• Korean Journal of Plant Taxonomy
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• v.36 no.3
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• pp.189-207
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• 2006

Goodyera rosulacea, which is morphologically similar to G. repens, is described recently as a new species based on its distinct morphological characters such as rosette-formed leaves, short rhizome and habitat. To verify the taxonomic identity of G. rosulacea and its taxonomic relationship within Korean Goodyera taxa, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the trnL region of cpDNA from 24 accessions including 1 outgroup accession were analyzed. Aligned sequences were analyzed using maximum parsimony and distance method, and the taxonomic identity and the taxonomic relationships among the related taxa were estimated by the existence of private marker gene and the phylogenetic tree of the aligned sequences. Molecular data indicate that G. rosulacea gas several private marker genes and shows monophyly in phylogenetic trees of both ITS and trnL sequences. the pairwise distance between G. rosulacea and the orher taxa of Korean Goodyera was 3.49-6.68% for ITS region and 5.05-9.53% for trnL region, indicating that G. rosulacea could be treated as an independent species. Therefore, our molecular data support the taxonomic of G. rosulacea as a distinct species of Korea. In phylogenetic trees, G. rosulacea formed same clade with G. repens, which has similar morphological characters with G. rosulacea, and showed the lowest pairwise distance with G. repens among Korean Goodyera taxa. These molecular data sugguested that G. rosulacea and G. repens are closely related taxa.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.6
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• pp.772-784
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• 2012

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-C), and various schemes (denoted cross program-A-E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3819-3823
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• 2013

Background: Hepatocellular carcinoma (HCC) is a major cause of cancer mortality worldwide. The outcome of HCC depends mainly on its early diagnosis. To date, the performance of traditional biomarkers is unsatisfactory. Talins were firstly identified as cytoplasmic protein partners of integrins but Talin-1 appears to play a crucial role in cancer formation and progression. Our study was conducted to assess the diagnostic value of serum Talin-1 (TLN1) compared to the most feasible traditional biomarker alpha-fetoprotein (AFP) for the diagnosis of HCC. Methods: TLN1 was detected using enzyme linked immunosorbent assay (ELISA) in serum samples from 120 Egyptian subjects including 40 with HCC, 40 with liver cirrhosis (LC) and 40 healthy controls (HC). Results: ROC curve analysis was used to create a predictive model for TLN1 relative to AFP in HCC diagnosis. Serum levels of TLN1 in hepatocellular carcinoma patients were significantly higher compared to the other groups (p<0.0001). The diagnostic accuracy of TLN1 was higher than that of AFP regarding sensitivity, specificity, positive predictive value and negative predictive value in diagnosis of HCC. Conclusions: The present study showed for the first time that Talin-1 (TLN1) is a potential diagnostic marker for HCC, with a higher sensitivity and specificity compared to the traditional biomarker AFP.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.268-274
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• 2011

Anabaena (Cyanobacteria, Nostocales) are important for water quality controls, because they are often responsible for freshwater green tides; moreover, some species are reported to produce hepatotoxin. In this study, we sequenced RNA polymerase beta subunit (rpoB) gene of Anabaena, and evaluated their sequences for the potential use of a molecular taxonomic marker in this taxon. Anabaena rpoB showed low DNA similarity and high genetic divergences when compared those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.01). Parsimony analyses showed the rpoB gene evolves 4.8-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each Anabaena strain more clearly compared with a 16S rRNA tree. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the species discrimination of Anabaena.

