scholarly journals Experimental Transmission of Pospiviroid Populations to Weed Species Characteristic of Potato and Hop Fields

2007 ◽  
Vol 81 (21) ◽  
pp. 11891-11899 ◽  
Author(s):  
J. Matoušek ◽  
L. Orctová ◽  
J. Ptáček ◽  
J. Patzak ◽  
P. Dědič ◽  
...  
Keyword(s):  
Wide Spectrum ◽  
Amaranthus Retroflexus ◽  
Rt Pcr ◽  
Weed Species ◽  
Experimental Transmission ◽  
Reverse Transcription Pcr ◽  
Weed Plants ◽  
Anthemis Arvensis ◽  
Galinsoga Ciliata ◽  
Rna And Dna

ABSTRACT Weed plants characteristic for potato and hop fields have not been considered in the past as potential hosts that could transmit and lead to spreading of potato spindle tuber (PSTVd) and hop stunt (HSVd) viroids, respectively. To gain insight into this problem, we biolistically inoculated these weed plants with viroid populations either as RNA or as cDNA. New potential viroid host species, collected in central Europe, were discovered. From 12 weed species characteristic for potato fields, high viroid levels, detectable by molecular hybridization, were maintained after both RNA and DNA transfers in Chamomilla reculita and Anthemis arvensis. Low viroid levels, detectable by reverse transcription-PCR (RT-PCR) only, were maintained after plant inoculations with cDNA in Veronica argensis and Amaranthus retroflexus. In these two species PSTVd concentrations were 105 and 103 times, respectively, lower than in tomato as estimated by real-time PCR. From 14 weeds characteristic for hop fields, high HSVd levels were detected in Galinsoga ciliata after both RNA and DNA transfers. HSVd was found, however, not to be transmissible by seeds of this weed species. Traces of HSVd were detectable by RT-PCR in HSVd-cDNA-inoculated Amaranthus retroflexus. Characteristic monomeric (+)-circular and linear viroid RNAs were present in extracts from weed species propagating viroids to high levels, indicating regular replication, processing, and circularization of viroid RNA in these weed species. Sequence analyses of PSTVd progenies propagated in C. reculita and A. arvensis showed a wide spectrum of variants related to various strains, from mild to lethal variants; the sequence variants isolated from A. retroflexus and V. argensis exhibited similarity or identity to the superlethal AS1 viroid variant. All HSVd clones from G. ciliata corresponded to a HSVdg variant, which is strongly pathogenic for European hops.

scholarly journals Sensitive Multiplex Real-Time Reverse Transcription-PCR Assay for the Detection of Human and Animal Noroviruses in Clinical and Environmental Samples

2007 ◽  
Vol 73 (17) ◽  
pp. 5464-5470 ◽  
Author(s):  
Sandro Wolf ◽  
Wendy M. Williamson ◽  
Joanne Hewitt ◽  
Malet Rivera-Aban ◽  
Susan Lin ◽  
...  
Keyword(s):  
Real Time ◽  
Reverse Transcription ◽  
Wide Spectrum ◽  
Clinical Diagnostics ◽  
Target Sequence ◽  
Rt Pcr ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Copy Numbers ◽  
Treated Drinking Water

ABSTRACT In this study, we developed a triplex real-time reverse transcription-PCR (RT-PCR)-based method that detects and distinguishs between noroviruses belonging to genogroups I, II, and III and that targets the junction between the regions of open reading frame 1 (ORF1) and ORF2. This is the first assay to include all three genogroups and the first real-time RT-PCR-based method developed for the detection of bovine noroviruses. The assay was shown to be broadly reactive against a wide spectrum of norovirus genotypes, including GI/1 through GI/7, GII/1 through GII/8, GII/10, GII/12, and GII/17, in different matrices (including fecal specimens, treated and raw sewage, source water, and treated drinking water). The assay is highly sensitive, detecting low copy numbers of plasmids that carry the target sequence. A new bovine norovirus, Bo/NLV/Norsewood/2006/NZL, was identified by this assay and was further genetically characterized. The results implicate a broad range of possible applications, including clinical diagnostics, tracing of fecal contaminants, and due to its sensitivity and broad reactivity, environmental studies.

