• Microbiology and Biotechnology Letters
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• v.48 no.3
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• pp.373-382
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• 2020

Candidatus Carsonella ruddii is an endosymbiont that resides in specialized cells within the body cavity of plant sap-feeding insects called psyllids. The establishment of symbiotic associations is considered one of the key factors for the evolutionary success of psyllids, as it may have helped them adapt to imbalanced food resources like plant sap. Although C. ruddii is defined as a psyllid primary symbiont, the genes for some essential amino acid pathways are absent. Complete genome sequences of several C. ruddii strains have been published. However, in-depth intra-species comparison of C. ruddii strains has not yet been done. This study therefore aimed to perform a comparative genome analysis of six C. ruddii strains, allowing the interrogation of phylogenetic group, functional category of genes, and biosynthetic pathway analysis. Accordingly, overall genome size, number of genes, and GC content of C. ruddii strains were reduced. Phylogenetic analysis based on the whole genome proteomes of 30 related bacterial strains revealed that the six C. ruddii strains form a cluster in same clade. Biosynthetic pathway analysis showed that complete sets of genes for biosynthesis of essential amino acids, except tryptophan, are absent in six C. ruddii strains. All genes for tryptophan biosynthesis are present in three C. ruddii strains (BC, BT, and YCCR). It is likely that the host may depend on a secondary symbiont to complement its deficient diet. Overall, it is therefore possible that C. ruddii is being driven to extinction and replacement by new symbionts.

• Ocean and Polar Research
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• v.31 no.2
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• pp.177-187
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• 2009

This study examined the multi-scale variabilities of sea surface temperature (SST) and salinity in the Japan/East Sea (JES) based on statistical analyses of observational data, with a focus on the northwestern part of the sea. The regionality of JES SST variability was estimated for different frequency ranges on semimonthly (11-17 days), monthly to seasonal (30-90 days), quasi-semiannual (157-220 days), and quasi-biennial (1.5-3 years) time scales using cluster analyses of daily gridded SST data for 1996 to 2007 from the Japan Meteorological Agency (JMA). Several significant peaks and regional cores were found in each frequency range of the SST anomaly (SSTA) oscillations. Quasi-semiannual SSTA oscillations with high amplitude were found in the south-southwestern part of the Japan Basin ($41-43^{\circ}N$) and were amplified in the area adjacent to Peter the Great Bay. Oscillations with periods of 79 and 55 days also prevailed over the southwest Japan Basin between the Yamato Rise and the continental slope. A similar method was applied to classify SST and the annual cycle of surface salinity using Generalized Digital Environmental Model (GDEM) gridded data. The Tatarskii Strait and adjacent area showed the most specific annual cycles and variability in salinity on interannual to interdecadal time scales. The most significant inverse relationship between surface salinity in the Tatarskii Strait and southern JES areas was found on the interdecadal time scale. Linkages of sea water salinity in the Tatarskii Strait with Amur River discharge and wind velocity over Amurskii Liman were also revealed.

• Parasites, Hosts and Diseases
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• v.55 no.3
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• pp.279-285
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• 2017

The present study was performed to analyze molecularly the phylogenetic positions of human-infecting Trichostrongylus species in Mazandaran Province, Iran, which is an endemic area for trichostrongyliasis. DNA from 7 Trichostrongylus infected stool samples were extracted by using in-house (IH) method. PCR amplification of ITS2-rDNA region was performed, and products were sequenced. Phylogenetic analysis of the nucleotide sequence data was performed using MEGA 5.0 software. Six out of 7 isolates had high similarity with Trichostrongylus colubriformis, while the other one showed high homology with Trichostrongylus axei registered in GenBank reference sequences. Intra-specific variations within isolates of T. colubriformis and T. axei amounted to 0-1.8% and 0-0.6%, respectively. Trichostrongylus species obtained in the present study were in a cluster with the relevant reference sequences from previous studies. BLAST analysis indicated that there was 100% homology among all 6 ITS2 sequences of T. colubriformis in the present study and most previously registered sequences of T. colubriformis from human, sheep, and goat isolates from Iran and also human isolates from Laos, Thailand, and France. The ITS2 sequence of T. axei exhibited 99.4% homology with the human isolate of T. axei from Thailand, sheep isolates from New Zealand and Iran, and cattle isolate from USA.

