• Molecules and Cells
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• v.19 no.1
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• pp.104-113
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• 2005

Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.

• Bulletin of the Korean Chemical Society
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• v.30 no.1
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• pp.205-213
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• 2009

This study reports on the geometry optimizations and electronic structure calculations for methyl pyropheophorbide (MPPa), tropolonyl methyl pyropheophorbides (TMPPa, ITMPPa), and cationic tropolonyl methyl pyropheophorbides ($TMPPa^+{{\cdot}BF_4}^-,\;ITMPPa^+{{\cdot}BF_4}^-,\;TMPPa^+,\;and\;ITMPPa^+$) using Local Spin Density Approximation (LSDA/ 6-31G*) and the Restricted Hatree-Fock (RHF/6-31G*) level theory. From the calculated results, we found that substituted cationic tropolonyl groups have larger structural effects than those of substituted neutral tropolonyl groups. The order of structural change effects is $ITMPPa^+ > ITMPPa^+{{\cdot}BF_4}^-$ > ITMPPa, as a result of the isopropyl group. Because it is an electron-releasing group, the substituted isopropyl group electronic effect on a 3-position tropolone increases the Highest Occupied Molecular Orbital and Lowest Unoccupied Molecular Orbital (HOMO-LUMO) energy gap. It was constituted that the larger the cationic characters of these photosensitizers, the smaller the HOMOLUMO band gaps are. The orbital energies of the cationic systems and the ions are stronger than those of a neutral system because of a strong electrostatic interaction. However, this stabilization of orbital energies are counteracted by the distortion of chlorin macrocycle, which results in a large destabilization of chlorin-based compound HOMOs and smaller destabilization of LUMOs as shown in TMPPa (ITMPPa), $TMPPa^+{{\cdot}BF_4}^- (ITMPPa^+{{\cdot}BF_4}^-),\;and\;TMPPa^+\;(ITMPPa^+)$ of Figure 6 and Table 6-7. These results are in reasonable agreement with normal-coordinate structural decomposition (NSD) results. The HOMO-LUMO gap is an important factor to consider in the development of photodynamic therapy (PDT).

• Polymer(Korea)
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• v.27 no.1
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• pp.3-8
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• 2003

Polysiloxanes with methacrylate groups at both terminals were synthesized by a hydrosilylation reaction between allyl methacrylate and hydride-terminated polysiloxanes. The polysiloxane methacrylates with high molecular weights could be prepared through the reaction of polysiloxane methacrylates and octamethylcyclotetrasiloxane with an acid catalyst. The structures of the prepared polysiloxane methacrylates were verified by $^1$H- and $^{29}Si-NMR.$ The polysiloxane methacrylates were freely miscible with silicone oils. Polysiloxane films with microphase-separated liquid silicone oil were prepared by photo-crosslinking the mixture of polysiloxane methacrylates and silicone oil. Scanning electron microscopy (SEM) of the films showed that the size of silicone oil droplets became smaller with a lower loading of silicone oil, lower molecular weight of polysiloxane methacrylate, and lower molecular weight of silicone oil.

• Molecules and Cells
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• v.21 no.2
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• pp.229-236
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• 2006

Gaegurin 4 (GGN4), a novel peptide isolated from the skin of a Korean frog, Rana rugosa, has broad spectrum antimicrobial activity. A number of amphipathic peptides closely related to GGN4 undergo a coil to helix transition with concomitant oligomerization in lipid membranes or membrane-mimicking environments. Despite intensive study of their secondary structures, the oligomeric states of the peptides before and after the transition are not well understood. To clarify the structural basis of its antibiotic action, we used analytical ultracentrifugation to define the aggregation state of GGN4 in water, ethyl alcohol, and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). The maximum size of GGN4 in 15% HFIP corresponded to a decamer, whereas it was monomeric in buffer. The oligomeric transition is accompanied by a cooperative 9 nm blue-shift of maximum fluorescence emission and a large secondary structure change from an almost random coil to an ${\alpha}$-helical structure. GGN4 induces pores in lipid membranes and, using electrophysiological methods, we estimated the diameter of the pores to be exceed $7.3{\AA}$, which suggests that the minimal oligomer structure responsible is a pentamer.

• Mycobiology
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• v.36 no.3
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• pp.173-177
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• 2008

The crude ethanol extracts (stem and fruits), their fractions and two triterpenes, $\beta$-Amyrin and 12-Oleanene 3$\beta$, 21$\beta$-diol, isolated as a mixture from the chloroform soluble fraction of an ethanolic extract of Duranta repens stem, were evaluated for antibacterial, antifungal activities by the disc diffusion method and cytotoxicity by brine shrimp lethality bioassay. The structures of the two compounds were confirmed by IR, $^1H$-NMR, $^{13}C$-NMR and LC-MS spectral data. The chloroform soluble fraction of stem and ethanol extract of fruits possess potent antishigellosis activity and also exhibited moderate activity against some pathogenic bacteria and fungi but the isolated compound 1 (mixture of $\beta$-Amyrin and 12-Oleanene 3$\beta$, 21$\beta$-diol) showed mild to moderate inhibitory activity to microbial growth. The minimum inhibitory concentrations (MICs) of the extracts (stem and fruits), their fractions and compound 1 were found to be in the range of 32$\sim$128 ${\mu}g/ml$. The chloroform soluble fractions of stem and ethanol extract of fruit showed significant cytotoxicity with $LC_{50}$ value of 0.94 ${\mu}g/ml$ and 0.49 ${\mu}g/ml$, respectively against brine shrimp larvae.

