scholarly journals Detection, Transmission, and Characterization of Grapevine Virus H in Croatia

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1578
Author(s):  
Martin Jagunić ◽  
Boris Lazarević ◽  
Kristina Nikolić ◽  
Domagoj Stupić ◽  
Darko Preiner ◽  
...  
Keyword(s):  
Transmission Rate ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Grapevine Virus ◽  
Coding Regions ◽  
Source Plant ◽  
One Step ◽  
Inoculation Access Period ◽  
Vine Mealybug

A survey of recently discovered vitiviruses was performed on 113 Croatian autochthonous grapevine cultivars from the national collection “Jazbina” using one-step RT-PCR. The presence of grapevine virus H (GVH) was confirmed in nine (7.9%) cultivars and grapevine virus G in eight (7.1%), while the presence of grapevine viruses I and J were not detected. GVH was transmitted by the vine mealybug (Planococcus ficus) from a source plant to grapevine seedlings with a 10.5% transmission rate using a combination of 10 first and second instars per plant with 48 and 72 h of acquisition and inoculation access period, respectively. Transmission correlated with the presence of grapevine leafroll-associated virus 3 (GLRaV-3) in the GVH-source plant and recipient seedlings. No alternative GVH host was identified. A comparison of 356 nt fragments of the RdRP and CP coding regions showed nucleotide identity between the Croatian GVH isolates in the range of 95.5–99.2% and 97.5–99.4% and amino acid identity between 95.8 and 100% and between 98.3 and 100%, respectively. Comparison with foreign isolates revealed nucleotide sequence similarity in the RdRP and CP between 94 and 100% and between 97.7–100%, respectively. To the best of our knowledge, this is the first report of GVH in Croatia and the first identification of the vine mealybug as a vector of GVH.

scholarly journals Taxogenomics of the Genus Cyclobacterium: Cyclobacterium xiamenense and Cyclobacterium halophilum as Synonyms and Description of Cyclobacterium plantarum sp. nov.

2020 ◽  
Vol 8 (4) ◽  
pp. 610 ◽  
Author(s):  
Azadeh Shahinpei ◽  
Mohammad Ali Amoozegar ◽  
Leila Mirfeizi ◽  
Mahdi Moshtaghi Nikou ◽  
Antonio Ventosa ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Threshold Value ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Average Amino Acid Identity ◽  
Halophytic Plant ◽  
Taxonomic Characterization ◽  
Current Species

The genus Cyclobacterium belongs to the phylum Bacteroidetes and includes eight species. Our study, based on the genomic parameters in silico DNA–DNA hybridization (GGDC), average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that all current species of Cyclobacterium belong to this genus and constitute a coherent phylogenomic group, but with species forming two separate branches. In addition, the genome-based analyses revealed that Cyclobacterium xiamenense and Cyclobacterium halophilum are members of the same species. Besides, we carried out a taxonomic characterization of the new strain GBPx2T, isolated from the halophytic plant Salicornia sp. Analysis of its 16S rRNA gene sequence showed the highest sequence similarity (97.5%) to Cyclobacterium lianum HY9T. Percentages of GGDC and OrthoANI between strain GBPx2T and species of the genus Cyclobacterium were lower than the threshold value for species delineation. The DNA G+C content was 43.0 mol%. The polar lipids included phosphatidylethanolamine as well as one unidentified phospholipid and four unidentified lipids, and its major cellular fatty acids were iso-C15:0 and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The only quinone present was menaquinone 7. Based on a combination of phenotypic, chemotaxonomic, and phylogenomic features, the GBPx2T strain represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium plantarum sp. nov. is proposed. The type strain of Cyclobacterium plantarum is GBPx2T (= IBRC-M 10634T = LMG 28551T).

scholarly journals Characterization of substrate specificity and novel autoprocessing mechanism of dipeptidase A from Prevotella intermedia

2020 ◽  
Vol 401 (5) ◽  
pp. 629-642 ◽  
Author(s):  
Mohammad Tanvir Sarwar ◽  
Yuko Ohara-Nemoto ◽  
Takeshi Kobayakawa ◽  
Mariko Naito ◽  
Takayuki K. Nemoto
Keyword(s):  
Substrate Specificity ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Lactobacillus Helveticus ◽  
Prevotella Intermedia ◽  
Gram Negative ◽  
Acid Identity ◽  
Mature Form ◽  
N Terminus

