• Title/Summary/Keyword: ITS2 secondary structure

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Morphology and phylogenetic relationships of Micractinium (Chlorellaceae, Trebouxiophyceae) taxa, including three new species from Antarctica

  • Chae, Hyunsik;Lim, Sooyeon;Kim, Han Soon;Choi, Han-Gu;Kim, Ji Hee
    • ALGAE
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    • v.34 no.4
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    • pp.267-275
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    • 2019
  • Three new species of the genus Micractinium were collected from five localities on the South Shetland Islands in maritime Antarctica, and their morphological and molecular characteristics were investigated. The vegetative cells are spherical to ellipsoidal and a single chloroplast is parietal with a pyrenoid. Because of their simple morphology, no conspicuous morphological characters of new species were recognized under light microscopy. However, molecular phylogenetic relationships were inferred from the concatenated small subunit rDNA, and internal transcribed spacer (ITS) sequence data indicated that the Antarctic microalgal strains are strongly allied to the well-supported genus Micractinium, including M. pusillum, the type species of the genus, and three other species in the genus. The secondary structure of ITS2 and compensatory base changes were used to identify and describe six Antarctic Micractinium strains. Based on their morphological and molecular characteristics, we characterized three new species of Micractinium: M. simplicissimum sp. nov., M. singularis sp. nov., and M. variabile sp. nov.

Emendation of Rhodomonas marina (Cryptophyceae): insights from morphology, molecular phylogeny and water-soluble pigment in an Arctic isolate

  • Niels Daugbjerg;Cecilie B. Devantier
    • ALGAE
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    • v.39 no.2
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    • pp.75-96
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    • 2024
  • Rhodomonas (Cryptophyceae) and species assigned to this genus have undergone numerous taxonomic revisions. This also applies to R. marina studied here as it was originally assigned as a species of Cryptomonas and later considered a variation of R. baltica, the type species. Despite being described more than 130 years ago, R. marina still lacks a comprehensive characterization. Light and electron microscopy were employed to delineate a strain from western Greenland. The living cells were 18 ㎛ long and 9 ㎛ wide, elliptical in shape with a pointed to rounded posterior and truncated anterior in lateral view. Two sub-equal flagella emerged from a vestibulum, where also a furrow extended. In transmission electron microscopy, the furrow was associated with a tubular gullet and the pyrenoid embedded in a deeply lobed chloroplast. The chloroplast contained DNA in perforations and was surrounded by starch grains. A tubular nucleomorph was enclosed within the pyrenoid matrix. In scanning electron microscopy, the inner periplast consisted of rectangular plates with rounded edges and posteriorly these were replaced by a sheet-like structure. The water-soluble pigment was Crypto-Phycoerythrin type I (Cr-PE 545). A phylogenetic inference based on SSU rDNA confirmed the identity of strain S18 as a species of Rhodomonas as it clustered with congeners but also Rhinomonas, Storeatula, and Pyrenomonas. These genera formed a monophyletic clade separated from a diverse assemblage of other cryptophyte genera. To further explore the phylogeny of R. marina a concatenated phylogenetic analysis based on the SSU rDNA-ITS1-5.8S rDNA-ITS2-LSU rDNA region was performed but included only closely related species. The secondary structure of nuclear internal transcribed spacer 2 was predicted and compared to similar structures in related species. Using morphological and molecular signatures as diagnostic features the description of R. marina was emended.

Design Methodology for Transformers Including Integrated and Center-tapped Structures for LLC Resonant Converters

  • Jung, Jee-Hoon;Choi, Jong-Moon;Kwon, Joong-Gi
    • Journal of Power Electronics
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    • v.9 no.2
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    • pp.215-223
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    • 2009
  • A design methodology for transformers including integrated and center-tapped structures for LLC resonant converters is proposed. In the LLC resonant converter, the resonant inductor in the primary side can be merged in the transformer as a leakage inductance. And, the absence of the secondary filter inductor creates low voltage stress on the secondary rectifiers and is cost-effective. A center-tapped structure of the transformer secondary side is widely used in commercial applications because of its higher efficiency and lower cost than full-bridge structures in the rectifying stages. However, this transformer structure has problems of resonance imbalance and transformer inefficiency caused by leakage inductance imbalance in the secondary side and the position of the air-gap in the transformer, respectively. In this paper, gain curves and soft-switching conditions are derived by first harmonic approximation (FHA) and operating circuit simulation. In addition, the effects of the transformer including integrated and center-tapped structures are analyzed by new FHA models and simulations to obtain an optimal design. Finally, the effects of the air-gap position are analyzed by an electromagnetic field simulator. The proposed analysis and design are verified by experimental results with a 385W LLC resonant converter.

