Fatima Osman - Academia.edu (original) (raw)

Papers by Fatima Osman

Plant Disease, Jun 1, 2011

Vitis and non-Vitis spp. surrounding nine Napa Valley vineyards were surveyed for Grapevine leafr... more Vitis and non-Vitis spp. surrounding nine Napa Valley vineyards were surveyed for Grapevine leafroll-associated virus (GLRaV)-1 to-5 and-9, Grapevine virus A (GVA), Grapevine virus B (GVB), and Grapevine virus D (GVD). Vitis spp. from three riparian areas not adjacent to vineyards were also included. DNA fingerprinting and probability analyses indicated that the Vitis samples consisted primarily of Vitis californica followed by V. californica × V. vinifera hybrids. Single and mixed infections of GLRaV-2,-3, GVA, or GVB were detected by conventional or quantitative reverse-transcription polymerase chain reaction in 6 of the 66 V. californica and 11 of the 19 V. californica × V. vinifera hybrids. GLRaV-1,-4,-5,-9, and GVD were not detected. Phylogenetic analysis of GLRaV-2 and-3 partial coat protein gene nucleotide sequences indicated that the isolates from V. californica and V. californica × V. vinifera hybrids were closely related to isolates from V. vinifera. Materials and Methods Vineyards and sample collection. In October and November 2008 and 2009, seven and two vineyards, respectively, were selected in Napa County, CA that had V. vinifera with red leaf symptoms typical of leafroll disease adjacent to areas with noncultivated Vitis and non-Vitis spp. Three riparian areas were also chosen that were not adjacent to vineyards but had a number of noncultivated Vitis plants with red leaves. Outside the vineyard, Vitis spp. and the most common woody non-Vitis spp. that were present within a 25m 2 area adjacent to symptomatic V. vinifera blocks were collected (Table 1). Within each vineyard, at least three vines from a block adjacent to noncultivated Vitis or non-Vitis spp. were collected. Composite samples of five to six canes per vine were collected and

Journal of Virological Methods, Feb 1, 2012

In this study different instruments and methods used for tissue homogenization, RNA extraction an... more In this study different instruments and methods used for tissue homogenization, RNA extraction and quantitative PCR (qPCR) based detection of grapevine RNA viruses were evaluated. Semi-automated and automated homogenization techniques were compared to process samples from grapevine petioles and cambial tissue. Four different high throughput automated nucleic acid extraction platforms were compared with the RNeasy plant extraction kit for their capacity and efficiency of extracting viral RNA from grapevine infected tissues. The RNA prepared from each extraction platform was then used as template for a comparative analysis of qPCR by One Step RT-qPCR, Two Step RT-qPCR and low density array (LDA) detection. This study showed that a thorough homogenization of grapevine tissues using the Tissue Lyser as well as DNase digestion of the purified RNA prior to cDNA synthesis improved the virus detection and yielded the lowest quantitation cycle (Cq) values in RT-qPCR. Comparison of different RNA extraction methods showed that methods implementing the magnetic bead-based technology were superior to other methods used. Comparing different qPCR detection methods, One Step RT-qPCR showed the lowest Cq values for the same sample tested compared to Two Step RT-qPCR and LDA.

Journal of Virological Methods, May 1, 2008

Low-density arrays (LDA) have been designed based on the real-time RT-PCR (TaqMan) assays for the... more Low-density arrays (LDA) have been designed based on the real-time RT-PCR (TaqMan) assays for the specific detection of 13 viruses that infect Grapevines in addition to the housekeeping gene 18S rRNA. The viruses included in the study are Grapevine leafroll associated viruses 1, 2, 3, 4, 5, and 9, Grapevine leafroll associated virus-2 Redglobe (GLRaV-2RG) strain, Ruspestris stem pitting associated virus, Grapevine vitivirus A, Grapevine vitivirus B, Grapevine fanleaf virus, Tomato ringspot virus (ToRSV), and Grapevine fleck virus (GFkV). This study includes three new TaqMan RT-PCR assays that have been developed for GLRaV-2RG, GFkV and ToRSV and have been included in the TaqMan RT-PCR and LDA detection. The LDAs were evaluated against a wide range of isolates distributed geographically. Geographical locations included Africa, Europe, Australia, Asia, Latin America and the United States. High-throughput detection of these viruses using LDAs was compared to RT-PCR and real-time TaqMan RT-PCR. The efficiency of different RNA extraction methodologies and buffers were compared for use in low-density array detection. In addition improving the RNA extraction technique and testing the quality of the RNA using the 18S ribosomal RNA TaqMan assay as an RNA specific internal control proved to generate better diagnostic assays. This is the first report on the use of LDA for the detection of plant viruses.