AbstractPrevotella intermedia, a Gram-negative anaerobic rod, is frequently observed in subgingival polymicrobial biofilms from adults with chronic periodontitis. Peptidases in periodontopathic bacteria are considered to function as etiological reagents. Prevotella intermedia OMA14 cells abundantly express an unidentified cysteine peptidase specific for Arg-4-methycoumaryl-7-amide (MCA). BAU17746 (locus tag, PIOMA14_I_1238) and BAU18827 (locus tag, PIOMA14_II_0322) emerged as candidates of this peptidase from the substrate specificity and sequence similarity with C69-family Streptococcus gordonii Arg-aminopeptidase. The recombinant form of the former solely exhibited hydrolyzing activity toward Arg-MCA, and BAU17746 possesses a 26.6% amino acid identity with the C69-family Lactobacillus helveticus dipeptidase A. It was found that BAU17746 as well as L. helveticus dipeptidase A was a P1-position Arg-specific dipeptidase A, although the L. helveticus entity, a representative of the C69 family, had been reported to be specific for Leu and Phe. The full-length form of BAU17746 was intramolecularly processed to a mature form carrying the N-terminus of Cys15. In conclusion, the marked Arg-MCA-hydrolyzing activity in Pre. intermedia was mediated by BAU17746 belonging to the C69-family dipeptidase A, in which the mature form carries an essential cysteine at the N-terminus.

scholarly journals Morphological and Molecular Characterization of a Cypovirus (Reoviridae) from the Mosquito Uranotaenia sapphirina (Diptera: Culicidae)

2005 ◽  
Vol 79 (15) ◽  
pp. 9430-9438 ◽  
Author(s):  
Alexandra Shapiro ◽  
Terry Green ◽  
Shujing Rao ◽  
Susan White ◽  
Gerry Carner ◽  
...  
Keyword(s):  
Inclusion Bodies ◽  
Transmission Rate ◽  
Sequence Similarity ◽  
Choristoneura Fumiferana ◽  
Mosquito Species ◽  
Electrophoretic Analysis ◽  
Antheraea Mylitta ◽  
Virus Particles ◽  
Large Numbers

ABSTRACT A novel cypovirus has been isolated from the mosquito Uranotaenia sapphirina (UsCPV) and shown to cause a chronic infection confined to the cytoplasm of epithelial cells of the gastric ceca and posterior stomach. The production of large numbers of virions and inclusion bodies and their arrangement into paracrystalline arrays gives the gut of infected insects a distinctive blue iridescence. The virions, which were examined by electron microscopy, are icosahedral (55 to 65 nm in diameter) with a central core that is surrounded by a single capsid layer. They are usually packaged individually within cubic inclusion bodies (polyhedra, ∼100 nm across), although two to eight virus particles were sometimes occluded together. The virus was experimentally transmitted per os to several mosquito species. The transmission rate was enhanced by the presence of magnesium ions but was inhibited by calcium ions. Most of the infected larvae survived to adulthood, and the adults retained the infection. Electrophoretic analysis of the UsCPV genome segments (using 1% agarose gels) generated a migration pattern (electropherotype) that is different from those of the 16 Cypovirus species already recognized. UsCPV genome segment 10 (Seg-10) showed no significant nucleotide sequence similarity to the corresponding segment of the other cypoviruses that have previously been analyzed, and it has different “conserved” termini. A BLAST search of the UsCPV deduced amino acid sequence also showed little similarity to Antheraea mylitta CPV-4 (67 of 290 [23%]) or Choristoneura fumiferana CPV-16 (33 of 111 [29%]). We conclude that UsCPV should be recognized as a member of a new Cypovirus species (Cypovirus 17, strain UsCPV-17).

scholarly journals Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

2021 ◽  
Vol 7 (3) ◽  
pp. 47
Author(s):  
Marios Lange ◽  
Rodiola Begolli ◽  
Antonis Giakountis
Keyword(s):  
Disease Onset ◽  
Cancer Genome ◽  
Driver Mutations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Coding Regions ◽  
Functional Variants ◽  
Coding Variants ◽  
Clinical Potential

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.

scholarly journals Exploiting the Amazing Diversity of Natural Source-Derived Polysaccharides: Modern Procedures of Isolation, Engineering, and Optimization of Antiviral Activities

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 136
Author(s):  
Bimalendu Ray ◽  
Martin Schütz ◽  
Shuvam Mukherjee ◽  
Subrata Jana ◽  
Sayani Ray ◽  
...  
Keyword(s):  
Structural Characteristics ◽  
Antiviral Drug ◽  
Natural Source ◽  
Target Interaction ◽  
Charge Densities ◽  
Linkage Pattern ◽  
Naturally Occurring ◽  
Antiviral Activities ◽  
One Step

Naturally occurring polysaccharide sulfates are highly diverse, owning variations in the backbone structure, linkage pattern and stereochemistry, branching diversity, sulfate content and positions of sulfate group(s). These structural characteristics bring about diverse sulfated polymers with dissimilar negative charge densities and structure–activity relationships. Herein, we start with a short discussion of techniques needed for extraction, purification, chemical sulfation, and structural characterization of polysaccharides. Processes of isolation and sulfation of plant-derived polysaccharides are challenging and usually involve two steps. In this context, we describe an integrated extraction-sulfation procedure that produces polysaccharide sulfates from natural products in one step, thereby generating additional pharmacological activities. Finally, we provide examples of the spectrum of natural source-derived polysaccharides possessing specific features of bioactivity, in particular focusing on current aspects of antiviral drug development and drug–target interaction. Thus, the review presents a detailed view on chemically engineered polysaccharides, especially sulfated derivatives, and underlines their promising biomedical perspectives.