Computational Analysis of the Three-Dimensional Flow Fields of Sirocco Fan

  • Hah, Jae-Hong;Moon, Young-J.;Park, Jin-Moo
    • International Journal of Air-Conditioning and Refrigeration
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    • v.9 no.2
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    • pp.44-50
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    • 2001
  • The Sirocco fan performance and its three-dimensional flow characteristics are numerically prediction by STAR-CD. Turbulent flow computations are performed using approximately 500,000 mesh points, and the performance results of tow computational methods, transient and quasi-static flow analyses are compared with experimental data. In the present study, our attention is focused on the three-dimensional flow characteristics of the Sirocco fan blades and the secondary flow structure in the scroll. For a design optimization study, the scroll shape is titled by $10^\circ$ to modify the secondary flow structure, which yields some improvement of the fan performance.

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Effect of substituent and dopant on properties of $LiMn_2O_4$ as cathode materials for lithium ion secondary batteries

  • Lee, Dae-Jin;Wai, Yin-Loo;Jee, Mi-Jung;Bae, Hyun;Choi, Byung-Hyun
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • 2007.11a
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    • pp.294-294
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    • 2007
  • Spinel cathode material $LiMn_2O_4$ is currently studied as a promising cathode material for lithium ion secondary batteries for future applications because of it is low cost, easy to be prepared and capable to be operated in high voltage range. However as a cathode material, $LiMn_2O_4$ performs a poor capacity retention which leads to short cycle life. In this study, stoichiometric $LiMn_2O_4$ was synthesized with granulation method with ion substitution to stabilize its structure and niobium doping to improve its conductivity. These well-mixed powders were calcined at $850^{\circ}C$ for 6 hours and its properties were investigated. Correlations of dopant and electrochemical properties were examined as well.

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Taxonomy and phylogeny of the genus Cryptomonas (Cryptophyceae, Cryptophyta) from Korea

  • Choi, Bomi;Son, Misun;Kim, Jong Im;Shin, Woongghi
    • ALGAE
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    • v.28 no.4
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    • pp.307-330
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    • 2013
  • The genus Cryptomonas is easily recognized by having two flagella, green brownish color, and a swaying behavior. They have relatively simple morphology, and limited diagnostic characters, which present a major difficulty in differentiating between species of the genus. To understand species delineation and phylogenetic relationships among Cryptomonas species, the nuclear-encoded internal transcribed spacer 2 (ITS2), partial large subunit (LSU) and small subunit ribosomal DNA (rDNA), and chloroplast-encoded psbA and LSU rDNA sequences were determined and used for phylogenetic analyses, using Bayesian and maximum likelihood methods. In addition, nuclear-encoded ITS2 sequences were predicted to secondary structures, and were used to determine nine species and four unidentified species from 47 strains. Sequences of helix I, II, and IIIb in ITS2 secondary structure were very useful for the identification of Cryptomonas species. However, the helix IV was the most variable region across species in alignment. The phylogenetic tree showed that fourteen species were monophyletic. However, some strains of C. obovata had chloroplasts with pyrenoid while others were without pyrenoid, which used as a key character in few species. Therefore, classification systems depending solely on morphological characters are inadequate, and require the use of molecular data.

A Study on the Secondary Buckling Behavior of Ship Plate (선체판부재의 2차좌굴거동에 관한 연구)

  • 고재용
    • Journal of the Korean Institute of Navigation
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    • v.20 no.1
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    • pp.47-58
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    • 1996
  • The use of high tensile steel plates is increasing in the fabrication of ship and offshore structures. The main portion of ship structure is usually composed of stiffened plates. In these structures, plate buckling is one of the most important design criteria and buckling load may usually be obtained as an eigenvalue solution of the governing equations for the plate. To use the high tensile steel plate effectively, its thickness may become thin so that the occurrence of buckling is inevitable and design allowing plate buckling may be necessary. When the panel elastic buckling is allowed, it is necessary to get precise understandings about the post-buckling behaviour of thin plates. It is well known that a thin flat plate undergoes secondary buckling after initial buckling took place and the deflection of the initial buckling mode was developed. From this point of view, this paper discusses the post-buckling behaviour of thin plates under thrust including the secondary buckling phenomenon. Series of elastic large deflection analyses were performed on rectangular plates with aspect ratio 3.6 using the analytical method and the FEM.

