• Journal of The Korean Society of Inherited Metabolic disease
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• v.3 no.1
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• pp.86-93
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• 2003

Background : The SCL began screening of newborns and high risk group blood spots with tandem mass spectrometry (MS/MS) in April 2001. Our goal was to determine approximate prevalence of metabolic disorders, optimization of decision criteria for estimation of preventive effect with early diagnosis. This report describes the ongoing effort to identify more than 30 metabolic disorders by MS/MS in South Korea. Methods : Blood spot was collected from day 2 to 30 (mostly from day 2 to 10) after birth for newborn. Blood spot of high risk group was from the pediatric patients in NICU, developmental delay, mental retardation, strong family history of metabolic disorders. One punch (3.2 mm ID) of dried blood spots was extracted with $150{\mu}L$ of methanol containing isotopically labelled amino acids (AA) and acylcarnitines (AC) internal standards. Butanolic HCl was added and incubated at $65^{\circ}C$ for 15 min. The butylated extract was introduced into the inlet of MS/MS. Neutral loss of m/z 102 and parent ion mode of m/z 85 were set for the analyses of AA and AC, respectively. Diagnosis was confirmed by repeating acylcarnitine profile, urine organic acid and plasma amino acid analysis, direct enzyme assay, or molecular testing. Results : Approximately 31,000 neonates and children were screened and the estimated prevalence (newborn/high risk group), sensitivity, specificity and recall rate amounted to 1:2384/1:2066, 96.55%, 99.98%, and 0.73%, respectively. Confirmed 28 (0.09%) multiple metabolic disorders (newborn/high risk) were as follows; 13 amino acid disorders [classical PKU (3/4), BH4 deficient-hyperphenylalaninemia (0/1), Citrullinemia (1/0), Homocystinuria (0/2), Hypermethioninemia (0/1), Tyrosinemia (1/0)], 8 organic acidurias [Propionic aciduria (2/1), Methylmalonic aciduria (0/1), Isovaleric aciduria (1/1), 3-methylcrotonylglycineuria (1/0), Glutaric aciduria type1 (1/0)], 7 fatty acid oxidation disorders [LCHAD def. (2/2), Mitochondrial TFP def. (0/1), VLCAD def. (1/0), LC3KT def. (0/1). Conclnsion : The relatively normal development of 10 patients with metabolic disorders among newborns (except for the expired) demonstrates the usefulness of newborn screening by MS/MS for early diagnosis and medical intervention. However, close coordination between the MS/MS screening laboratory and the metabolic clinic/biochmical geneticists is needed to determine proper decision of screening parameters, confirmation diagnosis, follow-up scheme and additional tests.

• Korean Journal of Food Science and Technology
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• v.40 no.2
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• pp.129-134
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• 2008

Five antioxidative active substances were isolated from the EtOAc layer (20 g/56.2 g) of Korean black raspberry (Rubus coreanus Miquel) wine (11 L, black raspberry 15.7 kg fresh wt. eq.) by various column chromatography and high performance liquid chromatography (HPLC). Proton nuclear magnetic resonance ($^1H$-NMR) spectroscopy and gas chromatography Electro Ionization-Mass Spectrometry (GC-EI-MS) identified these as 4-hydroxybenzoic acid (1, 0.1 mg), 3,4-dihydroxybenzoic acid (2, 0.3 mg), 4-(2-hydroxyethyl)-phenol (3, 0.6 mg; tyrosol), pyrocatechol (4, 0.3 mg), 3,4,5-trihydroxybenzoic acid ethyl ester (5, 0.6 mg; ethyl gallate). The presence of 1 and 2 in Korean black raspberry has previously been reported. However, the presence of 3-5 in Korean black raspberry, and the identification of 1-5 from the Korean black raspberry wine have never before been reported.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.737-750
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• 2015

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.11-18
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• 2019

Gaeumannomyces graminis var. tritici is a soil borne pathogenic fungus associated with wheat roots. The accurate quantification of gene expression during the process of infection might be helpful to understand the pathogenic molecular mechanism. However, this method requires suitable reference genes for transcript normalization. In this study, nine candidate reference genes were chosen, and the specificity of the primers were investigated by melting curves of PCR products. The expression stability of these nine candidates was determined with three programs-geNorm, Norm Finder, and Best Keeper. $TUB{\beta}$ was identified as the most stable reference gene. Furthermore, the exopolygalacturonase gene (ExoPG) was selected to verify the reliability of $TUB{\beta}$ expression. The expression profile of ExoPG assessed using $TUB{\beta}$ agreed with the results of digital gene expression analysis by RNA-Seq. This study is the first systematic exploration of the optimal reference genes in the infection process of Gaeumannomyces graminis var. tritici.

