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Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

  • Lee, Yu-No;Bang, Woo-Young;Kim, Song-Mi;Lazar, Prettina;Bahk, Jeong-Dong;Lee, Keun-Woo
    • Interdisciplinary Bio Central
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    • v.1 no.1
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    • pp.3.1-3.6
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    • 2009
  • Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

Results of Treatment for Children with Primary Brain Tumors : Long-Term Follow Up Results of a Single Institute (소아 원발성 뇌종양의 치료 결과 : 단일 기관에서의 장기간 추적 관찰)

  • Choi, Sung-Yeon;Won, Sung-Chul;Lyu, Chuhl-Joo;Oh, Seung-Hwan;Yang, Chang-Hyun;Suh, Chang-Ok;Choi, Joong-Uhn;Kim, Byung-Soo
    • Clinical and Experimental Pediatrics
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    • v.45 no.8
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    • pp.1016-1023
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    • 2002
  • Purpose : Brain tumors are the most common solid tumor in children. We retrospectively investigated the clinical characteristics of pediatric brain tumors, such as age, sex, tumor site and survival, as seen in a single institution over the last 15 years. We tried to evaluate the role of chemotherapy on the survival of some brain tumors. Methods : Three hundred fifty four children with primary brain tumor who were treated at Severance Hospital from Jan. 1985 to Sep. 2001 were enrolled. Results : Pediatric brain tumors were found most frequently in 10-15 years of age group(35.3%) and the ratio of male to female was 1.3 : 1. Supratentorial tumors(52%) were more frequent than infratentorial tumors(48%). Medulloblastoma/primitive neuroectodermal tumor(PNET) was the most common type(24.6%), followed by cerebellar astrocytoma(14.1%). Ten year survival rate of medulloblastoma, cerebellar astrocytoma and cerebral astrocytoma were 59.4%, 79.3% and 71%, respectively. The prognosis for brain stem glioma and glioblastoma multiforme were still grim with a 10 year survival rate of 12.7% and 13.3%, respectively. The addition of chemotherapy for high grade medulloblastoma led to an improved 10 year survival rate of 54.5%, compared with 40% without chemotherapy. Conclusion : The combined use of chemotherapy and radiation and surgery improved survival rate of pediatric brain tumors in our study. Chemotherapy for high grade medulloblastoma improved the 10 year survival rate. Further data analysis of the treatment modalities will lead to better comparisons.

Evaluation of short-term cardiac function by tissue Doppler imaging in pre and postoperative period of congenital heart disease (조직 도플러 영상을 이용한 선천성 심장병 수술 전후의 단기 심기능 평가)

  • Lee, Jun-Hwa;Kim, Yeo-Hyang;Hyun, Myung-Chul;Lee, Sang-Bum
    • Clinical and Experimental Pediatrics
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    • v.50 no.5
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    • pp.476-483
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    • 2007
  • Purpose : The objective of this study was to assess ventricular function by tissue Doppler imaging (TDI) in children with congenital heart disease (CHD) who have been undergoing open heart surgery (OHS) using cardiopulmonary bypass. We tried to compare the parameters of tissue Doppler imaging before and after OHS in patients with congenital heart disease. Methods : This study was conducted on 32 patients with CHD after OHS from January 2005 to December 2005 at Kyungpook National University hospital. Patients who underwent 2-D echocardiography before and after their OHS. All patients were divided into three groups, left ventricular volume overloading group (group 1), and right ventricular volume overloading group (group 2), and right ventricular pressure overloading group (group 3). The TDIs were examined before and 1 to 3 months after OHS. Peak early diastolic (E), and peak late diastolic (A) velocity of transmitral flow were measured by pulsed wave Doppler examination. Peak systolic (Sm), peak early diastolic (Em), and peak late diastolic (Am) velocity in apical 4-chamber and 2-chamber views were measured by TDI. The author calculated E/Em ratio. Results : The patients were 14 boys and 18 girls and the average age of patients was 2 years and 3 months. The congenital heart diseases which have to get OHS were ventricular septal defect (13 cases), atrial septal defect (7), atrioventricular septal defect (3), isolated pulmonary stenosis (2) and tetralogy of Fallot (7). There were significant decrease of Sm, Em, Am measured on tricuspid annulus and E/Em measured on mitral annulus in apical 4 chamber view (P<0.05). Conclusion : This study showed significant decrease of Sm, Em, Am measured on tricuspid annulus and E/Em measured on mitral annulus in apical 4 chamber view after OHS. These changes might be due to the effects of cardiopulmonary bypass in OHS and/or hemodynamic changes after correction of congenital heart disease. To clarify these changes, further study on more patients is needed.

