scholarly journals Molecular and Biological Characterization of a New Strawberry Cytorhabdovirus

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 982 ◽  
Author(s):  
Fránová ◽  
Přibylová ◽  
Koloniuk
Keyword(s):  
High Throughput Sequencing ◽  
Distinct Species ◽  
Aphis Fabae ◽  
Biological Characterization ◽  
Rt Pcr ◽  
Virus Diseases ◽  
Experimental Conditions ◽  
Ion Proton ◽  
Diagnostic Symptoms

Virus diseases of strawberry present several complex problems. More than 25 viruses have been described in the genus Fragaria thus far. Here, we describe a novel rhabdovirus, tentatively named strawberry virus 1 (StrV-1), that infects F. ananassa and F. vesca plants. Genomic sequences of three distinct StrV-1 genotypes co-infecting a single F. ananassa host were obtained using combined Illumina and Ion Proton high-throughput sequencing. StrV-1 was transmitted to herbaceous plants via Aphis fabae and A. ruborum, further mechanically transmitted to Nicotiana occidentalis 37B and sub-inoculated to N. benthamiana, N. benthamiana DCL2/4i, N. occidentalis 37B, and Physalis floridana plants. Irregular chlorotic sectors on leaf blades and the multiplication of calyx leaves seem to be the diagnostic symptoms for StrV-1 on indexed F. vesca clones. StrV-1 was detected in asymptomatic grafted plants and in 49 out of 159 field strawberry samples via RT-PCR followed by Sanger sequencing. The bacilliform shape of the virions, which have a cytoplasm-limited distribution, their size, and phylogenetic relationships support the assignment of StrV-1 to a distinct species of the genus Cytorhabdovirus. Acyrthosiphon malvae, A. fabae, and A. ruborum were shown to transmit StrV-1 under experimental conditions.

scholarly journals Molecular and biological characterization of a new strawberry Cytorhabdovirus

2019 ◽  
Author(s):  
Jana Fránová ◽  
Jaroslava Přibylová ◽  
Igor Koloniuk
Keyword(s):  
High Throughput Sequencing ◽  
Distinct Species ◽  
Aphis Fabae ◽  
Biological Characterization ◽  
Rt Pcr ◽  
Virus Diseases ◽  
Experimental Conditions ◽  
Ion Proton ◽  
Diagnostic Symptoms

Virus diseases of strawberry present several complex problems. More than 25 viruses have been described in the genus Fragaria thus far. Here, we describe a novel rhabdovirus, tentatively named strawberry virus 1 (StrV-1), that infects F. ananassa and F. vesca plants. Genomic sequences of three distinct StrV-1 genotypes co-infecting a single F. ananassa host were obtained using combined Illumina and Ion Proton high-throughput sequencing. StrV-1 was transmitted to herbaceous plants via Aphis fabae and A. ruborum, further mechanically transmitted to Nicotiana occidentalis 37B and sub-transferred to N. benthamiana, N. benthamiana DCL2/4i, N. occidentalis 37B and Physalis floridana plants. Irregular chlorotic sectors on leaf blades and the multiplication of calyx leaves seem to be the diagnostic symptoms for StrV-1 on indexed F. vesca clones. StrV-1 was detected in asymptomatic grafted plants and in 49 out of 159 field strawberry samples via RT-PCR followed by Sanger sequencing. The bacilliform shape of the virions, which have a cytoplasm-limited distribution, their size, and phylogenetic relationships support the assignment of StrV-1 to a distinct species of the genus Cytorhabdovirus. Acyrthosiphon malvae, A. fabae and A. ruborum were shown to transmit StrV-1 under experimental conditions.

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 Identification and characterization of a novel potyvirus infecting Paris yunnanensis

2021 ◽  
Author(s):  
Pingxiu Lan ◽  
Peng He ◽  
Mengji Cao ◽  
Guohua Zhou ◽  
Li Chenrong ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Pairwise Comparison ◽  
Distinct Species ◽  
Reading Frame ◽  
Single Clade ◽  
Terminal Poly ◽  
Identification And Characterization ◽  
Complete Genomic

Abstract The complete genomic sequence of a novel potyvirus from Paris yunnanensis was determined by high-throughput sequencing then confirmed by Sanger sequencing. Its genomic RNA consists 9600 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing a typical large open reading frame (ORF) of potyviruses and encoding a putative polyprotein of 3098 amino acids (aa). Pairwise comparison analysis showed the virus shares sequence identity with other members of Potyvirus was 53.0–57.8% at genome sequence level, and 39.3–51.2% at polyprotein sequence level. Phylogenetic analysis indicated that the virus was clustered as a single clade within the genus Potyvirus both using nt and aa level. These results suggest that the virus should be considered as a distinct species within the genus Potyvirus, and it was tentatively named as “Paris mottle virus” (PaMoV).

scholarly journals Identification and Characterization of a Novel Potyvirus Infecting Paris Yunnanensis

2021 ◽  
Author(s):  
Pingxiu Lan ◽  
Peng He ◽  
Mengji Cao ◽  
Guohua Zhou ◽  
Chenrong Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Pairwise Comparison ◽  
Distinct Species ◽  
Plum Pox Virus ◽  
Reading Frame ◽  
Terminal Poly ◽  
Chilli Veinal Mottle Virus ◽  
Identification And Characterization

Abstract The complete genomic sequence of a novel potyvirus from Paris yunnanensis was determined by high-throughput sequencing then confirmed by Sanger sequencing. Its genomic RNA consists 9600 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing a typical large open reading frame (ORF) of potyviruses and encoding a putative polyprotein of 3098 amino acids (aa). Pairwise comparison analysis showed the virus shares sequence identity with other members of Potyvirus was 53.0% to 57.8% at genome sequence level, and 39.3% to 51.2% at polyprotein sequence level. Phylogenetic analysis indicated that the virus was most closely related to the subgroup of plum pox virus and that of chilli veinal mottle virus within the genus Potyvirus. These results suggest that the virus should be considered as a distinct species within the genus Potyvirus and was tentatively named as “Paris mottle associated virus” (PMaV).

