• Research in Plant Disease
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• v.29 no.1
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• pp.52-59
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• 2023

Cucurbit chlorotic yellows virus (CCYV) is a plant virus that causes damage to cucurbit crops such as watermelon and cucumber, and is transmitted by an insect vector known as the whitefly. Since CCYV was first detected on cucumber in Chungbuk in 2018, it has been reported in other areas including Gyeongsang in Korea. In 2020, we performed field surveys of yellowing diseases in the greenhouses growing melon and watermelon in Chungbuk (Jincheon and Eumseong). Reverse transcription-polymerase chain reaction analysis of 79 collected samples including melon, watermelon, and weeds resulted in detection of CCYV in 4 samples: Three samples were singly infected with CCYV and one samples was mixed infected with CCYV, Cucurbit aphid borne yellows virus, and Watermelon mosaic virus. The complete genome sequences of the four collected CCYV melon isolates (ES 1-ES 4) were determined and genetically compared with those of previously reported CCYV isolates retrieved from GenBank. Phylogenetic analyses of RNA 1 and 2 sequences revealed that four ES isolates were clustered in one group and closely related to the CCYV isolates from China. The analysis also revealed very low genetic diversity among the CCYV ES isolates. In general, CCYV isolates showed little genetic diversity, regardless of host or geographic origins. CCYV has the potential to pose a serious threat to melon, watermelon, and cucumber production in Korea. Further studies are needed to examine the pathogenicity and transmissibility of CCYV in weeds and other cucurbits including watermelon.

• Journal of the Korean Society of International Agriculture
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• v.23 no.5
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• pp.560-569
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• 2011

In Japan, plant genomics research is mainly leaded by the national research institutes. The various structural studies such as rice genome has allowed researchers to analyze useful traits, and to focus their commercialization. With aims to facilitate structural and functional study in plant genome, NIAS (National Institute of Agrobiological Sciences) constructed Poaceae genome DB and RIKEN (Rikagaku Kenkyusho) built DB for Arabidopsis genome and plant full-length cDNA. NIG (National Institute of Genetics) constructed a national biological resources DB (National Bio Resource Project). This compiling DB provides a variety of genome-related research materials for researchers in the field. Recently, as an effort to resolve global issues of food supply and environmental problems, New Agri-genome Project has been performed aiming to develop an innovative agricultural technologies for the quantity, disease resistance and identifying useful genes related to environmental problems. In addition, in order to improve agricultural productivity in developing countries, JIRCAS assisted technical supports for the plant genome research and developed NERICA rice, which is suitable for African area. Such these approaches are expected to contribute to solving the global issues about food, energy and environment in the world.

• Korean journal of applied entomology
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• v.63 no.1
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• pp.43-51
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• 2024

Thrips infest hot peppers (Capsicum annuum) cultivating in open fields and give serious economic damages. This study reports their yearly occurrence from transplanting to harvest at three different places in Andong, an intense hot pepper-cultivating area. Two main occurrence peaks were detected in June and September. Two dominant thrips were the flower flowers, Frankliniella occidentalis and F. intonsa, which comprised of over 87% of the total occurring thrips. Other thrips did not follow the occurrence peaks of the two dominant species. Tomato spotted wilt virus (TSWV) was detected from the dominant two species, in which higher viruliferous rate was recorded in F. intonsa. Although the hot peppers were the resistant varieties against TSWV, some of them cultivating in the fields exhibited a characteristic disease symptom infected by the virus over the growing seasons. TSWV was isolated from the viruliferous thrips and assessed in NSs sequences encoded in S RNA segment of the virus. Compared to the known resistance breaking (RB) strains, the TSWV isolated from the viruliferous thrips in Andong did not show any RB mutations.

• Journal of Applied Biological Chemistry
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• v.66
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• pp.394-403
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• 2023

In the pursuit of sustainable and environmentally-friendly agricultural practices, we conducted an extensive study on the rhizosphere bacteria inhabiting soils that have been devoid of chemical fertilizers for an extended period exceeding 40 years. Through this investigation, we isolated a total of 80 species of plant growth-promoting rhizosphere bacteria and assessed their potential to enhance plant growth. Among these isolates, Burkholderia cepacia CD2 displayed remarkable plant growth-promoting activity, making it an optimal candidate for further analysis. Burkholderia cepacia CD2 exhibited a range of beneficial characteristics conducive to plant growth, including phosphate solubilization, siderophore production, denitrification, nitrate utilization, and urease activity. These attributes are well-known to positively influence the growth and development of plants. To validate the taxonomic classification of the strain, 16S rRNA gene sequencing confirmed its placement within the Burkholderia genus, providing further insights into its phylogenetic relationship. To delve deeper into the potential mechanisms underlying its plant growth-promoting properties, we sought to confirm the presence of specific genes associated with plant growth promotion in CD2. To achieve this, whole genome sequencing (WGS) was performed by Plasmidsaurus Inc. (USA) utilizing Oxford Nanopore technology (Abingdon, UK). The WGS analysis of the genome of CD2 revealed the existence of a subsystem function, which is thought to be a pivotal factor contributing to improved plant growth. Based on these findings, it can be concluded that Burkholderia cepacia CD2 has the potential to serve as a microbial fertilizer, offering a sustainable alternative to chemical fertilizers.

