• Journal of Animal Reproduction and Biotechnology
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• v.36 no.1
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• pp.35-44
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• 2021

A pregnancy diagnosis is an important standard for control of livestock's reproduction in paricular dairy cattle. High reproductive performance in dairy animals is a essential condition to realize of high life-time production. Pregnancy diagnosis is crucial to shortening the calving interval by enabling the farmer to identify open animals so as to treat or re-breed them at the earliest opportunity. MicroRNAs are short RNA molecules which are critically involved in regulating gene expression during both health and disease. This study is sought to establish the feasible of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from 12 non-pregnant cows ("open" cows: samples were collected before insemination (non-pregnant state) and after pregnancy check at the indicated time points) on weeks 0, 4, 8, 12 and 16. Using small RNA sequencing we identified a total of 115 miRNAs that were differentially expressed weeks 16 relative to non-pregnancy ("open" cows). Weeks 8, 12 and 16 of pregnancy commonly showed a distinct increase in circulating levels of miR-221 and miR-320a. Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with pregnancy in cattle. Their application in the field of reproductive biology has opened up opportunities for research communities to look for pregnancy biomarker molecules in dairy cattle.

• Animal Bioscience
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• v.37 no.6
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• pp.965-981
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• 2024

Objective: Milk composition varies considerably and depends on paratypical, genetic, and epigenetic factors. MiRNAs belong to the class of small non-coding RNAs; they are one of the key tools of epigenetic control because of their ability to regulate gene expression at the post-transcriptional level. We compared the relative expression levels of miR-106b, miR-191, and miR-30d in milk to demonstrate the relationship between the content of these miRNAs with protein and fat components of milk in Holstein and Ayrshire cattle. Methods: Milk fat, protein, and casein contents were determined in the obtained samples, as well as the content of the main fatty acids (g/100 g milk), including: saturated acids, such as myristic (C14:0), palmitic (C16:0), and stearic (C18:0) acids; monounsaturated acids, including oleic (C18:1) acid; as well as long-, medium- and short-chain, polyunsaturated, and trans fatty acids. Real-time stem-loop one-tube reverse transcription polymerase chain reaction with TaqMan probes was used to measure the miRNA expression levels. Results: The miRNA expression levels in milk samples were found to be decreased in the first two months in Holstein breed, and in the first four months in Ayrshire breed. Correlation analysis did not reveal any dependence between changes in the expression level of miRNA and milk fat content, but showed a multidirectional relationship with individual milk fatty acids. Positive associations between the expression levels of miR-106b and miR-30d and protein and casein content were found in the Ayrshire breed. Receiver operating characteristic curve analysis showed that miR-106b and miR-30d expression levels can cause changes in fatty acid and protein composition of milk in Ayrshire cows, whereas miR-106b expression level determines the fatty acid composition in Holsteins. Conclusion: The data obtained in this study showed that miR-106b, miR-191, and miR-30d expression levels in milk samples have peculiarities associated with breed affiliation and the lactation period.

• International Journal of Oral Biology
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• v.38 no.1
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• pp.21-27
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• 2013

Anginosus group streptococci (AGS) were classified based on the nucleotide sequences of the 16S rRNA gene (16S rDNA) and comprised Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus. It is known that AGS is a causative factor of oral and systematic diseases. The purpose of this study was to discriminate the 56 clinical strains of AGS isolated from Korean oral cavities using phylogenetic analysis of 16S rDNA and species-specific PCR at the species-level. The 16S rDNA of clinical strains of AGS was sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. PCR was performed to identify the clinical strains using species-specific primers described in previous studies and S. intermedius-specific PCR primers developed in our laboratory. The resulting phylogenetic data showed that the 16S rDNA sequences can delineate the S. anginosus, S. intermedius, and S. constellatus strains even though the 16S rDNA sequence similarity between S. intermedius and S. constellatus is above 98%. The PCR data showed that each species-specific PCR primer pair could discriminate between clinical strains at the species-level through phylogenetic analysis of 16S rDNA nucleotide sequences. These results suggest that phylogenetic analysis of 16S rDNA and PCR are useful tools for discriminating between AGS strains at the species-level.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.7
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• pp.3437-3445
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• 2016