Presenting White Blood Cell Count and Kinetics of Molecular Remission Predict Prognosis in Acute Promyelocytic Leukemia Treated With All-Trans Retinoic Acid: Result of the Randomized MRC Trial

Blood ◽  
1999 ◽  
Vol 93 (12) ◽  
pp. 4131-4143 ◽  
Author(s):  
Alan K. Burnett ◽  
David Grimwade ◽  
Ellen Solomon ◽  
Keith Wheatley ◽  
Anthony H. Goldstone
Keyword(s):  
Retinoic Acid ◽  
Promyelocytic Leukemia ◽  
Rt Pcr ◽  
Blood Cell Count ◽  
Relapse Risk ◽  
Trans Retinoic Acid ◽  
All Trans Retinoic Acid ◽  
To Receive ◽  
Risk Of Relapse

Abstract All-trans retinoic acid (ATRA) is an essential component of the treatment of acute promyelocytic leukemia (APL), but the optimal timing and duration remain to be determined. Molecular characterization of this disease can refine the diagnosis and could be potentially useful in monitoring response to treatment. Patients defined morphologically to have APL were randomized to receive a 5-day course of ATRA before commencing chemotherapy or to receive daily ATRA commencing with chemotherapy and continuing until complete remission (CR). The chemotherapy was that used in current MRC Leukaemia Trials. Outcome comparisons were by intention to treat with additional analysis for relevant risk factors. Patients were characterized by molecular techniques for the fusion products of the t(15;17) and monitored by reverse transcriptase-polymerase chain reaction (RT-PCR) during and after treatment. Two hundred thirty-nine patients were randomized. Treatment with extended ATRA resulted in a superior remission rate (87% v 70%, P < .001), due to fewer early and induction deaths (12% v 23%, P = .02), and less resistant disease (2% v 7%, P = .03), which was associated with a significantly more rapid recovery of neutrophils and platelets. Extended ATRA reduced relapse risk (20%v 36% at 4 years, P = .04) and resulted in superior survival (71% v 52% at 4 years, P = .005). Presenting white blood cell count (WBC) was a key determinant of outcome. The 70% of patients who presented with a WBC less than 10 × 109/L had a better CR (85% v62%, P = .0001) and reduced relapse risk (22% v42%, P = .002) and superior survival (69%v 43%, P < .0001). Within the low count group, extended ATRA resulted in a better CR (94% v 76%, P= .001), reduced relapse risk (13% v 35%, P = .04), and improved survival (80% v 57%, P = .0009). There was no evidence of benefit in patients presenting with a higher WBC (>10 × 109/L). Molecular monitoring after the third chemotherapy course had a correlation with risk of relapse. The relapse risk was 57% if the RT-PCR was positive versus 27% if the RT-PCR was negative (P = .006). APL patients who present with a low WBC derive substantial benefit from combining ATRA with induction chemotherapy until remission is achieved, whereas patients with a higher WBC did not benefit. Molecular characterization of disease can improve diagnostic precision and a positive RT-PCR after consolidation identifies patients at a higher risk of relapse.

scholarly journals Adsorption Studies on Magnetic Nanoparticles Functionalized with Silver to Remove Nitrates from Waters

Water ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 1757
Author(s):  
Yesica Vicente-Martínez ◽  
Manuel Caravaca ◽  
Antonio Soto-Meca ◽  
Miguel Ángel Martín-Pereira ◽  
María del Carmen García-Onsurbe
Keyword(s):  
Magnetic Nanoparticles ◽  
Nitrate Content ◽  
Adsorption Efficiency ◽  
Experimental Conditions ◽  
Dependent Behavior ◽  
Before And After ◽  
Naoh Solution ◽  
High Concentrations ◽  
Interference Studies

This paper presents a novel procedure for the treatment of contaminated water with high concentrations of nitrates, which are considered as one of the main causes of the eutrophication phenomena. For this purpose, magnetic nanoparticles functionalized with silver (Fe3O4@AgNPs) were synthesized and used as an adsorbent of nitrates. Experimental conditions, including the pH, adsorbent and adsorbate dose, temperature and contact time, were analyzed to obtain the highest adsorption efficiency for different concentration of nitrates in water. A maximum removal efficiency of 100% was reached for 2, 5, 10 and 50 mg/L of nitrate at pH = 5, room temperature, and 50, 100, 250 and 500 µL of Fe3O4@AgNPs, respectively. The characterization of the adsorbent, before and after adsorption, was performed by energy dispersive X-ray spectroscopy, scanning electron microscopy, Brunauer-Emmett-Teller analysis and Fourier-transform infrared spectroscopy. Nitrates can be desorbed, and the adsorbent can be reused using 500 µL of NaOH solution 0.01 M, remaining unchanged for the first three cycles, and exhibiting 90% adsorption efficiency after three regenerations. A deep study on equilibrium isotherms reveals a pH-dependent behavior, characterized by Langmuir and Freundlich models at pH = 5 and pH = 1, respectively. Thermodynamic studies were consistent with physicochemical adsorption for all experiments but showed a change from endothermic to exothermic behavior as the temperature increases. Interference studies of other ions commonly present in water were carried out, enabling this procedure as very selective for nitrate ions. In addition, the method was applied to real samples of seawater, showing its ability to eliminate the total nitrate content in eutrophized waters.

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