• Journal of Animal Science and Technology
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• 제58권4호
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• pp.17.1-17.7
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• 2016

Background: The Sapsaree (Canis familiaris) is a Korean native dog that is very friendly, protective, and loyal to its owner, and is registered as a natural monument in Korea (number: 368). To investigate large-scale gene expression profiles and identify the genes related to exercise-induced stress in the Sapsaree, we performed whole-transcriptome RNA sequencing and analyzed gene expression patterns before and after exercise performance. Results: We identified 525 differentially expressed genes in ten dogs before and after exercise. Gene Ontology classification and KEGG pathway analysis revealed that the genes were mainly involved in metabolic processes, such as programmed cell death, protein metabolic process, phosphatidylinositol signaling system, and cation binding in cytoplasm. The ten Sapsarees could be divided into two groups based on the gene expression patterns before and after exercise. The two groups were significantly different in terms of their basic body type ($p{\leq}0.05$). Seven representative genes with significantly different expression patterns before and after exercise between the two groups were chosen and characterized. Conclusions: Body type had a significant effect on the patterns of differential gene expression induced by exercise. Whole-transcriptome sequencing is a useful method for investigating the biological characteristics of the Sapsaree and the large-scale genomic differences of canines in general.

• Journal of Animal Science and Technology
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• 제54권6호
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• pp.419-425
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• 2012

The coordinated action of the detrusor muscle cells in the urinary bladder is governed by cell-cell communication through gap junction, consisted of connexin (Cx) molecules. Even though a number of researches have been mostly focused on expressional changes of a few Cx isoforms in clinically dysfunctional condition of the bladder, less attention has been paid for investigation of Cx isoforms present in the bladder. Using real-time PCR analysis, the present study examined Cx isoforms expressing in the male rat bladder during postnatal period. Also, expressional patterns of Cx isoforms were evaluated in the bladder at different postnatal ages. Of a total of 13 Cx isoforms tested in the present study, we were able to detect mRNAs of 6 Cx isoforms in the rat urinary bladder, including Cxs 31, 31.1, 32, 37, 40, and 45. The transcript levels of Cxs 31, 31.1, 37, 40, and 45 were gradually increased from 1 week of age until 25 days of age, followed by transient decreases at 45 days of age. However, abundance of Cx32 transcript was drastically increased at 15 days of age, followed by a sharp drop at 45 days of age. These results indicate that differential expression of Cx isoforms in the bladder during postnatal development would be necessary for maintaining proper function of the bladder. A question remains to be answered if significant decreases of transcript levels of some Cx isoforms at the elderly are associated with age-dependent dysfunction of the bladder.

• 생물정신의학
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• 제8권2호
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• pp.203-207
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• 2001

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information, new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.

• Molecules and Cells
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• 제20권2호
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• pp.247-255
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• 2005

Three different catalase cDNA clones (CaCat1, CaCat2, and CaCat3) were isolated from hot pepper (Capsicum annuum L.), and their expression patterns were analyzed at the levels of mRNA and enzyme activity. Northern hybridization showed that the three catalase genes were differentially expressed in various organs, and that expression of CaCat1 and CaCat2 was regulated differently by the circadian rhythm. In situ hybridization revealed different spatial distributions of CaCat1 and CaCat2 transcripts in leaf and stem. In response to wounding and paraquat treatment, CaCat1 mRNA increased at 4-12 h in both paraquat-treated and systemic leaves. In contrast, wounding had no significant effect on expression of the catalase genes. The increase of catalase activity in the paraquat-treated and systemic leaves paralleled that of CaCat1 mRNA, but did not match that of CaCat1 mRNA in paraquat-treated stems. Our results suggest that CaCat1 may play a role in responses to environmental stresses.

