operating characteristics curve analysis. We used the logistic score to generate receivers operating curves and to estimate the areas under the curves in order to compare different multivariate analyses. We compared the performance of each otoacoustic emission (transient, distorsion product) using three different multivariate analyses for each ear, when multi-frequency gold standards were used. We demonstrated that all multivariate analyses provided high values of the area under the curve proving the performance of the otoacoustic emissions. Each otoacoustic emission test presented high

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

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Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-20

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. 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. 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.

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.

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.

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Xi, Zhenxiang; Liu, Liang; Davis, Charles C

2015-11-01

The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014). Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

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Weerachai Jaratlerdsiri

Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

KAUST Repository

Jimenez Infante, Francy M.; Ngugi, David; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan; Blom, Jochen; Bajic, Vladimir B.; Stingl, Ulrich

2015-01-01

The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs

KAUST Repository

Jimenez Infante, Francy M.

2015-12-11

The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs playing important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (designated here as MBRS-H7) from the ultra-oligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species, which forms a distinct cluster together with isolate KB13 from Hawaii (H-RS cluster) that is separate from that represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S–23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low chlorophyll and/or high temperature provinces for the H-RS cluster, but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of H-RS include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely the existence of the NADH:quinone oxidoreductase NUO system in the H-RS and the non-homologous NQR system in HTCC2181, which might have implications on their overall energetic yields.

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

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Merchant, Sabeeha S

2007-04-09

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins.

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Staats, Charley Christian; Junges, Angela; Guedes, Rafael Lucas Muniz; Thompson, Claudia Elizabeth; de Morais, Guilherme Loss; Boldo, Juliano Tomazzoni; de Almeida, Luiz Gonzaga Paula; Andreis, Fábio Carrer; Gerber, Alexandra Lehmkuhl; Sbaraini, Nicolau; da Paixão, Rana Louise de Andrade; Broetto, Leonardo; Landell, Melissa; Santi, Lucélia; Beys-da-Silva, Walter Orlando; Silveira, Carolina Pereira; Serrano, Thaiane Rispoli; de Oliveira, Eder Silva; Kmetzsch, Lívia; Vainstein, Marilene Henning; de Vasconcelos, Ana Tereza Ribeiro; Schrank, Augusto

2014-09-29

Metarhizium anisopliae is an entomopathogenic fungus used in the biological control of some agricultural insect pests, and efforts are underway to use this fungus in the control of insect-borne human diseases. A large repertoire of proteins must be secreted by M. anisopliae to cope with the various available nutrients as this fungus switches through different lifestyles, i.e., from a saprophytic, to an infectious, to a plant endophytic stage. To further evaluate the predicted secretome of M. anisopliae, we employed genomic and transcriptomic analyses, coupled with phylogenomic analysis, focusing on the identification and characterization of secreted proteins. We determined the M. anisopliae E6 genome sequence and compared this sequence to other entomopathogenic fungi genomes. A robust pipeline was generated to evaluate the predicted secretomes of M. anisopliae and 15 other filamentous fungi, leading to the identification of a core of secreted proteins. Transcriptomic analysis using the tick Rhipicephalus microplus cuticle as an infection model during two periods of infection (48 and 144 h) allowed the identification of several differentially expressed genes. This analysis concluded that a large proportion of the predicted secretome coding genes contained altered transcript levels in the conditions analyzed in this study. In addition, some specific secreted proteins from Metarhizium have an evolutionary history similar to orthologs found in Beauveria/Cordyceps. This similarity suggests that a set of secreted proteins has evolved to participate in entomopathogenicity. The data presented represents an important step to the characterization of the role of secreted proteins in the virulence and pathogenicity of M. anisopliae.

Creating global comparative analyses of tectonic rifts, monogenetic volcanism and inverted relief

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van Wyk de Vries, Benjamin

2016-04-01

I have been all around the world, and to other planets and have travelled from the present to the Archaean and back to seek out the most significant tectonic rifts, monogenetic volcanoes and examples of inverted relief. I have done this to provide a broad foundation of the comparative analysis for the Chaîne des Puys - Limagne fault nomination to UNESCO world Heritage. This would have been an impossible task, if not for the cooperation of the scientific community and for Google Earth, Google Maps and academic search engines. In preparing global comparisons of geological features, these quite recently developed tools provide a powerful way to find and describe geological features. The ability to do scientific crowd sourcing, rapidly discussing with colleagues about features, allows large numbers of areas to be checked and the open GIS tools (such as Google Earth) allow a standardised description. Search engines also allow the literature on areas to be checked and compared. I will present a comparative study of rifts of the world, monogenetic volcanic field and inverted relief, integrated to analyse the full geological system represented by the Chaîne des Puys - Limagne fault. The analysis confirms that the site is an exceptional example of the first steps of continental drift in a mountain rift setting, and that this is necessarily seen through the combined landscape of tectonic, volcanic and geomorphic features. The analysis goes further to deepen the understanding of geological systems and stresses the need for more study on geological heritage using such a global and broad systems approach.

Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

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Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

2015-05-01

The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

Comparative analyses of bidirectional promoters in vertebrates

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Taylor James

2008-05-01

Full Text Available Abstract Background Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions. Results Our mapping of bidirectional promoters from humans to fish shows that many such promoters emerged after the divergence of chickens and fish. Furthermore, annotations of promoters in deep phylogenies enable detection of missing data or assembly problems present in higher vertebrates. The functional importance of bidirectional promoters is indicated by selective pressure to maintain the arrangement of genes regulated by the promoter over long evolutionary time spans. Characteristics unique to bidirectional promoters are further elucidated using a technique for unsupervised classification, known as ESPERR. Conclusion Results of these analyses will aid in our understanding of the evolution of bidirectional promoters, including whether the regulation of two genes evolved as a consequence of their proximity or if function dictated their co-regulation.

A phylogenomic analysis of Marek's disease virus reveals independent paths to virulence in Eurasia and North America.

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Trimpert, Jakob; Groenke, Nicole; Jenckel, Maria; He, Shulin; Kunec, Dusan; Szpara, Moriah L; Spatz, Stephen J; Osterrieder, Nikolaus; McMahon, Dino P

2017-12-01

Virulence determines the impact a pathogen has on the fitness of its host, yet current understanding of the evolutionary origins and causes of virulence of many pathogens is surprisingly incomplete. Here, we explore the evolution of Marek's disease virus (MDV), a herpesvirus commonly afflicting chickens and rarely other avian species. The history of MDV in the 20th century represents an important case study in the evolution of virulence. The severity of MDV infection in chickens has been rising steadily since the adoption of intensive farming techniques and vaccination programs in the 1950s and 1970s, respectively. It has remained uncertain, however, which of these factors is causally more responsible for the observed increase in virulence of circulating viruses. We conducted a phylogenomic study to understand the evolution of MDV in the context of dramatic changes to poultry farming and disease control. Our analysis reveals evidence of geographical structuring of MDV strains, with reconstructions supporting the emergence of virulent viruses independently in North America and Eurasia. Of note, the emergence of virulent viruses appears to coincide approximately with the introduction of comprehensive vaccination on both continents. The time-dated phylogeny also indicated that MDV has a mean evolutionary rate of ~1.6 × 10 -5 substitutions per site per year. An examination of gene-linked mutations did not identify a strong association between mutational variation and virulence phenotypes, indicating that MDV may evolve readily and rapidly under strong selective pressures and that multiple genotypic pathways may underlie virulence adaptation in MDV.

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

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Zhang, Jin; Ruhlman, Tracey A; Mower, Jeffrey P; Jansen, Robert K

2013-12-29

Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition

Parametric analyses of summative scores may lead to conflicting inferences when comparing groups: A simulation study.

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Khan, Asaduzzaman; Chien, Chi-Wen; Bagraith, Karl S

2015-04-01

To investigate whether using a parametric statistic in comparing groups leads to different conclusions when using summative scores from rating scales compared with using their corresponding Rasch-based measures. A Monte Carlo simulation study was designed to examine between-group differences in the change scores derived from summative scores from rating scales, and those derived from their corresponding Rasch-based measures, using 1-way analysis of variance. The degree of inconsistency between the 2 scoring approaches (i.e. summative and Rasch-based) was examined, using varying sample sizes, scale difficulties and person ability conditions. This simulation study revealed scaling artefacts that could arise from using summative scores rather than Rasch-based measures for determining the changes between groups. The group differences in the change scores were statistically significant for summative scores under all test conditions and sample size scenarios. However, none of the group differences in the change scores were significant when using the corresponding Rasch-based measures. This study raises questions about the validity of the inference on group differences of summative score changes in parametric analyses. Moreover, it provides a rationale for the use of Rasch-based measures, which can allow valid parametric analyses of rating scale data.

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

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Gelfand Mikhail S

2009-02-01

Full Text Available Abstract Background Nickel (Ni and cobalt (Co are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i transport systems, and (ii metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH, ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts have a tendency for loss of Ni/Co utilization. Conclusion Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three

Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics.

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Yoon, Sook Hee; Kim, Jaemin; Shin, Donghyun; Cho, Seoae; Kwak, Woori; Lee, Hak-Kyo; Park, Kyoung-Do; Kim, Heebal

2017-04-01

The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.

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Vinuesa, Pablo; Ochoa-Sánchez, Luz E; Contreras-Moreira, Bruno

2018-01-01

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

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Pablo Vinuesa

2018-05-01

Full Text Available The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM, computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT. The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as

Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution.

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Smith, Silvia E; Showers-Corneli, Patrice; Dardenne, Caitlin N; Harpending, Henry H; Martin, Darren P; Beiko, Robert G

2012-01-01

The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer (M. abscessus to Segniliparus and M. smegmatis to Streptomyces), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case (M. vanbaalenii to Streptomyces) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

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Burke, Sean V.; Wysocki, William P.; Clark, Lynn G.

2018-01-01

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD

Genomes-based phylogeny of the genus Xanthomonas

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Rodriguez-R Luis M

2012-03-01

Full Text Available Abstract Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

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Xing-Xing Shen

2016-12-01

Full Text Available Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence and two data matrices (amino acids or the first two codon positions yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Science.gov (United States)

Shen, Xing-Xing; Zhou, Xiaofan; Kominek, Jacek; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, Antonis

2016-01-01

Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast. PMID:27672114

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

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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.

Comparative sequence analyses of genome and transcriptome ...

Indian Academy of Sciences (India)

2015-12-04

Dec 4, 2015 ... 2011), unique vocal communication. (Payne 2003; Nair et al. ... induction of apoptosis when compared to human cells. In this study, we have .... based on calculated Pearson correlation and displayed based on centroid of the ...

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

Science.gov (United States)

Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

2015-01-01

The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

Comparing of Normal Stress Distribution in Static and Dynamic Soil-Structure Interaction Analyses

International Nuclear Information System (INIS)

Kholdebarin, Alireza; Massumi, Ali; Davoodi, Mohammad; Tabatabaiefar, Hamid Reza

2008-01-01

It is important to consider the vertical component of earthquake loading and inertia force in soil-structure interaction analyses. In most circumstances, design engineers are primarily concerned about the analysis of behavior of foundations subjected to earthquake-induced forces transmitted from the bedrock. In this research, a single rigid foundation with designated geometrical parameters located on sandy-clay soil has been modeled in FLAC software with Finite Different Method and subjected to three different vertical components of earthquake records. In these cases, it is important to evaluate effect of footing on underlying soil and to consider normal stress in soil with and without footing. The distribution of normal stress under the footing in static and dynamic states has been studied and compared. This Comparison indicated that, increasing in normal stress under the footing caused by vertical component of ground excitations, has decreased dynamic vertical settlement in comparison with static state

Semantics bias in cross-national comparative analyses

DEFF Research Database (Denmark)

Schnohr, Christina W.; Gobina, Inese; Santos, Teresa

2016-01-01

indicates that there are what may be called semantic issues affecting comparability in international studies, since the same original word (in an English original) is interpreted differently across countries and cultures. The paper test and discuss a few possible explanations to this, however, only leaving...

Comparative analyses on dynamic performances of photovoltaic–thermal solar collectors integrated with phase change materials

International Nuclear Information System (INIS)

Su, Di; Jia, Yuting; Alva, Guruprasad; Liu, Lingkun; Fang, Guiyin

2017-01-01

Highlights: • The dynamic model of photovoltaic–thermal collector with phase change material was developed. • The performances of photovoltaic–thermal collector are performed comparative analyses. • The performances of photovoltaic–thermal collector with phase change material were evaluated. • Upper phase change material mode can improve performances of photovoltaic–thermal collector. - Abstract: The operating conditions (especially temperature) of photovoltaic–thermal solar collectors have significant influence on dynamic performance of the hybrid photovoltaic–thermal solar collectors. Only a small percentage of incoming solar radiation can be converted into electricity, and the rest is converted into heat. This heat leads to a decrease in efficiency of the photovoltaic module. In order to improve the performance of the hybrid photovoltaic–thermal solar collector, we performed comparative analyses on a hybrid photovoltaic–thermal solar collector integrated with phase change material. Electrical and thermal parameters like solar cell temperature, outlet temperature of air, electrical power, thermal power, electrical efficiency, thermal efficiency and overall efficiency are simulated and analyzed to evaluate the dynamic performance of the hybrid photovoltaic–thermal collector. It is found that the position of phase change material layer in the photovoltaic–thermal collector has a significant effect on the performance of the photovoltaic–thermal collector. The results indicate that upper phase change material mode in the photovoltaic–thermal collector can significantly improve the thermal and electrical performance of photovoltaic–thermal collector. It is found that overall efficiency of photovoltaic–thermal collector in ‘upper phase change material’ mode is 10.7% higher than that in ‘no phase change material’ mode. Further, for a photovoltaic–thermal collector with upper phase change material, it is verified that 3 cm

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.

Whole-genome analyses resolve early branches in the tree of life of modern birds

DEFF Research Database (Denmark)

Sicheritz-Pontén, Thomas; Li, Cai; Li, Bo

2014-01-01

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister...... or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator...... and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high...

Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

Science.gov (United States)

Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

2015-01-01

Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

International comparative analyses of healthcare risk management.

Science.gov (United States)

Sun, Niuyun; Wang, Li; Zhou, Jun; Yuan, Qiang; Zhang, Zongjiu; Li, Youping; Liang, Minghui; Cheng, Lan; Gao, Guangming; Cui, Xiaohui

2011-02-01

Interpretation of the growing body of global literature on health care risk is compromised by a lack of common understanding and language. This series of articles aims to comprehensively compare laws and regulations, institutional management, and administration of incidence reporting systems on medical risk management in the United Kingdom, the United States, Canada, Australia, and Taiwan, so as to provide evidence and recommendations for health care risk management policy in China. We searched the official websites of the healthcare risk management agencies of the four countries and one district for laws, regulatory documents, research reports, reviews and evaluation forms concerned with healthcare risk management and assessment. Descriptive comparative analysis was performed on relevant documents. A total of 146 documents were included in this study, including 2 laws (1.4%), 17 policy documents (11.6%), 41 guidance documents (28.1%), 37 reviews (25.3%), and 49 documents giving general information (33.6%). The United States government implemented one law and one rule of patient safety management, while the United Kingdom and Australia each issued professional guidances on patient safety improvement. The four countries implemented patient safety management policy on four different levels: national, state/province, hospital, and non-governmental organization. The four countries and one district adopted four levels of patient safety management, and the administration modes can be divided into an "NGO-led mode" represented by the United States and Canada and a "government-led mode" represented by the United Kingdom, Australia, and Taiwan. © 2011 Blackwell Publishing Asia Pty Ltd and Chinese Cochrane Center, West China Hospital of Sichuan University.

Methodology for Analysing Energy Demand in Biogas Production Plants—A Comparative Study of Two Biogas Plants

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Emma Lindkvist

2017-11-01

Full Text Available Biogas production through anaerobic digestion may play an important role in a circular economy because of the opportunity to produce a renewable fuel from organic waste. However, the production of biogas may require energy in the form of heat and electricity. Therefore, resource-effective biogas production must consider both biological and energy performance. For the individual biogas plant to improve its energy performance, a robust methodology to analyse and evaluate the energy demand on a detailed level is needed. Moreover, to compare the energy performance of different biogas plants, a methodology with a consistent terminology, system boundary and procedure is vital. The aim of this study was to develop a methodology for analysing the energy demand in biogas plants on a detailed level. In the methodology, the energy carriers are allocated to: (1 sub-processes (e.g., pretreatment, anaerobic digestion, gas cleaning, (2 unit processes (e.g., heating, mixing, pumping, lighting and (3 a combination of these. For a thorough energy analysis, a combination of allocations is recommended. The methodology was validated by applying it to two different biogas plants. The results show that the methodology is applicable to biogas plants with different configurations of their production system.

Comparative transcriptomic analyses of vegetable and grain pea (Pisum sativum L. seed development

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Na eLiu

2015-11-01

Full Text Available Understanding the molecular mechanisms regulating pea seed developmental process is extremely important for pea breeding. In this study, we used high-throughput RNA-Seq and bioinformatics analyses to examine the changes in gene expression during seed development in vegetable pea and grain pea, and compare the gene expression profiles of these two pea types. RNA-Seq generated 18.7 G of raw data, which were then de novo assembled into 77,273 unigenes with a mean length of 930 bp. Our results illustrate that transcriptional control during pea seed development is a highly coordinated process. There were 459 and 801 genes differentially expressed at early and late seed maturation stages between vegetable pea and grain pea, respectively. Soluble sugar and starch metabolism related genes were significantly activated during the development of pea seeds coinciding with the onset of accumulation of sugar and starch in the seeds. A comparative analysis of genes involved in sugar and starch biosynthesis in vegetable pea (high seed soluble sugar and low starch and grain pea (high seed starch and low soluble sugar revealed that differential expression of related genes at late development stages results in a negative correlation between soluble sugar and starch biosynthetic flux in vegetable and grain pea seeds. RNA-Seq data was validated by using real-time quantitative RT-PCR analysis for 30 randomly selected genes. To our knowledge, this work represents the first report of seed development transcriptomics in pea. The obtained results provide a foundation to support future efforts to unravel the underlying mechanisms that control the developmental biology of pea seeds, and serve as a valuable resource for improving pea breeding.

The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains

DEFF Research Database (Denmark)

Soares, Siomar C; Silva, Artur; Trost, Eva

2013-01-01

, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic...

Functional and comparative genomics analyses of pmp22 in medaka fish

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Kawarabayasi Yutaka

2009-06-01

Full Text Available Abstract Background Pmp22, a member of the junction protein family Claudin/EMP/PMP22, plays an important role in myelin formation. Increase of pmp22 transcription causes peripheral neuropathy, Charcot-Marie-Tooth disease type1A (CMT1A. The pathophysiological phenotype of CMT1A is aberrant axonal myelination which induces a reduction in nerve conduction velocity (NCV. Several CMT1A model rodents have been established by overexpressing pmp22. Thus, it is thought that pmp22 expression must be tightly regulated for correct myelin formation in mammals. Interestingly, the myelin sheath is also present in other jawed vertebrates. The purpose of this study is to analyze the evolutionary conservation of the association between pmp22 transcription level and vertebrate myelin formation, and to find the conserved non-coding sequences for pmp22 regulation by comparative genomics analyses between jawed fishes and mammals. Results A transgenic pmp22 over-expression medaka fish line was established. The transgenic fish had approximately one fifth the peripheral NCV values of controls, and aberrant myelination of transgenic fish in the peripheral nerve system (PNS was observed. We successfully confirmed that medaka fish pmp22 has the same exon-intron structure as mammals, and identified some known conserved regulatory motifs. Furthermore, we found novel conserved sequences in the first intron and 3'UTR. Conclusion Medaka fish undergo abnormalities in the PNS when pmp22 transcription increases. This result indicates that an adequate pmp22 transcription level is necessary for correct myelination of jawed vertebrates. Comparison of pmp22 orthologs between distantly related species identifies evolutionary conserved sequences that contribute to precise regulation of pmp22 expression.

A phylogenomic study of human, dog, and mouse.

Directory of Open Access Journals (Sweden)

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.

Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

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Eunyoung Seo

2016-08-01

Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

Cost Analyses in the US and Japan: A Cross-Country Comparative Analysis Applied to the PRONOUNCE Trial in Non-Squamous Non-Small Cell Lung Cancer.

Science.gov (United States)

Hess, Lisa M; Rajan, Narayan; Winfree, Katherine; Davey, Peter; Ball, Mark; Knox, Hediyyih; Graham, Christopher

2015-12-01

Health technology assessment is not required for regulatory submission or approval in either the United States (US) or Japan. This study was designed as a cross-country evaluation of cost analyses conducted in the US and Japan based on the PRONOUNCE phase III lung cancer trial, which compared pemetrexed plus carboplatin followed by pemetrexed (PemC) versus paclitaxel plus carboplatin plus bevacizumab followed by bevacizumab (PCB). Two cost analyses were conducted in accordance with International Society For Pharmacoeconomics and Outcomes Research good research practice standards. Costs were obtained based on local pricing structures; outcomes were considered equivalent based on the PRONOUNCE trial results. Other inputs were included from the trial data (e.g., toxicity rates) or from local practice sources (e.g., toxicity management). The models were compared across key input and transferability factors. Despite differences in local input data, both models demonstrated a similar direction, with the cost of PemC being consistently lower than the cost of PCB. The variation in individual input parameters did affect some of the specific categories, such as toxicity, and impacted sensitivity analyses, with the cost differential between comparators being greater in Japan than in the US. When economic models are based on clinical trial data, many inputs and outcomes are held consistent. The alterable inputs were not in and of themselves large enough to significantly impact the results between countries, which were directionally consistent with greater variation seen in sensitivity analyses. The factors that vary across jurisdictions, even when minor, can have an impact on trial-based economic analyses. Eli Lilly and Company.

Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae Using a modification of the finite supragenome model

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Yu Susan

2011-04-01

Full Text Available Abstract Background Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the differential gene content among strains is of interest. Results We sequenced three clinical strains and combined these data with 13 publically available human isolates and one bovine strain for comparative genomic analyses. All genomes were annotated using RAST, and then their gene similarities and differences were delineated. Gene clustering yielded 3,155 orthologous gene clusters, of which 2,266 were core, 755 were distributed, and 134 were unique. Individual genomes contained between 2,524 and 2,648 genes. Gene-content comparisons among all possible S. aureus strain pairs (n = 136 revealed a mean difference of 296 genes and a maximum difference of 476 genes. We developed a revised version of our finite supragenome model to estimate the size of the S. aureus supragenome (3,221 genes, with 2,245 core genes, and compared it with those of Haemophilus influenzae and Streptococcus pneumoniae. There was excellent agreement between RAST's annotations and our CDS clustering procedure providing for high fidelity metabolomic subsystem analyses to extend our comparative genomic characterization of these strains. Conclusions Using a multi-species comparative supragenomic analysis enabled by an improved version of our finite supragenome model we provide data and an interpretation explaining the relatively larger core genome of S. aureus compared to other opportunistic nasopharyngeal pathogens. In addition, we provide independent validation for the efficiency and effectiveness of our orthologous gene clustering algorithm.

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals.

Science.gov (United States)

Romiguier, Jonathan; Ranwez, Vincent; Delsuc, Frédéric; Galtier, Nicolas; Douzery, Emmanuel J P

2013-09-01

Despite the rapid increase of size in phylogenomic data sets, a number of important nodes on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal tree is still a controversial issue. One difficulty lies in the pervasive phylogenetic conflicts among genes, with each one telling its own story, which may be reliable or not. Here, we identified a simple criterion, that is, the GC content, which substantially helps in determining which gene trees best reflect the species tree. We assessed the ability of 13,111 coding sequence alignments to correctly reconstruct the placental phylogeny. We found that GC-rich genes induced a higher amount of conflict among gene trees and performed worse than AT-rich genes in retrieving well-supported, consensual nodes on the placental tree. We interpret this GC effect mainly as a consequence of genome-wide variations in recombination rate. Indeed, recombination is known to drive GC-content evolution through GC-biased gene conversion and might be problematic for phylogenetic reconstruction, for instance, in an incomplete lineage sorting context. When we focused on the AT-richest fraction of the data set, the resolution level of the placental phylogeny was greatly increased, and a strong support was obtained in favor of an Afrotheria rooting, that is, Afrotheria as the sister group of all other placentals. We show that in mammals most conflicts among gene trees, which have so far hampered the resolution of the placental tree, are concentrated in the GC-rich regions of the genome. We argue that the GC content-because it is a reliable indicator of the long-term recombination rate-is an informative criterion that could help in identifying the most reliable molecular markers for species tree inference.

Fracture analyses of WWER reactor pressure vessels

International Nuclear Information System (INIS)

Sievers, J.; Liu, X.

1997-01-01

In the paper first the methodology of fracture assessment based on finite element (FE) calculations is described and compared with simplified methods. The FE based methodology was verified by analyses of large scale thermal shock experiments in the framework of the international comparative study FALSIRE (Fracture Analyses of Large Scale Experiments) organized by GRS and ORNL. Furthermore, selected results from fracture analyses of different WWER type RPVs with postulated cracks under different loading transients are presented. 11 refs, 13 figs, 1 tab

Fracture analyses of WWER reactor pressure vessels

Energy Technology Data Exchange (ETDEWEB)

Sievers, J; Liu, X [Gesellschaft fuer Anlagen- und Reaktorsicherheit mbH (GRS), Koeln (Germany)

1997-09-01

In the paper first the methodology of fracture assessment based on finite element (FE) calculations is described and compared with simplified methods. The FE based methodology was verified by analyses of large scale thermal shock experiments in the framework of the international comparative study FALSIRE (Fracture Analyses of Large Scale Experiments) organized by GRS and ORNL. Furthermore, selected results from fracture analyses of different WWER type RPVs with postulated cracks under different loading transients are presented. 11 refs, 13 figs, 1 tab.

Comparative physical-chemical characterization of encapsulated lipid-based isotretinoin products assessed by particle size distribution and thermal behavior analyses

Energy Technology Data Exchange (ETDEWEB)

Guimaraes, Carla Aiolfi, E-mail: carlaaiolfi@usp.br [Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil); Menaa, Farid [Department of Dermatology, School of Medicine Wuerzburg, Wuerzburg 97080 (Germany); Fluorotronics, Inc., 1425 Russ Bvld, San Diego Technology Incubator, San Diego, CA 92101 (United States); Menaa, Bouzid, E-mail: bouzid.menaa@gmail.com [Fluorotronics, Inc., 1425 Russ Bvld, San Diego Technology Incubator, San Diego, CA 92101 (United States); Quenca-Guillen, Joyce S. [Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil); Matos, Jivaldo do Rosario [Department of Fundamental Chemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil); Mercuri, Lucildes Pita [Department of Exact and Earth Sciences, Federal University of Sao Paulo, Diadema, SP 09972-270 (Brazil); Braz, Andre Borges [Department of Engineering of Mines and Oil, Polytechnical School, University of Sao Paulo, SP 05508-900 (Brazil); Rossetti, Fabia Cristina [Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP 14015-120 (Brazil); Kedor-Hackmann, Erika Rosa Maria; Santoro, Maria Ines Rocha Miritello [Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP 05508-000 (Brazil)

2010-06-10

Isotretinoin is the drug of choice for the management of severe recalcitrant nodular acne. Nevertheless, some of its physical-chemical properties are still poorly known. Hence, the aim of our study consisted to comparatively evaluate the particle size distribution (PSD) and characterize the thermal behavior of the three encapsulated isotretinoin products in oil suspension (one reference and two generics) commercialized in Brazil. Here, we show that the PSD, estimated by laser diffraction and by polarized light microscopy, differed between the generics and the reference product. However, the thermal behavior of the three products, determined by thermogravimetry (TGA), differential thermal (DTA) analyses and differential scanning calorimetry (DSC), displayed no significant changes and were more thermostable than the isotretinoin standard used as internal control. Thus, our study suggests that PSD analyses in isotretinoin lipid-based formulations should be routinely performed in order to improve their quality and bioavailability.

Taking a comparative approach: analysing personality as a multivariate behavioural response across species.

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Alecia J Carter

Full Text Available Animal personality, repeatable behaviour through time and across contexts, is ecologically and evolutionarily important as it can account for the exhibition of sub-optimal behaviours. Interspecific comparisons have been suggested as important for understanding the evolution of animal personality; however, these are seldom accomplished due, in part, to the lack of statistical tools for quantifying differences and similarities in behaviour between groups of individuals. We used nine species of closely-related coral reef fishes to investigate the usefulness of ecological community analyses for the analysis of between-species behavioural differences and behavioural heterogeneity. We first documented behavioural carryover across species by observing the fishes' behaviour and measuring their response to a threatening stimulus to quantify boldness. Bold fish spent more time away from the reef and fed more than shy fish. We then used ecological community analysis tools (canonical variate analysis, multi-response permutation procedure, and permutational analysis of multivariate dispersion and identified four 'clusters' of behaviourally similar fishes, and found that the species differ in the behavioural variation expressed; some species are more behaviourally heterogeneous than others. We found that ecological community analysis tools are easily and fruitfully applied to comparative studies of personality and encourage their use by future studies.

A comparative study between xerographic, computer-assisted overlay generation and animated-superimposition methods in bite mark analyses.

Science.gov (United States)

Tai, Meng Wei; Chong, Zhen Feng; Asif, Muhammad Khan; Rahmat, Rabiah A; Nambiar, Phrabhakaran

2016-09-01

This study was to compare the suitability and precision of xerographic and computer-assisted methods for bite mark investigations. Eleven subjects were asked to bite on their forearm and the bite marks were photographically recorded. Alginate impressions of the subjects' dentition were taken and their casts were made using dental stone. The overlays generated by xerographic method were obtained by photocopying the subjects' casts and the incisal edge outlines were then transferred on a transparent sheet. The bite mark images were imported into Adobe Photoshop® software and printed to life-size. The bite mark analyses using xerographically generated overlays were done by comparing an overlay to the corresponding printed bite mark images manually. In computer-assisted method, the subjects' casts were scanned into Adobe Photoshop®. The bite mark analyses using computer-assisted overlay generation were done by matching an overlay and the corresponding bite mark images digitally using Adobe Photoshop®. Another comparison method was superimposing the cast images with corresponding bite mark images employing the Adobe Photoshop® CS6 and GIF-Animator©. A score with a range of 0-3 was given during analysis to each precision-determining criterion and the score was increased with better matching. The Kruskal Wallis H test showed significant difference between the three sets of data (H=18.761, p<0.05). In conclusion, bite mark analysis using the computer-assisted animated-superimposition method was the most accurate, followed by the computer-assisted overlay generation and lastly the xerographic method. The superior precision contributed by digital method is discernible despite the human skin being a poor recording medium of bite marks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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...

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

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Davide Michetti

Full Text Available The psychrophilic and mesophilic endonucleases A (EndA from Aliivibrio salmonicida (VsEndA and Vibrio cholera (VcEndA have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

Comparative Analysis of Upper Ocean Heat Content Variability from Ensemble Operational Ocean Analyses

Science.gov (United States)

Xue, Yan; Balmaseda, Magdalena A.; Boyer, Tim; Ferry, Nicolas; Good, Simon; Ishikawa, Ichiro; Rienecker, Michele; Rosati, Tony; Yin, Yonghong; Kumar, Arun

2012-01-01

Upper ocean heat content (HC) is one of the key indicators of climate variability on many time-scales extending from seasonal to interannual to long-term climate trends. For example, HC in the tropical Pacific provides information on thermocline anomalies that is critical for the longlead forecast skill of ENSO. Since HC variability is also associated with SST variability, a better understanding and monitoring of HC variability can help us understand and forecast SST variability associated with ENSO and other modes such as Indian Ocean Dipole (IOD), Pacific Decadal Oscillation (PDO), Tropical Atlantic Variability (TAV) and Atlantic Multidecadal Oscillation (AMO). An accurate ocean initialization of HC anomalies in coupled climate models could also contribute to skill in decadal climate prediction. Errors, and/or uncertainties, in the estimation of HC variability can be affected by many factors including uncertainties in surface forcings, ocean model biases, and deficiencies in data assimilation schemes. Changes in observing systems can also leave an imprint on the estimated variability. The availability of multiple operational ocean analyses (ORA) that are routinely produced by operational and research centers around the world provides an opportunity to assess uncertainties in HC analyses, to help identify gaps in observing systems as they impact the quality of ORAs and therefore climate model forecasts. A comparison of ORAs also gives an opportunity to identify deficiencies in data assimilation schemes, and can be used as a basis for development of real-time multi-model ensemble HC monitoring products. The OceanObs09 Conference called for an intercomparison of ORAs and use of ORAs for global ocean monitoring. As a follow up, we intercompared HC variations from ten ORAs -- two objective analyses based on in-situ data only and eight model analyses based on ocean data assimilation systems. The mean, annual cycle, interannual variability and longterm trend of HC have

The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae.

Science.gov (United States)

de Santana Lopes, Amanda; Gomes Pacheco, Túlio; Nimz, Tabea; do Nascimento Vieira, Leila; Guerra, Miguel P; Nodari, Rubens O; de Souza, Emanuel Maltempi; de Oliveira Pedrosa, Fábio; Rogalski, Marcelo

2018-04-01

The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae: structural comparative analysis, gene content and microsatellite detection

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Andrew W. Gichira

2017-01-01

Full Text Available Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp, with a pair of Inverted Repeats (IR 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp and a small single copy (SSC, 18,696. H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

Science.gov (United States)

Gichira, Andrew W; Li, Zhizhong; Saina, Josphat K; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W; Wang, Qingfeng; Chen, Jinming

2017-01-01

Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica 's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene ( infA ) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica . A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

Spectral analyses of the Forel-Ule Ocean colour comparator scale

NARCIS (Netherlands)

Wernand, M.; van der Woerd, H.J.

2010-01-01

François Alphonse Forel (1890) and Willi Ule (1892) composed a colour comparator scale, with tints varying from indigo-blue to cola brown, to quantify the colour of natural waters, like seas, lakes and rivers. For each measurement, the observer compares the colour of the water above a submersed

Interpersonal trust and mutually beneficial exchanges: Measuring social capital for comparative analyses

Czech Academy of Sciences Publication Activity Database

Matějů, Petr; Vitásková, Anna

2006-01-01

Roč. 42, č. 3 (2006), s. 493-516 ISSN 0038-0288 R&D Projects: GA MPS(CZ) 1J/005/04-DP2; GA ČR(CZ) GA403/03/0340 Institutional research plan: CEZ:AV0Z70280505 Keywords : social capital * trust * komparative analyse Subject RIV: AO - Sociology, Demography Impact factor: 0.128, year: 2006

Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Science.gov (United States)

Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

2016-01-01

Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

Comparative proteomic analyses of macular and peripheral retina of cynomolgus monkeys (Macaca fascicularis).

