• Genomics & Informatics
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• v.16 no.4
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• The Plant Pathology Journal
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• v.38 no.4
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• pp.261-271
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• 2022

Root-knot nematodes are the most important plant-parasitic nematodes worldwide. Many efforts have been made to find non-chemical, risk-free, and environmentally friendly methods for nematode control. In this study, the effects of compost and vermicompost of arugula (Eruca sativa) on Meloidogyne javanica were investigated in three glasshouse experiments. In addition, the expression of the defense-related genes nonexpressor of pathogenesis-related 1 (NPR1) and lipoxygenase 1 (LOX1) was detected in tomato plants treated with vermicompost of arugula at 0, 2, 7, and 14 days after nematode inoculation. The result showed that the vermicompost of arugula significantly reduced the reproduction factor of the nematode by 54.4% to 70.5% in the three experiments and increased the dry weight of shoots of infected tomato plants. Gene expression analysis showed that LOX1 expression increased on the second and seventh day after nematode inoculation, while NPR1 expression decreased. The vermicompost of arugula showed stronger nematode inhibitory potential than the vermicompost of animal manure. The vermicompost of arugula is superior to arugula compost in suppressing the activity of M. javaniva and reducing its impact. It manipulates the expression of resistance genes and could induce systemic resistance against root-knot nematodes.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.2
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• pp.685-689
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• 2013

Objective: To study the effects of down-regulation of HDAC6 expression on proliferation, cell cycling and migration of esophageal squamous cell carcinoma (ESCC) cells and related molecular mechanisms. Methods: ESCC cell line EC9706 cells were randomly divided into untreated (with no transfection), control siRNA (transfected with control siRNA) and HDAC6 siRNA (transfected with HDAC6 small interfering RNA) groups. Effects of HDAC6 siRNA interference on expression of HDAC6 mRNA and protein in EC9706 cells were investigated by semi-quantitative RT-PCR, Western blotting and immunocytochemistry methods. Effects of down-regulation of HDAC6 expression on cell proliferation, cell cycle, and cell migration were studied using a CCK-8 kit, flow cytometry and Boyden chambers, respectively. Changes of mRNA and protein expression levels of cell cycle related factor (p21) and cell migration related factor (E-cadherin) were investigated by semi-quantitative RT-PCR and Western blotting methods. Results: After transfection of HDAC6 siRNA, the expression of HDAC6 mRNA and protein in EC9706 cells was significantly downregulated. In the HDAC6 siRNA group, cell proliferation was markedly inhibited, the percentage of cells in G0/G1 phase evidently increased and the percentage of cells in S phase decreased, and the number of migrating cells significantly and obviously decreased. The mRNA and protein expression levels of p21 and E-cadherin in the HDAC6 siRNA group were significantly higher than those in the untreated group and the control siRNA group, respectively. Conclusions: HDAC6 siRNA can effectively downregulate the expression of HDAC6 mRNA and protein in EC9706 cells. Down-regulation of HDAC6 expression can obviously inhibit cell proliferation, arrest cell cycling in the G0/G1 phase and reduce cell migration. The latter two functions may be closely related with the elevation of mRNA and protein expression of p21 and E-cadherin.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.30 no.3
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• pp.193-202
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• 2004

