• Genomics & Informatics
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• 제19권3호
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• pp.33.1-33.10
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• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.210-210
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• 2022

Silybum marianum is an annual or biennial plant from the Asteraceae family. It can grow in low-nutrient soil and drought conditions, making it easy to cultivate. From the seed, a specialized plant metabolite called silymarin (flavonolignan complex) is produced and is known to alleviate the liver from hepatitis and toxins damages. To infer the phylogenetic placement of a Korean milk thistle, we conducted a chloroplast assembly and annotation following by a comparison with existing Chinese reference genome (NC_028027). The chloroplast genome structure was highly similar with an assembly size of 152,642 bp, an 153,202 bp for Korean and Chinese milk thistle respectively. Moreover, there were similarities at the gene level, coding sequence (n = 82), transfer RNA (n = 31) and ribosomal RNA (n = 4). From all coding sequences gene set, the phylogenetic tree inference placed the Korean cultivar into the milk thistle clade; corroborating the expected tree. Moreover, an investigation the tree based only on the ycf1 gene confirmed the same tree; suggesting that ycf1 gene is a potential marker for DNA barcoding and population diversity study in milk thistle genus. Overall, the provided data represents a valuable resource for population genomics and species-centered determination since several species have been reported in the Silybum genus.

• 한국산림과학회지
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• 제108권3호
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• pp.364-371
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• 2019

본 연구는 전라도 지역의 주요 수종인 소나무와 편백의 흉고직경에 따른 우세목의 수고생장모델과 지위지수곡선을 개발하여 합리적인 경영과 지속가능한 산림경영체계의 기초자료를 제공할 목적으로 실시하였다. 데이터는 맞춤형 조림지도 제작을 위한 전라도 지역에 생육하고 있는 소나무 3,055본(611개 표본점), 편백 3,345본(669개 표본점)에 대한 표고, 경사도, 방위, 토양형, 우세목의 수고와 흉고직경, 수령 등을 측정하여 수집하였다. 전라도 지역 소나무와 편백에 대한 흉고직경에 따른 우세목의 수고생장모델은 Petterson식, Michailow식, Log식을 이용하였으며, 연령에 따른 우세목의 수고생장모델은 Chapman-Richards식, Schumacher식, Gompertz식을 이용하여 개발하였다. 흉고직경에 따른 우세목의 수고생장모델은 소나무와 편백 모두 잔차평균제곱의 값이 가장 낮은 Pettersosn식을 선정하였다. 연령에 따른 우세목의 수고생장모델은 국가수준에서 사용하고 있는 Chapman-Richards식을 선정하였다. 지위지수의 추정을 위하여 기준임령(Base age)은 30년을 사용하였다. 그 결과 소나무는 지위지수 6~18, 편백은 지위지수 6~22로 국가수준에서 사용하고 있는 지위지수곡선에 비해 매우 다양하게 지위를 추정할 수 있어, 현실임분의 합리적인 경영을 위한 자료제공에 적합한 것으로 판단된다.

• 셀메드
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• 제4권1호
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• pp.6.1-6.12
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• 2014

Anthrax is the deadly disease for human being caused by Bacillus anthracis. Instantaneous research work on the mode of infection of the organism revealed that different proteases are involved in different steps of pathogenesis. Present study reports the in silico characterization and the detection of pathogenic proteases involved in anthrax infection through protein-protein interaction. A total of 13 acid, 9 neutral, and 1 alkaline protease of Bacillus anthracis were selected for analysing the physicochemical parameter, the protein superfamily and family search, multiple sequence alignment, phylogenetic tree construction, protein-protein interactions and motif finding. Among the 13 acid proteases, 10 were found as extracellular enzymes that interact with immune inhibitor A (InhA) and help the organism to cross the blood brain barrier during the process of infection. Multiple sequence alignment of above acid proteases revealed the position 368, 489, and 498-contained 100% conserved amino acids which could be used to deactivate the protease. Among the groups analyzed, only acid protease were found to interact with InhA, which indicated that metalloproteases of acid protease group have the capability to develop pathogenesis during B. anthracis infection. Deactivation of conserved amino acid position of germination protease can stop the sporulation and germination of B anthracis cell. The detailed interaction study of neutral and alkaline proteases could also be helpful to design the interaction network for the better understanding of anthrax disease.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2000년도 The 7th International Symposium
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• pp.114-115
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• 2000