Science.gov (United States)

Okamoto, Haru; Umeda, Shinsuke; Nozawa, Takehiro; Suzuki, Michihiro T; Yoshikawa, Yasuhiro; Matsuura, Etsuko T; Iwata, Takeshi

2010-01-01

The central region of the primate retina is called the macula. The fovea is located at the center of the macula, where the photoreceptors are concentrated to create a neural network adapted for high visual acuity. Damage to the fovea, e.g., by macular dystrophies and age-related macular degeneration, can reduce central visual acuity. The molecular mechanisms leading to these diseases are most likely dependent on the proteins in the macula which differ from those in the peripheral retina in expression level. To investigate whether the distribution of proteins in the macula is different from the peripheral retina, proteomic analyses of tissues from these two regions of cynomolgus monkeys were compared. Two-dimensional gel electrophoresis and mass spectrometry identified 26 proteins that were present only in the macular gel spots. The expression levels of five proteins, cone photoreceptor specific arrestin-C, gamma-synuclein, epidermal fatty acid binding protein, tropomyosin 1alpha chain, and heterogeneous nuclear ribonucleoproteins A2/B1, were significantly higher in the macula than in the peripheral retina. Immunostaining of macula sections by antibodies to each identified protein revealed unique localization in the retina, retinal pigment epithelial cells and the choroidal layer. Some of these proteins were located in cells with higher densities in the macula. We suggest that it will be important to study these proteins to determine their contribution to the pathogenesis and progression of macula diseases.

Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.

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Wei Liu

Full Text Available Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.

Comparative Physiological and Molecular Analyses of Two Contrasting Flue-Cured Tobacco Genotypes under Progressive Drought Stress

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Xinhong Su

2017-05-01

Full Text Available Drought is a major environmental factor that limits crop growth and productivity. Flue-cured tobacco (Nicotiana tabacum is one of the most important commercial crops worldwide and its productivity is vulnerable to drought. However, comparative analyses of physiological, biochemical and gene expression changes in flue-cured tobacco varieties differing in drought tolerance under long-term drought stress are scarce. In this study, drought stress responses of two flue-cured tobacco varieties, LJ851 and JX6007, were comparatively studied at the physiological and transcriptional levels. After exposing to progressive drought stress, the drought-tolerant LJ851 showed less growth inhibition and chlorophyll reduction than the drought-sensitive JX6007. Moreover, higher antioxidant enzyme activities and lower levels of H2O2, Malondialdehyde (MDA, and electrolyte leakage after drought stress were found in LJ851 when compared with JX6007. Further analysis showed that LJ851 plants had much less reductions than the JX6007 in the net photosynthesis rate and stomatal conductance during drought stress; indicating that LJ851 had better photosynthetic performance than JX6007 during drought. In addition, transcriptional expression analysis revealed that LJ851 exhibited significantly increased transcripts of several categories of drought-responsive genes in leaves and roots under drought conditions. Together, these results indicated that LJ851 was more drought-tolerant than JX6007 as evidenced by better photosynthetic performance, more powerful antioxidant system, and higher expression of stress defense genes during drought stress. This study will be valuable for the development of novel flue-cured tobacco varieties with improved drought tolerance by exploitation of natural genetic variations in the future.

Localisation of nursery areas based on comparative analyses of the horizontal and vertical distribution patterns of juvenile Baltic cod (Gadus morhua)

DEFF Research Database (Denmark)

Nielsen, J. Rasmus; Lundgren, Bo; Kristensen, Kasper

2013-01-01

Baltic cod are determined, and their nursery areas are localised according to the environmental factors affecting them. Comparative statistical analyses of biological, hydrographic and hydroacoustic data are carried out based on standard ICES demersal trawl surveys and special integrated trawl...... and acoustic research surveys. Horizontal distribution maps for the 2001–2010 cohorts of juvenile cod are further generated by applying a statistical log-Gaussian Cox process model to the standard trawl survey data. The analyses indicate size-dependent horizontal and distinct vertical and diurnal distribution...... in deep sea localities down to a 100 m depth and at oxygen concentrations between 2–4 ml O2.l−1. The vertical, diurnally stratified and repeated trawling and hydroacoustic target strength-depth distributions obtained from the special surveys show juvenile cod concentrations in frontal zone water layers...

Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes.

Science.gov (United States)

Grim, Christopher J; Kozlova, Elena V; Sha, Jian; Fitts, Eric C; van Lier, Christina J; Kirtley, Michelle L; Joseph, Sandeep J; Read, Timothy D; Burd, Eileen M; Tall, Ben D; Joseph, Sam W; Horneman, Amy J; Chopra, Ashok K; Shak, Joshua R

2013-04-23

Aeromonas hydrophila has increasingly been implicated as a virulent and antibiotic-resistant etiologic agent in various human diseases. In a previously published case report, we described a subject with a polymicrobial wound infection that included a persistent and aggressive strain of A. hydrophila (E1), as well as a more antibiotic-resistant strain of A. hydrophila (E2). To better understand the differences between pathogenic and environmental strains of A. hydrophila, we conducted comparative genomic and functional analyses of virulence-associated genes of these two wound isolates (E1 and E2), the environmental type strain A. hydrophila ATCC 7966(T), and four other isolates belonging to A. aquariorum, A. veronii, A. salmonicida, and A. caviae. Full-genome sequencing of strains E1 and E2 revealed extensive differences between the two and strain ATCC 7966(T). The more persistent wound infection strain, E1, harbored coding sequences for a cytotoxic enterotoxin (Act), a type 3 secretion system (T3SS), flagella, hemolysins, and a homolog of exotoxin A found in Pseudomonas aeruginosa. Corresponding phenotypic analyses with A. hydrophila ATCC 7966(T) and SSU as reference strains demonstrated the functionality of these virulence genes, with strain E1 displaying enhanced swimming and swarming motility, lateral flagella on electron microscopy, the presence of T3SS effector AexU, and enhanced lethality in a mouse model of Aeromonas infection. By combining sequence-based analysis and functional assays, we characterized an A. hydrophila pathotype, exemplified by strain E1, that exhibited increased virulence in a mouse model of infection, likely because of encapsulation, enhanced motility, toxin secretion, and cellular toxicity. Aeromonas hydrophila is a common aquatic bacterium that has increasingly been implicated in serious human infections. While many determinants of virulence have been identified in Aeromonas, rapid identification of pathogenic versus nonpathogenic

The cost-effectiveness of rotavirus vaccination: Comparative analyses for five European countries and transferability in Europe.

Science.gov (United States)

Jit, Mark; Bilcke, Joke; Mangen, Marie-Josée J; Salo, Heini; Melliez, Hugues; Edmunds, W John; Yazdan, Yazdanpanah; Beutels, Philippe

2009-10-19

Cost-effectiveness analyses are usually not directly comparable between countries because of differences in analytical and modelling assumptions. We investigated the cost-effectiveness of rotavirus vaccination in five European Union countries (Belgium, England and Wales, Finland, France and the Netherlands) using a single model, burden of disease estimates supplied by national public health agencies and a subset of common assumptions. Under base case assumptions (vaccination with Rotarix, 3% discount rate, health care provider perspective, no herd immunity and quality of life of one caregiver affected by a rotavirus episode) and a cost-effectiveness threshold of euro30,000, vaccination is likely to be cost effective in Finland only. However, single changes to assumptions may make it cost effective in Belgium and the Netherlands. The estimated threshold price per dose for Rotarix (excluding administration costs) to be cost effective was euro41 in Belgium, euro28 in England and Wales, euro51 in Finland, euro36 in France and euro46 in the Netherlands.

Correlation of Klebsiella pneumoniae comparative genetic analyses with virulence profiles in a murine respiratory disease model.

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Ramy A Fodah

Full Text Available Klebsiella pneumoniae is a bacterial pathogen of worldwide importance and a significant contributor to multiple disease presentations associated with both nosocomial and community acquired disease. ATCC 43816 is a well-studied K. pneumoniae strain which is capable of causing an acute respiratory disease in surrogate animal models. In this study, we performed sequencing of the ATCC 43816 genome to support future efforts characterizing genetic elements required for disease. Furthermore, we performed comparative genetic analyses to the previously sequenced genomes from NTUH-K2044 and MGH 78578 to gain an understanding of the conservation of known virulence determinants amongst the three strains. We found that ATCC 43816 and NTUH-K2044 both possess the known virulence determinant for yersiniabactin, as well as a Type 4 secretion system (T4SS, CRISPR system, and an acetonin catabolism locus, all absent from MGH 78578. While both NTUH-K2044 and MGH 78578 are clinical isolates, little is known about the disease potential of these strains in cell culture and animal models. Thus, we also performed functional analyses in the murine macrophage cell lines RAW264.7 and J774A.1 and found that MGH 78578 (K52 serotype was internalized at higher levels than ATCC 43816 (K2 and NTUH-K2044 (K1, consistent with previous characterization of the antiphagocytic properties of K1 and K2 serotype capsules. We also examined the three K. pneumoniae strains in a novel BALB/c respiratory disease model and found that ATCC 43816 and NTUH-K2044 are highly virulent (LD50<100 CFU while MGH 78578 is relatively avirulent.

Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain

Science.gov (United States)

2013-01-01

Background Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia (EP), a mild, chronic pneumonia of swine. Despite presenting with low direct mortality, EP is responsible for major economic losses in the pig industry. To identify the virulence-associated determinants of M. hyopneumoniae, we determined the whole genome sequence of M. hyopneumoniae strain 168 and its attenuated high-passage strain 168-L and carried out comparative genomic analyses. Results We performed the first comprehensive analysis of M. hyopneumoniae strain 168 and its attenuated strain and made a preliminary survey of coding sequences (CDSs) that may be related to virulence. The 168-L genome has a highly similar gene content and order to that of 168, but is 4,483 bp smaller because there are 60 insertions and 43 deletions in 168-L. Besides these indels, 227 single nucleotide variations (SNVs) were identified. We further investigated the variants that affected CDSs, and compared them to reported virulence determinants. Notably, almost all of the reported virulence determinants are included in these variants affected CDSs. In addition to variations previously described in mycoplasma adhesins (P97, P102, P146, P159, P216, and LppT), cell envelope proteins (P95), cell surface antigens (P36), secreted proteins and chaperone protein (DnaK), mutations in genes related to metabolism and growth may also contribute to the attenuated virulence in 168-L. Furthermore, many mutations were located in the previously described repeat motif, which may be of primary importance for virulence. Conclusions We studied the virulence attenuation mechanism of M. hyopneumoniae by comparative genomic analysis of virulent strain 168 and its attenuated high-passage strain 168-L. Our findings provide a preliminary survey of CDSs that may be related to virulence. While these include reported virulence-related genes, other novel virulence determinants were also detected. This new information will form

Selective insectivory at Toro-Semliki, Uganda: comparative analyses suggest no 'savanna' chimpanzee pattern.

Science.gov (United States)

Webster, Timothy H; McGrew, William C; Marchant, Linda F; Payne, Charlotte L R; Hunt, Kevin D

2014-06-01

Chimpanzee (Pan troglodytes) insectivory across Africa is ubiquitous. Insects provide a significant nutritional payoff and may be important for chimpanzees in dry, open habitats with narrow diets. We tested this hypothesis at Semliki, Uganda, a long-term dry study site. We evaluated prospects for insectivory by measuring insect abundance along de novo transects and trails, monitoring social insect colonies, and surveying available raw materials for elementary technology. We determined the frequency and nature of insectivory through behavioral observation and fecal analysis. We then compared our results with those from 15 other long-term chimpanzee study sites using a cluster analysis. We found that Semliki chimpanzees are one of the most insectivorous populations studied to date in terms of frequency of consumption, but they are very selective in their insectivory, regularly consuming only weaver ants (Oecophylla longinoda) and honey and bees from hives of Apis mellifera. This selectivity obtains despite having a full range of typical prey species available in harvestable quantities. We suggest that Semliki chimpanzees may face ecological time constraints and therefore bias their predation toward prey taxa that can be quickly consumed. Geographical proximity correlated with the results of the cluster analysis, while rainfall, a relatively gross measure of environment, did not. Because broad taxonomic groups of insects were used in analyses, prey availability was unlikely to have a strong effect on this pattern. Instead, we suggest that transmission of cultural knowledge may play a role in determining chimpanzee prey selection across Africa. Further study is needed to test these hypotheses. Copyright © 2014 Elsevier Ltd. All rights reserved.

phyloXML: XML for evolutionary biology and comparative genomics.

Science.gov (United States)

Han, Mira V; Zmasek, Christian M

2009-10-27

Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org.

Contesting Citizenship: Comparative Analyses

DEFF Research Database (Denmark)

Siim, Birte; Squires, Judith

2007-01-01

The pursuit of equal citizenship has been complicated by two recent developments: the emergence of multi-level governance (and with it the growing importance of local, regional and global levels of citizenship practices) and the emrgence of group recognition claims (which signals the growing impo...

Anti-Vascular Endothelial Growth Factor Comparative Effectiveness Trial for Diabetic Macular Edema: Additional Efficacy Post Hoc Analyses of a Randomized Clinical Trial.

Science.gov (United States)

Jampol, Lee M; Glassman, Adam R; Bressler, Neil M; Wells, John A; Ayala, Allison R

2016-12-01

Post hoc analyses from the Diabetic Retinopathy Clinical Research Network randomized clinical trial comparing aflibercept, bevacizumab, and ranibizumab for diabetic macular edema (DME) might influence interpretation of study results. To provide additional outcomes comparing 3 anti-vascular endothelial growth factor (VEGF) agents for DME. Post hoc analyses performed from May 3, 2016, to June 21, 2016, of a randomized clinical trial performed from August 22, 2012, to September 23, 2015, of 660 participants comparing 3 anti-VEGF treatments in eyes with center-involved DME causing vision impairment. Randomization to intravitreous aflibercept (2.0 mg), bevacizumab (1.25 mg), or ranibizumab (0.3 mg) administered up to monthly based on a structured retreatment regimen. Focal/grid laser treatment was added after 6 months for the treatment of persistent DME. Change in visual acuity (VA) area under the curve and change in central subfield thickness (CST) within subgroups based on whether an eye received laser treatment for DME during the study. Post hoc analyses were performed for 660 participants (mean [SD] age, 61 [10] years; 47% female, 65% white, 16% black or African American, 16% Hispanic, and 3% other). For eyes with an initial VA of 20/50 or worse, VA improvement was greater with aflibercept than the other agents at 1 year but superior only to bevacizumab at 2 years. Mean (SD) letter change in VA over 2 years (area under curve) was greater with aflibercept (+17.1 [9.7]) than with bevacizumab (+12.1 [9.4]; 95% CI, +1.6 to +7.3; P grid laser treatment was performed for DME, the only participants to have a substantial reduction in mean CST between 1 and 2 years were those with a baseline VA of 20/50 or worse receiving bevacizumab and laser treatment (mean [SD], -55 [108] µm; 95% CI, -82 to -28 µm; P grid laser treatment, ceiling and floor effects, or both may account for mean thickness reductions noted only in bevacizumab-treated eyes between 1 and 2 years

Comparative and Predictive Multimedia Assessments Using Monte Carlo Uncertainty Analyses

Science.gov (United States)

Whelan, G.

2002-05-01

Multiple-pathway frameworks (sometimes referred to as multimedia models) provide a platform for combining medium-specific environmental models and databases, such that they can be utilized in a more holistic assessment of contaminant fate and transport in the environment. These frameworks provide a relatively seamless transfer of information from one model to the next and from databases to models. Within these frameworks, multiple models are linked, resulting in models that consume information from upstream models and produce information to be consumed by downstream models. The Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES) is an example, which allows users to link their models to other models and databases. FRAMES is an icon-driven, site-layout platform that is an open-architecture, object-oriented system that interacts with environmental databases; helps the user construct a Conceptual Site Model that is real-world based; allows the user to choose the most appropriate models to solve simulation requirements; solves the standard risk paradigm of release transport and fate; and exposure/risk assessments to people and ecology; and presents graphical packages for analyzing results. FRAMES is specifically designed allow users to link their own models into a system, which contains models developed by others. This paper will present the use of FRAMES to evaluate potential human health exposures using real site data and realistic assumptions from sources, through the vadose and saturated zones, to exposure and risk assessment at three real-world sites, using the Multimedia Environmental Pollutant Assessment System (MEPAS), which is a multimedia model contained within FRAMES. These real-world examples use predictive and comparative approaches coupled with a Monte Carlo analysis. A predictive analysis is where models are calibrated to monitored site data, prior to the assessment, and a comparative analysis is where models are not calibrated but

Systematic comparative and sensitivity analyses of additive and outranking techniques for supporting impact significance assessments

International Nuclear Information System (INIS)

Cloquell-Ballester, Vicente-Agustin; Monterde-Diaz, Rafael; Cloquell-Ballester, Victor-Andres; Santamarina-Siurana, Maria-Cristina

2007-01-01

Assessing the significance of environmental impacts is one of the most important and all together difficult processes of Environmental Impact Assessment. This is largely due to the multicriteria nature of the problem. To date, decision techniques used in the process suffer from two drawbacks, namely the problem of compensation and the problem of identification of the 'exact boundary' between sub-ranges. This article discusses these issues and proposes a methodology for determining the significance of environmental impacts based on comparative and sensitivity analyses using the Electre TRI technique. An application of the methodology for the environmental assessment of a Power Plant project within the Valencian Region (Spain) is presented, and its performance evaluated. It is concluded that contrary to other techniques, Electre TRI automatically identifies those cases where allocation of significance categories is most difficult and, when combined with sensitivity analysis, offers greatest robustness in the face of variation in weights of the significance attributes. Likewise, this research demonstrates the efficacy of systematic comparison between Electre TRI and sum-based techniques, in the solution of assignment problems. The proposed methodology can therefore be regarded as a successful aid to the decision-maker, who will ultimately take the final decision

Characterization of Aeromonas hydrophila Wound Pathotypes by Comparative Genomic and Functional Analyses of Virulence Genes

Science.gov (United States)

Grim, Christopher J.; Kozlova, Elena V.; Sha, Jian; Fitts, Eric C.; van Lier, Christina J.; Kirtley, Michelle L.; Joseph, Sandeep J.; Read, Timothy D.; Burd, Eileen M.; Tall, Ben D.; Joseph, Sam W.; Horneman, Amy J.; Chopra, Ashok K.; Shak, Joshua R.

2013-01-01

ABSTRACT Aeromonas hydrophila has increasingly been implicated as a virulent and antibiotic-resistant etiologic agent in various human diseases. In a previously published case report, we described a subject with a polymicrobial wound infection that included a persistent and aggressive strain of A. hydrophila (E1), as well as a more antibiotic-resistant strain of A. hydrophila (E2). To better understand the differences between pathogenic and environmental strains of A. hydrophila, we conducted comparative genomic and functional analyses of virulence-associated genes of these two wound isolates (E1 and E2), the environmental type strain A. hydrophila ATCC 7966T, and four other isolates belonging to A. aquariorum, A. veronii, A. salmonicida, and A. caviae. Full-genome sequencing of strains E1 and E2 revealed extensive differences between the two and strain ATCC 7966T. The more persistent wound infection strain, E1, harbored coding sequences for a cytotoxic enterotoxin (Act), a type 3 secretion system (T3SS), flagella, hemolysins, and a homolog of exotoxin A found in Pseudomonas aeruginosa. Corresponding phenotypic analyses with A. hydrophila ATCC 7966T and SSU as reference strains demonstrated the functionality of these virulence genes, with strain E1 displaying enhanced swimming and swarming motility, lateral flagella on electron microscopy, the presence of T3SS effector AexU, and enhanced lethality in a mouse model of Aeromonas infection. By combining sequence-based analysis and functional assays, we characterized an A. hydrophila pathotype, exemplified by strain E1, that exhibited increased virulence in a mouse model of infection, likely because of encapsulation, enhanced motility, toxin secretion, and cellular toxicity. PMID:23611906

Comparative analyses of tooth wear in free-ranging and captive wild equids.

Science.gov (United States)

Taylor, L A; Müller, D W H; Schwitzer, C; Kaiser, T M; Castell, J C; Clauss, M; Schulz-Kornas, E

2016-03-01

Captive breeding has played a crucial role in the conservation of threatened equid species. Grazing ruminants and rhinoceros in captivity have less abrasion-dominated tooth wear than their free-ranging conspecifics, with potential negative consequences for their health. However, a similar study on wild equids in captivity is missing. The aim was to establish if different tooth wear patterns are exhibited by free-ranging and captive equids. Cross-sectional study of museum specimens comparing free-ranging and captive equids. Dental casts of maxillary cheek teeth of 228 museum specimens (122 from free-ranging and 106 from captive individuals) of 7 wild equid species were analysed using the extended mesowear method. Although teeth showing specific abnormalities were not scored, the presence of focal overgrowths (hooks) of the rostral premolars (106, 206) was recorded. Captive Equus ferus przewalskii, E. grevyi, E. hemionus, E. quagga boehmi and E. zebra hartmannae have less abrasion-dominated tooth wear on their premolars than their free-ranging conspecifics (P<0.001). Fewer differences were exhibited between populations in the molars. No differences were exhibited in the distal cusp of the molars (110, 210) between populations, except in a small sample of E. kiang. Captive equids exhibited more homogeneous wear along the tooth row whereas free-ranging equids exhibited a tooth wear gradient, with more abrasion on premolars than molars. There were more rostral hooks on the premolars (106, 206) in the captive than the free-ranging population (P = 0.02). Captive equids did experience less abrasion-dominated tooth wear than their free-ranging conspecifics, but the differences in tooth wear were less pronounced than those between captive and free-ranging wild ruminant and rhinoceros species. This indicates that feeding regimes for captive equids deviate less from natural diets than those for captive ruminants and rhinoceros but that factors leading to hook

Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.

Science.gov (United States)

Lv, Changda; Li, Qi; Kong, Lingfeng

2018-01-01

Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

Science.gov (United States)

Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

2015-05-04

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Comparative Proteomic and Morphological Change Analyses of Staphylococcus aureus During Resuscitation From Prolonged Freezing

Science.gov (United States)

Suo, Biao; Yang, Hua; Wang, Yuexia; Lv, Haipeng; Li, Zhen; Xu, Chao; Ai, Zhilu

2018-01-01

When frozen, Staphylococcus aureus survives in a sublethally injured state. However, S. aureus can recover at a suitable temperature, which poses a threat to food safety. To elucidate the resuscitation mechanism of freezing survived S. aureus, we used cells stored at -18°C for 90 days as controls. After resuscitating the survived cells at 37°C, the viable cell numbers were determined on tryptic soy agar with 0.6% yeast extract (TSAYE), and the non-injured-cell numbers were determined on TSAYE supplemented with 10% NaCl. The results showed that the total viable cell number did not increase within the first 3 h of resuscitation, but the osmotic regulation ability of freezing survived cells gradually recovered to the level of healthy cells, which was evidenced by the lack of difference between the two samples seen by differential cell enumeration. Scanning electron microscopy (SEM) showed that, compared to late exponential stage cells, some frozen survived cells underwent splitting and cell lysis due to deep distortion and membrane rupture. Transmission electron microscopy (TEM) showed that, in most of the frozen survived cells, the nucleoids (low electronic density area) were loose, and the cytoplasmic matrices (high electronic density area) were sparse. Additionally, a gap was seen to form between the cytoplasmic membranes and the cell walls in the frozen survived cells. The morphological changes were restored when the survived cells were resuscitated at 37°C. We also analyzed the differential proteome after resuscitation using non-labeled high-performance liquid chromatography–mass spectrometry (HPLC-MS). The results showed that, compared with freezing survived S. aureus cells, the cells resuscitated for 1 h had 45 upregulated and 73 downregulated proteins. The differentially expressed proteins were functionally categorized by gene ontology enrichment, KEGG pathway, and STRING analyses. Cell membrane synthesis-related proteins, oxidative stress resistance

Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

Directory of Open Access Journals (Sweden)

Li Chuan

2012-05-01

Full Text Available Abstract Background Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP genes, fructosyltransferase (FST genes, and many C-repeat binding factor (CBF genes are Pooideae specific and important in low temperature responses. Here we used comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand its potential as a model species for agriculturally important temperate grasses. Results Brachypodium distachyon contains cold responsive IRIP genes which have evolved through Brachypodium specific gene family expansions. A large cold responsive CBF3 subfamily was identified in B. distachyon, while CBF4 homologs are absent from the genome. No B. distachyon FST gene homologs encode typical core Pooideae FST-motifs and low temperature induced fructan accumulation was dramatically different in B. distachyon compared to core Pooideae species. Conclusions We conclude that B. distachyon can serve as an interesting model for specific molecular mechanisms involved in low temperature responses in core Pooideae species. However, the evolutionary history of key genes involved in low temperature responses has been different in Brachypodium and core Pooideae species. These differences limit the use of B. distachyon as a model for holistic studies relevant for agricultural core Pooideae species.

Analyse comparative entre la distribution des fréquences de ...

African Journals Online (AJOL)

2016 International Formulae Group. All rights reserved. Mots clés: Hydrogéochimie, conductivité électrique, diagramme de Piper, socle cristallin et cristallophyllien, Côte d'Ivoire. English Title: Comparative analysis of electrical conductivity frequencies distribution and geochemical facies of hard rock aquifers waters (Ivory ...

Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

Science.gov (United States)

Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A.; Janke, Axel

2015-01-01

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. PMID:26019166

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

Science.gov (United States)

Glicksberg, Benjamin S.; Li, Li; Badgeley, Marcus A.; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D.; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L.; Hoffman, Gabriel E.; Dan Li, Shuyu; Schadt, Eric E.; Patel, Chirag J.; Chen, Rong; Dudley, Joel T.

2016-01-01

Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. Contacts: rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307606

Comparative genomics of Serratia spp.: two paths towards endosymbiotic life.

Directory of Open Access Journals (Sweden)

Alejandro Manzano-Marín

Full Text Available Symbiosis is a widespread phenomenon in nature, in which insects show a great number of these associations. Buchnera aphidicola, the obligate endosymbiont of aphids, coexists in some species with another intracellular bacterium, Serratia symbiotica. Of particular interest is the case of the cedar aphid Cinara cedri, where B. aphidicola BCc and S. symbiotica SCc need each other to fulfil their symbiotic role with the insect. Moreover, various features seem to indicate that S. symbiotica SCc is closer to an obligate endosymbiont than to other facultative S. symbiotica, such as the one described for the aphid Acirthosyphon pisum (S. symbiotica SAp. This work is based on the comparative genomics of five strains of Serratia, three free-living and two endosymbiotic ones (one facultative and one obligate which should allow us to dissect the genome reduction taking place in the adaptive process to an intracellular life-style. Using a pan-genome approach, we have identified shared and strain-specific genes from both endosymbiotic strains and gained insight into the different genetic reduction both S. symbiotica have undergone. We have identified both retained and reduced functional categories in S. symbiotica compared to the Free-Living Serratia (FLS that seem to be related with its endosymbiotic role in their specific host-symbiont systems. By means of a phylogenomic reconstruction we have solved the position of both endosymbionts with confidence, established the probable insect-pathogen origin of the symbiotic clade as well as the high amino-acid substitution rate in S. symbiotica SCc. Finally, we were able to quantify the minimal number of rearrangements suffered in the endosymbiotic lineages and reconstruct a minimal rearrangement phylogeny. All these findings provide important evidence for the existence of at least two distinctive S. symbiotica lineages that are characterized by different rearrangements, gene content, genome size and branch lengths.

Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms.

Science.gov (United States)

Sun, Luchao; Rai, Amit; Rai, Megha; Nakamura, Michimi; Kawano, Noriaki; Yoshimatsu, Kayo; Suzuki, Hideyuki; Kawahara, Nobuo; Saito, Kazuki; Yamazaki, Mami

2018-05-07

The three Forsythia species, F. suspensa, F. viridissima and F. koreana, have been used as herbal medicines in China, Japan and Korea for centuries and they are known to be rich sources of numerous pharmaceutical metabolites, forsythin, forsythoside A, arctigenin, rutin and other phenolic compounds. In this study, de novo transcriptome sequencing and assembly was performed on these species. Using leaf and flower tissues of F. suspensa, F. viridissima and F. koreana, 1.28-2.45-Gbp sequences of Illumina based pair-end reads were obtained and assembled into 81,913, 88,491 and 69,458 unigenes, respectively. Classification of the annotated unigenes in gene ontology terms and KEGG pathways was used to compare the transcriptome of three Forsythia species. The expression analysis of orthologous genes across all three species showed the expression in leaf tissues being highly correlated. The candidate genes presumably involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were screened as co-expressed genes. They express highly in the leaves of F. viridissima and F. koreana. Furthermore, the three unigenes annotated as acyltransferase were predicted to be associated with the biosynthesis of acteoside and forsythoside A from the expression pattern and phylogenetic analysis. This study is the first report on comparative transcriptome analyses of medicinally important Forsythia genus and will serve as an important resource to facilitate further studies on biosynthesis and regulation of therapeutic compounds in Forsythia species.

Retrospective analyses versus RCTs: comparing like with like?

Directory of Open Access Journals (Sweden)

Baron R

2017-03-01

Full Text Available Ralf Baron,1 Lieven Nils Kennes,2 Christian Elling31Division of Neurological Pain Research and Therapy, Department of Neurology, University Hospital of Schleswig-Holstein, Kiel Campus, Kiel, 2Department of Economics and Business Administration, University of Applied Sciences Stralsund, Stralsund, 3Grünenthal GmbH, Medical Affairs Europe and North America, Aachen, GermanyIn their recent retrospective analysis assessing oxycodone/naloxone (OXN vs. tapentadol (TAP treatment for chronic low-back pain with a neuropathic component, Ueberall and Mueller-Schwefe1 compare their results to the findings of an earlier phase 3b/4 study.2 In our opinion, a proper comparison to the prospective, randomized, controlled, open-label study by Baron and colleagues is scientifically not appropriate. Although Ueberall and Mueller-Schwefe use the terms “prospective,” “randomly,” and “blinded” and refer to the PROBE design (prospective, randomized, open-label, blinded endpoint,3 their database study is retrospective, nonrandomized, and nonblinded with the treatment choice left to the discretion of the physicians. In this context, the use of the term “intention-to-treat (ITT population” is inappropriate because ITT is unambiguously defined as including all randomized subjects and thus inseparable from true randomization (ICH E9.4View original paper by Ueberall and Mueller-Schwefe.

Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis.

Science.gov (United States)

Holubar, Marisa; Stavroulakis, Maria Christina; Maldonado, Yvonne; Ioannidis, John P A; Contopoulos-Ioannidis, Despina

2017-01-01

Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the adoption of the target

Comparative analyses of industrial-scale human platelet lysate preparations.

Science.gov (United States)

Pierce, Jan; Benedetti, Eric; Preslar, Amber; Jacobson, Pam; Jin, Ping; Stroncek, David F; Reems, Jo-Anna

2017-12-01

Efforts are underway to eliminate fetal bovine serum from mammalian cell cultures for clinical use. An emerging, viable replacement option for fetal bovine serum is human platelet lysate (PL) as either a plasma-based or serum-based product. Nine industrial-scale, serum-based PL manufacturing runs (i.e., lots) were performed, consisting of an average ± standard deviation volume of 24.6 ± 2.2 liters of pooled, platelet-rich plasma units that were obtained from apheresis donors. Manufactured lots were compared by evaluating various biochemical and functional test results. Comprehensive cytokine profiles of PL lots and product stability tests were performed. Global gene expression profiles of mesenchymal stromal cells (MSCs) cultured with plasma-based or serum-based PL were compared to MSCs cultured with fetal bovine serum. Electrolyte and protein levels were relatively consistent among all serum-based PL lots, with only slight variations in glucose and calcium levels. All nine lots were as good as or better than fetal bovine serum in expanding MSCs. Serum-based PL stored at -80°C remained stable over 2 years. Quantitative cytokine arrays showed similarities as well as dissimilarities in the proteins present in serum-based PL. Greater differences in MSC gene expression profiles were attributable to the starting cell source rather than with the use of either PL or fetal bovine serum as a culture supplement. Using a large-scale, standardized method, lot-to-lot variations were noted for industrial-scale preparations of serum-based PL products. However, all lots performed as well as or better than fetal bovine serum in supporting MSC growth. Together, these data indicate that off-the-shelf PL is a feasible substitute for fetal bovine serum in MSC cultures. © 2017 AABB.

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era.

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Smith, Stephen A; Brown, Joseph W; Walker, Joseph F

2018-01-01

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. "Gene shopping", wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated

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

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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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

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Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Comparative analyses of diffusion coefficients for different extraction processes from thyme

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Petrovic Slobodan S.

2012-01-01

Full Text Available This work was aimed to analyze kinetics and mass transfer phenomena for different extraction processes from thyme (Thymus vulgaris L. leaves. Different extraction processes with ethanol were studied: Soxhlet extraction and ultrasound-assisted batch extraction on the laboratory scale as well as pilot plant batch extraction with mixing. The extraction processes with ethanol were compared to the process of supercritical carbon dioxide extraction performed at 10 MPa and 40°C. Experimental data were analyzed by mathematical model derived from the Fick’s second law to determine and compare diffusion coefficients in the periods of constant and decreasing extraction rate. In the fast extraction period, values of diffusion coefficients were one to three orders of magnitude higher compared to those determined for the period of slow extraction. The highest diffusion coefficient was reported for the fast extraction period of supercritical fluid extraction. In the case of extraction processes with ethanol, ultrasound, stirring and extraction temperature increase enhanced mass transfer rate in the washing phase. On the other hand, ultrasound contributed the most to the increase of mass transfer rate in the period of slow extraction.

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

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Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T

2016-06-15

Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway

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Wattam, Alice R.; Inzana, Thomas J.; Williams, Kelly P.; Mane, Shrinivasrao P.; Shukla, Maulik; Almeida, Nalvo F.; Dickerman, Allan W.; Mason, Steven; Moriyón, Ignacio; O’Callaghan, David; Whatmore, Adrian M.; Sobral, Bruno W.; Tiller, Rebekah V.; Hoffmaster, Alex R.; Frace, Michael A.; De Castro, Cristina; Molinaro, Antonio; Boyle, Stephen M.; De, Barun K.; Setubal, João C.

2012-01-01

ABSTRACT Brucella species are Gram-negative bacteria that infect mammals. Recently, two unusual strains (Brucella inopinata BO1T and B. inopinata-like BO2) have been isolated from human patients, and their similarity to some atypical brucellae isolated from Australian native rodent species was noted. Here we present a phylogenomic analysis of the draft genome sequences of BO1T and BO2 and of the Australian rodent strains 83-13 and NF2653 that shows that they form two groups well separated from the other sequenced Brucella spp. Several important differences were noted. Both BO1T and BO2 did not agglutinate significantly when live or inactivated cells were exposed to monospecific A and M antisera against O-side chain sugars composed of N-formyl-perosamine. While BO1T maintained the genes required to synthesize a typical Brucella O-antigen, BO2 lacked many of these genes but still produced a smooth LPS (lipopolysaccharide). Most missing genes were found in the wbk region involved in O-antigen synthesis in classic smooth Brucella spp. In their place, BO2 carries four genes that other bacteria use for making a rhamnose-based O-antigen. Electrophoretic, immunoblot, and chemical analyses showed that BO2 carries an antigenically different O-antigen made of repeating hexose-rich oligosaccharide units that made the LPS water-soluble, which contrasts with the homopolymeric O-antigen of other smooth brucellae that have a phenol-soluble LPS. The results demonstrate the existence of a group of early-diverging brucellae with traits that depart significantly from those of the Brucella species described thus far. PMID:22930339

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.