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Charge-discharge behaviour of $LiNi_{0.85}Co_{0.15}O_2>/MPCF$ cell ($LiNi_{0.85}Co_{0.15}O_2/MPCF$전지의 충방전 특성)

  • 김상필;조정수;박정후;윤문수
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • 1998.11a
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    • pp.25-28
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    • 1998
  • Lithiated cobalt and nickel oxides are becoming very attractive as active cathode materials for secondary lithium ion secondary battery. $LiCoO_2$ is easily synthesized from lithium cobalt salts, but has a relatively high oxidizing potential on charge. LiNiOz is synthesized by a more complex procedure and its nonstoichiometry significantly degraded the charge-discharge characteristics. But $LiNiO_2$ has a lower charge potential which increases the system stability. Lithiated cobalt and nickel oxides are iso-structure which make the preparation of solid solutions of $LiNi_{1-x}Co_xO_2$ for O$LiCoO_2 and LiNiO_2$ electrode. The aim of the presentb paper is to study the electrochemical behaviour, as weU as the possibilities for practical application of layered Iithiated nickel oxide stabilized by $Co^{3+}$ substitution as active cathode materials in lithium ion secondary battery.

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Structure and Antibiotic Activity of a Porcine Myeloid Antibacterial Peptide, PMAP-23 and its Analogues

  • Shin, Song-Yub;Kang, Joo-Hyun;Jang, So-Yun;Kim, Kil-Lyong;Hahm, Kyung-Soo
    • BMB Reports
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    • v.33 no.1
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    • pp.49-53
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    • 2000
  • PMAP-23 is a 23-residue antimicrobial peptide derived from porcine myloid cells. In order to investigate the effects of two Pro residues at positions 12 and 15 of PMAP-23 on antibiotic activity, two analogues in which Ala was substituted for Pro residue at position 12 or 15 were synthesized. $Pro^{12}{\rightarrow}Ala$ (PMAPl) or $Pro^{15}{\rightarrow}Ala$(PMAP2) substitution in PMAP-23 caused a significant reduction on antitumor and phospholipid vesicle-disrupting activities, but did not cause a significant effect on antibacterial activity. PMAP-23 displayed the type I ${\beta}-turn$ structure with a negative ellipticity at near 205 om in SDS micelle, whereas PMAP1 and PMAP2 had a somewhat ${\alpha}-helical$ propensity in TFE solution, as compared to PMAP-23. These results suggest that two Pro residues of positions 12 and 15 in PMAP-23 play important roles in the formation of ${\beta}-turn$ structure on lipid membrane and its ${\beta}-turn$ structure may be essential for antibiotic activity including phospholipid vesicle-disrupting property.

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Structural characterization of calmodulin like domain of ryanodine receptor type 1

  • Song, Yonghyun;Kang, Sunmi;Park, Sunghyouk
    • Journal of the Korean Magnetic Resonance Society
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    • v.19 no.2
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    • pp.74-82
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    • 2015
  • Ryanodine receptor (RyR) is one of the two major $Ca^{2+}$ channels in membranes of intracellular $Ca^{2+}$ stores and is found in sarcoplasmic reticulum (SR), endoplasmic reticulum (ER). RyR1 is also the major calmodulin-binding protein of sarcoplasmic reticulum membranes. Residues 4064-4210 in the RyR1 polypeptide chain has similar primary sequence with calmodulin (CaM) and was designated as CaM-like domain (CaMLD). When expressed as a recombinant peptide, CaMLD showed several CaM-like properties in previous studies. Still, previous studies of CaMLD were focused on protein-protein interactions rather than its own properties. Here, we studied the expression of CaMLD and its sub-domains corresponding to each lobe of CaM in Escherichia coli. CaMLD could be obtained only as inclusion body, and it was refolded using urea solubilization followed by dialysis. Using spectroscopic approaches, such as NMR, circular dichroism, and gel filtration experiment, we found that the refolded CaMLD exists as nonspecific aggregate, even though it has alpha helical secondary structure. In comparison, the first half of CaMLD (R4061-4141) could be obtained as natively soluble protein with thioredoxin fusion. After the removal of the fusion tag, it exhibited folded and helical properties as shown by NMR and circular dichroism experiments. Its oligomeric status was different from CaMLD, existing as dimeric form in solution. However, the second half of the protein could not be obtained as soluble protein regardless of fusion tag. Based on these results, we believe that CaMLD, although similar to CaM in sequence, has quite different physicochemical properties and that the second half of the protein renders it the aggregative properties.