A Study of Correlation among the Knowledge of the Disease, Health Promoting Behaviors and the Quality of Life in the Female Patients with Osteoporosis (여성 골다공증환자의 골다공증에 대한 지식, 건강증진행위 및 삶의 질과의 관계 연구)

  • Lee, Hye-Young
    • Journal of muscle and joint health
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    • v.8 no.1
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    • pp.65-85
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    • 2001
  • Osteoporosis is the disease that is the most controversial issue with the aging tendency in 1990. It is an important issue in dealing with the health management for women in middle life. This study is designed to determine the relationships among the level of the knowledge of osteoporosis, the health promoting behaviors and the quality of life. The test has conducted a questionnaire survey of women with osteoporosis. This is a study that focused an interrelation of above issues and its purpose is to gain a foundation of a nursing intervention that can help to improve the qualify of life of an osteoporosis patients. The method of collecting data is collecting a questionnaire survey, individual interviews and records and the collected 123 questionnaire surveys are utilized for an data analysis. Questionnaire surveys are conducted in K and S Universities infirmaries and K general hospital in Seoul and C and J general hospital in near Seoul area from Sep. 27th to Nov. 4th, 2000. The instruments of this study were as follows: Yoon's used the revised and supplemented instrument to test the level of the knowledge of osteoporosis and she referred to the substance of Cassells & Knotz. Lee's revised and supplemented the instrument called Health Promoting Life style Profile that were invented by Walker, Sechrist & Pender and she used it to test the health promoting behaviors with the questionnaires added by this researcher. They are not related to the quality of life but relevant to the patients. Ro's tested the quality of life with the instrument that was invented by herself. The results of this study were as follows. 1. The general characteristics of this study subjects showed that the age of the patients was concentrated from 50 to 59. The periods after menopause was mainly from 6 to 10 years. Subjective symptoms that patients usually complain were musculoskelectal symptoms. 2. The results of measuring the level of the knowledge of osteoporosis, the health promoting behaviors and the quality of life were following. The level of the knowledge was the score 19.83 and it was above middle score out of the score 27 as full marks. In the result of the health promoting behaviors test, the score average was 2.58 with 4 point rating scale and it was about middle score. The quality of life test showed that average score was 2.92 with 5 point rating scale and it indicated that the quality was also around middle score. 3. The statistical test in the activities for promoting health according to the general characteristics of the patients showed that only monthly income has statistically significant difference(F-4.761, p=.004). The same test for the qualify of life indicated that the quality of life was higher from 1 to 5 years after menopause but it was not meaningful statistically. 4. In the correlation among the level of knowledge of osteoporosis, the health promoting behaviors and the qualify of life of the patients, showed a relationship between the health promoting behaviors and the qualify of life. The higher the health promoting behaviors, it was also higher the quality of life. But it was statistically significant with significant positive correlation.

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Comparative Pathology of chickens Experimentally Inoculated with Virulent Viscerotropic Newcastle Disease Viruses isolated in Korea (강병원성 뉴캣슬병 바이러스 한국분리주의 SPF 닭 접종에 따른 병리학적 변화 비교)

  • I. P. Mo;Y. K. Kwon;M. G. Han;H. W. Seong
    • Korean Journal of Poultry Science
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    • v.28 no.2
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    • pp.99-106
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    • 2001
  • Pathologic changes and distribution of viral antigen as determined by immunohistochemistry were compared among 4-wk-old specific-pathogen free (SPF) chickens inoculated intratracheally with velogenic vis-cerotropic Newcastle disease virus isolated in Korea. Although the pattern of organ involvement and severity of lesion was different among chickens infected with different velogenic viscerotropic Newcastle disease (VVND) viruses, the pathological types of lesion was similar among the chickens. Severe lymphocytic necrosis and depletion were main histologic lesions in the immune related organs such as thymus, Fabricius bursa and spleen. The frequency of IP positive staining was variable depends on the types of tissues but not types of the kinds of VVND viruses infected. Brain, Fabricius bursa, thymus, cecal tonsil and trachea were IP positive with fairly high frequency and spleen, lung, proventriculus, intestine, pancreas, liver, kidney, heart and Harderian gland were with relatively low frequency. These results suggest that histologic evaluation and viral antigen specific immunohistochemical staining methods to determine virus distribution will be useful for pathogenic study of velogenic viscerotropic Newcastle disease virus infection in chicken.

