scholarly journals Polerovirus Genomic Variation

2021 ◽  
Author(s):  
Katherine LaTourrette ◽  
Natalie M Holste ◽  
Hernan Garcia-Ruiz
Keyword(s):  
Host Plants ◽  
Aphid Transmission ◽  
Virus Genome ◽  
Aphid Species ◽  
Genomic Variation ◽  
Virus Species ◽  
Mutational Robustness ◽  
Practical Applications ◽  
Wide Range ◽  
Positive Strand Rna

Abstract The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single, positive strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3) and a read-through domain (ORF5) that is fused to the CP to form a CP-RT protein. The genus Polerovirus contains 26 virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and VPg contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. Results described here suggest that using contrasting mechanisms, P0, VPg and CP-RT mediate adaptation to host plants, to vectors, and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, identification of susceptibility genes, and contributes to our understanding of virus interactions with their host, vectors, and environment.

scholarly journals Occurrence, Distribution, Evolutionary Relationships, Epidemiology, and Management of Orthotospoviruses in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhongkai Zhang ◽  
Kuanyu Zheng ◽  
Lihua Zhao ◽  
Xiaoxia Su ◽  
Xue Zheng ◽  
...  
Keyword(s):  
Host Plants ◽  
Spatial Clustering ◽  
Systemic Infection ◽  
Early Warning Systems ◽  
Host Cells ◽  
Future Research ◽  
Evolutionary Relationships ◽  
Virus Species ◽  
Wide Range ◽  
Underlying Mechanisms

Orthotospoviruses are responsible for serious crop losses worldwide. Orthotospoviral diseases have spread rapidly in China over the past 10 years and are now found in 19 provinces. Currently, 17 Orthotospovirus species have been reported in China, including eight newly identified species from this genus. The number of new highly pathogenic Orthotospovirus strains or species has increased, likely because of the virus species diversity, the wide range of available hosts, adaptation of the viruses to different climates, and multiple transmission routes. This review describes the distribution of Orthotospovirus species, host plants, typical symptoms of infection under natural conditions, the systemic infection of host plants, spatial clustering characteristics of virus particles in host cells, and the orthotospoviral infection cycle in the field. The evolutionary relationships of orthotospoviruses isolated from China and epidemiology are also discussed. In order to effectively manage orthotospoviral disease, future research needs to focus on deciphering the underlying mechanisms of systemic infection, studying complex/mixed infections involving the same or different Orthotospovirus species or other viruses, elucidating orthotospovirus adaptative mechanisms to multiple climate types, breeding virus-resistant plants, identifying new strains and species, developing early monitoring and early warning systems for plant infection, and studying infection transmission routes.

Barley yellow dwarf viruses in, and aphids on, grasses (including cereals) in Tasmania

1987 ◽  
Vol 38 (1) ◽  
pp. 139 ◽  
Author(s):  
PL Guy ◽  
GR Johnstone ◽  
DI Morris
Keyword(s):  
Poa Pratensis ◽  
Aphid Transmission ◽  
Aphid Species ◽  
Yellow Dwarf ◽  
Serological Tests ◽  
Hyalopterus Pruni ◽  
Barley Yellow Dwarf ◽  
Wide Range ◽  
Sitobion Fragariae ◽  
Cereal Plants

Samples of 2077 grasses and cereal plants representative of the Poaceae found in Tasmania were collected from a wide range of habitats throughout the State. Each sample was examined for infestation with aphids and then checked for infection with viruses causing barley yellow dwarf by both aphid transmission and serological tests. Aphid species found among the samples were Hyalopterus pruni, Rhopalosiphum maidis, R. padi and Sitobion fragariae. R. padi transmitted a vector non-specific type of barley yellow dwarf (PAV) and a vector specific type (RPV), either alone or together, while S. fragariae transmitted PAV alone and occasionally RPV when present in plants together with PAV. The other aphid species did not transmit. A total of 189 samples contained virus. Incidence was greatest in samples from the Bambusoideae subfamily (31%) and least in the Arundinoideae (4%). There was no difference in the level of infection between the native and introduced species that were represented. The Arundinoideae and Panicoideae were predominantly infected with RPV types, while the Pooideae, with the exception of Dactylis glomerata and Poa pratensis, were predominantly infected with PAV types. Many more infected plants contained both PAV and RPV (11.9%) than would have been expected had the two types of virus infected independently (2.5%). No infected plants were found among samples from 25 of the 56 species tested, and some of these may prove useful in breeding for resistance to barley yellow dwarf viruses.

