• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.565-573
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• 2010

Thinning of apple fruitlets is one of the most laborious and important works for the improvement of fruit quality and for the promotion of sufficient flower bud formation to prevent alternate bearing in commercial cultivars. Lateral fruits of self-thinning apple cultivars fall naturally within 30 days after full bloom and only central fruit remains to mature. Differences of gene expression between central fruit and lateral fruit were investigated by differential display (DD) PCR. Partial cDNAs of 30 clones from the central fruit and 24 clones from the lateral fruit were selected for nucleotide sequence determination and homology searches. The levels of transcripts coding for proteins involved in pathogenesis related proteins, senescence, temperature stress, protein degradation, fruit browning, sorbitol metabolism were significantly higher in pedicels of lateral fruit than in pedicels of central fruit. On the other hand, the up-regulation of proteins involved in anthocyanin and flavanol biosynthesis and ethylene synthesis were observed in pedicels of central fruit. In Real time PCR analysis, cytochrome P450 gene was confirmed as showing a higher expression level in lateral fruit than in central fruit. The results of this study indicate that differentially expressed genes are related to self-thinning characteristics in apple tree.

• Korean Journal of Environmental Biology
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• v.39 no.3
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• pp.319-328
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• 2021

Tomato spotted wilt virus (TSWV) is one of the most destructive viruses worldwide, which causes severe damage to economically important crops, such as pepper and tomato. In this study, we examined the molecular and biological characterization of a TSWV isolate (SW-TO2) infecting tomato and compared it to the recently reported isolates from boxthorn, butterbur, and angelica plants. The phylogenetic analysis based on the complete genome sequences confirmed that SW-TO2 was clustered with those of isolates from boxthorn and pepper in Korea with the maximum nucleotide identities ranging from 98% to 99%. We developed the bioassay method for screening TSWV resistance and tested some commercial pepper and tomato cultivars for resistance evaluation of four isolates of TSWV. TSWV resistance was evaluated as TSWV resistance when all the following three conditions were satisfied: first, when symptoms of necrotic spots or no symptoms were present in the inoculated leaves; second, when there were no symptoms in the upper leaves; and third, when the upper leaves were negative as a result of RT-PCR diagnosis.

• Research in Plant Disease
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• v.27 no.1
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• pp.32-37
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• 2021

In May 2020, necrosis and necrotic ring patterns were observed on leaves of three of 140 Iris domestica plants in a demonstration garden in Wanju, Jeollabuk-do. Three symptomatic plants were found to be infected by tomato spotted wilt virus (TSWV). To analyze the whole genomic sequence of one TSWV isolate, 'Blackberry lily-kr1', L, M, and S genome segments were sequenced and analyzed by comparison of nucleotide sequences of the three segments with corresponding sequences of other TSWV isolates. 'Blackberry lily-kr1' isolate was most closely related to 'JJ' isolate (MF159046) or 'HJ' isolate (LC273305) in the L segment, and to 'JJ' isolate (MF159058 and KY021439) in the M and S segments, respectively. Phylogenetic analysis by Maximum likelihood method using MEGA X program with 'Blackberry lily-kr1' isolate showed high relationship with 'JJ' pepper isolate or 'HJ' Humulus japonicas isolate in the all three segment. Necrosis and double ring patterns on leaves were formed in the glasshouse after inoculation of healthy I. domestica plants with sap of 'Blackberry lily-kr1'-infected Nicotiana rustica plants. This result suggests that I. domestica plants showing necrotic ring patterns in the open field are caused by TSWV infection. This is the first report of TSWV infection of I. domestica in Korea.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.12 no.2
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• pp.94-101
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• 2007

Analysis of population structure of Oncorhynchus keta, the most abundant salmon in the East Sea of Korea, has not been much carried out despite its importance as a fishery resource in the North Pacific. Currently, molecular methods are being applied to stock identification and a method of using single nucleotide polymorphisms (SNPs) is getting more popular. In this study, we analyzed the 720 bp long sequence of the mtDNA COIII-ND3-ND4L region in order to examine genetic similarity-dissimilarity among the Korea chum salmons of each stream and their relationship with the Japan chum salmons. A total of 152 individuals were analyzed, 108 from 3 locations of Korea and 44 from 2 locations of japan, which resulted in as many as 29 different haplotypes. Pairwise $F_{ST}$ and AMOVA tests of the populations show that there is no significant population-level genetic difference among the chum salmons analyzed ($F_{ST}<0.07$). On the other hand, haplotype relationships among the individuals reveal that approximately 25% of the Korea salmons consist genetic lineages independent of Japan salmons and also that a genetic lineage exists in the Puk river and the Namdae river salmons independent of the Wangpi river salmons of Korea.

