• Journal of Korean Medicine Rehabilitation
• /
• v.30 no.4
• /
• pp.17-30
• /
• 2020

Objectives The purpose of this study is to evaluate the healing effect of Yukmijihwang-tang (YM) on femur fractured mice. Methods Mice were randomly divided into 6 groups: normal, control, positive control, YM with low, medium, high dosage each. All groups were prepared with femur fracture and treated diffrently. In order to measure bone regeneration effects, we analysed the levels of cyclooxygenase-2 (COX2), bone morphogenetic protein-2 (BMP2), collagen type II alpha 1 chain (Col2a1), Sox9, runt-related transcription factor 2 (Runx2), and osterix genes expressed in bone. For morphological analysis, muscles were removed and femur was observed with naked eye. Results COX2 gene expression in bone marrow significantly decreased. BMP2 gene expression significantly increased. Col2a1 gene expression significantly increased. Sox9 gene expression increased as well. Runx2 gene expression in bone marrow increased, but there was no statistical significance. Osterix gene expression significantly increased. Union of the fracture site progressed more in YM group compared to the control group. The fracture union score was significantly decreased in YM group compared to the control group. Conclusions YM showed anti-inflammatory effect, promoted bone regeneration by stimulating the bone regeneration factor. In conclusion, YM can help fracture healing and it well be applied clinically to patients with fracture.

• Reproductive and Developmental Biology
• /
• v.37 no.1
• /
• pp.1-8
• /
• 2013

In order to investigate genetic stability and gene expression profile after cloning procedure, two groups of cloned pigs were used for swine leukocyte antigen (SLA) gene nucleotide alteration and microarray analyses. Each group was consist of cloned pigs derived from same cell line (n=3 and 4, respectively). Six SLA loci were analyzed for cDNA sequences and protein translations. In total, 16 SLA alleles were identified and there were no evidence of SLA nucleotide alteration. All SLA sequences and protein translations were identical among the each pig in the same group. On the other hand, microarray assay was performed for profiling gene expression of the cloned pigs. In total, 43,603 genes were analyzed and 2,150~4,300 reliably hybridized spots on the each chip were selected for further analysis. Even though the cloned pigs in the same group had identical genetic background, 18.6~47.3% of analyzed genes were differentially expressed in between each cloned pigs. Furthermore, on gene clustering analysis, some cloned pigs showed abnormal physiological phenotypes such as inflammation, cancer or cardiomyopathy. We assumed that individual environmental adaption, sociality and rank in the pen might have induced these different phenotypes. In conclusion, the results of the present study indicate that SLA locus genes appear to be stable following SCNT. However, gene expressions and phenotypes between cloned pigs derived from the same cell line were not identical even under the same rearing conditions.

• Animal cells and systems
• /
• v.7 no.2
• /
• pp.159-164
• /
• 2003

The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. The RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA-RNA helicase activities. To examine the extent of conservation of structure and function of a S. pombe RAD3 during eukaryotic evolution, the RAD3 homolog gene was isolated by screening of genomic DNA library. The isolated gene was designated as HRD3 (homolog of RAD3 gene). Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as HRD3 gene and this gene exists as a single copy in S. pombe. The transcript of 2.8 kb was detected by Northern blot analysis, The level of transcripts increased by ultraviolet (UV) irradiation, indicating that HRD3 is one of the UV-inducible genes in S. pombe. Furthermore, the predicted partial sequence of HRD3 protein has 60％ identity to S. cerevisiae RAD3 gene. This homology was particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that the HRD3 gene is essential for viability and DNA repair function. These observations suggest evolutionary conservation of other protein components with which HRD3 might interact in mediating its DNA repair and viability functions.

• Journal of Korean Medicine Rehabilitation
• /
• v.30 no.2
• /
• pp.47-66
• /
• 2020

Objectives The purpose of this study is to evaluate the bone healing effect of Dohongsamul-tang (Taohongsiwu-tang; DH) on femur fractured mice. Methods Mice were randomly divided into 4 groups (naive, control, positive control and DH). All groups except naive group were subjected to bone fracture on both hind limb femurs. Naive group received no treatment at all. Control group was fed with normal saline, and positive control group was orally medicated with tramadol. DH-treated group was orally medicated with DH. We analysed the levels of BMP2, COX2, Col2a1, Sox9, Runx2, and Osterix genes on 3, 7 and 14 days after fracture. Alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, blood urea nitrogen, creatinine, total cholesterol, and triglyceride levels were measured for safety assessment. Results In morphological, histological analysis, callus formation process of DH-treated group was faster than the control group. BMP2, Sox9 gene expression were significantly increased at 7 days after fracture compared to the control group. COX2, Col2a1 gene expression were significantly increased at 14 days after fracture compared to the control group. Total cholesterol was significantly increased by DH at 3 days. Triglyceride was significantly decreased by DH at 3, 7 days after fracture compared to the control group. Conclusions Dohongsamul-tang promoted bone healing process after fracture by stimulating the bone regeneration factors. And DH shows no hepatotoxicity, nephrotoxicity and serum lipid abnormality. In conclusion, it seems that DH helps to promote fracture regeneration after bone fracture by regulating gene expressions related to bone repair.

• Journal of the Korean Institute of Intelligent Systems
• /
• v.18 no.4
• /
• pp.471-475
• /
• 2008

Microarray technology in biological science enables molecular level observations and analyses on the biological phenomina by allowing to measure the RNA expression profiles in cells. Microarray data analysis is applied in various purposes such as identifying significant genes which react to drug treatment, understanding the genome scale phenomina. In drug response experiments, the microarray-based gene expression analysis could provide meaningful information. It is sometimes needed to identify the genes which shows different expression behavior for treatment group and normal group each other. When the normal group shows the medium level expression, it is not easy to discriminate the group just by expression level comparison. This paper proposes a method which selects group-wise representative values for each gene and sets the value range of the groups in order to filter out the genes with specific pattern. It also shows some experiment results.