A New Detector System For The HB5 Stem Instrument

1985 ◽  
Vol 43 ◽  
pp. 134-135
Author(s):  
J.M. Cowley
Keyword(s):  
Dark Field ◽  
Detector System ◽  
Electron Holography ◽  
Small Specimen ◽  
Bright Field ◽  
Multiple Images ◽  
Practical Applications ◽  
Wide Range ◽  
Diffraction Patterns ◽  
Operational Modes

The HB5 STEM instrument at ASU has been modified previously to include an efficient two-dimensional detector incorporating an optical analyser device and also a digital system for the recording of multiple images. The detector system was built to explore a wide range of possibilities including in-line electron holography, the observation and recording of diffraction patterns from very small specimen regions (having diameters as small as 3Å) and the formation of both bright field and dark field images by detection of various portions of the diffraction pattern. Experience in the use of this system has shown that sane of its capabilities are unique and valuable. For other purposes it appears that, while the principles of the operational modes may be verified, the practical applications are limited by the details of the initial design.

First Detection of Tobacco Mosaic Virus in Tobacco Fields in Northern Lebanon

2020 ◽  
Vol 20 ◽  
Author(s):  
Rami Obeid ◽  
Elias Wehbe ◽  
Mohamad Rima ◽  
Mohammad Kabara ◽  
Romeo Al Bersaoui ◽  
...  
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Viral Genome ◽  
Virus Genome ◽  
Enzyme Linked Immunosorbent Assay ◽  
Virus Family ◽  
Crop Fields ◽  
Wide Range ◽  
Almost All ◽  
Das Elisa

Background: Tobacco mosaic virus (TMV) is the most known virus in the plant mosaic virus family and is able to infect a wide range of crops, in particularly tobacco, causing a production loss. Objectives: Herein, and for the first time in Lebanon, we investigated the presence of TMV infection in crops by analyzing 88 samples of tobacco, tomato, cucumber and pepper collected from different regions in North Lebanon. Methods: Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), revealed a potential TMV infection of four tobacco samples out of 88 crops samples collected. However, no tomato, cucumber and pepper samples were infected. The TMV+ tobacco samples were then extensively analyzed by RT-PCR to detect viral RNA using different primers covering all the viral genome. Results and Discussion: PCR results confirmed those of DAS-ELISA showing TMV infection of four tobacco samples collected from three crop fields of North Lebanon. In only one of four TMV+ samples, we were able to amplify almost all the regions of viral genome, suggesting possible mutations in the virus genome or an infection with a new, not yet identified, TMV strain. Conclusion: Our study is the first in Lebanon revealing TMV infection in crop fields, and highlighting the danger that may affect the future of agriculture.

scholarly journals Ring-Forming Polymerization toward Perfluorocyclobutyl and Ortho-Diynylarene-Derived Materials: From Synthesis to Practical Applications

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1486
Author(s):  
Eugene B. Caldona ◽  
Ernesto I. Borrego ◽  
Ketki E. Shelar ◽  
Karl M. Mukeba ◽  
Dennis W. Smith
Keyword(s):  
Chemical Resistance ◽  
Structural Features ◽  
Review Article ◽  
Aryl Ether ◽  
Aromatic Rings ◽  
Practical Applications ◽  
Repeat Units ◽  
Wide Range ◽  
Synthetic Routes ◽  
The Cost

Many desirable characteristics of polymers arise from the method of polymerization and structural features of their repeat units, which typically are responsible for the polymer’s performance at the cost of processability. While linear alternatives are popular, polymers composed of cyclic repeat units across their backbones have generally been shown to exhibit higher optical transparency, lower water absorption, and higher glass transition temperatures. These specifically include polymers built with either substituted alicyclic structures or aromatic rings, or both. In this review article, we highlight two useful ring-forming polymer groups, perfluorocyclobutyl (PFCB) aryl ether polymers and ortho-diynylarene- (ODA) based thermosets, both demonstrating outstanding thermal stability, chemical resistance, mechanical integrity, and improved processability. Different synthetic routes (with emphasis on ring-forming polymerization) and properties for these polymers are discussed, followed by their relevant applications in a wide range of aspects.

