• Genomics & Informatics
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• v.21 no.2
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• pp.22.1-22.15
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• 2023

Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OS-kirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.

• Korean Journal of Biological Psychiatry
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• v.22 no.4
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• pp.173-178
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• 2015

Objectives Previous genome-wide association studies have indicated the association between ankyrin 3 (ANK3) and the vulnerability of schizophrenia. We investigated the association between single nucleotide polymorphisms (SNPs) covering the whole ANK3 locus and schizophrenia in the Korean population. Methods The study subjects were 582 patients with schizophrenia and 502 healthy controls. Thirty-eight tag SNPs on ANK3 and five additional SNPs showing significant association with schizophrenia in previous studies were genotyped. Results Three (rs10994181, rs16914791, rs1938526) of 43 SNPs showed a nominally significant association (p < 0.05) with at least one genotype model. But none of these associations remained significant after adjusting for multiple testing errors with Bonferroni's correction. Conclusions We could not identify a significant association between ANK3 and schizophrenia in the Korean population. However, three SNPs showing an association signal with nominal significance need to be investigated in future studies with higher statistical power and more specific phenotype crossing the current diagnostic categories.

• Archives of Pharmacal Research
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• v.26 no.12
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• pp.1009-1013
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• 2003

A new pterocarpan, (-)-maackiain 3-sulfate (1) was isolated from the methanol extract of roots of Sophora subprostarata together with (-)-maackiain(2), trifolirhizin (3), lupeol (4), ononin (5),7,4'-dihydroxyflavone (5), and (+)-syringaresinol (7). The structure of 1 was determined by analyses of 2D NMR and HRFABMS. Compounds 5-7 were isolated from this plant for the first time.

• Journal of Life Science
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• v.26 no.3
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• pp.331-337
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• 2016

Although fibroblast growth factor 23 (FGF23) is exclusively produced in osteoblasts and osteocytes, its main target is the kidney, where it decreases phosphate reabsorption by suppressing Na-phosphate cotransporters. Independently of its action on phosphate homeostasis, FGF23 also inhibits bone formation in vivo. In a calvarial osteoblastic cell model, FGF23 was shown to negatively affect extracellular matrix mineralization. This study investigated whether FGF23 had similar effects on osteoblast maturation, including differentiation and mineralization of bone marrow-derived mesenchymal stem cells (MSCs). D1 MSCs were cultured in an osteogenic medium containing β-glycerophosphate, ascorbic acid, and dexamethazone. Osteoblastic differentiation was evaluated by alkaline phosphatase (Alp) staining, and matrix mineralization was evaluated by alizarin red staining and calcium deposition. The expression of differentiation-stimulating genes Runx2, Alp, and osteocalcin and mineralization-inhibiting genes Enpp1 and Ank was analyzed using semiquantitative RT-PCR. Supraphysiological doses of FGF23 did not stimulate proliferation or osteoblastic differentiation of MSCs. Matrix mineralization 1, 2, and 3 weeks after the FGF23 treatment did not vary between control and FGF23 groups, although time-dependent enhancement of mineralization was obvious. Calcium deposition was also unchanged after the FGF23 treatment. mRNA expression levels of differentiation- and mineralization-related genes were also similar between the groups. Despite these negative findings, FGF23 signaling through FGF receptors seemed to function normally, with phosphorylation of the Erk protein more evident in the FGF23 group than in controls. These findings suggest that unlike calvarial osteoblasts, FGF23 is not likely to affect osteoblastic differentiation and mineralization of MSCs.

• Journal of Biomedical Engineering Research
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• v.17 no.3
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• pp.379-386
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• 1996

This paper describes an approach for classifying myoelectric patterns using a multilayer perceptrons (MLP's) and hidden Markov models (HMM's) hybrid classifier. The dynamic aspects of EMG are important for tasks such as continuous prosthetic control or vari- ous time length EMG signal recognition, which have not been successfully mastered by the most neural approaches. It is known that the hidden Markov model (HMM) is suitable for modeling temporal patterns. In contrasts the multilayer feedforward networks are suitable for static patterns. Ank a lot of investigators have shown that the HMM's to be an excellent tool for handling the dynamical problems. Considering these facts, we suggest the combination of MLP and HMM algorithms that might lead to further improved EMG recognition systems.

• International Journal of Industrial Entomology and Biomaterials
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• v.37 no.2
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• pp.49-54
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• 2018

To artificially enhance antimicrobial peptide expression in Bombyx mori, we constructed genetically engineered silkworms overexpressing Rel family transcription factor. The truncated BmRelish1 (BmRelish1t) gene contained a Rel homolog domain (RHD), nuclear localization signal (NLS), acidic and hydrophobic amino acid (AHAA)-rich region, and death domain (DD), but no ankyrin-repeat (ANK) domain. The BmRelish1t gene was controlled by B. mori cytoplasmic actin 3 promoter in the PiggyBac transposon vector. Chromosome analysis of G1 generations of a transgenic silkworm with EGFP expression confirmed stable insertion of BmRelish1t. BmRelish1t gene overexpression in transgenic silkworms resulted in higher mRNA expression levels of B. mori antimicrobial peptides such as lebocin(~20.5-fold), moricin(~8.7-fold), and nuecin(~17.4-fold) than those in normal silkworms.

