• Korean Journal of Mineralogy and Petrology
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• v.35 no.3
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• pp.173-182
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• 2022

Dongsuak crater, located in the mid-mountainous region of Jeju Island, is located at an altitude of about 700 m, and the newly discovered Dongsuak spinel peridotites was enclosed in Dongsuak alkaline basalt. The Dongsuak spinel peridotites are composed of olivine, orthopyroxene, clinopyroxene, and spinel with porphyroclastic texture under the an equilibrium state. The variations of mineral major and trace compositions indicates that the Dongsuak spinel peridotites originate at depth from 66 to 88 km under an equilibrium temperature of about 960℃~1068℃. The Dongsuak spinel peridotites have been undergone about 1~3% fractional melting. The LREE-enriched characteristics indicate that the Dongsuak spinel peridotites have been undergone cryptic metasomatism by silicate melt without new minerals.

• ALGAE
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• v.38 no.1
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• pp.1-22
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• 2023

An enormous body of research is focused on finding ways to commercialize carotenoids produced by the unicellular green alga, Haematococcus, often without the benefit of a sound phylogenetic assessment. Evidence of cryptic diversity in the genus means that comparing results of pigment studies may be confounded by the absence of a phylogenetic framework. Moreover, previous work has identified unnamed strains that are likely candidates for species status. We reconstructed the phylogeny of an expanded sampling of Haematococcus isolates utilizing data from nuclear ribosomal markers (18S rRNA gene, 26S rRNA gene, internal transcribed spacer [ITS]-1, 5.8S rRNA gene, and ITS-2) and the rbcL gene. In addition, we gathered morphological, ultrastructural and pigment data from key isolates of Haematococcus. Our expanded data and taxon sampling support the concept of a new species, H. privus, found exclusively in North America. Despite overlap in numerous morphological traits, results indicate that ratios of protoplast length to width and akinete diameter may be useful for discriminating Haematococcus lineages. High growth rate and robust astaxanthin yield indicate that H. rubicundus (SAG 34-1c) is worthy of additional scrutiny as a pigment source. With the description of H. privus, the evidence supports the existence of at least five, species-level lineages in the genus. Our phylogenetic assessment provides the tools to frame future pigment investigations of Haematococcus in an updated evolutionary context. In addition, our investigation highlighted open questions regarding polyploidy and sexuality in Haematococcus which demonstrate that much remains to be discovered about this green flagellate.

• Korean Journal of Mineralogy and Petrology
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• v.36 no.4
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• pp.365-376
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• 2023

Songaksan, formed about 3800 year ago, is one of the tuff rings in the Jeju Island. Mantle xenoliths, spinel peridotites, are enclosed in the Songaksan Trachybasalt. The spinel peridotites are less than 2 cm in size and are composed of olivine, orthopyroxene, clinopyroxene, and spinel. The uniform compositions of the minerals from core to rim indicate that equilibrium was reached in the spinel peridotites before these were enclosed in the host magma. The spinel peridotites originated at depths between 55 and 60 km with equilibrium temperatures ranging from 915 to 968℃. The spinel peridotites from Songaksan reveal porphyroclastic texture with a lot of neoblast minerals. Olivines display strong kink banding, indicating that the upper mantle of Songaksan has been deformed. The spinel peridotites from Songaksan have undergone about 5~7% fractional melting, and cryptic metasomatism by an silicate melt. The period of entrainment and transport of the spinel peridotites in the host magma is about 15 days.

• Genomics & Informatics
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• v.21 no.4
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• pp.47.1-47.12
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• 2023

Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.

• ALGAE
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• v.26 no.2
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• pp.109-140
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• 2011

