포도나무 갈색무늬병과 줄기혹병에 감염된 포도나무의 대사물질 유형

학위논문 (박사)-- 서울대학교 대학원 : 농생명공학부, 2017. 2. 김영호.In this study, profilings of disease-related metabolites were assessed for characterizing two major grapevine diseases, leaf spot caused by Pseudocercospora vitis and crown gall caused by Agrobacterium vitis, respectively, for both of which GC-MS and multivariate data analysis were applied as the analytical instrumentation and statistical validation. For the leaf spot, a total of 20 metabolites were determined to have their relations with lesion symptoms and the periphery of the leaf spot symptoms, most of which were increased in their contents in the periphery of the symptoms compared with the necrotic lesions. For the crown gall, 13 metabolites increased significantly in relation to the response types, mostly at post-inoculation stages, more prevalently (8 metabolites) at two days after inoculation than other stages, and more related to the susceptible response type (SS) (7 metabolites) than resistant (RR) (3 metabolites) or moderately resistant (SR) (one metabolite) response type. This suggests that most of the disease-related metabolites may be induced by the pathogen infection largely for facilitating gall development except resveratrol, a phytoalexin involved in the resistance response (RR). A total of six metabolites were identified from the comparison of the metabolite profiling between the leaf tissues with and without leaf spot symptoms, including maltotriose, glucoheptonic acid and tartronic acid, a phenolic compound 1-hydroxyanthraquinone and two amino acids aspartic acid and L-threonine. This suggests these may be the disease-related metabolites occurring widely around the infection sites of the leaf tissues with the leaf spot. For the crown gall, most numerous metabolites related to the infection or wound significantly occurred at 2 days after inoculation (DAI) (post-1) (8 for infection in SS, 4 for wound in RR), second-most at 7 DAI (post-2) (3 for infection in SS, 6 and 1 for wounding in SS and RR, respectively), and least at 30 DAI (post-3) (all 3 for infection in RR or SR), suggesting that the responses to the pathogen infection mostly occur in the susceptible grapevines at post-1, and those to wounding (wound healing) occur earlier in the grapevines with RR than those with SS or SR. It also suggests the responses to wounding should be completed and no more wound-related metabolites are detected at post-3. All of the results suggest that plant resistance and wound healing responses are inter-related, enhancing the other responses to increase resistance to the pathogen infection and to speed up the wound healing processes. These disease characteristics revealed by metabolite profiling would provide valuable information and new insights on the understandings of the diseases so as to be used for the development of grapevine disease management strategies.GENERAL INTRODUCTION 1 LITERATURE CITED 8 CHAPTER 1. Metabolic profiles of four different tissues located in grape leaf spot disease caused by Pseudocercospora vitis 14 ABSTRACT 15 INTRODUCTION 16 MATERIALS AND METHODS 19 I. Plant materials 19 II. Sample extraction 19 III. GC-MS analysis 21 IV. Multivariate analysis 22 RESULTS 23 I. Leaf metabolites differences with unsupervised analysis (PCA) 23 II. Leaf metabolites differences with supervised analysis (OPLS-DA) 25 DISCUSSION. 29 LITERATURE CITED 34 CHAPTER 2. Metabolic profiles of grapevine internode tissues infected with Agrobacterium vitis 39 ABSTRACT 40 INTRODUCTION 41 MATERIALS AND METHODS 44 I. Grapevine, pathogen, and pathogen inoculation 44 II. Evaluation for response of Vitis species to Agrobacterium vitis K306 infection 45 III. Tissue sampling 45 IV. Extraction of total metabolites from the sampled tissue 46 V. GC-MS analysis 46 VI. Multivariate data analysis 47 RESULTS 49 I. Responses of grapevine species to Agrobacterium vitis K306 infection in the inoculation test 49 II. GC-MS analysis 49 III. Multivariate data analysis 52 DISCUSSION 58 LITERATURE CITED 65 CHAPTER 3. Metadata analysis of GC-MS metabolites profiling of grapevine infected with Pseudocercospora vitis and Agrobacterium vitis 72 ABSTRACT 73 INTRODUCTION 75 MATERIALS AND METHODS 77 I. Plant materials 77 II. GC-MS analysis and multivariate data analysis 78 RESULTS AND DISCUSSION. 79 I. Leaf spot caused by Psuedocercospora vitis 79 II. The crown gall caused by Agrobacterium vitis 85 LITERATURE CITED 98 ABSTRACT IN KOREAN 105Docto