• BMB Reports
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• 제39권1호
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• pp.26-36
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• 2006

Differential Display PCR technique (DD-PCR) was used for the analysis of altered gene expression in hemocytes of Vibrio harveyi-infected Penaeus monodon. Forty-four combinations of arbitrary and oligo(dT) primers were used to screen for differentially expressed genes. A total of 79 differentially expressed bands could be identified from 33 primer combinations. These included 48 bands (61%) whose expression level increased and 31 bands (39%) decreased after V. harveyi challenge. Subsequently, forty-eight differential display fragments were successfully reamplified and cloned. A total of 267 clones were randomly selected and sequenced. The sequence analysis showed that 85 (31%) out of 267 clones were matched with sequences in the GenBank database which represented 24 different genes with known functions. Among the known genes, glucose transporter 1, interferon-related developmental regulator 1, lysozyme, profilin, SERPINB3, were selected for further confirmation of their differentially expression patterns by real-time PCR. The results showed increasing in expression level of the selected genes in shrimp hemocytes after microbial challenge suggesting the involvement of such genes in bacterial response in shrimp. The anti-lipopolysaccharide factor type 3 (ALFPm3) gene, previously reported in P. monodon (Supungul et al., 2002) was found among the up-regulated genes but diversity due to amino acid changes was observed. Increase in ALFPm3 transcripts upon V. harveyi injection is in accordance with that found in the previous study.

• Clinical and Experimental Reproductive Medicine
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• 제46권2호
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• pp.76-86
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• 2019

Objective: This study was performed to explore the possibility that each oocyte and its surrounding cumulus cells might have different genetic expression patterns that could affect human reproduction. Methods: Differential gene expression analysis was performed for 10 clusters of cumulus cells obtained from 10 cumulus-oocyte complexes from 10 patients. Same procedures related to oocyte maturation, microinjection, and microarray analyses were performed for each group of cumulus cells. Two differential gene expression analyses were performed: one for the outcome of clinical pregnancy and one for the outcome of live birth. Results: Significant genes resulting from these analyses were selected and the top 20 affected pathways in each group were analyzed. Circadian entrainment is determined to be the most affected pathway for clinical pregnancy, and proteoglycans in cancer pathway is the most affected pathway for live birth. Circadian entrainment is also amongst the 12 pathways that are found to be in top 20 affected pathways for both outcomes, and has both lowest p-value and highest number of times found count. Conclusion: Although further confirmatory studies are necessary, findings of this study suggest that these pathways, especially circadian entrainment in cumulus cells, may be essential for embryo development and pregnancy.

• Journal of Animal Science and Technology
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• 제55권4호
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• pp.249-255
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• 2013

Intercellular interactions are important for the proper development and regulation of tissue function. This is especially necessary in the epididymis, a part of male reproductive tract where sperm become mature and acquire their fertilizing capacity. The caput region of the epididymis consists of several types of cells, including principal, basal, and apical cells. Direct intercellular communication is thus required to precisely regulate the functions of the caput epididymis. In this regard, connexin (Cx) is a molecule that forms channels, which allow the direct exchange of small molecules between cells, enabling intercellular communication. In this study, the expression of Cx isoforms in the caput epididymis at different postnatal ages was determined by using quantitative real-time polymerase chain reaction analysis. Nine of 13 Cx isoforms were detected. The transcript levels of Cx30.3, 31, 31.1, 32, and 40 were highest at 45 days of age, while the expression of Cx43 and 45 gradually decreased with age. A substantial fluctuation of Cx26 expression was detected, with significant decreases before and during puberty, followed by a transient increase at adult-hood and rapid decreases at an old age. A significant increase in Cx37 transcript was observed at 25 days of age, followed by gradual decreases at adult and old ages. These results indicate the significant differential expression of various Cx isoforms in the caput epididymis during postnatal development. It further suggests that the functional regulation and developmental maturation of the caput epididymis are highly related to the postnatal age-related differential expression of Cx isoforms.