Distraction osteogenesis(DO) is defined as a gradual mechanical process of mechanical stretching two vascularized bone surface apart with a critical rate and rhythm such that new bone forms within the expanding gap, reliably bridges the gap, and ultimately remodels to normal structure. DO has become a mainstay in bone tissue engineering and has significantly improved our armamentarium for reconstructive craniomaxillofacial procedures. But the molecular and biological mechanisms that regulate the formation of new bone during distraction osteogenesis are not completely understood. BMPs are potent osteoinductive agents. Our hypothesis was that BMPs, especially BMP-2 and BMP-4, might play an importent role in the signaling pathways that link the mechanical forces created by distraction to biological responses and in promting new bone formation. Using a rabbit's mandible, we investigated the expression of BMP-2, -4 at different time points during distraction osteogenesis. The purpose of this study is to research the pattern of expression of BMP-2, -4 in new bone formation during distraction osteogenesis of the rabbit mandible. The experimental group was applied gradual distraction (0.7mm a day by twice a day, 4.9mm in total, for 7 days) and the control group was carried out osteotomy alone. They were examined clinically, histologically, and by RT-PCR analysis. On 3 days after osteotomy, the high level of expression of BMP-2, -4 was detected. But, the expression of BMP-4 was decreased during latency period. As distraction was started, its expression was increased and maintained till postoperative 28days. In control group, the expression of BMP-4was remarkably decreased till postoperative 14 days. On the other hand, the expression of BMP-2 was no difference between experimental group and control group. The expression of BMP-4 was maintanined at high level during the entire experimental period in both group. These findings suggested that excellent bone formation during distraction osteogenesis is associated with enhanced expression of BMP-4 genes by mechanical tension stress.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.34 no.5
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• pp.543-549
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• 2008

Distraction osteogenesis is a commonly used technique for mandibular lengthening, but changes in the temporomandibular joint(TMJ) have not been well documented. The TMJ is one of the most complex joint in the body and is composed of a fibrous surface layer, a proliferative zone, hypertrophic cartilage, and bone. The shape and role of the TMJ change and modify during a person's life-time. Possible complications that can arise after mandibular distraction include failure of the formation, failure of callus, infection, disturbance of TMJ and of occlusion. However, there are only a few reports on changes in the TMJ as a result of distraction osteogenesis. Hence, the goal of this study was to evaluate the change of the TMJ after experimental distraction of mandibular ramus in rabbit. We studied histological changes of mandibular condyle, articular disk and retrodiscal tissue, and also examined the collagen I gene expression and MMP-1 gene expression. The results were as follows. 1. In the histological staining, experimental condylar surface showed more thick fibrous articular layer and proliferative layer, compared with the control condyle and experimental articular disc showed thick and dense collagen fibers compared with the control disc. 2. In the collagen I and MMP-1 gene RT-PCR analysis, experimental discs showed increased collagen I expression compared with the control disc, while MMP-1 gene expression was decreased compared with the control disc. The retrodiscal tissue was almost equal expressions of the collagen I and MMP-1 genes compared with the control retrodiscal tissue. These findings suggest that histological and biomolecular changes occur in condyles and discs after unilateral mandibular distraction osteogenesis.

• The Journal of Korean Physical Therapy
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• v.22 no.3
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• pp.87-92
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• 2010

Purpose: The purpose of this study was to investigate the effect of electrical stimulation (ES) on the wound closure rate, collagen deposition, and TGF-${\beta}$1 mRNA expression in skin wound of rat. Methods: Twenty male Sprague-Dawley rats (222~271 g) were randomly divided into ES (n=10) and control group (n=10). The ES group received a cathodal stimulation with 50 V at 100 pps for 30 minutes for 7 days, while the control group was not given electrical stimulation. The wound closure rate, collagen density and TGF-${\beta}$1 mRNA ratio were measured. Results: The mean wound closure rates in the ES and control groups were $83.79{\pm}16.35$% and $51.57{\pm}17.76$%, respectively (p<0.001). The collagen density in the ES and control groups were $46.67{\pm}10.68$% and $25.03{\pm}13.09$%, respectively (p<0.001). The TGF-${\beta}$1 mRNA ratio in the ES and control groups were $1.35{\pm}0.60$ and $0.63{\pm}0.30$, respectively at 6 hours post-wound (p<0.01) and $1.69{\pm}0.47$ and $1.32{\pm}0.28$, respectively, at 7 days post-wound (p<0.05). Conclusions: ES accelerated the wound closure rate of skin incision wounds and was accompanied by an increase in collagen deposition in the regenerating dermis. In addition, ES increased TGF-${\beta}$1 mRNA expression during wound healing process. These findings suggest that ES may activate TGF-${\beta}$1 expression, and may increase synthesis activities of fibroblasts in regenerating skin wounds in rats.

