• Parasites, Hosts and Diseases
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• v.57 no.5
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• pp.531-536
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• 2019

Cryptosporidium parvum and Giardia duodenalis are the main diarrhea-causing parasitic pathogens; however, their prevalence in Korea is unknown. Here, we conducted a survey to determine the prevalence and genotype distribution of these 2 pathogens causing acute diarrhea in 8,571 patients hospitalized in 17 Regional Institute of Health Environment sites in Korea, during 2013-2016. C. parvum and G. duodenalis were detected and genotyped by nested PCR, and the isolate were molecularly characterized by sequencing the glycoprotein 60 (Gp60) and ${\beta}-giardin$ genes, respectively. The overall prevalence of C. parvum and G. duodenalis was 0.37% (n=32) and 0.55% (n=47), respectively, and both pathogens were more prevalent in children under 9 years old. Molecular epidemiological analysis showed that the C. parvum isolates belonged to the IIa family and were subtyped as IIaA13G2R1, IIaA14G2R1, IIaA15G2R1, and IIaA18G3R1. Analysis of the ${\beta}-giardin$ gene fragment from G. duodenalis showed that all positive strains belong to assemblage A. This is the first report on the molecular epidemiology and subtyping of C. parvum and G. duodenalis in such a large number of diarrheal patients in Korea. These results highlight the need for continuous monitoring of these zoonotic pathogens and provide a basis for implementing control and prevention strategies. Further, the results might be useful for epidemiological investigation of the source of outbreak.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.43-43
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• 2019

The collection, evaluation and conservation of crop germplasm have been treated as one of the basics to breeding program. An understanding of genetic relationships among germplasm resources is vital for future breeding process like yield, quality, and resistance. In the present study, EST-SSR markers were employed to assess the polymorphism and genetic diversity of 192 accessions of Proso millet preserved in the National Agrobiodiversity Center of RDA. We evaluated the efficiency of EST-SSR markers developed for proso millet species. A total of 98 alleles were detected with an average allele number of 4.5 per locus among 192 proso millet millet accessions using 22 EST-SSR markers. The averaged values of gene diversity ($H_E$) and polymorphism information content (PIC) for each EST-SSR marker were 0.362 and 0.404 within populations, respectively. Our results showed the moderate level of the molecular diversity among the proso millet accessions from diverse countries. A phylogenetic tree revealed three major groups of accessions that did not correspond with geographical distribution patterns with a few exceptions. The less correlation between the clusters and their geographic location might be considered due to their type difference. Our study provided a better understanding of genetic relationships among various germplasm collections, and it could contribute to more efficient utilization of valuable genetic resources. The EST-SSR markers developed here will serve as a valuable resource for genetic studies, like linkage mapping, diversity analysis, quantitative trait locus/association mapping, and molecular breeding.

• Proceedings of the Korea Water Resources Association Conference
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• 2016.05a
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• pp.521-521
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• 2016