scholarly journals Active Trachoma Is Associated with Increased Conjunctival Expression ofIL17Aand Profibrotic Cytokines

2011 ◽  
Vol 79 (12) ◽  
pp. 4977-4983 ◽  
Author(s):  
Matthew J. Burton ◽  
Athumani Ramadhani ◽  
Helen A. Weiss ◽  
Victor Hu ◽  
Patrick Massae ◽  
...  
Keyword(s):  
Dna Isolation ◽  
Rt Pcr ◽  
Cross Sectional Survey ◽  
Proinflammatory Response ◽  
Cross Sectional ◽  
Active Trachoma ◽  
Content Type ◽  
Reverse Transcription Pcr ◽  
Rna And Dna ◽  
Proinflammatory Factors

ABSTRACTThe immunological basis of scarring trachoma is not well understood. It is unclear whether it is driven primarily through cell-mediated adaptive or epithelial-cell-derived innate responses. The purpose of this study was to investigate the expression of the inflammatory and fibrogenic mediators which may be involved. We conducted a cross-sectional survey of children living in an untreated trachoma-endemic community in Tanzania. The children were examined for signs of trachoma, and swabs were collected for bacteriological culture and RNA and DNA isolation.Chlamydia trachomatiswas detected by the Amplicor PCR test. The expression of the following genes was measured by quantitative reverse transcription-PCR (RT-PCR):S100A7,IL1B,IL17A,IL23A,CXCL5,CCL18,TLR2,NLRP3,KLRD1,CTGF, andMMP9. Four hundred seventy children under the age of 10 years were included. Follicular trachoma (TF) was detected in 65 children (14%),C. trachomatiswas detected in 25 (5%), and bacterial pathogens were cultured in 161 (34%). TF was associated with significantly increased expression ofS100A7,IL17A,CCL18,CXCL5, andCTGF.Expression was increased further in the presence of papillary inflammation. Nonchlamydial bacterial infection was associated with increased expression ofIL17A,CXCL5,CCL18, andKLRD1.IL17Aexpression was associated with increased expression ofS100A7,CXCL5,CCL18,KLRD1, andCTGF.These data are consistent with a role for IL-17A in orchestrating the proinflammatory response in trachoma. Its activity may be promoted either as part of the cell-mediated response or through innate pathways. It may drive a range of proinflammatory factors leading to excessive tissue damage and repair involving fibrosis.

Detection of Nucleic Acids in Cells or Tissue Sections Using In situ Polymerase Chain Reaction (PCR)

1996 ◽  
Vol 54 ◽  
pp. 16-17
Author(s):  
J. R. Hully ◽  
K. R. Luehrsen ◽  
K. Aoyagi ◽  
C. Shoemaker ◽  
R. Abramson
Keyword(s):  
Nucleic Acids ◽  
Viral Infections ◽  
Anatomical Location ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Cellular Source ◽  
Gene Transcripts ◽  
Initial Description ◽  
In Cells

The development of PCR technology has greatly accelerated medical research at the genetic and molecular levels. Until recently, the inherent sensitivity of this technique has been limited to isolated preparations of nucleic acids which lack or at best have limited morphological information. With the obvious exception of cell lines, traditional PCR or reverse transcription-PCR (RT-PCR) cannot identify the cellular source of the amplified product. In contrast, in situ hybridization (ISH) by definition, defines the anatomical location of a gene and/or it’s product. However, this technique lacks the sensitivity of PCR and cannot routinely detect less than 10 to 20 copies per cell. Consequently, the localization of rare transcripts, latent viral infections, foreign or altered genes cannot be identified by this technique. In situ PCR or in situ RT-PCR is a combination of the two techniques, exploiting the sensitivity of PCR and the anatomical definition provided by ISH. Since it’s initial description considerable advances have been made in the application of in situ PCR, improvements in protocols, and the development of hardware dedicated to in situ PCR using conventional microscope slides. Our understanding of the importance of viral latency or viral burden in regards to HIV, HPV, and KSHV infections has benefited from this technique, enabling detection of single viral copies in cells or tissue otherwise thought to be normal. Clearly, this technique will be useful tool in pathobiology especially carcinogenesis, gene therapy and manipulations, the study of rare gene transcripts, and forensics.

