• Asian-Australasian Journal of Animal Sciences
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• v.30 no.4
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• pp.462-469
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• 2017

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.3
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• pp.398-407
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• 2020

Objective: The Yip1 domain family (YIPF) proteins were proposed to function in endoplasmic reticulum (ER) to Golgi transport and maintenance of the morphology of the Golgi, which were homologues of yeast Yip1p and Yif1p. YIPF3, the member 3 of YIPF family was a homolog of Yif1p. The aim of present study was to investigate the expression and regulation mechanism of porcine YIPF3. Methods: Quantitative realtime polymerase chain reaction (qPCR) was used to analyze porcine YIPF3 mRNA expression pattern in different tissues and pig kidney epithelial (PK15) cells stimulated by polyinosine-polycytidylic acid (poly [I:C]). Site-directed mutations combined with dual luciferase reporter assays and electrophoretic mobility shift assay (EMSA) were employed to reveal transcription regulation mechanism of porcine YIPF3. Results: Results showed that the mRNA of porcine YIPF3 (pYIPF3) was widely expressed with the highest levels in lymph and lung followed by spleen and liver, while weak in heart and skeletal muscle. Subcellular localization results indicated that it expressed in Golgi apparatus and plasma membranes. Upon stimulation with poly (I:C), the level of this gene was dramatically up-regulated in a time- and concentration-dependent manner. pYIPF3 core promoter region harbored three cis-acting elements which were bound by ETS proto-oncogene 2 (ETS2), zinc finger and BTB domain containing 4 (ZBTB4), and zinc finger and BTB domain containing 14 (ZBTB14), respectively. In which, ETS2 and ZBTB4 both promoted pYIPF3 transcription activity while ZBTB14 inhibited it, and these three transcription factors all played important regulation roles in tumorigenesis and apoptosis. Conclusion: The pYIPF3 mRNA expression was regulated by ETS2, ZBTB4, and ZBTB14, and its higher expression in immune organs might contribute to enhancing ER to Golgi transport of proteins, thus adapting to the immune response.

• Journal of Life Science
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• v.22 no.8
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• pp.1018-1023
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• 2012

Snail is a zinc finger transcription factor that induces epithelial-to-mesenchymal transition (EMT), which promotes tumor invasion and metastasis by repressing E-cadherin expression. In addition, Snail restricts the cellular apoptotic response to apoptotic stimuli or survival factor withdrawal; however, its molecular mechanism remains largely unknown. In this study, we have investigated the mechanism underlying Snail-mediated chemoresistance to 5-fluorouracil (5-FU), one of the most widely used anti-cancer drugs. When Snail was overexpressed by doxycycline (DOX) in MCF-7 #5 cells, it inhibited 5-FU-induced apoptotic cell death and switched the cell death mode to necrosis. Snail expression, either by DOX treatment in MCF-7 #5 cells or by the transfection of Snail expression vectors pCR3.1-Snail-Flg, phosphorylation-resistant pCR3.1-S104, and 107A Snail-Flg in MCF-7 cells specifically induced PTEN down-regulation/inactivation and Akt/PKB activation, without affecting ERK1/2 activity. In addition, Snail prominently suppressed 5-FU-induced increases in p53 levels. These findings demonstrate that Snail switches 5-FU-induced apoptosis to necrosis through the activation of Akt/PKB and the down-regulation of p53 levels.

• Korean Journal of Microbiology
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• v.42 no.4
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• pp.246-251
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• 2006

A lot of mutants which cannot initiate sexual development were screened and several loci including nsdA, nsdB, nsdC, and nsdD were identified in homothallic ascomycetes Aspergillus nidulans. The NSD206, which has nsdC6 allele, showed typical phenotype of NSD (Never in sexual development) mutants. The nsdC gene was cloned by transforming NSDP697 ($nsdC^-$, $pryG^-$) with AMA1-NotI genomic library. The transforming library DNA recovered from several transformants showing wild phenotype carried about 10 kb genomic DNA insert. The DNA sequence of nsdC was analysed using GPS (Genome priming system). The nsdC gene has an open reading frame (ORF) of 1,929 bp encoding a putative polypeptide of 643 amino acids. The NsdC carries $C_2H_2C_2H_2C_2HC$ type zinc finger DNA binding domains in the middle of the polypeptide. A coiled-coil domain at its C terminus were also found. In nsdC6 allele, a single T insertion was occurred between 407-408 bp leading to the frameshift mutation and early termination of translation producing the truncated protein which has only 139 amino acids.