상수도 관망은 수원에서 수요절점까지 물을 안정적으로 공급하는 것을 목표로 한다. 상수도 관망의 최적설계는 수리학적 제한조건 (절점의 수압, 관로의 유속)을 만족하는 범위에서 비용을 최소화하는 설계안을 얻는 것으로 Savic and Walters (1997)는 유전 알고리즘 (Genetic Algorithms, Holland 1975)을 적용한 상수도 관망 설계 프로그램인 GANET를 제안하였고, Maier et al. (1996)은 개미군집알고리즘 (Ant Colony Optimization Algorithm, Dorigo et al. 1996)을 상수도 관망 최적설계에 적용한 후 그 결과가 유전 알고리즘에 비해 우수함을 증명하는 등 상수도 관망 최적설계에 관한 연구가 활발히 진행되어 오고 있다. 유전알고리즘은 선택, 교차, 돌연변이의 반복계산 과정을 통하여 최적해를 찾는 최적화 기법이다. 이 과정에서 결정변수는 유전자 (Gene)의 집합으로 표현되며, 염색체 (Chromosome) 내에서 근접한 유전 인자들은 일종의 Building Block을 형성하게 된다. Building Block은 좋은 해를 갖는 유전 인자를 높은 확률로 보관하여 지역해에 빠질 가능성을 줄이는 반면, 유전형 (Genotype)이 표현형 (Phenotype)을 충분히 모방하여 표현하지 못한 경우 오히려 최적해의 탐색을 방해할 수 있다는 한계점을 갖는다. 유전 알고리즘을 상수도 관망 최적설계에 적용하였을 때에도 이 한계점은 여실히 드러난다. 관로의 관경을 결정변수로 설정한 후 유전형으로 표현하였을 때, 관망도 상에서 근접하지 않은 두 관로가 염색체 내에서 연속으로 나열된다면 두 관로 간의 연관성이 실제보다 크게 고려되기 때문이다. 한편, 하모니써치 (Harmony Search, Geem et al. 2001) 알고리즘은 즉흥 연주 (Improvisation)를 통해 최상의 화음을 만들어내는 현상으로부터 착안하여 만들어진 최적화기법으로 연산 기법은 무작위선택, 기억회상, 피치조정 등으로 구성되어 있으며, 결정변수에 해당하는 연주자가 독립적으로 행동하며 해를 탐색한다는 점에서 유전알고리즘과 큰 차이를 갖는다. 본 연구에서는 유전알고리즘의 Building Block에 의해 발생하는 오류를 개선하고자, 상수도 관망 최적설계 연구에 많이 사용되는 Hanoi 관망 (Fujiwara and Khang 1990) 관로의 정렬 순서를 여러 가지 기준으로 설정하여 관망데이터를 구축한 후 하모니써치와 유전 알고리즘을 적용하여 최적화를 수행하였고 그 결과를 비교하였다. 그 결과 유전 알고리즘과 달리 하모니써치 알고리즘의 경우, 관로의 나열 순서와 상관없이 우수한 최적해 탐색 결과를 보이는 것을 확인할 수 있었다.

• Korean Journal of Soil Science and Fertilizer
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• v.48 no.5
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• pp.442-450
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• 2015

This study was conducted to investigate the effect of Psy-2A-CrtI (PAC), a genetically modified (GM) rice with enhanced ${\beta}$-carotene, on the soil microbial community. The soil used to cultivate GM rice and its wild-type, Nakdong, was analyzed for population density, denaturing gradient gel electrophoresis (DGGE), and pyrosequencing. It was found that the bacterial, fungal and actinomycetes population densities of the PAC soils were within the range of those of the non-GM rice cultivar, Nakdong. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The pyrosequencing result showed a temporal difference in microorganism taxon and distribution ratio, but no significant difference between GM and non-GM was found. The persistence of the transgene DNA in the plant and surrounding soil were investigated for different time periods. There were differences in the persistence within the plant depending on the gene, but they could not be detected after 5 weeks. Also the transgenes were not detected in the surrounding soil. These results indicate that soil microbial communities are unaffected by the cultivation of a PAC rice within the experimental time frame.

• Journal of Veterinary Science
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• v.22 no.4
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• pp.50.1-50.10
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• 2021

Background: Bovine papillomatosis is a type of proliferative tumor disease of skin and mucosae caused by bovine papillomavirus (BPV). As a transboundary and emerging disease in cattle, it poses a potential threat to the dairy industry. Objectives: The aim of this study is to detect and clarify the genetic diversity of BPV circulating in dairy cows in Xinjiang, China. Methods: 122 papilloma skin lesions from 8 intensive dairy farms located in different regions of Xinjiang, China were detected by polymerase chain reaction. The genetic evolution relationships of various types of BPVs were analyzed by examining this phylogenetic tree. Results: Ten genotypes of BPV (BPV1, BPV2, BPV3, BPV6, BPV7, BPV8, BPV10, BPV11, BPV13, and BPV14) were detected and identified in dairy cows. These were the first reported detections of BPV13 and BPV14 in Xinjiang, Mixed infections were detected, and there were geographical differences in the distribution of the BPV genotypes. Notably, the BPV infection rate among young cattle (< 1-year-old) developed from the same supply of frozen sperm was higher than that of the other young cows naturally raised under the same environmental conditions. Conclusions: Genotyping based on the L1 gene of BPV showed that BPVs circulating in Xinjiang China displayed substantial genetic diversity. This study provided valuable data at the molecular epidemiology level, which is conducive to developing deep insights into the genetic diversity and pathogenic characteristics of BPVs in dairy cows.