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 Effect of Clay, Soil Organic Matter, and Soil pH on Initial and Residual Weed Control with Flumioxazin

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1326
Author(s):  
Calvin F. Glaspie ◽  
Eric A. L. Jones ◽  
Donald Penner ◽  
John A. Pawlak ◽  
Wesley J. Everman
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Weed Control ◽  
Soil Ph ◽  
Organic Matter Content ◽  
Amaranthus Retroflexus ◽  
Matter Content ◽  
Weed Species ◽  
Soil Organic Matter Content ◽  
Field Soils

Greenhouse studies were conducted to evaluate the effects of soil organic matter content and soil pH on initial and residual weed control with flumioxazin by planting selected weed species in various lab-made and field soils. Initial control was determined by planting weed seeds into various lab-made and field soils treated with flumioxazin (71 g ha−1). Seeds of Echinochloa crus-galli (barnyard grass), Setaria faberi (giant foxtail), Amaranthus retroflexus (redroot pigweed), and Abutilon theophrasti (velvetleaf) were incorporated into the top 1.3 cm of each soil at a density of 100 seeds per pot, respectively. Emerged plants were counted and removed in both treated and non-treated pots two weeks after planting and each following week for six weeks. Flumioxazin control was evaluated by calculating percent emergence of weeds in treated soils compared to the emergence of weeds in non-treated soils. Clay content was not found to affect initial flumioxazin control of any tested weed species. Control of A. theophrasti, E. crus-galli, and S. faberi was reduced as soil organic matter content increased. The control of A. retroflexus was not affected by organic matter. Soil pH below 6 reduced flumioxazin control of A. theophrasti, and S. faberi but did not affect the control of A. retroflexus and E. crus-galli. Flumioxazin residual control was determined by planting selected weed species in various lab-made and field soils 0, 2, 4, 6, and 8 weeks after treatment. Eight weeks after treatment, flumioxazin gave 0% control of A. theophrasti and S. faberi in all soils tested. Control of A. retroflexus and Chenopodium album (common lambsquarters) was 100% for the duration of the experiment, except when soil organic matter content was greater than 3% or the soil pH 7. Eight weeks after treatment, 0% control was only observed for common A. retroflexus and C. album in organic soil (soil organic matter > 80%) or when soil pH was above 7. Control of A. theophrasti and S. faberi decreased as soil organic matter content and soil pH increased. Similar results were observed when comparing lab-made soils to field soils; however, differences in control were observed between lab-made organic matter soils and field organic matter soils. Results indicate that flumioxazin can provide control ranging from 75–100% for two to six weeks on common weed species.

Comet and cup genes in Drosophila spermatogenesis: the first demonstration of post-meiotic transcription

2008 ◽  
Vol 36 (3) ◽  
pp. 540-542 ◽  
Author(s):  
Carine Barreau ◽  
Elizabeth Benson ◽  
Helen White-Cooper
Keyword(s):  
In Situ Hybridization ◽  
Expression Pattern ◽  
Reverse Transcription ◽  
Protein Product ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Single Cyst ◽  
Reverse Transcription Pcr

Post-meiotic transcription is widespread in mammalian spermatogenesis, but is generally believed to be absent from Drosophila spermatogenesis. Genes required during meiosis, in early spermatids or later in spermiogenesis are typically transcribed in primary spermatocytes in Drosophila. Their mRNAs are then stored in the cytoplasm until the protein product is needed. Recently, using in situ hybridization, we identified 17 Drosophila genes, collectively named ‘comets’ and ‘cups’, whose mRNAs are most abundant in, and localize to the distal ends of, elongating spermatids. Using a single-cyst quantitative RT–PCR (reverse transcription–PCR) assay, we confirmed this unusual expression pattern and conclusively demonstrate the existence of post-meiotic transcription in Drosophila spermatids. We found that transcription of comets and cups occurs just before protamines can be detected in spermatid nuclei.