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A Survey of Japanese Perception of and Preference for Korean Foods (한국음식에 대한 일본인의 인식 및 기호도 조사)

  • ;;;;Kimiko Otan;Takahisa Minamide
    • Korean journal of food and cookery science
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    • v.14 no.2
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    • pp.188-194
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    • 1998
  • The purpose of this study was to provide those abroad with information about Korean foods and food culture by investigating the Japanese perception and preference for Korean foods. The results were as follows: 53.2% of the Japanese students had much interest in Korean foods and most of students (93.2%) were experience In eating Korean foods. On their first impression of Korean foods, 67.8% of the students answered that it was 'good', and 74.1% of answered their impression after eating Korean foods was 'good'. 83.1% of the students also answered that Korean foods suited their taste because they were 'delicious'. But 16.9% of the students answered that the Korean foods did not suit them because they were too spicey. The most well-known (99.3%) and eaten (96.3%) Korean food by Japanese stutents turned out to be Kimchi. In the preference test for Korean foods, Samgyetang was estimated the most delicious food. In the comparision between Korean Kimchi and Japanese Kimchi, the former was estimated more delicious and spicier than the latter.

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Study of Utilization of Dental High School and according to the Pain Experienced Dental Fear (고등학생의 치과이용실태와 통증 경험에 따른 치과공포에 대한 연구)

  • Jun, Bo-Hye;Choi, Young-Suk
    • Journal of dental hygiene science
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    • v.14 no.1
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    • pp.59-66
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    • 2014
  • The purpose of this study was to study of utilization of dental high school and according to the pain experienced dental fear and anxiety. This survey was conducted on 370 high school students in Suwon from November 21 to 23, 2011. A total of 352 questionnaires were collected and analyzed. The collected data was analyzed using the statistical package SPSS 15.0 using frequency, mean and standard deviation analysis, t-test, one-way ANOVA, Duncan's test correlation analysis and Stepwise multiple regression analysis. The results state that students feel fear and anxiety were feeling anesthetic needle ($3.19{\pm}1.43$), seeing anesthetic needle ($3.14{\pm}1.44$). We found that students feel more rear and anxiety from caries treatment than scaling. It influence that having dental fear with past dental pain experienced during dental treatment and also hearing dental treatment of pain from their family and friends. We found out that there are some influencing factors on dental fear and anxiety, gender, oral health condition, smoking, pain experienced during dental treatment. We need to care dental fear and anxiety continuously and have prevention program. We have to try understanding students have dental fear and anxiety. So it's better they have good experience visiting dental clinic. We should develop the system and specially treat well while they have dental treatment with anesthesia and some sharp instruments.

Effects of Ethanol Extracts from Commonly Consumed Vegetables in Korea on Differentiation and Secretion of MCP-1 and Adiponectin in 3T3-L1 Adipocytes and Lipid Accumulation in HepG2 Hepatocytes (한국인 다소비 채소의 에탄올 추출물이 3T3-L1 지방세포와 HepG2 간장세포의 지질축적, MCP-1과 Adiponectin의 분비에 미치는 영향)

  • Ahn, Eun Mi;Kang, Hyun Ju;Kim, Young;Choe, Jeong Sook;Kang, Min-Sook
    • Journal of the East Asian Society of Dietary Life
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    • v.25 no.1
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    • pp.99-110
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    • 2015
  • The purpose of this study was to evaluate the inhibitory effects of commonly consumed vegetables in Korea on lipid accumulation and production of pro-inflammatory cytokines related to obesity/metabolic syndrome. Using KNHANES (Korea National Health and Nutrition Examination Survey) raw data ($1^{st}$; 1998, $5^{th}$; 2010, 2011) and a literature search, we selected vegetables for study. Edible portions of samples were prepared, ethanol-extracted, and then freeze-dried. 3T3-L1 adipocytes and HepG2 hepatocytes cells were used as in vitro models. Lipid accumulation determined by Oil-red O staining showed that all samples except bracken had inhibitory effects on lipid accumulation in 3T3-L1 adipocytes. Especially, crown daisy and mugwort effectively reduced accumulation of lipids, and their inhibition rates were more than 60% of the control group. Young pumpkin, leeks, crown daisy, and mugwort showed significantly decreased MCP-1 levels compared to the control group. However, adiponectin protein level did not increase in the vegetables experimental group. In HepG2 hepatocytes, all samples showed inhibitory effects on lipid accumulation at one of the two concentrations. Although adiponectin protein levels did not increase, MCP-1 protein levels decreased in adipocytes. Further, lipid accumulation in adipocytes and hepatocytes decreased. In conclusion, all samples showed one or more improved obesity/metabolic syndrome indicators. Among them, young pumpkin, leeks, crown daisy, and mugwort were selected as the most effective portions of vegetables based on improvement of obesity/metabolic syndrome-related indicators.

