• Horticultural Science & Technology
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• v.29 no.6
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• pp.633-640
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• 2011

Brassica rapa is an A genome model species for Brassica crop genetics, genomics, and breeding. With the completion of sequencing the B. rapa genome, functional analysis of the genome is forthcoming issue. The expressed sequence tags are fundamental resources supporting annotation and functional analysis of the genome including identification of tissue-specific genes and promoters. As of July 2011, 147,217 ESTs from 39 cDNA libraries of B. rapa are reported in the public database. However, little information can be retrieved from the sequences due to lack of organized databases. To leverage the sequence information and to maximize the use of publicly-available EST collections, the Brassica rapa tissue-specific EST database (BrTED) is developed. BrTED includes sequence information of 23,962 unigenes assembled by StackPack program. The unigene set is used as a query unit for various analyses such as BLAST against TAIR gene model, functional annotation using MIPS and UniProt, gene ontology analysis, and prediction of tissue-specific unigene sets based on statistics test. The database is composed of two main units, EST sequence processing and information retrieving unit and tissue-specific expression profile analysis unit. Information and data in both units are tightly inter-connected to each other using a web based browsing system. RT-PCR evaluation of 29 selected unigene sets successfully amplified amplicons from the target tissues of B. rapa. BrTED provided here allows the user to identify and analyze the expression of genes of interest and aid efforts to interpret the B. rapa genome through functional genomics. In addition, it can be used as a public resource in providing reference information to study the genus Brassica and other closely related crop crucifer plants.

• Korean Journal of Poultry Science
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• v.46 no.1
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• pp.31-37
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• 2019

A chicken clathrin-associated adaptor protein $3-{\delta}$ subunit 2 (AP3S2) is a subunit of AP3, which is involved in cargo protein trafficking to target membrane with clathrin-coated vesicles. AP3S2 may play a role in virus entry into host cells through clathrin-dependent endocytosis. AP3S2 is also known to participate in metabolic disease developments of progressions, such as liver fibrosis with hepatitis C virus infection and type 2 diabetes mellitus. Chicken AP3S2 (chAP3S2) gene was originally identified as one of the differentially expressed genes (DEGs) in chicken kidney which was fed with different calcium doses. This study aims to characterize the molecular characteristics, gene expression patterns, and transcriptional regulation of chAP3S2 in response to the stimulation of Toll-like receptor 3 (TLR3) to understand the involvement of chAP3S2 in metabolic disease in chicken. As a result, the structure prediction of chAP3S2 gene revealed that the gene is highly conserved among AP3S2 orthologs from other species. Evolutionarily, it was suggested that chAP3S2 is relatively closely related to zebrafish, and fairly far from mammal AP3S2. The transcriptional profile revealed that chAP3S2 gene was highly expressed in chicken lung and spleen tissues, and under the stimulation of poly (I:C), the chAP3S2 expression was down-regulated in DF-1 cells (P<0.05). However, the presence of the transcriptional inhibitors, BAY 11-7085 (Bay) as an inhibitor for nuclear factor ${\kappa}B$ ($NF{\kappa}B$) or Tanshinone IIA (Tan-II) as an inhibitor for activated protein 1 (AP-1), did not affect the expressional level of chAP3S2, suggesting that these transcription factors might be dispensable for TLR3 mediated repression. These results suggest that chAP3S2 gene may play a significant role against viral infection and be involved in TLR3 signaling pathway. Further study about the transcriptional regulation of chAP3S2 in TLR3 pathways and the mechanism of chAP3S2 upon virus entry shall be needed.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.63 no.1
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• pp.25-34
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• 2018

This study was conducted to investigate the germination and proteome profile characteristics of wheat seeds treated under various concentrations of abscisic acid (ABA). After-ripening, the seeds of three wheat cultivars (Baegjoong, Keumkang, and Uri) showing different levels of dormancy were used. Germination index and germination rate of the cultivars was higher than 0.95% and 98%, respectively, and these were not significantly different under 0, 10, 30, and $50{\mu}M$ ABA at 7 d after germination. However, the growth of the shoot and radicle was significantly inhibited at 10, 30, and $50{\mu}M$ ABA compared to that at $0{\mu}M$ ABA. Mean ABA content of the embryos of seeds germinated at 0 and $50{\mu}M$ ABA for 7 d was 0.8 and $269.0ngmg^{-1}DW$, respectively. Proteins extracted from embryos germinated for 4 d were analyzed by two-dimensional gel electrophoresis, and proteins showing a difference of 1.5-fold or greater in their spot volume relative to that of $0{\mu}M$ ABA were identified. The expression of four protein spots increased at $50{\mu}M$ ABA and two protein spots were detected only at $50{\mu}M$ ABA; these six proteins were all identified as globulin types. Conversely, the expression of three protein spots decreased at $50{\mu}M$ ABA and were identified as cytosolic glutamine sysnthetase, isocitrate dehydrogenase, and S-adenosylmethionine synthetase 2. In conclusion, ABA did not inhibit the germination rate regardless of pre-harvest sprouting characteristics of the cultivars. However, the growth of the shoot and radicle was significantly inhibited by ABA, most likely through the down regulation of glutamine, methyl group donor, and polyamines biosynthesis, among others, while accompanied by globulin accumulation in the embryos.