• Animal Bioscience
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• v.36 no.1
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• pp.144-155
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• 2023

Objective: Adipocyte differentiation is regulated by a variety of functional genes and noncoding RNAs. However, the role of miRNAs in lipid deposition of goat white adipose tissue is still unclear. Therefore, this study revealed the miRNA expression profile in goat subcutaneous adipocytes by sRNA-seq. Methods: The miRNA expressed in goat subcutaneous preadipocytes and the mature adipocytes were sequenced by sRNA-seq. The differentially expressed miRNAs (DEm) were screened and gene ontology (GO) and Kyoto encyclopedia for genes and genomes (KEGG) analyses were performed. Gain-of-function and loss-of-function combined with oil red O staining, Bodipy staining, and quantitative reverse-transcription polymerase chain reaction (qPCR) were utilized to determine the effect of miR-133a-3p on adipocyte differentiation. Results: A total of 218 DEm were screened out. The target genes of these DEm were significantly enriched in GO items such as biological regulation and in KEGG terms such as FAK signaling pathway and MAPK signaling pathway. qPCR verified that the expression trend of miRNA was consistent with miRNA-seq. The gain-of-function or loss-of-function of miR-133a-3p showed that it promoted or inhibited the accumulation of lipid droplets, and CCAAT enhancer binding protein α (C/EBPα) and C/EBPβ were extremely significantly up-regulated or down-regulated respectively (p<0.01), the loss-of-function also led to a significant down-regulation of peroxisome proliferator activated receptor gamma (PPARγ) (p<0.01). Conclusion: This study successfully identified miRNAs expression patterns in goat subcutaneous adipocytes, and functional identification indicates that miR-133a-3p is a positive regulator of the differentiation process of goat subcutaneous adipocytes. Our results lay the foundation for the molecular mechanism of lipid deposition in meat-source goats from the perspective of miRNA.

• Animal Bioscience
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• v.36 no.4
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• pp.570-583
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• 2023

Objective: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R² = 0.92-0.95, p<0.01). Conclusion: This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.

• Animal Bioscience
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• v.36 no.10
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• pp.1517-1529
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• 2023

Objective: The objective of this study was to investigate the phylogenetic and expression analysis of the angiopoietin-like (ANGPTL) gene family and their role in lipid metabolism in pigs. Methods: In this study, the amino acid sequence analysis, phylogenetic analysis, and chromosome adjacent gene analysis were performed to identify the ANGPTL gene family in pigs. According to the body weight data from 60 Jinhua pigs, different tissues of 6 pigs with average body weight were used to determine the expression profile of ANGPTL1-8. The ileum, subcutaneous fat, and liver of 8 pigs with distinct fatness were selected to analyze the gene expression of ANGPTL3, ANGPTL4, and ANGPTL8. Results: The sequence length of ANGPTLs in pigs was between 1,186 and 1,991 bp, and the pig ANGPTL family members shared common features with human homologous genes, including the high similarity of the amino acid sequence and chromosome flanking genes. Amino acid sequence analysis showed that ANGPTL1-7 had a highly conserved domain except for ANGPTL8. Phylogenetic analysis showed that each ANGPTL homologous gene shared a common origin. Quantitative reverse-transcription polymerase chain reaction analysis showed that ANGPTL family members had different expression patterns in different tissues. ANGPTL3 and ANGPTL8 were mainly expressed in the liver, while ANGPTL4 was expressed in many other tissues, such as the intestine and subcutaneous fat. The expression levels of ANGPTL3 in the liver and ANGPTL4 in the liver, intestine and subcutaneous fat of Jinhua pigs with low propensity for adipogenesis were significantly higher than those of high propensity for adipogenesis. Conclusion: These results increase our knowledge about the biological role of the ANGPTL family in this important economic species, it will also help to better understand the role of ANGPTL3, ANGPTL4, and ANGPTL8 in lipid metabolism of pigs, and provide innovative ideas for developing strategies to improve meat quality of pigs.