Background: There is an increasing concern in the role of microRNA (miRNA) in the pathogenesis of bone metastasis (BM) secondary to prostate cancer (CaP). In this exploratory study, we hypothesized that the expression of vinculin (VCL) and chemokine X3C ligand 1 (CX3CL1) might be down-regulated in clinical samples, most likely due to the post-transcriptional modification by microRNAs. Targeted genes would be up-regulated upon transfection of the bone metastatic prostate cancer cell line, PC3, with specific microRNA inhibitors. Materials and Methods: MicroRNA software predicted that miR-21 targets VCL while miR-29a targets CX3CL1. Twenty benign prostatic hyperplasia (BPH) and 16 high grade CaP formalin-fixed paraffin embedded (FFPE) specimens were analysed. From the bone scan results, high grade CaP samples were further classified into CaP with no BM and CaP with BM. Transient transfection with respective microRNA inhibitors was done in both RWPE-1 (normal) and PC3 cell lines. QPCR was performed in all FFPE samples and transfected cell lines to measure VCL and CX3CL1 levels. Results: QPCR confirmed that VCL messenger RNA (mRNA) was significantly down-regulated while CX3CL1 was up-regulated in all FFPE specimens. Transient transfection with microRNA inhibitors in PC3 cells followed by qPCR of the targeted genes showed that VCL mRNA was significantly upregulated while CX3CL1 mRNA was significantly down-regulated compared to the RWPE-1 case. Conclusions: The down-regulation of VCL in FFPE specimens is most likely regulated by miR-21 based on the in vitro evidence but the exact mechanism of how miR-21 can regulate VCL is unclear. Up-regulated in CaP, CX3CL1 was found not regulated by miR-29a. More microRNA screening is required to understand the regulation of this chemokine in CaP with bone metastasis. Understanding miRNA-mRNA interactions may provide additional knowledge for individualized study of cancers.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.1037-1047
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• 2017

Objective: Despite an increasing number of investigations into the pathophysiology of necrotic enteritis (NE) disease, etiology of NE-associated diseases, and gene expression profiling of NE-affected tissues, the microRNA (miRNA) profiles of NE-affected poultry have been poorly studied. The aim of this study was to induce NE disease in the genetically disparate Fayoumi chicken lines, and to perform non-coding RNA sequencing in the intestinal mucosal layer. Methods: NE disease was induced in the Fayoumi chicken lines (M5.1 and M15.2), and non-coding RNA sequencing was performed in the intestinal mucosal layer of both NE-affected and uninfected chickens to examine the differential expression of miRNAs. Next, quantitative real-time polymerase chain reaction (real-time qPCR) was performed to further examine four miRNAs that showed the highest fold differences. Finally, bioinformatics analyses were performed to examine the four miRNAs target genes involvement in the signaling pathways, and to examine their interaction. Results: According to non-coding RNA sequencing, total 50 upregulated miRNAs and 26 downregulated miRNAs were detected in the NE-induced M5.1 chickens. While 32 upregulated miRNAs and 11 downregulated miRNAs were detected in the NE-induced M15.2 chickens. Results of real-time qPCR analysis on the four miRNAs (gga-miR-9-5p, gga-miR-20b-5p, ggamiR-196-5p, and gga-let-7d) were mostly correlated with the results of RNAseq. Overall, ggamiR-20b-5p was significantly downregulated in the NE-induced M5.1 chickens and this was associated with the upregulation of its top-ranking target gene, mitogen-activated protein kinase, kinase 2. Further bioinformatics analyses revealed that 45 of the gene targets of gga-miR-20b-5p were involved in signal transduction and immune system-related pathways, and 35 of these targets were predicted to interact with each other. Conclusion: Our study is a novel report of miRNA expression in Fayoumi chickens, and could be very useful in understanding the role of differentially expressed miRNAs in a NE disease model.

• Communications of the Korean Mathematical Society
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• v.16 no.1
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• pp.95-102
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• 2001

We consider a Cantor set with overlaps Λ in R$^1$. We calculate its correlation dimension with respect to the push-down measure on Λ comparing with its similarity dimension.

• Proceedings of the Korean Society of Life Science Conference
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• 2007.10a
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• pp.70.1-70.1
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• 2007

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• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.399-403
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• 2013

