scholarly journals Hidden diversity and macroevolutionary mode of Caulimoviridae uncovered by euphyllophyte paleoviruses

2017 ◽  
Author(s):  
Zhen Gong ◽  
Guan-Zhu Han
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Repetitive Elements ◽  
Molecular Fossils ◽  
Copy Numbers ◽  
Minor Part ◽  
Endogenous Viral Elements ◽  
A Minor ◽  
Endogenous Plant

AbstractFew viruses have been documented in plants outside angiosperms. Endogenous viral elements (paleoviruses) provide ‘molecular fossils’ for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread across angiosperms, but little is known about EPRVs in earlier branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as Caulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs in the genomes of gymnosperms and ferns. The known angiosperm viruses only constitute a minor part of the Caulimoviridae diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of Caulimoviridae, raising the possibility that many exogenous Caulimoviridae remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs define a unique group of repetitive elements and represent major components of euphyllophyte genomes. Phylogenetic analyses reveal an ancient monilophyte origin of Caulimoviridae and at least three independent origins of Caulimoviridae in angiosperms by cross-division transmissions. Our findings uncover the remarkable diversity of Caulimoviridae and have important implications in understanding the origin and macroevolution of plant pararetroviruses.

scholarly journals Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode ofCaulimoviridae

2018 ◽  
Vol 92 (10) ◽  
Author(s):  
Zhen Gong ◽  
Guan-Zhu Han
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Repetitive Elements ◽  
Content Type ◽  
Molecular Fossils ◽  
Copy Numbers ◽  
Minor Part ◽  
Endogenous Viral Elements ◽  
A Minor ◽  
Endogenous Plant

ABSTRACTEndogenous viral elements (paleoviruses) provide “molecular fossils” for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms, but little is known about EPRVs in earlier-branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known asCaulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs within the genomes of gymnosperms and ferns. The known angiosperm viruses constitute only a minor part of theCaulimoviridaediversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity ofCaulimoviridae, raising the possibility that many exogenousCaulimoviridaeremain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs might define a unique group of repetitive elements and represent important components of euphyllophyte genomes. Evolutionary analyses suggest an ancient origin ofCaulimoviridaeand at least three independent origins ofCaulimoviridaein angiosperms. Our findings reveal the remarkable diversity ofCaulimoviridaeand have important implications for understanding the origin and macroevolution of plant pararetroviruses.IMPORTANCEFew viruses have been documented in plants outside angiosperms. Viruses can occasionally integrate into host genomes, forming endogenous viral elements (EVEs). Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms. In this study, we performed comprehensive comparative and phylogenetic analyses of EPRVs and found that EPRVs are present in the genomes of gymnosperms and ferns. We identified numerous EPRVs in gymnosperm and fern genomes, revealing an unprecedented depth in the diversity of plant pararetroviruses. Plant pararetroviruses mainly underwent cross-species transmission, and angiosperm pararetroviruses arose at least three times. Our study provides novel insights into the diversity and macroevolution of plant pararetroviruses.

scholarly journals Energy release and conversion by reconnection in the magnetotail

2005 ◽  
Vol 23 (10) ◽  
pp. 3365-3373 ◽  
Author(s):  
J. Birn ◽  
M. Hesse
Keyword(s):  
Energy Transfer ◽  
Energy Release ◽  
Large Scale ◽  
Magnetic Energy ◽  
Minor Role ◽  
Ohmic Dissipation ◽  
Particle Simulations ◽  
Minor Part ◽  
Reconnection Site ◽  
A Minor

Abstract. Magnetic reconnection is the crucial process in the release of magnetic energy previously stored in the magnetotail in association with substorms. However, energy transfer and dissipation in the vicinity of the reconnection site is only a minor part of the energy conversion. We discuss the energy release, transport, and conversion based on large-scale resistive MHD simulations of magnetotail dynamics and more localized full particle simulations of reconnection. We address in particular, where the energy is released, how it propagates and where and how it is converted from one form into another. We find that Joule (or ohmic) dissipation plays only a minor role in the overall energy transfer. Bulk kinetic energy, although locally significant in the outflow from the reconnection site, plays a more important role as mediator or catalyst in the transfer between magnetic and thermal energy. Generator regions with potential auroral consequences are located primarily off the equatorial plane in the boundary regions of the plasma sheet.