• The Journal of Korean Medicine
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• v.23 no.4
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• pp.98-104
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• 2002

Objectives: Calpain, a calcium-dependent cysteine proteinase, may be one of the proteolytic enzymes that mediate cartilage degradation associated with rheumatoid arthritis. The object of this study is to ascertain immunohistochemically whether calpain is present in the inflamed joints of collagen-induced arthritis of rats, and examine the effect of Cortex Acanthopanacis Senticosi on the expression of calpain. Methods: Male Lewis rats, around 200g of body weight, were immunized with bovine type II collagen. After 3 weeks from first immunization, rats were divided into arthritic control (n=6) group and Cortex Acanthopanacis Senticosi-treated (n=6) group. Non-immunized rats served as the normal (n=6) group. All animals were sacrificed at 15 days post-treatment and tibiotarsal joints were removed. Calpain immunohistochemistry was performed on the midsagittal section of the tibiotarsal joint. Results: All animals of the control and treated groups showed ankylosing osteoarthritis. However, the animals of the treated group showed alleviation in the fibrous ankylosis, destruction of articular cartilage and destruction of subchondral bony tissue compared with the animals of the control group. Calpain was expressed in the chondrocyte lacunae of growing articular cartilage, in the skeletal muscle fibers, in the peripheral nerves, and in the vessel walls around the joints of all groups. In the control and treated groups, calpain was also expressed in proliferating synovial epithelia, subsynovial stroma cells, surface of articular cartilage, and fibrous pannus around destructive subchondral bony tissue. However, the expression density of calpain in the treated group was diminished compared with the control group, especially in surface of articular cartilage and fibrous pannus. Conclusions: These observations indicated that calpain plays an important role in the destruction of cartilage and bone in collagen-induced arthritis of rats, and also indicated that Cortex Acanthopanacis Senticosi inhibits the development of arthritis by decreasing the expression of calpain.

• Journal of Korean Neurosurgical Society
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• v.53 no.6
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• pp.337-341
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• 2013

Objective : After spinal cord injury (SCI), functional and structural reorganization occurs at multiple levels of brain including motor cortex. However, the underlying mechanism still remains unclear. The current study was performed to investigate the alterations in the expression of the main regulators of neuronal development, survival and death, in the brain following thoracic contusive SCI in a mouse model. Methods : Eight-week-old female imprinting control region mice (n=60; 30-35 g) were used in this study. We analyzed the expression levels of regulators such as brain-derived neurotrophic factor (BDNF), glial cell line-derived neurotrophic factor (GDNF), nerve growth factor (NGF) and histone deacetylase (HDAC) 1 in the brain following thoracic contusive SCI. Results : The expression of BDNF levels were elevated significantly compared with control group at 2 weeks after injury (p<0.05). The expression of NGF levels were elevated at 2, 4 weeks compared with control group, but these difference were not significant (p>0.05). The GDNF levels were elevated at 2 week compared with control group, but these differences were not significant (p>0.05). The difference of HDAC1 levels were not significant at 2, 4 and 8 weeks compared with control group (p>0.05). Conclusion : These results demonstrate that the upregulation of BDNF may play on important role in brain reorganization after SCI.