• Journal of Microbiology and Biotechnology
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• v.34 no.7
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• pp.1475-1483
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• 2024

Three Gram-stain-positive, aerobic, rod-shaped, and non-motile bacteria, labelled as W11^T, SW19^T, and YR1^T, were isolated from soil, and performed their polyphasic taxonomic investigation. The phylogenetic and 16S rRNA gene sequence analysis showed that strains W11^T, SW19^T, and YR1^T belonged to the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Strain W11^T was closely affiliated with Agromyces cavernae SYSU K20354^T (98.1%), strain SW19^T showed the closest affiliation with Rathayibacter rubneri ZW T2_19^T (97.0%), and strain YR1^T was most closely related to Nocardioides marmorisolisilvae KIS18-7^T (98.0%). The genome sizes of strains W11^T, SW19^T, and YR1^T were 4,181,720 bp, 4,740,677 bp, and 4,228,226 bp, respectively, with DNA G+C contents of 70.5%, 64.2%, and 69.7%, respectively. Average nucleotide identity and digital DNA-DNA hybridization values of W11^T, SW19^T, and YR1^T with their respective reference species were <79.6% and <23.6%, respectively. The predominant cellular fatty acids detected in strain W11^T were anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0. In strain SW19^T, they were summed feature 9 (C_16:0 10-methyl and/or iso-C_17:1ω 9c), anteiso-C_17:0, and anteiso-C_15:0. Strain YR1^T exhibited C_18:1ω 9c, C_18:0 10-methyl, TBSA, and anteiso-C_15:0 as its major cellular fatty acids. Overall, the polyphasic taxonomic comparisons indicated that strains W11^T, SW19^T, and YR1^T represent novel species within the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Accordingly, we propose the names Agromyces silvae sp. nov., with the type strain W11^T (=KCTC 49818^T =NBRC 115999^T), Rathayibacter soli sp. nov., with the type strain SW19^T (=KCTC 49860^T =NBRC 116108^T), and Nocardioides terrisoli sp. nov., with the type strain YR1^T (=KCTC 49863^T =NBRC 116165^T).

• The Korean Journal of Malacology
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• v.32 no.4
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• pp.263-268
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• 2016

Metallothionein (MT) family of metal-binding proteins are involved in maintaining homeostasis and heavy metal poisoning. Recently, MT has been considered as a biomarker that can identify a particular species, very similar to the use of cytochrome oxidase I (COI) gene. Satsuma myomphala species of land snails have been reported from North-East Asia, including South Korea and Japan. In particular, the land snail species have been known from only a limited area of Geoje Island, Gyeongsangnam-do province of South Korea. Genetic studies of S. myomphala has been limited with only 6 nucleotide, 2 protein registered on the NCBI server. For elucidating the genetic information of S. myomphala, we conducted RNA sequencing analysis using Illumina HiSeq 2500 next-generation platform. We screened the MT gene from the RNA-Seq database to confirm the molecular phylogenetic relationship. After sequencing, the de novo analysis and clustering generated 103,774 unigenes. After annotation against PANM database using BLAST program, we obtained MT sequence of 74 amino acid residues containing the coding region of 222 bp. Based on this sequence, we found about 53 sequences using the BLAST program in NCBI nr database. Using ClustalX alignment, Maximum-Likehood Tree of MEGA program, we confirmed the molecular phylogenetic relationships that showed similarity with mollusks such as Helix pomatia and H. aspersa, Megathura crenulata.

• Research in Plant Disease
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• v.12 no.3
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• pp.213-220
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• 2006

In year 2003, a soybean(Glycine max) sample showing severe dwarfing symptom was collected from a farmers' field in Cheongsong in Korea. The results from the diagnosis of the sample by RT-PCR revealed that it was infected by Soybean dwarf virus(SbDV), SbDV-L81. This study could be the first report of the occurrence of the virus in Korea. To further characterize the virus, the partial nucleotide sequence of the genomic RNA of SbDV-L81 was determined by RT-PCR using species-specific primers. The sequences were analyzed and subsequently compared to previously characterized strains of SbDV based on the pattern of symptom expression and vector specificities. The intergenic region between ORF 2 and 3 and the coding regions of ORF 2, 3 and 4 were relatively similar to those of dwarfing strains(SbDV-DS and DP) rather than those of yellowing strains(SbDV-YS and YP). Likewise, the result from the analysis of 5'-half of the coding region of ORF5 indicated that SbDV-L81 was closely related to strains(SbDV-YP and DP) transmitted by Acyrthosiphon pisum. These data from the natural symptom and the comparisons of five regions of nucleotide sequences of SbDV suggested that SbDV-L81 might be closely related SbDV-DP.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.4 no.1
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• pp.28-33
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• 2001

