• Title/Summary/Keyword: root fusion

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Epigenetic control of LTR retrotransposons in plant germline and somatic cells

  • Lee, Seung Cho;Parent, Jean-Sebastien;Ernst, Evan;Berger, Frederic;Grimanelli, Daniel;Martienssen, Robert A.
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.20-20
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    • 2017
  • Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.

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Epigenetic control of LTR retrotransposons in plant germline and somatic cells

  • Lee, Seung Cho;Parent, Jean-Sebastien;Ernst, Evan;Berger, Frederic;Grimanelli, Daniel;Martienssen, Robert A.
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.97-97
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    • 2017
  • Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.

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STUDIES ON THE TISSUE CULTURE OF PANAX GINSENG

  • Harn C
    • Proceedings of the Ginseng society Conference
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    • 1974.09a
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    • pp.9-22
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    • 1974
  • Unlike the tissue culture in animals and human being, in higher plants various parts of the plant are cultured for varied purposes, and they are named variously depending on which parts are used as explants or what purposes they are cultured for. Followings are some of the names of culture used frequently: organ culture, tissue culture, callus culture, single cell culture, meristem culture, mericlone culture, ovary culture, ovule culture, embryo culture, endosperm culture, anther culture, pollen culture, protoplast culture, etc.. As the names of the culture indicate, in some kinds of culture the explants used for culture are actually not tissues, but organs, single cells, or protoplasts. It seems, however, convenient to call all of the above-mentioned cultures grossly as tissue culture. Several kinds of tissue culture were attempted using Panax ginseng as material and some of the results were summarized below. 1. Callus culture After dormancy of the sed was broken, whole embryo or parts (hypocotyl, cotyledon and epicotyl) of partly grown embryo were cultured in the media supplemented with growth regulators. Rapid swelling occurred in a few weeks, but most of the swelling was observed only in the basal part of epicotyl, changes in the other parts of embryo appearing in much later stages. The swelling or increase in size, however, was resulted not from the divisions of cells, but from the mere expansion of cell. Real calli were formed about two months after inoculation of explants. Callus tissues developed from cortex, pith, and vascular bundle in the cases of hypo- and epicotyl, from mesophyl tissue in the case of cotyledon. Shoots developed more easily from cotyledons regardless of whether they are detached from or attached to the embryo proper. 2. Culture in the Knudson C medium When cotyledons, detached from or attached to the embryo proper, were cultured in the growth regulator-free Knudson C medium comprision only several kinds of mineral compounds and sucrose, shoot primordium or callus developed profusely and finally plantlets were produced directly from shoot primordium or indirectly through callus. In this medium epidermal cells as well as mesophyl cells of the cotyledon became meristematic and divided, changing into multinucleate cells or multicellular bodies, developing eventually into either shoot primordia or calli. 3. Anther culture Anthers were cultured in the media supplemented with various growth regulators applied singly or in combinations. Callus was formed mostly in the connective tissue of anther. Cells of anther wall layers changed in appearance, but no division occurred. Microspores of all stages in development were not changed, ruling out the possibility that microspore-originated callus might be formed. 4. Isolation of protoplast Protoplasts were isolated from young root, leaf, and epicotyl, using 0.7M D-mannitols as osmoticum and using macerozyme and cellulase respectively for maceration and digestion of the cell wall. Production in large number of naked intact protoplast was rather difficult as compared with other plant species. Fusion of protoplasts occurred infrequently mainly due to the fewer number of naked protoplasts in the solution.

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A comparative study of periodontal conditions around mesially tipped molars by a tipping degree (대구치의 근심 경사 정도에 따른 치주 상태의 비교 연구)

  • Park, So-Young;Choi, Seoung-Hwan;Lee, Su-Jeong;Chang, Moon-Taek;Kim, Hyung-Seop
    • Journal of Periodontal and Implant Science
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    • v.32 no.1
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    • pp.41-49
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    • 2002
  • The aim of this study was to compare periodontal conditions around mesially tipped molars by a tipping degree. Patients who had been consecutively treated at the Department of Periodontology, Chonbuk National University Hospital from October 1999 to August 2001 were assessed with radiographs taken at their molar regions. Of all molars investigated, 142 molars of 116 patients tipped mesially more than 10 degrees to the line perpendicular to an occlusal plane were selected for the study. The tipped molars were divided into 2 groups with a reference to a tipping degree, i.e., 66 slightly tipped(group 1 : <$30^{\circ}$) and 76 severely tipped molars (group 2 : ${\geq}30^{\circ}$). Probing depth(PD), plaque retention index(PRI) at mesial surfaces of tipped molars and tooth mobility(TM) were recorded at the clinical examination. Tipping degree(TD) and alveolar bony defect(ABD) at the mesial surface of the molars were measured in a radiograph. The results showed that no statistical differences were found between groups in all measured variables. In Pearson correlation analysis performed in the same group, a positive relationship was shown between PRI and PD in the group 1 and, in the group 2, between PRI and PD as well as PRI and ABD(p < 0.01). However, no statistically significant relationship was found between TD and all other variables in both groups. Within limitations of this study, it may be concluded that tipping degree did not seem to influence periodontal conditions, i.e., PD, ABD and TM of mesially tipped molars per se, but plaque presence/absence seemed to mainly affect the periodontal conditions of the tipped molars.