• BMB Reports
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• 제43권2호
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• pp.115-121
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• 2010

A large data set of Hanwoo (Korean cattle) ESTs was analyzed to obtain differential gene expression results for the following three libraries: intramuscular fat, longissimus dorsi muscle and liver. To better understand the gene expression profiles, we identified differentially expressed genes (DEGs) via digital gene expression analysis. Hierarchical clustering of genes was performed according to their relative abundance within the six separate groups (Hanwoo fat versus non-Hanwoo fat, Hanwoo muscle versus non-Hanwoo muscle and Hanwoo liver versus non-Hanwoo liver), producing detailed patterns of gene expression. We determined the quantitative traits associated with the highly expressed genes. We also provide the first list of putative regulatory elements associated with differential tissue expression in Hanwoo cattle. In addition, we conducted evolutionary analysis that suggests a subset of genes accelerated in the bovine lineage are strongly correlated with their expression in Hanwoo muscle.

• The Plant Pathology Journal
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• 제36권5호
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• pp.450-458
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• 2020

Pepper and tomato plants infected with two Clavibacter species, C. capsici and C. michiganensis have shown different patterns of disease development depending on their virulence. Here, we investigated how pepper and tomato plants respond to infection by the high-virulent or low-virulent Clavibacter strains. For this, we chose two strains of each Clavibacter species to show different virulence level in the host plants. Although low-virulent strains showed less disease symptoms, they grew almost the same level as the high-virulent strains in both plants. To further examine the response of host plants to Clavibacter infection, we analyzed the expression patterns of plant defense-related genes in the leaves inoculated with different strains of C. capsici and C. michiganensis. Pepper plants infected with high-virulent C. capsici strain highly induced the expression of CaPR1, CaDEF, CaPR4b, CaPR10, and CaLOX1 at 5 days after inoculation (dai), but their expression was much less in low-virulent Clavibacter infection. Expression of CaSAR8.2 was induced at 2 dai, regardless of virulence level. Expression of GluA, Pin2, and PR2 in tomato plants infected with high-virulent C. michiganensis were much higher at 5 dai, compared with mock or low-virulent strain. Expression of PR1a, Osmotin-like, Chitinase, and Chitinase class 2 was increased, regardless of virulence level. Expression of LoxA gene was not affected by Clavibacter inoculation. These results suggested that Clavibacter infection promotes induction of certain defense-related genes in host plants and that differential expression of those genes by low-virulent Clavibacter infection might be affected by their endophytic lifestyle in plants.

• Fisheries and Aquatic Sciences
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• 제18권1호
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• pp.73-80
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• 2015

To examine the interrelationship between transgenic insertion patterns and transgene expression profiles in established transgenic fish lines, four stable transgenic marine medaka Oryzias dancena germlines harboring ${\beta}$-actin regulator-driven RFP reporter constructs were selected. The established transgenic strains were characterized with regard to their transgenic genotypes (insertion pattern, concatemer formation, and transgene copy number based on genomic Southern blot hybridization and qPCR assay) and expression characteristics at the mRNA (qRT-PCR), protein (western blot), and phenotypic (fluorescent appearance) levels. From comparative examinations, it was found that transgenic expression at both the transcription and translation levels could be significantly downregulated in transgenic strains, potentially through methylation-mediated transgene silencing that was particularly associated with the formation of a long tail-to-head tandem concatemer in the chromosomal integration site(s). When this occurred, an inverse relationship between the transgene copy number and fluorescence intensity was observed in the resultant transgenic fish. However, with the other transgenic genotype, transgenic individuals with an identical Southern blot hybridization pattern, containing a tandem concatemer(s), had very different expression levels (highly robust vs. low expression strengths), which was possibly related to the differential epigenetic modifications and/or degrees of methylation. The concatemer-dependent downregulation of transgene activity could be induced in transgenic fish, but the overall pattern was strain-specific. Our data suggest that neither a low (or single) transgene copy number nor tandem transgene concatemerization is indicative of strong or silenced transgene expression in transgenic fish carrying a ubiquitous transgene. Hence, a sufficient number of transgenic lineages, with different genotypes, should be considered to ensure the establishment of the best-performance transgenic line(s) for practical applications.