Interference mitigation in point to point wireless sensor networks using LSP protocol and time division multiplexing approach

2020 ◽  
Vol 39 (4) ◽  
pp. 5449-5458
Author(s):  
A. Arokiaraj Jovith ◽  
S.V. Kasmir Raja ◽  
A. Razia Sulthana
Keyword(s):  
Energy Consumption ◽  
Large Scale ◽  
Control Parameter ◽  
Interference Mitigation ◽  
Wireless Sensor ◽  
Point To Point ◽  
A Minor ◽  
Two Stages ◽  
Time Division ◽  
And Control

Interference in Wireless Sensor Network (WSN) predominantly affects the performance of the WSN. Energy consumption in WSN is one of the greatest concerns in the current generation. This work presents an approach for interference measurement and interference mitigation in point to point network. The nodes are distributed in the network and interference is measured by grouping the nodes in the region of a specific diameter. Hence this approach is scalable and isextended to large scale WSN. Interference is measured in two stages. In the first stage, interference is overcome by allocating time slots to the node stations in Time Division Multiple Access (TDMA) fashion. The node area is split into larger regions and smaller regions. The time slots are allocated to smaller regions in TDMA fashion. A TDMA based time slot allocation algorithm is proposed in this paper to enable reuse of timeslots with minimal interference between smaller regions. In the second stage, the network density and control parameter is introduced to reduce interference in a minor level within smaller node regions. The algorithm issimulated and the system is tested with varying control parameter. The node-level interference and the energy dissipation at nodes are captured by varying the node density of the network. The results indicate that the proposed approach measures the interference and mitigates with minimal energy consumption at nodes and with less overhead transmission.

THE ROLE OF ANTHROPONYMS IN THE SEMANTIC FIELD OF ARTISTIC WORKS

2019 ◽  
Vol 2019 (29) ◽  
pp. 66-77
Author(s):  
Lidiya Derbenyova
Keyword(s):  
Literary Work ◽  
Main Theme ◽  
Semantic Field ◽  
New Meanings ◽  
Minor Part ◽  
The One ◽  
A Minor ◽  
And Storage ◽  
Horizon Of Expectations

The article explores the role of antropoetonyms in the reader’s “horizon of expectation” formation. As a kind of “text in the text”, antropoetonyms are concentrating a large amount of information on a minor part of the text, reflecting the main theme of the work. As a “text” this class of poetonyms performs a number of functions: transmission and storage of information, generation of new meanings, the function of “cultural memory”, which explains the readers’ “horizon of expectations”. In analyzing the context of the literary work we should consider the function of antropoetonyms in vertical context (the link between artistic and other texts, and the groundwork system of culture), as well as in the context of the horizontal one (times’ connection realized in the communication chain from the word to the text; the author’s intention). In this aspect, the role of antropoetonyms in the structure of the literary text is extremely significant because antropoetonyms convey an associative nature, generating a complex mechanism of allusions. It’s an open fact that they always transmit information about the preceding text and suggest a double decoding. On the one hand, the recipient decodes this information, on the other – accepts this as a sort of hidden, “secret” sense.

Electrostatic effects on ionization equilibria: An MNDO study of proton and hydrogen transfer reactions of 4-fluorobutylamine

1990 ◽  
Vol 55 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Zdeněk Friedl ◽  
Stanislav Böhm
Keyword(s):  
Hydrogen Transfer ◽  
Substituent Effects ◽  
Radical Cations ◽  
Transfer Reactions ◽  
Protonated Forms ◽  
Minor Part ◽  
Bond Strengths ◽  
Ionization Equilibria ◽  
A Minor ◽  
Gas Phase Basicities