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Durham, Bryndan P; Grote, Jana; Whittaker, Kerry A; Bender, Sara J; Luo, Haiwei; Grim, Sharon L; Brown, Julia M; Casey, John R; Dron, Antony; Florez-Leiva, Lennin; Krupke, Andreas; Luria, Catherine M; Mine, Aric H; Nigro, Olivia D; Pather, Santhiska; Talarmin, Agathe; Wear, Emma K; Weber, Thomas S; Wilson, Jesse M; Church, Matthew J; DeLong, Edward F; Karl, David M; Steward, Grieg F; Eppley, John M; Kyrpides, Nikos C; Schuster, Stephan; Rappé, Michael S

2014-06-15

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

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Daniel Garrido-Sanz

Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

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Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

2016-02-01

Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics.

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Hazen, Tracy H; Leonard, Susan R; Lampel, Keith A; Lacher, David W; Maurelli, Anthony T; Rasko, David A

2016-08-01

Enteroinvasive Escherichia coli (EIEC) is a unique pathovar that has a pathogenic mechanism nearly indistinguishable from that of Shigella species. In contrast to isolates of the four Shigella species, which are widespread and can be frequent causes of human illness, EIEC causes far fewer reported illnesses each year. In this study, we analyzed the genome sequences of 20 EIEC isolates, including 14 first described in this study. Phylogenomic analysis of the EIEC genomes demonstrated that 17 of the isolates are present in three distinct lineages that contained only EIEC genomes, compared to reference genomes from each of the E. coli pathovars and Shigella species. Comparative genomic analysis identified genes that were unique to each of the three identified EIEC lineages. While many of the EIEC lineage-specific genes have unknown functions, those with predicted functions included a colicin and putative proteins involved in transcriptional regulation or carbohydrate metabolism. In silico detection of the Shigella virulence plasmid (pINV), which is essential for the invasion of host cells, demonstrated that a form of pINV was present in nearly all EIEC genomes, but the Mxi-Spa-Ipa region of the plasmid that encodes the invasion-associated proteins was absent from several of the EIEC isolates. The comparative genomic findings in this study support the hypothesis that multiple EIEC lineages have evolved independently from multiple distinct lineages of E. coli via the acquisition of the Shigella virulence plasmid and, in some cases, the Shigella pathogenicity islands. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Efficacy and tolerability of naproxen/esomeprazole magnesium tablets compared with non-specific NSAIDs and COX-2 inhibitors: a systematic review and network analyses

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Datto C

2013-02-01

Full Text Available Catherine Datto,1 Richard Hellmund,1 Mohd Kashif Siddiqui21AstraZeneca Pharmaceuticals LP, Wilmington, DE, USA; 2HERON PVT India, Chandigarh, UT, IndiaAbstract: Non-steroidal anti-inflammatory drugs (NSAIDs, such as non-selective NSAIDs (nsNSAIDs or selective cyclooxygenase-2 (COX-2 inhibitors, are commonly prescribed for arthritic pain relief in patients with osteoarthritis (OA, rheumatoid arthritis (RA, or ankylosing spondylitis (AS. Treatment guidelines for chronic NSAID therapy include the consideration for gastroprotection for those at risk of gastric ulcers (GUs associated with the chronic NSAID therapy. The United States Food and Drug Administration has approved naproxen/esomeprazole magnesium tablets for the relief of signs and symptoms of OA, RA, and AS, and to decrease the risk of developing GUs in patients at risk of developing NSAID-associated GUs. The European Medical Association has approved this therapy for the symptomatic treatment of OA, RA, and AS in patients who are at risk of developing NSAID-associated GUs and/or duodenal ulcers, for whom treatment with lower doses of naproxen or other NSAIDs is not considered sufficient. Naproxen/esomeprazole magnesium tablets have been compared with naproxen and celecoxib for these indications in head-to-head trials. This systematic literature review and network meta-analyses of data from randomized controlled trials was performed to compare naproxen/esomeprazole magnesium tablets with a number of additional relevant comparators. For this study, an original review examined MEDLINE®, Embase®, and the Cochrane Controlled Trials Register from database start to April 14, 2009. Using the same methodology, a review update was conducted to December 21, 2009. The systematic review and network analyses showed naproxen/esomeprazole magnesium tablets have an improved upper gastrointestinal tolerability profile (dyspepsia and gastric or gastroduodenal ulcers over several active comparators (naproxen

Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) - phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation.

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Stervander, Martin; Illera, Juan Carlos; Kvist, Laura; Barbosa, Pedro; Keehnen, Naomi P; Pruisscher, Peter; Bensch, Staffan; Hansson, Bengt

2015-05-01

Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences. © 2015 John Wiley & Sons Ltd.

Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

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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.

Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

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Bidon, Tobias; Schreck, Nancy; Hailer, Frank; Nilsson, Maria A; Janke, Axel

2015-05-27

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Circular job-related spatial mobility in Germany:Comparative analyses of two representative surveys on the forms, prevalence and relevance in the context of partnership and family development

Directory of Open Access Journals (Sweden)

Heiko Rüger

2012-01-01

In this regard, the present article aims at achieving three essential objectives. First, we will introduce a common indicator for circular job mobility patterns found in the two surveys. On the basis of this common indicator, we will comparatively analyse the prevalence of different mobility forms and their composition according to key socio-demographic characteristics. In addition, we will use multivariate analyses to illustrate the relevance of job mobility for partnership and family development. Results suggest mobility patterns to be an important individual context factor when explaining processes relevant to partnerships and family. In particular, women who exhibit some degree of job mobility are less often married and rarely have children.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

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Li, Gang; Gandolfi, Barbara; Khan, Razib; Aken, Bronwen L.; Searle, Steven M. J.; Minx, Patrick; Hillier, LaDeana W.; Koboldt, Daniel C.; Davis, Brian W.; Driscoll, Carlos A.; Barr, Christina S.; Blackistone, Kevin; Quilez, Javier; Lorente-Galdos, Belen; Marques-Bonet, Tomas; Alkan, Can; Thomas, Gregg W. C.; Hahn, Matthew W.; Menotti-Raymond, Marilyn; O’Brien, Stephen J.; Wilson, Richard K.; Lyons, Leslie A.; Murphy, William J.; Warren, Wesley C.

2014-01-01

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae. PMID:25385592

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

Science.gov (United States)

Montague, Michael J; Li, Gang; Gandolfi, Barbara; Khan, Razib; Aken, Bronwen L; Searle, Steven M J; Minx, Patrick; Hillier, LaDeana W; Koboldt, Daniel C; Davis, Brian W; Driscoll, Carlos A; Barr, Christina S; Blackistone, Kevin; Quilez, Javier; Lorente-Galdos, Belen; Marques-Bonet, Tomas; Alkan, Can; Thomas, Gregg W C; Hahn, Matthew W; Menotti-Raymond, Marilyn; O'Brien, Stephen J; Wilson, Richard K; Lyons, Leslie A; Murphy, William J; Warren, Wesley C

2014-12-02

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.

Comparative exergy analyses of gasoline and hydrogen fuelled ices

International Nuclear Information System (INIS)

Nieminen, J.; Dincer, I.; Yang, Y.

2009-01-01

Comparative exergy models for naturally aspirated gasoline and hydrogen fuelled spark ignition internal combustion engines were developed according to the second laws of thermodynamics. A thorough graphical analysis of heat transfer, work, thermo mechanical, and intake charge exergy functions was made. An irreversibility function was developed as a function of entropy generation and graphed. A second law analysis yielded a proportional exergy distribution as a fraction of the intake charge exergy. It was found that the hydrogen fuelled engine had a greater proportion of the intake charge exergy converted into work exergy, indicating a second law efficiency of 50.13% as opposed to 44.34% for a gasoline fuelled engine. The greater exergy due to heat transfer or thermal availability associated with the hydrogen fuelled engine is postulated to be a part of the reason for decreased work output of a hydrogen engine. Finally, a second law analysis of both hydrogen and gasoline combustion reactions indicate a greater combustion irreversibility associated with gasoline combustion. A percentage breakdown of the combustion irreversibilities were also constructed according to information found in literature searches. (author)

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli.

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Hazen, Tracy H; Michalski, Jane; Luo, Qingwei; Shetty, Amol C; Daugherty, Sean C; Fleckenstein, James M; Rasko, David A

2017-06-14

Escherichia coli that are capable of causing human disease are often classified into pathogenic variants (pathovars) based on their virulence gene content. However, disease-associated hybrid E. coli, containing unique combinations of multiple canonical virulence factors have also been described. Such was the case of the E. coli O104:H4 outbreak in 2011, which caused significant morbidity and mortality. Among the pathovars of diarrheagenic E. coli that cause significant human disease are the enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC). In the current study we use comparative genomics, transcriptomics, and functional studies to characterize isolates that contain virulence factors of both EPEC and ETEC. Based on phylogenomic analysis, these hybrid isolates are more genomically-related to EPEC, but appear to have acquired ETEC virulence genes. Global transcriptional analysis using RNA sequencing, demonstrated that the EPEC and ETEC virulence genes of these hybrid isolates were differentially-expressed under virulence-inducing laboratory conditions, similar to reference isolates. Immunoblot assays further verified that the virulence gene products were produced and that the T3SS effector EspB of EPEC, and heat-labile toxin of ETEC were secreted. These findings document the existence and virulence potential of an E. coli pathovar hybrid that blurs the distinction between E. coli pathovars.

Comparative Analyses of Phenotypic Trait Covariation within and among Populations.

Science.gov (United States)

Peiman, Kathryn S; Robinson, Beren W

2017-10-01

Many morphological, behavioral, physiological, and life-history traits covary across the biological scales of individuals, populations, and species. However, the processes that cause traits to covary also change over these scales, challenging our ability to use patterns of trait covariance to infer process. Trait relationships are also widely assumed to have generic functional relationships with similar evolutionary potentials, and even though many different trait relationships are now identified, there is little appreciation that these may influence trait covariation and evolution in unique ways. We use a trait-performance-fitness framework to classify and organize trait relationships into three general classes, address which ones more likely generate trait covariation among individuals in a population, and review how selection shapes phenotypic covariation. We generate predictions about how trait covariance changes within and among populations as a result of trait relationships and in response to selection and consider how these can be tested with comparative data. Careful comparisons of covariation patterns can narrow the set of hypothesized processes that cause trait covariation when the form of the trait relationship and how it responds to selection yield clear predictions about patterns of trait covariation. We discuss the opportunities and limitations of comparative approaches to evaluate hypotheses about the evolutionary causes and consequences of trait covariation and highlight the importance of evaluating patterns within populations replicated in the same and in different selective environments. Explicit hypotheses about trait relationships are key to generating effective predictions about phenotype and its evolution using covariance data.

Phylogenomic analysis of the GIY-YIG nuclease superfamily

Directory of Open Access Journals (Sweden)

Bujnicki Janusz M

2006-04-01

Full Text Available Abstract Background The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported. Results We carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for extending the GIY-YIG superfamily to include members of COG3680 and a number of proteins not classified in COGs and to predict that these proteins may function as nucleases, potentially involved in DNA recombination and/or repair. Finally, all old and new members of the GIY-YIG superfamily were compared and analyzed to infer the phylogenetic tree. Conclusion An evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation of all (subfamilies. It provides a comprehensive picture of sequence-structure-function relationships in this superfamily of nucleases, which will help to design experiments to study the mechanism of action of known members (especially the uncharacterized ones and will facilitate the prediction of function for the newly discovered ones.

Exergoeconomic and environmental analyses of CO

NARCIS (Netherlands)

Mosaffa, A. H.; Garousi Farshi, L; Infante Ferreira, C.A.; Rosen, M. A.

2016-01-01

Exergoeconomic and environmental analyses are presented for two CO₂/NH₃ cascade refrigeration systems equipped with (1) two flash tanks and (2) a flash tank along with a flash intercooler with indirect subcooler. A comparative study is performed for the proposed systems, and

Comparison with Russian analyses of meteor impact

Energy Technology Data Exchange (ETDEWEB)

Canavan, G.H.

1997-06-01

The inversion model for meteor impacts is used to discuss Russian analyses and compare principal results. For common input parameters, the models produce consistent estimates of impactor parameters. Directions for future research are discussed and prioritized.

Comparing EFT and Exact One-Loop Analyses of Non-Degenerate Stops

CERN Document Server

Drozd, Aleksandra; Quevillon, Jeremie; You, Tevong

2015-01-01

We develop a universal approach to the one-loop effective field theory (EFT) using the Covariant Derivative Expansion (CDE) method. We generalise previous results to include broader classes of UV models, showing how expressions previously obtained assuming degenerate heavy-particle masses can be extended to non-degenerate cases. We apply our method to the general MSSM with non-degenerate stop squarks, illustrating our approach with calculations of the coefficients of dimension-6 operators contributing to the $hgg$ and $h\\gamma\\gamma$ couplings, and comparing with exact calculations of one-loop Feynman diagrams. We then use present and projected future sensitivities to these operator coefficients to obtain present and possible future indirect constraints on stop masses. The current sensitivity is already comparable to that of direct LHC searches, and future FCC-ee measurements could be sensitive to stop masses above a TeV. The universality of our one-loop EFT approach facilitates extending these constraints to...

Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

Science.gov (United States)

Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

2014-01-01

ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits.

Science.gov (United States)

Oueslati, Amel; Salhi-Hannachi, Amel; Luro, François; Vignes, Hélène; Mournet, Pierre; Ollitrault, Patrick

2017-01-01

The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the "small citrus" modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the "phylogenomic karyotypes" of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening

The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

Science.gov (United States)

Rothfels, Carl J; Li, Fay-Wei; Sigel, Erin M; Huiet, Layne; Larsson, Anders; Burge, Dylan O; Ruhsam, Markus; Deyholos, Michael; Soltis, Douglas E; Stewart, C Neal; Shaw, Shane W; Pokorny, Lisa; Chen, Tao; dePamphilis, Claude; DeGironimo, Lisa; Chen, Li; Wei, Xiaofeng; Sun, Xiao; Korall, Petra; Stevenson, Dennis W; Graham, Sean W; Wong, Gane K-S; Pryer, Kathleen M

2015-07-01

• Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies. © 2015 Botanical Society of America, Inc.

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Directory of Open Access Journals (Sweden)

Catherine L Worth

Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Science.gov (United States)

Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

2009-09-16

Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

Self-sampling with HPV mRNA analyses from vagina and urine compared with cervical samples.

Science.gov (United States)

Asciutto, Katrin Christine; Ernstson, Avalon; Forslund, Ola; Borgfeldt, Christer

2018-04-01

In order to increase coverage in the organized cervical screening program, self-sampling with HPV analyses has been suggested. The aim was to compare human papillomavirus (HPV) mRNA detection in vaginal and urine self-collected samples with clinician-taken cervical samples and the corresponding clinician-taken histological specimens. Self-collected vaginal, urine and clinician-taken cervical samples were analyzed from 209 women with the Aptima mRNA assay (Hologic Inc, MA, USA). Cervical cytology, colposcopy, biopsy and/or the loop electrosurgical excision procedure (LEEP) were performed in every examination. The sensitivity of the HPV mRNA test in detecting high-grade squamous intraepithelial lesions (HSIL)/adenocarcinoma in situ (AIS)/cancer cases was as follows: for the vaginal self-samples 85.5% (95% CI; 75.0-92.8), the urinary samples 44.8% (95% CI; 32.6-57.4), and for routine cytology 81.7% (95% CI; 70.7-89.9). For the clinician-taken cervical HPV samples the sensitivity of the HPV mRNA test in detecting HSIL/AIS/cancer was 100.0% (95% CI; 94.9-100.0). The specificity of the HPV mRNA was similar for the clinician-taken cervical HPV samples and the self-samples: 49.0% vs. 48.1%. The urinary HPV samples had a specificity of 61.9% and cytology had a specificity of 93.3%. The sensitivity of the Aptima HPV mRNA test in detecting HSIL/AIS/cancer from vaginal self-samples was similar to that of routine cytology. The Aptima HPV mRNA vaginal self-sampling analysis may serve as a complement in screening programs. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparative analyses of seven technologies to facilitate the integration of fluctuating renewable energy sources

DEFF Research Database (Denmark)

Mathiesen, Brian Vad; Lund, Henrik

2009-01-01

An analysis of seven different technologies is presented. The technologies integrate fluctuating renewable energy sources (RES) such as wind power production into the electricity supply, and the Danish energy system is used as a case. Comprehensive hour-by-hour energy system analyses are conducted...... of a complete system meeting electricity, heat and transport demands, and including RES, power plants, and combined heat and power production (CHP) for district heating and transport technologies. In conclusion, the most fuel-efficient and least-cost technologies are identified through energy system...

A theoretical framework for analysing preschool teaching

DEFF Research Database (Denmark)

Chaiklin, Seth

2014-01-01

This article introduces a theoretical framework for analysing preschool teaching as a historically-grounded societal practice. The aim is to present a unified framework that can be used to analyse and compare both historical and contemporary examples of preschool teaching practice within and across...... national traditions. The framework has two main components, an analysis of preschool teaching as a practice, formed in relation to societal needs, and an analysis of the categorical relations which necessarily must be addressed in preschool teaching activity. The framework is introduced and illustrated...

High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T.

Science.gov (United States)

Ramaloko, Winnie Thabisa; Koen, Nadine; Polliack, Shamara; Aliyu, Habibu; Lebre, Pedro Humberto; Mohr, Teresa; Oswald, Florian; Zwick, Michaela; Zeigler, Daniel Ray; Neumann, Anke; Syldatk, Christoph; Cowan, Don Arthur; De Maayer, Pieter

2018-01-01

The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of Geobacillus uzenensis (DSM 23175 T ), G. thermocatenulatus (DSM 730 T ) and Parageobacillus galactosidasius (DSM 18751 T ). Phylogenomic analyses revealed that DSM 18751 T and DSM 23175 T represent later heterotypic synonyms of P. toebii and G. subterraneus , respectively, while DSM 730 T represents the type strain for the species G. thermocatenulatus . These genome sequences will contribute towards a deeper understanding of the ecological and biological diversity and the biotechnological exploitation of the 'geobacilli'.

Neuromuscular Structure, Evolution and Development in Meiofaunal Annelids with Special Focus on Dinophilus gyrociliatus (Dinophilidae)

DEFF Research Database (Denmark)

Kerbl, Alexandra

less complex sensory structures. Yet, very little is still known on how these small brains are organized to fulfil basic functions. This study addresses the structure, evolution and development of neuromuscular systems within two exclusively meiofaunal lineages Lobatocerebridae and Dinophilidae....... RESULTS: Both families were shown to be nested within annelids in phylogenomic analyses based on transcriptomic data, which also suggest the Spiralian ancestor to be meiofaunal (Manuscript 4). The annelid affinity of the enigmatic Lobatocerebridae was further tested by detailed morphological examinations...... warranting further studies to uncover how the genetic domains influence the configuration of the brain...

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

KAUST Repository

Ngugi, David

2014-08-08

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate \\'switch\\' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

KAUST Repository

Ngugi, David; Blom, Jochen; Alam, Intikhab; Rashid, Mamoon; Ba Alawi, Wail; Zhang, Guishan; Hikmawan, Tyas I.; Guan, Yue; Antunes, Andre; Siam, Rania; El-Dorry, Hamza A A; Bajic, Vladimir B.; Stingl, Ulrich

2014-01-01

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.

Science.gov (United States)

Kamanda Ngugi, David; Blom, Jochen; Alam, Intikhab; Rashid, Mamoon; Ba-Alawi, Wail; Zhang, Guishan; Hikmawan, Tyas; Guan, Yue; Antunes, Andre; Siam, Rania; El Dorry, Hamza; Bajic, Vladimir; Stingl, Ulrich

2015-02-01

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

Comparing Postural Stability Entropy Analyses to Differentiate Fallers and Non-fallers.

Science.gov (United States)

Fino, Peter C; Mojdehi, Ahmad R; Adjerid, Khaled; Habibi, Mohammad; Lockhart, Thurmon E; Ross, Shane D

2016-05-01

The health and financial cost of falls has spurred research to differentiate the characteristics of fallers and non-fallers. Postural stability has received much of the attention with recent studies exploring various measures of entropy. This study compared the discriminatory ability of several entropy methods at differentiating two paradigms in the center-of-pressure of elderly individuals: (1) eyes open (EO) vs. eyes closed (EC) and (2) fallers (F) vs. non-fallers (NF). Methods were compared using the area under the curve (AUC) of the receiver-operating characteristic curves developed from logistic regression models. Overall, multiscale entropy (MSE) and composite multiscale entropy (CompMSE) performed the best with AUCs of 0.71 for EO/EC and 0.77 for F/NF. When methods were combined together to maximize the AUC, the entropy classifier had an AUC of for 0.91 the F/NF comparison. These results suggest researchers and clinicians attempting to create clinical tests to identify fallers should consider a combination of every entropy method when creating a classifying test. Additionally, MSE and CompMSE classifiers using polar coordinate data outperformed rectangular coordinate data, encouraging more research into the most appropriate time series for postural stability entropy analysis.

A Simple, Reliable Precision Time Analyser

Energy Technology Data Exchange (ETDEWEB)

Joshi, B. V.; Nargundkar, V. R.; Subbarao, K.; Kamath, M. S.; Eligar, S. K. [Atomic Energy Establishment Trombay, Bombay (India)

1966-06-15

A 30-channel time analyser is described. The time analyser was designed and built for pulsed neutron research but can be applied to other uses. Most of the logic is performed by means of ferrite memory core and transistor switching circuits. This leads to great versatility, low power consumption, extreme reliability and low cost. The analyser described provides channel Widths from 10 {mu}s to 10 ms; arbitrarily wider channels are easily obtainable. It can handle counting rates up to 2000 counts/min in each channel with less than 1% dead time loss. There is a provision for an initial delay equal to 100 channel widths. An input pulse de-randomizer unit using tunnel diodes ensures exactly equal channel widths. A brief description of the principles involved in core switching circuitry is given. The core-transistor transfer loop is compared with the usual core-diode loops and is shown to be more versatile and better adapted to the making of a time analyser. The circuits derived from the basic loop are described. These include the scale of ten, the frequency dividers and the delay generator. The current drivers developed for driving the cores are described. The crystal-controlled clock which controls the width of the time channels and synchronizes the operation of the various circuits is described. The detector pulse derandomizer unit using tunnel diodes is described. The scheme of the time analyser is then described showing how the various circuits can be integrated together to form a versatile time analyser. (author)

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

Science.gov (United States)

Leaché, Adam D.; Chavez, Andreas S.; Jones, Leonard N.; Grummer, Jared A.; Gottscho, Andrew D.; Linkem, Charles W.

2015-01-01

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus. PMID:25663487

Review of radionuclide source terms used for performance-assessment analyses

International Nuclear Information System (INIS)

Barnard, R.W.

1993-06-01

Two aspects of the radionuclide source terms used for total-system performance assessment (TSPA) analyses have been reviewed. First, a detailed radionuclide inventory (i.e., one in which the reactor type, decay, and burnup are specified) is compared with the standard source-term inventory used in prior analyses. The latter assumes a fixed ratio of pressurized-water reactor (PWR) to boiling-water reactor (BWR) spent fuel, at specific amounts of burnup and at 10-year decay. TSPA analyses have been used to compare the simplified source term with the detailed one. The TSPA-91 analyses did not show a significant difference between the source terms. Second, the radionuclides used in source terms for TSPA aqueous-transport analyses have been reviewed to select ones that are representative of the entire inventory. It is recommended that two actinide decay chains be included (the 4n+2 ''uranium'' and 4n+3 ''actinium'' decay series), since these include several radionuclides that have potentially important release and dose characteristics. In addition, several fission products are recommended for the same reason. The choice of radionuclides should be influenced by other parameter assumptions, such as the solubility and retardation of the radionuclides

How narrow-band and broad-band uvb irradiation influences the immunohistochemistry analyses of experimental animals’ skin – a comparative study. Part II

Directory of Open Access Journals (Sweden)

Katarzyna Borowska

2017-09-01

Full Text Available This is the second part of the artcle series impact narrow-band UVB radiation (NB-UVB and broad-band UVB radiation (BB-UVB on experimental animals’ skin (white Wistar female rats. The aim of this comparative study was immunohistochemistry analyses containing expression of p53 protein. Expression of p53 protein was performed on two experimental groups. One – exposed to NB-UVB; the other – exposed to BB-UVB radiation. The results indicate that p53 protein takes an active part in the process of apoptosis that is induced by both NB-UVB and BB-UVB. The results showed an increase in p53 expressing cells following BB-UVB than NB-UVB phototherapy.

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

Science.gov (United States)

Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

2017-01-01

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach

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González, Vanessa L.; Bieler, Rüdiger; Giribet, Gonzalo

2016-01-01

Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix (Matrix 3: 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea. PMID:27358369

Comparative accident analyses for a KONVOI-type PWR using the integral codes ASTEC V1.33 and MELCOR 1.8.6

International Nuclear Information System (INIS)

Reinke, Nils; Erdmann, Walter; Nowack, Holger; Sonnenkalb, Martin

2010-08-01

In the frame of the project RS1180 funded by the German Federal Ministry for Economics and Technology (BMWi) calculations have been carried out with the integral code ASTEC V1.33 p3 developed by GRS for two postulated accidents in a nuclear power plant with KONVOI type a pressurized water reactor and compared to calculations with MELCOR 1.8.6 YU. Major objective was to assess the capability of ASTEC for application in level 2 probabilistic safety analyses (PSA). In particular, it was investigated to which extent ASTEC is able to perform such integral calculations meeting criteria with regard to both reasonable calculation time and specific boundary conditions necessary for PSA analyses. Two exemplary accidents were selected: - A transient with loss of steam generator feed water, - A small break loss of coolant accident (50 cm 2 ) in the cold leg of the coolant line connected to the pressurizer. In principle, the results demonstrate the capability of ASTEC V1.33 to carry out such PSA level 2 calculations. In addition, it has to be noted that for both ASTEC and MELCOR the requirements in view of the quality of the results leads to prolonged calculation times due to more detailed nodalisations of the whole plant. This is valid for the core region as well as for the primary circuit and for the containment. Consequently, calculation times in the order of one day to two weeks are accomplished, thereby excluding extensive parameter analyses in order to assess the sensitivity of the calculation results. Concerning the quality of the results a good agreement can be stated between ASTEC and MELCOR results in terms of global data. In detail some results are sensitive to user effects. Here, the nodalisation seems to be of major influence besides differences in modeling specific phenomena. The comparison suggests that in particular the influence of the nodalisation defined by the user and depending on the user's experience should be carefully evaluated. Since some

Distinctive Architecture of the Chloroplast Genome in the Chlorodendrophycean Green Algae Scherffelia dubia and Tetraselmis sp. CCMP 881.

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Turmel, Monique; de Cambiaire, Jean-Charles; Otis, Christian; Lemieux, Claude

2016-01-01

The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.

Co-diversification of Enterococcus faecium core genomes and PBP5: evidences of pbp5 horizontal transfer

Directory of Open Access Journals (Sweden)

Carla Novais

2016-10-01

Full Text Available Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18 and ST78 in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180-280 kb chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.

Analyses of MHD instabilities

International Nuclear Information System (INIS)

Takeda, Tatsuoki

1985-01-01

In this article analyses of the MHD stabilities which govern the global behavior of a fusion plasma are described from the viewpoint of the numerical computation. First, we describe the high accuracy calculation of the MHD equilibrium and then the analysis of the linear MHD instability. The former is the basis of the stability analysis and the latter is closely related to the limiting beta value which is a very important theoretical issue of the tokamak research. To attain a stable tokamak plasma with good confinement property it is necessary to control or suppress disruptive instabilities. We, next, describe the nonlinear MHD instabilities which relate with the disruption phenomena. Lastly, we describe vectorization of the MHD codes. The above MHD codes for fusion plasma analyses are relatively simple though very time-consuming and parts of the codes which need a lot of CPU time concentrate on a small portion of the codes, moreover, the codes are usually used by the developers of the codes themselves, which make it comparatively easy to attain a high performance ratio on the vector processor. (author)

Cloning, characterisation, and comparative quantitative expression analyses of receptor for advanced glycation end products (RAGE) transcript forms.

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Sterenczak, Katharina A; Willenbrock, Saskia; Barann, Matthias; Klemke, Markus; Soller, Jan T; Eberle, Nina; Nolte, Ingo; Bullerdiek, Jörn; Murua Escobar, Hugo

2009-04-01

RAGE is a member of the immunoglobulin superfamily of cell surface molecules playing key roles in pathophysiological processes, e.g. immune/inflammatory disorders, Alzheimer's disease, diabetic arteriosclerosis and tumourigenesis. In humans 19 naturally occurring RAGE splicing variants resulting in either N-terminally or C-terminally truncated proteins were identified and are lately discussed as mechanisms for receptor regulation. Accordingly, deregulation of sRAGE levels has been associated with several diseases e.g. Alzheimer's disease, Type 1 diabetes, and rheumatoid arthritis. Administration of recombinant sRAGE to animal models of cancer blocked tumour growth successfully. In spite of its obvious relationship to cancer and metastasis data focusing sRAGE deregulation and tumours is rare. In this study we screened a set of tumours, healthy tissues and various cancer cell lines for RAGE splicing variants and analysed their structure. Additionally, we analysed the ratio of the mainly found transcript variants using quantitative Real-Time PCR. In total we characterised 24 previously not described canine and 4 human RAGE splicing variants, analysed their structure, classified their characteristics, and derived their respective protein forms. Interestingly, the healthy and the neoplastic tissue samples showed in majority RAGE transcripts coding for the complete receptor and transcripts showing insertions of intron 1.

Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics.

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Bourguignon, Thomas; Tang, Qian; Ho, Simon Y W; Juna, Frantisek; Wang, Zongqing; Arab, Daej A; Cameron, Stephen L; Walker, James; Rentz, David; Evans, Theodore A; Lo, Nathan

2017-04-01

Following the acceptance of plate tectonics theory in the latter half of the 20th century, vicariance became the dominant explanation for the distributions of many plant and animal groups. In recent years, however, molecular-clock analyses have challenged a number of well-accepted hypotheses of vicariance. As a widespread group of insects with a fossil record dating back 300 My, cockroaches provide an ideal model for testing hypotheses of vicariance through plate tectonics versus transoceanic dispersal. However, their evolutionary history remains poorly understood, in part due to unresolved relationships among the nine recognized families. Here, we present a phylogenetic estimate of all extant cockroach families, as well as a timescale for their evolution, based on the complete mitochondrial genomes of 119 cockroach species. Divergence dating analyses indicated that the last common ancestor of all extant cockroaches appeared ∼235 Ma, ∼95 My prior to the appearance of fossils that can be assigned to extant families, and before the breakup of Pangaea began. We reconstructed the geographic ranges of ancestral cockroaches and found tentative support for vicariance through plate tectonics within and between several major lineages. We also found evidence of transoceanic dispersal in lineages found across the Australian, Indo-Malayan, African, and Madagascan regions. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these insects.

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology.

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Yuan, Zhaohe; Fang, Yanming; Zhang, Taikui; Fei, Zhangjun; Han, Fengming; Liu, Cuiyu; Liu, Min; Xiao, Wei; Zhang, Wenjing; Wu, Shan; Zhang, Mengwei; Ju, Youhui; Xu, Huili; Dai, He; Liu, Yujun; Chen, Yanhui; Wang, Lili; Zhou, Jianqing; Guan, Dian; Yan, Ming; Xia, Yanhua; Huang, Xianbin; Liu, Dongyuan; Wei, Hongmin; Zheng, Hongkun

2017-12-22

Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Comparative analyses of forest fuels in a life cycle perspective with a focus on transport systems

Energy Technology Data Exchange (ETDEWEB)

Eriksson, Lisa Naeslund [Ecotechnology, Department of Engineering, Physics and Mathematics, Mid Sweden University, SE-831 25 Oestersund (Sweden)

2008-08-15

Local, national and international transportation of forest fuels with regard to costs, primary energy use and CO{sub 2} emission was analysed. The main issue was the extent to which both mode and distance of transport affect the monetary cost, CO{sub 2} emission and primary energy use arising from the use of various types of forest residues for energy purpose. Local applications proved the most efficient options of those studied. Chipping of bundles at a terminal, for transport by rail and sea to national or international end-users, has low costs and produces only modest CO{sub 2} emissions. For the pellet options, the cost is about the same as for chipping, but require more primary energy and emit more CO{sub 2}. The traditional chipping system is more expensive than the other options. The costs of the international options over a transport distance of 1100 km vary between 21 and 28 EUR{sub 2007}/MWh, whereas pellet options cost between 22 and 25 EUR{sub 2007}/MWh. The primary energy required for transport of logging residues vis-a-vis pellets falls in the range 4-7% and 2-4%, respectively, of the bio-energy delivered. The primary energy needed to produce pellets gives them a lower fossil fuel substitution rate per hectare, compared with bundle systems. Similarly, for chip systems vis-a-vis bundle systems, the biomass delivered to the conversion plant is reduced by the greater physical dry-matter losses entailed by chipping systems in the forest-fuel chain. (author)

Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats

Science.gov (United States)

Zhang, Nan; Yang, Dongqing; Kendall, Joshua R. A.; Borriss, Rainer; Druzhinina, Irina S.; Kubicek, Christian P.; Shen, Qirong; Zhang, Ruifu

2016-01-01

Bacillus subtilis and its sister species B. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. Many of these strains are used as plant growth-promoting rhizobacteria (PGPR) in agriculture and a plant-specialized subspecies of B. amyloliquefaciens—B. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: B. amyloliquefaciens NJN-6 isolated from Musa sp. (banana) and B. subtilis HJ5 from Gossypium sp. (cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in different niches. Phylogenomic analysis indicated that strains isolated from plant-associated (PA) habitats could be distinguished from those from non-plant-associated (nPA) niches in both species. The core genomes of PA strains are more abundant in genes relevant to intermediary metabolism and secondary metabolites biosynthesis as compared with those of nPA strains, and they also possess additional specific genes involved in utilization of plant-derived substrates and synthesis of antibiotics. A further gene gain/loss analysis indicated that only a few of these specific genes (18/192 for B. amyloliquefaciens and 53/688 for B. subtilis) were acquired by PA strains at the initial divergence event, but most were obtained successively by different subgroups of PA stains during the evolutional process. This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production. PMID:28066362

Comparative proteomic analyses reveal that FlbA down-regulates gliT expression and SOD activity in Aspergillus fumigatus.