Taylor's (1960) floristic treatment of the benthic marine algae of the tropical and subtropical western Atlantic and Wynne's (2011) "checklist: third revision" serve as benchmarks in a review of changes made in the past half-century period. There has been a great increase in the number of recognized taxa of red, brown and green algae at all taxonomic ranks: from 758 to 1,393 species, an increase of 84%; from 231 to 406 genera, an increase of 75%; and from 63 to 106 families, an increase of 68%. In regard to recognized infraspecific taxa, the increase was less dramatic, from 140 to 185, thus a 32% change in the 50-year period. This review addresses the question: What factors were responsible for this proliferation of taxa that are now recognized in this domain of the tropical and subtropical western Atlantic? The answer is that many reasons contributed to these changes. Foremost among these causes have been the advances in gene-sequencing technologies. Revised phylogenetic relationships have led to many genera being divided into more than one genus, as well as new families and orders being delineated. Numerous examples of cryptic species have been discovered by gene-sequence and DNA-bar coding studies. This trend is depicted by case studies. Examples of genera being divided are Galaxaura, Liagora and Laurencia. Tricleocarpa and Dichotomaria have been segregated from Galaxaura. Trichogloeopsis, Ganonema, Izziella, Yamadaella, and Titanophycus have been segregated from Liagora. Chondrophycus, Osmundea, Palisada, and Yuzurura have been segregated from Laurencia. Examples are given of other genera present in this region of the western Atlantic that have been split up. Many genera have increased in terms of the number of species now assigned to them. Taylor's (1960) treatment recognized only two species in Hypoglossum, whereas Wynne's (2011) checklist contained a total of 9 species of Hypoglossum. Taylor's account included only two species of Botryocladia, but this number had grown to 15 in Wynne's checklist. Examples of new genera and species occurring in the region of the western Atlantic are given, and examples of taxa being newly reported for this domain are provided. An increase in the number of phycologists in Latin and South America, exploration of previously unexplored regions, and the increasing use of SCUBA for collecting and at greater depths have all contributed to the increase in the number of algal taxa that are now recognized as occurring in the tropical and subtropical western Atlantic.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.17 no.2
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• pp.59-75
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• 2012

The species composition of plankton is essential to understand the material and energy cycling within marine ecosystem. It also provides the useful information for understanding the properties of marine environments due to its sensitivity to the physicochemical characteristics and variability of water masses. In this study we adopted metagenomics to evaluate eukaryotic plankton species diversity from coastal waters off Busan. Characteristics of water masses at sampling sites is expected to be very complex due to the mixing of various water masses; Nakdong River runoff, Changjiang diluted water (CDW), South Sea coastal water, and Tsushima warm current. 18S rDNA clone libraries were constructed from surface waters at the three sites off Busan. Clone libraries revealed 94 unique phylotypes from 370 clones; Dinophyceae(42 phylotypes), Ciliophora(15 phylotypes), Bacillariophyta(7 phylotypes), Chlorophyta(2 phylotypes), Haptophyceae(1 phylotype), Metazoa(Arthropoda( 17 phylotypes), Chaetognatha(1 phylotypes), Cnidaria(2 phylotypes), Chordata(1 phylotype)), Rhizaria (Acantharea(2 phylotypes), Polycystinea(1 phylotype)), Telonemida(1 phylotype), Fungi(2 phylotypes). The difference in species diversity at the closely located three sites off Busan may be attributed to the various physicochemical properties of water masses at these sites by the mixture of water masses of various origins. Metagenomic study of species composition may provide useful information for understanding marine ecosystem of coastal waters with various physicochemical properties in the near feature.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.1999-2006
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• 2016

Background: Acute promyelocytic leukemia (APML) is characterized by the reciprocal translocation t(15;17) (p22;p12) resulting in the PML-$RAR{\alpha}$ fusion gene. A dual diagnostic and follow up approach was applied including cytogenetic demonstration of the t(15;17) translocation and detection dg PML-$RAR{\alpha}$ chimeric transcripts by molecular means. Purpose: Conventional cytogenetics involving bone marrow is beset with high probability of poor metaphase index and was substituted with phytohemagglutinin (PHA)-induced peripheral blood culture based cytogenetic analysis as a diagnostic & follow up modality in APML patients of Kashmir (North India). Both qualitative (RT-PCR) and quantitative (Q-PCR) tests were simultaneously carried out to authenticte the modified cytogenetics. Materials and Method: Patient samples were subjected to the said techniques to establish their baseline as well as follow-up status. Results: Initial cytogenetics revealed 30 patients (81%) Positive for t(15;17) whereas 7 (19%) had either cryptic translocation or were negative for t(15;17). Two cases had chromosome 16q deletion and no hallmark translocation t(15;17). Q-PCR status for PML-$RAR{\alpha}$ was found to be positive for all patients. All the APML patients were reassessed at the end of consolidation phase and during maintenance phase of chemotherapy where 6 patients had molecular relapse, wherein 4 also demonstrated cytogenetic relapse. Conclusions: It was found that PHA-induced peripheral blood cytogenetics along with molecular analysis could prove a reliable modality in the diagnosis and assessment of follow up response of APML patients.