The relative enthalpies of proton transfer δ ΔH0and homolytic bond strengths δDH0(B-H+) were calculated by the MNDO method for the sp and ap conformers of 4-flurobutylamine. The data obtained, along with the experimental gas phase basicities, are compared with the values predicted by the electrostatic theory. It is shown that the substituent polar effects FD on the basicities of amines are predominantly due to interactions in their protonated forms (X-B-H+) and/or radical-cations (X-B+.), those in the neutral species (X-B) playing a minor part. A contribution, which is considerably more significant in the sp conformer than in the ap conformer, arises probably also from substituent effects on the homolytic bond strength DH0(B-H+.

scholarly journals Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2688
Author(s):  
Tobias Goris ◽  
Rafael R. C. Cuadrat ◽  
Annett Braune
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Health Impact ◽  
Gut Bacteria ◽  
Human Gut ◽  
Positive Health ◽  
Human Gut Microbiome ◽  
Nutritional Recommendations ◽  
Genes Encoding ◽  
A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

scholarly journals Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽  
2021 ◽  
pp. eabf2946
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals TreeMerge: a new method for improving the scalability of species tree estimation methods

2019 ◽  
Vol 35 (14) ◽  
pp. i417-i426 ◽  
Author(s):  
Erin K Molloy ◽  
Tandy Warnow
Keyword(s):  
Large Scale ◽  
Species Tree ◽  
New Method ◽  
Divide And Conquer ◽  
Supplementary Information ◽  
Estimation Methods ◽  
Running Time ◽  
Tree Estimation ◽  
Computationally Intensive ◽  
A Minor

Abstract Motivation At RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant limitations: it can fail to return a tree and, when used within the proposed divide-and-conquer framework, has O(n5) running time for datasets with n species. Results Here we present a new method called ‘TreeMerge’ that improves on NJMerge in two ways: it is guaranteed to return a tree and it has dramatically faster running time within the same divide-and-conquer framework—only O(n2) time. We use a simulation study to evaluate TreeMerge in the context of multi-locus species tree estimation with two leading methods, ASTRAL-III and RAxML. We find that the divide-and-conquer framework using TreeMerge has a minor impact on species tree accuracy, dramatically reduces running time, and enables both ASTRAL-III and RAxML to complete on datasets (that they would otherwise fail on), when given 64 GB of memory and 48 h maximum running time. Thus, TreeMerge is a step toward a larger vision of enabling researchers with limited computational resources to perform large-scale species tree estimation, which we call Phylogenomics for All. Availability and implementation TreeMerge is publicly available on Github (http://github.com/ekmolloy/treemerge). Supplementary information Supplementary data are available at Bioinformatics online.

Formation and dynamics of Saturn and its disk simulated by using a new N-body model

Open Physics ◽  
2003 ◽  
Vol 1 (4) ◽  
Author(s):  
A. Pavlov ◽  
Y. Pavlova
Keyword(s):  
Surface Density ◽  
Electromagnetic Interaction ◽  
The Core ◽  
Body Model ◽  
Magnetic Forces ◽  
Axis Of Rotation ◽  
Gravitational Model ◽  
Minor Part ◽  
Body Self ◽  
A Minor

AbstractThe formation of Saturn and its disk is simulated using a new N-body self-gravitational model. It is demonstrated that the formation of the disk and the planet is the result of gravitational contraction of a slowly rotated particle cloud that have a shape of slightly deformed sphere. The sphere was flattened by a coefficient of 0.8 along the axis of rotation. During the gravitational contraction, the major part of the cloud transformed into a planet and a minor part transformed into a disk. The thin structured disk is a result of the electromagnetic interaction in which the magnetic forces acting on charged particles of the cloud originate in the core of the planet. The simulation program gives such parameters of Saturn as the escape velocity of about 35 km/s at the surface, density, rotational velocities of the rings and temperature distribution.

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

2017 ◽  
Vol 74 (7) ◽  
pp. 1875-1884 ◽  
Author(s):  
Dmitry N. Kulagin ◽  
Tatiana V. Neretina
Keyword(s):  
Atlantic Ocean ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Maturity Stage ◽  
Congeneric Species ◽  
Morphological Examination ◽  
Posterior Teeth ◽  
Biogeographic Patterns ◽  
True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

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