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Genome-wide survey and expression analysis of F-box genes in wheat

  • Kim, Dae Yeon;Hong, Min Jeong;Seo, Yong Weon
    • Proceedings of the Korean Society of Crop Science Conference
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    • pp.141-141
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    • 2017
  • The ubiquitin-proteasome pathway is the major regulatory mechanism in a number of cellular processes for selective degradation of proteins and involves three steps: (1) ATP dependent activation of ubiquitin by E1 enzyme, (2) transfer of activated ubiquitin to E2 and (3) transfer of ubiquitin to the protein to be degraded by E3 complex. F-box proteins are subunit of SCF complex and involved in specificity for a target substrate to be degraded. F-box proteins regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence. However, little is known about the F-box genes in wheat. The draft genome sequence of wheat (IWGSC Reference Sequence v1.0 assembly) used to analysis a genome-wide survey of the F-box gene family in wheat. The Hidden Markov Model (HMM) profiles of F-box (PF00646), F-box-like (PF12937), F-box-like 2 (PF13013), FBA (PF04300), FBA_1 (PF07734), FBA_2 (PF07735), FBA_3 (PF08268) and FBD (PF08387) domains were downloaded from Pfam database were searched against IWGSC Reference Sequence v1.0 assembly. RNA-seq paired-end libraries from different stages of wheat, such as stages of seedling, tillering, booting, day after flowering (DAF) 1, DAF 10, DAF 20, and DAF 30 were conducted and sequenced by Illumina HiSeq2000 for expression analysis of F-box protein genes. Basic analysis including Hisat, HTseq, DEseq, gene ontology analysis and KEGG mapping were conducted for differentially expressed gene analysis and their annotation mappings of DEGs from various stages. About 950 F-box domain proteins identified by Pfam were mapped to wheat reference genome sequence by blastX (e-value < 0.05). Among them, more than 140 putative F-box protein genes were selected by fold changes cut-offs of > 2, significance p-value < 0.01, and FDR<0.01. Expression profiling of selected F-box protein genes were shown by heatmap analysis, and average linkage and squared Euclidean distance of putative 144 F-box protein genes by expression patterns were calculated for clustering analysis. This work may provide valuable and basic information for further investigation of protein degradation mechanism by ubiquitin proteasome system using F-box proteins during wheat development stages.

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Comparative physiological and proteomic analysis of leaf in response to cadmium stress in sorghum

  • Roy, Swapan Kumar;Cho, Seong-Woo;Kwon, Soo Jeong;Kamal, Abu Hena Mostafa;Kim, Sang-Woo;Lee, Moon-Soon;Chung, Keun-Yook;Woo, Sun-Hee
    • Proceedings of the Korean Society of Crop Science Conference
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    • pp.124-124
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    • 2017
  • Cadmium (Cd) is of particular concern because of its widespread occurrence and high toxicity and may cause serious morpho-physiological and molecular abnormalities in in plants. The present study was performed to explore Cd-induced morpho-physiological alterations and their potentiality associated mechanisms in Sorghum bicolor leaves at the protein level. Ten-day-old sorghum seedlings were exposed to different concentrations (0, 100, and $150{\mu}M$) of $CdCl_2$, and different morpho-physiological responses were recorded. The effects of Cd exposure on protein expression patterns in S. bicolor were investigated using two-dimensional gel electrophoresis (2-DE) in samples derived from the leaves of both control and Cd-treated seedlings. The observed morphological changes revealed that the plants treated with Cd displayed dramatically altered shoot lengths, fresh weights, and relative water content. In addition, the concentration of Cd was markedly increased by treatment with Cd, and the amount of Cd taken up by the shoots was significantly and directly correlated with the applied level of Cd. Using the 2-DE method, a total of 33 differentially expressed protein spots were analyzed using MALDI-TOF/TOF MS. Of these, treatment with Cd resulted in significant increases in 15 proteins and decreases in 18 proteins. Significant changes were absorbed in the levels of proteins known to be involved in carbohydrate metabolism, transcriptional regulation, translation and stress responses. Proteomic results revealed that Cd stress had an inhibitory effect on carbon fixation, ATP production and the regulation of protein synthesis. In addition, the up-regulation of glutathione S-transferase and cytochrome P450 may play a significant role in Cd-related toxicity and stress responses. Our study provides insights into the integrated molecular mechanisms involved in response to Cd and the effects of Cd on the growth and physiological characteristics of sorghum seedlings. The upregulation of these stress-related genes may be candidates for further research and use in genetic manipulation of sorghum tolerance to Cd stress.