• Korean Journal of Plant Taxonomy
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• v.45 no.4
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• pp.353-361
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• 2015

Spatio-temporal variation in fruit set in orchids would affect long-term population viability and will influence genetic diversity over many generations. The aim of this study was to examine the breeding system of the nectariferous terrestrial orchid Epipactis thunbergii, to specifically determine levels of fruit set in terms of time and space under natural conditions. We examined pollination under natural conditions and conducted hand pollination experiments during a 2-year survey in four populations located along 1.5 km of coastal line in Jinguiri (rual village) [Jeollanam-do (province), southern Korea]. We found that, over a 2-year period, levels of percentage of fruit set were similar within patches of the four populations. By contrast, we detected significant differences in the percentage of fruit set among patches. We also found that plants with larger inflorescence size produced significantly more fruits than plants with fewer flowers. Over a 2-year period, the percentage of fruit set for E. thunbergii was similar but low (14.1%) compared to that averaged for eighty-four rewarding species (37.1%). However, an increase in fruit set was achieved by hand-pollinations: artificial self-pollination (90.5-95.2%), artificial geitonogamy (94.7-95.0%), and cross-pollination (artificial xenogamy, 91.3-91.4%). No emasculated flowers produced fruits and no automatic pollination was found in E. thunbergii. Our findings suggest that E. thunbergii is a self-compatible terrestrial orchid that depends on pollinators (insects) to achieve fruit set in natural habitats, and that local environmental conditions were similar over a period of 2 years in the study area. Our results also highlight the cryptic variation of fruit production in time, but more pronounced variability in space.

• Journal of Microbiology and Biotechnology
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• v.23 no.4
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• pp.545-554
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• 2013

Plasmid isolation of kimchi-derived Weissella cibaria KLC140 revealed six different plasmids. The smallest plasmid, pKW2124, was DNA sequenced and characterized, showing 2,126 bp with a GC content of 36.39% and five putative open reading frames (ORFs). In silico analysis of these ORFs showed ORF1 encodes a putative replication protein similar to rolling circular replication proteins from other lactic acid bacteria. However, a single-stranded intermediate was not detected when S1 nuclease was treated, suggesting it may follow theta replication. Interestingly, the replication initiation site of this plasmid is 100% identical to other plasmids from lactic acid bacteria, suggesting it may function for replication initiation. To construct a surface layer expression vector, pTSLGFP, slpA encoding the surface layer protein from Lactobacillus acidophilus was PCR amplified and fused with the gfp gene, forming a SLGFP fused gene. The plasmid pKW2124 was cloned into the XbaI site of pUC19, forming an Weissella-E. coli shuttle vector pKUW22. NheI-linearized pTSLGFP was ligated into pKUWCAT containing pKUW22 and the chloramphenicol acetyltransferase gene from pEK104, resulting in an 8.6 kb pKWCSLGFP surface layer expression vector. After transformation of this vector into W. cibaria KLC140, a GFP fluorescence signal was detected on the surface of the transformant, substantiating production of SLGFP fused protein and its secretion. This is the first report for construction of a Weissella surface layer expression vector, which may be useful for surface layer production of beneficial proteins in Weissella.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.156-169
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• 2021

Traditional morphological identification difficulties, such as phenotypic plasticity, misidentification of cryptic species, and larval stage species, can be compensated for by using DNA analysis techniques, such as DNA barcoding, in surveying zooplankton populations, including species identification. Recently, the rapid development of DNA sequencing techniques has allowed DNA-based community analysis not only for zooplankton assemblages in various aquatic ecosystems but also for the gut contents of zooplankton that are limited by conventional methods such as visual and microscopic identification. Therefore, the application of DNA sequencing can help understand biological interactions through the analysis of zooplankton food sources. The present paper introduces the major DNA-based approaches in zooplankton research topics, including taxonomic approaches by DNA barcoding, community-level approaches by metabarcoding, and gut content analyses, summarizes the analysis methods, and finally suggests the methodological topics that need to be considered for future applications.