Browsing by Author "Sipahioglu, H.M."

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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 and Partial Characterization of Two Distinct Walnut Isolates of Cherry Leaf Roll Virus (Clrv)
(Academic Journals, 2011) Sipahioglu, H.M.; Tekin, Z.; Usta, M.
Two new cherry leaf roll virus (CLRV) isolates (Ah and Ad) were isolated and detected from traditionally-grown walnuts that showed severe apical necrosis and chlorotic spots in systemically infected Cheneopodium amaranticolor, in the eastern part of Turkey. The 404 and 405 bp long DNA fragments of the 3'-non-coding region of both isolates from PCR reactions were cloned and sequenced. A significant genetic variability (up to 14% divergence between sequences) was found within the 3' terminal region of viral genome of CLRV Turkish isolates compared with the isolates in databases. The sequence of Ad isolate was found to share 84 to 98% and the Ah isolate was found to share 85 to 97% nucleotide identity with corresponding sequences of the selected world isolates. An RNA riboprobe generated for CLRV-Ad isolate reacted also with the CLRV-Ah isolate in dot blot molecular hybridization test. Positive reactions were still visible in hybridization test when the extracts of infected fresh and dried leaf tissues of C. amaranticolor diluted 1:20. Western blot analysis revealed that the molecular mass of the coat protein of about 52 kDa for both isolates. © 2011 Academic Journals.
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.
Detection of Arbuscular Mycorrhizal Fungi Within Colonised Roots of the Gramineae Family Members by Nested-Polymerase Chain Reaction (Pcr)
(2011) Demir, S.; Sipahioglu, H.M.; Kaya, I.; Usta, M.; Savur, O.B.
In this study, it is aimed to asses the association of arbuscular mycorrhizal (AM) fungi within colonised rhizosphere of Gramineae family members through a survey by using nested polymerase chain reaction method in Van province (Turkey). From 24 agro-ecological fields, a total of 82 samples belonging to Gramineae family were tested by molecular methods. The presence of Glomus intraradices and Glomus mosseae was ascertained in 10 plants belonging to eight different species by using fungus specific primers. Root colonisation ranged from 6 to 37% within rhizosphere of Gramineae family members and the average root colonisation by AM fungi was 22%. © 2011 Copyright Taylor and Francis Group, LLC.
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.
Partial Characterisation of a Cherry Isolate of a Newly Emerging Stone Fruit Virus: Plum Bark Necrosis Stem Pitting Associated Virus
(Taylor and Francis Ltd., 2011) Sipahioglu, H.M.; Usta, M.; Oksuz, T.
Plum bark necrosis stem pitting associated virus (PBNSPaV) has occurred globally over the last two decades and is becoming one of the major agricultural issues of stone fruits. The virus was detected for the first time in plums and has been reported in the other stone fruit species. The agent, whose dissemination mode is still unknown, has been first reported in cherries in Turkey grown in Malatya province. In this study, the K1 isolate of PBNSPaV, identified in a sweet cherry plant with severe stem pitting and gumming symptoms on its trunk, was partially characterised. A fragment of Hsp70h gene located on ORF3 of viral genome has been cloned, sequenced and analysed phylogenetically (Accession number. FJ231498). The PBNSPaV-K1 isolate showed 93-96% nucleotide sequence identity to sequences of Italian and American isolates in databases. An RNA probe has been raised for fast and reliable detection of the agent by molecular hybridisation. The studies on development of genome specific primers for the detection of the isolate by one-tube RT-PCR have failed. © 2011 Taylor & Francis.
Sanitary Status of Stone-Fruit Trees in East Anatolia (Turkey) With Particular Reference To Apricot
(1999) Sipahioglu, H.M.; Myrta, A.; Abou-Ghanem, N.; Di Terlizzi, B.; Savino, V.
Field surveys were carried out in the main stone-fruit-growing areas of East Anatolia (Turkey) to assess the sanitary status of varietal collections, mother blocks and commercial orchards. The presence of virus and virus-like diseases was ascertained by enzyme-linked immunosorbent assay (ELISA), sap transmission to herbaceous hosts, graft transmission to peach cv. GF305 and molecular hybridization tests. A total of 1019 samples was tested by ELISA (859 apricot, 120 cherry, 21 almond and 19 peach). The sanitary status of apricot was extremely satisfactory, as the infection level was less than 0.3%. Cherry and almond, however, showed 21% and 33% infection respectively. The viruses identified were apple chlorotic leaf spot trichovirus (ACLSV), prune dwarf ilarvirus (PDV) and prunus necrotic ringspot ilarvirus (PNRSV). The commonest virus was PDV. Plum pox potyvirus (PPV), apple mosaic ilarvirus (ApMV) and the nepoviruses tomato black ring (TBRV), raspberry ringspot (RpRSV), strawberry latent ringspot (SLRV), cherry leaf roll (CLRV), arabis mosaic (ArMV) and tomato ringspot (ToRSV) were not encountered. Peach latent mosaic viroid (PLMVd) and hop stunt viroid (HSVd) were not detected either. © 1999 Wiley. All rights reserved.