• The Plant Pathology Journal
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• v.34 no.6
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• pp.514-531
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• 2018

Tomato spotted wilt virus (TSWV; Genus Orthotospovirus: Family Tospoviridae) is one of the most destructive viruses affecting a wide range of horticultural crops on a worldwide basis. In 2015 and 2016, 171 leaf and fruit samples from tomato (Solanum lycopersicum) plants with viral symptoms were collected from the fields in various regions of Iran. ELISA test revealed that the samples were infected by TSWV. The results of RT-PCR showed that the expected DNA fragments of about 819 bp in length were amplified using a pair of universal primer corresponding to the RNA polymerase gene and DNA fragments of ca 777 bp and 724 bp in length were amplified using specific primers that have been designed based on the nucleocapsid (N) and non-structural (NSs) genes, respectively. The amplified fragments were cloned into pTG19-T and sequenced. Sequence comparisons with those available in the GenBank showed that the sequences belong to TSWV. The high nucleotide identity and similarities of new sequences based on the L, N, and NSs genes showed that minor evolutionary differences exist amongst the isolates. The phylogenetic tree grouped all isolates six clades based on N and NSs genes. Phylogenetic analysis showed that the Iranian isolates were composed a new distinct clade based on a part of polymerase, N and NSs genes. To our knowledge, this is the first detailed study on molecular characterization and genetic diversity of TSWV isolates from tomato in Iran that could be known as new clade of TSWV isolates.

• The Plant Pathology Journal
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• v.37 no.6
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• pp.619-631
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• 2021

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

• Research in Plant Disease
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• v.27 no.4
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• pp.137-148
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• 2021

Plant RNA viruses are one of the most destructive pathogens that cause a significant loss in crop production worldwide. They have evolved with high genetic diversity and adaptability due to the short replication cycle and high mutation rate during genome replication, which are characteristics of RNA viruses. Plant RNA viruses exist as quasispecies with high genetic diversity; thereby, a rapid population transition with new fitness can occur due to selective pressure resulting from environmental changes. Plant resistance can act as selective pressure and affect the fitness of the virus, which may lead to the emergence of resistance-breaking variants. In this paper, we introduced the evolutionary perspectives of plant RNA viruses and the driving forces in their evolution. Based on this, we discussed the mechanism of the emergence of variant viruses that overcome plant resistance. In addition, strategies for deploying plant resistance to viral diseases and improving resistance durability were discussed.

• The Plant Pathology Journal
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• v.38 no.4
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• pp.383-394
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• 2022

In Japan, the P1 protein (S-type) encoded by leek yellow stripe virus (LYSV) isolates detected in Honshu and southward is shorter than the P1 (N-type) of LYSV isolates from garlic grown in Hokkaido due to a large deletion in the N-terminal half. In garlic fields in Hokkaido, two types of LYSV isolate with N- and S-type P1s are sometimes found in mixed infections. In this study, we confirmed that N- and S-type P1 sequences were present in the same plant and that they belong to different evolutionary phylogenetic groups. To investigate how LYSV with S-type P1 (LYSV-S) could have invaded LYSV with N-type P1 (LYSV-N)-infected garlic, we examined wild Allium spp. plants in Hokkaido and found that LYSV was almost undetectable. On the other hand, in Honshu, LYSV-S was detected at a high frequency in Allium spp. other than garlic, suggesting that the LYSV-S can infect a wider host range of Allium spp. compared to LYSV-N. Because P1 proteins of potyviruses have been reported to promote RNA silencing suppressor (RSS) activity of HC-Pro proteins, we analyzed whether the same was true for P1 of LYSV. In onion, contrary to expectation, the P1 protein itself had RSS activity. Moreover, the RSS activity of S-type P1 was considerably stronger than that of N-type P1, suggesting that LYSV P1 may be able to enhance its RSS activity when the deletion is in the N-terminal half and that acquiring S-type P1 may have enabled LYSV to expand its host range.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2000.11a
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• pp.149-152
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• 2000

This paper addresses the wavelet fuzzy modeling using Virus-Evolutionary Genetic Algorithm (VEGA). We build a fuzzy system model which is equivalent to the wavelet transform after identifying the coefficients of wavelet transform. We can obtain an accurate system model with a small number of coefficients due to the energy compaction property of the wavelet transform. It thus means that we can construct a fuzzy system model with a small number of rules. In order to identify the wide-ranged coefficients of the wavelet transform, VEGA is adopted, which has prominent ability to avoid premature local convergence that is suitable to complex optimization problems. We demonstrate the superiority of our proposed fuzzy system modeling method over the previous results by modeling nonlinear function.

