scholarly journals Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1119
Author(s):  
Emese Demian ◽  
Aliz Holczbauer ◽  
Zsuzsanna Nagyne Galbacs ◽  
Nikoletta Jaksa-Czotter ◽  
Mihaly Turcsan ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Latent Infection ◽  
High Variability ◽  
Grapevine Virus ◽  
Rt Pcr ◽  
Grapevine Cultivar ◽  
Long Time ◽  
High Diversity

Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT had not yet been described. A re-analysis of our sRNA HTS datasets and a survey of grapevines by RT-PCR revealed the presence of GVT in most of the vineyards tested, while at rootstock fields its presence was very rare. The presence and high variability of the virus in the country was confirmed by sequence analysis of strains originating from different vineyards. In this study, we demonstrate the presence of GVT in Hungary and show its high diversity, suggesting that GVT presence may not seriously affect grapevine health and that it could have been present in European vineyards for a long time as a latent infection.

scholarly journals First Report of Plum Bark Necrosis and Stem Pitting-Associated Virus Infecting Grapevine in China

2020 ◽  
Author(s):  
Yang Yang ◽  
Yifan Sun ◽  
Qingliang Li ◽  
Wu Yufeng ◽  
Deya Wang
Keyword(s):  
Small Rna ◽  
Virus Disease ◽  
Neighbor Joining ◽  
Rna Seq ◽  
Rt Pcr ◽  
First Report ◽  
Reverse Transcription Pcr ◽  
Grapevine Cultivar ◽  
Field Samples ◽  
Stem Pitting

Abstract Background: Virus disease is one of the main diseases in grapevine, and there has been no report on Plum bark necrosis and stem pitting-associated virus infecting grapevine in China.Objective: The leaf samples of grapevine cultivar 'Cabernet Gernischt' were collected from Shandong province, which the leaves suffered from viral-like symptoms with spotting and crinkle.Methods: Small RNA-seq combined with reverse transcription PCR (RT-PCR) were performed to detect the potential viruses in these field samples. Phylogenetic tree was constructed using the neighbor joining method in MEGA 5.1Conclusions: This is the first report of PBNSPaV infecting grapevine in China, contributing to a better understanding of the epidemiology and host range distribution of this pathogen.

scholarly journals First report of Plum bark necrosis stem pitting-associated virus infecting grapevine in China

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Yang Yang ◽  
Yifan Sun ◽  
Qingliang Li ◽  
Yufeng Wu ◽  
Deya Wang
Keyword(s):  
Small Rna ◽  
Virus Disease ◽  
Neighbor Joining ◽  
Rna Seq ◽  
Rt Pcr ◽  
First Report ◽  
Reverse Transcription Pcr ◽  
Grapevine Cultivar ◽  
Field Samples ◽  
Stem Pitting

Abstract Background Virus disease is one of the main diseases in grapevine, and there has been no report on Plum bark necrosis and stem pitting-associated virus infecting grapevine in China. Objective The leaf samples of grapevine cultivar 'Cabernet Gernischt' were collected from Shandong province, which the leaves suffered from viral-like symptoms with spotting and crinkle. Methods Small RNA-seq combined with reverse transcription PCR (RT-PCR) were performed to detect the potential viruses in these field samples. Phylogenetic tree was constructed using the neighbor joining method in MEGA 5.1 Conclusions This is the first report of PBNSPaV infecting grapevine in China, contributing to a better understanding of the epidemiology and host range distribution of this pathogen.

scholarly journals First Report of Plum bark necrosis stem pitting-associated virus Infecting Grapevine in China

2020 ◽  
Author(s):  
Yang Yang ◽  
Yifan Sun ◽  
Qingliang Li ◽  
Wu Yufeng ◽  
Deya Wang
Keyword(s):  
Small Rna ◽  
Virus Disease ◽  
Neighbor Joining ◽  
Rna Seq ◽  
Rt Pcr ◽  
First Report ◽  
Reverse Transcription Pcr ◽  
Grapevine Cultivar ◽  
Field Samples ◽  
Stem Pitting

Abstract Background: Virus disease is one of the main diseases in grapevine, and there has been no report on Plum bark necrosis and stem pitting-associated virus infecting grapevine in China.Objective: The leaf samples of grapevine cultivar 'Cabernet Gernischt' were collected from Shandong province, which the leaves suffered from viral-like symptoms with spotting and crinkle.Methods: Small RNA-seq combined with reverse transcription PCR (RT-PCR) were performed to detect the potential viruses in these field samples. Phylogenetic tree was constructed using the neighbor joining method in MEGA 5.1Conclusions: This is the first report of PBNSPaV infecting grapevine in China, contributing to a better understanding of the epidemiology and host range distribution of this pathogen.