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Shin, Kwang-Soo; Park, Hee-Soo; Kim, Young-Hwan; Yu, Jae-Hyuk

2013-07-11

FlbA is a regulator of G-protein signaling protein that plays a central role in attenuating heterotrimeric G-protein mediated vegetative growth signaling in Aspergillus. The deletion of flbA (∆flbA) in the opportunistic human pathogen Aspergillus fumigatus results in accelerated cell death and autolysis in submerged culture. To further investigate the effects of ∆flbA on intracellular protein levels we carried out 2-D proteome analyses of 2-day old submerged cultures of ∆flbA and wild type (WT) strains and observed 160 differentially expressed proteins. Via nano-LC-ESI-MS/MS analyses, we revealed the identity of 10 and 2 proteins exhibiting high and low level accumulation, respectively, in ∆flbA strain. Notably, the GliT protein is accumulated at about 1800-fold higher levels in ∆flbA than WT. Moreover, GliT is secreted at high levels from ∆flbA strain, whereas Sod1 (superoxide dismutase) is secreted at a higher level in WT. Northern blot analyses reveal that ∆flbA results in elevated accumulation of gliT mRNA. Consequently, ∆flbA strain exhibits enhanced tolerance to gliotoxin toxicity. Finally, ∆flbA strain displayed enhanced SOD activity and elevated resistance to menadione and paraquat. In summary, FlbA-mediated signaling control negatively affects cellular responses associated with detoxification of reactive oxygen species and of exogenous gliotoxin in A. fumigatus. Regulator of G protein Signaling (RGS) proteins play crucial roles in fundamental biological processes in filamentous fungi. FlbA is the first studied filamentous fungal RGS protein, yet much remains to be understood about its roles in the opportunistic human pathogen Aspergillus fumigatus. In the present study, we examined the effects of the deletion of flbA using comprehensive analyses of the intra- and extracellular proteomes of A. fumigatus wild type and the flbA deletion mutant. Via MS analyses, we identified 10 proteins exhibiting high level accumulation in the flbA deletion

Reliability and vulnerability analyses of critical infrastructures: Comparing two approaches in the context of power systems

International Nuclear Information System (INIS)

Johansson, Jonas; Hassel, Henrik; Zio, Enrico

2013-01-01

Society depends on services provided by critical infrastructures, and hence it is important that they are reliable and robust. Two main approaches for gaining knowledge required for designing and improving critical infrastructures are reliability analysis and vulnerability analysis. The former analyses the ability of the system to perform its intended function; the latter analyses its inability to withstand strains and the effects of the consequent failures. The two approaches have similarities but also some differences with respect to what type of information they generate about the system. In this view, the main purpose of this paper is to discuss and contrast these approaches. To strengthen the discussion and exemplify its findings, a Monte Carlo-based reliability analysis and a vulnerability analysis are considered in their application to a relatively simple, but representative, system the IEEE RTS96 electric power test system. The exemplification reveals that reliability analysis provides a good picture of the system likely behaviour, but fails to capture a large portion of the high consequence scenarios, which are instead captured in the vulnerability analysis. Although these scenarios might be estimated to have small probabilities of occurrence, they should be identified, considered and treated cautiously, as probabilistic analyses should not be the only input to decision-making for the design and protection of critical infrastructures. The general conclusion that can be drawn from the findings of the example is that vulnerability analysis should be used to complement reliability studies, as well as other forms of probabilistic risk analysis. Measures should be sought for reducing both the vulnerability, i.e. improving the system ability to withstand strains and stresses, and the reliability, i.e. improving the likely behaviour

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

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Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

2018-01-01

Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing

Comparative analyses of plastid sequences between native and introduced populations of aquatic weeds Elodea canadensis and E. nuttallii.

Directory of Open Access Journals (Sweden)

Tea Huotari

Full Text Available Non-indigenous species (NIS are species living outside their historic or native range. Invasive NIS often cause severe environmental impacts, and may have large economical and social consequences. Elodea (Hydrocharitaceae is a New World genus with at least five submerged aquatic angiosperm species living in fresh water environments. Our aim was to survey the geographical distribution of cpDNA haplotypes within the native and introduced ranges of invasive aquatic weeds Elodea canadensis and E. nuttallii and to reconstruct the spreading histories of these invasive species. In order to reveal informative chloroplast (cp genome regions for phylogeographic analyses, we compared the plastid sequences of native and introduced individuals of E. canadensis. In total, we found 235 variable sites (186 SNPs, 47 indels and two inversions between the two plastid sequences consisting of 112,193 bp and developed primers flanking the most variable genomic areas. These 29 primer pairs were used to compare the level and pattern of intraspecific variation within E. canadensis to interspecific variation between E. canadensis and E. nuttallii. Nine potentially informative primer pairs were used to analyze the phylogeographic structure of both Elodea species, based on 70 E. canadensis and 25 E. nuttallii individuals covering native and introduced distributions. On the whole, the level of variation between the two Elodea species was 53% higher than that within E. canadensis. In our phylogeographic analysis, only a single haplotype was found in the introduced range in both species. These haplotypes H1 (E. canadensis and A (E. nuttallii were also widespread in the native range, covering the majority of native populations analyzed. Therefore, we were not able to identify either the geographic origin of the introduced populations or test the hypothesis of single versus multiple introductions. The divergence between E. canadensis haplotypes was surprisingly high, and future

Comparative analyses of plastid sequences between native and introduced populations of aquatic weeds Elodea canadensis and E. nuttallii.

Science.gov (United States)

Huotari, Tea; Korpelainen, Helena

2013-01-01

Non-indigenous species (NIS) are species living outside their historic or native range. Invasive NIS often cause severe environmental impacts, and may have large economical and social consequences. Elodea (Hydrocharitaceae) is a New World genus with at least five submerged aquatic angiosperm species living in fresh water environments. Our aim was to survey the geographical distribution of cpDNA haplotypes within the native and introduced ranges of invasive aquatic weeds Elodea canadensis and E. nuttallii and to reconstruct the spreading histories of these invasive species. In order to reveal informative chloroplast (cp) genome regions for phylogeographic analyses, we compared the plastid sequences of native and introduced individuals of E. canadensis. In total, we found 235 variable sites (186 SNPs, 47 indels and two inversions) between the two plastid sequences consisting of 112,193 bp and developed primers flanking the most variable genomic areas. These 29 primer pairs were used to compare the level and pattern of intraspecific variation within E. canadensis to interspecific variation between E. canadensis and E. nuttallii. Nine potentially informative primer pairs were used to analyze the phylogeographic structure of both Elodea species, based on 70 E. canadensis and 25 E. nuttallii individuals covering native and introduced distributions. On the whole, the level of variation between the two Elodea species was 53% higher than that within E. canadensis. In our phylogeographic analysis, only a single haplotype was found in the introduced range in both species. These haplotypes H1 (E. canadensis) and A (E. nuttallii) were also widespread in the native range, covering the majority of native populations analyzed. Therefore, we were not able to identify either the geographic origin of the introduced populations or test the hypothesis of single versus multiple introductions. The divergence between E. canadensis haplotypes was surprisingly high, and future research may

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Science.gov (United States)

Wrzeszczynski, Kazimierz O; Frank, Mayu O; Koyama, Takahiko; Rhrissorrakrai, Kahn; Robine, Nicolas; Utro, Filippo; Emde, Anne-Katrin; Chen, Bo-Juen; Arora, Kanika; Shah, Minita; Vacic, Vladimir; Norel, Raquel; Bilal, Erhan; Bergmann, Ewa A; Moore Vogel, Julia L; Bruce, Jeffrey N; Lassman, Andrew B; Canoll, Peter; Grommes, Christian; Harvey, Steve; Parida, Laxmi; Michelini, Vanessa V; Zody, Michael C; Jobanputra, Vaidehi; Royyuru, Ajay K; Darnell, Robert B

2017-08-01

To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs. More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts. The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible. NCT02725684.

Working regime identification for natural circulation loops by comparative thermalhydraulic analyses with three fluids under identical operating conditions

International Nuclear Information System (INIS)

Sarkar, Milan K.S.; Basu, Dipankar N.

2015-01-01

Highlights: • Thermalhydraulic analyses of NCL to justify the use of supercritical condition. • Mass flow rate of supercritical loop increases with heater power till a maxima. • Supercritical loop suffer from HTD beyond the maxima with jump in fluid temperature. • HTD is pronounced at higher sink temperatures and pressures just above critical. • Supercritical CO_2 is preferred fluid till the HTD and single-phase water afterwards. - Abstract: Computational investigation for comparative thermalhydraulic analyses of rectangular natural circulation loops is performed to propose a guideline for selecting the working fluid and nature of the loop, subcritical or supercritical, under identical levels of operating parameters like pressure, heating power and coolant temperature. A 3-d uniform-diameter loop geometry is developed with horizontal heating and cooling. Heating is provided in constant heat flux mode, whereas cooling is through a constant temperature sink. Due to favourable thermophysical properties and environmental conformity, water, CO_2 and R134a are selected as possible working fluids. Operational parameters are set so as to have sub- to supercritical condition for CO_2, supercritical for R134a and single-phase liquid for water. Mass flow rate for supercritical fluid rapidly increases with heater power, when the fluid is allowed to cross the pseudocritical point during its passage through the heater, and exhibits a maxima. Drastic fall in mass flow rate can be observed beyond the maxima, accompanied by a jump in maximum fluid temperature and a rapid decline in sink-side heat transfer coefficient. That can be identified as heat transfer deterioration in supercritical natural circulation loops, a highly undesirable situation from loop safety point of view. Allowable working range of heater power can be enhanced by increasing system pressure and decreasing sink temperature. For any specified set of operating conditions, CO_2-based supercritical loops

Working regime identification for natural circulation loops by comparative thermalhydraulic analyses with three fluids under identical operating conditions

Energy Technology Data Exchange (ETDEWEB)

Sarkar, Milan K.S.; Basu, Dipankar N., E-mail: dipankar.n.basu@gmail.com

2015-11-15

Highlights: • Thermalhydraulic analyses of NCL to justify the use of supercritical condition. • Mass flow rate of supercritical loop increases with heater power till a maxima. • Supercritical loop suffer from HTD beyond the maxima with jump in fluid temperature. • HTD is pronounced at higher sink temperatures and pressures just above critical. • Supercritical CO{sub 2} is preferred fluid till the HTD and single-phase water afterwards. - Abstract: Computational investigation for comparative thermalhydraulic analyses of rectangular natural circulation loops is performed to propose a guideline for selecting the working fluid and nature of the loop, subcritical or supercritical, under identical levels of operating parameters like pressure, heating power and coolant temperature. A 3-d uniform-diameter loop geometry is developed with horizontal heating and cooling. Heating is provided in constant heat flux mode, whereas cooling is through a constant temperature sink. Due to favourable thermophysical properties and environmental conformity, water, CO{sub 2} and R134a are selected as possible working fluids. Operational parameters are set so as to have sub- to supercritical condition for CO{sub 2}, supercritical for R134a and single-phase liquid for water. Mass flow rate for supercritical fluid rapidly increases with heater power, when the fluid is allowed to cross the pseudocritical point during its passage through the heater, and exhibits a maxima. Drastic fall in mass flow rate can be observed beyond the maxima, accompanied by a jump in maximum fluid temperature and a rapid decline in sink-side heat transfer coefficient. That can be identified as heat transfer deterioration in supercritical natural circulation loops, a highly undesirable situation from loop safety point of view. Allowable working range of heater power can be enhanced by increasing system pressure and decreasing sink temperature. For any specified set of operating conditions, CO{sub 2}-based

New Insights into the Diversity of the Genus Faecalibacterium

Directory of Open Access Journals (Sweden)

Leandro Benevides

2017-09-01

Full Text Available Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST, Average Nucleotide Identity (ANI, gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters—A, B, and C—composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach

Comparative trials in registration files of cardiovascular drugs : Comparator drugs and dosing schemes.

NARCIS (Netherlands)

Wieringa, NF; Vos, R; de Graeff, PA

Registration files of 13 cardiovascular drugs were analysed with respect to the number of double-blind phase-III clinical trials, the use of placebo and active comparator drugs and their dosing schemes. Half of the 146 double-blind trials used active comparator drugs. The majority of files included

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

Science.gov (United States)

Kamanda Ngugi, David; Blom, Jochen; Alam, Intikhab; Rashid, Mamoon; Ba-Alawi, Wail; Zhang, Guishan; Hikmawan, Tyas; Guan, Yue; Antunes, Andre; Siam, Rania; El Dorry, Hamza; Bajic, Vladimir; Stingl, Ulrich

2015-01-01

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate ‘switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA. PMID:25105904

Comparative analyses of microbial structures and gene copy numbers in the anaerobic digestion of various types of sewage sludge.

Science.gov (United States)

Hidaka, Taira; Tsushima, Ikuo; Tsumori, Jun

2018-04-01

Anaerobic co-digestion of various sewage sludges is a promising approach for greater recovery of energy, but the process is more complicated than mono-digestion of sewage sludge. The applicability of microbial structure analyses and gene quantification to understand microbial conditions was evaluated. The results show that information from gene analyses is useful in managing anaerobic co-digestion and damaged microbes in addition to conventional parameters like total solids, pH and biogas production. Total bacterial 16S rRNA gene copy numbers are the most useful tools for evaluating unstable anaerobic digestion of sewage sludge, rather than mcrA and total archaeal 16S rRNA gene copy numbers, and high-throughput sequencing. First order decay rates of gene copy numbers during pH failure were higher than typical decay rates of microbes in stable operation. The sequencing analyses, including multidimensional scaling, showed very different microbial structure shifts, but the results were not consistent. Copyright © 2017 Elsevier Ltd. All rights reserved.

Value of MR histogram analyses for prediction of microvascular invasion of hepatocellular carcinoma.

Science.gov (United States)

Huang, Ya-Qin; Liang, He-Yue; Yang, Zhao-Xia; Ding, Ying; Zeng, Meng-Su; Rao, Sheng-Xiang

2016-06-01

The objective is to explore the value of preoperative magnetic resonance (MR) histogram analyses in predicting microvascular invasion (MVI) of hepatocellular carcinoma (HCC).Fifty-one patients with histologically confirmed HCC who underwent diffusion-weighted and contrast-enhanced MR imaging were included. Histogram analyses were performed and mean, variance, skewness, kurtosis, 1th, 10th, 50th, 90th, and 99th percentiles were derived. Quantitative histogram parameters were compared between HCCs with and without MVI. Receiver operating characteristics (ROC) analyses were generated to compare the diagnostic performance of tumor size, histogram analyses of apparent diffusion coefficient (ADC) maps, and MR enhancement.The mean, 1th, 10th, and 50th percentiles of ADC maps, and the mean, variance. 1th, 10th, 50th, 90th, and 99th percentiles of the portal venous phase (PVP) images were significantly different between the groups with and without MVI (P histogram analyses-in particular for 1th percentile for PVP images-held promise for prediction of MVI of HCC.

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

Science.gov (United States)

Svartström, Olov; Alneberg, Johannes; Terrapon, Nicolas; Lombard, Vincent; de Bruijn, Ino; Malmsten, Jonas; Dalin, Ann-Marie; Muller, Emilie E.L.; Shah, Pranjul; Wilmes, Paul; Henrissat, Bernard; Aspeborg, Henrik; Andersson, Anders F.

2017-01-01

The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to eleven prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes, and were overall overrepresented in the moose microbiome compared to other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci (PULs), which has never been reported before. The almost one hundred CAZyme-annotated genomes reconstructed in this study provides an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries. PMID:28731473

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

Science.gov (United States)

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

2018-02-28

To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided

Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

International Nuclear Information System (INIS)

Bao, Guanhui; Dong, Hongjun; Zhu, Yan; Mao, Shaoming; Zhang, Tianrui; Zhang, Yanping; Chen, Zugen; Li, Yin

2014-01-01

Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance

Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

Energy Technology Data Exchange (ETDEWEB)

Bao, Guanhui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); University of Chinese Academy of Sciences, Beijing (China); Dong, Hongjun; Zhu, Yan; Mao, Shaoming [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Zhang, Tianrui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin (China); Zhang, Yanping [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Chen, Zugen [Department of Human Genetics, School of Medicine, University of California, Los Angeles, CA 90095 (United States); Li, Yin, E-mail: yli@im.ac.cn [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China)

2014-08-08

Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance.

Finite element analyses of a linear-accelerator electron gun

Science.gov (United States)

Iqbal, M.; Wasy, A.; Islam, G. U.; Zhou, Z.

2014-02-01

Thermo-structural analyses of the Beijing Electron-Positron Collider (BEPCII) linear-accelerator, electron gun, were performed for the gun operating with the cathode at 1000 °C. The gun was modeled in computer aided three-dimensional interactive application for finite element analyses through ANSYS workbench. This was followed by simulations using the SLAC electron beam trajectory program EGUN for beam optics analyses. The simulations were compared with experimental results of the assembly to verify its beam parameters under the same boundary conditions. Simulation and test results were found to be in good agreement and hence confirmed the design parameters under the defined operating temperature. The gun is operating continuously since commissioning without any thermal induced failures for the BEPCII linear accelerator.

Finite element analyses of a linear-accelerator electron gun

Energy Technology Data Exchange (ETDEWEB)

Iqbal, M., E-mail: muniqbal.chep@pu.edu.pk, E-mail: muniqbal@ihep.ac.cn [Centre for High Energy Physics, University of the Punjab, Lahore 45590 (Pakistan); Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Wasy, A. [Department of Mechanical Engineering, Changwon National University, Changwon 641773 (Korea, Republic of); Islam, G. U. [Centre for High Energy Physics, University of the Punjab, Lahore 45590 (Pakistan); Zhou, Z. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)

2014-02-15

Thermo-structural analyses of the Beijing Electron-Positron Collider (BEPCII) linear-accelerator, electron gun, were performed for the gun operating with the cathode at 1000 °C. The gun was modeled in computer aided three-dimensional interactive application for finite element analyses through ANSYS workbench. This was followed by simulations using the SLAC electron beam trajectory program EGUN for beam optics analyses. The simulations were compared with experimental results of the assembly to verify its beam parameters under the same boundary conditions. Simulation and test results were found to be in good agreement and hence confirmed the design parameters under the defined operating temperature. The gun is operating continuously since commissioning without any thermal induced failures for the BEPCII linear accelerator.

Finite element analyses of a linear-accelerator electron gun

International Nuclear Information System (INIS)

Iqbal, M.; Wasy, A.; Islam, G. U.; Zhou, Z.

2014-01-01

Thermo-structural analyses of the Beijing Electron-Positron Collider (BEPCII) linear-accelerator, electron gun, were performed for the gun operating with the cathode at 1000 °C. The gun was modeled in computer aided three-dimensional interactive application for finite element analyses through ANSYS workbench. This was followed by simulations using the SLAC electron beam trajectory program EGUN for beam optics analyses. The simulations were compared with experimental results of the assembly to verify its beam parameters under the same boundary conditions. Simulation and test results were found to be in good agreement and hence confirmed the design parameters under the defined operating temperature. The gun is operating continuously since commissioning without any thermal induced failures for the BEPCII linear accelerator

GIS-based Approaches to Catchment Area Analyses of Mass Transit

DEFF Research Database (Denmark)

Andersen, Jonas Lohmann Elkjær; Landex, Alex

2009-01-01

Catchment area analyses of stops or stations are used to investigate potential number of travelers to public transportation. These analyses are considered a strong decision tool in the planning process of mass transit especially railroads. Catchment area analyses are GIS-based buffer and overlay...... analyses with different approaches depending on the desired level of detail. A simple but straightforward approach to implement is the Circular Buffer Approach where catchment areas are circular. A more detailed approach is the Service Area Approach where catchment areas are determined by a street network...... search to simulate the actual walking distances. A refinement of the Service Area Approach is to implement additional time resistance in the network search to simulate obstacles in the walking environment. This paper reviews and compares the different GIS-based catchment area approaches, their level...

Graphite analyser upgrade for the IRIS spectrometer at ISIS

International Nuclear Information System (INIS)

Campbell, S.I.; Telling, M.T.F.; Carlile, C.J.

1999-01-01

Complete text of publication follows. The pyrolytic graphite (PG) analyser bank on the IRIS high resolution inelastic spectrometer [1] at ISIS is to be upgraded. At present the analyser consists of 1350 graphite pieces (6 rows by 225 columns) cooled to 25K [2]. The new analyser array, however, will provide a three-fold increase in area and employ 4212 crystal pieces (18 rows by 234 columns). In addition, the graphite crystals will be cooled close to liquid helium temperature to further reduce thermal diffuse scattering (TDS) and improve the sensitivity of the spectrometer [2]. For an instrument such as IRIS, with its analyser in near back-scattering geometry, optical aberration and variation in the time-of-flight of the analysed neutrons is introduced as one moves out from the horizontal scattering plane. To minimise such effects, the profile of the analyser array has been redesigned. The concept behind the design of the new analyser bank and factors that effect the overall resolution of the instrument are discussed. Results of Monte Carlo simulations of the expected resolution and intensity of the complete instrument are presented and compared to the current instrument performance. (author) [1] C.J. Carlile et al, Physica B 182 (1992) 431-440.; [2] C.J. Carlile et al, Nuclear Instruments and Methods In Physics Research A 338 (1994) 78-82

A tale of two phylogenies: comparative analyses of ecological interactions.

Science.gov (United States)

Hadfield, Jarrod D; Krasnov, Boris R; Poulin, Robert; Nakagawa, Shinichi

2014-02-01

The evolution of traits involved in ecological interactions such as predator-prey, host-parasite, and plant-pollinator interactions, are likely to be shaped by the phylogenetic history of both parties. We develop generalized linear mixed-effects models (GLMM) that estimate the effect of both parties' phylogenetic history on trait evolution, both in isolation but also in terms of how the two histories interact. Using data on the incidence and abundance of 206 flea species on 121 mammal species, we illustrate our method and compare it to previously used methods for detecting host-parasite coevolution. At large spatial scales we find that the phylogenetic interaction effect was substantial, indicating that related parasite species were more likely to be found on related host species. At smaller spatial scales, and when sampling effort was not controlled for, phylogenetic effects on the number and types of parasite species harbored by hosts were found to dominate. We go on to show that in situations where these additional phylogenetic effects exist, then previous methods have very high Type I error rates when testing for the phylogenetic interaction. Our GLMM method represents a robust and reliable approach to quantify the phylogenetic effects of traits determined by, or defined by, ecological interactions and has the advantage that it can easily be extended and interpreted in a broader context than existing permutation tests.

Seismic risk analyses in the German Risk Study, phase B

International Nuclear Information System (INIS)

Hosser, D.; Liemersdorf, H.

1991-01-01

The paper discusses some aspects of the seismic risk part of the German Risk Study for Nuclear Power Plants, Phase B. First simplified analyses in Phase A of the study allowed only a rough classification of structures and systems of the PWR reference plant according to their seismic risk contribution. These studies were extended in Phase B using improved models for the dynamic analyses of buildings, structures and components as well as for the probabilistic analyses of seismic loading, failure probabilities and event trees. The methodology of deriving probabilistic seismic load descriptions is explained and compared with the methods in Phase A of the study and in other studies. Some details of the linear and nonlinear dynamic analyses of structures are reported in order to demonstrate the influence of different assumptions for material behaviour and failure criteria. The probabilistic structural and event tree analyses are discussed with respect to distribution assumptions, acceptable simplifications and model uncertainties. Some results for the PWR reference plant are given. (orig.)

Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes.

Science.gov (United States)

Huotari, Tea; Korpelainen, Helena

2012-10-15

Elodea canadensis is an aquatic angiosperm native to North America. It has attracted great attention due to its invasive nature when transported to new areas in its non-native range. We have determined the complete nucleotide sequence of the chloroplast (cp) genome of Elodea. Taxonomically Elodea is a basal monocot, and only few monocot cp genomes representing early lineages of monocots have been sequenced so far. The genome is a circular double-stranded DNA molecule 156,700 bp in length, and has a typical structure with large (LSC 86,194 bp) and small (SSC 17,810 bp) single-copy regions separated by a pair of inverted repeats (IRs 26,348 bp each). The Elodea cp genome contains 113 unique genes and 16 duplicated genes in the IR regions. A comparative analysis showed that the gene order and organization of the Elodea cp genome is almost identical to that of Amborella trichopoda, a basal angiosperm. The structure of IRs in Elodea is unique among monocot species with the whole cp genome sequenced. In Elodea and another monocot Lemna minor the borders between IRs and LSC are located upstream of rps 19 gene and downstream of trnH-GUG gene, while in most monocots, IR has extended to include both trnH and rps 19 genes. A phylogenetic analysis conducted using Bayesian method, based on the DNA sequences of 81 chloroplast genes from 17 monocot taxa provided support for the placement of Elodea together with Lemna as a basal monocot and the next diverging lineage of monocots after Acorales. In comparison with other monocots, the Elodea cp genome has gone through only few rearrangements or gene losses. IR of Elodea has a unique structure among the monocot species studied so far as its structure is similar to that of a basal angiosperm Amborella. This result together with phylogenetic analyses supports the placement of Elodea as a basal monocot to the next diverging lineage of monocots after Acorales. So far, only few cp genomes representing early lineages of monocots have been

Analysing the Wrongness of Killing

DEFF Research Database (Denmark)

Di Nucci, Ezio

2014-01-01

This article provides an in-depth analysis of the wrongness of killing by comparing different versions of three influential views: the traditional view that killing is always wrong; the liberal view that killing is wrong if and only if the victim does not want to be killed; and Don Marquis‟ future...... of value account of the wrongness of killing. In particular, I illustrate the advantages that a basic version of the liberal view and a basic version of the future of value account have over competing alternatives. Still, ultimately none of the views analysed here are satisfactory; but the different...

Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy.

Science.gov (United States)

Sheng, Xihui; Wang, Ligang; Ni, Hemin; Wang, Lixian; Qi, Xiaolong; Xing, Shuhan; Guo, Yong

2016-01-01

The molecular mechanism regulated by microRNAs (miRNAs) that underlies postnatal hypertrophy of skeletal muscle is complex and remains unclear. Here, the miRNAomes of longissimus dorsi muscle collected at five postnatal stages (60, 120, 150, 180, and 210 days after birth) from Large White (commercial breed) and Min pigs (indigenous breed of China) were analyzed by Illumina sequencing. We identified 734 miRNAs comprising 308 annotated miRNAs and 426 novel miRNAs, of which 307 could be considered pig-specific. Comparative analysis between two breeds suggested that 60 and 120 days after birth were important stages for skeletal muscle hypertrophy and intramuscular fat accumulation. A total of 263 miRNAs were significantly differentially expressed between two breeds at one or more developmental stages. In addition, the differentially expressed miRNAs between every two adjacent developmental stages in each breed were determined. Notably, ssc-miR-204 was significantly more highly expressed in Min pig skeletal muscle at all postnatal stages compared with its expression in Large White pig skeletal muscle. Based on gene ontology and KEGG pathway analyses of its predicted target genes, we concluded that ssc-miR-204 may exert an impact on postnatal hypertrophy of skeletal muscle by regulating myoblast proliferation. The results of this study will help in elucidating the mechanism underlying postnatal hypertrophy of skeletal muscle modulated by miRNAs, which could provide valuable information for improvement of pork quality and human myopathy.

Soil microbial community structure in diverse land use systems:A comparative study using Biolog,DGGE,and PLFA analyses

Institute of Scientific and Technical Information of China (English)

XUE Dong; YAO Huai-Ying; GE De-Yong; HUANG Chang-Yong

2008-01-01

Biolog,16S rRNA gene denaturing gradient gel electrophoresis (DGGE),and phospholipid fatty acid (PLFA) analyses were used to assess soil microbial community characteristics in a chronosequence of tea garden systems (8-,50-,and 90year-old tea gardens),an adjacent wasteland,and a 90-year-old forest.Biolog analysis showed that the average well color development (AWCD) of all carbon sources and the functional diversity based on the Shannon index decreased (P＜0.05)in the following order:wasteland＞forest＞tea garden.For the DGGE analysis,the genetic diversity based on the Shannon index was significantly lower in the tea garden soils than in the wasteland.However,compared to the 90-year-old forest,the tea garden soils showed significantly higher genetic diversity.PLFA analysis showed that the ratio of Gram positive bacteria to Gram negative bacteria was significantly higher in the tea garden soils than in the wasteland,and the highest value was found in the 90-year-old forest.Both the fungal PLFA and the ratio of fungi to bacteria were significantly higher in the three tea garden soils than in the wasteland and forest,indicating that fungal PLFA was significantly affected by land-use change.Based on cluster analysis of the soil microbial community structure,all three analytical methods showed that land-use change had a greater effect on soil microbial community structure than tea garden age.

Comparative clinical effectiveness of management strategies for sciatica: systematic review and network meta-analyses.

Science.gov (United States)

Lewis, Ruth A; Williams, Nefyn H; Sutton, Alex J; Burton, Kim; Din, Nafees Ud; Matar, Hosam E; Hendry, Maggie; Phillips, Ceri J; Nafees, Sadia; Fitzsimmons, Deborah; Rickard, Ian; Wilkinson, Clare

2015-06-01

There are numerous treatment approaches for sciatica. Previous systematic reviews have not compared all these strategies together. To compare the clinical effectiveness of different treatment strategies for sciatica simultaneously. Systematic review and network meta-analysis. We searched 28 electronic databases and online trial registries, along with bibliographies of previous reviews for comparative studies evaluating any intervention to treat sciatica in adults, with outcome data on global effect or pain intensity. Network meta-analysis methods were used to simultaneously compare all treatment strategies and allow indirect comparisons of treatments between studies. The study was funded by the UK National Institute for Health Research Health Technology Assessment program; there are no potential conflict of interests. We identified 122 relevant studies; 90 were randomized controlled trials (RCTs) or quasi-RCTs. Interventions were grouped into 21 treatment strategies. Internal and external validity of included studies was very low. For overall recovery as the outcome, compared with inactive control or conventional care, there was a statistically significant improvement following disc surgery, epidural injections, nonopioid analgesia, manipulation, and acupuncture. Traction, percutaneous discectomy, and exercise therapy were significantly inferior to epidural injections or surgery. For pain as the outcome, epidural injections and biological agents were significantly better than inactive control, but similar findings for disc surgery were not statistically significant. Biological agents were significantly better for pain reduction than bed rest, nonopioids, and opioids. Opioids, education/advice alone, bed rest, and percutaneous discectomy were inferior to most other treatment strategies; although these findings represented large effects, they were statistically equivocal. For the first time, many different treatment strategies for sciatica have been compared in the

A case study of discordant overlapping meta-analyses: vitamin d supplements and fracture.

Directory of Open Access Journals (Sweden)

Mark J Bolland

Full Text Available BACKGROUND: Overlapping meta-analyses on the same topic are now very common, and discordant results often occur. To explore why discordant results arise, we examined a common topic for overlapping meta-analyses- vitamin D supplements and fracture. METHODS AND FINDINGS: We identified 24 meta-analyses of vitamin D (with or without calcium and fracture in a PubMed search in October 2013, and analysed a sample of 7 meta-analyses in the highest ranking general medicine journals. We used the AMSTAR tool to assess the quality of the meta-analyses, and compared their methodologies, analytic techniques and results. Applying the AMSTAR tool suggested the meta-analyses were generally of high quality. Despite this, there were important differences in trial selection, data extraction, and analytical methods that were only apparent after detailed assessment. 25 trials were included in at least one meta-analysis. Four meta-analyses included all eligible trials according to the stated inclusion and exclusion criteria, but the other 3 meta-analyses "missed" between 3 and 8 trials, and 2 meta-analyses included apparently ineligible trials. The relative risks used for individual trials differed between meta-analyses for total fracture in 10 of 15 trials, and for hip fracture in 6 of 12 trials, because of different outcome definitions and analytic approaches. The majority of differences (11/16 led to more favourable estimates of vitamin D efficacy compared to estimates derived from unadjusted intention-to-treat analyses using all randomised participants. The conclusions of the meta-analyses were discordant, ranging from strong statements that vitamin D prevents fractures to equally strong statements that vitamin D without calcium does not prevent fractures. CONCLUSIONS: Substantial differences in trial selection, outcome definition and analytic methods between overlapping meta-analyses led to discordant estimates of the efficacy of vitamin D for fracture prevention

Switching to olanzapine long-acting injection from either oral olanzapine or any other antipsychotic: comparative post hoc analyses

Directory of Open Access Journals (Sweden)

Ciudad A

2013-11-01

Full Text Available Antonio Ciudad,1 Ernie Anand,2 Lovisa Berggren,3 Marta Casillas,4 Alexander Schacht,3 Elena Perrin5 1Department of Clinical Research and Development, Eli Lilly & Co, Madrid, Spain; 2Neuroscience Medical Affairs – EU, Lilly Research Centre, Windlesham, Surrey, UK; 3Global Statistical Sciences, Eli Lilly & Co, Bad Homburg, Germany; 4European Scientific Communications, Eli Lilly & Co, Madrid, Spain; 5Medical Department, Eli Lilly & Co, Suresnes, Paris, France Background: A considerable proportion of patients suffering from schizophrenia show suboptimal responses to oral antipsychotics due to inadequate adherence. Hence, they are likely to benefit from switching to a long-acting injectable formulation. These post hoc analyses assessed the clinical effects of switching to olanzapine long-acting injection (OLAI from either oral olanzapine (OLZ or other antipsychotics (non-OLZ. Methods: Post hoc analyses were done based on two randomized studies (one short-term, one long-term conducted in patients suffering from schizophrenia and treated with OLAI. The short-term study was an 8-week placebo-controlled, double-blind trial in acute patients, and the long-term study was a 2-year, oral olanzapine-controlled, open-label, follow-up of stabilized outpatients. Results: These analyses used data from 62 OLAI-treated patients (12 switched from OLZ, 50 from non-OLZ from the short-term study and 190 OLAI-treated patients (56 switched from OLZ, 134 from non-OLZ from the long-term study. Kaplan–Meier survival analyses of time to all-cause discontinuation of OLAI treatment did not differ significantly between OLZ and non-OLZ patients in the short-term study (P=0.209 or long-term study (P=0.448. Similarly, the proportions of OLZ and non-OLZ patients that discontinued OLAI were not statistically different in the short-term (16.7% versus 36.0%, respectively; P=0.198 or long-term (57.1% versus 47.8% respectively; P=0.238 studies. In the short-term study, no

Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

Science.gov (United States)

Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

2018-04-16

Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

Comparative proteomic and metabolomic analyses reveal mechanisms of improved cold stress tolerance in bermudagrass (Cynodon dactylon (L.) Pers.) by exogenous calcium.