Changes of General Components and Aromatic Constituents in Codonopsis lanceolata Grown at The Native and Cultivated Area (재배장소에 따른 더덕의 일반성분과 향기성분의 조성변화)

  • 이승필
    • Korean Journal of Plant Resources
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    • v.9 no.3
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    • pp.230-238
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    • 1996
  • The experiment was carried out to find aromatic constituent composition of Codonopsis lanceolata species grown in the native(Mt. lrwol, Youngyang, Kyungpuk Province) and the cultivated(Andong, Kyungpuk Province) areas from 1994 to 1995. The results were as follows : Air temperature and soil temperature at the native area were lower to $2{\sim}3^{\circ}C$, and to $2^{\circ}C$ than the cultivated area. Organic matter contents of plant grown at the native area higher than that of plants at the cultivated area by 4.8%. Crude protein content was higher in plant grown at native area than the plant grown in wild area but in case of crude saponin, plants grown at wild area was higher than that of native area. For inorganic element contents. K content is much higher than in the domesticated area as compared with wild area above ten over. And other elements such as Cu, Mn, Na and Mg were not remarkably different in contents. In the free amino acid compositions, argine was highest compared with other free amino acids, and Arginine content was higher in dometicated area. Recovery yield of essential oil of wild species grown at the cultivated showed 0.005%, but domesticated species was 0.004%. But both species at the native area were the same by 0.004%. Although composition of aromatic constituents in the two areas and species varied, total aromatic constituent was 21 kinds. Most aromatic constituents were aliphatic alcohols such as 1-hexanol, eis-3-hexanol, and trans-2-hexanol occupied by approximately 90% over. But three constituets as amylalcohol, furfuryl acetate, and 2-methoxy-4-vinyl phenol(MVP) were detected only in domesticated species.

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Protection of UV-derived Skin Cell Damage and Anti-irritation Effect of Juniperus chinensis Xylem Extract (향나무추출물의 광손상으로부터 피부세포 보호와 자극완화 효과에 대한 연구)

  • 김진화;박성민;심관섭;이범천;표형배
    • Journal of the Society of Cosmetic Scientists of Korea
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    • v.30 no.1
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    • pp.63-71
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    • 2004
  • The human skin is constantly exposed to environmental irritants such as ultraviolet, smoke, chemicals. Free radicals and reactive oxygen species (ROS) caused by these environmental facts play critical roles in cellular damage. These irritants are in themselves damaging to the skin structure but they also participate the immensely complex inflammatory reaction. The purpose of this study was to investigate the skin cell protective effect of Juniperus chinensis xylem extract on the UV and SLS-induced skin cell damages. We tested free radical and superoxide scavenging effect in vitro. We found that Juniperus chinensis xylem extracts had potent radical scavenging effect by 98% at 100 $\mu\textrm{g}$/mL. Fluorometric assays of the proteolytic activities of matrix metalloproteinase-l(MMP-1, collagenase) were performed using fluorescent collagen substrates. UV A induced MMP-1 synthesis and activity were analyzed by enzyme-linked immunosorbent assay (ELISA) and gelatin-based zymography in skin fibroblasts. The extract of Juniperus chinensis showed strong inhibitory effect on MMP-1 activities by 97% at 100 $\mu\textrm{g}$/mL and suppressed the UVA induced expression of MMP-1 by 79% at 25 $\mu\textrm{g}$/mL. This extract also showed strong inhibition on MMP-2 activity in UVA irradiated fibroblast by zymography. We also examined anti-inflammatory effects by the determination test of proinflammatory cytokine, interleukin 6 in HaCaT keratinocytes. In this test Juniperus chinensis decreased expression of interleukin 6 about 30%. Expression of prostaglandin E$_2$, (PGE$_2$) after UVB irradiation was measured by competitive enzyme immunoassay (EIA) using PGE$_2$ monoclonal antibody. At the concentrations of 5-50 $\mu\textrm{g}$/mL of the extracts, the production of PGE$_2$ by HaCaT keratinocytes (24 hours after 10 mJ/$\textrm{cm}^2$ UVB irradiation) was significantly inhibited in culture supernatants (p〈0.05). The viability of cultured HaCaT keratinocytes was significantly reduced at the doses of above 10 mJ/$\textrm{cm}^2$ of UVB irradiation, but the presence of these extracts improved cell viability comparing to control after UVB irradiation. We also investigated the protective effect of this extract in sodium lauryl sulfate (SLS)-induced irritant skin reactions from 24 hour exposure. Twice a day application of the extract for reducing local inflammation in human skin was done. Irritant reactions were assessed by various aspects of skin condition, that is, erythema (skin color reflectance) and transepidermal water loss (TEWL). After 5 days the extract was found to reduce SLS-induced skin erythema and improve barrier regeneration when compared to untreated symmetrical test site. In conclusion, our results suggest that Juniperus chinensis can be effectively used for the prevention of UV and SLS-induced adverse skin reactions such as radical production, inflammation and skin cell damage.