Journal of Virological Methods, Apr 1, 2007

This article was originally published in a journal published by Elsevier, and the attached copy i... more This article was originally published in a journal published by Elsevier, and the attached copy is provided by Elsevier for the author's benefit and for the benefit of the author's institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues that you know, and providing a copy to your institution's administrator.

PhytoFrontiers™

An updated real-time multiplex quantitative polymerase chain reaction (qPCR) assay was designed a... more An updated real-time multiplex quantitative polymerase chain reaction (qPCR) assay was designed and validated for the simultaneous detection of three ‘ Candidatus Liberibacter species’ (CLsp), ‘ Ca. Liberibacter asiaticus’ (CLas), ‘africanus’ (CLaf), and ‘americanus’ (CLam), associated with the huanglongbing disease of citrus. The multiplex assay was designed based on the qPCR assay published in 2006 by Li et al., considering all available CLsp 16S rRNA gene sequences in GenBank and the MIQE guidelines and workflow for qPCR optimization, which became available after 2006. When using the updated multiplex CLsp qPCR assay compared with singleplex qPCR, no significant increase in quantitative cycle (Cq) values was detected. The specificity and sensitivity of the updated qPCR assay was optimal, and measuring the intra- and interassay variations confirmed the reproducibility and repeatability of the assay. The assay was also successfully used with a large number of diverse samples at ind...

Phytopathology, Jun 8, 2011

International Organization of Citrus Virologists Conference Proceedings (1957-2010), 1976

Average number of local lesions per half-leaf of petunia leaves. Thirty-two replicates.

Journal of Plant Pathology, 2012

Plant Disease, 2021

Pathogen-tested foundation plant stocks are the cornerstone of sustainable specialty crop product... more Pathogen-tested foundation plant stocks are the cornerstone of sustainable specialty crop production. They provide the propagative units that are used to produce clean planting materials, which are essential as the first-line management option of diseases caused by graft-transmissible pathogens such as viruses, viroids, bacteria, and phytoplasmas. In the United States, efforts to produce, maintain, and distribute pathogen-tested propagative material of specialty crops are spearheaded by centers of the National Clean Plant Network (NCPN). Agricultural economists collaborated with plant pathologists, extension educators, specialty crop growers, and regulators to investigate the impacts of select diseases caused by graft-transmissible pathogens and to estimate the return on investments in NCPN centers. Economic studies have proven valuable to the NCPN in (i) incentivizing the use of clean planting material derived from pathogen-tested foundation plant stocks; (ii) documenting benefits ...

Journal of Plant Pathology, Mar 1, 2012

The USDA National Clonal Germplasm Repository (NGCR) at the University of California, Davis is re... more The USDA National Clonal Germplasm Repository (NGCR) at the University of California, Davis is recognized as one of the richest sources of Prunus species material in the US. The repository maintains more than 2450 trees representing 96 taxa collected from around the world. However, the phytosanitary status of the NCGR Prunus collection has not been thoroughly evaluated. In this study, a comprehensive screening of a selected subset of the collection for virus and virus-like diseases affecting Prunus trees has been completed. Two factors were considered for selecting the trees: the country of origin and the observation of suspicious disease symptoms. A total of 221 trees representing 185 different cultivars of cherry, almond, peach, apricot and plum were sampled. Conventional RT-PCR detection was used to test for 13 different viruses and two viroids. The pathogens included in the survey were Prunus necrotic ringspot virus (PNRSV), Prune dwarf virus (PDV), Plum bark necrosis stem pitting-associated virus (PBNSPaV), American plum line pattern virus (APLPV), Cherry virus A (CVA), Cherry leafroll virus (CLRV), Cherry rasp leaf virus (CRLV), Cherry green ring mottle virus (CGRMV), Cherry necrotic rusty mottle virus (CNRMV), Apple chlorotic leafspot virus (ACLSV) Tomato ringspot virus (ToRSV), Little cherry virus 1 (LChV-1), Little cherry virus 2 (LChV-2), Peach latent mosaic viroid (PLMVd) and Hop stunt viroid (HSVd). Though the majority of these trees were asymptomatic, all tested pathogens were detected except for ToRSV and CRLV. Two of the viruses detected (ACLSV and LChV-2) had never been reported from California. Incidence of PNRSV in tested trees was the highest (55 trees) followed by the two viroids (PLMVd and HSVd), with 33 and 32 infected trees, respectively. The incidence for the rest of the pathogens ranged between 0 to 19 trees. The infection rate of all tested samples ranged from 0.5% to 24.9%.