• Molecules and Cells
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• v.26 no.5
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• pp.474-480
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• 2008

OsMADS1 is a rice MADS box gene necessary for floral development. To identify the key cis-regulatory regions for its expression, we utilized transgenic rice plants expressing GUS fusion constructs. Histochemical analysis revealed that the 5.7-kb OsMADS1 intragenic sequences, encompassing exon 1, intron 1, and a part of exon 2, together with the 1.9-kb 5' upstream promoter region, are required for the GUS expression pattern that coincides with flower-preferential expression of OsMADS1. In contrast, the 5' upstream promoter sequence lacking this intragenic region caused ectopic expression of the reporter gene in both vegetative and reproductive tissues. Notably, incorporation of the intragenic region into the CaMV35S promoter directed the GUS expression pattern similar to that of the endogenous spatial expression of OsMADS1 in flowers. In addition, our transient gene expression assay revealed that the large first intron following the CaMV35S minimal promoter enhances flower-preferential expression of GUS. These results suggest that the OsMADS1 intragenic sequence, largely intron 1, contains a key regulatory region(s) essential for expression.

• The Journal of Korean Medicine
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• v.23 no.2
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• pp.211-224
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• 2002

Background and Objective : In order to investigate the effects of Gilgyunglwedok-tang (GRT) on antitumor activity and antimetastatic activity, studies were done experimentally. Materials and Methods : Experimental studies were perfonned for the cytotoxic effect on BALB/c mouse lung fibroblast cells, the proliferating effect of splenic lymphocyte, the expression of CD3e/CD4, CD3e/CD8, and B220 in peripheral blood mononuclear cells (PBMCs), the cytotoxic effect on A549, SK-OV-3, SK-MEL-2, MCF-7 cells, the inhibitory effect on the activity of DNA topoisomerase I, the T/C% in ICR mice bearing S-180, the inhibitory effect of Cell adhesive of A549 Cells and SK-OY-3 Cells to complex extracellular matrix, the inhibitory effect on lung colonies, the change of lung tissue, the antiangiogenic activity, and the effect on MMP-2 and MMP-9 gene expression in the RT1080 cell line. Results and Conclusion : The results were obtained as follows : 1. In the cytotoxic effect on BALB/C mouse lung fibroblast Cell, GHT didn't show the significant cytotoxic effect on BALB/C mouse lung fibroblast cell compared to the control group. 2. In thymidine uptake assay, GHT showed the significant proliferating effect of splenic lymphocyte in proportion to the concentration. 3. In the expression of CD3e/CD4, CD3e/CD8, and B220 in peripheral blood mononuclea cells (PBMCs) of mice, GRT had no significant change to the normal group in CD4. However, GRT showed an increase to the normal group in CD8 and GHT in the only $1\mu\textrm{g}/ml$ category showed an increase to the normal group in B220. 4. In the cytotoxic effect of GRT on A549, SK-OY-3, SK-MEL-2 and MCF-7 cells, there was no significant cytotoxic effect compared to the control group. 5. In the inhibitory effect on the activity of DNA topoisomerase I, GHT in the $10\mu\textrm{g}/ml$ category showed the inhibitory effect on the activity of DNA topoisomerase I in proportion to the concentration. 6. In the T/C% in ICRmice bearing S-180, GHTtreated group showed 123.7% of T/C% compared to the control group. 7. In the inhibitory effect of cell adhesive of A549 Cells and SK-OV-3 Cells to complex extracellular matrix, GRT in the only $100\mu\textrm{g}/ml$ category showed the significant inhibitory effect compared to the control group. 8. In the inhibitory effect on lung colonies, GHT showed the significant inhibitory effect on lung colonies compared to the control group. 9. In the change of lung tissue, GHT showed a significant decrease of lung cancer growth, interalveolar fibrosis and hyaline material compared to the control group. In the development of lymphocyte around lung cancer cells and lung parenchymal, GHT showed the significant inducement efficacy compared to the control group. 10. In CAM assay, the antiangiogenic activity of GHT showed 30%. 11. In the effect on MMP-2 and MMP-9 gene expression in the RT1080 cell line, GHT had no significant inhibitory effect on MMP-2 and MMP-9 gene expression compared to the control group. According to the above results, it could be suggested that GHT has an antitumor activity and antimetastatic activity.