• Genomics & Informatics
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• v.13 no.4
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• pp.137-145
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• 2015

Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc. These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.

• Animal Bioscience
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• v.37 no.5
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• pp.807-816
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• 2024

Objective: This study aims to identify the significant regions and candidate genes of growth-related traits (adjusted backfat thickness [ABF], average daily gain [ADG], and days to 90 kg [DAYS90]) in Korean commercial GGP pig (Duroc, Landrace, and Yorkshire) populations. Methods: A genome-wide association study (GWAS) was performed using single-nucleotide polymorphism (SNP) markers for imputation to Illumina PorcineSNP60. The BayesB method was applied to calculate thresholds for the significance of SNP markers. The identified windows were considered significant if they explained ≥1% genetic variance. Results: A total of 28 window regions were related to genetic growth effects. Bayesian GWAS revealed 28 significant genetic regions including 52 informative SNPs associated with growth traits (ABF, ADG, DAYS90) in Duroc, Landrace, and Yorkshire pigs, with genetic variance ranging from 1.00% to 5.46%. Additionally, 14 candidate genes with previous functional validation were identified for these traits. Conclusion: The identified SNPs within these regions hold potential value for future marker-assisted or genomic selection in pig breeding programs. Consequently, they contribute to an improved understanding of genetic architecture and our ability to genetically enhance pigs. SNPs within the identified regions could prove valuable for future marker-assisted or genomic selection in pig breeding programs.

• ALGAE
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• v.33 no.2
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• pp.181-189
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• 2018

Emiliania huxleyi (a haptophyte) is the most abundant coccolithophore species that produces delicate calcite scales called coccoliths. In this study, we identified several candidate genes associated with coccolith production by comparing the transcriptomes of the calcifying (CCMP 371) and non-calcifying (CCMP 2090) strains of E. huxleyi. Among the candidates, genes highly expressed in CCMP 371 were identified. To confirm whether these genes are associated with calcification, we modulated coccolith production in CCMP 371 by culturing it at different calcium concentrations. At an ambient (10 mM) concentration of calcium in the growth medium, CCMP 371 sustained its calcifying ability. However, at a low (0.1 mM) concentration or absence of calcium, there was no calcite formation, demonstrating that calcium-limiting conditions negatively affect calcification. We also evaluated the expression patterns of the putative genes in cells grown at different calcium concentrations by quantitative reverse transcription polymerase chain reaction. In addition, we showed that the growth rate of cells cultured under calcium-limiting conditions does not differ from that under ambient conditions. Further studies are required to investigate the roles of the putative calcification-associated genes at the molecular level.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.114-114
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• 2003

Epidermal growth factor (EGF) induces well-documented mitogenic and differentiating effects on murine and bovine preimplantation embryos. However, the effects of EGF on apoptosis and implantation-related gene expression in bovine embryos developing in vitro have not been evaluated. The objective of this study was to determine the effects of exogenous EGF in the presence and absence of BSA on the preimplantation development of bovine embryos. In addition, we measured cell number, apoptosis, and expression of apoptosis and implantation-related genes of the blastocysts that developed in these culture conditions. In vitro produced bovine embryos were randomly cultured in the same medium containing 0 or 10 ng/ml EGF in the presence and absence of 0.8% BSA. More 2-cell embryos developed into blastocysts at day 7 when BSA was present than when BSA was absent. The addition of 10 ng/$m\ell$ EGF into the medium did not significantly increase the developmental rate and the cell numbers per blastocyst. However, addition of EGF in the presence of 0.8% BSA significantly reduced the degree of apoptosis in the blastocysts (P<0.01). To investigate whether EGF modulates mRNA expression of apoptosis-related genes, mRNA was prepared from single blastocysts and each preparation was subjected to RT-PCR for Bcl-2 and Bax transcripts. EGF did not alter the relative abundance of Bax gene expression in the presence of BSA, but increase Bcl-2 (P<0.01) The relative abundance of Interferon tau expression was increased by EGF treatment in the presence of BSA. These results suggest that EGF and BSA synergistically enhance Bcl-2 and interferone tau gene expression, which may result in a net increase in viability in bovine embryos.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.99-99
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• 2003