• Journal of Applied Biological Chemistry
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• v.61 no.2
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• pp.141-150
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• 2018

In this study, the inflammation of ethanol extracts from Caryopteris incana (CI) and fermented C. incana (FCI) on induced to lipopolysaccharide with Raw 264.7 cell was tested. The composition profile of L. plantarum was changed by fermentation, and confirmed by HPLC analysis. We performed the 3-[4,5-dimethylthiazol]-2-yl]-2,5-diphenyltetrazolium bromide assay to evaluate the toxicity of CI and FCI extracts. In cell viability, cell toxicity was not shown at 5, 10 and $15{\mu}g/mL$ of CI extracts and 10, 20, 30 and $40{\mu}g/mL$ of FCI extracts. The results of inducible nitric oxide synthase and cyclooxygenase-2 protein production were confirmed to be inhibitory in a concentration-dependent manner, respectively. Additionally, protein expression of nitric oxide and prostaglandin $E_2$ by CI and FCI extracts were also inhibited in a concentration-dependent manner. In the result of pro-inflammatory cytokine, $15{\mu}g/mL$ concentration of CI extracts was showed tumar necrosis factor $(TNF)-{\alpha}$ (57.3%), interleukin (IL)-6 (35.2%), and $IL-1{\beta}$ (48.0%), respectively. And $40{\mu}g/mL$ of FCI extracts was showed $TNF-{\alpha}$ (34.6%), IL-6 (32.1%), and $IL-1{\beta}$ (30.0%), respectively. These results suggest that FCI extracts showed better effect of anti-inflammatory than CI extracts. Therefore, it was found that both CI and FCI can be used as an excellent material for the development of new anti-inflammatory resource.

• Journal of Oral Medicine and Pain
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• v.32 no.2
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• pp.137-150
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• 2007

Trees emit phytoncide into atmosphere to protect them from predation. Phytoncide from different trees has its own unique fragrance that is referred to as forest bath. Phytoncide, which is essential oil of trees, has microbicidal, insecticidal, acaricidal, and deodorizing effect. The present study was performed to examine the effect of phytoncide on Porphyromonas gingivalis, which is one of the most important causative agents of periodontitis and halitosis. P. gingivalis 2561 was incubated with or without phytoncide extracted from Hinoki (Chamaecyparis obtusa Sieb. et Zucc.; Japanese cypress) and then changes were observed in its cell viability, antibiotic sensitivity, morphology, and biochemical/molecular biological pattern. The results were as follows: 1. The phytoncide appeared to have a strong antibacterial effect on P. gingivalis. MIC of phytoncide for the bacterium was determined to be 0.008%. The antibacterial effect was attributed to bactericidal activity against P. gingivalis. It almost completely suppressed the bacterial cell viability (>99.9%) at the concentration of 0.01%, which is the MBC for the bacterium. 2. The phytoncide failed to enhance the bacterial susceptibility to ampicillin, cefotaxime, penicillin, and tetracycline but did increase the susceptibility to amoxicillin. 3. Numbers of electron dense granules, ghost cell, and vesicles increased with increasing concentration of the phytoncide, 4. RT-PCR analysis revealed that expression of superoxide dismutase was increased in the bacterium incubated with the phytoncide. 5. No distinct difference in protein profile between the bacterium incubated with or without the phytoncide was observed as determined by SDS-PAGE and immunoblot. Overall results suggest that the phytoncide is a strong antibacterial agent that has a bactericidal action against P. gingivalis. The phytoncide does not seem to affect much the profile of the major outer membrane proteins but interferes with antioxidant activity of the bacterium. Along with this, yet unknown mechanism may cause changes in cell morphology and eventually cell death.