• Korean Journal of Microbiology
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• v.47 no.4
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• pp.281-288
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• 2011

To screen downstream genes of Aspergillus nidulans MsnA showing amino acid sequence similarity to the zinc finger region of Msn2/4 stress response transcription factors in Saccharomyces cerevisiae, differentially expressed genes (DEG) in MsnA overexpressed or msnA null mutant strains compared to wild type have been isolated. The cognate gene IDs were identified by DNA sequencing of the selected DEGs. Among those, DEG6 was known as mstB encoding a putative monosaccharide transporter. Expression level of mstB mRNA was increased in MsnA overproducing strains and MsnA bound directly to the promoter region of mstB in vitro. MstB containing twelve transmembrane domains exhibited 80% of amino acid sequence identities to A. niger MstA a high-affinity monosaccharide transporter. A null mutant of mstB was phenotypically undistinguishable to wild type. On the other hand, forced overexpression of MstB caused the increased formation of sexual structure cleistothecia in 0.1% glucose condition where wild type showed almost no cleistothecia. This result implies that mstB is involved in transport of monosaccharide required for sexual differentiation.

• Journal of Life Science
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• v.17 no.12
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• pp.1729-1733
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• 2007

Brassinolide insensitive associated receptor kinase 1(BAK1) is a critical component that play an important roles in signaling of brassinosteroid biosynthesis. Brassinosteroid-deficient and -insensitive mutants showed the characteristic of dwarf symptom. The nutrient deficient tomato showing stunt phenomenon was selected from soiless cultivation system using modified Sonneveld hydroponic solution. Twenty eight protein spots showing different expression levels compared to the control were isolated from extracts of stunted tomato leaves by 2D PAGE analyses. Significantly down-regulated 6 protein spots out of 28 protein spots were analyzed and sequenced by MALDI-TOF mass spectrometry. The protein spot having pI=4.5 and MW=24 kDa was identified as a signal protein, BAK1, which is directly related to brassinosteroid biosynthesis. In addition, five other protein spots were identified as BCK1, cystein proteinase, sulfutase, peroxidase and zinc finger factor respectively, and they were also signal proteins related to brassinosteroid biosynthesis. Furthermore, amplification of 500bp of BAK1 mRNA by RT-PCR using a primer set of peptide matched regions was inhibited conpared to that of the wild type. The results sugested that the BAK1 might be regulated at the transcription level in response to nutrition applications.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.64 no.1
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• pp.1-17
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• 2019

A quantitative trait loci (QTL) analysis of traits related to heading and yield was performed develop rice cultivars that are both early maturing and panicle weight type varieties. Our analysis included 120 strains of the Cheongcheong Nagdong doubled haploid (CNDH) variety. An observational growth experiment was conducted to identify genetic agronomic traits of CNDH. Heading date, ten plant weight, moisture, thousand grain weight, and yield had a normal distribution based on the frequency distribution table of the observational growth data. The QTL analysis found one heading-related and nine yield-related QTLs. The LOD of 2.85 was the largest in QTLs for heading date (QHD), 5.39 in QTLs for ten plant weight (QTPW), 3.92 in QTLs for moisture (QM), 4.80 in QTLs for thousand grain weight (QTGW), and 3.7 in QTLs for yield (QY). Genomic analysis detected 58 candidate genes on chromosome 2, 3, 7, 8, and 10. Among those, we found Rcd1 protein and OsERF3 gene in QM, MtN3 and zinc finger protein genes in QTGW, and OsNAC3 protein gene in QY. If further analysis reveals the presence of genes related to water content, thousand grain weight or yield in the CNDH stains, we can develop a selection of varieties that will be capable of coping with climate change and will contribute to global food problems.

• Journal of Life Science
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• v.32 no.3
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• pp.241-248
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• 2022