Science.gov (United States)

Shi, Haitao; Ye, Tiantian; Zhong, Bao; Liu, Xun; Chan, Zhulong

2014-11-01

As an important second messenger, calcium is involved in plant cold stress response, including chilling (Cynodon dactylon (L.) Pers.). Physiological analyses showed that CaCl2 treatment alleviated the reactive oxygen species (ROS) burst and cell damage triggered by chilling stress, via activating antioxidant enzymes, non-enzymatic glutathione antioxidant pool, while EGTA treatment had the opposite effects. Additionally, comparative proteomic analysis identified 51 differentially expressed proteins that were enriched in redox, tricarboxylicacid cycle, glycolysis, photosynthesis, oxidative pentose phosphate pathway, and amino acid metabolisms. Consistently, 42 metabolites including amino acids, organic acids, sugars, and sugar alcohols were regulated by CaCl2 treatment under control and cold stress conditions, further confirming the common modulation of CaCl2 treatment in carbon metabolites and amino acid metabolism. Taken together, this study reported first evidence of the essential and protective roles of endogenous and exogenous calcium in bermudagrass response to cold stress, partially via activation of the antioxidants and modulation of several differentially expressed proteins and metabolic homeostasis in the process of cold acclimation. © 2014 Institute of Botany, Chinese Academy of Sciences.

Environmental analyses of land transportation systems in The Netherlands

NARCIS (Netherlands)

Bouwman, Mirjan E.; Moll, Henri C.

Environmental analyses of the impact of transportation systems on the environment from the cradle to the grave are rare. This article makes a comparison of various Dutch passenger transportation systems by studying their complete life-cycle energy use. Moreover, systems are compared according to

Comparative modeling analyses of Cs-137 fate in the rivers impacted by Chernobyl and Fukushima accidents

Energy Technology Data Exchange (ETDEWEB)

Zheleznyak, M.; Kivva, S. [Institute of Environmental Radioactivity, Fukushima University (Japan)

2014-07-01

The consequences of two largest nuclear accidents of the last decades - at Chernobyl Nuclear Power Plant (ChNPP) (1986) and at Fukushima Daiichi NPP (FDNPP) (2011) clearly demonstrated that radioactive contamination of water bodies in vicinity of NPP and on the waterways from it, e.g., river- reservoir water after Chernobyl accident and rivers and coastal marine waters after Fukushima accident, in the both cases have been one of the main sources of the public concerns on the accident consequences. The higher weight of water contamination in public perception of the accidents consequences in comparison with the real fraction of doses via aquatic pathways in comparison with other dose components is a specificity of public perception of environmental contamination. This psychological phenomenon that was confirmed after these accidents provides supplementary arguments that the reliable simulation and prediction of the radionuclide dynamics in water and sediments is important part of the post-accidental radioecological research. The purpose of the research is to use the experience of the modeling activities f conducted for the past more than 25 years within the Chernobyl affected Pripyat River and Dnieper River watershed as also data of the new monitoring studies in Japan of Abukuma River (largest in the region - the watershed area is 5400 km{sup 2}), Kuchibuto River, Uta River, Niita River, Natsui River, Same River, as also of the studies on the specific of the 'water-sediment' {sup 137}Cs exchanges in this area to refine the 1-D model RIVTOX and 2-D model COASTOX for the increasing of the predictive power of the modeling technologies. The results of the modeling studies are applied for more accurate prediction of water/sediment radionuclide contamination of rivers and reservoirs in the Fukushima Prefecture and for the comparative analyses of the efficiency of the of the post -accidental measures to diminish the contamination of the water bodies. Document

Validation of a fully autonomous phosphate analyser based on a microfluidic lab-on-a-chip

DEFF Research Database (Denmark)

Slater, Conor; Cleary, J.; Lau, K.T.

2010-01-01

of long-term operation. This was proven by a bench top calibration of the analyser using standard solutions and also by comparing the analyser's performance to a commercially available phosphate monitor installed at a waste water treatment plant. The output of the microfluidic lab-on-a-chip analyser...

Evaluating Phylogenetic Congruence in the Post-Genomic Era

Science.gov (United States)

Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Science.gov (United States)

Bushley, Kathryn E.; Raja, Rajani; Jaiswal, Pankaj; Cumbie, Jason S.; Nonogaki, Mariko; Boyd, Alexander E.; Owensby, C. Alisha; Knaus, Brian J.; Elser, Justin; Miller, Daniel; Di, Yanming; McPhail, Kerry L.; Spatafora, Joseph W.

2013-01-01

The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role

Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis.

Science.gov (United States)

Teixeira, Marcus M; de Almeida, Luiz G P; Kubitschek-Barreira, Paula; Alves, Fernanda L; Kioshima, Erika S; Abadio, Ana K R; Fernandes, Larissa; Derengowski, Lorena S; Ferreira, Karen S; Souza, Rangel C; Ruiz, Jeronimo C; de Andrade, Nathalia C; Paes, Hugo C; Nicola, André M; Albuquerque, Patrícia; Gerber, Alexandra L; Martins, Vicente P; Peconick, Luisa D F; Neto, Alan Viggiano; Chaucanez, Claudia B; Silva, Patrícia A; Cunha, Oberdan L; de Oliveira, Fabiana F M; dos Santos, Tayná C; Barros, Amanda L N; Soares, Marco A; de Oliveira, Luciana M; Marini, Marjorie M; Villalobos-Duno, Héctor; Cunha, Marcel M L; de Hoog, Sybren; da Silveira, José F; Henrissat, Bernard; Niño-Vega, Gustavo A; Cisalpino, Patrícia S; Mora-Montes, Héctor M; Almeida, Sandro R; Stajich, Jason E; Lopes-Bezerra, Leila M; Vasconcelos, Ana T R; Felipe, Maria S S

2014-10-29

The fungal genus Sporothrix includes at least four human pathogenic species. One of these species, S. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in Brazil. Elsewhere, sapronoses are caused by S. schenckii and S. globosa. The major aims on this comparative genomic study are: 1) to explore the presence of virulence factors in S. schenckii and S. brasiliensis; 2) to compare S. brasiliensis, which is cat-transmitted and infects both humans and cats with S. schenckii, mainly a human pathogen; 3) to compare these two species to other human pathogens (Onygenales) with similar thermo-dimorphic behavior and to other plant-associated Sordariomycetes. The genomes of S. schenckii and S. brasiliensis were pyrosequenced to 17x and 20x coverage comprising a total of 32.3 Mb and 33.2 Mb, respectively. Pair-wise genome alignments revealed that the two species are highly syntenic showing 97.5% average sequence identity. Phylogenomic analysis reveals that both species diverged about 3.8-4.9 MYA suggesting a recent event of speciation. Transposable elements comprise respectively 0.34% and 0.62% of the S. schenckii and S. brasiliensis genomes and expansions of Gypsy-like elements was observed reflecting the accumulation of repetitive elements in the S. brasiliensis genome. Mitochondrial genomic comparisons showed the presence of group-I intron encoding homing endonucleases (HE's) exclusively in S. brasiliensis. Analysis of protein family expansions and contractions in the Sporothrix lineage revealed expansion of LysM domain-containing proteins, small GTPases, PKS type1 and leucin-rich proteins. In contrast, a lack of polysaccharide lyase genes that are associated with decay of plants was observed when compared to other Sordariomycetes and dimorphic fungal pathogens, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style. Comparative genomic data suggest a unique ecological shift in the

Next generation sequencing and comparative analyses of Xenopus mitogenomes

Directory of Open Access Journals (Sweden)

Lloyd Rhiannon E

2012-09-01

Full Text Available Abstract Background Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell’s major energy producing apparatus, the mitochondrial respiratory chain. Additonally, their nucleotide and amino acid sequences are of great utility as markers for systematics, molecular ecology and forensics. Their characterization through nucleotide sequencing is a fundamental starting point in mitogenomics. Methods to amplify complete mitochondrial genomes rapidly and efficiently from microgram quantities of tissue of single individuals are, however, not always available. Here we validate two approaches, which combine long-PCR with Roche 454 pyrosequencing technology, to obtain two complete mitochondrial genomes from individual amphibian species. Results We obtained two new xenopus frogs (Xenopus borealis and X. victorianus complete mitochondrial genome sequences by means of long-PCR followed by 454 of individual genomes (approach 1 or of multiple pooled genomes (approach 2, the mean depth of coverage per nucleotide was 9823 and 186, respectively. We also characterised and compared the new mitogenomes against their sister taxa; X. laevis and Silurana tropicalis, two of the most intensely studied amphibians. Our results demonstrate how our approaches can be used to obtain complete amphibian mitogenomes with depths of coverage that far surpass traditional primer-walking strategies, at either the same cost or less. Our results also demonstrate: that the size, gene content and order are the same among xenopus mitogenomes and that S. tropicalis form a separate clade to the other xenopus, among which X. laevis and X. victorianus were most closely related. Nucleotide and amino acid diversity was found to vary across the xenopus mitogenomes, with the greatest diversity observed in the Complex 1 gene nad4l and the least diversity observed in Complex 4 genes (cox1-3. All protein

Comparative Analyses of Physics Candidates Scores in West African and National Examinations Councils

Science.gov (United States)

Utibe, Uduak James; Agah, John Joseph

2015-01-01

The study is a comparative analysis of physics candidates' scores in West African and National Examinations Councils. It also investigates influence of gender. Results of 480 candidates were randomly selected form three randomly selected Senior Science Colleges using the WASSCE and NECOSSCE computer printout sent to the schools, transformed using…

Hydrogen-combustion analyses of large-scale tests

International Nuclear Information System (INIS)

Gido, R.G.; Koestel, A.

1986-01-01

This report uses results of the large-scale tests with turbulence performed by the Electric Power Research Institute at the Nevada Test Site to evaluate hydrogen burn-analysis procedures based on lumped-parameter codes like COMPARE-H2 and associated burn-parameter models. The test results: (1) confirmed, in a general way, the procedures for application to pulsed burning, (2) increased significantly our understanding of the burn phenomenon by demonstrating that continuous burning can occur, and (3) indicated that steam can terminate continuous burning. Future actions recommended include: (1) modification of the code to perform continuous-burn analyses, which is demonstrated, (2) analyses to determine the type of burning (pulsed or continuous) that will exist in nuclear containments and the stable location if the burning is continuous, and (3) changes to the models for estimating burn parameters

Hydrogen-combustion analyses of large-scale tests

International Nuclear Information System (INIS)

Gido, R.G.; Koestel, A.

1986-01-01

This report uses results of the large-scale tests with turbulence performed by the Electric Power Research Institute at the Nevada Test Site to evaluate hydrogen burn-analysis procedures based on lumped-parameter codes like COMPARE-H2 and associated burn-parameter models. The test results (a) confirmed, in a general way, the procedures for application to pulsed burning, (b) increased significantly our understanding of the burn phenomenon by demonstrating that continuous burning can occur and (c) indicated that steam can terminate continuous burning. Future actions recommended include (a) modification of the code to perform continuous-burn analyses, which is demonstrated, (b) analyses to determine the type of burning (pulsed or continuous) that will exist in nuclear containments and the stable location if the burning is continuous, and (c) changes to the models for estimating burn parameters

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Energy Technology Data Exchange (ETDEWEB)

Mahajabeen, Padamsee; Kumas, T. K. Arun; Riley, Robert; Binder, Manfred; Boyd, Alex; Calvo, Ann M.; Furukawa, Kentaro; Hesse, Cedar; Hohmann, Stefan; James, Tim Y.; LaButti, Kurt; Lapidus, Alla; Lindquist, Erika; Lucas, Susan; Miller, Kari; Shantappa, Sourabha; Grigoriev, Igor V.; Hibbett, David S.; McLaughlin, David J.; Spatafora, Joseph W.; Aime, Mary C.

2011-09-03

Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identied 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebito colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is conrmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were idented although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic

Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar.

Science.gov (United States)

Besnard, Guillaume; Christin, Pascal-Antoine; Malé, Pierre-Jean G; Coissac, Eric; Ralimanana, Hélène; Vorontsova, Maria S

2013-10-01

An accurate characterization of biodiversity requires analyses of DNA sequences in addition to classical morphological descriptions. New methods based on high-throughput sequencing may allow investigation of specimens with a large set of genetic markers to infer their evolutionary history. In the grass family, the phylogenetic position of the monotypic genus Lecomtella, a rare bamboo-like endemic from Madagascar, has never been appropriately evaluated. Until now its taxonomic treatment has remained controversial, indicating the need for re-evaluation based on a combination of molecular and morphological data. The phylogenetic position of Lecomtella in Poaceae was evaluated based on sequences from the nuclear and plastid genomes generated by next-generation sequencing (NGS). In addition, a detailed morphological description of L. madagascariensis was produced, and its distribution and habit were investigated in order to assess its conservation status. The complete plastid sequence, a ribosomal DNA unit and fragments of low-copy nuclear genes (phyB and ppc) were obtained. All phylogenetic analyses place Lecomtella as an isolated member of the core panicoids, which last shared a common ancestor with other species >20 million years ago. Although Lecomtella exhibits morphological characters typical of Panicoideae, an unusual combination of traits supports its treatment as a separate group. The study showed that NGS can be used to generate abundant phylogenetic information rapidly, opening new avenues for grass phylogenetics. These data clearly showed that Lecomtella forms an isolated lineage, which, in combination with its morphological peculiarities, justifies its treatment as a separate tribe: Lecomtelleae. New descriptions of the tribe, genus and species are presented with a typification, a distribution map and an IUCN conservation assessment.

Integrated Waste Treatment Unit (IWTU) Input Coal Analyses and Off-Gass Filter (OGF) Content Analyses

Energy Technology Data Exchange (ETDEWEB)

Jantzen, Carol M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Missimer, David M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Guenther, Chris P. [National Energy Technology Lab. (NETL), Morgantown, WV (United States); Shekhawat, Dushyant [National Energy Technology Lab. (NETL), Morgantown, WV (United States); VanEssendelft, Dirk T. [National Energy Technology Lab. (NETL), Morgantown, WV (United States); Means, Nicholas C. [AECOM Technology Corp., Oak Ridge, TN (United States)

2015-04-23

in process piping and materials, in excessive off-gas absorbent loading, and in undesired process emissions. The ash content of the coal is important as the ash adds to the DMR and other vessel products which affect the final waste product mass and composition. The amount and composition of the ash also affects the reaction kinetics. Thus ash content and composition contributes to the mass balance. In addition, sodium, potassium, calcium, sulfur, and maybe silica and alumina in the ash may contribute to wall-scale formation. Sodium, potassium, and alumina in the ash will be overwhelmed by the sodium, potassium, and alumina from the feed but the impact from the other ash components needs to be quantified. A maximum coal particle size is specified so the feed system does not plug and a minimum particle size is specified to prevent excess elutriation from the DMR to the Process Gas Filter (PGF). A vendor specification was used to procure the calcined coal for IWTU processing. While the vendor supplied a composite analysis for the 22 tons of coal (Appendix A), this study compares independent analyses of the coal performed at the Savannah River National Laboratory (SRNL) and at the National Energy Technology Laboratory (NETL). Three supersacks a were sampled at three different heights within the sack in order to determine within bag variability and between bag variability of the coal. These analyses were also compared to the vendor’s composite analyses and to the coal specification. These analyses were also compared to historic data on Bestac coal analyses that had been performed at Hazen Research Inc. (HRI) between 2004-2011.

Physico-Chemical and Bacteriological Analyses of Water Used for ...

African Journals Online (AJOL)

Samuel Olaleye

Physicochemical and bacteriological analyses were carried out on well water, stream water and river water used for drinking and swimming purposes in. Abeokuta, Nigeria. The results obtained were compared with WHO and EPA standards for drinking and recreational water. With the exception of Sokori stream and a well ...

UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes

Directory of Open Access Journals (Sweden)

Nomin Batnyam

2012-01-01

Full Text Available Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.

Directory of Open Access Journals (Sweden)

Petr Smýkal

2017-04-01

Full Text Available The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320 and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor and recombinant inbred lines (RILs. Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography–electrospray ionization/mass spectrometry and Laser desorption/ionization–mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin, quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082, peroxisomal membrane PEX14-like protein (MACE-S108, 4-coumarate CoA ligase (MACE-S131, and UDP-glucosyl transferase (MACE-S139 was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE data. In

Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae.

Directory of Open Access Journals (Sweden)

Tristan Lefébure

Full Text Available Streptococcus pyogenes, is an important human pathogen classified within the pyogenic group of streptococci, exclusively adapted to the human host. Our goal was to employ a comparative evolutionary approach to better understand the genomic events concomitant with S. pyogenes human adaptation. As part of ascertaining these events, we sequenced the genome of one of the potential sister species, the agricultural pathogen S. canis, and combined it in a comparative genomics reconciliation analysis with two other closely related species, Streptococcus dysgalactiae and Streptococcus equi, to determine the genes that were gained and lost during S. pyogenes evolution. Genome wide phylogenetic analyses involving 15 Streptococcus species provided convincing support for a clade of S. equi, S. pyogenes, S. dysgalactiae, and S. canis and suggested that the most likely S. pyogenes sister species was S. dysgalactiae. The reconciliation analysis identified 113 genes that were gained on the lineage leading to S. pyogenes. Almost half (46% of these gained genes were phage associated and 14 showed significant matches to experimentally verified bacteria virulence factors. Subsequent to the origin of S. pyogenes, over half of the phage associated genes were involved in 90 different LGT events, mostly involving different strains of S. pyogenes, but with a high proportion involving the horse specific pathogen S. equi subsp. equi, with the directionality almost exclusively (86% in the S. pyogenes to S. equi direction. Streptococcus agalactiae appears to have played an important role in the evolution of S. pyogenes with a high proportion of LGTs originating from this species. Overall the analysis suggests that S. pyogenes adaptation to the human host was achieved in part by (i the integration of new virulence factors (e.g. speB, and the sal locus and (ii the construction of new regulation networks (e.g. rgg, and to some extent speB.

Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics.

Science.gov (United States)

Breinholt, Jesse W; Earl, Chandra; Lemmon, Alan R; Lemmon, Emily Moriarty; Xiao, Lei; Kawahara, Akito Y

2018-01-01

The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing

Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees

Science.gov (United States)

Liang, Zhengzheng S.; Mattila, Heather R.; Rodriguez-Zas, Sandra L.; Southey, Bruce R.; Seeley, Thomas D.; Robinson, Gene E.

2014-01-01

Individual differences in behaviour are often consistent across time and contexts, but it is not clear whether such consistency is reflected at the molecular level. We explored this issue by studying scouting in honeybees in two different behavioural and ecological contexts: finding new sources of floral food resources and finding a new nest site. Brain gene expression profiles in food-source and nest-site scouts showed a significant overlap, despite large expression differences associated with the two different contexts. Class prediction and ‘leave-one-out’ cross-validation analyses revealed that a bee's role as a scout in either context could be predicted with 92.5% success using 89 genes at minimum. We also found that genes related to four neurotransmitter systems were part of a shared brain molecular signature in both types of scouts, and the two types of scouts were more similar for genes related to glutamate and GABA than catecholamine or acetylcholine signalling. These results indicate that consistent behavioural tendencies across different ecological contexts involve a mixture of similarities and differences in brain gene expression. PMID:25355476

Castor-1C spent fuel storage cask decay heat, heat transfer, and shielding analyses

International Nuclear Information System (INIS)

Rector, D.R.; McCann, R.A.; Jenquin, U.P.; Heeb, C.M.; Creer, J.M.; Wheeler, C.L.

1986-12-01

This report documents the decay heat, heat transfer, and shielding analyses of the Gesellschaft fuer Nuklear Services (GNS) CASTOR-1C cask used in a spent fuel storage demonstration performed at Preussen Elektra's Wurgassen nuclear power plant. The demonstration was performed between March 1982 and January 1984, and resulted in cask and fuel temperature data and cask exterior surface gamma-ray and neutron radiation dose rate measurements. The purpose of the analyses reported here was to evaluate decay heat, heat transfer, and shielding computer codes. The analyses consisted of (1) performing pre-look predictions (predictions performed before the analysts were provided the test data), (2) comparing ORIGEN2 (decay heat), COBRA-SFS and HYDRA (heat transfer), and QAD and DOT (shielding) results to data, and (3) performing post-test analyses if appropriate. Even though two heat transfer codes were used to predict CASTOR-1C cask test data, no attempt was made to compare the two codes. The codes are being evaluated with other test data (single-assembly data and other cask data), and to compare the codes based on one set of data may be premature and lead to erroneous conclusions

Should processed or raw image data be used in mammographic image quality analyses? A comparative study of three full-field digital mammography systems

International Nuclear Information System (INIS)

Borg, Mark; Badr, Ishmail; Royle, Gary

2015-01-01

The purpose of this study is to compare a number of measured image quality parameters using processed and unprocessed or raw images in two full-field direct digital units and one computed radiography mammography system. This study shows that the difference between raw and processed image data is system specific. The results have shown that there are no significant differences between raw and processed data in the mean threshold contrast values using the contrast-detail mammography phantom in all the systems investigated; however, these results cannot be generalised to all available systems. Notable differences were noted in contrast-to-noise ratios and in other tests including: response function, modulation transfer function, noise equivalent quanta, normalised noise power spectra and detective quantum efficiency as specified in IEC 62220-1-2. Consequently, the authors strongly recommend the use of raw data for all image quality analyses in digital mammography. (authors)

Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily?

Directory of Open Access Journals (Sweden)

Reitzel Adam M

2011-02-01

Full Text Available Abstract Background Nuclear receptors (NRs are an ancient superfamily of metazoan transcription factors that play critical roles in regulation of reproduction, development, and energetic homeostasis. Although the evolutionary relationships among NRs are well-described in two prominent clades of animals (deuterostomes and protostomes, comparatively little information has been reported on the diversity of NRs in early diverging metazoans. Here, we identified NRs from the phylum Ctenophora and used a phylogenomic approach to explore the emergence of the NR superfamily in the animal kingdom. In addition, to gain insight into conserved or novel functions, we examined NR expression during ctenophore development. Results We report the first described NRs from the phylum Ctenophora: two from Mnemiopsis leidyi and one from Pleurobrachia pileus. All ctenophore NRs contained a ligand-binding domain and grouped with NRs from the subfamily NR2A (HNF4. Surprisingly, all the ctenophore NRs lacked the highly conserved DNA-binding domain (DBD. NRs from Mnemiopsis were expressed in different regions of developing ctenophores. One was broadly expressed in the endoderm during gastrulation. The second was initially expressed in the ectoderm during gastrulation, in regions corresponding to the future tentacles; subsequent expression was restricted to the apical organ. Phylogenetic analyses of NRs from ctenophores, sponges, cnidarians, and a placozoan support the hypothesis that expansion of the superfamily occurred in a step-wise fashion, with initial radiations in NR family 2, followed by representatives of NR families 3, 6, and 1/4 originating prior to the appearance of the bilaterian ancestor. Conclusions Our study provides the first description of NRs from ctenophores, including the full complement from Mnemiopsis. Ctenophores have the least diverse NR complement of any animal phylum with representatives that cluster with only one subfamily (NR2A. Ctenophores and

Revisit of analytical methods for the process and plant control analyses during reprocessing of fast reactor fuels

International Nuclear Information System (INIS)

Subba Rao, R.V.

2016-01-01

CORAL (COmpact facility for Reprocessing of Advanced fuels in Lead cell) is an experimental facility for demonstrating the reprocessing of irradiated fast reactor fuels discharged from the Fast Breeder Test Reactor (FBTR). The objective of the reprocessing plant is to achieve nuclear grade plutonium and uranium oxides with minimum process waste volumes. The process flow sheet for the reprocessing of spent Fast Reactor Fuel consists of Transport of spent fuel, Chopping, Dissolution, Feed conditioning, Solvent Extraction cycle, Partitioning Cycle and Re-conversion of Plutonium nitrate and uranium nitrate to respective oxides. The efficiency and performance of the plant to achieve desired objective depends on the analyses of various species in the different steps adopted during reprocessing of fuels. The analytical requirements in the plant can be broadly classified as 1. Process control Analyses (Analyses which effect the performance of the plant- PCA); 2. Plant control Analyses (Analyses which indicates efficiency of the plant-PLCA); 3. Nuclear Material Accounting samples (Analyses which has bearing on nuclear material accounting in the plant - NUMAC) and Quality control Analyses (Quality of the input bulk chemicals as well as products - QCA). The analytical methods selected are based on the duration of analyses, precision and accuracies required for each type analytical requirement classified earlier. The process and plant control analyses requires lower precision and accuracies as compared to NUMAC analyses, which requires very high precision accuracy. The time taken for analyses should be as lower as possible for process and plant control analyses as compared to NUMAC analyses. The analytical methods required for determining U and Pu in process and plant samples from FRFR will be different as compared to samples from TRFR (Thermal Reactor Fuel Reprocessing) due to higher Pu to U ratio in FRFR as compared TRFR and they should be such that they can be easily

Comparative genomics of Westiellopsis prolifica a freshwater cyanobacteria uncovers the prolific and distinctive metabolic potentials

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Vineeta Verma

2017-10-01

Full Text Available Cyanobacteria are one of the ancient Micro-organisms that originated about 2.5 billion years ago. They are a very rich source for production of various natural compounds that are largely scalable in pharmaceutical and biotechnology industries. The unicellular Cyanobacteria are more ancient than the multicellular forms. In this study, we are exploring the genomes of a multi cellular, heterocystous, true branching Cyanobacteria, Westiellopsis prolifica belonging to order Nostocales. Complete genome is essential to serve as a reference for other sequencing projects and from which we can confirm the presence of various useful metabolic genes which are important for manufacturing pharmaceutical products. Here we report the draft assembly of Westiellopsis prolifica genome of 7.2 Mb with 19 scaffolds and the N50 and largest contig sizes are 2650655 bp and 3476031 bp, respectively. The phylogenomic studies from the literature reveal the closest relative of Westiellopsis prolifica are Fischerella sp. pcc 9431, Fischerella sp. pcc 9939 and Hapalosiphon welwitschii. Our preliminary comparative genomic analysis revealed that the sequence identity with the neighbouring clades were less, although we observed the large set of genes were syntenic and arranged in conserved in clusters. Genome mining on these organisms identified several clusters of NRPS, polyketide biosynthesis, two-component system, heterocyst differentiation genes and Nif genes were conserved in these genomes. We identified 21 clusters of secondary metabolites, which include NRPS and polyketide genes. For extraction of metabolites, we used several organic solvents. These extract contain various metabolic products which can be further exploited for the large scale production by genetic engineering approaches. Our Future work includes checking the RNAseq expressions of these metabolite producing genes.

COGNATE: comparative gene annotation characterizer.

Science.gov (United States)

Wilbrandt, Jeanne; Misof, Bernhard; Niehuis, Oliver

2017-07-17

The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https

Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

Science.gov (United States)

Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

2017-04-12

Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen

Discrete sensors distribution for accurate plantar pressure analyses.

Science.gov (United States)

Claverie, Laetitia; Ille, Anne; Moretto, Pierre

2016-12-01

The aim of this study was to determine the distribution of discrete sensors under the footprint for accurate plantar pressure analyses. For this purpose, two different sensor layouts have been tested and compared, to determine which was the most accurate to monitor plantar pressure with wireless devices in research and/or clinical practice. Ten healthy volunteers participated in the study (age range: 23-58 years). The barycenter of pressures (BoP) determined from the plantar pressure system (W-inshoe®) was compared to the center of pressures (CoP) determined from a force platform (AMTI) in the medial-lateral (ML) and anterior-posterior (AP) directions. Then, the vertical ground reaction force (vGRF) obtained from both W-inshoe® and force platform was compared for both layouts for each subject. The BoP and vGRF determined from the plantar pressure system data showed good correlation (SCC) with those determined from the force platform data, notably for the second sensor organization (ML SCC= 0.95; AP SCC=0.99; vGRF SCC=0.91). The study demonstrates that an adjusted placement of removable sensors is key to accurate plantar pressure analyses. These results are promising for a plantar pressure recording outside clinical or laboratory settings, for long time monitoring, real time feedback or for whatever activity requiring a low-cost system. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Analyse comparative de pratiques d’animation d’une discussion à visée démocratique et philosophique vues sous l’angle de la temporalité

OpenAIRE

Pierrisnard, Christine

2015-01-01

Cette étude s’intéresse à la manière dont l’outil « Discussion à Visée Démocratique et Philosophique » (DVDP) est transformé par ses utilisateurs en instrument au fil des situations. L’analyse comparative des pratiques d’un animateur plutôt novice et d’un animateur expert fait apparaître trois éléments cruciaux de représentation temporelle de la situation de DVDP. Un empan temporel large, ancré dans le temps long pour le nécessaire recul de la pensée ; le kaïros, ancré dans l’immédiateté et l...

Consumer Brand Choice: Individual and Group Analyses of Demand Elasticity

Science.gov (United States)

Oliveira-Castro, Jorge M.; Foxall, Gordon R.; Schrezenmaier, Teresa C.

2006-01-01

Following the behavior-analytic tradition of analyzing individual behavior, the present research investigated demand elasticity of individual consumers purchasing supermarket products, and compared individual and group analyses of elasticity. Panel data from 80 UK consumers purchasing 9 product categories (i.e., baked beans, biscuits, breakfast…

Le français du tourisme dans le contexte universitaire chinois : analyse comparative des besoins

Directory of Open Access Journals (Sweden)

LI Lu

2016-11-01

Full Text Available Cette recherche vise à dévoiler la situation de l’enseignement du français du tourisme dans le contexte universitaire chinois. A travers une analyse des besoins, nous tâchons de vérifier si la formation actuelle correspond aux besoins des apprenants ainsi qu’à la demande du marché du travail. Des enquêtes ont été menées auprès d’étudiants, d’enseignants et de professionnels. Les résultats montrent que les publics se diversifient avec des besoins variés et que la rupture de l’ensei gnement avec le secteur professionnel est évidente. Trois propositions sont ainsi formulées en vue de fournir des conseils à l’amélioration et à l’innovation de la formation du français du tourisme dans les universités chinoises.

Comparing Political Journalism

DEFF Research Database (Denmark)

Comparing Political Journalism is a systematic, in-depth study of the factors that shape and influence political news coverage today. Using techniques drawn from the growing field of comparative political communication, an international group of contributors analyse political news content drawn...... Comparing Political Journalism offers an unparalleled scope in assessing the implications for the ongoing transformation of Western media systems, and addresses core concepts of central importance to students and scholars of political communication world-wide....... from newspapers, television news, and news websites from 16 countries, to assess what kinds of media systems are most conducive to producing quality journalism. Underpinned by key conceptual themes, such as the role that the media are expected to play in democracies and quality of coverage...

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

Science.gov (United States)

Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

2012-05-01

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

Science.gov (United States)

Wallace, Lalena; Daugherty, Sean C.; Nagaraj, Sushma; Johnson, J. Kristie; Harris, Anthony D.

2016-01-01

Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen. PMID:27458211

Comparative in silico analyses of Cannabis sativa, Prunella vulgaris and Withania somnifera compounds elucidating the medicinal properties against rheumatoid arthritis.

Science.gov (United States)

Zaka, Mehreen; Sehgal, Sheikh Arslan; Shafique, Shagufta; Abbasi, Bilal Haider

2017-06-01

From last decade, there has been progressive improvement in computational drug designing. Several diseases are being cured from different plant extracts and products. Rheumatoid Arthritis (RA) is the most shared disease among auto-inflammatory diseases. Tumour necrosis factor (TNF)-α is associated with RA pathway and has adverse effects. Extensive literature review showed that plant species under study (Cannabis sativa, Prunella vulgaris and Withania somnifera) possess anti-inflammatory, anti-arthritic and anti-rheumatic properties. 13 anti-inflammatory compounds were characterised and filtered out from medicinal plant species and analysed for RA by targeting TNF-α through in silico analyses. By using ligand based pharmacophore generation approach and virtual screening against natural products libraries we retrieved twenty unique molecules that displayed utmost binding affinity, least binding energies and effective drug properties. The docking analyses revealed that Ala-22, Glu-23, Ser-65, Gln-67, Tyr-141, Leu-142, Asp-143, Phe-144 and Ala-145 were critical interacting residues for receptor-ligand interactions. It is proposed that the RA patients should use reported compounds for the prescription of RA by targeting TNF-α. This report is opening new dimensions for designing innovative therapeutic targets to cure RA. Copyright © 2017 Elsevier Inc. All rights reserved.

Parental conflict in birds: comparative analyses of offspring development, ecology and mating opportunities

Science.gov (United States)

Olson, V.A; Liker, A; Freckleton, R.P; Székely, T

2007-01-01

Parents often conflict over how much care to provide to their offspring. This conflict is expected to produce a negative relationship between male and female parental care, the strength of which may be mediated by both ecological and life-history variables. Previous studies have observed such trade-offs, but it is not known how generally they occur. Traditional views of sexual conflict place great importance on ecological factors in determining levels of parental care, whereas alternative views propose that the key determinant is mating opportunity. We carried out a broad-scale comparative study of parental conflict using 193 species from 41 families of birds. Using phylogenetic comparative analysis, we establish the generality of intersexual parental care conflict. We also show that parental conflict, as indicated by the disparity in care between the male and the female, depends on offspring development and mating opportunities, since in precocial species both males and females responded to increased mating opportunities. Altricial birds, however, failed to show these relationships. We also found little influence of breeding climate on parental conflict. Taken together, our results suggest that sexual conflict is a key element in the evolution of parental care systems. They also support the view that the major correlates of the intersexual conflict are mating opportunities for both sexes, rather than the breeding environment. PMID:18029303

Twenty years of meta-analyses in orthopaedic surgery: has quality kept up with quantity?

Science.gov (United States)

Dijkman, Bernadette G; Abouali, Jihad A K; Kooistra, Bauke W; Conter, Henry J; Poolman, Rudolf W; Kulkarni, Abhaya V; Tornetta, Paul; Bhandari, Mohit

2010-01-01

As the number of studies in the literature is increasing, orthopaedic surgeons highly depend on meta-analyses as their primary source of scientific evidence. The objectives of this review were to assess the scientific quality and number of published meta-analyses on orthopaedics-related topics over time. We conducted, in duplicate and independently, a systematic review of published meta-analyses in orthopaedics in the years 2005 and 2008 and compared them with a previous systematic review of meta-analyses from 1969 to 1999. A search of electronic databases (MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews) was performed to identify meta-analyses published in 2005 and 2008. We searched bibliographies and contacted content experts to identify additional relevant studies. Two investigators independently assessed the quality of the studies, using the Oxman and Guyatt index, and abstracted relevant data. We included forty-five and forty-four meta-analyses from 2005 and 2008, respectively. While the number of meta-analyses increased fivefold from 1999 to 2008, the mean quality score did not change significantly over time (p = 0.067). In the later years, a significantly lower proportion of meta-analyses had methodological flaws (56% in 2005 and 68% in 2008) compared with meta-analyses published prior to 2000 (88%) (p = 0.006). In 2005 and 2008, respectively, 18% and 30% of the meta-analyses had major to extensive flaws in their methodology. Studies from 2008 with positive conclusions used and described appropriate criteria for the validity assessment less often than did those with negative results. The use of random-effects and fixed-effects models as pooling methods became more popular toward 2008. Although the methodological quality of orthopaedic meta-analyses has increased in the past twenty years, a substantial proportion continues to show major to extensive flaws. As the number of published meta-analyses is increasing, a routine checklist for

Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea

DEFF Research Database (Denmark)

Karlsson, Magnus; Durling, Mikael Brandström; Choi, Jaeyoung

2015-01-01

lifestyle. The genome of C. rosea is estimated to 58.3 Mbp, and contains 14268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/saprotrophic Trichoderma species in an ancestral position. A comparative analysis...... (multidrug resistance-associated proteins) is evident in T. virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes were induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone...

