RT-PCR

ralkowni's picture

Detection of Genomic Variations in Grapevine Rupestris Stem Pitting Associated Virus, Leading For Identification of New Virus Isolates and Developing Of Molecular Tool for Their Specific Detection

Journal Title, Volume, Page: 
Hebron University Research Journal 08/2008; 3(2):36-48
Year of Publication: 
2008
Authors: 
Raed Alkowni
Department of Biology and Biotechnology, Faculty of Science, An-Najah National University, Nablus, Palestine
Current Affiliation: 
Department of Biology and Biotechnology, Faculty of Science, An-Najah National University, Nablus, Palestine
Preferred Abstract (Original): 

Grapevine rupestris stem pitting associated virus (GRSPaV) is a component of the rugose wood disease complex. The vast majority of collected samples through field surveys in Californian vineyards that showing rugose wood disease complex symptoms, were tested negative for viruses typically associated with graft union disorders, meanwhile 50% were found positive for GRSPaV using RT-PCR methodology. The dsRNA extracted from GRSPaV-positively tested samples were used as a template for cDNA construction. Molecular analysis of the several sequenced clones from different vines, using ClustalW bioinformatics program revealing significant variations in the virus genome. Two different GRSPaV-isolates named later as GRSPaV-SY and GRSPaV-PN had been identified, showing significant nucleotide sequence variability reached up to 29%. Specific pairs of primers were designed and optimized to detect each isolate specifically, using one step RT-PCR techniques. The use of these detection primers in studying the etiology of GRSPaV and correlation of the symptoms variation will be inevitable.

ralkowni's picture

Genomic Study and Detection of a New Variant of Grapevine Rupestris Stem Pitting Associated Virus in Declining California Pinot Noir Grapevines

Journal Title, Volume, Page: 
Journal of Plant Pathology, Vol 91, No 1 (2009)
Year of Publication: 
2009
Authors: 
M. Lima
Department of Plant Pathology, University of California, 95616 Davis, CA, USA
R. Alkowni
Department of Biology and Biotechnology, The Arab American University, Jenin, Palestine
Current Affiliation: 
Department of Biology and Biotechnology, Faculty of Science, An-Najah National University, Nablus, Palestine
J.K. Uyemoto
Department of Biology and Biotechnology, The Arab American University, Jenin, Palestine
A. Rowhani
Department of Plant Pathology, University of California, 95616 Davis, CA, USA
Preferred Abstract (Original): 

Declining cv. Pinot noir clone 23 plants on 3309 Couderc rootstock were observed in different vineyards in California exhibiting severe stunting, solid red leaves and rootstocks with stem necrosis-distortion. High molecular weight dsRNA of ca. 8.7 kbp was extracted from symptomatic vines, used as a template for cDNA libraries construction and sequencing and identified as a new strain of Grapevine rupestris stem pitting-associated virus designated as Pinot noir strain (GRSPaV-PN). Molecular characterization of GRSPaV-PN genome revealed that the complete nucleotide sequence was composed of 8,724 nt, excluding the poly-A tail. This strain shared nucleotide identity of 76% to 78% with other GRSPaV sequences present in the GenBank. Its genome organization included six open reading frames where its replicase gene had 76% and 85% nucleotide and deduced amino acid identities, respectively, to other GRSPaV sequences. The coat protein gene was the most conserved with nucleotide and amino acid identities of 81-88% and 91.8-95%, respectively. Limited field survey revealed that GRSPaV-PN was present mainly in Pinot noir clone 23. However, the causal nature of GRSPaVPN and 3309C stem necrosis-distortion is not known.

Hani Al-Ahmad's picture

Gene Expression Profiling of Resistant And Susceptible Soybean Lines Infected With Soybean Cyst Nematode

Journal Title, Volume, Page: 
TAG Theoretical and Applied Genetics DOI: 10.1007/s00122-011-1659-8
Year of Publication: 
2011
Authors: 
Mitra Mazarei
Department of Plant Sciences, The University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN 37996, USA
Wusheng Liu
Department of Plant Sciences, The University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN 37996, USA
Hani Al-Ahmad
Department of Plant Sciences, The University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
Current Affiliation: 
Department of Biology & Biotechnology, Faculty of Science, An-Najah National University, Nablus. Palestine
Prakash R. Arelli
Crop Genetics Research Unit, USDA-ARS, 605 Airways Blvd, Jackson, TN 38301, USA
Vincent R. Pantalone
Department of Plant Sciences, The University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN 37996, USA
C. Neal Stewart
Department of Plant Sciences, The University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN 37996, USA
Preferred Abstract (Original): 

Soybean cyst nematode (SCN) is the most devastating pathogen of soybean. Information about the molecular basis of soybean–SCN interactions is needed to assist future development of effective management tools against this pathogen. Toward this end, soybean transcript abundance was measured using the Affymetrix Soybean Genome Array in a susceptible and a resistant reaction of soybean to SCN infection. Two genetically related soybean sister lines TN02-226 and TN02-275, which are resistant and susceptible, respectively, to the SCN race 2 infection were utilized in these experiments. Pairwise comparisons followed by false discovery rate analysis indicated that the expression levels of 162 transcripts changed significantly in the resistant line, of which 84 increased while 78 decreased. However, in the susceptible line, 1,694 transcripts changed significantly, of which 674 increased while 1,020 decreased. Comparative analyses of these transcripts indicated that a total of 51 transcripts were in common between resistance and susceptible responses. In this set, 42 transcripts increased in the resistant line, but decreased in the susceptible line. Quantitative real-time reverse-transcription polymerase chain reaction confirmed the results of microarray analysis. Of the transcripts to which a function could be assigned, genes were associated with metabolism, cell wall modification, signal transduction, transcription, and defense. Microarray analyses examining two genetically related soybean lines against the same SCN population provided additional insights into the specific changes in gene expression of a susceptible and a resistant reaction beneficial for identification of genes involved in defense.

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