Analysis of Co-registration Performance According to Geometric Processing Level of KOMPSAT-3/3A Reference Image (KOMPSAT-3/3A 기준영상의 기하품질에 따른 상호좌표등록 결과 분석)

  • Yun, Yerin;Kim, Taeheon;Oh, Jaehong;Han, Youkyung
    • Korean Journal of Remote Sensing
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    • v.37 no.2
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    • pp.221-232
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    • 2021
  • This study analyzed co-registration results according to the geometric processing level of reference image, which are Level 1R and Level 1G provided from KOMPSAT-3 and KOMPSAT-3A images. We performed co-registration using each Level 1R and Level 1G image as a reference image, and Level 1R image as a sensed image. For constructing the experimental dataset, seven Level 1R and 1G images of KOMPSAT-3 and KOMPSAT-3A acquired from Daejeon, South Korea, were used. To coarsely align the geometric position of the two images, SURF (Speeded-Up Robust Feature) and PC (Phase Correlation) methods were combined and then repeatedly applied to the overlapping region of the images. Then, we extracted tie-points using the SURF method from coarsely aligned images and performed fine co-registration through affine transformation and piecewise Linear transformation, respectively, constructed with the tie-points. As a result of the experiment, when Level 1G image was used as a reference image, a relatively large number of tie-points were extracted than Level 1R image. Also, in the case where the reference image is Level 1G image, the root mean square error of co-registration was 5 pixels less than the case of Level 1R image on average. We have shown from the experimental results that the co-registration performance can be affected by the geometric processing level related to the initial geometric relationship between the two images. Moreover, we confirmed that the better geometric quality of the reference image achieved the more stable co-registration performance.

Suggestion of Community Design for the Efficiency of CPTED - Focused on Community Furniture - (범죄예방환경설계(CPTED)의 효율성 증대를 위한 커뮤니티디자인 제안 - 커뮤니티퍼니쳐를 중심으로 -)

  • Lee, Ho Sang
    • Korea Science and Art Forum
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    • v.29
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    • pp.305-318
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    • 2017
  • The need for recognizing the crime in the urban spaces as a social problem and finding out specific approaches such as the study of space design and various guidelines for crime prevention is increasing. In this regard, "Crime Prevention Through Environmental Design" (marked as "CPTED") is actively underway. Yeomri-dong Salt Way is the first place to which the Seoul Crime Prevention Design Project was appled. The business objective of improving the local environment has been implemented rationally through cooperation and voluntary participation between subject of the project executives and community members. Since its efficiency has been proven, the sites have been expanded since then and becomes a benchmarking example of each local government.This kind of problem solving effort has the same context in purpose and direction of the 'Village Art Project' which has been implemented since 2009 with the aim of promoting the culture of the underdeveloped area and encouraging the participation of the residents by introducing the public art. It is noteworthy that this trend is centered around the characteristics of community functions and values. The purpose of this study is to propose the application method of community furniture as a way to increase the efficiency of CPTED to improve the 'quality of life' of residents. To do this, we reviewed CPTED, community design, public art literature and prior research, and identified the problems and implications based on the site visit Yeomri-dong of Seoul and Gamcheon Village of Pusan which is the successful model of "Seoul Root out Crime by Design" and 'Maeulmisul Art Project' respectively. The common elements of the two case places identified in this study are as follows: First, the 'lives' of community residents found its place in the center through the activation of community by collaborative activities in addition to the physical composition of the environment. Second, community design and introduction of public art created a new space, and thereby many people came to visit the village and revitalize the local economy. Third, it strengthened the natural monitoring, the territoriality and control, and the activity increase among the CPTED factors. The psychological aspect of CPTED and the emotional function of public art are fused with the 'community furniture', thereby avoiding a vague or tremendous approach to the public space through a specific local context based on the way of thinking and emotion of local people and it will be possible to create an environment beneficial for all. In this way, the possibility and implication of the fusion of CPTED and public art are expected to be able to reduce the social cost through the construction of the crime prevention infrastructure such as expansion of the CPTED application space, and to suggest a plan to implement the visual amenity as a design strategy to regenerate city.