• The Plant Pathology Journal
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• v.29 no.4
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• pp.397-409
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• 2013

The full-genome sequences of fourteen isolates of Broad bean wilt virus 2 (BBWV2), collected from broad bean, pea, spinach, bell pepper and paprika plants in Korea during the years 2006-2012, were determined and analyzed comparatively along with fifteen previously reported BBWV2 genome sequences. Sequence analyses showed that RNA-1 and RNA-2 sequences of BBWV2 Korean isolates consisted of 5950-5956 and 3568-3604 nucleotides, respectively. Full-length genome sequence-based phylogenetic analyses revealed that the BBWV2 Korean isolates could be divided into three major groups comprising GS-I (isolates BB2 and RP7) along with isolate IP, GS-II (isolates BB5, P2, P3 and RP3) along with isolate B935, and GS-III including 16 BBWV2 Korean isolates. Interestingly, GS-III appears to be newly emerged and predominant in Korea. Recombination analyses identified two recombination events in the analyzed BBWV2 population: one in the RNA-1 of isolate K and another one in the RNA-2 of isolate XJ14-3. However, no recombination events were detected in the other 21 Korean isolates. On the other hand, out of 29 BBWV2 isolates, 16 isolates were found to be re-assortants, of which each RNA segment (i.e. RNA1 and RNA2) was originated from different parental isolates. Our findings suggested that reassortment rather than recombination is a major evolutionary force in the genetic diversification of BBWV population in Korea.

• The Plant Pathology Journal
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• v.29 no.3
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• pp.260-273
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• 2013

The incidence and distribution of Tobacco mosaic virus (TMV) and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP) gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100%) among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each subgroup was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population.

• Clinical and Experimental Vaccine Research
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• v.12 no.3
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• pp.179-192
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• 2023

The world has watched the emergence of numerous animal viruses that may threaten animal health which were added to the perpetual growing list of animal pathogens. This emergence drew the attention of the experts and animal health groups to the fact that it has become necessary to work on vaccine development. The current review aims to explore the perspective vaccines for emerging viral diseases in farm animals. This aim was fulfilled by focusing on modern technologies as well as next generation vaccines that have been introduced in the field of vaccines, either in clinical developments pending approval, or have already come to light and have been applied to animals with acceptable results such as viral-vectored vaccines, virus-like particles, and messenger RNA-based platforms. Besides, it shed the light on the importance of differentiation of infected from vaccinated animals technology in eradication programs of emerging viral diseases. The new science of nanomaterials was explored to elucidate its role in vaccinology. Finally, the role of Bioinformatics or Vaccinomics and its assist in vaccine designing and developments were discussed. The reviewing of the published manuscripts concluded that the use of conventional vaccines is considered an out-of-date approach in eliminating emerging diseases. However, these types of vaccines are considered the suitable plan especially in countries with few resources and capabilities. Piloted vaccines that rely on genetic-based technologies with continuous analyses of current viruses should be the aim of future vaccinology. Smart genomics of emerging viruses will be the gateway to choosing appropriate vaccines, regardless of the evolutionary rates of viruses.

• The Bulletin of The Korean Astronomical Society
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• v.36 no.2
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• pp.68.1-68.1
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• 2011

Type Ia 초신성을 이용한 거리측정은 암흑에너지의 존재를 암시하는 가장 직접적인 증거를 제시하며, 이것은 Type Ia 초신성의 밝기가 표준화된 광도에서 모두 같다고 하는 가정하에서 성립한다. 하지만 최근 표준화된 Type Ia 초신성의 광도가 모은하의 특성과 상관관계가 있음을 보이는 연구결과들이 등장하여 이러한 가정에 대한 의문이 제기되었다. Gallagher et al. (2008)은 조기형 모은하의 나이와 중원소 함량이 Type Ia 초신성의 밝기와 갖는 상관관계에 대하여 시도하였으나, 전체 은하의 표본갯수와 나이측정, 그리고 Hubble Residual을 구하는 과정에서 오차로 인한 한계가 있었다. 우리는 Type Ia 초신성에 나타나는 광도진화효과를 확인하기 위하여 가까운 거리에 있는 Type Ia 초신성의 조기형 모은하에 대하여 CTIO 1.5m, 보현산 1.8m, LCO 2.5 m 망원경의 긴 슬릿 분광기를 이용한 분광관측을 수행하고 있다. 관측된 모은하의 분광스펙트럼으로부터 방출선에 의한 영향을 제거한 뒤, 흡수선의 세기를 이용하여 Lick/IDS indices를 측정하고 있으며 이를Yonsei Evolutionary Population Synthesis model (YEPS)과 비교하여 은하의 나이와 중원소 함량을 추정하였다. 이 결과를 이용하여 Type Ia 초신성의 Hubble Residual과 항성종족의 나이 및 중원소 함량간의 상관관계를 통하여 Type Ia 초신성의 광도진화효과에 대해 분석할 예정이다. 현재까지 조기형 모은하 20여개에 대한 분광관측을 진행하였으며, 앞으로 긴 슬릿 분광기와 McDonald 2.7m 망원경의 VIRUS-P를 이용한 모은하의 분광관측을 추가로 수행할 예정이다.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2001.05a
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• pp.126-130
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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 FBFE, 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 identifying 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.

• International journal of advanced smart convergence
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• v.8 no.1
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• pp.1-8
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• 2019

Coronaviruses are known respiratory pathogens. In the past, most human coronaviruses were thought to cause mild symptoms such as cold. However recently, as seen in the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS), infectious diseases with severe pulmonary disease and respiratory symptoms are caused by coronaviruses, making research on coronaviruses become important. Considering previous studies, we constructed 'HCoV-IMDB (Human Corona Virus Immune Database)' to systematically provide genetic information on human coronavirus and host immune information, which can be used to analyze the interaction between human coronavirus and host immune proteins. The 'HCoV-IMDB' constructed in the study can be used to search for genetic information on human coronavirus and host immune protein and to download data. A BLAST search specific to the human coronavirus, one of the database functions, can be used to infer genetic information and evolutionary relationship about the query sequence.