• The Plant Pathology Journal
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• v.34 no.6
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• pp.499-505
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• 2018

Huanglongbing (HLB, Citrus greening disease) is one of the most devastating diseases that threaten citrus production worldwide. Although HLB presents systemically, low titer and uneven distribution of these bacteria within infected plants can make reliable detection difficult. It was known loop-mediated isothermal amplification (LAMP) method has the advantages of being highly specific, rapid, efficient, and laborsaving for detection of plant pathogens. We developed a new LAMP method targeting gene contained tandem repeat for more rapid and sensitive detection of Candidatus Liberibacter asiaticus (CLas), putative causal agent of the citrus huanglongbing. This new LAMP method was 10 folds more sensitive than conventional PCR in detecting the HLB pathogen and similar to that of real-time PCR in visual detection assay by adding SYBR Green I to mixture and 1% agarose gel electrophoresis. Positive reactions were achieved in reaction temperature 57, 60 and $62^{\circ}C$ but not $65^{\circ}C$. Although this LAMP method was not more sensitive than real-time PCR, it does not require a thermocycler for amplification or agarose gel electrophoresis for resolution. Thus, we expect that this LAMP method shows strong promise as a reliable, rapid, and cost-effective method of detecting the CLas in citrus and can be applied for rapid diagnosis is needed.

• The Plant Pathology Journal
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• v.35 no.5
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• pp.508-520
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• 2019

Interplay between Cymbidium mosaic virus (CymMV)/Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infecting viruses. In this study, for the first time, we characterized viral small interfering RNAs (vsiRNAs) profiles in P. equestris co-infected with CymMV and ORSV through small RNA sequencing technology. CymMV and ORSV small interfering RNAs (siRNAs) demonstrated several general and specific/new characteristics. vsiRNAs, with A/U bias at the first nucleotide, were predominantly 21-nt long and they were derived predominantly (90%) from viral positive-strand RNA. 21-nt siRNA duplexes with 0-nt overhangs were the most abundant 21-nt duplexes, followed by 2-nt overhangs and then 1-nt overhangs 21-nt duplexes in infected P. equestris. Continuous but heterogeneous distribution and secondary structures prediction implied that vsiRNAs originate predominantly by direct Dicer-like enzymes cleavage of imperfect duplexes in the most folded regions of the positive strand of both viruses RNA molecular. Furthermore, we totally predicted 54 target genes by vsiRNAs with psRNATarget server, including disease/stress response-related genes, RNA interference core components, cytoskeleton-related genes, photosynthesis or energy supply related genes. Gene Ontology classification showed that a majority of the predicted targets were related to cellular components and cellular processes and performed a certain function. All target genes were down-regulated with different degree by vsiRNAs as shown by real-time reverse transcription polymerase chain reaction. Taken together, CymMV and ORSV siRNAs played important roles in interplay with P. equestris by down modulating the expression levels of endogenous genes in host plant.

