Identification and Expression Analysis of Genes Induced in Response to Tomato chlorosis virus Infection in Tomato

Sahin-Cevik, Mehtap,Sivri, Emine Dogus,Cevik, Bayram The Korean Society of Plant Pathology 2019 Plant Pathology Journal Vol.35 No.3

Tomato (Solanum lycopersicum) is one of the most widely grown and economically important vegetable crops in the world. Tomato chlorosis virus (ToCV) is one of the recently emerged viruses of tomato distributed worldwide. ToCV-tomato interaction was investigated at the molecular level for determining changes in the expression of tomato genes in response to ToCV infection in this study. A cDNA library enriched with genes induced in response to ToCV infection were constructed and 240 cDNAs were sequenced from this library. The macroarray analysis of 108 cDNAs revealed that the expression of 92 non-redundant tomato genes was induced by 1.5-fold or greater in response to ToCV infection. The majority of ToCV-induced genes identified in this study were associated with a variety of cellular functions including transcription, defense and defense signaling, metabolism, energy, transport facilitation, protein synthesis and fate and cellular biogenesis. Twenty ToCV-induced genes from different functional groups were selected and induction of 19 of these genes in response to ToCV infection was validated by RT-qPCR assay. Finally, the expression of 6 selected genes was analyzed in different stages of ToCV infection from 0 to 45 dpi. While the expression of three of these genes was only induced by ToCV infection, others were induced both by ToCV infection and wounding. The result showed that ToCV induced the basic defense response and activated the defense signaling in tomato plants at different stages of the infection. Functions of these defense related genes and their potential roles in disease development and resistance to ToCV are also discussed.

AN EXAMPLE OF LARGE GROUPS

Cevik, Ahmet Sinan Korean Mathematical Society 2020 대한수학회보 Vol.57 No.1

The fundamental idea of this article is to present an effective way to obtain the large groups in terms of the split extension obtained by a finite cyclic group and a free abelian group rank 2. The proof of the main result on largeness property of this specific split extension groups will be given by using the connection of large groups with the groups having deficiency one presentations.

The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains

Cevik, Bayram,Yardimci, Nejla,Korkmaz, Sava The Korean Society of Plant Pathology 2013 Plant Pathology Journal Vol.29 No.1

The presence of Citrus tristeza virus (CTV) has previously been reported in citrus growing regions of Turkey. All serologically and biologically characterized isolates including I$\breve{g}$d${\i}$r, which was the first identified CTV isolates from Turkey, were considered mild isolates. In this study, molecular characteristics of the I d r isolate were determined by different methods. Analysis of the I$\breve{g}$d${\i}$r isolate by western blot and BD-RT-PCR assays showed the presence of MCA13 epitope, predominantly found in severe isolates, in the I$\breve{g}$d${\i}$r isolate revealing that it contains a severe component. For further characterization, the coat protein (CP) and the RNA-depen-dent RNA polymerase (RdRp) genes representing the 3' and 5' half of CTV genome, respectively, were amplified from dsRNA by RT-PCR. Both genes were cloned separately and two clones for each gene were sequenced. Comparisons of nucleotide and deduced amino acid sequences showed that while two CP gene sequences were identical, two RdRp clones showed only 90% and 91% sequence identity in their nucleotide and amino acid sequences, respectively, suggesting a mixed infection with different strains. Phylogenetic analyses of the CP and RdRp genes of I$\breve{g}$d${\i}$r isolate with previously characterized CTV isolates from different citrus growing regions showed that the CP gene was clustered with NZRB-TH30, a resistance breaking isolate from New Zealand, clearly showing the presence of severe component. Furthermore, two different clones of the RdRp gene were clustered separately with different CTV isolates with a diverse biological activity. While the RdRp-1 was clustered with T30 and T385, two well-characterized mild isolates from Florida and Spain, respectively, the RdRp-2 was most closely related to NZRB-G90 and NZRB-TH30, two well-characterized resistance breaking and stem pitting (SP) isolates from New Zealand confirming the mixed infection. These results clearly demonstrated that the I$\breve{g}$d${\i}$r isolate, which was previously described as biologically a mild isolate, actually contains a mixture of mild and severe strains.

