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Identity and Sequence Diversity of Begomovirus Associated with Yellow Leaf Curl Disease of Tomato in Indonesia  [cached]
Microbiology Indonesia , 2008,
Abstract: Infection of tomato by Begomovirus is known to cause serious disease and yield losses. Samples of tomato plants showing typical symptoms of begomovirus infection were collected from eight locations in Java and Sumatra. Amplification of a putative AV1 gene was performed using AV1 specific primers for Geminivirus, total nucleic acid isolated from tomato samples exhibiting leaf curl disease as the template, and the PCR technique. Direct sequencing of PCR product was carried out, followed by nucleotide and predicted amino acid sequence analysis using the BLAST program. Positive results were obtained, the PCR amplification proved that diseased tomato samples collected from eight locations in Java and Sumatra were infected with Begomovirus. When nucleic acid and amino acid sequences of the eight isolates were compared to other begomovirus’s sequences present in the GenBank it was found that the isolates determined in this research were Indonesian isolates of AYVV. Further phylogenetic analysis of eight Begomovirus isolates identified in this study indicated they belonged into two different clades. Results of this research also suggest that the existence of Begomovirus genetic diversity in various regions in Indonesia needs further investigation. Moreover, the prevalence of distinct Begomovirus species or isolates also need investigation.
Detection and Sequence Diversity of Begomovirus Associated with Yellow Leaf Curl Disease of Pepper (Capsicum annuum) in West Sumatra, Indonesia  [cached]
Microbiology Indonesia , 2009,
Abstract: Yellow leaf curl disease of pepper has become an emerging important disease in West Sumatra since early 2000. Several attempts have been made, including disease survey and detection, in order to identify the causal agent of the disease. Pepper (Capsicum annuum) plants showing yellow leaf curl from West Sumatra were analyzed for presence of Begomovirus employing Polymerase Chain Reaction (PCR) with degenerate primers pAL1v 1978 and pARc 715. A DNA fragment of 1.6 kb was successfully amplified and subjected to direct sequencing. A stem loop region was found in the nucleotide sequence obtained, which contains the conserved nucleotide signature sequence TAATATTAC present in begomoviruses. Based on the stem loop region comparisons and phylogenetic analysis, the virus isolates from West Sumatra showed the closest relationship to Pepper yellow leaf curl Indonesia virus (PYLVIV) and Tomato yellow leaf curl Indonesia virus (TYLCIV). The sequence was different from other Asia Begomoviruses reported earlier. These isolates were divided into three groups which were tentatively called Pepper yellow leaf curl Indonesia virus-West Sumatra-[group 1], -[group 2] and -[group 3] {PYLCIV-WS-[group1], -[group2], and -[group3]}.
Response of Various Tomato Genotypes to Begomovirus Infection and Its Improved Diagnostic  [PDF]
HAYATI Journal of Biosciences , 2007,
Abstract: Begomovirus infection was identified from tomato growing areas in West Java (Bogor), Central Java (Boyolali), and D.I. Yogyakarta (Kaliurang). Efforts to reduce the infection among others are planting resistance varieties. This research was undertaken to evaluate 14 tomato genotypes for their response to the infection. Dot blot hybridization using nonradioactive (digoxigenin) DNA probe was employed to determine the presence of begomovirus in inoculated plants. Polymerase chain reaction-amplified product of DNA clone of tobacco leaf curl virus –Indonesia was used as a source of DNA probe. All of tomato genotypes evaluated in this study was infected separately by three strain of begomovirus (GVPSlm, GVABy, GVCBgr). Tomato genotypes Bonanza, Jelita, Safira, Permata, Presto, PSPT 8, PSPT 5B, Apel-Belgia, Karibia, Mitra, PSPT 9, Marta, and PSPT 2, showed susceptible or highly susceptible response to the three strains of begomovirus. Exception to those was shown by cv. Intan which resulted in moderate resistance when inoculated with GVCBgr although it resulted susceptible response with the other two strains. Dot-blot hybridization technique was proved to be a powerful tool to detect begomovirus infection in plants showing symptom as well as symptom-less plants. Accumulation of the virus in those plants was relatively high, except in cv. Bonanza and Apel-Belgia. Dot-blot hybridization technique using DIG-labeled DNA probe was able to detect begomovirus DNA in infected tissue up to 10-2 dilution factor.
