• BMB Reports
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• v.50 no.1
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• pp.12-19
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• 2017

Traditionally, biologists have devoted their careers to studying individual biological entities of their own interest, partly due to lack of available data regarding that entity. Large, high-throughput data, too complex for conventional processing methods (i.e., "big data"), has accumulated in cancer biology, which is freely available in public data repositories. Such challenges urge biologists to inspect their biological entities of interest using novel approaches, firstly including repository data retrieval. Essentially, these revolutionary changes demand new interpretations of huge datasets at a systems-level, by so called "systems biology". One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype changes. In this review, we introduce the repositories of cancer big data and cutting-edge systems biology tools for network generation, and improved identification of therapeutic targets.

• Molecules and Cells
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• v.38 no.5
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• pp.390-395
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• 2015

Degradation of chlorophyll (Chl) by Chl catabolic enzymes (CCEs) causes the loss of green color that typically occurs during senescence of leaves. In addition to CCEs, STAYGREEN1 (SGR1) functions as a key regulator of Chl degradation. Although sgr1 mutants in many plant species exhibit a staygreen phenotype, the biochemical function of the SGR1 protein remains elusive. Many recent studies have examined the physiological and molecular roles of SGR1 and its homologs (SGR2 and SGR-LIKE) in Chl metabolism, finding that these proteins have different roles in different species. In this review, we summarize the recent studies on SGR and discuss the most likely functions of SGR homologs.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.6 no.2
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• pp.116-130
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• 2020

The aging society is globally one of biggest issue because it is related with various degenerative brain disease such as dementia, Parkinson's disease, Alzheimer's disease, multiple sclerosis, and cerebrovascular disease. These diseases are characterized by misfolded-protein aggregation; another pathological trait is "neuroinflammation". In physiological state, the resting microglia cells are activated and it removes abnormal synapses and cell membrane debris to maintain the homeostasis. In pathological state, however, microglia undergo morphological change form 'resting' to 'activated amoeboid phenotype' and the microglia cells are accumulated by neuronal damage, the inflammatory reactions induced nerve metamorphosis with a variety of neurotoxic factors including cytokines, chemokines, and reactive oxygen species. Thus, the activated microglia cell with various receptors (TSPO, COX, CR, P2XR, etc.) was perceived as important biomarkers for imaging the inflammatory progression. In this review, we would like to introduce the current status of the development of radiotracers that can image activated microglia.

• BMB Reports
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• v.31 no.3
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• pp.269-273
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• 1998

The objective of this study was to evaluate the reversal of multi drug resistance of human cell lines by specific inhibitors of ${\alpha}-glycosidase$ and mannosidases that had been reported to be involved in N-linked oligosaccharide processing of glycoproteins. N-methyldeoxynojirimycin, I-deoxynojirimycin, and castanospermine, which were known to be potent inhibitors of both ${\alpha}-glycosidase$ I and II, showed no activity against the multidrug resistant phenotype of the cell lines of SNU1DOX, KB-V1, and MCF-7/ADR. In contrast, I-deoxymannojirimycin, an inhibitor of mannosidase I, resulted in a slight reversal for the vinblastine resistance of the KB-V1 cell line, but did not show any activity toward the other cell lines. Parallel experiments with tunicamycin, an inhibitor of N-linked glycosylation, also resulted in no significant changes in multidrug resistant (MDR) phenotype of the cell lines tested in this work. These observations suggest that the unglycosylation of P-glycoprotein associated with the inhibitor treatments might not be correlated with the reversal of multidrug resistance of the cell lines tested in this study.

• BMB Reports
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• v.46 no.11
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• pp.550-554
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• 2013

The platelet-derived growth factor (PDGF) signaling pathway is essential for inducing a dedifferentiated state of vascular smooth muscle cells (VSMCs). Activation of PDGF inhibits smooth muscle cell (SMC)-specific gene expression and increases the rate of proliferation and migration, leading to dedifferentiation of VSMCs. Recently, microRNAs have been shown to play a critical role in the modulation of the VSMC phenotype in response to extracellular signals. However, little is known about microRNAs regulated by PDGF in VSMCs. Herein, we identify microRNA- 15b (miR-15b) as a mediator of VSMC phenotype regulation upon PDGF signaling. We demonstrate that miR-15b is induced by PDGF in pulmonary artery smooth muscle cells and is critical for PDGF-mediated repression of SMC-specific genes. In addition, we show that miR-15b promotes cell proliferation. These results indicate that PDGF signaling regulates SMC-specific gene expression and cell proliferation by modulating the expression of miR-15b to induce a dedifferentiated state in the VSMCs.

• BMB Reports
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• v.45 no.12
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• pp.686-692
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• 2012

Phenotypic analysis of gene-specific knockout (KO) mice has revolutionized our understanding of in vivo gene functions. As the use of mouse embryonic stem (ES) cells is inevitable for conventional gene targeting, the generation of knockout mice remains a very time-consuming and expensive process. To accelerate the large-scale production and phenotype analyses of KO mice, international efforts have organized global consortia such as the International Knockout Mouse Consortium (IKMC) and International Mouse Phenotype Consortium (IMPC), and they are persistently expanding the KO mouse catalogue that is publicly available for the researches studying specific genes of interests in vivo. However, new technologies, adopting zinc-finger nucleases (ZFNs) or Transcription Activator-Like Effector (TALE) Nucleases (TALENs) to edit the mouse genome, are now emerging as valuable and effective shortcuts alternative for the conventional gene targeting using ES cells. Here, we introduce the recent achievement of IKMC, and evaluate the significance of ZFN/TALEN technology in mouse genetics.