Epidermal growth factor (EGF) induces well-documented mitegenic and differentiating effects on murine and bovine preimplantation embryos. However, the effects of EGF on apoptosis and implantation-related gene expression in bovine embryos developing in vitro have not been evaluated. The objective of this study was to determine the effects of exogenous EGF in the presence and absence of BSA on the preimplantation development of bovine embryos. In addition, we measured cell number, apoptosis, and expression of apoptosis and implantation-related genes of the blastocysts that developed in these culture conditions. In vitro produced bovine embryos were randomly cultured in the same medium containing 0 or 10 ng/$m\ell$ EGF in the presence and absence of 0.8% BSA. More 2-cell embryos developed into blastocysts at day 7 when BSA was present than when BSA was absent. The addition of 10 ng/$m\ell$ EGF into the medium did not significantly increase the developmental rate and the cell numbers per blastocyst. However, addition of EGF in the presence of 0.8% BSA significantly reduced the degree of apoptosis in the blastocysts (P< 0.01). To investigate whether EGF modulates mRNA expression of apoptosis-related genes, mRNA was prepared from single blastocysts and each preparation was subjected to RT-PCR for Bcl-2 and Bax transcripts. EGF did not alter the relative abundance of Bax gene expression in the presence of BSA, but increase Bcl-2 (P < 0.01). The relative abundance of Interferon tau expression was increased by EGF treatment in the presence of BSA. These results suggest that EGF and BSA synergistically enhance Bcl-2 and interferone tau gene expression, which may result in a net increase in viability in bovine embryos.

• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1390-1401
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• 2023

In this study, a 12-week feeding experiment was conducted to characterize the effects of exogenous α-amylase on the growth, feed utilization, digestibility, plasma α-amylase activity, feed degradation rate, and fecal particle size of olive flounder (Paralichthys olivaceus). Diet was supplemented with 0 (AA₀; control), 100 (AA₁₀₀), 200 (AA₂₀₀), or 400 (AA₄₀₀) mg/kg of α-amylase, respectively. Fish (273.1 ± 2.3 g) were stocked into 12 tanks (25 fish/1,000-L tank) and 3 tanks were randomly selected for each diet group. As a result, α-amylase was found to have no significant effects (p ≥ 0.05) on the growth, feed utilization parameters, and whole-body proximate compositions. α-Amylase-treated fish exhibited only a significant increase in the apparent digestibility coefficient of carbohydrates compared to the controls. In addition, in vitro analyses revealed that α-amylase dose-dependently increased (p < 0.05) the feed degradation rate, while photographs of the intestinal content after 2, 4, and 8 h of feeding demonstrated an improved degradation rate in the α-amylase-treated groups. Plasma α-amylase content was higher in the AA₂₀₀ and AA₄₀₀ groups, whereas the control group produced significantly larger-sized fecal particles (90% size class) than these two groups. In the intestine, no changes were observed in the expression levels of the immune-related TNF-α, IL-1β, IL-2, immunoglobulin-M, HSP-70, lysozyme, and amylase alpha-2A. However, growth-related genes IGF-1, IGF-2, TGF-β3, and growth hormone genes were upregulated in muscle tissues. Collectively, exogenous α-amylase has positive roles in the modulation of the digestibility coefficient, blood α-amylase concentration, growth-related gene expression, and diet degradation for improved digestion in olive flounder.

• Journal of Animal Science and Technology
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• v.65 no.1
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• pp.160-174
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• 2023

The purpose of this study was to compare marbling score, meat quality, juiciness, sarcomere length, and skeletal muscle satellite cell (SMSC) growth and related gene expression between Woori black pig (WB) and the Landrace, Yorkshire, and Duroc (LYD) crossbreed at different body weights (b.w.). WB was developed to improve meat quality and growth efficiency by crossbreeding Duroc with Korean native black pig. A total of 24 pigs were sacrificed when their b.w. reached about 50, 75, 100, and 120 kg. SMSC were isolated from the femoris muscles, and muscle and adipose tissues were sampled from the middle and the subcutaneous part of the femoris of hind legs, respectively. Expression levels of genes including Myoblast determination protein 1 (MyoD), Paired box gene 3 (Pax3), Myosin heavy chain (MyHC), and Myogenin, which are responsible for the growth and development of SMSC, were higher in LYD than the WB. Muscle growth inhibitor myostatin (MSTN), however, was expressed more in WB compared to LYD (p < 0.01). Numbers of SMSC extracted from femoris muscle of LYD at 50, 75, 100, and 120 kg b.w. were 8.5 ± 0.223, 8.6 ± 0.245, 7.2 ± 0.249, and 10.9 ± 0.795, and those from WB were 6.2 ± 0.32, 6.2 ± 0.374, 5.3 ± 0.423, and 17.1 ± 0.315, respectively. Expression of adipogenic genes in adipose tissue including CCAAT/enhancer-binding protein (CEBP)-β, peroxisome proliferator activated receptor (PPAR)-γ, and fatty acid synthase (FASN), were greater in WB when compared with LYD (p < 0.01). Results from the current study suggest that different muscle cell numbers between 2 different breeds might be affected by related gene expression and this warrants further investigation on other growth factors regulating animal growth and development.