Background: Several studies have reported the role of the miR-146a rs2910164 G > C polymorphism as a susceptibility factor for several digestive cancers. However, the results have been controversial. Therefore, we conducted the present meta-analysis to obtain the most reliable estimate of the association. Methods: PubMed, Embase and Web of Science databases were searched. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were extracted and pooled to assess the strength of the association between miR-146a rs2910164 G > C polymorphism and digestive cancer risk. A total of four eligible studies including 3,447 cases and 5,041 controls based on the search criteria were included. Results: We observed that miR-146a rs2910164 G > C polymorphism was not significantly correlated with digestive cancer risks when all studies were pooled into the meta-analysis. While we found that miR-146a rs2910164 polymorphism was not associated with gastric cancer, it was significantly linked with hepatocellular cancer risk (the homozygote codominant model: OR = 1.40, 95% CI = 1.04-1.87). In the stratified analysis by ethnicity, significant associations were observed in Chinese population for the allele contrast model (OR = 1.25; 95% CI = 1.12-1.38), for the homozygote codominant model (OR = 1.62; 95% CI = 1.28-2.04), and for the recessive model (OR = 1.38; 95% CI = 1.16-1.64). However, studies with Asian groups presented no significant association for all genetic models. Conclusions: This meta-analysis suggests that the miR-146a rs2910164 G > C polymorphism is a low-penetrant risk factor for digestive cancers in Chinese.

• Journal of fish pathology
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• v.32 no.2
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• pp.69-80
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• 2019

We performed MLSA (multilocus sequence analysis) and phenotypic characterization of Aliivibrio species isolated from walleye pollock (Gadus chalcogrammus) maintained in 3 different facilities of Gangwon Province, the east coast of Korea. Of 38 Aliivibrio species identified by 16S rDNA sequences, 12 strains were randomly selected and MLSA was conducted with 5 house-keeping genes (gapA, gyrB, pyrH, recA and rpoA) and 16S rDNA gene. Phylogenetic analysis and homology of the concatenated sequences (4,580 bp) with other Vibrionaceae genera revealed that 4 strains (GNGc16.1, YYGc16.1, YYGc16.2, GSGc18.1) were identified as Aliivibrio logei and one strain (GSGc16.1) as A. wodanis. One strain (GSGc17.1) was tentatively identified as A. logei, but needs further analysis because it did not belong to the same clade with A. logei type strain. 6 strains (GSGc17.2, GNGc16.2, GSGc16.2, GSGc17.3, GSGc18.2, GSGc17.4) need further investigation as potential novel species. Either phenotypic characterization or 16S rDNA sequence alone did not provide enough information for identification of Aliivibrio strains at the species level. A. logei and A. wodanis are generally known as non-pathogenic bacteria, but also known as opportunistic or secondary pathogens of cold water fishes. Cares should be taken to prevent potential outbreaks due to these bacteria, although there was no outbreaks during the sampling period.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1824-1836
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• 2020

Objective: On the hypothesis that grazing of cattle prompts organs to secrete or internalize circulating microRNAs (c-miRNAs) in parallel with changes in energy metabolism, we aimed to clarify biological events in adipose, skeletal muscle, and liver tissues in grazing Japanese Shorthorn (JSH) steers by a transcriptomic approach. Methods: The subcutaneous fat (SCF), biceps femoris muscle (BFM), and liver in JSH steers after three months of grazing or housing were analyzed using microarray and quantitative polymerase chain reaction (qPCR), followed by gene ontology (GO) and functional annotation analyses. Results: The results of transcriptomics indicated that SCF was highly responsive to grazing compared to BFM and liver tissues. The 'Exosome', 'Carbohydrate metabolism' and 'Lipid metabolism' were extracted as the relevant GO terms in SCF and BFM, and/or liver from the >1.5-fold-altered mRNAs in grazing steers. The qPCR analyses showed a trend of upregulated gene expression related to exosome secretion and internalization (charged multivesicular body protein 4A, vacuolar protein sorting-associated protein 4B, vesicle associated membrane protein 7, caveolin 1) in the BFM and SCF, as well as upregulation of lipolysis-associated mRNAs (carnitine palmitoyltransferase 1A, hormone-sensitive lipase, perilipin 1, adipose triglyceride lipase, fatty acid binding protein 4) and most of the microRNAs (miRNAs) in SCF. Moreover, gene expression related to fatty acid uptake and inter-organ signaling (solute carrier family 27 member 4 and angiopoietin-like 4) was upregulated in BFM, suggesting activation of SCF-BFM organ crosstalk for energy metabolism. Meanwhile, expression of plasma exosomal miR-16a, miR-19b, miR-21-5p, and miR-142-5p was reduced. According to bioinformatic analyses, the c-miRNA target genes are associated with the terms 'Endosome', 'Caveola', 'Endocytosis', 'Carbohydrate metabolism', and with pathways related to environmental information processing and the endocrine system. Conclusion: Exosome and fatty acid metabolism-related gene expression was altered in SCF of grazing cattle, which could be regulated by miRNA such as miR-142-5p. These changes occurred coordinately in both the SCF and BFM, suggesting involvement of exosome in the SCF-BFM organ crosstalk to modulate energy metabolism.