• Journal of Life Science
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• v.30 no.3
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• pp.285-290
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• 2020

Foot-and-mouth disease virus (FMDV), a member of the genus Aphthovirus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. FMDV causes various clinical symptoms, including severe inflammation in infected tissue. Genome RNA of FMDV shows a positive single-strand chain approximately 8.3 kb long and encodes a single long open reading frame (ORF). The ORF is translated into structural and non-structural proteins by viral proteases. The FMDV 2C protein is one of the non-structural proteins encoded by FMDV and plays a critical role in FMD pathogenesis, including inflammation, apoptosis, and viral replication. In this study, we examined whether FMDV 2C induces intracellular expression of pro-inflammatory cytokine tumor necrosis factor alpha (TNFα). FMDV 2C expression in pig IBRS-2 cells increased mRNA and protein expression of TNFα at the transcriptional level via activation of TNFα promoter. Treatment with 4-phenylbutyric acid, an endoplasmic reticulum (ER) stress reducer, decreased TNFα expression induced by FMDV 2C. Activating transcription factor 4 (ATF4), a transcription factor mediating ER stress response, induced transactivation of TNFα promoter and expression of mRNA and protein of TNFα. However, the dominant negative mutant of ATF4 did not induce FMDV 2C-mediated TNFα expression. The results indicate that FMDV 2C protein increases clinical inflammation via ATF4-mediated TNFα expression and is associated with ER stress induction.

• Microbiology and Biotechnology Letters
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• v.37 no.2
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• pp.118-124
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• 2009

Esterase EM2L8 gene isolated from deep sea sediment was expressed in Escherichia coli BL21 (DE3) and the esterase activity of the cell-free extract was assayed using p-nitrophenyl butyrate-spectrophotometric method. Its optimum temperature was $40-45^{\circ}C$ and 45% activity of the maximum activity was retained at $15^{\circ}C$. The activation energy at $15-45^{\circ}C$ was calculated to be 4.9 kcal/mol showing that esterase EM2L8 was a typical cold-adapted enzyme. Enzyme activity was maintained for 6 h and 4 weeks at $30^{\circ}C$ and $4^{\circ}C$, respectively. When each ethanol, methanol, and acetone was added to the reaction mixture to 15% concentration, enzyme activity was maintained. In the case of DMSO, enzyme activity was kept up to 40% concentration. (S)-4-Chloro-3-hydroxy butyric acid is a chiral intermediate for the synthesis of Atorvastatin, a hyperlipemia drug. When esterase EM2L8 (40 U) was added to buffer solution (1.2 mL, pH 9.0) containing ethyl-(R,S)-4-chloro-3-hydroxybutyrate (38 mM), it was hydrolyzed into 4-chloro-3-hydroxy butyric acid with a rate of $6.8\;{\mu}mole/h$. The enzyme hydrolyzed (S)-substrate more rapidly than (R)-substrate. When conversion yield was 80%, e.e.s value was 40%. When DMSO was added, hydrolysis rate increased to $10.4\;{\mu}mole/h$. The plots of conversion yield vs e.e.s in the presence or absence of DMSO were almost same, implying that the reaction enantioselectivity was not changed by the addition of DMSO. Taken together, esterase EM2L8 had high activity and stability at low temperatures as well as in various organic solvents/aqueous solutions. These properties suggested that it could be used as a biocatalyst in the synthesis of useful pharmaceuticals.

• Journal of Plant Biotechnology
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• v.35 no.3
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• pp.177-183
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• 2008

Ac/Ds mutant lines of this study were transgenic rice plants, each of which harbored the maize transposable element Ds together with a GUS coding sequence under the control of a promoterless(Ds-GUS). We selected the mutants that were GUS expressed lines, because the GUS positive lines will be useful for identifying gene function in rice. One of these mutants was identified knock-out at Oszinc626(NP_001049991) gene, encoding a RING-H2 zinc-finger protein, by Ds insertion. In this mutant, while primary root development is normal, secondary root development from lateral root was very poor and seed development was incomplete compare with normal plant. RING zinc-finger proteins play important roles in the regulation of development in a variety of organisms. In the plant kingdom, a few genes encoding RING zinc-finger proteins have been documented with visible effects on plant growth and development. The consensus of the RING-H2(C3-H2-C3 type) domain for this group of protein is $Cys-X_2-Cys-X_{28}-Cys-X-His-X_2-His-X_2-Cys-X_{14}-Cys-X_2-Cys$. Oszinc626 encodes a predicted protein product of 445 amino acids residues with a molecular mass of 49 kDa, with a RING-zinc-finger motif located at the extreme end of the C-terminus. RT-PCR analysis indicated that the expression of Oszinc626 gene was induced by IAA, cold, dehydration, high-salinity and abscisic acid, but not by 2,4-D, and the transcription of Oszinc626 gene accumulated primarily in rice immature seeds, root meristem and shoots. The gene accumulation patterns were corresponded with GUS expression.