• 제어로봇시스템학회:학술대회논문집
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• 2002.10a
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• pp.120.3-120
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• 2002

1. Introduction $\textbullet$ Immune system is an evolutionary biological system to protect innumerable foreign materials such as virus, germ cell, and etc. Immune algorithm is the modeling of this system's response that has adaptation and reliableness when disturbance occur. $\textbullet$ In this paper, Immune algorithm is applied to the Steering Controller of AGV in container yard. $\textbullet$ And then the computer simulation result from the viewpoint of yaw rate and lateral displacement is analyzed and compared with result of conventional PID controller. 2. Dynamic Modeling of AGV $\textbullet$ Dynamic modeling has high degree of freedom. But, basic assumptions of this model are that the center of gravity(CG)...

• Proceedings of the KIEE Conference
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• 2002.07d
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• pp.2824-2826
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• 2002

Immune system is an evolutionary biological system to protect innumerable foreign materials such as virus, germ cell, and etcetera. Immune algorithm is the modeling of this systems response that has adaptation and reliability when disturbance occur. In this paper, immune algorithm is proposed to control four wheels steering AGV(Automated Guided Vehicle) in container yard. The adaptive immune system is applied to the PID controller. For design the PID controller using immune algorithm, we tune PID parameters by off-line manner, in order to avoid the damage from abrupt control force. Repeatedly, the PID parameters are adjusted to be accurate by on-line fine tuner of immune algorithm. And then the computer simulation result from the viewpoint of yaw rate and lateral displacement are analyzed and compared with result of conventional PID controller.

• Proceedings of the Korean Institute of Navigation and Port Research Conference
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• 2002.03a
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• pp.229-234
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• 2002

Immune system is an evolutionary biological system to protect Innumerable foreign materials such as virus, germ cell, and et cetera. Immune algorithm is the modeling of this system'response that has adaptation and reliableness when disturbance occur. In this paper, immune algorithm controller was proposed to control four wheels steering(4ws) Automated Guided vehicle(AGV) in container yard. And then the simulation result was analysed and compared with the results of NN-PID controller.

• Journal of Veterinary Science
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• v.24 no.6
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• pp.78.1-78.6
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• 2023

Avian-origin H3N2 canine influenza A viruses (CIVs) have become enzootic in China and Korea and have sporadically transmitted to North America, causing multiple epidemics. We isolated six CIVs in Korea from CIV-infected patients during 2014-2017 and conducted whole genome sequencing and phylogenetic analyses. Results revealed that CIVs have circulated and evolved in Korea since the early 2000s and then diversified into a new clade, probably contributing to multiple epidemics in China, the USA, and Canada. Our findings bridge an evolutionary gap for understanding the global transmission of CIVs, emphasizing the significance of continuous monitoring of CIVs.

• Journal of the Korean Institute of Intelligent Systems
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• v.11 no.4
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• pp.359-365
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• 2001

In this paper, we propose the design methodology of target tracking system using fuzzy basis function expansion(FBFE) based on virus evolutionary genetic algorithm (VEGA). In general, the objective of target tracking is to estimate the future trajectory of the target based on the past position of the target obtained from the sensor. In the conventional and mathematical nonlinear filtering method such as extended Kalman filter(EKF), the performance of the system may be deteriorated in highly nonlinear situation. To resolve these problems of nonlinear filtering technique, by appling artificial intelligent technique to the tracking control of moving targets, we combine the advantages of both traditional and intelligent control technique. In the proposed method, after composing training datum from the parameters of extended Kalman filter, by combining FDFE, which has the strong ability for the approximation, with VEGA, which prevent GA from converging prematurely in the case of lack of genetic diversity of population, and by idenLifying the parameters and rule numbers of fuzzy basis function simultaneously, we can reduce the tracking error of EKF. Finally, the proposed method is applied to three dimensional tracking problem, and the simulation results shows that the tracking performance is improved by the proposed method.