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

Science.gov (United States)

Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

Directory of Open Access Journals (Sweden)

Fagen Li

Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC Lineages

Directory of Open Access Journals (Sweden)

Sabiha Shaik

2017-10-01

Full Text Available Escherichia coli sequence type 131 (ST131, a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12, ST405 (n = 10, and ST648 (n = 18, and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.

Comparative Proteomics Analyses of Kobresia pygmaea Adaptation to Environment along an Elevational Gradient on the Central Tibetan Plateau

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Li, Xiong; Yang, Yunqiang; Ma, Lan; Sun, Xudong; Yang, Shihai; Kong, Xiangxiang; Hu, Xiangyang; Yang, Yongping

2014-01-01

Variations in elevation limit the growth and distribution of alpine plants because multiple environmental stresses impact plant growth, including sharp temperature shifts, strong ultraviolet radiation exposure, low oxygen content, etc. Alpine plants have developed special strategies to help survive the harsh environments of high mountains, but the internal mechanisms remain undefined. Kobresia pygmaea, the dominant species of alpine meadows, is widely distributed in the Southeastern Tibet Plateau, Tibet Autonomous Region, China. In this study, we mainly used comparative proteomics analyses to investigate the dynamic protein patterns for K. pygmaea located at four different elevations (4600, 4800, 4950 and 5100 m). A total of 58 differentially expressed proteins were successfully detected and functionally characterized. The proteins were divided into various functional categories, including material and energy metabolism, protein synthesis and degradation, redox process, defense response, photosynthesis, and protein kinase. Our study confirmed that increasing levels of antioxidant and heat shock proteins and the accumulation of primary metabolites, such as proline and abscisic acid, conferred K. pygmaea with tolerance to the alpine environment. In addition, the various methods K. pygmaea used to regulate material and energy metabolism played important roles in the development of tolerance to environmental stress. Our results also showed that the way in which K. pygmaea mediated stomatal characteristics and photosynthetic pigments constitutes an enhanced adaptation to alpine environmental stress. According to these findings, we concluded that K. pygmaea adapted to the high-elevation environment on the Tibetan Plateau by aggressively accumulating abiotic stress-related metabolites and proteins and by the various life events mediated by proteins. Based on the species'lexible physiological and biochemical processes, we surmised that environment change has only a slight

Comparative proteomics analyses of Kobresia pygmaea adaptation to environment along an elevational gradient on the central Tibetan Plateau.

Directory of Open Access Journals (Sweden)

Xiong Li

Full Text Available Variations in elevation limit the growth and distribution of alpine plants because multiple environmental stresses impact plant growth, including sharp temperature shifts, strong ultraviolet radiation exposure, low oxygen content, etc. Alpine plants have developed special strategies to help survive the harsh environments of high mountains, but the internal mechanisms remain undefined. Kobresia pygmaea, the dominant species of alpine meadows, is widely distributed in the Southeastern Tibet Plateau, Tibet Autonomous Region, China. In this study, we mainly used comparative proteomics analyses to investigate the dynamic protein patterns for K. pygmaea located at four different elevations (4600, 4800, 4950 and 5100 m. A total of 58 differentially expressed proteins were successfully detected and functionally characterized. The proteins were divided into various functional categories, including material and energy metabolism, protein synthesis and degradation, redox process, defense response, photosynthesis, and protein kinase. Our study confirmed that increasing levels of antioxidant and heat shock proteins and the accumulation of primary metabolites, such as proline and abscisic acid, conferred K. pygmaea with tolerance to the alpine environment. In addition, the various methods K. pygmaea used to regulate material and energy metabolism played important roles in the development of tolerance to environmental stress. Our results also showed that the way in which K. pygmaea mediated stomatal characteristics and photosynthetic pigments constitutes an enhanced adaptation to alpine environmental stress. According to these findings, we concluded that K. pygmaea adapted to the high-elevation environment on the Tibetan Plateau by aggressively accumulating abiotic stress-related metabolites and proteins and by the various life events mediated by proteins. Based on the species'lexible physiological and biochemical processes, we surmised that environment change

Comparative phenotypic and genotypic analyses of Salmonella Rissen that originated from food animals in Thailand and United States.

Science.gov (United States)

Pornsukarom, S; Patchanee, P; Erdman, M; Cray, P F; Wittum, T; Lee, J; Gebreyes, W A

2015-03-01

Salmonella enterica serovar Rissen has been recognized as one of the most common serovar among humans and pork production systems in different parts of the world, especially Asia. In the United States, this serovar caused outbreaks but its epidemiologic significance remains unknown. The objectives of this study were to compare the phenotypic (antimicrobial susceptibility) and genotypic attributes of Salmonella Rissen isolated in Thailand (Thai) and the United States (US). All the Thai isolates (n = 30) were recovered from swine faecal samples. The US isolates (n = 35) were recovered from swine faecal samples (n = 29), cattle (n = 2), chicken (n = 2), dog (n = 1) and a ready-to-eat product (n = 1). The antimicrobial susceptibility of isolates was determined using the Kirby-Bauer disk diffusion method with a panel of 12 antimicrobials. Pulse-field gel electrophoresis (PFGE) was used to determine the genotypic diversity of isolates. All Thai isolates showed multidrug resistance (MDR) with the most frequent antibiotic resistance shown against ampicillin (100%), sulfisoxazole (96.7%), tetracycline (93.3%), streptomycin (90%) and chloramphenicol (30%). About half of the isolates of USA origin were pan-susceptible and roughly 30% were resistant to only tetracycline (R-type: Te). Salmonella Rissen isolated from Thailand and the USA in this study were found to be clonally unrelated. Genotypic analyses indicated that isolates were clustered primarily based on the geographic origin implying the limited clonality among the strains. Clonal relatedness among different host species within the same geography (USA) was found. We found genotypic similarity in Thai and US isolates in few instances but with no epidemiological link. Further studies to assess propensity for increased inter-regional transmission and dissemination is warranted. © 2014 Blackwell Verlag GmbH.

New genes often acquire male-specific functions but rarely become essential in Drosophila.

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Kondo, Shu; Vedanayagam, Jeffrey; Mohammed, Jaaved; Eizadshenass, Sogol; Kan, Lijuan; Pang, Nan; Aradhya, Rajaguru; Siepel, Adam; Steinhauer, Josefa; Lai, Eric C

2017-09-15

Relatively little is known about the in vivo functions of newly emerging genes, especially in metazoans. Although prior RNAi studies reported prevalent lethality among young gene knockdowns, our phylogenomic analyses reveal that young Drosophila genes are frequently restricted to the nonessential male reproductive system. We performed large-scale CRISPR/Cas9 mutagenesis of "conserved, essential" and "young, RNAi-lethal" genes and broadly confirmed the lethality of the former but the viability of the latter. Nevertheless, certain young gene mutants exhibit defective spermatogenesis and/or male sterility. Moreover, we detected widespread signatures of positive selection on young male-biased genes. Thus, young genes have a preferential impact on male reproductive system function. © 2017 Kondo et al.; Published by Cold Spring Harbor Laboratory Press.

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

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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

Cost-of-illness studies and cost-effectiveness analyses in anxiety disorders: a systematic review.

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Konnopka, Alexander; Leichsenring, Falk; Leibing, Eric; König, Hans-Helmut

2009-04-01

To review cost-of-illness studies (COI) and cost-effectiveness analyses (CEA) conducted for anxiety disorders. Based on a database search in Pubmed, PsychINFO and NHS EED, studies were classified according to various criteria. Cost data were inflated and converted to 2005 US-$ purchasing power parities (PPP). We finally identified 20 COI and 11 CEA of which most concentrated on panic disorder (PD) and generalized anxiety disorder (GAD). Differing inclusion of cost categories limited comparability of COI. PD and GAD tended to show higher direct costs per case, but lower direct cost per inhabitant than social and specific phobias. Different measures of effectiveness severely limited comparability of CEA. Overall CEA analysed 26 therapeutic or interventional strategies mostly compared to standard treatment, 8 of them resulting in lower better effectiveness and costs than the comparator. Anxiety disorders cause considerable costs. More research on phobias, more standardised inclusion of cost categories in COI and a wider use of comparable effectiveness measures (like QALYs) in CEA is needed.

The Hanford study: issues in analysing and interpreting data from occupational studies

International Nuclear Information System (INIS)

Gilbert, E.S.

1987-01-01

Updated analyses of workers at the Hanford Site provided no evidence of a correlation of radiation exposure and mortality from all cancers or mortality from leukemia. Potentially confounding factors were examined, and to the extent possible taken account of in these analyses. Risk estimates for leukemia and for all cancers except leukemia were calculated and compared with those from other sources. For leukemia, consideration was given to modifying factors such as age at exposure and time from exposure. (author)

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms.

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Chavda, Kalyan D; Chen, Liang; Fouts, Derrick E; Sutton, Granger; Brinkac, Lauren; Jenkins, Stephen G; Bonomo, Robert A; Adams, Mark D; Kreiswirth, Barry N

2016-12-13

Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed bla KPC-2 , 40 had bla KPC-3 , 2 had bla KPC-4 , and 2 had bla NDM-1 Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups-18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of bla KPC -harboring plasmids between different phylogenomic groups, and repeated transposition of the bla KPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique bla KPC -harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this

Nuclear analyses of the Pietroasa gold hoard

International Nuclear Information System (INIS)

Cojocaru, V.; Besliu, C.

1999-01-01

By means of nuclear analyses the concentrations of Au, Ag, Cu, Ir, Os, Pt, Co and Hg were measured in the 12 artifacts of the gold hoard discovered in 1837 at Pietroasa, Buzau country in Romania. The concentrations of the first four elements were used to compare different stylistic groups assumed by historians. Comparisons with gold nuggets from the old Dacian territory and gold Roman imperial coins were also made. A good agreement was found with the oldest hypothesis which considers that the hoard is represented by three styles appropriated mainly by the Goths. (author)

Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease.

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Gomez-Valero, Laura; Rusniok, Christophe; Rolando, Monica; Neou, Mario; Dervins-Ravault, Delphine; Demirtas, Jasmin; Rouy, Zoe; Moore, Robert J; Chen, Honglei; Petty, Nicola K; Jarraud, Sophie; Etienne, Jerome; Steinert, Michael; Heuner, Klaus; Gribaldo, Simonetta; Médigue, Claudine; Glöckner, Gernot; Hartland, Elizabeth L; Buchrieser, Carmen

2014-01-01

The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains.

Comparison of metformin and insulin versus insulin alone for type 2 diabetes: systematic review of randomised clinical trials with meta-analyses and trial sequential analyses.

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Hemmingsen, Bianca; Christensen, Louise Lundby; Wetterslev, Jørn; Vaag, Allan; Gluud, Christian; Lund, Søren S; Almdal, Thomas

2012-04-19

To compare the benefits and harms of metformin and insulin versus insulin alone as reported in randomised clinical trials of patients with type 2 diabetes. Systematic review of randomised clinical trials with meta-analyses and trial sequential analyses. The Cochrane Library, Medline, Embase, Science Citation Index Expanded, Latin American Caribbean Health Sciences Literature, and Cumulative Index to Nursing and Allied Health Literature until March 2011. We also searched abstracts presented at the American Diabetes Association and European Association for the Study of Diabetes Congresses, contacted relevant trial authors and pharmaceutical companies, hand searched reference lists of included trials, and searched the US Food and Drug Administration website. Two authors independently screened titles and abstracts for randomised clinical trials comparing metformin and insulin versus insulin alone (with or without placebo) in patients with type 2 diabetes, older than 18 years, and with an intervention period of at least 12 weeks. We included trials irrespective of language, publication status, predefined outcomes, antidiabetic interventions used before randomisation, and reported outcomes. We included 26 randomised trials with 2286 participants, of which 23 trials with 2117 participants could provide data. All trials had high risk of bias. Data were sparse for outcomes relevant to patients. Metformin and insulin versus insulin alone did not significantly affect all cause mortality (relative risk 1.30, 95% confidence interval 0.57 to 2.99) or cardiovascular mortality (1.70, 0.35 to 8.30). Trial sequential analyses showed that more trials were needed before reliable conclusions could be drawn regarding these outcomes. In a fixed effect model, but not in a random effects model, severe hypoglycaemia was significantly more frequent with metformin and insulin than with insulin alone (2.83, 1.17 to 6.86). In a random effects model, metformin and insulin resulted in reduced Hb

Comparative Factor Analyses of the Personal Attributes Questionnaire and the Bem Sex-Role Inventory.

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Antill, John K.; Cunningham, John D.

1982-01-01

Compared the Personal Attributes Questionnaire (PAQ) and the Bem Sex Role Inventory (BSRI) as measures of androgyny. Results showed that femininty (Concern for Others) and masculinity (Dominance) accounted for most of the variance, but for PAQ, clusters of male- and female-valued items (i.e., Extroversion and Insecurity) formed subsidiary factors.…

The comparative ecology and biogeography of parasites

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Poulin, Robert; Krasnov, Boris R.; Mouillot, David; Thieltges, David W.

2011-01-01

Comparative ecology uses interspecific relationships among traits, while accounting for the phylogenetic non-independence of species, to uncover general evolutionary processes. Applied to biogeographic questions, it can be a powerful tool to explain the spatial distribution of organisms. Here, we review how comparative methods can elucidate biogeographic patterns and processes, using analyses of distributional data on parasites (fleas and helminths) as case studies. Methods exist to detect phylogenetic signals, i.e. the degree of phylogenetic dependence of a given character, and either to control for these signals in statistical analyses of interspecific data, or to measure their contribution to variance. Parasite–host interactions present a special case, as a given trait may be a parasite trait, a host trait or a property of the coevolved association rather than of one participant only. For some analyses, it is therefore necessary to correct simultaneously for both parasite phylogeny and host phylogeny, or to evaluate which has the greatest influence on trait expression. Using comparative approaches, we show that two fundamental properties of parasites, their niche breadth, i.e. host specificity, and the nature of their life cycle, can explain interspecific and latitudinal variation in the sizes of their geographical ranges, or rates of distance decay in the similarity of parasite communities. These findings illustrate the ways in which phylogenetically based comparative methods can contribute to biogeographic research. PMID:21768153

Application of energy dispersive X-ray spectrometers with semiconductor detectors in radiometric analyses

International Nuclear Information System (INIS)

Jugelt, P.; Schieckel, M.

1983-01-01

Problems and possibilities of applying semiconductor detector spectrometers in radiometric analyses are described. A summary of the state of the art and tendencies of device engineering and spectra evaluation is given. Liquid-nitrogen cooled Li-drifted Si-detectors and high-purity Ge-detectors are compared. Semiconductor detectors working at room temperature are under development. In this connection CdTe and HgI 2 semiconductor detectors are compared. The use of small efficient computers in the spectrometer systems stimulates the development of algorithms for spectra analyses and for determining the concentration. Fields of application of energy dispersive X-ray spectrometers are X-ray diffraction and X-ray macroanalysis in investigating the structure of extensive surface regions

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

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Springer, Mark S; Gatesy, John

2018-02-26

coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful

Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

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Carolyn A. Young

2015-04-01

Full Text Available The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization. The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine.

The Evolution of Arthropod Body Plans: Integrating Phylogeny, Fossils, and Development-An Introduction to the Symposium.

Science.gov (United States)

Chipman, Ariel D; Erwin, Douglas H

2017-09-01

The last few years have seen a significant increase in the amount of data we have about the evolution of the arthropod body plan. This has come mainly from three separate sources: a new consensus and improved resolution of arthropod phylogeny, based largely on new phylogenomic analyses; a wealth of new early arthropod fossils from a number of Cambrian localities with excellent preservation, as well as a renewed analysis of some older fossils; and developmental data from a range of model and non-model pan-arthropod species that shed light on the developmental origins and homologies of key arthropod traits. However, there has been relatively little synthesis among these different data sources, and the three communities studying them have little overlap. The symposium "The Evolution of Arthropod Body Plans-Integrating Phylogeny, Fossils and Development" brought together leading researchers in these three disciplines and made a significant contribution to the emerging synthesis of arthropod evolution, which will help advance the field and will be useful for years to come. © The Author 2017. 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.

A new approach to analyse longitudinal epidemiological data with an excess of zeros.

Science.gov (United States)

Spriensma, Alette S; Hajos, Tibor R S; de Boer, Michiel R; Heymans, Martijn W; Twisk, Jos W R

2013-02-20

Within longitudinal epidemiological research, 'count' outcome variables with an excess of zeros frequently occur. Although these outcomes are frequently analysed with a linear mixed model, or a Poisson mixed model, a two-part mixed model would be better in analysing outcome variables with an excess of zeros. Therefore, objective of this paper was to introduce the relatively 'new' method of two-part joint regression modelling in longitudinal data analysis for outcome variables with an excess of zeros, and to compare the performance of this method to current approaches. Within an observational longitudinal dataset, we compared three techniques; two 'standard' approaches (a linear mixed model, and a Poisson mixed model), and a two-part joint mixed model (a binomial/Poisson mixed distribution model), including random intercepts and random slopes. Model fit indicators, and differences between predicted and observed values were used for comparisons. The analyses were performed with STATA using the GLLAMM procedure. Regarding the random intercept models, the two-part joint mixed model (binomial/Poisson) performed best. Adding random slopes for time to the models changed the sign of the regression coefficient for both the Poisson mixed model and the two-part joint mixed model (binomial/Poisson) and resulted into a much better fit. This paper showed that a two-part joint mixed model is a more appropriate method to analyse longitudinal data with an excess of zeros compared to a linear mixed model and a Poisson mixed model. However, in a model with random slopes for time a Poisson mixed model also performed remarkably well.

Design factors analyses of second-loop PRHRS

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ZHANG Hongyan

2017-05-01

Full Text Available In order to study the operating characteristics of a second-loop Passive Residual Heat Removal System (PRHRS, the transient thermal analysis code RELAP5 is used to build simulation models of the main coolant system and second-loop PRHRS. Transient calculations and comparative analyses under station blackout accident and one-side feed water line break accident conditions are conducted for three critical design factors of the second-loop PRHRS:design capacity, emergency makeup tank and isolation valve opening speed. The impacts of the discussed design factors on the operating characteristics of the second-loop PRHRS are summarized based on calculations and analyses. The analysis results indicate that the system safety and cooling rate should be taken into consideration in designing PRHRS's capacity,and water injection from emergency makeup tank to steam generator can provide advantage to system cooling in the event of accident,and system startup performance can be improved by reducing the opening speed of isolation valve. The results can provide references for the design of the second-loop PRHRS in nuclear power plants.

Overview of cooperative international piping benchmark analyses

International Nuclear Information System (INIS)

McAfee, W.J.

1982-01-01

This paper presents an overview of an effort initiated in 1976 by the International Working Group on Fast Reactors (IWGFR) of the International Atomic Energy Agency (IAEA) to evaluate detailed and simplified inelastic analysis methods for piping systems with particular emphasis on piping bends. The procedure was to collect from participating member IAEA countries descriptions of tests and test results for piping systems or bends (with emphasis on high temperature inelastic tests), to compile, evaluate, and issue a selected number of these problems for analysis, and to compile and make a preliminary evaluation of the analyses results. Of the problem descriptions submitted three were selected to be used: a 90 0 -elbow at 600 0 C with an in-plane transverse force; a 90 0 -elbow with an in-plane moment; and a 180 0 -elbow at room temperature with a reversed, cyclic, in-plane transverse force. A variety of both detailed and simplified analysis solutions were obtained. A brief comparative assessment of the analyses is contained in this paper. 15 figures

Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi.

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Richards, Thomas A; Soanes, Darren M; Foster, Peter G; Leonard, Guy; Thornton, Christopher R; Talbot, Nicholas J

2009-07-01

Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in the ancestry of many microbes. The role of HGT in plant evolutionary history is, however, largely unexplored. Here, we compare the genomes of six plant species with those of 159 prokaryotic and eukaryotic species and identify 1689 genes that show the highest similarity to corresponding genes from fungi. We constructed a phylogeny for all 1689 genes identified and all homolog groups available from the rice (Oryza sativa) genome (3177 gene families) and used these to define 14 candidate plant-fungi HGT events. Comprehensive phylogenetic analyses of these 14 data sets, using methods that account for site rate heterogeneity, demonstrated support for nine HGT events, demonstrating an infrequent pattern of HGT between plants and fungi. Five HGTs were fungi-to-plant transfers and four were plant-to-fungi HGTs. None of the fungal-to-plant HGTs involved angiosperm recipients. These results alter the current view of organismal barriers to HGT, suggesting that phagotrophy, the consumption of a whole cell by another, is not necessarily a prerequisite for HGT between eukaryotes. Putative functional annotation of the HGT candidate genes suggests that two fungi-to-plant transfers have added phenotypes important for life in a soil environment. Our study suggests that genetic exchange between plants and fungi is exceedingly rare, particularly among the angiosperms, but has occurred during their evolutionary history and added important metabolic traits to plant lineages.

Quantitative metagenomic analyses based on average genome size normalization

DEFF Research Database (Denmark)

Frank, Jeremy Alexander; Sørensen, Søren Johannes

2011-01-01

provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data...... marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how......). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis....

Comparison study of inelastic analyses for high temperature structure subjected to cyclic creep loading

International Nuclear Information System (INIS)

Kim, J. B.; Lee, H. Y.; Lee, J. H.

2002-01-01

It is necessary to develop a reliable numerical analysis method to simulate the plasticity and creep behavior of LMR high temperature structures. Since general purpose finite element analysis codes such as ABAQUS and ANSYS provide various models for plastic hardening and creep equation of Norton's power law, it is possible to perform the separate iscoplasticity analysis. In this study, the high temperature structural analysis program(NONSTA-VP) implementing Chaboche's unified visco plasticity equation into ABAQUS has been developed and the viscoplastic response of the 316 SS plate having a circular hole subjected to a cyclic creep loading has been analyzed. The results among the separate visco plasticity analyses and the unified visco plasticity analysis using NONSTA-VP have been compared and the results from NONSTA-VP shows remarkable responses of stress relaxation and creep behavior during hold time compared to those from separate visco plasticity analyses. Also, it is anticipated to reduce the conservatism arising from using elastic approach for creep-fatigue damage analysis since the stress range and the strain range from the unified visco plasticity analysis has been greatly reduced compared to those from separate visco plasticity analyses and elastic analysis

Financial relationships in economic analyses of targeted therapies in oncology.

Science.gov (United States)

Valachis, Antonis; Polyzos, Nikolaos P; Nearchou, Andreas; Lind, Pehr; Mauri, Davide

2012-04-20

A potential financial relationship between investigators and pharmaceutical manufacturers has been associated with an increased likelihood of reporting favorable conclusions about a sponsor's proprietary agent in pharmacoeconomic studies. The purpose of this study is to investigate whether there is an association between financial relationships and outcome in economic analyses of new targeted therapies in oncology. We searched PubMed (last update June 2011) for economic analyses of targeted therapies (including monoclonal antibodies, tyrosine-kinase inhibitors, and mammalian target of rapamycin inhibitors) in oncology. The trials were qualitatively rated regarding the cost assessment as favorable, neutral, or unfavorable on the basis of prespecified criteria. Overall, 81 eligible studies were identified. Economic analyses that were funded by pharmaceutical companies were more likely to report favorable qualitative cost estimates (28 [82%] of 34 v 21 [45%] of 47; P = .003). The presence of an author affiliated with manufacturer was not associated with study outcome. Furthermore, if only studies including a conflict of interest statement were included (66 of 81), studies that reported any financial relationship with manufacturers (author affiliation and/or funding and/or other financial relationship) were more likely to report favorable results of targeted therapies compared with studies without financial relationship (32 [71%] of 45 v nine [43%] of 21; P = .025). Our study reveals a potential threat for industry-related bias in economic analyses of targeted therapies in oncology in favor of analyses with financial relationships between authors and manufacturers. A more balanced funding of economic analyses from other sources may allow greater confidence in the interpretation of their results.

Comparative analyses identified species-specific functional roles in oral microbial genomes

Science.gov (United States)

Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

2017-01-01

ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to

Numerical analyses for efficient photoionization by nonmonochromatic fields

International Nuclear Information System (INIS)

Hasegawa, Shuichi; Suzuki, Atsuyuki

2000-01-01

Numerical analyses on excitation and ionization probabilities of atoms with hyperfine structures were performed in order to compare two different excitation methods, adiabatic excitation and broadband excitation. The lifetime of the intermediate states was considered in order to investigate the effect of the absorption line broadening. The dependences of the two excitation methods on the lifetime were found to be quite different. The ionization probability by the adiabatic excitation is higher than that by the broadband excitation for identical excitation laser intensity. (author)

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

DEFF Research Database (Denmark)

Schubert, Mikkel; Ermini, Luca; Der Sarkissian, Clio

2014-01-01

a variety of computational tools. Here we present PALEOMIX (http://geogenetics.ku.dk/publications/paleomix), a flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. Starting with next...

Optical region elemental abundance analyses of B and A stars

International Nuclear Information System (INIS)

Adelman, S.J.; Young, J.M.; Baldwin, H.E.

1984-01-01

Abundance analyses using optical region data and fully line blanketed model atmospheres have been performed for two sharp-lined hot Am stars o Pegasi and σ Aquarii and for the sharp-lined marginally peculiar A star v Cancri. The derived abundances exhibit definite anomalies compared with those of normal B-type stars and the Sun. (author)

Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems

Science.gov (United States)

Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.

2010-03-01

Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

Outsourcing medical data analyses: can technology overcome legal, privacy, and confidentiality issues?

Science.gov (United States)

Brumen, Bostjan; Heričko, Marjan; Sevčnikar, Andrej; Završnik, Jernej; Hölbl, Marko

2013-12-16

Medical data are gold mines for deriving the knowledge that could change the course of a single patient's life or even the health of the entire population. A data analyst needs to have full access to relevant data, but full access may be denied by privacy and confidentiality of medical data legal regulations, especially when the data analyst is not affiliated with the data owner. Our first objective was to analyze the privacy and confidentiality issues and the associated regulations pertaining to medical data, and to identify technologies to properly address these issues. Our second objective was to develop a procedure to protect medical data in such a way that the outsourced analyst would be capable of doing analyses on protected data and the results would be comparable, if not the same, as if they had been done on the original data. Specifically, our hypothesis was there would not be a difference between the outsourced decision trees built on encrypted data and the ones built on original data. Using formal definitions, we developed an algorithm to protect medical data for outsourced analyses. The algorithm was applied to publicly available datasets (N=30) from the medical and life sciences fields. The analyses were performed on the original and the protected datasets and the results of the analyses were compared. Bootstrapped paired t tests for 2 dependent samples were used to test whether the mean differences in size, number of leaves, and the accuracy of the original and the encrypted decision trees were significantly different. The decision trees built on encrypted data were virtually the same as those built on original data. Out of 30 datasets, 100% of the trees had identical accuracy. The size of a tree and the number of leaves was different only once (1/30, 3%, P=.19). The proposed algorithm encrypts a file with plain text medical data into an encrypted file with the data protected in such a way that external data analyses are still possible. The results

A phylogenomic analysis of the bacterial phylum Fibrobacteres

Directory of Open Access Journals (Sweden)

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.

Early Versus Delayed Motion After Rotator Cuff Repair: A Systematic Review of Overlapping Meta-analyses.

Science.gov (United States)

Houck, Darby A; Kraeutler, Matthew J; Schuette, Hayden B; McCarty, Eric C; Bravman, Jonathan T

2017-10-01

Previous meta-analyses have been conducted to compare outcomes of early versus delayed motion after rotator cuff repair. To conduct a systematic review of overlapping meta-analyses comparing early versus delayed motion rehabilitation protocols after rotator cuff repair to determine which meta-analyses provide the best available evidence. Systematic review. A systematic review was performed by searching PubMed and Cochrane Library databases. Search terms included "rotator cuff repair," "early passive motion," "immobilization," "rehabilitation protocol," and "meta-analysis." Results were reviewed to determine study eligibility. Patient outcomes and structural healing were extracted from these meta-analyses. Meta-analysis quality was assessed using the Oxman-Guyatt and Quality of Reporting of Meta-analyses (QUOROM) systems. The Jadad decision algorithm was then used to determine which meta-analyses provided the best level of evidence. Seven meta-analyses containing a total of 5896 patients met the eligibility criteria (1 Level I evidence, 4 Level II evidence, 2 Level III evidence). None of these meta-analyses found immobilization to be superior to early motion; however, most studies suggested that early motion would increase range of motion (ROM), thereby reducing time of recovery. Three of these studies suggested that tear size contributed to the choice of rehabilitation to ensure proper healing of the shoulder. A study by Chan et al in 2014 received the highest QUOROM and Oxman-Guyatt scores, and therefore this meta-analysis appeared to have the highest level of evidence. Additionally, a study by Riboh and Garrigues in 2014 was selected as the highest quality study in this systematic review according to the Jadad decision algorithm. The current, best available evidence suggests that early motion improves ROM after rotator cuff repair but increases the risk of rotator cuff retear. Lower quality meta-analyses indicate that tear size may provide a better strategy in

The hemispherical deflector analyser revisited

Energy Technology Data Exchange (ETDEWEB)

Benis, E.P. [Institute of Electronic Structure and Laser, P.O. Box 1385, 71110 Heraklion, Crete (Greece)], E-mail: benis@iesl.forth.gr; Zouros, T.J.M. [Institute of Electronic Structure and Laser, P.O. Box 1385, 71110 Heraklion, Crete (Greece); Department of Physics, University of Crete, P.O. Box 2208, 71003 Heraklion, Crete (Greece)

2008-04-15

Using the basic spectrometer trajectory equation for motion in an ideal 1/r potential derived in Eq. (101) of part I [T.J.M. Zouros, E.P. Benis, J. Electron Spectrosc. Relat. Phenom. 125 (2002) 221], the operational characteristics of a hemispherical deflector analyser (HDA) such as dispersion, energy resolution, energy calibration, input lens magnification and energy acceptance window are investigated from first principles. These characteristics are studied as a function of the entry point R{sub 0} and the nominal value of the potential V(R{sub 0}) at entry. Electron-optics simulations and actual laboratory measurements are compared to our theoretical results for an ideal biased paracentric HDA using a four-element zoom lens and a two-dimensional position sensitive detector (2D-PSD). These results should be of particular interest to users of modern HDAs utilizing a PSD.

The hemispherical deflector analyser revisited

International Nuclear Information System (INIS)

Benis, E.P.; Zouros, T.J.M.

2008-01-01

Using the basic spectrometer trajectory equation for motion in an ideal 1/r potential derived in Eq. (101) of part I [T.J.M. Zouros, E.P. Benis, J. Electron Spectrosc. Relat. Phenom. 125 (2002) 221], the operational characteristics of a hemispherical deflector analyser (HDA) such as dispersion, energy resolution, energy calibration, input lens magnification and energy acceptance window are investigated from first principles. These characteristics are studied as a function of the entry point R 0 and the nominal value of the potential V(R 0 ) at entry. Electron-optics simulations and actual laboratory measurements are compared to our theoretical results for an ideal biased paracentric HDA using a four-element zoom lens and a two-dimensional position sensitive detector (2D-PSD). These results should be of particular interest to users of modern HDAs utilizing a PSD

Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system.

Science.gov (United States)

Richter, Sandy; Helm, Conrad; Meunier, Frederic A; Hering, Lars; Campbell, Lahcen I; Drukewitz, Stephan H; Undheim, Eivind A B; Jenner, Ronald A; Schiavo, Giampietro; Bleidorn, Christoph

2017-03-04

We present the first molecular characterization of glycerotoxin (GLTx), a potent neurotoxin found in the venom of the bloodworm Glycera tridactyla (Glyceridae, Annelida). Within the animal kingdom, GLTx shows a unique mode of action as it can specifically up-regulate the activity of Ca v 2.2 channels (N-type) in a reversible manner. The lack of sequence information has so far hampered a detailed understanding of its mode of action. Our analyses reveal three ~3.8 kb GLTx full-length transcripts, show that GLTx represents a multigene family, and suggest it functions as a dimer. An integrative approach using transcriptomics, quantitative real-time PCR, in situ hybridization, and immunocytochemistry shows that GLTx is highly expressed exclusively in four pharyngeal lobes, a previously unrecognized part of the venom apparatus. Our results overturn a century old textbook view on the glycerid venom system, suggesting that it is anatomically and functionally much more complex than previously thought. The herein presented GLTx sequence information constitutes an important step towards the establishment of GLTx as a versatile tool to understand the mechanism of synaptic function, as well as the mode of action of this novel neurotoxin.

Micro‐CT analyses of apical enlargement and molar root canal complexity

DEFF Research Database (Denmark)

Markvart, M.; Darvann, Tron Andre; Larsen, P.

2012-01-01

Markvart M, Darvann TA, Larsen P, Dalstra M, Kreiborg S, Bjørndal L. Micro‐CT analyses of apical enlargement and molar root canal complexity. International Endodontic Journal, 45, 273–281, 2012. Aim To compare the effectiveness of two rotary hybrid instrumentation techniques with focus on apical...

Comparison of Numerical Analyses with a Static Load Test of a Continuous Flight Auger Pile

Directory of Open Access Journals (Sweden)

Hoľko Michal

2014-12-01

Full Text Available The article deals with numerical analyses of a Continuous Flight Auger (CFA pile. The analyses include a comparison of calculated and measured load-settlement curves as well as a comparison of the load distribution over a pile's length. The numerical analyses were executed using two types of software, i.e., Ansys and Plaxis, which are based on FEM calculations. Both types of software are different from each other in the way they create numerical models, model the interface between the pile and soil, and use constitutive material models. The analyses have been prepared in the form of a parametric study, where the method of modelling the interface and the material models of the soil are compared and analysed.

New insights into survival trend analyses in cancer population-based studies: the SUDCAN methodology.