Purpose: H. pylori infection is thought to contribute to iron-deficiency anemia, especially during puberty. The ferritin protein Pfr of H. pylori is homologous to eukaryotic and prokaryotic ferritins. The purpose of this study was to analyze the H. pylori pfr status in gastric biopsy specimens according to clinical data, including antral gastritis with or without iron-deficiency anemia. Methods: A total of 26 H. pylori-positive patients aged from ten to 18 years were categorized into subgroups based on the presence or absence of iron-deficiency anemia. All of them had antral gastritis. Sixteen patients were proved to have iron-deficiency anemia by hematological study, two of which had a duodenal ulcer. The other ten patients showed normal hematological findings. DNA isolation was performed from each of the gastric biopsy specimens. PCR amplification of the pfr gene coding was done using two sets of primers. The pfr region, 501 bp, was generated by linking the sequences of the two PCR products. The nucleotide and protein sequences were compared between the pfr regions from Korean H. pylori strains and the NCTC 11638, 26695, and J99 strain, which were obtained from the Genbank. Sequence comparisons were also performed for the pfr regions between the iron-deficiency anemia (+) and (-) groups. Results: Analysis of the complete coding region of pfr gene revealed three sites of mutation. The Ser39Ala mutation was found in 100% (26/26), Gly111Asn in 26.9% (7/26), and Gly82Ser in 11.5% (3/26). There were no significant differences in the mutations of the pfr regions between the iron deficiency anemia (+) and (-) groups. Conclusion: The mutation in the pfr gene did not relate with the clinical phenotype, iron deficiency anemia. Further studies are needed on the aspects of host side or other complex factors to elucidate anemia. Further studies are needed on the aspects of host side or other complex factors to elucidate the mechanisms by which the H. pylori infection might lead to iron deficiency anemia.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.139-145
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• 2013

There are several loci controlling the feather color of birds, of which one of the most studied is Extended black (E) encoding the melanocortin 1-receptor (MC1R). Mutations in this gene affect the relative distribution of eumelanin, phaeomelanin. The association of feather color and sequence polymorphism in the melanocortin 1-receptor (MC1R) gene was investigated using Korean native chicken H breed (H_PL) and 'Woorimatdag' commercial chickens (Woorimatdag_CC). In order to correlate gene mutation to Korean native chicken feather color, single nucleotide polymorphism (SNP) from MC1R gene sequence were investigated. A total of 307 birds from H_PL and Woorimatdag_CC were used. H_PL have black, black-brown feather color and Woorimatdag_CC have black with brown spots or brown with black spots. There are 6 SNPs in MC1R gene, locus T69C, C212T, A274G, G376A, G636A, T637C. 3 SNPs are nonsynonymous that change amino acid. But it is difficult to find correlation of feather color and polymorphisms. It will be needed to increase the population of Korean native chicken H breed and correlation analysis of genetic variation with feather colors.

• Journal of Genetic Medicine
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• v.5 no.1
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• pp.26-33
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• 2008

Purpose : Phenylketonuria(PKU) is an inborn error of metabolism and a genetic disorder resulting from a deficiency of phenylalanine hydroxylase(PAH) and decreased activity of tetrahydrobiopterin(BH4).In this study the correlation between the DNA mutation and clinical manifestations was investigated and PAH DNA mutations were compared bewteen Asian and Caucasian populations. Methods : DNA was isolated from peripheral leukocytes. The PAH gene was amplified by Polymerase Chain Reaction(PCR) and the sequence was analyzed with Multiplex Ligation-dependent Probe Amplification(MLPA). Results : We characterized the PAH gene of 102 independent Korean patients with PKU. PAH nucleotide sequence analysis revealed 44 different mutations, including 10 novel mutations comprising 9 missense mutations(N207D, K95del, A447P, G344D, P69S, S391I, A202T, G103S, and I306L) and 1 novel splice-site variant mutation(IVS10-3C>G). R243Q was the most prevalent mutation in this study. A259T has not previously been reported in Asian populations, but we found that this mutation had a frequency of 10.1% in our study. Furthermore, the genotypes of $BH_4$ responsive patients were analyzed and were divided into two groups: $BH_4$ medication-only group and $BH_4$ medication with diet therapy group. In the $BH_4$ medication-only group and $BH_4$ medication with diet therapy group, R241C was the most common mutation. Conclusion : Novel mutations in the PAH gene of PKU patients are still being discovered. Additional information as to the frequency of mutations in the tetrahydrobiopterine responsive gene is also accumulating. We anticipate that knowledge of these PKU gene mutations will assist the diagnosis, genetic counseling, and therapeutic treatment of PKU patients in future.