scholarly journals Sensing of Nickel(II) Ions by Immobilizing Ligands and Using Different SPEs

2021 ◽  
Vol 6 (1) ◽  
pp. 2
Author(s):  
Liliana Anchidin-Norocel ◽  
Sonia Amariei ◽  
Gheorghe Gutt
Keyword(s):  
Bismuth Oxide ◽  
Human Population ◽  
Raw Materials ◽  
Sensor Technology ◽  
Cyclic Voltammogram ◽  
Accurate Analysis ◽  
Nickel Allergy ◽  
Nickel Ions ◽  
Practical Applications ◽  
Wide Range

The aim of this paper is the development of a sensor for the quantification of nickel ions in food raw materials and foods. It is believed that about 15% of the human population suffers from nickel allergy. In addition to digestive manifestations, food intolerance to nickel may also have systemic manifestations, such as diffuse dermatitis, diffuse itching, fever, rhinitis, headache, altered general condition. Therefore, it is necessary to control this content of nickel ions for the health of the human population by developing a new method that offers the advantages of a fast, not expensive, in situ, and accurate analysis. For this purpose, bismuth oxide-screen-printed electrodes (SPEs) and graphene-modified SPEs were used with a very small amount of dimethylglyoxime and amino acid L-histidine that were deposited. A potentiostat that displays the response in the form of a cyclic voltammogram was used to study the electrochemical properties of nickel standard solution with different concentrations. The results were compared and the most sensitive sensor proved to be bismuth oxide-SPEs with dimethylglyoxime (Bi2O3/C-dmgH2) with a linear response over a wide range (0.1–10 ppm) of nickel concentrations. Furthermore, the sensor shows excellent selectivity in the presence of common interfering species. The Bi2O3/C-dmgH2 sensor showed good viability for nickel analysis in food samples (cocoa, spinach, cabbage, and red wine) and demonstrated significant advancement in sensor technology for practical applications.

scholarly journals Assessment of Linearization Approaches for Multibody Dynamics Formulations

2017 ◽  
Vol 12 (4) ◽  
Author(s):  
Francisco González ◽  
Pierangelo Masarati ◽  
Javier Cuadrado ◽  
Miguel A. Naya
Keyword(s):  
Mechanical System ◽  
Multibody Dynamics ◽  
Equations Of Motion ◽  
Differential Algebraic Equations ◽  
Algebraic Equations ◽  
Practical Applications ◽  
Linearization Methods ◽  
Highly Nonlinear ◽  
Wide Range ◽  
The Way

Formulating the dynamics equations of a mechanical system following a multibody dynamics approach often leads to a set of highly nonlinear differential-algebraic equations (DAEs). While this form of the equations of motion is suitable for a wide range of practical applications, in some cases it is necessary to have access to the linearized system dynamics. This is the case when stability and modal analyses are to be carried out; the definition of plant and system models for certain control algorithms and state estimators also requires a linear expression of the dynamics. A number of methods for the linearization of multibody dynamics can be found in the literature. They differ in both the approach that they follow to handle the equations of motion and the way in which they deliver their results, which in turn are determined by the selection of the generalized coordinates used to describe the mechanical system. This selection is closely related to the way in which the kinematic constraints of the system are treated. Three major approaches can be distinguished and used to categorize most of the linearization methods published so far. In this work, we demonstrate the properties of each approach in the linearization of systems in static equilibrium, illustrating them with the study of two representative examples.

Periodic wavelet descriptor of plant leaf and its application in botany

2015 ◽  
Vol 13 (06) ◽  
pp. 1550043 ◽  
Author(s):  
Qing-Mao Zeng ◽  
Tong-Lin Zhu ◽  
Xue-Ying Zhuang ◽  
Ming-Xuan Zheng
Keyword(s):  
Species Identification ◽  
Plant Species ◽  
Shape Descriptor ◽  
Plant Leaf ◽  
Practical Applications ◽  
Wide Range ◽  
Periodic Wavelet ◽  
Plant Species Identification ◽  
Botanical Research ◽  
Wavelet Descriptor

Leaf is one of the most important organs of plant. Leaf contour or outline, usually a closed curve, is a fundamental morphological feature of leaf in botanical research. In this paper, a novel shape descriptor based on periodic wavelet series and leaf contour is presented, which we name as Periodic Wavelet Descriptor (PWD). The PWD of a leaf actually expresses the leaf contour in a vector form. Consequently, the PWD of a leaf has a wide range in practical applications, such as leaf modeling, plant species identification and classification, etc. In this work, the plant species identification and the leaf contour reconstruction, as two practical applications, are discussed to elaborate how to employ the PWD of a plant leaf in botanical research.

