scholarly journals Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease

2015 ◽  
Vol 105 (9) ◽  
pp. 1262-1269 ◽  
Author(s):  
Jean-Sébastien Reynard ◽  
Pierre H. H. Schneeberger ◽  
Jürg Ernst Frey ◽  
Santiago Schaerer
Keyword(s):  
Large Scale ◽  
Amino Acid Identity ◽  
Biological Properties ◽  
Enzyme Linked Immunosorbent Assay ◽  
Subgroup Ii ◽  
Leafroll Disease ◽  
Serological Data ◽  
Pyrosequencing Technology ◽  
Divergent Strain

The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera ‘Otcha bala’ from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.

scholarly journals Characterization of the Gene Cassette Required for Biosynthesis of the (α1→6)-LinkedN-Acetyl-d-Mannosamine-1-Phosphate Capsule of Serogroup A Neisseria meningitidis

1998 ◽  
Vol 180 (6) ◽  
pp. 1533-1539 ◽  
Author(s):  
John S. Swartley ◽  
Li-Jun Liu ◽  
Yoon K. Miller ◽  
Larry E. Martin ◽  
Srilatha Edupuganti ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Intergenic Region ◽  
Gene Cassette ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Capsule Production ◽  
Reading Frames

ABSTRACT The (α1→6)-linkedN-acetyl-d-mannosamine-1-phosphate meningococcal capsule of serogroup A Neisseria meningitidisis biochemically distinct from the sialic acid-containing capsules produced by other disease-associated meningococcal serogroups (e.g., B, C, Y, and W-135). We defined the genetic cassette responsible for expression of the serogroup A capsule. The cassette comprised a 4,701-bp nucleotide sequence located between the outer membrane capsule transporter gene, ctrA, and galE, encoding the UDP-glucose-4-epimerase. Four open reading frames (ORFs) not found in the genomes of the other meningococcal serogroups were identified. The first serogroup A ORF was separated from ctrA by a 218-bp intergenic region. Reverse transcriptase (RT) PCR and primer extension studies of serogroup A mRNA showed that all four ORFs were cotranscribed in the opposite orientation to ctrA and that transcription of the ORFs was initiated from the intergenic region by a ς-70-type promoter that overlapped the ctrA promoter. The first ORF exhibited 58% amino acid identity with the UDP-N-acetyl-d-glucosamine (UDP-GlcNAc) 2-epimerase of Escherichia coli, which is responsible for the conversion of UDP-GlcNAc into UDP-N-acetyl-d-mannosamine. Polar or nonpolar mutagenesis of each of the ORFs resulted in an abrogation of serogroup A capsule production as determined by colony immunoblots and enzyme-linked immunosorbent assay. Replacement of the serogroup A biosynthetic gene cassette with a serogroup B cassette by transformation resulted in capsule switching from a serogroup A capsule to a serogroup B capsule. These data indicate that assembly of the serogroup A capsule likely begins with monomeric UDP-GlcNAc and requires proteins encoded by three other genes found in the serogroup A N. meningitidis-specific operon located betweenctrA and galE.

scholarly journals Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
M. Ahsan ◽  
M. Ashfaq ◽  
H. Riaz ◽  
Z. Khan ◽  
M. Z. Hamza ◽  
...  
Keyword(s):  
Spinacia Oleracea ◽  
Balancing Selection ◽  
Statistical Tests ◽  
Disease Incidence ◽  
Phylogenetic Reconstruction ◽  
Enzyme Linked Immunosorbent Assay ◽  
Subgroup Ii ◽  
Cmv Disease ◽  
Indel Event

Abstract Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour-joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the values 2.02535, 0.01468, and 0.71862 of Tajima's D, Fu, & Li’s F* and D* respectively, demonstrating that the CMV population is under balancing selection.

scholarly journals Biological and Molecular Characterization of a New Cucurbit-Infecting Tobamovirus

2001 ◽  
Vol 91 (6) ◽  
pp. 565-571 ◽  
Author(s):  
Y. Antignus ◽  
Y. Wang ◽  
M. Pearlsman ◽  
O. Lachman ◽  
N. Lavi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Genome Organization ◽  
Economic Losses ◽  
Its Sequence ◽  
Subgroup Ii ◽  
Cucumber Fruit ◽  
The Family ◽  
Serological Data

An uncharacterized virus was isolated from greenhouse-grown cucumber plants. Biological and serological data described in the present study indicated that the virus belonged in the genus Tobamovirus. The host range of the virus included several plant species within the family Cucurbitaceae. The virus designated Cucumber fruit mottle mosaic virus (CFMMV) causes severe mottling or mosaic on cucumber fruits, and its fast spread within greenhouses could lead to significant economic losses in cucumber crops. The genome of CFMMV has been completely sequenced and its genome organization was typical of a Tobamovirus. However, its sequence was distinct from other described viruses within the group of cucurbit-infecting Tobamoviruses. Comparisons of sequences and phylogenetic analysis suggested that the cucurbit-infecting Tobamoviruses be separated into two subgroups: subgroup I comprising the strains and isolates referred to in the literature as Cucumber green mottle mosaic virus (CGMMV) (CV3, CV4, CGMMV-W, CGMMV-SH, and CGMMV-Is) and subgroup II comprising CFMMV, Kyuri green mottle mosaic virus (KGMMV), and the Yodo strain of CGMMV, which is closely related to KGMMV and may be considered a strain of it.

