Browsing by Author "Ocak, M."

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Cherry Leafroll Virus in Juglans Regia in the Lake Van Basin of Turkey
(Springer, 2008) Ozturk, M. O.; Sipahioglu, H. M.; Ocak, M.; Usta, M.
Walnut orchards of the Lake Van basin (Turkey) were surveyed from June to October 2006 to determine the incidence of viral infections. ELISA and RT-PCR were used to investigate the presence of Cherry leaf roll virus (CLRV) and Plum pox virus (PPV), testing a total of 870 samples collected from traditional seed-grown plantations. Whereas no PPNT was detected in any of the samples, CLRV was found for the first time in the surveyed locations with an average incidence of 12.9%. Two viral isolates from Edremit were mechanically transmitted to Chenopodium amaranticolor in which they caused local chlorotic spots followed by development of small leaves and apical. necrosis. A 366 bp DNA fragment was amplified by RT-PCR from the 3' non-coding region of RNA-2 of both viral isolates and sequenced. Isolate Edremit-2 was 93-98% identical to the comparable sequences of other isolates for which information is available, whereas isolate Edremit-1 had a lower sequence identity (53-46%). The size of the coat protein subunits of both viral isolates was 52.4 kDa as determined by electropboresis.
Comparison of Three Conventional Extraction Methods for the Detection of Plant Virus/Viroid Rnas From Heat Dried High-Phenolic Host Leaves
(Asian Network for Scientific Information, 2007) Sipahioglu, H.M.; Ocak, M.; Usta, M.
The presence of virus/viroid infections can go unnoticed since symptoms appear only if additional viruses are present. Detection of Plum bark necrosis stem pitting associated virus (PBNSPaV), Apricot latent virus (ApLV), Apple scar skin viroid (ASSVd), Prunus necrotic ringspot virus (PNRSV) and Potato virus Y (PVY) by reverse transcriptase polymerase chain reaction (RT-PCR) or nested-RT-PCR is possible; however, these assays could be unreliable if the tissue contains interfering compounds. This study reports on use of three extraction procedures in recently developed heat-dried virus/viroid preserved plant tissues. The methods tested were lithium chloride, silica-capture and citric buffer. The results showed that (1) the silica-capture RNA extraction method appears to be superior for total RNA extraction; (2) the increase in volume of silica improves the efficiency of RNA extraction from dried infected leaves and (3) the use of silica method minimizes the fragmentation of PCR products and improves the PCR detection of tested pathogens. The results of study indicate that the use of appropriate RNA extraction method is crucial for a successful PCR and an appreciable yield of PCR product from heat-dried infected leaves. © 2007 Asian Network for Scientific Information.
Detection of Apricot Latent Virus and Plum Bark Necrosis Stem Pitting-Associated Virus by Rt-Pcr in Eastern Anatolia (Turkey)
(2007) Ustai, M.; Sipahioglu, H.M.; Ocak, M.; Myrta, A.
Field surveys were carried out to determine presence and incidence of Apricot latent virus (ApLV) and Plum bark necrosis stempilting-associated virus (PBNSPaV) in the main stone fruit growing areas of Eastern Anatolia. RT-PCR and nested-RT-PCR techniques were used to detect ApLV and PBNSPaV, respectively. Three apricot samples out of 224 tested positive for ApLV, although infected trees showed no apparent disease symptoms. Of 45 sweet cherry and plum trees tested for PBNSPaV, 35 tested positive. Stem pitting symptoms were observed on the trunks of PBNSPaV-infected sweet cherries. Trunk bark was spongy and thick; pits and grooves were observed on the woody cylinder. The overall incidence of ApLV was 1.3% and of PBNSPaV was 77%. This is the first report of ApLV and PBNSPaV in Eastern Anatolia, Turkey. © 2007 OEPP/EPPO.
Development of a Rapid Enzymatic Cdna Amplification Test for the Detection of Apple Scar Skin Viroid (Assvd) in Apple Trees From Eastern Anatolia, Turkey
(2009) Sipahioglu, H.M.; Usta, M.; Ocak, M.
A validated RT-PCR method was used to investigate the presence of Apple scar skin viroid (ASSVd) in the commercial apple orchards of eastern Anatolia. Among three modified and simplified silica-capture based extraction methods, one was used for mass extraction to ascertain the presence of ASSVd. The test was initially performed from an ASSVd-infected source and then applied to total RNA preparations from fresh leaf tissues of apple trees collected from eastern Anatolia. ASSVd was found to occur in apple trees. Among 263 apple samples, 121 were positive for ASSVd. The infected trees showed no apparent disease symptoms on the leaves other than scarring on fruit skin. Overall incidence of ASSVd was 46% in eastern Anatolia. The presence of ASSVd reported for the first time in Turkey. Among three total RNA preparation methods, Method II was determined to be the best procedure for large scale routine analysis. The improved test can be used in a certification or clean stock program to contribute to the prevention of the spread of ASSVd in the eastern Anatolia.
The Effect of Gradient Temperature Pattern on Annealing Efficiency
(int Soc Horticultural Science, 2008) Ocak, M.; Sipahioglu, H. M.; Usta, M.
The specific complementary association due to hydrogen bonding of single stranded nucleic acids is referred to as annealing. Successful primer annealing is of critical importance in a polymerase chain reaction (PCR). In this study, the effect of gradually increased and decreased annealing temperatures on PCR reactions were investigated. In the annealing tests, the isolates of Plum bark necrosis stem pitting associated virus (PBNSPaV), Apricot latent virus (ApLV), Apple scar skin viroid (ASSVd) and Potato virus Y (PVY) were used as reference isolates. The effects of annealing temperature alterations were tested by nested reverse transcriptase polymerase chain reaction (nested-RT-PCR) for PBNSPaV and RT-PCR for ApLV, ASSVd and PVY. The PCR products were analyzed and evaluated by polyacrylamide gel electrophoresis (PAGE). Gradient temperatures (2 to 4 degrees C) below and above annealing temperature resulted in increased primer annealing by both methods. Higher gradients (8-12 degrees C) never resulted in appreciable yields of a unique PCR product, as the likelihood of primer annealing was reduced. Both high and low gradients of annealing temperature gave the yield in PCR reactions, confirming flexible nature of annealing temperature.
Occurrence of Cherry Green Ring Mottle Virus in Turkey
(Wiley, 2008) Sipahioglu, H. M.; Usta, M.; Ocak, M.