• Molecules and Cells
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• v.21 no.1
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.

• Molecules and Cells
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• v.28 no.5
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• pp.447-453
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• 2009

The quorum sensing (QS) inhibitors that antagonize TraR, a receptor protein for N-3-oxo-octanoyl-L-homoserine lactones (3-oxo-C8-HSL), a QS signal of Agrobacterium tumefaciens were developed. The structural analogues of 3-oxo-C8-HSL were designed by in silico molecular modeling using SYBYL packages, and synthesized by the solid phase organic synthesis (SPOS) method, where the carboxamide bond of 3-oxo-C8-HSL was replaced with a nicotinamide or a sulfonamide bond to make derivatives of N-nicotinyl-L-homoserine lactones or N-sulfonyl-L-homoserine lactones. The in vivo inhibitory activities of these compounds against QS signaling were assayed using reporter systems and compared with the estimated binding energies from the modeling study. This comparison showed fairly good correlation, suggesting that the in silico interpretation of ligand-receptor structures can be a valuable tool for the pre-design of better competitive inhibitors. In addition, these inhibitors also showed anti-biofilm activities against Pseudomonas aeruginosa.

• Journal of The Korean Society of Grassland and Forage Science
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• v.37 no.3
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• pp.248-253
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• 2017

Humic acid (HA) is known to consist of various kinds of polymeric organics, their detailed structures can vary depend on sample sources such as organic manure, composts, peat, and lignite brown coal, and largely exists in grassland soils. HA possesses diverse positive effects that not only increase plant growth but also improve soil fertility. Recently, we have manufactured a co-polymeric product of catechol and vanillic acid (CAVA) synthesized artificially, and found that CAVA as a HA mimic increases seed germination and salt tolerance in Arabidopsis. In this study, we examined whether HA or CAVA affects to seedling growth in alfalfa. Foliar application of HA or CAVA increased alfalfa seedling growth including aerial and in root parts. HA or CAVA dramatically enhanced size of leaf and root, whereas HA significantly displayed higher bioactivity than CAVA. Taken together, CAVA acts like as a HA mimic in alfalfa that could apply as an alternation supplement to enhance plant growth and productivity.

• Polymer(Korea)
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• v.36 no.1
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• pp.29-33
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• 2012

Solution type pressure sensitive acrylic adhesives were synthesized from 2-ethylhexyl acrylate (2-EHA) as a base monomer and acrylic acid as a functional monomer. The surface energy and basic physical properties of synthesized PSA (pressure sensitive adhesives) were investigated as a function of contents of acrylic acid and crosslinking agent. The structures of adhesive were identified by FTIR. Viscosities and molecular weights of PSA were measured by a Brookfield viscometer and GPC, respectively. Consequently, molecular weight and viscosity increased as the contents of acrylic acid increased up to 6 wt% and then decreased at higher contents. Surface energy increased as the contents of acrylic acid increased owing to the increase of COOH groups, which yielded the enhancement of polarity of PSA. On the other hands, their peel strengths were inversely proportional to molecular weight and showed tendencies of decreasing as the contents of acrylic acid and crosslinking agent increased.

• Korean Journal of Food Science and Technology
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• v.51 no.5
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• pp.432-437
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• 2019

The objective of this study was to determine the molecular/crystalline structures and phase transition properties of starches isolated from six rice cultivars grown in Korea. Apparent amylose content was highest in starch obtained from the Saemimyeon cultivar (30.8%) and lowest in that obtained from the Sheonhyangheukmi cultivar (20.3%). Starch from the Saemimyeon cultivar had a lower proportion of short chains (DP 6-12) and a the higher proportion of long chains (DP${\geq}37$) than that seen in other rice starches. Saemimyeon had relatively higher pasting temperature ($86.5^{\circ}C$), gelatinization temperature ($72.1^{\circ}C$) and gelatinization enthalpy (14.2 J/g) than these values found for other rice starches. The onset temperature and enthalpy for ice crystallization of rice starch ranged from $-27.1{\sim}-20.2^{\circ}C$ and 241.1~264.8 J/g, respectively. The ice melting enthalpy measured in excess water (67% water content) of rice starches was 282.4~310.1 J/g. Among the rice starches examined, starch obtained from Sheonhyangheukmi, with the lowest amylose content, showed the lowest glass transition temperature (${T_g}^{\prime}$).