• Journal of Animal Science and Technology
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• v.63 no.1
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• pp.25-35
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• 2021

The purpose of this study is to estimate the single nucleotide polymorphism (SNP) effect for pH values affecting Berkshire meat quality. A total of 39,603 SNPs from 1,978 heads after quality control and 882 pH values were used estimate SNP effect by single step genomic best linear unbiased prediction (ssGBLUP) method. The average physical distance between adjacent SNP pairs was 61.7kbp and the number and proportion of SNPs whose minor allele frequency was below 10% were 9,573 and 24.2%, respectively. The average of observed heterozygosity and polymorphic information content was 0.32 ± 0.16 and 0.26 ± 0.11, respectively and the estimate for average linkage disequilibrium was 0.40. The heritability of pH45m and pH24h were 0.10 and 0.15 respectively. SNPs with an absolute value more than 4 standard deviations from the mean were selected as threshold markers, among the selected SNPs, protein-coding genes of pH45m and pH24h were detected in 6 and 4 SNPs, respectively. The distribution of coding genes were detected at pH45m and were detected at pH24h.

• Journal of the Korean earth science society
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• v.34 no.4
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• pp.313-328
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• 2013

Jurassic granitoids in the northeastern part of the Yeongnam Massif are possibly the result of intensive magmatic activities that occurred in response to subduction of the proto-Pacific plate beneath the northeast portion of the Eurasian plate. Geochemical studies on the granitic rocks are carried out in order to constrain the petrogenesis of the granitic magma and to establish the paleotectonic environment of the area. Whole rock chemical data of the Uljin granitoids in the northeastern part of the Yeongnam Massif indicate that all of the rocks have the characteristics of calcalkaline series in subalkaline field. The overall major element trends show systematic variations in each granitic body, but the source materials of each granitoids seem to have different chemical composition. The Uljin granitoids are different from other granitic rocks, which distributed vicinity of the study area, in the contents of $Al_2O_3$ and trace elements such as Cr, Co, Ni, Sr, Y and Nb. The Uljin granitoids have geochemical features similar to slab-derived adakites such as high $Al_2O_3$, Sr contents and high Sr/Y, La/Yb ratios, but they have low Y and Yb contents. The major ($SiO_2$, $Al_2O_3$, MgO) and trace element (Sr, Y, La, Yb) contents of the Uljin granitoids fall well within the adakitic field. The Uljin granitoids have similar geochemical characteristics, paleotectonic environments and intrusion ages to those of the Yatsuo plutonic rocks of Hida belt located on northwestern part of Japan. Chondrite normalized REE patterns show generally enriched LREEs ($(La/Yb)_{CN}=10.6-103.4$) and are slight negative to flat Eu anomalies. On the ANK vs. A/CNK and tectonic discrimination diagrams, parental magma type of the granites corresponds to I-type and volcanic arc granite (VAG). Interpretations of the chemical characteristics of the granitic rocks favor their emplacement in a compressional tectonic regime at the continental margin during the subduction of Izanagi plate in Jurassic period.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.3
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• pp.303-309
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• 2014

The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.

• Journal of the Korean earth science society
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• v.30 no.4
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• pp.427-443
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• 2009

Cretaceous intrusive and extrusive rocks in the southwestern part of the Yeongnam Massif are possibly the result of intensive magmatism which occurred in response to subduction of the Pacific plate beneath the northeast portion of the Eurasian plate. Geochemical and petrological study on the granitic rocks were carried out in order to constrain the petrogenesis of the granitic magma and to establish the paleotectonic environment of the area. Whole rock chemical data of the granitic rocks from the study area indicate that all the rocks have characteristics of calc-alkaline series in the subalkaline field. The overall geochemical features show systematic variations in each granitic body, but the source materials of each granitic body are thought to have been different in their chemical composition. The granodiorites distributed around Donggyori in the Bognae area (DGd) are different from other granitic rocks within the study area in the contents and differentiation trends of $Al_2O_3$ and MgO as well as in the contents of the trace elements such as Ba, Sr, Pb, Ni, Cr and Y DGd have geochemical features similar to slab-derived adakites such as high $Al_2O_3$, Sr contents and high Sr/Y, La/Yb ratios, but low Y and Yb contents. The major and trace element contents of the DGd fall well within the adakitic field, whereas other Cretaceous granites in the study area are plotted in the island arc ADR area in Sr/Y vs. Y diagram. On the ANK vs. A/CNK and tectonic discrimination diagrams, parental magma type of the granites corresponds to I-type and volcanic arc granite (VAG). Interpretations of the chemical characteristics of the granitic rocks favor their emplacement in a compressional tectonic regime at continental margin during the subduction of Pacific plate. The geochemical and tectonic features reveal that adakite-like signatures of the DGd were generated by the interaction of mantle peridotite and subducted slab-derived adakitic melts (caused by the thermal effect of ridge subduction), and which slightly modified by crustal contamination during emplacement.