scholarly journals Characterization of a novel recombination event in the Deformed wing bee virus polymerase gene

2018 ◽  
Vol 68 (4) ◽  
pp. 661 ◽  
Author(s):  
G GORAS ◽  
IGA RUETHER ◽  
CH TANANAKI ◽  
S GOUNARI ◽  
V LIOLIOS ◽  
...  
Keyword(s):  
Recombination Event ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Rna Dependent Rna Polymerase ◽  
Reverse Transcription Pcr ◽  
Plot Analysis ◽  
Recombination Point ◽  
Bee Virus ◽  
Similarity Plot

Honeybee populations are known to be infected by numerous viruses. Reverse transcription-PCR (RT-PCR) of regions of the RNA-dependent RNA polymerase is often used to diagnose the presence in apiaries and also to classify the type of virus detected. In this report, through analysis of the RdRp gene, we describe a novel recombination event in the DWV genome. Similarity plot analysis amplified from hundred positive individuals identified a previously undescribed recombination point in the 5’ region of the polymerase gene. To our knowledge this is the first description of recombination in the DWV polymerase gene and highlights the continuous genetic evolution of these viruses.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene

2020 ◽  
Vol 64 (8) ◽  
pp. 556-562
Author(s):  
Mozafar Hajijafari Anaraki ◽  
Nariman Sheikhi ◽  
Hadi Haghbin Nazarpak ◽  
Gholamreza Nikbakht Brujeni
Keyword(s):  
Rna Polymerase ◽  
Molecular Characterization ◽  
Infectious Bronchitis Virus ◽  
Polymerase Gene ◽  
Rna Dependent Rna Polymerase ◽  
Infectious Bronchitis ◽  
Rna Polymerase Gene

Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize

2011 ◽  
Vol 30 (7) ◽  
pp. 1347-1363 ◽  
Author(s):  
Yexiong Qian ◽  
Ying Cheng ◽  
Xiao Cheng ◽  
Haiyang Jiang ◽  
Suwen Zhu ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Gene Families ◽  
Polymerase Gene ◽  
Rna Dependent Rna Polymerase ◽  
Identification And Characterization ◽  
Rna Polymerase Gene

scholarly journals Characterization of the Serpin-Encoding Gene of Bifidobacterium breve 210B

2010 ◽  
Vol 76 (10) ◽  
pp. 3206-3219 ◽  
Author(s):  
Francesca Turroni ◽  
Elena Foroni ◽  
Mary O'Connell Motherway ◽  
Francesca Bottacini ◽  
Vanessa Giubellini ◽  
...  
Keyword(s):  
Transcriptional Start Site ◽  
Northern Hybridization ◽  
Rt Pcr ◽  
Significant Similarity ◽  
Bifidobacterium Breve ◽  
Polycistronic Mrna ◽  
Reverse Transcription Pcr ◽  
Number Of Genes ◽  
Encoding Gene

ABSTRACT Members of the serpin (serine protease inhibitor) superfamily have been identified in higher multicellular eukaryotes, as well as in bacteria, although examination of available genome sequences has indicated that homologs of the bacterial serpin-encoding gene (ser) are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least 5, and perhaps up to 9, of the 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria produce serpins that form a separate clade. We characterized the ser 210B locus of Bifidobacterium breve 210B, which encompasses a number of genes whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, microarray, reverse transcription-PCR (RT-PCR), and quantitative real-time PCR (qRT-PCR) analyses revealed that a 3.5-kb polycistronic mRNA encompassing the ser 210B operon with a single transcriptional start site is strongly induced following treatment of B. breve 210B cultures with some proteases. Interestingly, transcription of other bifidobacterial ser homologs appears to be triggered by different proteases.

scholarly journals Identification and Functional Characterization of a new Sunflower Germacrene A Synthase (HaGAS3)

2010 ◽  
Vol 5 (5) ◽  
pp. 1934578X1000500 ◽  
Author(s):  
Jens Göpfert ◽  
Anna-Katharina Bülow ◽  
Otmar Spring
Keyword(s):  
Sesquiterpene Lactones ◽  
Glandular Trichomes ◽  
Functional Characterization ◽  
Plant Tissues ◽  
Rt Pcr ◽  
Plant Organs ◽  
Reverse Transcription Pcr ◽  
Engineered Yeast

Sesquiterpenes and sesquiterpene lactones are major natural compounds found in linear and capitate glandular trichomes of sunflower, Helianthus annuus L. In addition to two recently identified germacrene A synthases HaGAS1 and HaGAS2, found in capitate trichome gland cells, reverse transcription-PCR experiments have now allowed identification of a third enzyme of this type, HaGAS3. Its cDNA sequence was established and its functional characterization as a germacrene A synthase was achieved through in vitro expression in engineered yeast, and by GC-MS experiments. PCR and RT-PCR experiments with cDNA from different plant organs revealed that the new enzyme is expressed independently from the other two. While these latter two were expressed in plant organs bearing capitate glandular trichomes and in roots, the new enzyme occurred in plant tissues not linked to the presence of specific trichomes (for example, cotyledons), and was absent in roots. The experiments show that independently regulated pathways for the first cyclic sesquiterpene, germacrene A, are present in sunflower.