• Asian-Australasian Journal of Animal Sciences
• /
• v.9 no.4
• /
• pp.405-410
• /
• 1996

Phylogenetic analyses were carried out using four Indonesian native chicken breeds; Kampung, Bangkok, Pelung and Kedu. Gene frequencies of four blood group (A, B, D and E) and eight electrophoretic loci (akp, Akp-2, Es-1, Amy-1, Alb, Tf, Pas and Pa-1) were examined. Geographical and breed specific trends in the gene frequencies were not found in the local population of Kampung breed or in four native breeds. The values of average heterozygosity were estimated as 0.35-0.45. Genetic distances among the local populations of Kampung breed and other native breeds were comparatively small. In a cluster analysis, the Bangkok breed and Kampung E population showed distance from another cluster. The coefficient of gene differentiation for local populations of Kampung breed was estimated as 0.099.

• The KIPS Transactions:PartB
• /
• v.18B no.2
• /
• pp.67-72
• /
• 2011

Single nucleotide polymorphisms (SNPs) are a very important tool for the study of human genome structure. Cluster analysis of the large amount of gene expression data is useful for identifying biologically relevant groups of genes and for generating networks of gene-gene interactions. In this paper we compared the clusters of SNPs within asthma group and normal control group obtained by using hierarchical cluster analysis method with entropy distance. It appears that the 5-cluster collections of the two groups are significantly different. We searched the best set of SNPs that are useful for diagnosing the two types of asthma using representative SNPs of the clusters of the asthma group. Here support vector machines are used to evaluate the prediction accuracy of the selected combinations. The best combination model turns out to be the five-locus SNPs including one on the gene ALOX12 and their accuracy in predicting aspirin tolerant asthma disease risk among asthmatic patients is 66.41%.

• The Plant Pathology Journal
• /
• v.33 no.3
• /
• pp.296-306
• /
• 2017

Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5-99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.

• Ocean and Polar Research
• /
• v.32 no.3
• /
• pp.309-319
• /
• 2010

To assess community structure and diversity of archaea, a clone sequencing analysis based on an archaeal 16S rRNA gene was conducted at three sediment depths of the continental slope and Ulleung Basin in the East Sea. A total of 311 and 342 clones were sequenced at the slope and basin sites, respectively. Marine Group I, which is known as the ammonia oxidizers, appeared to predominate in the surface sediment of both sites (97.3% at slope, 88.5% at basin). In the anoxic subsurface sediment of the slope and basin, the predominant archaeal group differed noticeably. Marine Benthic Group B dominated in the subsurface sediment of the slope. Marine Benthic Group D and Miscellaneous Crenarchaeotal Group were the second largest archaeal group at 8-9 cm and 18-19 cm depth, respectively. Marine Benthic Group C of Crenarchaeota occupied the highest proportion by accounting for more than 60% of total clones in the subsurface sediments of the basin site. While archaeal groups that use metal oxide as an electron acceptor were relatively more abundant at the basin sites with manganese (Mn) oxide-enriched surface sediment, archaeal groups related to the sulfur cycle were more abundant in the sulfidogenic sediments of the slope. Overall results indicate that archaeal communities in the Ulleung Basin show clear spatial variation with depth and sites according to geochemical properties the sediment. Archaeal communities also seem to play a significant role in the biogeochemical carbon (C), nitrogen (N), sulfur (S), and metal cycles at each site.

• The Journal of Korean Medicine
• /
• v.31 no.2
• /
• pp.91-108
• /
• 2010

Background & Objective: The aim of this study was to investigate the effect of P. radix on the inflammatory related gene expression in IL-$1{\beta}$-stimulated primary human gingival fibroblast using Whole Transcript Sense Target (WT-ST). Method: Human gingival fibroblast was incubated with P. radix [100 or $200\;{\mu}g/ml$], and IL-$1{\beta}$ [$1ng/m{\ell}$] added an hour later. After 24h, total RNA was extracted using RNeasy Mini Kit and the whole gene expression patterns were performed using WT-ST Labeling $Assay^{(R)}$. Result: In the DEG results, 782 genes were up-regulated in the IL-$1{\beta}$-treated group as compared to control and among those, 43 genes were associated with inflammation. 981 genes were down-regulated after treatment with IL-$1{\beta}$ and of those 7 genes were associated with inflammation. 1439 genes were up-regulated after treatment with P. radix plus IL-$1{\beta}$-treated when compared to IL-$1{\beta}$-treated alone group and 1225 genes were down-regulated in the same condition. Among the down-regulated genes, 5 were associated with inflammation- and inhibitor genes such as GDF15 and LIF. In the analysis of the P. radix plus IL-$1{\beta}$-treated group, the most significant pathways were the cytokine-cytokine receptor interaction, toll-like receptor signaling, JAK-STAT signaling and tyrosine metabolism. The gene expression patterns in the P. radix $200{\mu}g/m{\ell}$ plus IL-$1{\beta}$-treated group appear to be more involved in the metabolism-related pathways than in the $100{\mu}g/m{\ell}$ plus IL-$1{\beta}$-treated group. Conclusion & Discussion: By microarray analysis of gene expression data, we are able to identify gene expression patterns associated with not only anti-inflammation effect but also transcription function of P. radix.