• Journal of Plant Biotechnology
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• v.49 no.3
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• pp.178-186
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• 2022

The tetraploid Solanum acaule is a wild potato species from Bolivia widely used for potato breeding because of its diverse attractive traits, including resistance to frost, late blight, potato virus X, potato virus Y, potato leafroll virus, potato spindle tuber viroid, and cyst nematode. However, the introgression of useful traits into cultivated potatoes via crossing has been limited by differences in endosperm balance number between species. Somatic fusion could be used to overcome sexual reproduction barriers and the development of molecular markers is essential to select proper fusion products. The chloroplast genome of S. acaule was sequenced using next-generation sequencing technology and specific markers for S. acaule were developed by comparing the obtained sequence with those of seven other Solanum species. The total length of the chloroplast genome is 155,570 bp, and 158 genes were annotated. Structure and gene content were very similar to other Solanum species and maximum likelihood phylogenetic analysis with 12 other species belonging to the Solanaceae family revealed that S. acaule is very closely related to other Solanum species. Sequence alignment with the chloroplast genome of seven other Solanum species revealed four InDels and 79 SNPs specific to S. acaule. Based on these InDel and SNP regions, one SCAR marker and one CAPS marker were developed to discriminate S. acaule from other Solanum species. These results will aid in exploring evolutionary aspects of Solanum species and accelerating potato breeding using S. acaule.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.250-256
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• 2009

Acinetobacter strain $KNF2022^T$ was isolated from tobacco plant roots during the screening of antiviral substances having inhibitory effects on Tobacco mosaic virus (TMV) and examined by phenotypic, chemotaxonomic, and genetic characterization. It was a nonmotile, Gram-negative bacterium. This strain contained Q-9 as the main respiratory quinone. The major cellular fatty acids of the isolate were 16:0, 18:1 w9c, and 16:1 w7c/15 iso 2OH. The DNA base composition was 44 mol%. Phylogenetic analysis based on the 16S rRNA sequence revealed that the isolate formed an evolutionary lineage distinct from other Acinetobacter species. Based on the evaluation of morphologic, physiologic, and chemotaxonomic characteristics, DNA-DNA hybridization values, and 16S rRNA sequence comparison, we propose the new species Acinetobacter antiviralis sp. nov., the type strain of which is $KNF2022^T$ (=KCTC $0699BP^T$).

• Korean Journal of Poultry Science
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• v.28 no.2
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• pp.143-153
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• 2001

Using bioinformatic tools for searching the massive genome databases, it is possible to Identify new genes in few minutes for initial discoveries based on evolutionary conservation, domain homology, and tissue expression patterns, followed by further verification and characterization using the bench-top works. The development of high-density two-dimensional arrays has allowed the analysis of the expression of thousands of genes simultaneously in the humans, mice, rats, yeast, and bacteria to elucidate the genes and pathways involved in physiological processes. In addition, rapid and automated protein identification is being achieved by searching protein and nucleotide sequence databases directly with data generated from mass spectrometry. Recently, analysis at the bio-chemical level such as biochemical screening and metabolic profiling (Biochemical genomics) has been introduced as an additional approach for categorical assignment of gene function. To make advantage of recent achievements in computational approaches for facilitated gene discoveries in the avian model, chicken expression sequence tags (ESTs) have been reported and deposited in the international databases. By searching EST databases, a chicken heparanase gene was identified and functionally confirmed by subsequent experiments. Using combination of sub-tractive hybridization assay and Genbank database searches, a chicken heme -binding protein family (cSOUL/HBP) was isolated in the retina and pineal gland of domestic chicken and verified by Northern blot analysis. Microarrays have identified several host genes whose expression levels are elevated following infection of chicken embryo fibroblasts (CEF) with Marek's disease virus (MDV). The ongoing process of chicken genome projects and new discoveries and breakthroughs in genomics and proteomics will no doubt reveal new and exciting information and advances in the avian research.

• Journal of Life Science
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• v.30 no.11
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• pp.947-955
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• 2020

The foot-and-mouth disease virus (FMDV), a member of the Aphthovirus genus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. During replication of the FMDV RNA (ribonucleic acid) genome, FMDV-encoding RNA polymerase 3D acts in a highly location-specific manner. This suggests that specific RNA structures recognized by 3D polymerase within non-coding regions of the FMDV genome assist with binding during replication. One such region is the cis-acting replication element (CRE), which functions as a template for RNA replication. The FMDV CRE adopts a stem-loop conformation with an extended duplex stem, supporting a novel 15-17 nucleotide loop that derives stability from base-stacking interactions, with the exact RNA nucleotide sequence of the CRE producing different RNA secondary structures. Here, we show that CRE sequences of FMDVs isolated in Korea from 2010 to 2017 exhibit A and O genotypes. Interestingly, variations in the RNA secondary structure of the Korean FMDVs are consistent with the phylogenetic relationships between these viruses and reveal the specificity of FMDV infections for particular host species. Therefore, we conclude that each genetic clade of Korean FMDV is characterized by a unique functional CRE and that the evolutionary success of new genetic lineages may be associated with the invention of a novel CRE motif. Therefore, we propose that the specific RNA structure of a CRE is an additional criterion for FMDV classification dependent on the host species. These findings will help correctly analyze CRE sequences and indicate the specificity of host species for future FMDV epidemics.