• Biomedical Science Letters
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• v.17 no.3
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• pp.197-202
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• 2011

Mitosis count is one of the most helpful morphologic features for distinguishing pulmonary typical carcinoid (TC) from atypical carcinoid (AC). However, identifying areas of highest mitotic activity is tedious and time-consuming, and mitosis count may vary substantially among pathologists. Anti-phosphohistone H3 (PHH3) is an antibody that specifically detects histone H3 only when phosphorylated at serine 10 or serine 28, an event that is concurrent with mitotic chromatin condensation and not observed during apoptosis. In this study, immunohistochemical staining for PHH3 was performed to determine whether PHH3 was a reliable and objective mitosis-specific marker for pulmonary carcinoid tumors. Seventeen cases of surgically resected pulmonary carcinoid tumors (12 TCs and 5 ACs) were obtained and classified according to the 2004 World Health Organization classification. Mitotic counts determined by PHH3 correlated to ones determined by hematoxylin and eosin (H&E) staining; however, PHH3 mitotic counts (mean mitotic counts: 1 in TCs and 3.2 in ACs) were slightly higher than H&E mitotic counts (mean mitotic counts: 0.25 in TCs and 1.8 in ACs). The mitotic counts determined by experienced observer were more correlated to those determined by inexperienced observer with the PHH3-based method (R=0.968, P<0.001) rather than H&E staining (R=0.658, P<0.001). These results suggest that the PHH3 mitotic counting method was more sensitive and simple for detecting mitoses compared to traditional H&E staining. Therefore, PHH3 immunohistochemistry may contribute to more accurate and reproducible diagnosis of pulmonary carcinoid tumors and may be a valuable aid for administrating appropriate clinical treatment.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.418-427
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• 2020

Xanthomonas campestris pv. campestris (Xcc), the pathogen of black rot which is the most destructive disease of Brassica vegetables throughout the world. Here, we reported two novel sequence-characterized amplified region (SCAR) markers (i.e., XccR6-60 and XccR6-67) for the detection of Xcc race 6 via re-alignment of the complete genome sequences of Xcc races/strains/pathovars. The specificity of SCAR primer sets was verified by mean of PCR amplification using the genomic DNA template of Xcc races/strains/pathovars and two other plant infecting bacterial strains. The PCR result revealed that the XccR6-60 and XccR6-67 primer sets amplified 692-bp and 917-bp DNA fragments, respectively, specifically from race 6, while no visible amplification was detected in other samples. In addition, the SCAR primers were highly sensitive and can detect from a very low concentration of genomic DNA of Xcc race 6. However, the complete genome sequence of Xcc race 6 is not yet publicly available. Therefore, the cloning and sequencing of XccR6-60 and XccR6-67 fragments from race 6 provide more evidence of the specificity of these markers. These results indicated that the newly developed SCAR markers can successfully, effectively and rapidly detect Xcc race 6 from other Xcc races/strains/pathovars as well as other plant pathogenic bacteria. This is the first report for race-specific molecular markers for Xcc race 6.

• Asian Journal of Atmospheric Environment
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• v.11 no.3
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• pp.165-175
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• 2017

In Japan, the primary carbonaceous particles emitted from motor vehicles and waste incinerators have been reduced due to strict regulations against exhaust gas. However, the relative contribution of carbonaceous particles derived from plants and biomass has been increasing. Accordingly, compositional analysis of carbonaceous particles has become increasingly important to determine the sources and types of particles produced. To reveal the sources of the organic particles contained in particulate matter with diameters of ${\leq}2.5{\mu}m$ ($PM_{2.5}$) and the processes involved in their generation, we analyzed molecular marker compounds (2-methyltetrols, cis-pinonic acid, and levoglucosan) derived from the plants and biomass in the $PM_{2.5}$ collected during daytime- and nighttime-sampling periods in summer (July and August) and autumn (November) in Kazo, which is in the northern area of Saitama prefecture, Japan. We also measured $^{14}C$ carbonaceous concentrations in the same $PM_{2.5}$ samples. The concentrations of 2-methyltetrols were higher in the summer than in the autumn. Because the deciduous period overlaps with this decrease in the levels of 2-methyltetrols, we considered the emission source to broad-leaved trees. In contrast, the emission source of the cis-pinonic acid precursor was considered to be conifers, because its concentration remained almost constant throughout the year. The concentration of levoglucosan was considerably increased in the autumn due to frequent biomass open burning. The ratio of plant-derived carbon to total carbon, obtained by measuring of $^{14}C$, in summer $PM_{2.5}$ sample was higher in the nighttime, and could be influenced by anthropogenic sources during the daytime.

