• Journal of the Korea Academia-Industrial cooperation Society
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• v.20 no.9
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• pp.211-226
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• 2019

Pig CD45, the leukocyte common antigen, is encoded by the PTPRC gene and CD45 is a T cell-type specific tyrosine phosphatase with alternative splicing of its exons. The CD45 is a coordinated regulator of T cell antigen receptor (TCR) signal transduction achieved by dephosphorylating the phosphotyrosine of its substances, including $CD3{\zeta}$ chain of TCR, Lck, Fyn, and Zap-70 kinase. A dysregulation of CD45 is associated with a multitude of immune disease and has been a target for immuno-drug discovery. To characterize its key structural features with the effects of regulating TCR signaling, this study predicted the unknown structure of pig CD45RO (the smallest isoform) and the complex structure bound to the ITAM (REEpYDV) of $CD3{\zeta}$ chain via homology modeling and docking the peptide, based on the known human CD45 structures. These features were integrated into the structural plasticity of extracellular domains and functional KNRY and PTP signature motifs (the role of a narrow entrance into ITAM binding site) of the tyrosine phosphatase domains in a cytoplasmic region from pig CD45RO. This contributes to the selective recognition of phosphotyrosine from its substrates by adjusting the structural stability and binding affinity of the complex. The characterized features of pigCD45RO can be applied in virtual screening of the T-cell specific immunomodulator.

• Journal of Life Science
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• v.29 no.1
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• pp.84-89
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• 2019

Previous screening of novel antibacterial agents revealed that some bacterial isolates exhibited antibiotic activity against both gram-positive and gram-negative bacteria and that they showed antibacterial activity, even against methicillin-resistant Staphylococcus aureus (MRSA). Among these isolates, one bacterial strain, BCNU 1204, was identified as Pseudomonas aeruginosa using phenetic and phylogenetic analysis, based on 16S ribosomal RNA gene sequences. The maximum productivities of antimicrobial substances of BCNU 1204 were obtained after being cultured at $35^{\circ}C$ and pH 7.0 for 4 d in King's medium B (KMB). Dichloromethane (DCM) and ethylacetate (EA) extracts of P. aeruginosa BCNU 1204 exhibited strong antimicrobial activity, particularly against gram-positive bacteria. The EA extracts exhibited broad-spectrum activity against antibiotic resistant strains. Fraction 5-2, was obtained by recycling preparative liquid chromatography (LC) and preparative thin-layer chromatography (TLC) and was identified as phenazine-1-carboxylic acid belonging to phenazines using gas chromatography and mass spectrometry (GC/MS). Its minimum inhibitory concentration (MIC) values were $25{\mu}g/ml$, $50{\mu}g/ml$, ${\geq}25{\mu}g/ml$, and ${\geq}50{\mu}g/ml$ for MRSA CCARM 3089, 3090, 3091, and 3095 strains, respectively. P. aeruginosa BCNU 1204 may be a potential resource for the development of anti-MRSA antibiotics. Additional research is required to identify the active substance from P. aeruginosa BCNU 1204.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.64-64
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• 2019

Screening and identification of genetic resources based on their phytoconstituents and morphological characters potentially provide baseline data for researchers, breeders, and nutraceutical companies who wish to formulate a nutrient-dense diet and health beneficial supplement. Thus, we evaluated the amount of total phenolic content and major phenolic compounds; examined if phenolic compounds could be used as distinguishing factors for perilla genetic resources; and investigated the relation between some quantitative and qualitative morphological characters with the contents of phenolic compounds in 360 accessions obtained from National Agrobiodiversity Center gene bank, Jeonju, Korea. Total phenolic content (TPC) was estimated using Folin-Ciocalteu colorimetric assay. Individual phenolic compounds were determined using an Ultra-High Performance Liquid Chromatography system equipped with Photodiode Array detector. Considerable variations were observed in TPC (7.99 to 117.47 mg GAE/g DE), rosmarinic acid (RA) (ND to 19.19 mg/g DE), caffeic acid (CA) (ND to 0.72 mg/g DE), apigenin-7-O-diglucuronide (ADG) (ND to 1.24 mg luteolin equivalent (LUE)/g DE), scutellarein-7-O-glucuronide (SG) (ND to 4.32 mg LUE/g DE), and apigenin-7-O-glucuronide (AG) (ND to 1.60 mg LUE/g DE). RA was the most dominant phenolic compound in most accessions (95.3%) followed by SG. The adaxial leaf color was light green, green and dark green in 13.8%, 65.0%, and 21.1 % of the accessions, respectively. 78.8% of the accessions had light green color at the abaxial side with the remaining being described as green. Most of the accessions (96.9%) were cordate shape, the remaining being eclipse. Intensities of green pigment at abaxial and adaxial leaf surfaces were correlated with contents of individual phenolic compounds and TPC whereas leaf length and width had no correlation with TPC, CA and RA, and negatively correlated with ADG, AG, and SG. Leaf shape was not related with content of phenolic compounds, color of leaves, or the length or width of leaves. Accessions IT57426, IT157434, IT267710, and IT267712 which contained relatively high contents of TPC and major phenolic compounds (RA and SG) could be used for further research in breeding and bioassay test. Our study result showed the contents of total phenolics and individual phenolic compounds along with the morphological characters could be useful distinguishing factors for perilla genetic resources.

• 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.