• Journal of Applied Biological Chemistry
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• v.52 no.1
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• pp.1-7
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• 2009

For the development of qualitative PCR detection method of genetically modified (CM) rice, rice species-specific gene, OsCc-1 (rice cytochrome c gene), was selected as suitable far use as an endogenous gene in rice. The primer pair OsCytC-5'/3'with 111 bp amplicon was used for PCR amplification of the rice endogenous gene, OsCc-1 and no amplified product was observed from 8 different crops as templates. Qualitative PCR method was carried out with stack traits of L528$\times$CryIAc1 GM rice developed in Korea. For the qualitative PCRs, some primer pairs were designed with a construct-specific and event-specific type based on T-DNA and junction sequences of T-DNA in GM rice. Actck-5'/3' amplifying between actin promoter and OsCK1 gene introduced in LS28 gave rise to an amplicon 306 bp; also, CrLB-5'/3' from CryIAcl and CKRB-5'/3'amplifying the junction region of T-DNA and genome sequence from LS28 as event-specific primers gave rise to an amplicon 142 bp and 91 bp, respectively. These primer pairs for the detection of event-specific targets not produced PCR amplicons on non-CM rice and various crops in contrast to event lines. Therefore, in this study we verified that event-specific primers were effective to specifically detect stack trait lines and demonstrated that this method presented could be provided with the detection-method data for risk assessment analysis of GM rice to be commercialized.

• Journal of Animal Science and Technology
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• v.46 no.3
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• pp.301-306
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• 2004

This study was conducted to develop new markers at the region that was related to QTL affecting intramuscular fat and backfat thickness on chromosome 6q28 - 6q32 in pigs. Dozens of repeated sequences were founded using shotgun sequencing of several BAC clones corresponding to that region, of which five new microstellite markers that identified polymorphism were discovered. The mean number of alleles at each locus observed 2.13(KP0290F2), 4.63(KP0248Cll), 7.38(KP1231C91), 2.75(KPI23IC92) and 6.2S(KP1231C93) in 8 breeds(Landrace, Korean native pig, Duroc, Yorkshire, Berkshire, Wuzhishan pig, Xiang pig, Min pig). The average estimated heterozygosity values at each locus varied from 0.2100(KP0290F2) to 0.8304(KPI23IC91) in all populations. In other hand, the average allele of all loci WlL'I within range of 0.4517(Berkshire) and 0.6957 (Yorkshire). Of these markers, KP0248C11, KP1231C91 and KP1231C93 were identified to have optimal number of alleles, high heterozygosity values and low standard deviation values. Especially, KPI23IC91 and KPI231C93 might be considered as a useful marker for genetic mapping and diversity study.

• Research in Plant Disease
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• v.10 no.4
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• pp.241-247
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• 2004

Recently, we reported a satellite RNA (Paf-satRNA) which is encapsidated in a pepper isolate of Cucumber mosaic virus (CMV-Paf) regulated symptom attenuation of the helper virus. To characterize mild symptom domain of Paf-satRNA, a series of chimeric cDNAs of satRNAs were created by using full-length cDNA clones of Paf-satRNA and a Pep-satRNA, chlorosis-inducing satRNA in pepper plants, and analyzed for determinants of symptom attenuation. When compared the nucleotide sequences, the 3' and 5' terminal sequences of the two wild-type (wt) satRNAs contained relatively conserved sequences which are the typical to CMV satRNA. Ten bases insertions were found in PepY-satRNA, and two variable regions, 81st to 113th and 183rd to 265th from the 5'-end, were located in the middle parts of the satRNAs. To delineate the attenuated symptom-related domain for the Paf-satRNA, in vitro transcripts RNAs transcribed from the wt cDNAs and constructed chimeric cDNAs were combined with genomic RNAs, RNA1, RNA2 and RNA3, of CMV-Fny and inoculated onto Nicotiana benthamiana plants. These transcripts were fully infectious onto the N. benthamiana and infectivity was confirmed by the RT-PCR. Chimeric Paf(H/N)-satRNA and PepY(N/A)-satRNA as well as Paf-satRNA induced very mild mosaic or symptomless infection on N. benthamiana. By contrast, typical mosaic symptom and stunting of infected plants were induced when PepY-satRNA, PepY(H/N)-satRNA and Paf(N/A)-satRNA were infected to N. benthamiana. Paf-satRNA coinfected with CMV-Fny RNAs induced very mild to sympomless on pepper plants whereas PepY-satRNA-infected pepper expressed typical chlorosis mosaic symptom. Two kinds of chimeric mutants, Paf(H/N)-satRNA and PepY(N/A)-satRNA, induced mild mosaic or symptomless infection onto pepper plants, while PepY(H/N)-satRNA and Paf(N/A)-satRNA showed typical chlorosis and mosaic symptom with stunting. This results suggest that mild symptom-related domain for the Paf-satRNA was located on HpaI-NarI region.