• Journal of Korean Society for Atmospheric Environment
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• v.31 no.2
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• pp.105-117
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• 2015

Sources related to road dust is one of the biggest sources, which is responsible for a large portion of emission. In particular, PM2.5 is a potential cause for respiratory diseases, thus it should be managed and a mitigation plan using results of statistical apportionment modeling such as chemical mass balance needs to be established. Recently, identifying sources of PM2.5 and analyzing the contribution of the road dust through a contribution assessment is required. Therefore, this study provides the chemical source profiles of PM2.5 using IC, GC/MS, OCEC, and XRF for both paved sidewalk and paved roadway collected at seven different sampling sites. As a result, for paved sidewalk, $NH{_4}^+$ (70%), $NO{_3}^-$ (12%), $PO{_4}^-$ (9%), and $SO{_4}^{2-}$ (9%) have been analyzed in PM2.5 mass. Major molecular marker such as Si has been indicated as $12.0{\pm}3.4%$ and $13.6{\pm}6.9%$ for paved sidewalk and roadway, respectively. PAHs such as Fluoranthene, Pyrene, Chrysene, and 1,3,5-Triphenylbenzene are suggested as molecular markers for road dust.

• Animal cells and systems
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• v.11 no.2
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• pp.165-168
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• 2007

The nucleotide sequences of a male-specific marker sex determining region Y (SRY) gene and a mitochondrial cytochrome B (CYTB) gene were characterized and analyzed to establish a molecular method for identification of species and sex of Korean roe deer (Capreolus pygargus tianschanicus). Similarity search result of SRY sequences showed very similar result to those reported in Moose (Alces alces) and Reindeer (Rangifer tarandus), both of which had 95.9% similarity in identity. CYTB genes were very similar to those reported in Siberian roe deer (C. pygargus pygargus) which had 98.6% similarity and not to European roe deer (C. capreolus), suggesting that the DNA samples tested were of Siberian roe deer lineage. Polymerase chain reaction (PCR)-based sex typing successfully discriminated between carcasses of male and female roe deer. Males had SRY band on agarose gels and females did not. The result of this molecular sex typing provided similar information with that obtained by genital organ observation. Therefore, this molecular method using male specific marker SRY and mitochondrial CYTB genes would be very useful for identification of the species and sex of the carcass remains of roe deer.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.5
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• pp.429-433
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• 2004

A single recessive gene, rxp, controls the bacterial leaf pustule (BLP) resistance in soybean and in our previous article, it has been mapped on linkage group (LG) D2 of molecular genetic map of soybean. A total of 130 recombinant inbred lines (RILs) from a cross between BLP-resistant SS2-2 and BLP-susceptible Jangyeobkong were used to identify molecular markers linked to rxp. Fifteen simple sequence repeat (SSR) markers on LG D2 were screened to construct a genetic map of rxp locus. Only four SSR markers, Satt135, Satt372, Satt448, and Satt486, showed parental polymorphisms. Using these markers, genetic scaffold map was constructed covering 26.2cM. Based on the single analysis of variance, Satt372 among these four SSR markers was the most significantly associated with the resistance to BLP. To develop new amplified fragment length polymorphism (AFLP) marker linked to the resistance gene, bulked segregant analysis (BSA) was employed. Resistance and susceptible bulks were made by pooling equal amount of genomic DNAs from ten of each in the segregating population. A total of 192 primer combinations were used to identify specific bands to the resistance, selecting three putative AFLP markers. These AFLP markers produced the fragment present in SS2-2 and the resistant bulk, and not in Jangyeobkong and the susceptible bulk. Linkage analysis revealed that McctEact97 $(P=0.0004,\;R^2=14.67\%)$ was more significant than Satt372, previously reported as the most closely linked marker.