• Natural Product Sciences
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• v.17 no.2
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• pp.147-159
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• 2011

A high-performance liquid chromatography-electrospray ionization-tandem mass spectrometric method was developed to determine simultaneously eight marker constituents of Forsythiae fructus, and subsequently applied it to classify its two botanical origins. The marker compounds of Forsythia suspensa were phillyrin, pinoresinol, phillygenin, lariciresinol and forsythiaside; those of F.viridissima were arctiin, arctigenin and matairesinol. Separation of the eight analytes was achieved on a phenyl-hexyl column (150${\times}$2.0 mm i.d., 3 ${\mu}M$) using gradient elution with the mobile phase: (A) 10% acetonitrile in 0.5% acetic acid, (B) 40% aqueous acetonitrile. A few fragment ions specific to the types of lignans, among the product ions generated by collisonally induced dissociation (CID) of molecular ion clusters, such as [M-H]$^-$ or [M+OAc]$^-$ were used not only for fingerprinting analysis but for the quantification of each epimer by using multiple-reaction monitoring mode. It was shown good linearity ($r^2{\geq}$ 0.9998) over the wide range of all analytes; intra- and inter-day precisions (RSD, %) were within 9.14% and the accuracy ranged from 84.3 to 115.1%. The analytical results of 40 drug samples, combined with multivariate statistical analyses - principal component analysis (PCA) and hierarchical cluster analysis (HCA) - clearly demonstrated the classification of the test samples according to their botanical origins. This method would provide a practical strategy for assessing the authenticity or quality of the herbal drug.

• YAKHAK HOEJI
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• v.56 no.5
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• pp.280-287
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• 2012

A high-performance liquid chromatography (HPLC) combined with ultraviolet (UV) method for the simultaneous determination of ${\alpha}$-cyperone and nootkatone was developed for the quality control of Cyperus rotundus Linne. The separation was performed on a KR100-$5C_{18}$ ($4.6{\times}250mm$) column, and an elution gradient composed of methanol and water with a flow-rate of 1.0 ml/min. Detection wavelength was set at 254 nm. The optimum extraction for the detection of the ${\alpha}$-cyperone and nookatone was achieved by ultrasonic with methanol for an hour. Two marker compounds ${\alpha}$-cyperone and nootkatone in Cyperi Rhizoma showed good linearity ($R^2$ >0.999) in the concentration range of $12.5{\mu}g/ml$ to $200{\mu}g/ml$. The developed method provided satisfactory precision and accuracy with overall intra-day and inter-day variations of 0.04~1.23% and 0.08~0.68%, respectively, and the overall recoveries of 97.45~105.58% for the two compounds analyzed. Additionally, a difference was observed in the cluster analysis and principal component analysis between Cyperi Rhizoma in Korea and China. The result demonstrated that the principal component analysis is useful to distinguish between Cyperi Rhizoma in Korea and China.

• Bulletin of the Korean Chemical Society
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• v.30 no.1
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• pp.137-144
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• 2009

In this study, quantitative and pattern recognition analyses for the quality evaluation of Herba Epimedii using HPLC was developed. For quantitative analysis, five major bioactive constituents, hyperin, epimedin A, epimedin B, epimedin C, and icariin were determined. Analysis was carried out on Capcell pak $C_{18}$ column ($250{\time}4.6$ mm, 5 ${\mu}m$) with a mobile phase of mixture of acetonitrile and 0.1% formic acid, using UV detection at 270 nm. The linear behavior was observed over the investigated concentration range (2-50 ${\mu}g/mL;\;r_2\;>$ 0.99) for all analytes. The intraand inter-day precisions were lower than 4.3% (as a relative standard deviation, RSD) and accuracies between 95.1% and 104.4%. The HPLC analytical method for pattern recognition analysis was validated by repeated analysis of one reference sample. The RSD of intra- and inter-day variation of relative retention time (RRT) and relative peak area (RPA) of the 12 selected common peaks were below 0.8% and 4.7%, respectively. The developed methods were applied to analysis of twenty Herba Epimedii extract samples. Contents of hyperin, epimedin A, epimedin B, epimedin C, and icariin were calculated to be 0$\sim$0.79, 0.69$\sim$1.91, 0.93$\sim$9.58, 0.65$\sim$3.05, and 2.43$\sim$11.8 mg/g dried plant. Principal component analysis (PCA) showed that most samples were clustered together with the reference samples but several apart from the main cluster in the PC score plot, indicating differences in overall chemical composition between two clusters. The present study suggests that quantitative determination of marker compounds combined with pattern-recognition method can provide a comprehensive approach for the quality assessment of herbal medicines.