Long-offset moveout for VTI using Padé approximation

Geophysics ◽  
2016 ◽  
Vol 81 (5) ◽  
pp. C219-C227 ◽  
Author(s):  
Hanjie Song ◽  
Yingjie Gao ◽  
Jinhai Zhang ◽  
Zhenxing Yao
Keyword(s):  
Padé Approximation ◽  
Pade Approximation ◽  
Practical Applications ◽  
Long Offset ◽  
Wide Range ◽  
Isotropic Media ◽  
Transversally Isotropic ◽  
Error Accumulation ◽  
Anisotropy Parameters ◽  
Vti Media

The approximation of normal moveout is essential for estimating the anisotropy parameters of the transversally isotropic media with vertical symmetry axis (VTI). We have approximated the long-offset moveout using the Padé approximation based on the higher order Taylor series coefficients for VTI media. For a given anellipticity parameter, we have the best accuracy when the numerator is one order higher than the denominator (i.e., [[Formula: see text]]); thus, we suggest using [4/3] and [7/6] orders for practical applications. A [7/6] Padé approximation can handle a much larger offset and stronger anellipticity parameter. We have further compared the relative traveltime errors between the Padé approximation and several approximations. Our method shows great superiority to most existing methods over a wide range of offset (normalized offset up to 2 or offset-to-depth ratio up to 4) and anellipticity parameter (0–0.5). The Padé approximation provides us with an attractive high-accuracy scheme with an error that is negligible within its convergence domain. This is important for reducing the error accumulation especially for deeper substructures.

scholarly journals Polinton-like viruses are abundant in aquatic ecosystems

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Christopher M. Bellas ◽  
Ruben Sommaruga
Keyword(s):  
Capsid Protein ◽  
Major Capsid Protein ◽  
Virus Detection ◽  
Virus Genome ◽  
Alpine Lake ◽  
Virus Particles ◽  
Wide Range ◽  
Extracellular Form ◽  
Eukaryotic Organisms ◽  
Dsdna Viruses

Abstract Background Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they have been found to encode virus capsid genes, suggesting they may actually be integrated viruses; however, an extracellular form has yet to be detected. Recently, circa 25 Polinton-like viruses have been discovered in environmental metagenomes and algal genomes, which shared distantly related genes to both Polintons and virophages (Lavidaviridae). These entities could be the first members of a major class of ancient eukaryotic viruses; however, owing to the lack of available genomes for analysis, information on their global diversity, evolutionary relationships, eukaryotic hosts, and status as free virus particles is limited. Results Here, we analysed the metaviromes of an alpine lake to show that Polinton-like virus genome sequences are abundant in the water column. We identify major capsid protein genes belonging to 82 new Polinton-like viruses and use these to interrogate publicly available metagenomic datasets, identifying 543 genomes and a further 16 integrated into eukaryotic genomes. Using an analysis of shared gene content and major capsid protein phylogeny, we define large groups of Polinton-like viruses and link them to diverse eukaryotic hosts, including a new group of viruses, which possess all the core genes of virophages and infect oomycetes and Chrysophyceae. Conclusions Our study increased the number of known Polinton-like viruses by 25-fold, identifying five major new groups of eukaryotic viruses, which until now have been hidden in metagenomic datasets. The large enrichment (> 100-fold) of Polinton-like virus sequences in the virus-sized fraction of this alpine lake and the fact that their viral major capsid proteins are found in eukaryotic host transcriptomes support the hypothesis that Polintons in unicellular eukaryotes are viruses. In summary, our data reveals a diverse assemblage of globally distributed viruses, associated with a wide range of unicellular eukaryotic hosts. We anticipate that the methods we have developed for Polinton-like virus detection and the database of over 20,000 genes we present will allow for continued discovery and analysis of these new viral groups.

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