Science.gov (United States)

Uhry, Zoé; Bossard, Nadine; Remontet, Laurent; Iwaz, Jean; Roche, Laurent

2017-01-01

The main objective of the SUDCAN study was to compare, for 15 cancer sites, the trends in net survival and excess mortality rates from cancer 5 years after diagnosis between six European Latin countries (Belgium, France, Italy, Portugal, Spain and Switzerland). The data were extracted from the EUROCARE-5 database. The study period ranged from 6 (Portugal, 2000-2005) to 18 years (Switzerland, 1989-2007). Trend analyses were carried out separately for each country and cancer site; the number of cases ranged from 1500 to 104 000 cases. We developed an original flexible excess rate modelling strategy that accounts for the continuous effects of age, year of diagnosis, time since diagnosis and their interactions. Nineteen models were constructed; they differed in the modelling of the effect of the year of diagnosis in terms of linearity, proportionality and interaction with age. The final model was chosen according to the Akaike Information Criterion. The fit was assessed graphically by comparing model estimates versus nonparametric (Pohar-Perme) net survival estimates. Out of the 90 analyses carried out, the effect of the year of diagnosis on the excess mortality rate depended on age in 61 and was nonproportional in 64; it was nonlinear in 27 out of the 75 analyses where this effect was considered. The model fit was overall satisfactory. We analysed successfully 15 cancer sites in six countries. The refined methodology proved necessary for detailed trend analyses. It is hoped that three-dimensional parametric modelling will be used more widely in net survival trend studies as it has major advantages over stratified analyses.

Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporum

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Gustavo Bravo-Ruiz

2017-09-01

Full Text Available Penicillium occitanis is a model system for enzymatic regulation. A mutant strain exhibiting constitutive overproduction of different pectinolytic enzymes both under inducing (pectin or repressing conditions (glucose was previously isolated after chemical mutagenesis. In order to identify the molecular basis of this regulatory mechanism, the genomes of the wild type and the derived mutant strain were sequenced and compared, providing the first reference genome for this species. We used a phylogenomic approach to compare P. occitanis with other pectinolytic fungi and to trace expansions of gene families involved in carbohydrate degradation. Genome comparison between wild type and mutant identified seven mutations associated with predicted proteins. The most likely candidate was a mutation in a highly conserved serine residue of a conserved fungal protein containing a GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain and a fungus-specific transcription factor regulatory middle homology region. To functionally characterize the role of this candidate gene, the mutation was recapitulated in the predicted orthologue Fusarium oxysporum, a vascular wilt pathogen which secretes a wide array of plant cell wall degrading enzymes, including polygalacturonases, pectate lyases, xylanases and proteases, all of which contribute to infection. However, neither the null mutant nor a mutant carrying the analogous point mutation exhibited a deregulation of pectinolytic enzymes. The availability, annotation and phylogenomic analysis of the P. occitanis genome sequence represents an important resource for understanding the evolution and biology of this species, and sets the basis for the discovery of new genes of biotechnological interest for the degradation of complex polysaccharides.

Comparative Analyses of Tomato yellow leaf curl virus C4 Protein-Interacting Host Proteins in Healthy and Infected Tomato Tissues

Directory of Open Access Journals (Sweden)

Namgyu Kim

2016-10-01

Full Text Available Tomato yellow leaf curl virus (TYLCV, a member of the genus Begomovirus, is one of the most important viruses of cultivated tomatoes worldwide, mainly causing yellowing and curling of leaves with stunting in plants. TYLCV causes severe problems in sub-tropical and tropical countries, as well as in Korea. However, the mechanism of TYLCV infection remains unclear, although the function of each viral component has been identified. TYLCV C4 codes for a small protein involved in various cellular functions, including symptom determination, gene silencing, viral movement, and induction of the plant defense response. In this study, through yeast-two hybrid screenings, we identified TYLCV C4-interacting host proteins from both healthy and symptom-exhibiting tomato tissues, to determine the role of TYLCV C4 proteins in the infection processes. Comparative analyses of 28 proteins from healthy tissues and 36 from infected tissues showing interactions with TYLCV C4 indicated that TYLCV C4 mainly interacts with host proteins involved in translation, ubiquitination, and plant defense, and most interacting proteins differed between the two tissues but belong to similar molecular functional categories. Four proteins—two ribosomal proteins, S-adenosyl-L-homocysteine hydrolase, and 14-3-3 family protein—were detected in both tissues. Furthermore, the identified proteins in symptom-exhibiting tissues showed greater involvement in plant defenses. Some are key regulators, such as receptor-like kinases and pathogenesis-related proteins, of plant defenses. Thus, TYLCV C4 may contribute to the suppression of host defense during TYLCV infection and be involved in ubiquitination for viral infection.

Construction and comparative analyses of highly dense linkage maps of two sweet cherry intra-specific progenies of commercial cultivars.

Directory of Open Access Journals (Sweden)

Carolina Klagges

Full Text Available Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L. intra-specific progenies derived from crosses between 'Black Tartarian' × 'Kordia' (BT×K and 'Regina' × 'Lapins'(R×L, high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F(1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1-LG8. These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.

Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates.

Directory of Open Access Journals (Sweden)

Daniel Wibberg

Full Text Available Rhizoctonia solani, a soil-born plant pathogenic basidiomycetous fungus, affects various economically important agricultural and horticultural crops. The draft genome sequence for the R. solani AG1-IB isolate 7/3/14 as well as a corresponding transcriptome dataset (Expressed Sequence Tags--ESTs were established previously. Development of a specific R. solani AG1-IB gene model based on GMAP transcript mapping within the eukaryotic gene prediction platform AUGUSTUS allowed detection of new genes and provided insights into the gene structure of this fungus. In total, 12,616 genes were recognized in the genome of the AG1-IB isolate. Analysis of predicted genes by means of different bioinformatics tools revealed new genes whose products potentially are involved in degradation of plant cell wall components, melanin formation and synthesis of secondary metabolites. Comparative genome analyses between members of different R. solani anastomosis groups, namely AG1-IA, AG3 and AG8 and the newly annotated R. solani AG1-IB genome were performed within the comparative genomics platform EDGAR. It appeared that only 21 to 28% of all genes encoded in the draft genomes of the different strains were identified as core genes. Based on Average Nucleotide Identity (ANI and Average Amino-acid Identity (AAI analyses, considerable sequence differences between isolates representing different anastomosis groups were identified. However, R. solani isolates form a distinct cluster in relation to other fungi of the phylum Basidiomycota. The isolate representing AG1-IB encodes significant more genes featuring predictable functions in secondary metabolite production compared to other completely sequenced R. solani strains. The newly established R. solani AG1-IB 7/3/14 gene layout now provides a reliable basis for post-genomics studies.

Thermo-economic analysis of recuperated Maisotsenko bottoming cycle using triplex air saturator: Comparative analyses

International Nuclear Information System (INIS)

Saghafifar, Mohammad; Omar, Amr; Erfanmoghaddam, Sepehr; Gadalla, Mohamed

2017-01-01

Highlights: • Proposing recuperated Maisotsenko bottoming cycle (RMBC) as a new combined cycle. • Introducing triplex air saturator for waste heat recovery application. • Conducting thermodynamic optimization to maximize RMBC thermal efficiency. • Conducting thermo-economic optimization to minimize RMBC cost of electricity. - Abstract: A recently recommended combined cycle power plant is to employ another gas turbine cycle for waste heat recovery as an air bottoming cycle (ABC). There are some studies conducted to improve ABC’s thermodynamic performance utilizing commonly power augmentation methods such as steam/water injection. In particular, it is proposed to employ Maisotsenko gas turbine cycle as a bottoming cycle, i.e. Maisotsenko bottoming cycle (MBC). Due to the promising performance of the MBC configuration, it is decided to investigate a recuperated MBC (RMBC) configuration by recommending the triplex air saturator. In this way, the air saturator consists of three sections. The first section is an indirect evaporative cooler while the other two sections are responsible for heat recovery from the topping and bottoming cycle turbines exhaust. In this paper, thermodynamic and thermo-economic analyses are carried out to study the main merits and demerits of RMBC against MBC configuration. Thermodynamic optimization results indicate that the maximum achievable efficiency for MBC and RMBC incorporation in a simple gas turbine power plant are 39.40% and 44.73%, respectively. Finally, thermo-economic optimization shows that the optimum levelized cost of electricity for MBC and RMBC power plants are 62.922 US$/MWh and 58.154 US$/MWh, respectively.

Comparing parametric and nonparametric regression methods for panel data

DEFF Research Database (Denmark)

Czekaj, Tomasz Gerard; Henningsen, Arne

We investigate and compare the suitability of parametric and non-parametric stochastic regression methods for analysing production technologies and the optimal firm size. Our theoretical analysis shows that the most commonly used functional forms in empirical production analysis, Cobb......-Douglas and Translog, are unsuitable for analysing the optimal firm size. We show that the Translog functional form implies an implausible linear relationship between the (logarithmic) firm size and the elasticity of scale, where the slope is artificially related to the substitutability between the inputs....... The practical applicability of the parametric and non-parametric regression methods is scrutinised and compared by an empirical example: we analyse the production technology and investigate the optimal size of Polish crop farms based on a firm-level balanced panel data set. A nonparametric specification test...

Lipid analyses of fumigated vs irradiated raw and roasted almonds

International Nuclear Information System (INIS)

Uthman, R.S.; Toma, R.B.; Garcia, R.; Medora, N.P.; Cunningham, S.

1998-01-01

The purpose of this study was to compare the effects of propylene oxide (PO) and irradiation treatments on the lipid analyses of raw and roasted almonds. Eight kilograms each of raw and roasted almonds were divided into four batches (2 kg each). Three of the batches were subjected to PO treatment or irradiation treatment with a dose of 6, 10·5 kGy. The untreated batch served as control samples, they were taken from all the batches at three consecutive times during storage (day 0, 8 weeks and 16 weeks) and analysed for iodine number, peroxide value and 2-thiobarbituric acid number. Overall, irradiated almonds incurred a higher variation in lipid stability than PO tested almonds while roasted almonds incurred a higher variation than raw almonds

A comparative study among methods used for wheat flour analysis and for measurements of gluten properties using the Wheat Gluten Quality Analyser (WGQA

Directory of Open Access Journals (Sweden)

Maria Cristina Ferrari

2014-06-01

Full Text Available This study aimed at comparing both the results of wheat flour quality assessed by the new equipment Wheat Gluten Quality Analyser (WGQA and those obtained by the extensigraph and farinograph. Fifty-nine wheat samples were evaluated for protein and gluten contents; the rheological properties of gluten and wheat flour were assessed using the WGQA and the extensigraph/farinograph methods, respectively, in addition to the baking test. Principal component analysis (PCA and linear regression were used to evaluate the results. The parameters of energy and maximum resistance to extension determined by the extensigraph and WGQA showed an acceptable level for the linear correlation within the range from 0.6071 to 0.6511. The PCA results obtained using WGQA and the other rheological apparatus showed values similar to those expected for wheat flours in the baking test. Although all equipment used was effective in assessing the behavior of strong and weak flours, the results of medium strength wheat flour varied. WGQA has shown to use less amount of sample and to be faster and easier to use in relation to the other instruments used.

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees.

Science.gov (United States)

Huang, Wen; Zhou, Guifang; Marchand, Melissa; Ash, Jeremy R; Morris, David; Van Dooren, Paul; Brown, Jeremy M; Gallivan, Kyle A; Wilgenbusch, Jim C

2016-12-01

Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License. © The Author 2016. 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.

Stress intensity factor analyses of surface cracks in three-dimensional structures

International Nuclear Information System (INIS)

Miyazaki, Noriyuki; Shibata, Katsuyuki; Watanabe, Takayuki; Tagata, Kazunori.

1983-11-01

The stress intensity factor analyses of surface cracks in various three-dimensional structures were performed using the finite element computer program EPAS-J1. The results obtained by EPAS-J1 were compared with other finite element solutions or results obtained by the simplified estimation methods. Among the simplified estimation methods, the equations proposed by Newman and Raju give the distributions of the stress intensity factor along a crack front, which were compared with the result obtained by EPAS-J1. It was confirmed by comparing the results that EPAS-J1 gives reasonable stress intensity factors of surface cracks in three-dimensional structures. (author)

Application of the portable pavement seismic analyser (PSPA) for pavement analysis

CSIR Research Space (South Africa)

Steyn, WJVDM

2007-07-01

Full Text Available at the selected locations were compared using a one-way ANOVA and a correlation matrix to analyse the repeatability of the PSPA data, and to determine whether there was a significant difference between the three observations obtained at a specific location... behaviour from pavement layers, the PSPA measurements were conducted at 90° angles at the same location. An ANOVA test and correlation matrix was set up for each point to evaluate the isotropy of the moduli. Unfortunately, no comparative data (such as FWD...

Proteomic analyses of host and pathogen responses during bovine mastitis.

Science.gov (United States)

Boehmer, Jamie L

2011-12-01

The pursuit of biomarkers for use as clinical screening tools, measures for early detection, disease monitoring, and as a means for assessing therapeutic responses has steadily evolved in human and veterinary medicine over the past two decades. Concurrently, advances in mass spectrometry have markedly expanded proteomic capabilities for biomarker discovery. While initial mass spectrometric biomarker discovery endeavors focused primarily on the detection of modulated proteins in human tissues and fluids, recent efforts have shifted to include proteomic analyses of biological samples from food animal species. Mastitis continues to garner attention in veterinary research due mainly to affiliated financial losses and food safety concerns over antimicrobial use, but also because there are only a limited number of efficacious mastitis treatment options. Accordingly, comparative proteomic analyses of bovine milk have emerged in recent years. Efforts to prevent agricultural-related food-borne illness have likewise fueled an interest in the proteomic evaluation of several prominent strains of bacteria, including common mastitis pathogens. The interest in establishing biomarkers of the host and pathogen responses during bovine mastitis stems largely from the need to better characterize mechanisms of the disease, to identify reliable biomarkers for use as measures of early detection and drug efficacy, and to uncover potentially novel targets for the development of alternative therapeutics. The following review focuses primarily on comparative proteomic analyses conducted on healthy versus mastitic bovine milk. However, a comparison of the host defense proteome of human and bovine milk and the proteomic analysis of common veterinary pathogens are likewise introduced.

Automated monosegmented flow analyser. Determination of glucose, creatinine and urea.

Science.gov (United States)

Raimundo Júnior, I M; Pasquini, C

1997-10-01

An automated monosegmented flow analyser containing a sampling valve and a reagent addition module and employing a laboratory-made photodiode array spectrophotometer as detection system is described. The instrument was controlled by a 386SX IBM compatible microcomputer through an IC8255 parallel port that communicates with the interface which controls the sampling valve and reagent addition module. The spectrophotometer was controlled by the same microcomputer through an RS232 serial standard interface. The software for the instrument was written in QuickBasic 4.5. Opto-switches were employed to detect the air bubbles limiting the monosegment, allowing precise sample localisation for reagent addition and signal reading. The main characteristics of the analyser are low reagent consumption and high sensitivity which is independent of the sample volume. The instrument was designed to determine glucose, creatinine or urea in blood plasma and serum without hardware modification. The results were compared against those obtained by the Clinical Hospital of UNICAMP using commercial analysers. Correlation coefficients among the methods were 0.997, 0.982 and 0.996 for glucose, creatinine and urea, respectively.

The intervals method: a new approach to analyse finite element outputs using multivariate statistics

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Jordi Marcé-Nogué

2017-10-01

Full Text Available Background In this paper, we propose a new method, named the intervals’ method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology. Methods The intervals’ method consists of generating a set of variables, each one defined by an interval of stress values. Each variable is expressed as a percentage of the area of the mandible occupied by those stress values. Afterwards these newly generated variables can be analysed using multivariate methods. Results Applying this novel method to the biological case study of whether armadillo mandibles differ according to dietary groups, we show that the intervals’ method is a powerful tool to characterize biomechanical performance and how this relates to different diets. This allows us to positively discriminate between specialist and generalist species. Discussion We show that the proposed approach is a useful methodology not affected by the characteristics of the finite element mesh. Additionally, the positive discriminating results obtained when analysing a difficult case study suggest that the proposed method could be a very useful tool for comparative studies in finite element analysis using multivariate statistical approaches.

The intervals method: a new approach to analyse finite element outputs using multivariate statistics

Science.gov (United States)

De Esteban-Trivigno, Soledad; Püschel, Thomas A.; Fortuny, Josep

2017-01-01

Background In this paper, we propose a new method, named the intervals’ method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology. Methods The intervals’ method consists of generating a set of variables, each one defined by an interval of stress values. Each variable is expressed as a percentage of the area of the mandible occupied by those stress values. Afterwards these newly generated variables can be analysed using multivariate methods. Results Applying this novel method to the biological case study of whether armadillo mandibles differ according to dietary groups, we show that the intervals’ method is a powerful tool to characterize biomechanical performance and how this relates to different diets. This allows us to positively discriminate between specialist and generalist species. Discussion We show that the proposed approach is a useful methodology not affected by the characteristics of the finite element mesh. Additionally, the positive discriminating results obtained when analysing a difficult case study suggest that the proposed method could be a very useful tool for comparative studies in finite element analysis using multivariate statistical approaches. PMID:29043107

Elemental composition of skin tissue by PIXE and INAA analyses

International Nuclear Information System (INIS)

Hollands, R.; Spyrou, N.M.

1997-01-01

Hypertrophic scars are a particular type of scar that can form after any type of dermal injury. They are unsightly, red, elevated above normal skin level, itchy and painful. At present no-one knows why these scars form. Due to the differences between scar tissue and normal skin it was decided to analyse skin tissue which at a later date would be compared to scar tissue. Spit skin graft (epidermis) samples as well as full thickness skin (epidermis to dermis) tissue were analysed using PIXE and RBS with a 2 MeV proton beam. The epidermis was compared to the dermis to see if there were any variations between the two. In all the samples P, S, Cl, K, Ca, Fe, and Cd were detected and in a majority of the samples Zn and Ba were found, using PIXE. It was found that, between the epidermis and dermis, there was an significant increase in P in the epidermis in both full thickness and split skin graft samples. Complementary elemental analysis was also performed using neutron activation, and Br, Na and Zn were detected. (author)

Bayesian models for comparative analysis integrating phylogenetic uncertainty

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Villemereuil Pierre de

2012-06-01

Full Text Available Abstract Background Uncertainty in comparative analyses can come from at least two sources: a phylogenetic uncertainty in the tree topology or branch lengths, and b uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow and inflated significance in hypothesis testing (e.g. p-values will be too small. Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible

Bayesian models for comparative analysis integrating phylogenetic uncertainty

Science.gov (United States)

2012-01-01

Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

Science.gov (United States)

Wisniewski-Dyé, Florence; Lozano, Luis; Acosta-Cruz, Erika; Borland, Stéphanie; Drogue, Benoît; Prigent-Combaret, Claire; Rouy, Zoé; Barbe, Valérie; Mendoza Herrera, Alberto; González, Victor; Mavingui, Patrick

2012-01-01

Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation. PMID:24705077

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

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Victor González

2012-09-01

Full Text Available Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510. The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis, and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.

Consensuses and discrepancies of basin-scale ocean heat content changes in different ocean analyses

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Wang, Gongjie; Cheng, Lijing; Abraham, John; Li, Chongyin

2018-04-01

Inconsistent global/basin ocean heat content (OHC) changes were found in different ocean subsurface temperature analyses, especially in recent studies related to the slowdown in global surface temperature rise. This finding challenges the reliability of the ocean subsurface temperature analyses and motivates a more comprehensive inter-comparison between the analyses. Here we compare the OHC changes in three ocean analyses (Ishii, EN4 and IAP) to investigate the uncertainty in OHC in four major ocean basins from decadal to multi-decadal scales. First, all products show an increase of OHC since 1970 in each ocean basin revealing a robust warming, although the warming rates are not identical. The geographical patterns, the key modes and the vertical structure of OHC changes are consistent among the three datasets, implying that the main OHC variabilities can be robustly represented. However, large discrepancies are found in the percentage of basinal ocean heating related to the global ocean, with the largest differences in the Pacific and Southern Ocean. Meanwhile, we find a large discrepancy of ocean heat storage in different layers, especially within 300-700 m in the Pacific and Southern Oceans. Furthermore, the near surface analysis of Ishii and IAP are consistent with sea surface temperature (SST) products, but EN4 is found to underestimate the long-term trend. Compared with ocean heat storage derived from the atmospheric budget equation, all products show consistent seasonal cycles of OHC in the upper 1500 m especially during 2008 to 2012. Overall, our analyses further the understanding of the observed OHC variations, and we recommend a careful quantification of errors in the ocean analyses.

Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions [version 1; referees: 2 approved

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Eugene V. Koonin

2016-07-01

Full Text Available The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly universal genes, translates into the notion of a statistical tree of life (STOL, which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

Embodied energy and emergy analyses of a concentrating solar power (CSP) system

International Nuclear Information System (INIS)

Zhang Meimei; Wang Zhifeng; Xu Chao; Jiang Hui

2012-01-01

Although concentrating solar power (CSP) technology has been projected as one of the most promising candidates to replace conventional power plants burning fossil fuels, the potential advantages and disadvantages of the CSP technology have not been thoroughly evaluated. To better understand the performance of the CSP technology, this paper presents an ecological accounting framework based on embodied energy and emergy analyses methods. The analyses are performed for the 1.5 MW Dahan solar tower power plant in Beijing, China and different evaluation indices used in the embodied energy and emergy analyses are employed to evaluate the plant performance. Our analysis of the CSP plant are compared with six Italian power plants with different energy sources and an American PV plant, which demonstrates the CSP is the superior technology. - Highlights: ► Embodied energy and emergy analyses are employed to evaluate the first solar tower power plant in China. ► Different evaluation indices are quantitatively analyzed to show the advantages of CSP technology. ► This analysis provides insights for making energy policy and investment decisions about CSP technology.

Diagnostic Comparison of Meteorological Analyses during the 2002 Antarctic Winter

Science.gov (United States)

Manney, Gloria L.; Allen, Douglas R.; Kruger, Kirstin; Naujokat, Barbara; Santee, Michelle L.; Sabutis, Joseph L.; Pawson, Steven; Swinbank, Richard; Randall, Cora E.; Simmons, Adrian J.;

Comparative analyses of transport proteins encoded within the genomes of Leptospira species.

Science.gov (United States)

Buyuktimkin, Bora; Saier, Milton H

2016-09-01

Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they all have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity arose in Leptospira correlating to progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles. Copyright © 2016. Published by Elsevier Ltd.

The complete chloroplast genome sequence of Dodonaea viscosa: comparative and phylogenetic analyses.

Science.gov (United States)

Saina, Josphat K; Gichira, Andrew W; Li, Zhi-Zhong; Hu, Guang-Wan; Wang, Qing-Feng; Liao, Kuo

2018-02-01

The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp. The annotation analysis revealed a total of 115 unique genes of which 81 were protein coding, 30 tRNA, and four ribosomal RNA genes. Comparative genome analysis with other closely related Sapindaceae members showed conserved gene order in the inverted and single copy regions. Phylogenetic analysis clustered D. viscosa with other species of Sapindaceae with strong bootstrap support. Finally, a total of 249 SSRs were detected. Moreover, a comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates in D. viscosa showed very low values. The availability of cp genome reported here provides a valuable genetic resource for comprehensive further studies in genetic variation, taxonomy and phylogenetic evolution of Sapindaceae family. In addition, SSR markers detected will be used in further phylogeographic and population structure studies of the species in this genus.

The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

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Zhitao Niu

2017-05-01

Full Text Available Orchidaceae (orchids is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5′trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae were sisters to a multi-stamened subfamily (i.e., Cypripedioideae rather than to the other one-stamened subfamily (Vanilloideae, suggesting that the living one-stamened orchids are paraphyletic.

Comparison of Genome-Wide Association Methods in Analyses of Admixed Populations with Complex Familial Relationships

DEFF Research Database (Denmark)

Kadri, Naveen; Guldbrandtsen, Bernt; Sørensen, Peter

2014-01-01

Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P) and family (K......) levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic...... corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree...

Phylogenomic Insights into Animal Evolution.

Science.gov (United States)

Telford, Maximilian J; Budd, Graham E; Philippe, Hervé

2015-10-05

Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of the animal kingdom - their relationships to each other and the evolution of their body plans - was based on a consideration of the morphological and developmental characteristics of the different animal groups. This morphology-based approach had many successes but important aspects of the evolutionary tree remained disputed. In the past three decades, molecular data, most obviously primary sequences of DNA and proteins, have provided an estimate of animal phylogeny largely independent of the morphological evolution we would ultimately like to understand. The molecular tree that has evolved over the past three decades has drastically altered our view of animal phylogeny and many aspects of the tree are no longer contentious. The focus of molecular studies on relationships between animal groups means, however, that the discipline has become somewhat divorced from the underlying biology and from the morphological characteristics whose evolution we aim to understand. Here, we consider what we currently know of animal phylogeny; what aspects we are still uncertain about and what our improved understanding of animal phylogeny can tell us about the evolution of the great diversity of animal life. Copyright © 2015 Elsevier Ltd. All rights reserved.

A phylogenomic profile of globins

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Dewilde Sylvia

2006-04-01

Full Text Available Abstract Background Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FAD-binding domain and the gene-regulating globin coupled sensors, with variable C-terminal domains. The single-domain globins encompass sequences related to chimeric globins and «truncated» hemoglobins with a 2-over-2 instead of the canonical 3-over-3 α-helical fold. Results A census of globins in 26 archaeal, 245 bacterial and 49 eukaryote genomes was carried out. Only ~25% of archaea have globins, including globin coupled sensors, related single domain globins and 2-over-2 globins. From one to seven globins per genome were found in ~65% of the bacterial genomes: the presence and number of globins are positively correlated with genome size. Globins appear to be mostly absent in Bacteroidetes/Chlorobi, Chlamydia, Lactobacillales, Mollicutes, Rickettsiales, Pastorellales and Spirochaetes. Single domain globins occur in metazoans and flavohemoglobins are found in fungi, diplomonads and mycetozoans. Although red algae have single domain globins, including 2-over-2 globins, the green algae and ciliates have only 2-over-2 globins. Plants have symbiotic and nonsymbiotic single domain hemoglobins and 2-over-2 hemoglobins. Over 90% of eukaryotes have globins: the nematode Caenorhabditis has the most putative globins, ~33. No globins occur in the parasitic, unicellular eukaryotes such as Encephalitozoon, Entamoeba, Plasmodium and Trypanosoma. Conclusion Although Bacteria have all three types of globins, Archaeado not have flavohemoglobins and Eukaryotes lack globin coupled sensors. Since the hemoglobins in organisms other than animals are enzymes or sensors, it is likely that the evolution of an oxygen transport function accompanied the emergence of multicellular animals.

Laser Beam Focus Analyser

DEFF Research Database (Denmark)

Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

2007-01-01

the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating......The quantitative and qualitative description of laser beam characteristics is important for process implementation and optimisation. In particular, a need for quantitative characterisation of beam diameter was identified when using fibre lasers for micro manufacturing. Here the beam diameter limits...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...

Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae: A Comparative Analysis and Phylogenetic Implications.

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Jie Cai

Full Text Available Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.

Steady-state and accident analyses of PBMR with the computer code SPECTRA

International Nuclear Information System (INIS)

Stempniewicz, Marek M.

2002-01-01

The SPECTRA code is an accident analysis code developed at NRG. It is designed for thermal-hydraulic analyses of nuclear or conventional power plants. The code is capable of analysing the whole power plant, including reactor vessel, primary system, various control and safety systems, containment and reactor building. The aim of the work presented in this paper was to prepare a preliminary thermal-hydraulic model of PBMR for SPECTRA, and perform steady state and accident analyses. In order to assess SPECTRA capability to model the PBMR reactors, a model of the INCOGEN system has been prepared first. Steady state and accident scenarios were analyzed for INCOGEN configuration. Results were compared to the results obtained earlier with INAS and OCTOPUS/PANTHERMIX. A good agreement was obtained. Results of accident analyses with PBMR model showed qualitatively good results. It is concluded that SPECTRA is a suitable tool for analyzing High Temperature Reactors, such as INCOGEN or for example PBMR (Pebble Bed Modular Reactor). Analyses of INCOGEN and PBMR systems showed that in all analyzed cases the fuel temperatures remained within the acceptable limits. Consequently there is no danger of release of radioactivity to the environment. It may be concluded that those are promising designs for future safe industrial reactors. (author)

Thermal analyses. Information on the expected baking process; Thermische analyses. Informatie over een te verwachten bakgedrag

Energy Technology Data Exchange (ETDEWEB)

Van Wijck, H. [Stichting Technisch Centrum voor de Keramische Industrie TCKI, Velp (Netherlands)

2009-09-01

The design process and the drying process for architectural ceramics and pottery partly determine the characteristics of the final product, but the largest changes occur during the baking process. An overview is provided of the different thermal analyses and how the information from these analyses can predict the process in practice. (mk) [Dutch] Het vormgevingsproces en het droogproces voor bouwkeramische producten en aardewerk bepalen voor een deel de eigenschappen van de eindproducten, maar de grootste veranderingen treden op bij het bakproces. Een overzicht wordt gegeven van de verschillende thermische analyses en hoe de informatie uit deze analyses het in de praktijk te verwachten gedrag kan voorspellen.

Comparative analyses of the bacterial microbiota of the human nostril and oropharynx.

Science.gov (United States)

Lemon, Katherine P; Klepac-Ceraj, Vanja; Schiffer, Hilary K; Brodie, Eoin L; Lynch, Susan V; Kolter, Roberto

2010-06-22

The nose and throat are important sites of pathogen colonization, yet the microbiota of both is relatively unexplored by culture-independent approaches. We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries. While the bacterial microbiota of the oropharynx was richer than that of the nostril, the oropharyngeal microbiota varied less among participants than did nostril microbiota. A few phyla accounted for the majority of the bacteria detected at each site: Firmicutes and Actinobacteria in the nostril and Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx. Compared to culture-independent surveys of microbiota from other body sites, the microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites. In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of that of skin, though Proteobacteria were much less prevalent. The distribution of Firmicutes, Proteobacteria, and Bacteroidetes in the oropharynx was most similar to that in saliva, with more Proteobacteria than in the distal esophagus or mouth. While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each. At both sites there was an inverse correlation between the prevalences of Firmicutes and another phylum: in the oropharynx, Firmicutes and Proteobacteria, and in the nostril, Firmicutes and Actinobacteria. In the nostril, this inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups.

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

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

Science.gov (United States)

Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

2017-07-18

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.

Contribution of thermo-fluid analyses to the LHC experiments

CERN Document Server

Gasser, G

2003-01-01

The big amount of electrical and electronic equipment that will be installed in the four LHC experiments will cause important heat dissipation into the detectors’ volumes. This is a major issue for the experimental groups, as temperature stability is often a fundamental requirement for the different sub-detectors to be able to provide a good measurement quality. The thermofluid analyses that are carried out in the ST/CV group are a very efficient tool to understand and predict the thermal behaviour of the detectors. These studies are undertaken according to the needs of the experimental groups; they aim at evaluate the thermal stability for a proposed design, or to compare different technical solutions in order to choose the best one for the final design. The usual approach to carry out these studies is first presented and then, some practical examples of thermo-fluid analyses are presented focusing on the main results in order to illustrate their contribution.

Numerical analyses of an aircraft crash on containment building

Energy Technology Data Exchange (ETDEWEB)

Sim, Jae Min; Kim, Seung Hyun; Chang, Yoon Suk [Kyunghee University, Yongin (Korea, Republic of)

2016-05-15

The containment building is responsible to isolate and protect internal devices against external conditions like earthquake, hurricane and impact loading. It has also to protect leakage of radioactivity, like LOCA (Loss Of Coolant Accident), when severe accidents occurred. Meanwhile, social awareness such as terrorism has been increased globally after international aircraft crashes at World Trade Center and Pentagon. In this paper, FE (Finite Element) analyses according to variation of crash locations and speeds were carried out to examine the aircraft crash impact on a domestic containment building. In this paper, numerical analyses of aircraft crash on NPP's containment building were performed taking into account different locations and aircraft speeds. (1) Amounts of concrete failure were dependent on the crash locations and the connector was the most delicate location comparing to the dome and wall part. (2) Maximum stress values generated at the liner plate and rebars did not exceed their UTS values.

Numerical analyses of an aircraft crash on containment building

International Nuclear Information System (INIS)

Sim, Jae Min; Kim, Seung Hyun; Chang, Yoon Suk

2016-01-01

The containment building is responsible to isolate and protect internal devices against external conditions like earthquake, hurricane and impact loading. It has also to protect leakage of radioactivity, like LOCA (Loss Of Coolant Accident), when severe accidents occurred. Meanwhile, social awareness such as terrorism has been increased globally after international aircraft crashes at World Trade Center and Pentagon. In this paper, FE (Finite Element) analyses according to variation of crash locations and speeds were carried out to examine the aircraft crash impact on a domestic containment building. In this paper, numerical analyses of aircraft crash on NPP's containment building were performed taking into account different locations and aircraft speeds. (1) Amounts of concrete failure were dependent on the crash locations and the connector was the most delicate location comparing to the dome and wall part. (2) Maximum stress values generated at the liner plate and rebars did not exceed their UTS values

Chromosome analyses of nuclear-power plant workers

International Nuclear Information System (INIS)

Bauchinger, M.; Kolin-Gerresheim, J.; Schmid, E.; Dresp, J.

1980-01-01

A brief report is given on chromosome aberration analyses of 57 healthy male employees of six German nuclear power plants. All had received annual doses below maximum permissible occupational limit of 5 rem and had worked with radiation for periods ranging from 1 - 14 years. Exposure was mainly due to external sources of γ rays and high energy x radiation. Controls were 11 healthy males with no radiation exposure except natural background. The yields of dicentrics and acentrics were significantly higher than in the unirradiated controls, but no dose dependence was apparent. These results are compared with the dose response dependence of dicentrics + rings found in nuclear dockyard workers by Evans et al. (1979). (U.K.)

Safety analyses of the nuclear-powered ship Mutsu with RETRAN

International Nuclear Information System (INIS)

Naruko, Y.; Ishida, T.; Tanaka, Y.; Futamura, Y.