• Journal of Plant Biotechnology
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• v.44 no.3
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• pp.271-286
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• 2017

GROWTH-REGULATING FACTOR (GRF) genes encode plant-specific transcription factors containing two conserved QLQ and WRC domains and play critical roles in regulating the growth and development of lateral organs, such as cotyledons, leaves, and flowers. To explore the agricultural potential of Brassica rapa GRF genes (BrGRFs), the researchers isolated seven BrGRFs (BrGRF3-1, 3-2, 5, 7, 8-1, 8-2, and 9) and constructed BrGRF-overexpressing Arabidopsis thaliana plants (BrGRF-OX). BrGRF-OX plants developed larger cotyledons, leaves, and flowers as well as longer roots than the wild type. The increase in size of these organs were due to increases in cell number, but not due to cell size. BrGRF-OX plants also had larger siliques and seeds. Furthermore, BrGRF-OX seeds produced more oil than the wild type. RT-PCR analysis revealed that BrGRFs regulated expression of a wide range of genes that are involved in gibberellin-, auxin-, cell division-related growth processes. Taken together, the data indicates that BrGRFs act as positive regulators of plant growth, thus raising the possibility that they may serve as a useful genetic source for crop improvement with respect to organ size and seed oil production.

• The Journal of the Korean Society for Microbiology
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• v.35 no.4
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• pp.299-308
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• 2000

Recently developed cDNA microarray or DNA chip technology allows expression monitoring of expression of hundreds and thousands of genes simultaneously and provides a format for identifying genes as well as changes in their activity. In order to search for changes in gene expression after X irradiation in HL60 cells, cDNA microarray technique was done. In this study, expression of 588 human genes (including oncogenes, tumor suppressor genes, cell cycle regulator genes, intracellular signal transduction modulator genes, apoptosis related genes, transcription factor genes, growth factors and receptor genes, cytokine genes, etc) were analyzed. For cDNA microarray analysis mRNAs were extracted from control and 8 Gy-irradiated HL60 cells. As a result the changes in expression of several genes were observed. This alteration of gene expression was confirmed by reverse transcription-polymerase chain reaction. The expression of heat shock 60 KD protein, c-jun, erythroid differentiation factor, CPP32, myeloid cell nuclear differentiation antigen, MAP kinase-activated protein kinase, interleukin-8, monocyte chemotactic peptide 1 and RANTES genes was increased, but the expression of p55CDC gene was decreased after X irradiation.

• Genomics & Informatics
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• v.21 no.4
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• pp.44.1-44.10
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• 2023

Tumor hypoxia, oxygen deprivation state, occurs in most cancers and promotes angiogenesis, enhancing the potential for metastasis. The vascular endothelial growth factor (VEGF) family genes play crucial roles in tumorigenesis by promoting angiogenesis. To investigate the malignant processes triggered by hypoxia-induced angiogenesis across pan-cancers, we comprehensively analyzed the relationships between the expression of VEGF family genes and hypoxic microenvironment based on integrated bioinformatics methods. Our results suggest that the expression of VEGF family genes differs significantly among various cancers, highlighting their heterogeneity effect on human cancers. Across the 33 cancers, VEGFB and VEGFD showed the highest and lowest expression levels, respectively. The survival analysis showed that VEGFA and placental growth factor (PGF) were correlated with poor prognosis in many cancers, including kidney renal cell and liver hepatocellular carcinoma. VEGFC expression was positively correlated with glioma and stomach cancer. VEGFA and PGF showed distinct positive correlations with hypoxia scores in most cancers, indicating a potential correlation with tumor aggressiveness. The expression of miRNAs targeting VEGF family genes, including hsa-miR-130b-5p and hsa-miR-940, was positively correlated with hypoxia. In immune subtypes analysis, VEGFC was highly expressed in C3 (inflammatory) and C6 (transforming growth factor β dominant) across various cancers, indicating its potential role as a tumor promotor. VEGFC expression exhibited positive correlations with immune infiltration scores, suggesting low tumor purity. High expression of VEGFA and VEGFC showed favorable responses to various drugs, including BLU-667, which abrogates RET signaling, an oncogenic driver in liver and thyroid cancers. Our findings suggest potential roles of VEGF family genes in malignant processes related with hypoxia-induced angiogenesis.