A mesoscopic model for B to Z-DNA transition

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B-DNA와 Z-DNA 사이의 전이에 관한 mesoscopic 모델

MasterIt is known that the left-handed DNA, called Z-DNA, exists in various situations of specific sequences and ionic environments. Transition between the right-handed B-DNA, the regular form in cell, and the Z-DNA is critical in regulating gene regulation. Within the mesoscopic model for double strand(ds) DNA recently developed, where the ds stacking is implemented by base-pairing, diagonal and stretching interactions, we incorporate a geometrical feature, i.e., the tilting angle of base plane, and the associated energy. This breaks the symmetry of the energy profile, otherwise symmetric, with respect to helical angles, showing the energy minimum at the positive (angle) of the B-DNA as well as the meta-stability of Z-DNA, when B-DNA potential parameters obtained by the B-DNA geometry are used in the energy model. On the other hand, when Z-DNA geometry is used to obtain the Z-DNA potential parameters, the energy profile indeed shows the minimum at the negative helical angle characteristic of Z-DNA. We find the potential parameters, the ranges and stiffness of the interactions, are all slightly smaller than those of B-DNA. We explain this difference within a simple argument based on the electrostatics of different ionic environments of B and Z-DNAs. It demonstrates the validity of our model that it can describe some physical condition or Z-DNA and the B-Z transition in an analytical manner

Advanced Importance Sampling for Complex Soft/Biological System

DoctorImportance sampling is widely applied to understand physical, chemical properties and mechanical processes in various scientific fields. Importance sampling introduces well-designed weight functions to gather useful information from collections of configurations of molecular systems. In this thesis, I develop an advanced importance sampling that uses clustering and non-Boltzmann distribution sampling, and compare its merits with conventional methods. Advanced importance-sampling methods effectively explore a whole configurational space, in which the free energy landscape has several local minima, and approximately identify important conformations from large simulation data. Thus I unveil the key interactions and mechanisms of complex soft systems and biological systems to explore unknown aspects of life processes. For real implementations, I apply the method to two important complex soft/biological systems (i.e., neurofilament brush (NB) and water molecules), and extract information about global configurational change. NBs domains are categorized into three types according to molecular weight: high (NF-H), medium (NF-M) and low (NF-L). We study the large-scale interactions between the projection domains in various conditions of monovalent salt in the presence of phosphorylation. In practical implementations, grand canonical Monte Carlo simulations are applied to a coarse-grained neurofilament brush model. We model a neurofilament as a uniformly-charged cylindrical backbone with tethered flexible projection tails. We introduce importance coordinates, average distances between amino acid (AA) residues and tethered surface, to quantitatively and intuitively describe the brush structure. We measure its typical looping and back-folding conformation to explain the conformal change under hyperphosphorylation. To obtain more-detailed insight, I apply metastable state analysis, which is a form of advanced importance sampling, by combining principal component analysis (PCA) and the density-based spatial clustering of applications with noise (DBSCAN) algorithm. By using this method, I depict novel major metastable states at different physical environments. Although water has crucial functions in biological systems, its physically and chemically anomalous behaviors, including its very complicated phase boundaries, are still not clearly understood. Numerical study is difficult because of thermodynamic instability during phase transition, which causes a sparsity of sampling in the transition (phase-change) zone. Here, I use the advanced importance sampling technique to study the vapor-liquid phase transition of water. To understand the microstructural mechanism and the nucleation process, the intermediate states during transition must be sampled efficiently. In this thesis I perform generalized canonical ensemble replica exchange molecular dynamics (gceREMD) simulations with an advanced importance sampling method, to extract novel micro-structure of the transient states for water droplets or gas bubbles near the vapor-liquid transition. I analyzed morphological changes of the interfaces between vapor and liquid under various pressures. The nucleation process differed greatly depending on the system pressure. At low pressure, the main liquid nucleus shape is approximately spherical and its dynamical process is well described by classical nucleation theory (CNT). However, CNT does not hold near the critical point in which a major liquid droplet already in a ramified shape formed even before the spinodal due to its small free energy cost for surface fluctuation. We provide quantitative comparisons of the order parameters that are related to variations of the interface shape under different system pressures