1982-01-01

To provide a quantitative basis for the safety evaluation of the N.S. Mutsu, a number of safety analyses were performed in the course of reexamination. With respect to operational transient analyses, the RETRAN computer code was used to predict plant performances on the basis of postulated transient scenarios. The COBRA-IV computer code was also used to obtain a value of the minimum DNBR for each transient, which is necessary to predict detailed thermal-hydraulic performances in the core region of the reactor. In the present paper, the following three operational transients, which were calculated as a part of the safety analyses, are being dealt with: a complete loss of load without reactor scram; an excessive load increase incident, which is followed by a 30 percent stepwise load increase in the steam dump flow; and an accidental depressurization of the primary system, which is followed by a sudden full opening of the pressurizer spray valve. A Mutsu two-loop RETRAN model and simulation results were described. The results being compared with those of land-based PWRs, the characteristic features of the Mutsu reactor were presented and the safety of the plant under the operational transient conditions was confirmed

INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Science.gov (United States)

Kjer, K M; Ware, J L; Rust, J; Wappler, T; Lanfear, R; Jermiin, L S; Zhou, X; Aspöck, H; Aspöck, U; Beutel, R G; Blanke, A; Donath, A; Flouri, T; Frandsen, P B; Kapli, P; Kawahara, A Y; Letsch, H; Mayer, C; McKenna, D D; Meusemann, K; Niehuis, O; Peters, R S; Wiegmann, B M; Yeates, D K; von Reumont, B M; Stamatakis, A; Misof, B

2015-07-31

Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a "roachoid" fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate. Copyright © 2015, American Association for the Advancement of Science.

Comparative analyses of genetic risk prediction methods reveal ...

Indian Academy of Sciences (India)

2015-03-12

Mar 12, 2015 ... 1National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. ... 2Institute of Post Graduate Medical Education and Research, J. C. Bose Road, ...... Torres D. M. and Harrison S. A 2008 Diagnosis and therapy of.

Comparative phytochemical analyses of two varieties of Adenia ...

African Journals Online (AJOL)

Dr Mrs Agoruyo

Adenia lobata is a medicinal plant that is traditionally used for the treatment of various diseases such as cancer in ... wrinkling of the skin, arthritis, Alzheimer's disease and much ..... Cancer Chemotherapy and Pharmacology,. 65: 277 – 287.

Comparative analyses of genetic risk prediction methods reveal ...

Indian Academy of Sciences (India)

0.85. 0.8. 0.95. 0.93. 0.81 rs1227756. 0.5. 0.56. 0.75. 0.55. 0.7. 0.71. 0.58. 0.81. 0.25. 0.5. 0.53. 0.48. 0.64. 0.58. 0.58. 0.8. 0.68. 0.78. 0.48. 0.65. NA. NA. NA. NA rs1501299. 0.64. 0.78. 0.75. 0.83. 0.83. 0.89. 0.83. 0.72. 0.63. 0.73. 0.78. 0.75. 0.84. 0.79. 0.61. 0.78. 0.78. 0.7. 0.73. 0.73. NA. NA. NA. NA rs16944. 0.64. 0.72. 0.68.

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

KAUST Repository

Haroon, Mohamed

2016-07-05

Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

KAUST Repository

Haroon, Mohamed; Thompson, Luke R.; Parks, Donovan H.; Hugenholtz, Philip; Stingl, Ulrich

2016-01-01

Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

Complete genome sequence of Bacillus velezensis QST713: a biocontrol agent that protects Agaricus bisporus crops against the green mould disease.

Science.gov (United States)

Pandin, Caroline; Le Coq, Dominique; Deschamps, Julien; Védie, Régis; Rousseau, Thierry; Aymerich, Stéphane; Briandet, Romain

2018-04-24

Bacillus subtilis QST713 is extensively used as a biological control agent in agricultural fields including in the button mushroom culture, Agaricus bisporus. This last use exploits its inhibitory activity against microbial pathogens such as Trichoderma aggressivum f. europaeum, the main button mushroom green mould competitor. Here, we report the complete genome sequence of this bacterium with a genome size of 4 233 757 bp, 4263 predicted genes and an average GC content of 45.9%. Based on phylogenomic analyses, strain QST713 is finally designated as Bacillus velezensis. Genomic analyses revealed two clusters encoding potential new antimicrobials with NRPS and TransATPKS synthetase. B. velezensis QST713 genome also harbours several genes previously described as being involved in surface colonization and biofilm formation. This strain shows a strong ability to form in vitro spatially organized biofilm and to antagonize T. aggressivum. The availability of this genome sequence could bring new elements to understand the interactions with micro or/and macroorganisms in crops. Copyright © 2018. Published by Elsevier B.V.

A catalogue of 136 microbial draft genomes from Red Sea metagenomes.

Science.gov (United States)

Haroon, Mohamed F; Thompson, Luke R; Parks, Donovan H; Hugenholtz, Philip; Stingl, Ulrich

2016-07-05

Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial diversity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.

Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs

Science.gov (United States)

Li, Hu; Leavengood, John M.; Chapman, Eric G.; Burkhardt, Daniel; Song, Fan; Jiang, Pei; Liu, Jinpeng; Cai, Wanzhi

2017-01-01

Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats. PMID:28878063

The Use of Statistical Process Control Tools for Analysing Financial Statements

Directory of Open Access Journals (Sweden)

Niezgoda Janusz

2017-06-01

Full Text Available This article presents the proposed application of one type of the modified Shewhart control charts in the monitoring of changes in the aggregated level of financial ratios. The control chart x̅ has been used as a basis of analysis. The examined variable from the sample in the mentioned chart is the arithmetic mean. The author proposes to substitute it with a synthetic measure that is determined and based on the selected ratios. As the ratios mentioned above, are expressed in different units and characters, the author applies standardisation. The results of selected comparative analyses have been presented for both bankrupts and non-bankrupts. They indicate the possibility of using control charts as an auxiliary tool in financial analyses.

USE OF BOUNDING ANALYSES TO ESTIMATE THE PREFORMANCE OF A SEISMICALLY ISOLATED STRUCTURE

Directory of Open Access Journals (Sweden)

Gökhan ÖZDEMİR

2017-03-01

Full Text Available Current design approach for seismic isolated structures is to perform bounding analyses. These analyses provide an envelope for the response of the seismic isolated structure rather than focusing on the actual performance. In this study, the success of bounding analyses to estimate performance of a seismic isolated structure, in which the isolation is provided by means of lead rubber bearings (LRBs, is evaluated in a comparative manner. For this purpose, nonlinear response history analyses were performed under the effect of bidirectional ground motion excitations. In bounding analyses, non-deteriorating hysteretic representations were used to model the hysteretic behavior of LRBs. On the other hand, to estimate the actual performance of both the superstructure and isolator units, deteriorating hysteretic idealizations were employed. The deterioration in strength of LRBs was defined as a function of temperature rise in the lead core. The analyzed structure is an existing seismically isolated hospital building and analytically modeled in accordance with its reported design properties for both isolation units and superstructure. Results obtained from analyses where LRBs are idealized by both deteriorating and non-deteriorating hysteretic representations are used in the comparisons. The response quantities used in the comparisons are maximum isolator displacement, maximum isolator force, maximum absolute floor acceleration, and maximum relative story displacements. In an average sense, bounding analyses is found to provide conservative estimates for the selected response quantities and fulfills its intended purpose. However, it is revealed that there may be individual cases where bounding analyses fails to provide a safe envelope.

A method for reducing memory errors in the isotopic analyses of uranium hexafluoride by mass spectrometry; Methode de reduction des erreurs de memoire dans les analyses isotopiques de l'hexafluorure d'uranium par spectrometrie de masse

Energy Technology Data Exchange (ETDEWEB)

Bir, R [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires

1961-07-01

One of the most serious causes of systematic error in isotopic analyses of uranium from UF{sub 6} is the tendency of this material to become fixed in various ways in the mass spectrometer. As a result the value indicated by the instrument is influenced by the isotopic composition of the substances previously analysed. The resulting error is called a memory error. Making use of an elementary mathematical theory, the various methods used to reduce memory errors are analysed and compared. A new method is then suggested, which reduces the memory errors to an extent where they become negligible over a wide range of {sup 235}U concentration. The method is given in full, together with examples of its application. (author) [French] Une des causes d'erreurs systematiques les plus graves dans les analyses isotopiques d'uranium a partir d'UF{sub 6} est l'aptitude de ce produit a se fixer de diverses manieres dans le spectrometre de masse. Il en resulte une influence de la composition isotopique des produits precedemment analyses sur la valeur indiquee par l'appareil. L'erreur resultante est appelee erreur de memoire. A partir d'une theorie mathematique elementaire, on analyse et on compare les differentes methodes utilisees pour reduire les erreurs de memoire. On suggere ensuite une nouvelle methode qui reduit les erreurs de memoire dans une proportion telle qu'elles deviennent negligeables dans un grand domaine de concentration en {sup 235}U. On donne le mode operatoire complet et des exemples d'application. (auteur)

Does the inclusion of grey literature influence estimates of intervention effectiveness reported in meta-analyses?

Science.gov (United States)

McAuley, L; Pham, B; Tugwell, P; Moher, D

2000-10-07

The inclusion of only a subset of all available evidence in a meta-analysis may introduce biases and threaten its validity; this is particularly likely if the subset of included studies differ from those not included, which may be the case for published and grey literature (unpublished studies, with limited distribution). We set out to examine whether exclusion of grey literature, compared with its inclusion in meta-analysis, provides different estimates of the effectiveness of interventions assessed in randomised trials. From a random sample of 135 meta-analyses, we identified and retrieved 33 publications that included both grey and published primary studies. The 33 publications contributed 41 separate meta-analyses from several disease areas. General characteristics of the meta-analyses and associated studies and outcome data at the trial level were collected. We explored the effects of the inclusion of grey literature on the quantitative results using logistic-regression analyses. 33% of the meta-analyses were found to include some form of grey literature. The grey literature, when included, accounts for between 4.5% and 75% of the studies in a meta-analysis. On average, published work, compared with grey literature, yielded significantly larger estimates of the intervention effect by 15% (ratio of odds ratios=1.15 [95% CI 1.04-1.28]). Excluding abstracts from the analysis further compounded the exaggeration (1.33 [1.10-1.60]). The exclusion of grey literature from meta-analyses can lead to exaggerated estimates of intervention effectiveness. In general, meta-analysts should attempt to identify, retrieve, and include all reports, grey and published, that meet predefined inclusion criteria.

Subgroup analyses on return to work in sick-listed employees with low back pain in a randomised trial comparing brief and multidisciplinary intervention

Directory of Open Access Journals (Sweden)

Petersen Karin D

2011-05-01

Full Text Available Abstract Background Multidisciplinary intervention is recommended for rehabilitation of employees sick-listed for 4-12 weeks due to low back pain (LBP. However, comparison of a brief and a multidisciplinary intervention in a randomised comparative trial of sick-listed employees showed similar return to work (RTW rates in the two groups. The aim of the present study was to identify subgroups, primarily defined by work-related baseline factors that would benefit more from the multidisciplinary intervention than from the brief intervention. Methods A total of 351 employees sick-listed for 3-16 weeks due to LBP were recruited from their general practitioners. They received a brief or a multidisciplinary intervention. Both interventions comprised clinical examination and advice by a rehabilitation doctor and a physiotherapist. The multidisciplinary intervention also comprised assignment of a case manager, who made a rehabilitation plan in collaboration with the patient and a multidisciplinary team. Using data from a national database, we defined RTW as no sickness compensation benefit disbursement for four consecutive weeks within the first year after the intervention. At the first interview in the clinic, it was ensured that sick leave was primarily due to low back problems.Questionnaires were used to obtain data on health, disability, demographic and workplace-related factors. Cox hazard regression analyses were used with RTW as outcome measure and hazard rate ratios (HRR = HRmultidisciplinary/HRbrief were adjusted for demographic and health-related variables. An interaction term consisting of a baseline variable*intervention group was added to the multivariable regression model to analyse whether the effects of the interventions were moderated by the baseline factor. Subsequently, a new study was performed that included 120 patients who followed the same protocol. This group was analyzed in the same way to verify the findings from the original

Topological variation in single-gene phylogenetic trees

OpenAIRE

Castresana, Jose

2007-01-01

A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.

Cladistic analyses of behavioural variation in wild Pan troglodytes: exploring the chimpanzee culture hypothesis.

Science.gov (United States)

Lycett, Stephen J; Collard, Mark; McGrew, William C

2009-10-01

Long-term field studies have revealed considerable behavioural differences among groups of wild Pan troglodytes. Here, we report three sets of cladistic analyses that were designed to shed light on issues relating to this interpopulation variation that are of particular relevance to palaeoanthropology. In the first set of analyses, we focused on the proximate cause of the variation. Some researchers have argued that it is cultural, while others have suggested that it is the result of genetic differences. Because the eastern and western subspecies of P. troglodytes are well differentiated genetically while groups within the subspecies are not, we reasoned that if the genetic hypothesis is correct, the phylogenetic signal should be stronger when data from the eastern and western subspecies are analysed together compared to when data from only the eastern subspecies are analysed. Using randomisation procedures, we found that the phylogenetic signal was substantially stronger with in a single subspecies rather than with two. The results of the first sets of analyses, therefore, were inconsistent with the predictions of the genetic hypothesis. The other two sets of analyses built on the results of the first and assumed that the intergroup behavioural variation is cultural in nature. Recent work has shown that, contrary to what anthropologists and archaeologists have long believed, vertical intergroup transmission is often more important than horizontal intergroup transmission in human cultural evolution. In the second set of analyses, we sought to determine how important vertical transmission has been in the evolution of chimpanzee cultural diversity. The first analysis we carried out indicated that the intergroup similarities and differences in behaviour are consistent with the divergence of the western and eastern subspecies, which is what would be expected if vertical intergroup transmission has been the dominant process. In the second analysis, we found that the

Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae.

Science.gov (United States)

Benjak, Andrej; Avanzi, Charlotte; Singh, Pushpendra; Loiseau, Chloé; Girma, Selfu; Busso, Philippe; Fontes, Amanda N Brum; Miyamoto, Yuji; Namisato, Masako; Bobosha, Kidist; Salgado, Claudio G; da Silva, Moisés B; Bouth, Raquel C; Frade, Marco A C; Filho, Fred Bernardes; Barreto, Josafá G; Nery, José A C; Bührer-Sékula, Samira; Lupien, Andréanne; Al-Samie, Abdul R; Al-Qubati, Yasin; Alkubati, Abdul S; Bretzel, Gisela; Vera-Cabrera, Lucio; Sakho, Fatoumata; Johnson, Christian R; Kodio, Mamoudou; Fomba, Abdoulaye; Sow, Samba O; Gado, Moussa; Konaté, Ousmane; Stefani, Mariane M A; Penna, Gerson O; Suffys, Philip N; Sarno, Euzenir Nunes; Moraes, Milton O; Rosa, Patricia S; Baptista, Ida M F Dias; Spencer, John S; Aseffa, Abraham; Matsuoka, Masanori; Kai, Masanori; Cole, Stewart T

2018-01-24

Leprosy is a chronic human disease caused by the yet-uncultured pathogen Mycobacterium leprae. Although readily curable with multidrug therapy (MDT), over 200,000 new cases are still reported annually. Here, we obtain M. leprae genome sequences from DNA extracted directly from patients' skin biopsies using a customized protocol. Comparative and phylogenetic analysis of 154 genomes from 25 countries provides insight into evolution and antimicrobial resistance, uncovering lineages and phylogeographic trends, with the most ancestral strains linked to the Far East. In addition to known MDT-resistance mutations, we detect other mutations associated with antibiotic resistance, and retrace a potential stepwise emergence of extensive drug resistance in the pre-MDT era. Some of the previously undescribed mutations occur in genes that are apparently subject to positive selection, and two of these (ribD, fadD9) are restricted to drug-resistant strains. Finally, nonsense mutations in the nth excision repair gene are associated with greater sequence diversity and drug resistance.

Biofilm-Growing Bacteria Involved in the Corrosion of Concrete Wastewater Pipes: Protocols for Comparative Metagenomic Analyses

Science.gov (United States)

Advances in high-throughput next-generation sequencing (NGS) technology for direct sequencing of environmental DNA (i.e. shotgun metagenomics) is transforming the field of microbiology. NGS technologies are now regularly being applied in comparative metagenomic studies, which pr...

Comparison of design and probabilistic analyses of nuclear power plants

International Nuclear Information System (INIS)

Maslenikov, O.R.; Johnson, J.J.; Campbell, R.D.

1995-01-01

A study was made to evaluate the margin of conservatism introduced into design in-structures response spectra by following standard design analysis procedures according to the U.S.Nuclear Regulatory Commission (NRC) Standard Review Plan and Regulatory Guides for comparing spectra produced by such a design analysis to response from median-centered probabilistic analyses. Three typical nuclear plant structures were studied: PWR reactor building, PWR auxiliary building and BWR reactor building. Each building was assumed to be situated on three idealized sites: a rock site, a medium and a soft soil site. All buildings were assumed to have embedded foundations. The PWR reactor building was also assumed to have a surface foundation. Each design analysis was performed inn accordance with the current SRP criteria. Each probabilistic analysis consisted of 30 earthquake simulations for which the free-field motions and soil and structural properties were varied; the simulated earthquakes were generated such that their mean-plus-one-standard-deviation free-field spectra approximated the Regulatory Guide (RG) 1.60 design spectra. In-structure response spectra from the design analyses were compared with the 84% non-exceedance probability (NEP) spectra from the probabilistic analyses. The comparisons showed that the design method produced conservative results for all cases. The smallest margin was about 10% for buildings on rock sites. Softer sides had larger margins of conservatism; the reactor buildings on the soft soil site had margins of as much as 100% (factor of 2),. The shorter structures and lower locations in all buildings had smaller margins. The margin of conservatism for the surface founded reactor building was about 20% more than for the embedded reactor building. (author). 3 refs., 5 figs., 1 tab

Comparative analyses reveal different consequences of two oxidative stress inducers, gamma irradiation and potassium tellurite, in the extremophile Deinococcus radiodurans

International Nuclear Information System (INIS)

Narasimha, Anaganti; Basu, Bhakti; Apte, Shree Kumar

2014-01-01

Proteomic and mass spectrometric analyses revealed differential responses of D. radiodurans to two oxidative stressors. While both elicited oxidative stress alleviation response, major divergence was observed at the level of DNA repair, metabolic pathways and protein homeostasis. Response to gamma irradiation was focused on DNA repair and ROS scavenging but supported metabolism as well as protein homeostasis. Tellurite, induced oxidative stress alleviation but decreased reducing affected and adversely affected metabolism and protein homeostasis

Comparative Analyses on OPR1000 Steam Generator Tube Rupture Event Emergency Operational Guideline

International Nuclear Information System (INIS)

Lee, Sang Won; Bae, Yeon Kyoung; Kim, Hyeong Teak

2006-01-01

The Steam Generator Tube Rupture (SGTR) event is one of the important scenarios in respect to the radiation release to the environment. When the SGTR occurs, containment integrity is not effective because of the direct bypass of containment via the ruptured steam generator to the MSSV and MSADV. To prevent this path, the Emergency Operational Guideline of OPR1000 indicates the use of Turbine Bypass Valves (TBVs) as an effective means to depressurize the main steam line and prevent the lifting of MSSV. However, the TBVs are not operable when the offsite power is not available (LOOP). In this situation, the RCS cool-down is achieved by opening the both intact and ruptured SG MSADV. But this action causes the large amount of radiation release to the environment. To minimize the radiation release to the environment, KSNP EOG adopts the improved strategy when the SGTR concurrently with LOOP is occurred. However, these procedures show some duplicated procedure and branch line that might confusing the operator for optimal recovery action. So, in this paper, the comparative analysis on SGTR and SGTR with LOOP is performed and optimized procedure is proposed

The ASSET intercomparison of stratosphere and lower mesosphere humidity analyses

Directory of Open Access Journals (Sweden)

H. E. Thornton

2009-02-01

Full Text Available This paper presents results from the first detailed intercomparison of stratosphere-lower mesosphere water vapour analyses; it builds on earlier results from the EU funded framework V "Assimilation of ENVISAT Data" (ASSET project. Stratospheric water vapour plays an important role in many key atmospheric processes and therefore an improved understanding of its daily variability is desirable. With the availability of high resolution, good quality Michelson Interferometer for Passive Atmospheric Sounding (MIPAS water vapour profiles, the ability of four different atmospheric models to assimilate these data is tested. MIPAS data have been assimilated over September 2003 into the models of the European Centre for Medium Range Weather Forecasts (ECMWF, the Belgian Institute for Space and Aeronomy (BIRA-IASB, the French Service d'Aéronomie (SA-IPSL and the UK Met Office. The resultant middle atmosphere humidity analyses are compared against independent satellite data from the Halogen Occultation Experiment (HALOE, the Polar Ozone and Aerosol Measurement (POAM III and the Stratospheric Aerosol and Gas Experiment (SAGE II. The MIPAS water vapour profiles are generally well assimilated in the ECMWF, BIRA-IASB and SA systems, producing stratosphere-mesosphere water vapour fields where the main features compare favourably with the independent observations. However, the models are less capable of assimilating the MIPAS data where water vapour values are locally extreme or in regions of strong humidity gradients, such as the southern hemisphere lower stratosphere polar vortex. Differences in the analyses can be attributed to the choice of humidity control variable, how the background error covariance matrix is generated, the model resolution and its complexity, the degree of quality control of the observations and the use of observations near the model boundaries. Due to the poor performance of the Met Office analyses the results are not included in

The ASSET intercomparison of stratosphere and lower mesosphere humidity analyses

Science.gov (United States)

Thornton, H. E.; Jackson, D. R.; Bekki, S.; Bormann, N.; Errera, Q.; Geer, A. J.; Lahoz, W. A.; Rharmili, S.

2009-02-01

This paper presents results from the first detailed intercomparison of stratosphere-lower mesosphere water vapour analyses; it builds on earlier results from the EU funded framework V "Assimilation of ENVISAT Data" (ASSET) project. Stratospheric water vapour plays an important role in many key atmospheric processes and therefore an improved understanding of its daily variability is desirable. With the availability of high resolution, good quality Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) water vapour profiles, the ability of four different atmospheric models to assimilate these data is tested. MIPAS data have been assimilated over September 2003 into the models of the European Centre for Medium Range Weather Forecasts (ECMWF), the Belgian Institute for Space and Aeronomy (BIRA-IASB), the French Service d'Aéronomie (SA-IPSL) and the UK Met Office. The resultant middle atmosphere humidity analyses are compared against independent satellite data from the Halogen Occultation Experiment (HALOE), the Polar Ozone and Aerosol Measurement (POAM III) and the Stratospheric Aerosol and Gas Experiment (SAGE II). The MIPAS water vapour profiles are generally well assimilated in the ECMWF, BIRA-IASB and SA systems, producing stratosphere-mesosphere water vapour fields where the main features compare favourably with the independent observations. However, the models are less capable of assimilating the MIPAS data where water vapour values are locally extreme or in regions of strong humidity gradients, such as the southern hemisphere lower stratosphere polar vortex. Differences in the analyses can be attributed to the choice of humidity control variable, how the background error covariance matrix is generated, the model resolution and its complexity, the degree of quality control of the observations and the use of observations near the model boundaries. Due to the poor performance of the Met Office analyses the results are not included in the intercomparison

The complete genome sequence of Bacillus velezensis 9912D reveals its biocontrol mechanism as a novel commercial biological fungicide agent.

Science.gov (United States)

Pan, Hua-Qi; Li, Qing-Lian; Hu, Jiang-Chun

2017-04-10

A Bacillus sp. 9912 mutant, 9912D, was approved as a new biological fungicide agent by the Ministry of Agriculture of the People's Republic of China in 2016 owing to its excellent inhibitory effect on various plant pathogens and being environment-friendly. Here, we present the genome of 9912D with a circular chromosome having 4436 coding DNA sequences (CDSs), and a circular plasmid encoding 59 CDSs. This strain was finally designated as Bacillus velezensis based on phylogenomic analyses. Genome analysis revealed a total of 19 candidate gene clusters involved in secondary metabolite biosynthesis, including potential new type II lantibiotics. The absence of fengycin biosynthetic gene cluster is noteworthy. Our data offer insights into the genetic, biological and physiological characteristics of this strain and aid in deeper understanding of its biocontrol mechanism. Copyright © 2017 Elsevier B.V. All rights reserved.

A journey into a Mediterranean diet and type 2 diabetes: a systematic review with meta-analyses

Science.gov (United States)

Esposito, Katherine; Maiorino, Maria Ida; Bellastella, Giuseppe; Chiodini, Paolo; Panagiotakos, Demosthenes; Giugliano, Dario

2015-01-01

Objectives To summarise the evidence about the efficacy of a Mediterranean diet on the management of type 2 diabetes and prediabetic states. Design A systematic review of all meta-analyses and randomised controlled trials (RCTs) that compared the Mediterranean diet with a control diet on the treatment of type 2 diabetes and prediabetic states was conducted. Electronic searches were carried out up to January 2015. Trials were included for meta-analyses if they had a control group treated with another diet, if they were of sufficient duration (at least 6 months), and if they had at least 30 participants in each arm. A random-effect model was used to pool data. Participants Adults with or at risk for type 2 diabetes. Interventions Dietary patterns that described themselves as using a ‘Mediterranean’ dietary pattern. Outcome measures The outcomes were glycaemic control, cardiovascular risk factors and remission from the metabolic syndrome. Results From 2824 studies, 8 meta-analyses and 5 RCTs were eligible. A ‘de novo’ meta-analysis of 3 long-term (>6 months) RCTs of the Mediterranean diet and glycaemic control of diabetes favoured the Mediterranean diet as compared with lower fat diets. Another ‘de novo’ meta-analysis of two long-term RCTs showed a 49% increased probability of remission from the metabolic syndrome. 5 meta-analyses showed a favourable effect of the Mediterranean diet, as compared with other diets, on body weight, total cholesterol and high-density lipoprotein cholesterol. 2 meta-analyses demonstrated that higher adherence to the Mediterranean diet reduced the risk of future diabetes by 19–23%. Conclusions The Mediterranean diet was associated with better glycaemic control and cardiovascular risk factors than control diets, including a lower fat diet, suggesting that it is suitable for the overall management of type 2 diabetes. PMID:26260349

Hearing loss among older construction workers: Updated analyses.

Science.gov (United States)

Dement, John; Welch, Laura S; Ringen, Knut; Cranford, Kim; Quinn, Patricia

2018-04-01

A prior study of this construction worker population found significant noise-associated hearing loss. This follow-up study included a much larger study population and consideration of additional risk factors. Data included audiometry, clinical chemistry, personal history, and work history. Qualitative exposure metrics for noise and solvents were developed. Analyses compared construction workers to an internal reference group with lower exposures and an external worker population with low noise exposure. Among participants (n = 19 127) an overall prevalence of hearing loss of 58% was observed, with significantly increased prevalence across all construction trades. Construction workers had significantly increased risk of hearing loss compared to reference populations, with increasing risk by work duration. Noise exposure, solvent exposure, hypertension, and smoking were significant risk factors in multivariate models. Results support a causal relationship between construction trades work and hearing loss. Prevention should focus on reducing exposure to noise, solvents, and cigarette smoke. © 2018 Wiley Periodicals, Inc.

On the Syntax of Canonical Comparatives in European Portuguese

Directory of Open Access Journals (Sweden)

Gabriela Matos

2002-06-01

Full Text Available Comparative constructions in English and other Germanic and Romance languages have been analysed either as subordinate or coordinate structures. Focussing European Portuguese (=EP we will argue, from a syntactic point of view, that there is evidence for the coordinate nature of canonical comparatives in this language. In fact, not only many properties of these constructions distinguish them from subordinate structures, but also most of the characteristics attributed to the subordinate status of comparatives can also be accounted for within the coordinate approach. In particular, the selection of the comparative phrase by the degree marker in the first term of comparison may be viewed as a case of correlative coordination. In the same line of reasoning, the islands effects exhibited by comparative clauses do not constitute a compelling evidence for the systematic presence of a wh-operator, since they may also arise in other cases of A-bar movement. So, though accepting that Comparative and Subcomparative deletions are two distinct cases of Operator-variable chain, relying on empirical evidence across other Romance languages, we will analyse Comparative Deletion in European Portuguese as an instance of (Quantified Null Object and we will impute Subcomparative deletion to Quantifier Raising at LF for scope assignment purposes.

Analysing home-ownership of couples: the effect of selecting couples at the time of the survey.

Science.gov (United States)

Mulder, C H

1996-09-01

"The analysis of events encountered by couple and family households may suffer from sample selection bias when data are restricted to couples existing at the moment of interview. The paper discusses the effect of sample selection bias on event history analyses of buying a home [in the Netherlands] by comparing analyses performed on a sample of existing couples with analyses of a more complete sample including past as well as current partner relationships. The results show that, although home-buying in relationships that have ended differs clearly from behaviour in existing relationships, sample selection bias is not alarmingly large." (SUMMARY IN FRE) excerpt

ATHENA/INTRA analyses for ITER, NSSR-2

International Nuclear Information System (INIS)

Shen, Kecheng; Eriksson, John; Sjoeberg, A.

1999-02-01

The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes

ATHENA/INTRA analyses for ITER, NSSR-2

Energy Technology Data Exchange (ETDEWEB)

Shen, Kecheng; Eriksson, John; Sjoeberg, A

1999-02-01

The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes 8 refs, 14 figs, 15 tabs

Safety and deterministic failure analyses in high-beta D-D tokamak reactors

International Nuclear Information System (INIS)

Selcow, E.C.

1984-01-01

Safety and deterministic failure analyses were performed to compare major component failure characteristics for different high-beta D-D tokamak reactors. The primary focus was on evaluating damage to the reactor facility. The analyses also considered potential hazards to the general public and operational personnel. Parametric designs of high-beta D-D tokamak reactors were developed, using WILDCAT as the reference. The size, and toroidal field strength were reduced, and the fusion power increased in an independent manner. These changes were expected to improve the economics of D-D tokamaks. Issues examined using these designs were radiation induced failurs, radiation safety, first wall failure from plasma disruptions, and toroidal field magnet coil failure

The Banana Genome Hub

Science.gov (United States)

Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

2013-01-01

Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

Agriproteomics of Bread Wheat: Comparative Proteomics and Network Analyses of Grain Size Variation.

Science.gov (United States)

Dawkar, Vishal V; Dholakia, Bhushan B; Gupta, Vidya S

2015-07-01

Agriproteomics signifies the merging of agriculture research and proteomics systems science and is impacting plant research and societal development. Wheat is a frequently consumed foodstuff, has highly variable grain size that in effect contributes to wheat grain yield and the end-product quality. Very limited information is available on molecular basis of grain size due to complex multifactorial nature of this trait. Here, using liquid chromatography-mass spectrometry, we investigated the proteomics profiles from grains of wheat genotypes, Rye selection 111 (RS111) and Chinese spring (CS), which differ in their size. Significant differences in protein expression were found, including 33 proteins uniquely present in RS111 and 32 only in CS, while 54 proteins were expressed from both genotypes. Among differentially expressed proteins, 22 were upregulated, while 21 proteins were downregulated in RS111 compared to CS. Functional classification revealed their role in energy metabolism, seed storage, stress tolerance and transcription. Further, protein interactive network analysis was performed to predict the targets of identified proteins. Significantly different interactions patterns were observed between these genotypes with detection of proteins such as Cyp450, Sus2, and WRKY that could potentially affect seed size. The present study illustrates the potentials of agriproteomics as a veritable new frontier of plant omics research.

Comparative Study of Daylighting Calculation Methods

Directory of Open Access Journals (Sweden)

Mandala Ariani

2018-01-01

Full Text Available The aim of this study is to assess five daylighting calculation method commonly used in architectural study. The methods used include hand calculation methods (SNI/DPMB method and BRE Daylighting Protractors, scale models studied in an artificial sky simulator and computer programs using Dialux and Velux lighting software. The test room is conditioned by the uniform sky conditions, simple room geometry with variations of the room reflectance (black, grey, and white color. The analyses compared the result (including daylight factor, illumination, and coefficient of uniformity value and examines the similarity and contrast the result different. The color variations trial is used to analyses the internally reflection factor contribution to the result.

Josephson comparator switching time

Energy Technology Data Exchange (ETDEWEB)

Herr, Quentin P; Miller, Donald L; Przybysz, John X [Northrop Grumman, Baltimore, MD (United States)

2006-05-15

Comparator performance can be characterized in terms of both sensitivity and decision time. Delta-sigma analogue-to-digital converters are tolerant of sensitivity errors but require short decision time due to feedback. We have analysed the Josephson comparator using the numerical solution of the Fokker-Planck equation, which describes the time evolution of the ensemble probability distribution. At balance, the result is essentially independent of temperature in the range 5-20 K. There is a very small probability, 1 x 10{sup -14}, that the decision time will be longer than seven single-flux-quantum pulse widths, defined as Phi{sub 0}/(I{sub c}R{sub n}). For junctions with a critical current density of 4.5 kA, this decision time is only 20 ps. Decision time error probability decreases rapidly with lengthening time interval, at a rate of two orders of magnitude per pulse width. We conclude that Josephson comparator performance is quite favourable for analogue-to-digital converter applications.

Consumer brand choice: individual and group analyses of demand elasticity.

Science.gov (United States)

Oliveira-Castro, Jorge M; Foxall, Gordon R; Schrezenmaier, Teresa C

2006-03-01

Following the behavior-analytic tradition of analyzing individual behavior, the present research investigated demand elasticity of individual consumers purchasing supermarket products, and compared individual and group analyses of elasticity. Panel data from 80 UK consumers purchasing 9 product categories (i.e., baked beans, biscuits, breakfast cereals, butter, cheese, fruit juice, instant coffee, margarine and tea) during a 16-week period were used. Elasticity coefficients were calculated for individual consumers with data from all or only 1 product category (intra-consumer elasticities), and for each product category using all data points from all consumers (overall product elasticity) or 1 average data point per consumer (interconsumer elasticity). In addition to this, split-sample elasticity coefficients were obtained for each individual with data from all product categories purchased during weeks 1 to 8 and 9 to 16. The results suggest that: 1) demand elasticity coefficients calculated for individual consumers purchasing supermarket food products are compatible with predictions from economic theory and behavioral economics; 2) overall product elasticities, typically employed in marketing and econometric research, include effects of interconsumer and intraconsumer elasticities; 3) when comparing demand elasticities of different product categories, group and individual analyses yield similar trends; and 4) individual differences in demand elasticity are relatively consistent across time, but do not seem to be consistent across products. These results demonstrate the theoretical, methodological, and managerial relevance of investigating the behavior of individual consumers.

Resolution analyses for selecting an appropriate airborne electromagnetic (AEM) system

DEFF Research Database (Denmark)

Christensen, N.B.; Lawrie, Ken

2012-01-01

is necessary and has to be approached in a pragmatic way involving a range of different aspects. In this paper, we concentrate on the resolution analysis perspective and demonstrate that the inversion analysis must be preferred over the derivative analysis because it takes parameter coupling into account, and...... resolution for a series of models relevant to the survey area by comparing the sum over the data of squares of noise-normalised derivatives. We compare this analysis method with a resolution analysis based on the posterior covariance matrix of an inversion formulation. Both of the above analyses depend......, furthermore, that the derivative analysis generally overestimates the resolution capability. Finally we show that impulse response data are to be preferred over step response data for near-surface resolution....