scholarly journals Single Step 2-Port Device De-Embedding Algorithm for Fixture-DUT-Fixture Network Assembly

Electronics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1275
Author(s):  
Simone Scafati ◽  
Enza Pellegrino ◽  
Francesco de Paulis ◽  
Carlo Olivieri ◽  
James Drewniak ◽  
...  
Keyword(s):  
Standard Technique ◽  
Single Step ◽  
Scattering Parameters ◽  
Linear Set ◽  
S Parameter ◽  
Parameter Conversion ◽  
Before And After ◽  
One Step ◽  
Typical Measurement

The de-embedding of measurement fixtures is relevant for an accurate experimental characterization of radio frequency and digital electronic devices. The standard technique consists in removing the effects of the measurement fixtures by the calculation of the transfer scattering parameters (T-parameters) from the available measured (or simulated) global scattering parameters (S-parameters). The standard de-embedding is achieved by a multiple steps process, involving the S-to-T and subsequent T-to-S parameter conversion. In a typical measurement setup, two fixtures are usually placed before and after the device under test (DUT) allowing the connection of the device to the calibrated vector network analyzer coaxial ports. An alternative method is proposed in this paper: it is based on the newly developed multi-network cascading algorithm. The matrices involved in the fixture-DUT-fixture cascading gives rise to a non-linear set of equations that is in one step analytically solved in closed form, obtaining a unique solution. The method is shown to be effective and at least as accurate as the standard multi-step de-embedding one.

scholarly journals A Versatile Approach to Access Trimetallic Complexes Based on Trisphosphinite Ligands

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 593
Author(s):  
Juan Miranda-Pizarro ◽  
Macarena G. Alférez ◽  
M. Dolores Fernández-Martínez ◽  
Eleuterio Álvarez ◽  
Celia Maya ◽  
...  
Keyword(s):  
Coordination Chemistry ◽  
Late Transition Metal ◽  
X Ray Diffraction ◽  
X Ray ◽  
Full Characterization ◽  
Metal Precursors ◽  
Straightforward Method ◽  
One Step ◽  
Late Transition

A straightforward method for the preparation of trisphosphinite ligands in one step, using only commercially available reagents (1,1,1-tris(4-hydroxyphenyl)ethane and chlorophosphines) is described. We have made use of this approach to prepare a small family of four trisphosphinite ligands of formula [CH3C{(C6H4OR2)3], where R stands for Ph (1a), Xyl (1b, Xyl = 2,6-Me2-C6H3), iPr (1c), and Cy (1d). These polyfunctional phosphinites allowed us to investigate their coordination chemistry towards a range of late transition metal precursors. As such, we report here the isolation and full characterization of a number of Au(I), Ag(I), Cu(I), Ir(III), Rh(III) and Ru(II) homotrimetallic complexes, including the structural characterization by X-ray diffraction studies of six of these compounds. We have observed that the flexibility of these trisphosphinites enables a variety of conformations for the different trimetallic species.

scholarly journals Genetic and Molecular Characterization of the Maizerp3Rust Resistance Locus

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 381-394 ◽  
Author(s):  
Craig A Webb ◽  
Todd E Richter ◽  
Nicholas C Collins ◽  
Marie Nicolas ◽  
Harold N Trick ◽  
...  
Keyword(s):  
Family Members ◽  
Crossing Over ◽  
Resistance Locus ◽  
Leucine Rich Repeat ◽  
Bac Contig ◽  
Puccinia Sorghi ◽  
Coding Regions ◽  
Complex Locus ◽  
Sequence Identities

AbstractIn maize, the Rp3 gene confers resistance to common rust caused by Puccinia sorghi. Flanking marker analysis of rust-susceptible rp3 variants suggested that most of them arose via unequal crossing over, indicating that rp3 is a complex locus like rp1. The PIC13 probe identifies a nucleotide binding site-leucine-rich repeat (NBS-LRR) gene family that maps to the complex. Rp3 variants show losses of PIC13 family members relative to the resistant parents when probed with PIC13, indicating that the Rp3 gene is a member of this family. Gel blots and sequence analysis suggest that at least 9 family members are at the locus in most Rp3-carrying lines and that at least 5 of these are transcribed in the Rp3-A haplotype. The coding regions of 14 family members, isolated from three different Rp3-carrying haplotypes, had DNA sequence identities from 93 to 99%. Partial sequencing of clones of a BAC contig spanning the rp3 locus in the maize inbred line B73 identified five different PIC13 paralogues in a region of ∼140 kb.

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