Xanthine Biosensor Based on XO/AuNP/PtNP/MWCNT Hybrid Nanocomposite Modified GCPE

Serdar Cevik 한국생물공학회 2016 Biotechnology and Bioprocess Engineering Vol.21 No.2

A new xanthine (X) biosensors based on a hybrid nanocomposite containing multi-walled carbon nanotubes (MWCNT), Pt nanoparticles (PtNP) and gold nanoparticle (AuNP) was presented. X biosensor was fabricated by dropping AuNP/PtNP/MWCNT onto xanthine oxidase (XO) modified glassy carbon paste electrode (GCPE). Resulted XO/AuNP/PtNP/MWCNT/GCPE biosensor showed two linearity between 2.0 and 50 μM and 0.25 and 6.0 mM for X. RSD value was calculated as 2.46 (n = 5). Finally, the biosensor was applied to the X detection in synthetic serum samples and good recovery value was obtained.

Neuro-Fuzzy modeling of torsional strength of RC beams

A. Cevik,R. Saracoglu,M.H. Arslan 사단법인 한국계산역학회 2012 Computers and Concrete, An International Journal Vol.9 No.6

This paper presents Neuro-Fuzzy (NF) based empirical modelling of torsional strength of RC beams for the first time in literature. The proposed model is based on fuzzy rules. The experimental database used for NF modelling is collected from the literature consisting of 76 RC beam tests. The input variables in the developed rule based on NF model are cross-sectional area of beams, dimensions of closed stirrups, spacing of stirrups, cross-sectional area of one-leg of closed stirrup, yield strength of stirrup and longitudinal reinforcement, steel ratio of stirrups, steel ratio of longitudinal reinforcement and concrete compressive strength. According to the selected variables, the formulated NFs were trained by using 60 of the 76 sample beams. Then, the method was tested with the other 16 sample beams. The accuracy rates were found to be about 96% for total set. The performance of accuracy of proposed NF model is furthermore compared with existing design codes by using the same database and found to be by far more accurate. The use of NF provided an alternative way for estimating the torsional strength of RC beams. The outcomes of this study are quite satisfactory which may serve NF approach to be widely used in further applications in the field of reinforced concrete structures.

Genetic-programming-based Modeling of RC Beam Torsional Strength

Abdulkadir Cevik,Musa Hakan Arslan,Mehmet Alpaslan Koroglu 대한토목학회 2010 KSCE Journal of Civil Engineering Vol.14 No.3

This study investigates the use of Genetic Programming (GP) to model Reinforced Concrete (RC) beam torsional strength. Experimental data of 76 rectangular RC beams from an existing database were used to develop the GP model. The following input parameters, which affect torsional strength, were selected: beam cross-sectional area, closed stirrup dimensions, stirrup spacing,closed stirrup cross-sectional area of one leg, stirrup and longitudinal reinforcement yield strength, stirrup steel ratio, longitudinal reinforcement steel ratio and concrete compressive strength. Moreover, a short review of well-known building codes in relation to the design of RC beams under pure torsion is presented. The accuracy of the codes in predicting the RC beam torsional strength was also compared with the proposed GP model using the same test data. The study concludes that the proposed GP model predicts RC beam torsional strength more accurately than building codes

Modelling the performance of self-compacting SIFCON of cement slurries using genetic programming technique

Abdulkadir Cevik,Mohammed Sonebi 사단법인 한국계산역학회 2008 Computers and Concrete, An International Journal Vol.5 No.5