scholarly journals Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Raziyeh Khalesi ◽  
Ehsan Razmara ◽  
Golareh Asgaritarghi ◽  
Ali Reza Tavasoli ◽  
Yasser Riazalhosseini ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Cerebral White Matter ◽  
Global Developmental Delay ◽  
Spastic Diplegia ◽  
Amplification Refractory Mutation System ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Mutation System ◽  
Warburg Micro Syndrome

Abstract Background The present study aimed to determine the underlying genetic factors causing the possible Warburg micro syndrome (WARBM) phenotype in two Iranian patients. Case presentation A 5-year-old female and a 4.5-year-old male were referred due to microcephaly, global developmental delay, and dysmorphic features. After doing neuroimaging and clinical examinations, due to the heterogeneity of neurodevelopmental disorders, we subjected 7 family members to whole-exome sequencing. Three candidate variants were confirmed by Sanger sequencing and allele frequency of each variant was also determined in 300 healthy ethnically matched people using the tetra-primer amplification refractory mutation system-PCR and PCR-restriction fragment length polymorphism. To show the splicing effects, reverse transcription-PCR (RT-PCR) and RT-qPCR were performed, followed by Sanger sequencing. A novel homozygous variant—NM_012233.2: c.151-5 T > G; p.(Gly51IlefsTer15)—in the RAB3GAP1 gene was identified as the most likely disease-causing variant. RT-PCR/RT-qPCR showed that this variant can activate a cryptic site of splicing in intron 3, changing the splicing and gene expression processes. We also identified some novel manifestations in association with WARBM type 1 to touch upon abnormal philtrum, prominent antitragus, downturned corners of the mouth, malaligned teeth, scrotal hypoplasia, low anterior hairline, hypertrichosis of upper back, spastic diplegia to quadriplegia, and cerebral white matter signal changes. Conclusions Due to the common phenotypes between WARBMs and Martsolf syndrome (MIM: 212720), we suggest using the “RABopathies” term that can in turn cover a broad range of manifestations. This study can per se increase the genotype-phenotype spectrum of WARBM type 1.

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.

scholarly journals Weed Interference Affects Dry Bean Yield and Growth

2012 ◽  
Vol 4 (3) ◽  
pp. 70-75 ◽  
Author(s):  
Hossein GHAMARI ◽  
Goudarz AHMADVAND
Keyword(s):  
Chenopodium Album ◽  
Growing Season ◽  
Amaranthus Retroflexus ◽  
Growth And Yield ◽  
Weed Competition ◽  
Weed Species ◽  
Dry Bean ◽  
Logistic Equations ◽  
Weed Interference ◽  
Minimum Number

Dry bean is one of the most important pulse crops in Iran. Field study was conducted in 2011 to evaluate effects of weed competition from a natural flora on growth and yield of dry bean (Phaseolus vulgaris L.). The treatments consisted of weed infestation and weed removal periods (10, 20, 30, 40 and 50 days) after crop emergence. Control plots kept weed-infested and weed-free throughout growing season. To assess the weed competition effect on crop characteristics, Richards, Gompertz and logistic equations were fitted to the data. The most abundant weed species were Chenopodium album and Amaranthus retroflexus. Increase in duration of weed interference decreased the stem height of dry bean. At the end of the growing season, dry bean was 20 cm taller in season-long weed-free treatment compared to the season-long weed-infested treatment. As the number of days of weed interference increased, a declining trend of LAI and number of pods was observed. The minimum number of pods was obtained in season-long weed-infested treatment (5.01 pods/plant). Weed interference during the whole growing season, caused a 60% reduction in yield. Considering 5% and 10% acceptable yield lost, the critical period of weed competition was determined from 20 to 68 and 23 to 55 days after planting (DAE), respectively.

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