Aralia elata is found in mountain areas all over Korean peninsula. Aralia elata is the scientific name for Japanese angelica tree. The tree belongs to the family Araliaceae, commonly known as ginseng family. Bud sprouts from apical shoot tip of the plants are rich in flavor and thus mainly used for both folk medicine and vegetable. The stalks with apical buds are gathered in the early spring and planted in sandy soil or water in the greenhouse. The sprouting buds are then collected and sold as fresh vegetable. Although the plants have been used for food, they have been cultivated in a very small scale. In spring, local farmers just go around mountain areas to search the trees and gather the stalks as much as they get and sell them to the market. No conservation efforts have been made to stop the exploitation or to save the dwindling population. We tried to provide local farmers with the plants that may be used as an alternative to stalks from wild populations. This will bel! p conserve the wild populations. However, it is hard to propagate them either by conventional cuttings or by seed germination in a short period of time. Mass propagation using tissue culture systems have shown a great promise with several woody plants. Recently we developed a mass propagation technique via somatic embryogenesis system using mature and/or juvenile explants for Aralia elata. Several factors affecting somatic embryogenesis system including SE(somatic embryo) induction, embryogenic callus proliferation, SE germination, plant regeneration and transplanting to field frill be presented. And some problems arising for the somatic embryogenesis system will be also discussed.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2000년도 제7차 국제 심포지움(생약자원개발에 관한연구) 및 추계정기 학술발표회 초록집
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• pp.16-17
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• 2000

Aralia elata is found in mountain areas all over Korean peninsula. Aralia elata is the scientific name for Japanese angelica tree. The tree belongs to the family Araliaceae, commonly known as ginseng family. Bud sprouts from apical shoot tip of the plants are rich in flavor and thus mainly used for both folk medicine and vegetable. The stalks with apical buds are gathered in the early spring and planted in sandy soil or water in the greenhouse. The sprouting buds are then collected and sold as fresh vegetable. Although the plants have been used for food, they have been cultivated in a very small scale. In spring, local farmers just go around mountain areas to search the trees and gather the stalks as much as they get and sell them to the market. No conservation efforts have been made to stop the exploitation or to save the dwindling population. We tried to provide local farmers with the plants that may be used as an alternative to stalks from wild populations. This will hel! p conserve the wild populations. However, it is hard to propagate them either by conventional cuttings or by seed germination in a short period of time. Mass propagation using tissue culture systems have shown a great promise with several woody plants. Recently we developed a mass propagation technique via somatic embryogenesis system using mature and/ or juvenile explants for Aralia elata. Several factors affecting somatic embryogenesis system including SE(somatic embryo) induction, embryogenic callus proliferation, SE germination, plant regeneration and transplanting to field will be presented. And some problems arising for the somatic embryogenesis system will be also discussed.lso discussed.

• 대한지역사회영양학회지
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• 제19권5호
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• pp.468-478
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• 2014

Objectives: Intake of fruits and vegetables has protective effects against stroke attack. This study intended to examine the status of consuming fruits and vegetables and to find out which factors may influence the frequency of consumption of fruits and vegetables in individuals with a history of stroke. Methods: The data of 208 subjects from 5th (2010, 2011) Korea National Health and Nutrition Examination Survey (KNHNES) who reported a stroke diagnosis was used for analysis. To identify major factors influencing the consumption of fruits and vegetables, a classification-tree analysis was carried out. Results: Among those who reported a stroke diagnosis, the frequencies of consumption of fruits and vegetables were influenced by their age, place of residence (urban or rural), economic status, educational level, occupation, number of family members, frequency of eating out, and having meals (breakfast or lunch) with family members. Two factors from fruits and three factors from vegetables were generated by exploratory factor analyses. Urban residents ate fruits and vegetables more frequently in all factors than rural residents. Eating frequencies of 'seasonal fruits (orange, apple, strawberry, melon, pear and watermelon)', 'easily-accessible fruits (persimmon, tangerine, grape, peach, banana)', and 'Western-style vegetables (cabbage, mushroom, carrot, tomato, spinach)' were influenced by the socioeconomic status. Eating frequencies of 'Korean-style vegetables (bean sprout, radish leaves, pumpkin/squash, sea weed)', 'preserved vegetables (Korean cabbage, radish, laver, cucumber)' were influenced by having breakfast with family members. Conclusions: The results of this study suggested that by eating more fruits and vegetables, more preventive effects against secondary stroke attack are expected in stroke patients who live in the rural areas and who do not eat breakfast with family members. In addition, more outreach and education programs are needed for them.