The paper explores the potential of applicability of Genetic programming approach (GP), adopted in this investigation, to model the combined effects of five independent variables to predict the mini-slump, the plate cohesion meter, the induced bleeding test, the J-fiber penetration value, and the compressive strength at 7 and 28 days of self-compacting slurry infiltrated fiber concrete (SIFCON). The variables investigated were the proportions of limestone powder (LSP) and sand, the dosage rates of superplasticiser (SP) and viscosity modifying agent (VMA), and water-to-binder ratio (W/B). Twenty eight mixtures were made with 10-50% LSP as replacement of cement, 0.02-0.06% VMA by mass of cement, 0.6-1.2% SP and 50-150% sand (% mass of binder) and 0.42-0.48 W/B. The proposed genetic models of the self-compacting SIFCON offer useful modelling approach regarding the mix optimisation in predicting the fluidity, the cohesion, the bleeding, the penetration, and the compressive strength.

Without Oil, How Do Gulf Countries Move? Non-hydrocarbon Business Cycles

( Ser Han Cevik ) 세종대학교 경제통합연구소 2014 Journal of Economic Integration Vol.29 No.2

This paper investigates the empirical characteristics of business cycles and the extent of cyclical comovement in the Gulf Cooperation Council (GCC) countries, using nonhydrocarbon GDP (excluding crude oil and natural gas sectors) and constituents of aggregate demand during the period 1990~2010. Although hydrocarbons still account for an overwhelming share of export earnings and fiscal revenues in the GCC countries leading to a higher degree of business cycle synchronicity at an aggregate level, this is driven largely by external factors influencing the price of crude oil and natural gas. By applying the Christiano-Fitzgerald asymmetric band-pass filter and a mean corrected concordance index, the results show that low level of synchronization in nonhydrocarbon business cycles across the GCC economies and a decline in the degree of synchronicity in the 2000s if Kuwait is excluded from the sample. It is partly because of divergent fiscal policies. The GCC countries do not appear to efficiently coordinate policies, let alone forming an optimal currency area.

Detection of Viruses Infecting Stone Fruits in Western Mediterranean Region of Turkey

Yardimci, Bayram Cevik Nejla,Culal-Klllc, Handan The Korean Society of Plant Pathology 2011 Plant Pathology Journal Vol.27 No.1

Field surveys were conducted in 45 stone fruit orchards in seven districts of Isparta Province located in western Mediterranean region of Turkey important for stone fruit production. Leaf samples were collected from 175 trees showing virus-like symptoms. These samples were first tested by ELISA for five different RNA viruses including Apple mosaic ilarvirus (ApMV), Prunus necrotic ringspot ilarvirus (PNRSV), Prune dwarf ilarvirus (PDV), Plum pox potyvirus (PPV), Apple chlorotic leafspot trichovirus (ACLSV). While no ApMV and PPV infection was found, 46, 24 and 16 samples were tested positive for PDV, ACLSV and PNRSV, respectively, in ELISA showing about 45% of symptomatic trees in the region were infected with at least one of these viruses. In addition, it was found that nine sweet cherry trees were mixed infected with two or three of these viruses and PDV with an infection rate of 26.3% was the most widespread virus in symptomatic trees in western Mediterranean region. Thirty samples were selected and tested by a multiplex RT-PCR (mRT-PCR) for simultaneous detection of these viruses. While PPV was not detected, more than half of the tested 20 samples were individually or mixed infected with ApMV, ACLSV, PNRSV and PDV. The mRT-PCR results were confirmed by detection of these viruses individually in some of the field samples using RT-PCR with primes specific to each virus. Comparison of ELSA and mRT-PCR results of 30 samples showed that numbers of infected and mixed infected samples as well as infection and mixed infection rates were significantly higher in RT-PCR (20 and 66.7%) than in ELISA (14 and 46.7%). The results confirm that mRT-PCR is more sensitive than ELISA.

An example of large groups

Ahmet Sinan Cevik 대한수학회 2020 대한수학회보 Vol.57 No.1

The fundamental idea of this article is to present an effective way to obtain the large groups in terms of the split extension obtained by a finite cyclic group and a free abelian group rank $2$. The proof of the main result on largeness property of this specific split extension groups will be given by using the connection of large groups with the groups having deficiency one presentations.