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Analysis on infection control of general hospital radiology (종합병원 영상의학과의 감염관리 대한 분석)

  • Shin, Jung-Sub;Park, Cheol-Woo;Jeon, Byeong-Kyou
    • Journal of the Korean Society of Radiology
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    • v.6 no.5
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    • pp.335-342
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    • 2012
  • This study aims to find a way to control infection of community radiology effectively by calculating the degree of contamination, culture and identifying the flora in radiology of five general hospitals in Gyeongsangbuk-do. Staphylococcus, Micrococcus, Pseudomonas stutzeri, Pseudomonas oryzihabitans were identified as surface flora. These are know to be pathogens of hospital acquired infection and there was no radiology-specific flora. Research subject hospitals were conducting similar infection control education but degree of contamination of each hospital showed significant difference. Difference in degree of contamination according to contact sources were analyzed by Contact sources were classified into technologist-using, patients-using and common-using materials. Analysis of each hospital's degree of contamination showed that patient-using materials were significantly more contaminated than technologist-using and common-using materials (p<0.001). Devices which are similar to each other in monthly average frequency of use showed no significant difference in degree of contamination, but general X-ray devices and chest boards which are used most frequently showed higher degree of contamination than others. In addition, hospital A, B and C which have heavier monthly average caseload showed relatively high degree of contamination on irradiation devices which are used by technologists only or by technologists and patients commonly, office desks and doorpulls. Hence it is considered that intensity of infection control education should be different according to the degree of monthly average caseload. This study provided an opportunity to aware that technologists' feeling of contamination is crucial for infection control of radiology, and the Accupoint ATP public hygiene monitoring system which was used in this study for measuring the degree of contamination was proved to be an effective measuring device for hospital acquired infection management.

Valproic Acid Reduces Reactive Oxygen Species in Fibroblast of X-linked Adrenoleukodystrophy (부신백질형성장애증 섬유모세포에서 발프로산의 항산화능)

  • Kang, Joon Won;Quan, Zhejiu;Jang, Jiho;Kang, Hoon-Chul
    • Journal of the Korean Child Neurology Society
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    • v.23 no.2
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    • pp.45-50
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    • 2015
  • Purpose: X-linked adrenoleukodystrophy (X-ALD) is a fatal, axonal demyelinating, neurodegenerative disease, and is caused by mutations the in ABCD1 (ATP-binding cassette transporter subfamily D member 1). Oxidative damage of proteins caused by very long chain fatty acid accumulating in X-ALD, is an early event in the neurodegenerative cascade. We evaluated valproic acid (VPA) as a possible option for oxidative damage in X-ALD. Method: We generated fibroblast of the childhood cerebral ALD from patient. We evaluated mRNA (ribonucleic acid) level of ABCD2 by real-time polymerase chain reaction, and reactive oxygen species (ROS) levels by flow cytometry. Results: VPA increased expression of ABCD2 in both control and ALD fibroblast. ABCD2 gene mRNA expression was increased 1.76 fold in normal fibroblasts, and 2.22 fold in the X-ALD fibroblasts. ROS levels were decreased in VPA treated X-ALD fibroblast, especially in treated with 1 mM of VPA. ROS levels revealed 13.7 in control fibroblast, on the other hand, 5.83 in X-ALD fibroblast treated with 1 mM of VPA. Conclusion: We propose VPA as a promising novel therapeutic approach in oxidant damage that warrants further clinical investigation in X-ALD.