Synthesis and Characterization of New Functional Brush Polymers Containing Electroactive Moieties

DoctorPolymeric memory devices have attracted a great amount of attention due to their low fabrication cost, good scalability, and simplicity of device structure Therefore, functional polymers have been considered as alternatives to traditional inorganic semiconductor materials for memory devices because they can be easily miniaturized indevice fabrication and their properties can easily be tailored through chemical synthesis. These merits have further accelerated the development of several types of polymer-based memory devices such as rewritable memory, write-once read-many times (WORM) memory, and dynamic random access memory (DRAM). However, none of reported studies can comprehensively account for the observed swiching properties of polymer memory, even though many operating mechanisms have benn proposed such as filamentary conduction, charge transfer, charge trapping and conformational chnge mechasinm. To figure out the operating mechanism of polymer memory device, the design of novel polymeric materials with controlled morphologies and electrical properties is required to elucidate the switching mechasnism because electrical behaviors is closely related to morphologies formed in thin films. First, different volume fraction of diblock copolymer is synthesized because block copolymers (BCP) can self-assemble into various ordered nanostructures (such as lamellae, cylinders, spheres and so on) with length scales ranging from 10 to 100 nm due to the repulsion between the chemically connected blocks. Secondly, correlation between memory and structure is studied by controlled morphologies and electrical properties. Lastly, development of a new polymeric materials system is needed for comprehensive understading, so various fluorinated brush polymers is synthesized and studied. In Chapter II, two series of crystalline-amorphous brush diblock copolymers bearing electroactive moieties were newly synthesized by sequential anionic ring-opening copolymerizations of glycidyl derivatives and subsequent selective post-functionalizations. Self-assembly structural details and electrical memory behaviors of these polymers in nanoscale thin films were investigated. The diblock copolymers revealed complex hierarchical self-assembly structures depending on the compositions. The self-assembly structure and orientation of the crystalline block chains were severely affected by the geometrical confinement (i.e., size and shape) resulted from phase-separation. Such film morphologies were found to cause significant influences on the electrical properties; they exhibited electrical properties from p-type permanent memory behavior to dielectric-like behavior. The permanent memory performances were further varied with the morphology parameters. The observed digital memory behaviors were originated from the electroactive moieties incorporated into the bristle ends. In Chapter III, perfluorinated and carbazole brush-containing block copolymer series, poly(3-((6-((7-(9H-carbazol-9-yl)heptanoyl)oxy)hexyl) thio)propyl glycidyl ether - b - glycidyl 12-((3,3,4,4,5,5,6,6,7,7,8,8,9, 9,10,10,10-heptadecafluorodecyl) oxy)-12-oxo dodecanoate) (PGCHHSP20-b-PGHFD60), (PGCHHSP40-b-PGHFD40), (PGCHHSP60-b-PGHFD20), were synthesized. The polymer was thermally stable up to 300 oC. Below the degradation temperature, it showed a glass transition, crystal melting transition, and a liquid crystal to isotropic melt transition. Most of the materials developed so far are only partially fluorinated materials with relatively low fluorine contents. Highly fluorinated polymers such as Teflon are difficult to process into high-quality films, thereby restricting their applicability. As a consequence, the innovative development of new types of highly fluorinated polymers with easy processability has become very attractive. Therefore, we demonstrates that well-defined linear homo polymer and diblock copolymers with the AGE and EEGE monomer, which are versatile and selectively functionalizable polyether platforms is used to synthesize polymer containing liquid crystalline and amorphous block for a variety of nanostructures and memory device applications. Most of all, synthesiezed brush diblock copolymer with different volume fraction is used to study relationship between memory and structure by controlled morphologies and electrical properties. In Chapter IV, fluorinated side chain liquid crystal polymers have been prepared and properties of synthesized polymers were studied. We report fluorinated polymers composed of hydrocarbon unit and semifluorinated side chain segments, where the number of fluorinated tails varies from one to eight. The polymeric structures described differed by the length of the perfluorinated chains and the spacer which joined the polymer backbone. The fluorinated brush polymers possessing different length of fluoroalkyl side group is used to study the correlation between the surface properties and liquid crystalline properties. By systematically probing the effect of structure on the surface organization of the fluorocarbon side chain, study of these brush polymers has helped optimize the semifluorinated side groups for creating low surface energy materials. In addition, electrical switching behaviors of fluorinated brush polymers are measured for memory device application, since research of electrical property with polymers bearing fluorine or fluuorocaron have not been reported except PVDF (polyvinylidene fluoride) and its copolymer. In Chapter V, we have prepared several polymers with mesogenic cores, coded PGBFn (PG : PolyGlycidyl-backbone, B : biphenyl-mesogenic core, Fn : the number of fluorocarbon-side chian). We designed the two types of polymer series with para-position and meta-position of biphenyl side group to study similarity and difference of crystalline structure and physical properties. The introduction of a mesogenic core will contributes to the stabilization and organization of fluorinated tails at the surface. The surface properties with contact angle measuremtn and surface energy is studied and all measured fluorinated brush polymer show the very low surface energy. This study will help us in the design of future liquid crystal polymers and low surface energy polymers opening an interesting field for the building of stable active surfaces with a favorable eco-toxic approach. In addition, quantitative studies on electrical properties of fluorinated polymer have not been carried out so far, electrical memory performance is measured with polymers which have the number of fluorinated tails varies from one to eight. In Chapter VI, we have synthesized a series of polymers bearing fluorinated aromatic ring side chains to investigate the effect of fluorine and trifluoromethyl group on the morphology, the crystal orientation, charge-carrier transport, and device performance. We have prepared several polymers with mesogenic cores and fluorinated aromatic ring, coded PGBaFbcCF3dP (PG : PolyGlycidyl-backbone, B : Biphenyl-mesogenic core, aFbcCF3dP : the number(a, c) and position(b, d) of fluorine or trifluoromethyl group on phenyl unit –fluorinated aromatic ring pendent). The fluorine atom has the highest Pauling electronegativity of 4.0 among electron-withdrawing groups and the electron density distribution of aromatic ring will be varied according to the position and the number of fluorine and trifluoromethyl group. This means the position of fluorine has significant effect on the crystalline behavior and thermal property