American Journal of Enology and Viticulture, Oct 30, 2017

A time course study was performed over two years to investigate the seasonal changes in copy numb... more A time course study was performed over two years to investigate the seasonal changes in copy numbers of different Grapevine leafroll associated virus (GLRaV) in infected grapevine (Vitis vinifera) in North America. Selected viruses were GLRaV-1,-2,-3,-4, and GLRaV-2RG. 17 One hundred and four different grapevines were selected from Davis grapevine virus collection 18 and from the USDA National Clonal Germplasm Repository (NCGR) located in Northern CA. 19 Grapevines, previously tested positive for one or more of these GLRaVs were assessed. Different 20 samples types were collected starting from the beginning of the growing season (Late April) as 21 follows; From April to November mature leaf petioles and from December to February cambial 22 scrapings from dormant grapevine cuttings. All samples were tested by RT-PCR and RT-qPCR. 23 RT-qPCR was found to be the more sensitive technique. Results showed that the GLRaVs were 24 more reliably detected when samples were collected between August and February. Grapevines 25 infected with GLRaV-2 were evenly detected throughout the year. More grapevines infected with 26

Additional file 1: Supplementary Table S1. BLASTn similarity search of Spiroplasma citri putative... more Additional file 1: Supplementary Table S1. BLASTn similarity search of Spiroplasma citri putative plasmid (contigs) against available Spiroplasma sequences deposited in NCBI database.

Additional file 2: Supplementary Table S2. GenBank accession numbers for the 16S rRNA Spiroplasma... more Additional file 2: Supplementary Table S2. GenBank accession numbers for the 16S rRNA Spiroplasma sequences used for phylogenetic analyses in Fig. 1.

Methods in Molecular Biology, 2021

High-throughput nucleic acid extraction is critical for the implementation of modern viroid detec... more High-throughput nucleic acid extraction is critical for the implementation of modern viroid detection assays. Successful large-scale nursery, field surveys, and other regulatory, quarantine, or research diagnostic programs are increasingly dependent on high-throughput tissue pulverization and nucleic acid extraction protocols. Magnetic bead-based approaches using semi-automated robotic equipment allow highthroughput extraction and purification of high-quality uniform total nucleic acids for each individual sample. Here, we describe a streamlined and optimized protocol for citrus tissue processing and RNA extraction that can be used for downstream applications such as viroid detection by reverse transcriptionquantitative polymerase chain reaction.

Journal of Plant Pathology, 2014

Reverse transcription quantitative PCR (RT-qPCR) assays were developed for the detection of the i... more Reverse transcription quantitative PCR (RT-qPCR) assays were developed for the detection of the ilarviruses Prunus necrotic ringspot virus (PNRSV), Prune dwarf virus (PDV), Apple mosaic virus (ApMV), and American plum line pattern virus (APLPV), and the nepoviruses Tomato ringspot virus (ToRSV) and Cherry leafroll virus (CLRV). These viruses affect various stone fruits such as apricots, cherries, peaches, plums, and almonds. The goal of this work was to improve the RT-qPCR detection of PNRSV, PDV, and ApMV in addition to developing three new RT-qPCR assays for the detection of APLPV, ToRSV and CLRV. Primers for conventional RT-PCR as well as primers and probes for RT-qPCR assays were designed after aligning coat protein (CP) gene sequences of geographically diverse isolates with the corresponding CP gene sequences from GenBank, targeting regions with 100% sequence identity. The efficiency of each RT-qPCR assay, as well as the intra- and inter-assay variability, were determined. Thes...

Frontiers in Microbiology, 2021

Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CY... more Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.

BMC Research Notes, 2020

Objectives: Spiroplasma citri is a bacterium with a wide host range and is the causal agent of ci... more Objectives: Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution. Data description: The whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4-25.6%.

American Journal of Enology and Viticulture, 2013

Cluster thinning (CT) is applied to reduce grapevine crop load and advance ripening parameters, b... more Cluster thinning (CT) is applied to reduce grapevine crop load and advance ripening parameters, but it also increases production costs and lowers yields. Riesling vines were subjected to four crop levels (nonthinned control and cluster thinned to 1, 1.5, and 2 ...

Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horse... more Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC2, C5, C189, LB319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas.Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri str...