Lukman Ade Putratama,Ulif Muhayyatin,Bambang Sri Kaloko
Academic Research International , 2012,
Abstract: Forecasting of Product Domestic Regional Bruto (PDRB) in Jember has been developed to successful in consistently predicting the performance of the Domestic Government. The complex set of problemprocesses within PDRB have made the development of analytical models to be a significant challenge. Advanced simulation tools are needed to become more accurately model of PDRB systems. As an alternative approach, we have begun development of PDRB modeling based on Levenberg Marquardt which uses Matlab 7.6.0(R2008b). A neural network based learning system method has been proposed forecasting of PDRB. Levenberg Marquardt based technique is used for learning PDRB. Thus a precision model of Levenberg Marquardt has been evaluated. The correlation coefficient of this model is 0.99 shows good results for the target and network output.
The Merging of Two Dynasties—Identification of an African Cotton Leaf Curl Disease-Associated Begomovirus with Cotton in Pakistan  [PDF]
Muhammad Nouman Tahir, Imran Amin, Rob W. Briddon, Shahid Mansoor
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0020366
Abstract: Cotton leaf curl disease (CLCuD) is a severe disease of cotton that occurs in Africa and Pakistan/northwestern India. The disease is caused by begomoviruses in association with specific betasatellites that differ between Africa and Asia. During survey of symptomatic cotton in Sindh (southern Pakistan) Cotton leaf curl Gezira virus (CLCuGV), the begomovirus associated with CLCuD in Africa, was identified. However, the cognate African betasatellite (Cotton leaf curl Gezira betasatellite) was not found. Instead, two Asian betasatellites, the CLCuD-associated Cotton leaf curl Multan betasatellite (CLCuMB) and Chilli leaf curl betasatellite (ChLCB) were identified. Inoculation of the experimental plant species Nicotiana benthamiana showed that CLCuGV was competent to maintain both CLCuMB and ChLCB. Interestingly, the enations typical of CLCuD were only induced by CLCuGV in the presence of CLCuMB. Also in infections involving both CLCuMB and ChLCB the enations typical of CLCuMB were less evident. This is the first time an African begomovirus has been identified on the Indian sub-continent, highlight the growing threat of begomoviruses and particularly the threat of CLCuD causing viruses to cotton cultivation in the rest of the world.
Molecular Detection and Partial Characterization of Begomovirus Associated with Leaf Curl Disease of Sunflower (Helianthus annuus) in Southern India  [PDF]
M.R. Govindappa,I. Shankergoud,K.S. Shankarappa,W.A.R.T. Wickramaarachchi
Plant Pathology Journal , 2011,
Abstract: The present study was conducted to investigate the etiology, mode of transmission and molecular relationship of the causal virus associated with Sunflower leaf curl disease with other related viruses. Leaf curl disease on sunflower caused by a begomovirus was observed to an extent of 40% for the first time on some hybrids grown in experimental plots at Main Research Station (MRS), Raichur, Karnataka, Southern India. Symptoms like curling, malformation of leaves, leaf thickening, leaf enations and severe stunting were observed on infected plants. The disease was successfully transmitted by whitefly, Bemisia tabaci. The experimentally inoculated plants produced symptoms similar to that of naturally infected plants. The causal virus was detected using two sets of begomovirus specific degenerate primers. The core Coat Protein (CP) gene fragment of 575 bases was amplified from naturally as well as whitefly inoculated plants. Phylogenetic analysis of the core CP gene sequence of the virus with those of other begomoviruses clustered next to Tomato Leaf Curl Karnataka Virus isolate Lucknow (ToLCKV-(Luc) (Accession No. EU604297.2) and Tomato Leaf Curl Virus-Bangalore II (ToLCBV-(Ban2) (Accession No. EU604297.2) and shared 97.5% nucleotide identities. Thus, its exact taxonomic status will require sequencing of the complete ssDNA viral genome. The begomovirus infecting sunflower, which we tentatively called Sunflower Leaf Curl Virus (SuLCV).