제2차 바이오 가스 포럼(최진하.박창영.정성민)

가. 출장목적 • 음식물류폐기물 바이오가스화사업 추진을 위한, 해외 공법사 실증플랜트 운영현황 파악 및 Risk요인 분석 • 해외 혐기성 바이오가스화 및 폐수처리기술의 운영/관리 전반에 대한 자료 및 정보수집 • 음식물류폐기물 바이오가스화 정책 담당공무원, 전문가, 이해관계자들이 참여함으로써 혐기소화 공법에 대한 인식증진 및 의사결정시 올바른 정책 참여 유도 - 이후 생략O 목 적 - 선도적 정책개발을 위한 선진사례 학습 - 연구원 전공분야의 새로운 이론 및 정책 습득으로 연구역량 강화 - 국가정책 변화 및 관련 국제동향 파악으로 향후 우리 지역 모범 적영 사례 도출 O 내 용 -기조발제)바이오가스화,폐수처리공법 실증 플랜트 현지조사 및 공법사 방문 기술협의_최진하(충청남도 정책특별보좌관) - 발표1)멤브레인을 이용한 바이오가스화 공법소개_박창영(코오롱글로벌 부장) - 발표2)혐기성소화조 공법과 성능 검증방법_정성민(ANNABINI 기술고문

Effect of C60 fullerene on the duplex structure of i-motif DNA with complementary DNA in solution

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Synchrotron X-ray and Neutron Scattering Studies of Nanostructures in Chemically Well-Defined Functional Polymers: Synthetic Polymers, Proteins, and DNAs

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