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 Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Derek Toms ◽  
Bo Pan ◽  
Yinshan Bai ◽  
Julang Li
Keyword(s):  
Granulosa Cells ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Ovarian Function ◽  
Ovarian Follicle ◽  
Small Rna Sequencing ◽  
Cell Fractionation ◽  
Steroid Synthesis ◽  
Non Coding Rna ◽  
Dna Binding Sites

AbstractNuclear small RNAs have emerged as an important subset of non-coding RNA species that are capable of regulating gene expression. A type of small RNA, microRNA (miRNA) have been shown to regulate development of the ovarian follicle via canonical targeting and translational repression. Little has been done to study these molecules at a subcellular level. Using cell fractionation and high throughput sequencing, we surveyed cytoplasmic and nuclear small RNA found in the granulosa cells of the pig ovarian antral preovulatory follicle. Bioinformatics analysis revealed a diverse network of small RNA that differ in their subcellular distribution and implied function. We identified predicted genomic DNA binding sites for nucleus-enriched miRNAs that may potentially be involved in transcriptional regulation. The small nucleolar RNA (snoRNA) SNORA73, known to be involved in steroid synthesis, was also found to be highly enriched in the cytoplasm, suggesting a role for snoRNA species in ovarian function. Taken together, these data provide an important resource to study the small RNAome in ovarian follicles and how they may impact fertility.

scholarly journals Overview of Safety Measures at Selected Airports during the COVID-19 Pandemic

2021 ◽  
Vol 13 (15) ◽  
pp. 8499
Author(s):  
Monika Blišťanová ◽  
Michaela Tirpáková ◽  
Ľubomíra Brůnová
Keyword(s):  
Time Frame ◽  
Organizational Changes ◽  
Rt Pcr ◽  
Final Phase ◽  
Chain Reaction ◽  
Scoring Method ◽  
Safety Measures ◽  
Long Time ◽  
Polymerase Chain ◽  
Cleaning And Disinfection

The year 2020 was very challenging for the whole world, given the outbreak of the ongoing coronavirus-related pandemic, and was marked in particular by overcoming new hitherto unknown obstacles. For air transport, in particular, airlines stopped flying altogether and were forced to ground hundreds of planes worldwide involuntarily. Airports had to close their terminals for a long time, wholly suspend operations, and its resumption required significant organizational changes. This article summarizes the measures related to the COVID-19 pandemic adopted by airports to minimize the risk of spreading the disease. The article focuses on countermeasures and their implementation at selected airports in a specific time frame and airports’ behavior during a pandemic which varies depending on country and time of the year. The results demonstrated that steps being taken at airports include the use of face coverings or masks, social distance, enhanced cleaning and disinfection, or temperature checks and/or symptoms (fever, loss of smell, chills, cough, shortness of breath), RT-PCR (reverse transcription-polymerase chain reaction) screening and data collection with health declaration. These measures have now become an essential standard for the operation of airports and can, therefore, be used to assess the level of airport safety achieved. In the final phase, the article evaluates the level of achieved airport safety based on the proposed scoring method.

scholarly journals Cloning, Sequencing, and the Expression of the Elusive Sarcomeric TPM4α Isoform in Humans

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Dipak K. Dube ◽  
Syamalima Dube ◽  
Lynn Abbott ◽  
Ruham Alshiekh-Nasany ◽  
Charles Mitschow ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Western Blot ◽  
Human Heart ◽  
Amino Acid Sequences ◽  
Rt Pcr ◽  
Adult Heart ◽  
Qrt Pcr ◽  
Long Time ◽  
Alternate Promoters ◽  
Computational Analyses

In mammals, tropomyosin is encoded by four known TPM genes (TPM1, TPM2, TPM3, and TPM4) each of which can generate a number of TPM isoforms via alternative splicing and/or using alternate promoters. In humans, the sarcomeric isoform(s) of each of the TPM genes, except for the TPM4, have been known for a long time. Recently, on the basis of computational analyses of the human genome sequence, the predicted sequence of TPM4α has been posted in GenBank. We designed primer-pairs for RT-PCR and showed the expression of the transcripts of TPM4α and a novel isoform TPM4δ in human heart and skeletal muscle. qRT-PCR shows that the relative expression of TPM4α and TPM4δ is higher in human cardiac muscle. Western blot analyses using CH1 monoclonal antibodies show the absence of the expression of TPM4δ protein (~28 kDa) in human heart muscle. 2D western blot analyses with the same antibody show the expression of at least nine distinct tropomyosin molecules with a mass ~32 kD and above in adult heart. By Mass spectrometry, we determined the amino acid sequences of the extracted proteins from these spots. Spot “G” reveals the putative expression of TPM4α along with TPM1α protein in human adult heart.

Comparison of high throughput sequencing to standard protocols for virus detection in berry crops

Plant Disease ◽  
2021 ◽  
Author(s):  
Dan Edward Veloso Villamor ◽  
Karen E Keller ◽  
Robert Martin ◽  
Ioannis Emmanouil Tzanetakis
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Wide Spectrum ◽  
Virus Detection ◽  
Rt Pcr ◽  
Host Interactions ◽  
Growing Seasons ◽  
Berry Crops ◽  
Sampling Times ◽  
Better Than

A comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium and 8 Rubus) with known virus profiles was completed. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, RT-PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared to RT-PCR on a wide spectrum of virus variants and discovery of novel viruses. More importantly, in most cases where the two protocols showed parallel virus detection, 11 viruses in 16 berry selections were not consistently detected by both methods at all sampling points. Based on these data we propose a four sampling times/two-year testing requirement for berry and potentially other crops to ensure that no virus remains undetected independent of titer, distribution or other virus/virus or virus/host interactions.

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