Mahmood-ur-Rahman,Khadim Hussain,Muhammad Azmatullah Khan,Abdul Qayyum Rao
Pure and Applied Biology , 2012, DOI: nil
Abstract: Genome of plant viruses consists of either RNA or DNA. DNA viruses can be categorized into two types, (1) circular double-stranded DNA (dsDNA), these viruses are able to replicate through the process of reverse transcription from RNA (the caulimoviruses and badnaviruses), (2) viruses that have circular single-stranded DNA (ssDNA), which replicate through a dsDNA intermediate (the Geminivirus and nanoviruses). Begomoviruses are whiteflies transmitted geminiviruses and infect many economically important dicotyledonous crops including cotton, potato, tomato, cassava and chili. Begomoviruses cause leaf curl disease in cotton. In this review article, the Cotton Leaf Curl Virus (CLCuV) has been introduced systematically.
Association of an Alphasatellite with Tomato Yellow Leaf Curl Virus and Ageratum Yellow Vein Virus in Japan Is Suggestive of a Recent Introduction  [PDF]
Muhammad Shafiq Shahid,Masato Ikegami,Abdul Waheed,Rob W. Briddon,Keiko T. Natsuaki
Viruses , 2014, DOI: 10.3390/v6010189
Abstract: Samples were collected in 2011 from tomato plants exhibiting typical tomato leaf curl disease symptoms in the vicinity of Komae, Japan. PCR mediated amplification, cloning and sequencing of all begomovirus components from two plants from different fields showed the plants to be infected by Tomato yellow leaf curl virus (TYLCV) and Ageratum yellow vein virus (AYVV). Both viruses have previously been shown to be present in Japan, although this is the first identification of AYVV on mainland Japan; the virus previously having been shown to be present on the Okinawa Islands. The plant harboring AYVV was also shown to contain the betasatellite Tomato leaf curl Java betasatellite (ToLCJaB), a satellite not previously shown to be present in Japan. No betasatellite was associated with the TYLCV infected tomato plants analyzed here, consistent with earlier findings for this virus in Japan. Surprisingly both plants were also found to harbor an alphasatellite; no alphasatellites having previously been reported from Japan. The alphasatellite associated with both viruses was shown to be Sida yellow vein China alphasatellite which has previously only been identified in the Yunnan Province of China and Nepal. The results suggest that further begomoviruses, and their associated satellites, are being introduced to Japan. The significance of these findings is discussed.
Phytochemical Composition of Selaginella spp. from Java Island Indonesia  [cached]
Tatik Chikmawati,Ahmad Dwi Setyawan,Miftahudin
Makara Seri Sains , 2012,
Abstract: For a long time, people in West Java, Indonesia have used Selaginella as a traditional cure for several ailments including fever, minor wounds, broken bones, women’s health disorders or postnatal bleeding. However, information on the active compounds of the plant from Java Island has not been fully expounded. The objective of the research was to reveal the diversity of bioactive compounds and amentoflavone content of Selaginella from Java Island in order to optimize the use of this plant as a medicinal plant. Selaginella plants collected from 29 locations in Java were extracted and subjected to colorimetric and thin layer chromatography test to qualitatively analyze the bioactive compounds of alkaloid, phenol, and steroid. In addition, high performance liquid chromatography was performed to analyze the amentofalvone content of Selaginella extract. The research result showed that all the examined Selaginella species contained alkaloid, flavonoid, saponin, tannin, and steroid, but they did not contain hydroquinone. Seven of them contained the biflavonoid type of amentoflavone. The highest amentoflavone concentration, 6.87 ppm, was found in S. subalpina that originated from Gedung Songo, Central Java. Those results indicated that more than one Selaginella species originating from Java Island had marked potential for use as medicinal plants.
Arsenic and Mercury Concentrations at Several Geothermal Systems in West Java, Indonesia  [PDF]
N.R. Herdianita,B. Priadi
ITB Journal of Science , 2008,
Abstract: A study at several geothermal systems in West Java, Indonesia shows that thermal waters could naturally contain up to 2.6 ppm As and 6.5 ppb Hg, and the surface hydrothermal alteration could contribute up to 50 ppm As and 800 ppb Hg. The higher the chloride content, the higher the contents of As and Hg of thermal waters. The amounts of As and Hg in an active geothermal system are influenced by the type of host rock, boiling and mixing processes, and adsorption of vapor and volcanic gases into thermal waters.
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