• Molecules and Cells
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• v.45 no.12
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• pp.896-910
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• 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and potentially fatal virus. So far, most comprehensive analyses encompassing clinical and transcriptional manifestation have concentrated on the lungs. Here, we confirmed evident signs of viral infection in the lungs and spleen of SARS-CoV-2-infected K18-hACE2 mice, which replicate the phenotype and infection symptoms in hospitalized humans. Seven days post viral detection in organs, infected mice showed decreased vital signs, leading to death. Bronchopneumonia due to infiltration of leukocytes in the lungs and reduction in the spleen lymphocyte region were observed. Transcriptome profiling implicated the meticulous regulation of distress and recovery from cytokine-mediated immunity by distinct immune cell types in a time-dependent manner. In lungs, the chemokine-driven response to viral invasion was highly elevated at 2 days post infection (dpi). In late infection, diseased lungs, post the innate immune process, showed recovery signs. The spleen established an even more immediate line of defense than the lungs, and the cytokine expression profile dropped at 7 dpi. At 5 dpi, spleen samples diverged into two distinct groups with different transcriptome profile and pathophysiology. Inhibition of consecutive host cell viral entry and massive immunoglobulin production and proteolysis inhibition seemed that one group endeavored to survive, while the other group struggled with developmental regeneration against consistent viral intrusion through the replication cycle. Our results may contribute to improved understanding of the longitudinal response to viral infection and development of potential therapeutics for hospitalized patients affected by SARS-CoV-2.

• Journal of Life Science
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• v.34 no.7
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• pp.509-519
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• 2024

A previous study showed that krill oil improved recognition and memory through anti-oxidative effects in an amyloid β model, but the authors noted that further investigations are necessary of alterations to neurotransmitters' states and of serum lipid profile improvements related to serum lipid peroxidation. Accordingly, in this study, ICR mice were pre-treated intraperitoneally with scopolamine prior to induced neurotransmission impairment, and the effects of krill oil provision on their capabilities of cognition were tested by performing a passive avoidance test (PAT), water maze test (WMT), and novel object recognition test. Then, parameters including the acetylcholine (ACh) concentration, acetylcholinesterase activity (AChE), lipid peroxidation, serum lipid levels, and nerve cell proliferation were investigated. The results showed that krill oil improved the mice's abilities in recognition and memory as the times taken to complete the PAT and WMT were reduced compared to the mice in a comparison scopolamine-treated group. Krill oil produced an increased concentration of Ach, and this was accompanied by a decrease in AChE. As shown in a scopolamine-treated SH-SY5Y cell line, krill oil reduced the activity of AChE. Moreover, the suppression of lipid peroxidation-reflected in the finding that malondialdehyde was decreased with krill oil provision-is speculated to affect the recorded serum triglyceride and cholesterol decreases and LDL cholesterol increase. The intake of krill oil was also found to produce an improvement in brain-derived neurotrophic factor expression by stimulating the activation of cyclic AMP response element binding protein in the brain tissue. Overall, the current results imply that the provision of krill oil raises the cognition and memory by elevating neurotransmitters and by improving the serum lipid profile and nerve cell proliferation, which occur as lipid peroxidation is suppressed in the brain tissue.

• Journal of Physiology & Pathology in Korean Medicine
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• v.16 no.5
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• pp.1025-1034
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• 2002

The herbal extract (YMT_02) is a modified herbal extracts from Yukmijihwang-tang (YMJ) to promote memory-enhancing. The YMJ extracts has been widely used as an anti-aging herbal medicine for hundred years in Asian countries. The purpose of this study is to; 1) quantitatively evaluate the memory-enhancing effect of YMT_02 by behavior task, 2) identify candidate genes responsible for enhancing memory by cDNA microarray and 3) assess the anti-oxidant effect of YMT_02 on PC12 cell. Memory retention abilities are addressed by passive avoidance task with Sprague-Dawley (SD) male rat. Before the training session, the rats are subdivided into four groups and administrated with YMT_02, Ginkgo biloba, Soya lecithin and normal saline for 10 days. The retention test was performed. 24 hours after the training session. The retention time of the YMT_02 group was significantly (p<0.05) delayed (～100%), whereas Ginkgo biloba and Soya lecithin treatment delayed 20% and 10% respectively. The hippocampi of YMT_02 and control group were dissected and mANA was further purified. After synthesizing cDNA using oligo-dT primer, the cDNA were applied to Incyte rat GEMTM 2 cDNA microarray. The microarray results show that prealbumin(transthyretin), phosphotidylethanolamine N-methyltransferase, and PEP-19 are expressed abundantly in the YMT_02 treated group. Especially, PEP-19 is a neuron-specific protein, which inhibits apoptotic processes in neuronal cell. On the other hand, transcripts of RAB15, glutamate receptor subunit 2 and CDK108 are abundant in control group. Besides, neuronal genes involved in neuronal death or neurodegeneration such as neuronal-pentraxin and spectrin are abundantly expressed in control group. Additionally, the YMT_02 shows an anti oxidative effect in the PC12 cell. The list of differentially expressed genes may implicate further insight on the action and mechanism behind the memory-enhancing effect of herbal extracts YMT_02, for example, anti-apoptotic, anti-oxidative, and neuroprotective effects.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.19
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• pp.8377-8382
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• 2014