scholarly journals APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins

2016 ◽  
Author(s):  
Malvika Sharan ◽  
Konrad U. Förstner ◽  
Ana Eulalio ◽  
Jörg Vogel
Keyword(s):  
Large Scale ◽  
Binding Proteins ◽  
Rna Binding ◽  
Markov Models ◽  
Rna Binding Proteins ◽  
Experimental Studies ◽  
Biological Properties ◽  
Computational Pipeline ◽  
Identification And Characterization

ABSTRACTRNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs), and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches.We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using Position Specific Scoring Matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot

Some applications of electron beam microanalysis techniques in VLSI process evaluation

1983 ◽  
Vol 41 ◽  
pp. 160-161
Author(s):  
Simon Thomas
Keyword(s):  
Integrated Circuits ◽  
Process Evaluation ◽  
Large Scale ◽  
Technology Development ◽  
Analytical Techniques ◽  
Successful Implementation ◽  
Analysis Of Failures ◽  
Characterization Of Materials ◽  
Circuits Vlsi

Trends in the technology development of very large scale integrated circuits (VLSI) have been in the direction of higher density of components with smaller dimensions. The scaling down of device dimensions has been not only laterally but also in depth. Such efforts in miniaturization bring with them new developments in materials and processing. Successful implementation of these efforts is, to a large extent, dependent on the proper understanding of the material properties, process technologies and reliability issues, through adequate analytical studies. The analytical instrumentation technology has, fortunately, kept pace with the basic requirements of devices with lateral dimensions in the micron/ submicron range and depths of the order of nonometers. Often, newer analytical techniques have emerged or the more conventional techniques have been adapted to meet the more stringent requirements. As such, a variety of analytical techniques are available today to aid an analyst in the efforts of VLSI process evaluation. Generally such analytical efforts are divided into the characterization of materials, evaluation of processing steps and the analysis of failures.

Characterization of Portuguese Propolis: Unraveling Biological Properties

Planta Medica ◽  
2014 ◽  
Vol 80 (16) ◽  
Author(s):  
CA Aguiar ◽  
AM Ferreira ◽  
R Oliveira ◽  
F Baltazar ◽  
A Cunha
Keyword(s):  
Biological Properties

TBE in Sweden

2020 ◽  
Keyword(s):  
Genetic Characterization ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Second Phase ◽  
Serum Samples ◽  
Tick Borne Encephalitis ◽  
Specific Immunoglobulin ◽  
Tick Borne Encephalitis Virus ◽  
First Time

Tick-borne encephalitis virus (TBEV) was isolated for the first time in Sweden in 1958 (from ticks and from 1 tick-borne encephalitis [TBE] patient).1 In 2003, Haglund and colleagues reported the isolation and antigenic and genetic characterization of 14 TBEV strains from Swedish patients (samples collected 1991–1994).2 The first serum sample, from which TBEV was isolated, was obtained 2–10 days after onset of disease and found to be negative for anti-TBEV immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA), whereas TBEV-specific IgM (and TBEV-specific immunoglobulin G/cerebrospinal fluid [IgG/CSF] activity) was demonstrated in later serum samples taken during the second phase of the disease.

Characterization of seawater reverse osmosis fouled membranes from large scale commercial desalination plant

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Reverse Osmosis ◽  
Large Scale ◽  
Retention Rate ◽  
Local Level ◽  
Microscopic Analysis ◽  
Transmembrane Pressure ◽  
Hydraulic Permeability ◽  
Seawater Reverse Osmosis ◽  
A Chain

The objective of this work is to study the ageing state of a used reverse osmosis (RO) membrane taken in Algeria from the Benisaf Water Company seawater desalination unit. The study consists of an autopsy procedure used to perform a chain of analyses on a membrane sheet. Wear of the membrane is characterized by a degradation of its performance due to a significant increase in hydraulic permeability (25%) and pressure drop as well as a decrease in salt retention (10% to 30%). In most cases the effects of ageing are little or poorly known at the local level and global measurements such as (flux, transmembrane pressure, permeate flow, retention rate, etc.) do not allow characterization. Therefore, a used RO (reverse osmosis) membrane was selected at the site to perform the membrane autopsy tests. These tests make it possible to analyze and identify the cause as well as to understand the links between performance degradation observed at the macroscopic scale and at the scale at which ageing takes place. External and internal visual observations allow seeing the state of degradation. Microscopic analysis of the used membranes surface shows the importance of fouling. In addition, quantification and identification analyses determine a high fouling rate in the used membrane whose foulants is of inorganic and organic nature. Moreover, the analyses proved the presence of a biofilm composed of protein.

Characterization of Interconnect Defects Using Scanning Thermal Conductivity Microscopy

2004 ◽  
Author(s):  
H.W. Ho ◽  
J.C.H. Phang ◽  
A. Altes ◽  
L.J. Balk
Keyword(s):  
Thermal Conductivity ◽  
Integrated Circuits ◽  
Large Scale

Abstract In this paper, scanning thermal conductivity microscopy is used to characterize interconnect defects due to electromigration. Similar features are observed both in the temperature and thermal conductivity micrographs. The key advantage of the thermal conductivity mode is that specimen bias is not required. This is an important advantage for the characterization of defects in large scale integrated circuits. The thermal conductivity micrographs of extrusion, exposed and subsurface voids are presented and compared with the corresponding topography and temperature micrographs.

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