• Molecules and Cells
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• v.41 no.2
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• pp.134-139
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• 2018

Here, we report isolation of multiple long non-coding RNAs (lncRNAs) expressed tissue-specifically during murine embryogenesis. One of these, subsequently came to be known as Redrum, is expressed in erythropoietic cells in fetal liver and adult bone marrow. Redrum transcription is also detected during pregnancy in the spleen where extramedullary hematopoiesis takes place. In order to examine the function of Redrum in vivo, we generated a gene-targeted murine model and analyzed its embryonic and adult erythropoiesis. The homozygous mutant embryo showed no apparent deficiency or defect in erythropoiesis. Adult erythropoiesis in bone marrow and in the spleen during pregnancy likewise showed no detectable phenotype as red blood cells matured in normal fashion. The phenotype is in contrast to the reported function of Redrum in vitro, and our observation implies that Redrum plays in vivo an accessory or supplementary role whose loss is compatible with normal erythropoiesis.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.23-27
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• 2010

The objective of this study was to map the gene for reduced embryo size in rice using DNA markers. The reduced embryo size mutant was induced from N-methyl-N-nitrosourea (MNU) treated Taichung 65. Genetic analysis revealed that the phenotype of the reduced embryo was controlled by a single recessive gene, designated as re-1. For mapping the gene controlling embryo size, an $F_2$ population was developed from a cross between the Korean Tongil-type, Milyang 23 (Oryza sativa ssp. indica) and the mutant. The ratio of $F_2$ seeds nearly fitted to 3:1 ratio, indicating that this phenotype was controlled by a single recessive gene. Bulked sergeant analysis was performed with SSR markers. The gene for the reduced embryo size was detected on chromosome 1. The gene was further mapped between two SSR markers, RM315 and RM265 on chromosome 1 (approximately 1.5 Mb interval). The linked markers will facilitate selection of this grain character in a breeding program and provide the foundation for positional cloning of this gene.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.14-14
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• 2022

Greenhouse gas emissions are one of the critical factors that drive change in rice cropping systems. Within this changing system, less water irrigation and chemical fertilizer are seriously considered, as well combining precision farming technologies with irrigation control. Water and phosphorus (P) fertilizer are two of the most critical inputs in rice cultivation. Due to the lack of water availability in the system, P fertilizer is not available, especially in acidic soil conditions. Moreover, the various types of abiotic stresses, such as drought, high temperature, salinity, submergence, and limited fertilizer result in significant yield loss in the system. Even in the late stage of growth, the waves caused by diseases and insects make the field more unfruitful. Therefore, agronomists and breeders need to identify the secondary phenotypes to estimate the yield loss of when stress appears. The prediction will be clearer if we have a set of markers tagging the causal variation and the associated precise phenotype indices. Although there have been various studies for abiotic stress tolerance, we still lack functional molecular markers and phenotype indices. This is due to the underlying challenges caused by environmental factors in highly unpredictable regional and yearly environmental conditions in the field system. Pupl (phosphorus uptake 1) is still known as the first QTL associated with phosphorus uptake and have been validated in different field crops. Interestingly, some pyramiding lines of Pupl and other QTLs for other stress tolerances showed preferable phenotypes in the yield. Precise physiological studies with the help of genomics are on-going and some results will be discussed.

• Journal of Genetic Medicine
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• v.4 no.2
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• pp.133-141
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• 2007

Purpose : Cri-du-Chat syndrome (CdCs) is a rare but clinically recongnizable condition with an estimated incidence of 1:50,000 live births. The clinical characteristics of the syndrome include severe psychomotor and mental retardation, microcephaly, hypertelorism, hypotonia, and slow growth. Also the size of the chromosome 5p deletion ranges were known from the region 5p13 to the terminal region. In this study, we report the spectrum of 5p deletion in Korean 20 pts. with CdCs and genotype-phenotype associations in CdCs. Methods : In order to delineate genotype-phenotype correlation, molecular cytogenetic studies including GTG banding and clinical characterization were performed on Korean 20 pts with CdCs including parents. CGH array and Fluorescence in situ hybridization (FISH) analysis were used to confirm a terminal deletion karyotype and map more precisely the location of the deletion breakpoint. Results : Molecular analysis of the spectrum of 5p deletion revealed 9 pts (45%) with a del (5)(p14), 7 pts. (35%) a del (5)(p13), 3 pts. (15%) a del (5)(p15.1) and 1 pt. (5%) a del (5)(p15.2) in 20 pts with CdCs. 4(20%)pts were identified to have additional chromosome abnormalites of deficiency and duplication involving chromosomes of 6, 8, 18, & 22. Parental study identified 3 familial case (2 paternal and 1 maternal origin) showing parents being a balanced translocation carrier. And the comparison study of the deletion break points among these 20 pts. with their phenotype has showed the varying clinical pheno-types in the CdCs critical region. Conclusion : The characterization of 5p deletion including parental study may help to delineate the genotypephenotype correlation in CdCs. Also these molecular cytogenetic analyses will be able to offer better information for accurate genetic diagnosis in CdCs and further make possible useful genetic counseling in pts. and family.