• Journal of the Korean housing association
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• v.15 no.2
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• pp.27-34
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• 2004

The purpose of this study has two folds. For the local government it gives a guide to establish the housing information system, which provides various housing information in order to promote service to the public on Internet. It also gives a guide for the local government to collect the fundamental data from local housing market and provide them to the policy makers as well as the housing producers (landlords, builders and owner-occupiers). Contents of housing information system website for the local government consist of three main parts. The first part provides housing policy and local housing market information to the upper level local government as well as housing producers. The second part provides housing information for the people who are looking for houses to move the own. Final part provides the procedures of building construction and development plan for landlords to the public. In case of Pyongtaek-City, this study makes them by cluster analysis of houses and households moving pattern as the Internet contents. Housing markets of Pyongtaek-City divide 3 sectors by housing type, tenure type and housing supply ratio etc. And populations prefer to move intra sectors. According to this information, policy-makers should define local housing problems and find solutions and housing producers can supply the house just in sites and in time. In conclusion, local government should provide valuable housing information based on local housing market research to the public for the effective housing policy. As local housing market is formed by various factors it is needed for local government to research housing sub-markets due to apply these research results to the local government for the future.

• Development and Reproduction
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• v.10 no.4
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• pp.227-238
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• 2006

Genomic DNAs(gDNAs) were isolated from the venus clam(Gomphina aequilatera) from Samcheok(venus clam from Samcheok; VCS) and Wonsan(venus clam from Wonsan; VCW) located in the East Sea of the Korean Peninsula. The amplified products were generated by agarose gel electrophoresis(AGE) with oligonucleotides primer, detected by staining with ethidium bromide and viewed by ultraviolet ray. The seven arbitrarily selected primers BION-21, BION-23, BION-25, BION-27, BION-29, BION-31 and BION-33 generated the shared loci, polymorphic, and specific loci, with the molecular sizes ranging from 150 bp to 2,400 bp. In this study, 147 polymorphic loci(147/954 loci, 15.41%) in VCS population and 274(274/996 loci, 27.51%) in VCW population were generated with seven primers. These results suggest the genetic variation in VCW population is higher than in VCS population. Especially, the 700 bp bands generated by the primer BION-21 were identified commonly in two Gomphina populations, which identified populations and/or species. This specific primer was found to be useful in the identification of individuals and/or population, resulting from the different DNA polymorphism among individuals/species/population. Two Gomphina populations between the individual SAMCHEOK no. 03 and WONSAN no. 22 showed the longest genetic distance(0.696) in comparison with other individuals used. The complete linkage cluster analysis indicating three genetic groupings and dendrogram revealed close relationships among individual identities within two geographical populations of venus clam(G. aequilatera) from the Samcheok and Wonsan. The intra-species classification and clustering analyses inferred from molecular markers supported the traditional taxonomy of the species based on morphological characters such as shell size, shape and color. Accordingly, as mentioned above, RAPD analysis showed that VCS population was more or less separated from VCW population.

• Journal of the Economic Geographical Society of Korea
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• v.15 no.1
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• pp.26-41
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• 2012

This study investigates the time-space characteristics of intra-urban passenger flows in the Metropolitan Seoul area. In particular, we analyze the relationships between transit ridership and land use through the use of the subway passenger flow data obtained from the transit transaction databases. For this purpose, the strength of each subway station, i.e., the number of total in-coming and out-going passengers at each station, in the morning, afternoon, and evening, is calculated and visualized, which reflects urban land use patterns. Then the subway stations are classified into four groups via a hierarchical analysis of the in-coming and out-going passenger flows at 353 stations. Each group appears to have characteristic properties according to the region, e.g., residential areas and central business districts. This has been confirmed by the analysis which probes explicitly the relationship between the local socio-economic variables and station groups. This analysis, disclosing the inter-relationship between the subway network and urban land use, may be useful at various stages in urban as well as transportation planning, and provides analytical tools for a wide spectrum of applications ranging from impact evaluation to decision-making and planning support.

• Progress in Medical Physics
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• v.15 no.4
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• pp.228-236
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• 2004

Retinal ganglion cells transmit visual scene as an action potential to visual cortex through optic nerve. Conventional recording method using single intra- or extra-cellular electrode enables us to understand the response of specific neuron on specific time. Therefore, it is not possible to determine how the nerve impulses in the population of retinal ganglion cells collectively encode the visual stimulus with conventional recording. This requires recording the simultaneous electrical signals of many neurons. Recent advances in multi-electrode recording have brought us closer to understanding how visual information is encoded by population of retinal ganglion cells. We examined how ganglion cells act together to encode a visual scene with multi-electrode array (MEA). With light stimulation (on duration: 2 sec, off duration: 5 sec) generated on a color monitor driven by custom-made software, we isolated three functional types of ganglion cell activities; ON (35.0$\pm$4.4%), OFF (31.4$\pm$1.9%), and ON/OFF cells (34.6$\pm$5.3%) (Total number of retinal pieces = 8). We observed that nearby neurons often fire action potential near synchrony (< 1 ms). And this narrow correlation is seen among cells within a cluster which is made of 6～8 cells. As there are many more synchronized firing patterns than ganglion cells, such a distributed code might allow the retina to compress a large number of distinct visual messages into a small number of ganglion cells.