• BMB Reports
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• v.56 no.10
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• pp.569-574
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• 2023

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments.

• Journal of the Korean Society of Food Science and Nutrition
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• v.39 no.1
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• pp.54-63
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• 2010

Baicalin, a flavonoid, was shown to have diverse effects such as anti-inflammatory, anti-cancer, anti-viral, anti-bacterial and others. Recently, we found that the baicalin inhibits adipogenesis through the modulations of anti-adipogenic and pro-adipogenic factors of the adipogenesis pathway. In the present study, we further characterized the molecular mechanism of the anti-adipogenic effect of baicalin using microarray technology. Microarray analyses were conducted to analyze the gene expression profiles during the differentiation time course (0 day, 2 day, 4 day and 7 day) in 3T3-L1 cells with or without baicalin treatment. We identified a total of 3972 genes of which expressions were changed more than 2 fold. These 3972 genes were further analyzed using hierarchical clustering analysis, resulting in 20 clusters. Four clusters among 20 showed clearly up-regulated expression patterns (cluster 8 and cluster 10) or clearly down-regulated expression patterns (cluster 12 and cluster 14) by baicalin treatment for over-all differentiation period. The cluster 8 and cluster 10 included many genes which enhance cell proliferation or inhibit adipogenesis. On the other hand, the cluster 12 and cluster 14 included many genes which are related with proliferation inhibition, cell cycle arrest, cell growth suppression or adipogenesis induction. In conclusion, these data provide detailed information on the molecular mechanism of baicalin-induced inhibition of adipogenesis.

• Horticultural Science & Technology
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• v.30 no.4
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• pp.345-356
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• 2012

We investigated the changes of fruit quality parameters, polysaccharide contents and cell wall components during maturation and ripening of two Korean pear cultivar 'Hanareum' and 'Manpungbae' compared with 'Niitaka' pear (Pyrus pyrifolia Nakai) which showed different physiological maturity based on days after full bloom (DAFB). Flesh firmness decreased continuously with fruit development and maturation, reaching a final level of 29.4, 33.5, and 27.4N at maturity in 'Hanareum' (127 DAFB), 'Manpungbae' (163 DAFB), and 'Niitaka' (170 DAFB), respectively. The level of ethylene production was very low in early season 'Hanareum' pear which showed at most 0.39 ${\mu}L{\cdot}L^{-1}$ at maturity and no ethylene was detected in 'Manpungbae' and 'Niitaka' at maturity. Fructose was the most abundant soluble sugar during fruit maturation in the pears tested and an increase of sucrose was observed during fruit ripening in the Asian pears commonly. Ethanol insoluble solids (EIS) content decreased gradually with different levels among the pear cultivars as fruit ripens consisted of 10.79, 12.72, and 12.75 $mg{\cdot}g^{-1}$ FW. The amount of total soluble polyuronides was higher in early season cultivars 'Hanareum' than those of mid-season cultivar 'Manpungbae' and 'Niitaka'. In 'Niitaka' which harvested most late season, the level of 4% KOH soluble hemicelluloses was lower than 'Hanareum' and 'Manpungbae' and maintained constantly during fruit ripening period. Cellulosic residues were determined high level in 'Niitaka' which showed 612.33 ${\mu}g{\cdot}mg^{-1}$ EIS at maturity when compared with 'Hanareum' (408.0 ${\mu}g{\cdot}mg^{-1}$ EIS) and 'Manpungbae' (538.67 ${\mu}g{\cdot}mg^{-1}$ EIS). The main constituents of cell wall neutral sugars which consisted of arabinose, xylose, galactose, and glucose were decreased gradually with onset of fruit ripening regardless of cultivar. Arabinose which was predominant in 'Hanareum' pear decreased at the last stage of ripening, but the changes of cell wall neutral sugar during ripening were not occurred in 'Niitaka' pear. The change of molecular mass distribution in water soluble pectin observed dominantly at the early stage of fruit development. Depolymerization of 4% KOH-soluble hemicelluloses and degradation of xyloglucan showed in early-season cultivar 'Hanareum' during fruit maturation, and degradation of those fractions were detected only at the early stage fruit development in mid-season cultivar 'Manpungbae' and 'Niitaka'. The molecular mass profile of CDTA soluble pectin, $Na_2CO_3$-SP and 24% KOH soluble hemicelluloses showed no significant change during fruit maturation regardless of cultivar.