NF-κB acts as a critical transcription factor in inflammation and innate immunity, and it is also closely involved in cell survival and tumorigenesis via induction of anti-apoptotic genes. In these processes, NF-κB cooperates with multiple other signaling molecules and pathways, and although many studies have demonstrated that Hsp90 regulates NF-κB activity, the exact mechanism is unclear. In this study, we investigated the relationship between Hsp90 and IKKγ in the regulation of NF-κB using expression plasmids of IKK complex components. Wild-type and deletion mutants of IKKγ were expressed together with Hsp90, and the combined regulatory effect of Hsp90 and IKKγ on NF-κB activation was assayed. The results show that Hsp90 activates NF-κB by promoting the phosphorylation and degradation of IκBα and that activation of NF-κB by NIK and LPS was increased by Hsp90. IKKγ elevated the effect of Hsp90 on NF-κB activation by increasing phosphorylation and degradation of IκBα. The positive regulation on NF-κB by Hsp90 and IKKγ was also proved in analysis with IKKβ-EE, the constitutively active form of IKKβ. In experiments with the deletion mutants of IKKγ, the N-terminal IKKβ binding domain, C-terminal leucine zipper, and zinc finger domains of IKKγ were found not necessary for the positive regulation of NF-κB activity. Additionally, the expression of pro-inflammatory cytokines was synergistically elevated by Hsp90 and IKKγ. These results indicate that inhibiting the interaction between Hsp90 and IKKγ is a possible strategic method for controlling NF-κB and related diseases.

• Oncology Letters
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• v.18 no.6
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• pp.6852-6868
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• 2019

There is a wide disparity in the incidence, malignancy and mortality of different types of cancer between each sex. The sex-specificity of cancer seems to be dependent on the type of cancer. Cancer incidence and mortality have been demonstrated as sex-specific in a number of different types of cancer, such as liver cancer, whereas sex-specificity is not noticeable in certain other types of cancer, including colon and lung cancer. The present study aimed to elucidate the molecular basis for sex-biased gene expression in cancer. The mRNA expression of the epithelial-to-mesenchymal transition-associated genes was investigated, including E-cadherin (also termed CDH1), vimentin (VIM), discoidin domain receptor 1 (DDR1) and zinc finger E-box binding homeobox 1 (ZEB1) in female- and male-derived cancer cell lines by reverse transcription (RT)-PCR and the Broad-Novartis Cancer Cell Line Encyclopedia (CCLE) database analysis. A negative correlation was observed between DDR1 and ZEB1 only in the female-derived cancer cell lines via RT-PCR analysis. A negative correlation between DDR1 index (defined by the logarithmic value of DDR1 divided by ZEB1, based on the mRNA data from the RT-PCR analysis) and an invasive phenotype was observed in cancer cell lines in a sex-specific manner. Analysis of the CCLE database demonstrated that DDR1 and ZEB1, which are already known to be sex-biased, were negatively correlated in female-derived liver cancer cell lines, but not in male-derived liver cancer cell lines. In contrast, cell lines of colon and lung cancer did not reveal any sex-dependent difference in the correlation between DDR1 and ZEB1. Kaplan-Meier survival curves using the transcriptomic datasets such as Gene Expression Omnibus, European Genome-phenome Archiva and The Cancer Genome Atlas databases suggested a sex-biased difference in the correlation between DDR1 expression pattern and overall survival in patients with liver cancer. The results of the present study indicate that sex factors may affect the regulation of gene expression, contributing to the sex-biased progression of the different types of cancer, particularly liver cancer. Overall, these findings suggest that analyses of the correlation between DDR1 and ZEB1 may prove useful when investigating sex-biased cancers.

• Reproductive and Developmental Biology
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• v.33 no.3
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• pp.183-187
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• 2009

This study analyzed change of proteins in granulosa cells during the porcine follicuar development by proteomics techniques. Granulosa cells of the follicles, of which the diameter is $2{\sim}4\;mm$ and $6{\sim}10\;mm$, were collected from ovary of slaughtered pig that each follicle of diameter $1{\sim}4\;mm$ and $6{\sim}10\;mm$. We extracted glanulosa cell proteins by M-PER Mammalian Protein Extraction Reagent. Proteins were refined by clean-up kit and quantified by Bradford method until total protein was $200{\mu}l$. Immobilized pH gradient(IPG) strip used 18 cm, $3{\sim}10\;NL$. SDS-PAGE used 10% acrylamide gel. After silver staining, Melanie 7 and naked eye test were used for spot analyzation. Increasing proteins in glanulosa cell of $6{\sim}10\;mm$ follicle were 7 spots. This spots were analyzed by MALDI-TOF MS and searched on NCBInr. In results, 7 spots were similar to zinc/ling finger protein 3 precursor (RING finger protein 203), angiomotin, heat shock 60 kDa protein 1 (chaperonin) isoform 1 (HSP60), similar to transducin-like enhancer protein 1 (TLE 1), SH3 and PX domains 2A (SH3PXD2A). Those proteins were related with transfer between cells. Increase of proteins has an effect on follicular development.