Background: Oral squamous cell carcinoma (OSCC) is the sixth most common malignancy worldwide. Cancer development and progression require inactivation of tumor suppressor genes and activation of proto-oncogenes. The well recognized mechanism of action demonstrated for chemotherapeutic agents is induction of apoptosis via reactivation of p53. In this context, we evaluate the efficacy of IV and oral routes of our novel PH and temperature sensitive doxorubicin-methotrexate-loaded nanoparticles (DOX-MTX NP) in affecting p53 profile in an OSCC rat model. Methods: In this study, 120 male rats were divided into 8 groups of 15 animals each. The new formulated DOX-MTX NP and free doxorubicin were IV and orally given to rats with 4-nitroquinoline-1-oxide induced OSCC. Results: Results showed that both DOX and DOX-MTX-NP caused significant increase in mRNA levels of P53 compared to the untreated group (p<0.000). With both DOX and DOX-MTX NP, the IV mode was more effective than the oral (gavage) route (p<0.000). Surprisingly, in oral mode, p53 mRNA was not affected in DOX treated groups (p>0.05), Nonetheless, both IV and oral administration of MTX-DOX NP showed superior activity (~3 fold) over free DOX in reactivation of p53 in OSCC (p<0.000). The effectiveness of oral route in group treated with nanodrug accounts for the enhanced bioavailability of nanoparticulated DOX-MTX compared to free DOX. Moreover, in treated groups, tumor stage was markedly related to the amount of p53 mRNA (p<0.05). Conclusion: Both oral and IV application of our novel nanodrug possesses superior activity over free DOX-in up-regulation of p53 in a OSCC model and this increase in p53 level associated with less aggressive tumors in our study. Although, impressive results obtained with IV form of nanodrug (-21 fold increase in p53 mRNA level) but both forms of nanodrug are effective in OSCC, with less toxicity normal cells.

• Journal of Nutrition and Health
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• v.51 no.5
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• pp.369-378
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• 2018

Purpose: Obesity is associated with a dysregulation of metabolic balance and is regarded as a low grade chronic inflammation. Western-style diet and physical inactivity are leading causes of obesity. This study examined the profiles of forty plasma cytokines and chemokines at the same time in the early stages of high-fat diet-induced obesity using a mouse model. Methods: A total of 30 male CD1 mice, 12 ~ 14 weeks of age, were enrolled. The mice were fed a high-fat diet for 6 weeks to induce obesity. The plasma glucose and triglyceride concentrations were measured using a hexokinase colorimetric assay kit and a serum triglyceride determination kit, respectively. The relative levels of multiple cytokines and chemokines in the plasma were determined using a mouse cytokine array kit. Results: The mice exhibited significant weight gain after 6 weeks of a high-fat diet. The genital fat depot was enlarged along with an increase in the number and the mean size of white adipocytes as early as 4 weeks after a high-fat diet. In addition, the plasma glucose and triglyceride levels increased significantly after 4 weeks of a high-fat diet. Cytokine array analysis revealed a remarkable increase in the expression of both CXCL12 and CXCL13, whereas the proinflammatory cytokines remained low after 4 weeks of a high-fat diet. Conclusion: A significant increase in plasma levels of CXCL12 and CXCL13 was observed after 4 weeks of a high-fat diet, which might induce the migration of B lymphocytes, T lymphocytes, and monocytes from the blood to expanding adipose tissue or fat associated lymphoid clusters, playing a key role in adipose tissue remodeling and local immunity during the early stages of high-fat diet-induced obesity.