• Journal of Food Hygiene and Safety
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• v.37 no.4
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• pp.277-284
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• 2022

To investigate the occurrence of fungi in dried ginseng products, we collected 24 white and 26 red ginseng samples from the retail market. Fungi were detected in 50% and 46% of white and red ginseng samples, respectively. The average level of fungal contamination was 0.5 and 0.2 log₁₀ CFU/g in white and red ginseng, respectively. In white ginseng, Penicillium polonicum, P. chrysogenum, and Rhizopus microsporus dominated with each having an occurrence of 18.2%. In red ginseng, Aspergillus spp. was dominant with an occurrence of 87.6%, with A. chevalieri having the highest occurrence (50%). PCR screening for mycotoxigenic potential showed that the 13 isolates of 4 species (P. polonicum, P. chrysogenum, P. melanoconidium, and A. chevalieri) tested were negative for the citrinin biosynthetic gene. These results show that the samples tested in this study had low risk of mycotoxin contamination. However, there is a possibility of dried ginseng products, such as white and red ginseng, being contaminated with fungi.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.23 no.1
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• pp.17-24
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• 2023

Purpose: In the past, detection of metabolic abnormalities in plasma amino acid (PAA) and urine organic acid (UOA) has been widely used to diagnose clinical mitochondrial diseases, such as mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS). In this study, the diagnostic values of PAA and UOA were reviewed, and their effectiveness in the diagnosis of MELAS was examined retrospectively. Methods: Blood and urine samples at the time of diagnosis were collected from all clinically diagnosed MELAS patients (n=31), and PAA and UOA tests were performed. All samples were collected in a fasting state to minimize artifacts in the results. The difference in the ratio of abnormal metabolites of PAA and UOA at initial diagnosis was statistically compared between the MELAS with genetic confirmation (n=19, m.3243A>G mutation) and MELAS without genetic confirmation (n=12) groups. The MELAS without genetic confirmation group was used as control. Results: Comparison of PAA and UOA between the two groups revealed that no abnormal metabolites showed characteristic differences between gene-confirmed MELAS patients with and those without genetic confirmation. Conclusions: Abnormal values of metabolites in PAA or UOA might be useful as a screening test but are not sufficient to diagnose MELAS patients.

• Korean Journal of Poultry Science
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• v.20 no.4
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• pp.177-188
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• 1993

This study was performed to find out the reasonable sexing methods In the chicken, obtain the basic information for the mechanisms related to chicken sexual differentiation and identify the genes which known to involved in chicken sex differentiation. The chromosome analysis of chicken embryonic fibroblast was a simple method to determine sex of chicken by means of Z and W chromosome identification. The bands of female chicken genomic DNA digested with Xho Ⅰ and Eco RI restriction endonuclease showed to be useful in direct sex determination and these repetitive sequences of Xho Ⅰ and Eco RI families were proposed to be very homologous in their sequences by colony hybridization analysis. Seven of 150 random primers were selected to amplify the W chromosome-specific band by using arbitrary primed PCR and three of them were useful to identify the sex of chicken. To identify the sex differentiation genes in the chicken, PCR for the amplification of ZFY and SRY sequences was performed. ZFY and SRY sequences were amplified successfully in the chicken genome, implying that chicken genome might have the sex-related conserved sequences similar to mammalian ones. The PCR products of ZFY amplification were the same in both sexes, suggesting that these sequences may be located on autosome or Z chromosome. The profile of PCR amplification for SRY sequences showed variation between sexes, but this result was not enough to specify whether the SRY gene in chicken is on the autosome or sex chromosome.

• Animal Bioscience
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• v.35 no.9
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.30-30
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• 2022

Philippines is the second world supplier of coconut by-products. As its first major genomics project, the Philippine Genome Center program for Agriculture (PGC-Agriculture) took the challenge to sequence and assemble the whole coconut genome. The project aims to provide advance genetics tools for our collaborating coconut researchers while taking the opportunity to initiate local capacity. Combination of different NGS platforms was explored and the Philippine 'Catigan Green Dwarf' (CATD) variety was selected with the breeders to be the crop's reference genome. A high quality genome assembly of CATD was generated and used to characterize important genes of coconut towards the development of resilient and outstanding varieties especially for added high-value traits. The talk will present the significant results of the project as published in various papers including the first report of whole genome sequence of a dwarf coconut variety. Updates will include the challenges hurdled and specific applications such as gene mining for host insect resistance and screening for least damaged coconuts (thus potentially insect resistant varieties). Genome-wide DNA markers as published and genes related to coconut oil qualitative/quantitative traits will also be presented, including initial molecular/biochemical studies that support nutritional and medicinal claims. A web-based genome database is currently built for ease access and wider utility of these genomics tools. Indeed, a major milestone accomplished by the coconut genomics research team, which was facilitated with the all-out government support and strong collaboration among multidisciplinary experts and partnership with advance research institutes.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.24 no.1
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• pp.17-25
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• 2024

Fabry disease (FD) is an X-linked lysosomal storage disorder. It is caused by mutations in the α-galactosidase A gene, which results in deficient or absent activity of α-galactosidase A (α-Gal A). This leads to a progressive accumulation of globotriaosylceramide (Gb3) in various tissues. Manifestations of Fabry disease include serious and progressive impairment of renal and cardiac function. In addition, patients experience pain, gastrointestinal disturbance, transient ischaemic attacks, and strokes. Additional effects on the skin, eyes, ears, lungs, and bones are often seen. Reduced life expectancy and deadly consequences are being caused by cardiac involvement. Chaperone therapy or enzyme replacement therapy (ERT) are two disease-specific treatments for FD. Thus, early detection of FD is critical for decreasing morbidity and mortality. Globotriaosysphingosine (lyso-Gb3) for identifying atypical FD variants and highly sensitive troponin T (hsTNT) for detecting cardiac involvement are both significant diagnostic indicators. This review aimed to offer a basic resource for the early diagnosis and update on the diagnosis of having FD. We will also provide a general diagnostic algorithm and information on ERT and its accompanying treatments.