• Asian-Australasian Journal of Animal Sciences
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• v.28 no.8
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• pp.1066-1074
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• 2015

In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five YSNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (${\pi}=5.6{\times}10^{-4}$) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (${\pi}=0.00000$) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.244-244
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• 2017

Soil salinity due to accumulation of salts particularly sodium chloride affects agricultural lands and their vegetation. Generally, rice is a moderately sensitive plant with some cultivars with varying tolerance to salinity. Though there are physiological differences between salt-sensitive and salt-tolerant rice cultivars, both are still affected especially during high salinity and prolonged exposure. This also ultimately affects their indigenous bacterial endophytes particularly those that inhabit the rice seed endosphere. This study investigates the dynamic structure of seed bacterial endophytes of salt-sensitive and tolerant rice cultivars grown in different levels of soil salinity. Endophytic bacterial diversity was studied Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Results revealed a very interesting pattern of diversity and shifts in community structure of bacterial endophytes in the rice seeds. There is a general decrease in diversity for the salt-sensitive rice cultivar, IR29 as soil salinity increases. For the salt-tolerant cultivars, IC32 and IC37, diversity interestingly increased at moderate salinity then decreased at high soil salinity. The patterns of community structure is also strikingly different for the salt-sensitive and salt-tolerant rice cultivars. IR29 has a more even distribution of abundance, but under soil salinity, the community shifted where Curtobacterium, Pantoea, Flavobacterium and Microbacterium become the more dominant bacterial communities. For IC32 and IC37, the dominant bacterial groups under normal stress conditions were also the dominant bacterial groups during salt stress conditions. Their seed bacterial community is dominated by endophytes belonging to Microbacterium, Flavobacterium, Pantoea, Kosakonia and Enterobacter. Stenotrophomonas and Xanthomonas have not changed in terms of abundance under different salinity stress level in the salt-sensitive and salt-tolerant rice cultivars. This study showed that soil salinity greatly influenced the seed bacterial communities of rice seeds irrespective of their physiological tolerance to salinity.

• The Plant Pathology Journal
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• v.32 no.5
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• pp.431-440
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• 2016

In 2004, bacterial spot-causing xanthomonads (BSX) were reclassified into 4 species-Xanthomonas euvesicatoria, X. vesicatoria, X. perforans, and X. gardneri. Bacterial spot disease on pepper plant in Korea is known to be caused by both X. axonopodis pv. vesicatoria and X. vesicatoria. Here, we reidentified the pathogen causing bacterial spots on pepper plant based on the new classification. Accordingly, 72 pathogenic isolates were obtained from the lesions on pepper plants at 42 different locations. All isolates were negative for pectolytic activity. Five isolates were positive for amylolytic activity. All of the Korean pepper isolates had a 32 kDa-protein unique to X. euvesicatoria and had the same band pattern of the rpoB gene as that of X. euvesicatoria and X. perforans as indicated by PCR-restriction fragment length polymorphism analysis. A phylogenetic tree of 16S rDNA sequences showed that all of the Korean pepper plant isolates fit into the same group as did all the reference strains of X. euvesicatoria and X. perforans. A phylogenetic tree of the nucleotide sequences of 3 housekeeping genes-gapA, gyrB, and lepA showed that all of the Korean pepper plant isolates fit into the same group as did all of the references strains of X. euvesicatoria. Based on the phenotypic and genotypic characteristics, we identified the pathogen as X. euvesicatoria. Neither X. vesicatoria, the known pathogen of pepper bacterial spot, nor X. perforans, the known pathogen of tomato plant, was isolated. Thus, we suggest that the pathogen causing bacterial spot disease of pepper plants in Korea is X. euvesicatoria.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.80-80
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• 2020

Glycyrrhizae Radix (GR), commomly known as liquorice, is a medicinal and edible plant widely used in East Asia with its pharmacological properties. Currently, Glycyrrhiza uralensis, G. glabra and G. inflata are used for pharmaceutical purposes in Korea and then the improved Glycyrrhiza varieties, WON-GAM (WG) has been developed by Korea Rural Development Administration. To evaluate equivalence of efficacy, several comparative studies between already-registered species and new cultivars have been conducted. To evaluate equivalence of efficacy, several comparative studies between already-registered species and new cultivars have been conducted. The aim of this study was to evaluate the effect of WG on fecal microbiota in DSS-induced colitis model. Fecal microbiota was analyzed by terminal restriction fragment length polymorphism (T-RFLP). The composition of the fecal microbiota did not show a specific pattern based on experimental groups; however, a tendency toward an increase in the proportion of Lactobacillales was observed. Glycyrrhiza varieties could change composition of fecal microbiota in DSS-induced colitis model. This work was carried out with the support of "Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ014246022020)" Rural Development Administration.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.28 no.5
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• pp.649-658
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• 1995