scholarly journals Survey and Genetic Diversity of Grapevine Leafroll Associated Virus 2 in Algeria

2015 ◽  
Vol 4 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Arezki Lehad ◽  
Ilhem Selmi ◽  
Meriem Louanchi ◽  
Mouni Aitouada ◽  
Naima Mahfoudhi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Synonymous Site ◽  
Rt Pcr ◽  
Synonymous Substitutions ◽  
Representative Sequence ◽  
Polymerase Chain ◽  
Das Elisa ◽  
Similarity Plot

Vineyards in western and center regions of Algeria were surveyed for the Grapevine leafroll-associated virus 2 (GLRaV-2). Analyses by DAS-ELISA and Reverse Transcription Polymerase Chain Reaction (RT-PCR) reveal 15, 8% prevalence. The genetic diversity of the GLRaV-2 population was studied by phylogenetic analyses of the HSP70h gene region of seven samples sequenced in this study and other sequences downloaded from GenBank. Results reveal segregation of the GLRav-2 population into six distinct groups. An estimation of the ratio of non-synonymous substitutions per non-synonymous site to synonymous substitutions per synonymous site indicated that HSP70h gene evolve under positive selection. Similarity plot constructed with representative sequence from each group confirmed previous results.  All Algerian isolates belong to group PN. As far as we know, this is the first characterization of GLRaV-2 isolates from Algeria.

scholarly journals The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey

2020 ◽  
Author(s):  
Karamese Murat ◽  
Ozgur Didem ◽  
Tarhan Ceyda ◽  
Dik Altintas Susamber ◽  
Caliskan Okan ◽  
...  
Keyword(s):  
Epidemiologic Studies ◽  
Screening Tests ◽  
Gene Fragment ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Rna Dependent Rna Polymerase ◽  
Final Study ◽  
The World ◽  
Study Population ◽  
Rna Polymerase Gene

ABSTRACTCOVID-19, is caused by SARS-CoV-2, has been started on December/2019 in Wuhan/China and spread all over the world. We analyzed RT-PCR results of 10,000 cases from April-2 to May-30, 2020 in three neighbor cities located on the Eastern of Turkey. The final study population was 7853 cases after excluded screening tests. RT-PCR were performed to detect the SARS-CoV-2-specific RdRp (RNA-dependent-RNA-polymerase) gene fragment. The number of total positive samples out of 7853 were 487; however, the number of non-repeating positive patient was 373 (4.8%). The cough and fever were the most common symptoms in positive cases. The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world.

scholarly journals Variability of the 3' terminal of the polymerase gene of Grapevine leafroll-associated virus 3 isolates from Vale do São Francisco, Brazil

2005 ◽  
Vol 30 (2) ◽  
pp. 173-176 ◽  
Author(s):  
Érico de C. Dianese ◽  
Eduardo D. Ramalho ◽  
Daniela M. Cerqueira ◽  
Daniela B. Lopes ◽  
Thor V.M. Fajardo ◽  
...  
Keyword(s):  
North America ◽  
Natural Variation ◽  
Amino Acid Change ◽  
Economic Importance ◽  
Southern Brazil ◽  
Polymerase Gene ◽  
Rt Pcr ◽  
Rna Dependent Rna Polymerase ◽  
Great Economic Importance ◽  
Vitis Spp

Many viral diseases, including leafroll, which is of great economic importance, affect grapevines (Vitis spp.). A complex of eight viruses [Grapevine leafroll-associated virus (GLRaV) -1 to 8] is associated with this disease. The objective of this study was to compare the variability of the 3' terminal region of the polymerase gene of three isolates of GLRaV-3 (Grapevine leafroll-associated virus-3), from Submédio do Vale do Rio São Francisco (Petrolina-PE) with that of other isolates available at the GenBank, including an isolate from North America and another from Southern Brazil. The viral RNA was extracted from three infected ELISA reactive plants and a fragment of 340 bp was amplified, by RT-PCR, using primers that recognize that portion of the polymerase gene found between nucleotides 8267 and 8606. The three isolates from Vale do Rio São Francisco named Pet-1, Pet-2 and Pet-3, showed similarities ranging from 98% and 94%, respectively to the isolates from North America (AF037268) and Southern Brazilian (AF438411). Considering the whole genome, the main variation found was one amino acid change at position 2766 (F2766Y). These preliminary data indicate the existence of a natural variation among GLRaV-3 isolates from grapevines. This could be due to the vegetative propagation and long cycle of the plant, associated with the error-prone nature of RNA-dependent RNA polymerase.

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