• Journal of Plant Biotechnology
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• 제49권4호
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• pp.271-291
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• 2022

Pectin methylesterase (PME) plays an important role in vegetative and reproductive development and biotic/abiotic stress responses by regulating the degree of methyl-esterification of pectic polysaccharides in the plant cell wall. PMEs are encoded by a large multigene family in higher land plant genomes. In general, the expression of plant PME genes shows tissue- or cell-specific patterns and is induced by endogenous and exogenous stimuli. In this study, we identified PME multigene family members (CsPMEs) from the sweet orange genome and report detailed molecular characterization and expression profiling in different citrus tissues and two fruit developmental stages. We also discussed the possible functional roles of some CsPME genes by comparing them with the known functions of PMEs from other plant species. We identified 48 CsPME genes from the citrus genome. A phylogenetic tree analysis revealed that the identified CsPMEs were divided into two groups/types. Some CsPMEs showed very close phylogenetic relationships with the PMEs whose functions were formerly addressed in Arabidopsis, tomato, and maize. Expression profiling showed that some CsPME genes are highly or specifically expressed in the leaf, root, flower, or fruit. Based on the phylogenetic relationships and gene expression profiling results, we suggest that some CsPMEs could play functional roles in pollen development, pollen tube growth, cross incompatibility, root development, embryo/seed development, stomata movement, and biotic/abiotic stress responses. Our results shed light on the biological roles of individual CsPME isoforms and contribute to the search for genetic variations in citrus genetic resources.

• 한국콘텐츠학회논문지
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• 제13권12호
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• pp.829-839
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• 2013

본 연구는 로지스틱 회귀분석과 의사결정나무 분석을 활용하여 일 대도시 주민의 우울에 영향을 주는 요인을 예측하고 비교하고자 시도된 서술적 조사연구이다. 연구대상은 20세에서 65세 미만의 일 대도시 주민 462명이었다. 자료 수집은 2011년 10월 7일부터 10월 21일까지이었으며, 자료 분석은 SPSS 18.0 프로그램을 이용하여 빈도, 백분율, 평균과 표준편차 및 ${\chi}^2$-test, t-test, 로지스틱 회귀분석, roc curve, 의사결정나무 분석으로 분석하였다. 본 연구 결과, 로지스틱 회귀분석과 의사결정나무 분석에서 공통적으로 나타난 우울 예측요인은 사회부적응, 주관적 신체증상 및 가족 지지이었다. 로지스틱 회귀분석에서 특이도 93.8%, 민감도 42.5%이었고, 본 연구의 모형 적합도를 roc curve 검증 한 결과 AUC=.84으로 본 연구 모형은 적합(p=<.001)하다고 할 수 있다. 우울예측에 대한 의사결정나무 분석은 분류에 대한 예측 정확도에서 특이도 98.3%, 민감도 20.8%이었고, 전체 분류 정확도는 로지스틱 회귀분석은 82.0%, 의사결정나무 분석은 80.5% 이었다. 본 연구 결과 민감성과 분류 정확도와 더 높게 나타난 로지스틱 회귀분석 방법이 지역 주민의 우울 예측 모형을 구축하는데 더 유용한 자료로 사용될 수 있으리라 사료된다.

• Genomics & Informatics
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• 제10권1호
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• pp.9-15
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• 2012

Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. $Cryptosporidium$ $parvum$ is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that $C.$ $parvum$ CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that $C.$ $parvum$ CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including $C.$ $parvum$, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that $C.$ $parvum$ regained cysQ from proteobacteria by HGT, although its functional role is elusive.