In order to estimate the level of genetic differences among the pleuronectid species, mitochondrial DNAs were isolated from four species: brown sole, Limanda herensteini; marbled sole, Limanda Yokohamae; stone flounder, Kareius bicoloratus; starry flounder, Platichthys stellatus, and the number of nucleotide substitutions was calculated by the restriction fragment length polymorphisms (RFIPs) generated by f4 sin base recognition restriction endonucleases. Total lengths of the mitochondrial DNA were measured as about 17.6 kbp in all species. Ten different composite genotypes were observed in brown sole, four different genotypes in marbled sole, and two different genotypes in starry flounder. However, only one genotype was observed in stone flounder. The calculated haplotypic diversity value of brown sole was higher than that of marbled sole. The average number of nucleotide substitutions per sites in four species was estimated to be 0.0045 in the intraspecies, 0.0344 in the interspecies, and 0.0457 in the genera, respectively. From these results, we could estimate that the genetic differences among interspecies were not influenced by nucleotide substitutions but genetical discontinuous.

• Tuberculosis and Respiratory Diseases
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• v.48 no.3
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• pp.308-314
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• 2000

Background : DNA fingerprinting of Mycobacterium tuberculosis with RFLP is a very useful tool for deciphering the molecular epidemiology of tuberculosis. An international comparison of the RFLP pattern became possible with the proposal to standardize RFLP methodology using Pvu-II restricted IS-6110, and the comparison has noted some predominance of RFLP pattern in East Asia. The RFLP patterns of tuberculosis strains collected at SNUH was studied and was compared with other strains from East Asia. Method : Fifty strains of M. tuberculosis were isolated from patients who visited 'or were admitted to the SNUH in 1998. Some isolates belonging to the Beijing family were also received. After the extraction of DNA from M. tuberculosis isolates, the chromosomal DNAs were digested with Pvu-II and analyzed by the Southern blot method with DNA probe to IS6110. Result : Six strains belonged to the Beijing family. The RFLP patterns of other 9 strains were similar to each other. No statistically significant endobronchial tuberculosis, presence of underlying disease. and the province of residence were found. Conclusion : Few groups of M. tuberculosis strains from SNUH showed similar RFLP patterns, but their clinical implications are not yet clear.

• Applied Biological Chemistry
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• v.47 no.2
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• pp.182-186
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• 2004

Morphological observation of roots and molecular technique were used to investigate the symbiotic relationships between arbuscular mycorrhizal (AM) fungi and ginseng roots. Korean ginseng, Panax ginseng, was collected from 8 sites in Korea. Colonization pattern of AM fungi in ginseng roots was determined as an Arum type under light microscopes. Nested PCR using AM fungal specific primers was employed to amplify a partial region on 18s rDNA of AM fungi from the root extracted mixed DNA. The amplified DNA was cloned and analyzed by random fragment length polymorphism (RFLP) with restriction enzymes, AluI, HinfI and AsuC21. One from each RFLP pattern was selected for sequencing. A total 16 clones were sequenced and identified as 2 species of AM fungi; Paraglomus brasilianum and Glomus spurcum. Paramglomus brasilianum was found from most of the ginseng roots, in this syudy suggesting that this species of AM fungi could have specific relationship with the ginseng root. Possible roles of AM fungal species in ginseng roots are discussed.

• Journal of Life Science
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• v.19 no.9
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• pp.1328-1332
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• 2009

Anisakidosis is caused by anisakid nematodes (family Anisakidae) larvae which can cause not only direct tissue damage but also a severe allergic response related to excretory-secretion products. Lots of different species of anisakid larvae, including Anisakis simplex, Contracaecum, Goezia, Pseudoterranova, and Hysterothylacium, cause the anisakidosis. But it is difficult to diagnosis the species of larvae since the morphologies of larval anisakid nematodes are almost indistinguishable. In order to diagnosis the differential infections of larval anisakid nematodes, polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) of 18S rDNA - was conducted. Three major species of anisakid larvae including A. simplex, C.ontracaecum spp, and Goezia spp. were collected from mackerel (Scomber japonicus), mullet (Mugil cephalus), founder (Paralichthys olivaceus), eel (Astroconger myriaster) and red sea bream (Pagrus major). PCR amplified 18S rDNA from each species of anisakid larvae was digested with eight restriction enzymes including Taq I, Hinf I, Hha I, Alu I, Dde I, Hae III, Sau96 I, and Sau3A I. The original sizes of PCR amplified 18S rDNA were 2.0Kb in both anisakid larvaes and Goezia. Restrction enzymes including Hinf 1, Alu 1, Hha I, Dde 1 and Hae III cut differently and distinguished the A. simplex and Contracaecum type C'. However, Contracaecum type A showed two different restriction enzyme cutting patterns by Taq 1, Hinf I, Alu 1, and Dde 1. One of the patterns was the same as those of A. simplex, Contracaecum type C' and Goezia and the other was unique. These results suggest that PCR-RFLP pattern by Hinf 1, Alu 1, Hae I, Dde 1 and Hae III can be applied to differential diagnosis of human infection with A. simplex and Contracaecum type C'. Contracaecum type A needs further study of classification by morphological characteristics and genetic analysis.