• Korean Journal of Plant Taxonomy
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• v.50 no.4
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• pp.385-394
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• 2020

To elucidate the molecular phylogeny of Neottia japonica, which is a terrestrial orchid distributed in East Asia, the internal transcribed spacer (ITS) of nuclear DNA and the matK of chloroplast DNA were used. A total 22 species of 69 accessions for ITS and 21 species of 114 accessions for matK phylogeny were analyzed with the maximum parsimony and Bayesian methods. In addition, we sought to establish a correlation between the distribution, morphology of the auricles and genetic association of N. japonica with phylogenetic data. The phylogenetic results suggest that N. japonica is monophyletic and a sister to N. suzukii in terms of the ITS phylogeny, while it is paraphyletic with N. suzukii in terms of the matK phylogeny. N. japonica and N. suzukii show similar morphologies of the lip and column, they both flower in April, and they are both distributed sympatrically in Taiwan. Therefore, it appears to be clear that N. japonica and N. suzukii are close taxa within Neottia, although there is incongruence between the nrDNA and cpDNA phylogenies of N. japonica. The incongruence between the two datasets may have various causes, meaning that further studies are needed to confirm the evolutionary process of N. japonica. The phylogenetic status of N. kiusiana, which was not included in previous studies, was as a sister to N. nidus-avis. Meanwhile, the ITS and matK phylogenies are unsuitable for identifying genetic associations with the characteristic of auricles. The phylogenetic topologies of Korean, Taiwanese and mainland Chinese individuals suggest that the populations of N. japonica in Korea originated from China's mainland and island areas. The characterization of regional gene differences could provide useful preliminary data for future studies.

• Journal of Korean Neurosurgical Society
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• v.64 no.4
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• pp.505-513
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• 2021

Objective : The adaptive immune response following subarachnoid hemorrhage (SAH) is not well understood. We evaluated and compared the T cell receptor (TCR) immune repertoire of good-grade and poor-grade SAH patients to elucidate the T cell immunology after ictus. Methods : Peripheral blood from six SAH patients was collected at two different times, admission and at the 7-day follow-up. Composition and variation of the TCR β-chain (TCRB) complimentary determining regions (CDR) 3 repertoire was examined using high-throughput sequencing; the analysis was based on sampling time and disease severity (good vs. poor-grade SAH). Results : Clonality at admission and follow-up were 0.059 (0.037-0.038) and 0.027 (0.014-0.082) (median, 25th-75th percentile). Poor-grade SAH (0.025 [0.011-0.038]) was associated with significantly lower clonality than good-grade SAH (0.095 [0.079-0.101]). Poor-grade SAH patients had higher diversity scores than good-grade SAH patients. CDR length was shorter in good-grade SAH vs. poor-grade SAH. Differences in clonotype distribution were more prominent in TCRBV gene segments than TCRBJ segments. TCRBV19-01/TCRBJ02-04 and TCRBV28-01/TCRBJ02-04 were the most increased and the most decreased V-J pairs in the 7-day follow-up compared to admission in good-grade SAH. The most increased and decreased V-J pairs in poor-grade SAH patients were TCRBV28-01/TCRBJ02-06 and TCRBV30-01/TCRBJ02-04, respectively. Conclusion : The TCRB repertoire is dynamic in nature following SAH. TCRB repertoire may facilitate our understanding of adaptive immune response according to SAH severity.

• Journal of Physiology & Pathology in Korean Medicine
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• v.34 no.4
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• pp.184-190
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• 2020

This study was performed to find antibacterial substances contained in Scutellariae Radix (SR) using a systems pharmacological analysis method and to establish an effective strategy for the prevention and treatment of infectious diseases. Analysis of the main active ingredients of SR was performed using Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and Analysis Platform. 36 active compounds were screened by the parameter values of Drug-Likeness (DL), Oral Bioavailability (OB), and Caco-2 permeability (Caco-2), which were based on the drug absorption, distribution, metabolism, and excretion indicators. The UniProt database was used to obtain information on 159 genes associated with active compounds. The main active compounds with antibacterial effects were wogonin, β-sitosterol, baicalein, acacetin and oroxylin-A. Target proteins associated with the antibacterial action were chemokine ligand 2, interleukin-6, tumor necrosis factor, caspase-8,9 and mitogen-activated protein kinase 14. In the future, systems pharmacological analysis of traditional medicine will be able to make it easy to find the important mechanism of action of active substances present in natural medicines and to optimize the efficacy of medicinal effects for combinations of major ingredients to help treat certain diseases.