• Korean Journal of Biological Psychiatry
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• v.12 no.2
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• pp.196-206
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• 2005

Objectives:The purpose of this study is to evaluate the pathophysiology of alcoholics by investigating the differences in frequency of Aldehyde Dehydrogenase 2(ALDH2) genotypes and ALDH2 alleles between patients with alcohol dependence and controls, and the differences of drinking and personality traits in Korean male alcoholics with ALDH2 genotype variances. Methods:The authors selected 98 patients with alcohol dependence and 53 controls. Self-report questionnaires for acute reponses after alcohol ingestion, the AUI(Alcohol Use Inventory), and the NEO-PI-R(NEO Personality Inventory Revised) were given to all patients with alcohol dependence. ALDH2 genotypes were typed with MboII RFLP(Restriction Fragment Length Polymorphism) method in 53 controls and 98 patients with alcohol dependence. The authors divided alcoholic patients into two groups according to the presence of variant $ALDH2^2$ allele;normal ALDH2 alcoholics(N=87) and variant ALDH2 alcoholics(N=11). Results:1) The genotypic frequencies of subjects with $ALDH2^{1/1}$ were higher and those with $ALDH2^{1/2}$ and $ALDH2^{2/2}$ were lower in patients than in controls. 2) Alcohol dependence could be found in $ALDH2^{2/2}$ homozygote individuals. 3) Variant ALDH2 alcoholics had more family problems in the AUI than normal ALDH2 alcoholics. 4) Variant ALDH2 alcoholics experienced more flushing and cardiovascular responses after alcohol ingestion than normal ALDH2 alcoholics. 5) Variant ALDH2 alcoholics had less altruistic personality traits in the NEO-PI-R than normal ALDH2 alcoholics. 6) Variant ALDH2 alcoholics tended to have more tolerance to alcohol than normal ALDH2 alcoholics. Conclusion:Variant $ALDH2^2$ allele might play a protective role in the pathogenesis of alcohol dependence and there were several significant differences of drinking and personality traits in Korean male alcoholics with ALDH2 genotype variances.

• Korean Journal of Biological Psychiatry
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• v.6 no.2
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• pp.176-188
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• 1999

Objective : The purpose of this study was to evaluate the effects of alcohol on neurocognitive function, psychomotor performance and subjective response in healthy Korean adults with different ALDH2 genotypes. Method : A total of 24 males, half with active $ALDH2^*1/2^*1$ and the other with inactive $ALDH2^*1/2^*2$, was selected through genotyping using restriction fragment length polymorphism. In a double-blind, placebo-controlled cross-over design, each subject consumed 0.5g/kg dose of alcohol, given as a mixture of 40% vodka and orange juice, and placebo(orange juice) on two separate occasions on an average of weekly intervals. The blood alcohol concentrations(BACs) were measured using a breath analyzer at baseline and at 30, 60 minutes after drinking. P300s were measured at baseline and at 30 minutes after alcohol and placebo intake. Vital signs and psychomotor performance[Critical Flicker Fusion Threshold(CFFT), Choice Reaction Time (CRT), Digit Symbol Substitution(DSS)] were measured at baseline and at 60 minutes after alcohol and placebo intake. Subjective responses were measured at the end of the study. The statistical analysis focused on whether there were any differences between groups with different ALDH2 genotypes. Results : The major results are as follows. 1) BACs in the inactive group were overall equivalent to those in the active group. Only in terms of time, BACs were significantly higher overall at 30 minutes than at 60 minutes after alcohol intake. 2) Pulse rates were significantly increased after alcohol intake compared with placebo, and the increase was greater in the inactive than in the active group. 3) P300 latencies in leads Fz(frontal), Cz(cental) and Pz(parietal) were significantly increased after alcohol intake compared to placebo, and the increase was greater in the inactive than in the active group. P300 amplitudes in leads Cz and Pz were significantly decreased overall after alcohol intake compared to placebo. 4) Compared with placebo, alcohol produced significant effect on the psychomotor performance : impairment in the inactive group, improvement in the active group. 5) Compared with placebo, alcohol significantly induced a negative or an intense effect on the subjective responses in the inactive group, but little negative and even a somewhat positive effect in the active group. Conclusions : These results suggest that ALDH isozyme variance might be an important factor to determine the effects of acute dose of alcohol on the various psychobehavioural functions and also to determine the alcohol use pattern and to predict the future development of alcohol overuse and/or abuse.