Potential Antitumor Activity of SIM-89 in Non-Small Cell Lung Cancer Cells

  • Pei, Jun;Chu, Tianqing;Shao, Minhua;Teng, Jiajun;Sha, Huifang;Gu, Aiqing;Li, Rong;Qian, Jialin;Mao, Weifeng;Li, Ying;Han, Baohui
    • Yonsei Medical Journal
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    • v.58 no.3
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    • pp.581-591
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    • 2017
  • Purpose: c-Met and its ligand, hepatocyte growth factor (HGF), play a critical role in oncogenesis and metastatic progression. The aim of this study was to identify inhibited enzymogram and to test the antitumor activity of SIM-89 (a c-Met receptor tyrosine kinase inhibitor) in non-small cell lung cancer. Materials and Methods: Z'-LYTE kinase assay was employed to screen the kinase enzymogram, and mechanism of action (MOA) analysis was used to identify the inhibited kinases. Cell proliferation was then analyzed by CCK8 assay, and cell migration was determined by transwell assay. The gene expression and the phosphorylation of c-Met were examined by realtime-PCR and western blotting, respectively. Finally, the secretion of HGF was detected by ELISA assay. Results: c-Met, activated protein kinase (AMPK), and tyrosine kinase A (TRKA) were inhibited by SIM-89 with the $IC_{50}$ values of 297 nmol/L, $1.31{\mu}mol/L$, and 150.2 nmol/L, respectively. SIM-89 exerted adenosine triphosphate (ATP) competitive inhibition on c-Met. Moreover, the expressions of STAT1, JAK1, and c-Met in H460 cells were decreased by SIM-89 treatment, and c-Met phosphorylation was suppressed in A549, H441, H1299, and B16F10 cells by the treatment. In addition, SIM-89 treatment significantly decreased the level of HGF, which accounted for the activation of c-Met receptor tyrosine kinase. Finally, we showed cell proliferation inhibition and cell migration suppression in H460 and H1299 cells after SIM-89 treatment. Conclusion: In conclusion, SIM-89 inhibits tumor cell proliferation, migration and HGF autocrine, suggesting it's potential antitumor activity.

Incidence and Related Factors of the Metabolic Syndrome in a University Hospital (대학병원 종합검진센터 수진자의 대사증후군 발생과 관련요인)

  • Choi, Se-Mook;Kim, Keon-Yeop;Lee, Tea-Yong;Jung, Jin-Gyu;Lee, Og-Kyoung
    • Korean Journal of Health Education and Promotion
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    • v.26 no.4
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    • pp.35-47
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    • 2009
  • Objectives: The purpose of this research was to investigate incidence and related factors of the MS in a university hospital Methods: This survey was conducted from January in 1997 to March in 2008. This study is a cohort study. The baseline subjects were 529 men and 609 women without metabolic syndrome(MS) who visited the health promotion center of Chungnam National University Hospital for general health check-up. The MS was diagnosed according to the definition by the NCEP ATP III. The abdominal obesity guidelines for waist circumference applied the Korean Society for the Study of Obesity Guideline Results: The survey exhibited that baseline risk factors that mainly affect odds ratio(OR) of the MS at follow-up were sex, ages, heavy drinking, uric acid and transpeptidase(GGT) in women. Incidence of the MS was 10.6% in total cases, 18.1% in men and 4.0% in women. The risk of the MS was significantly lower in women than men(OR=0.4, 95% confidence interval(CI: 0.2-0.9), significantly higher 50-59 Ages than < 40 ages(OR=3.4, 95% CI: 1.9-6.4), significantly high in women with heavy drinkers(OR=14.3, 95% CI: 1.2-177.5), significantly high in whole, men and women with high uric acid group(whole, OR=2.6, 95% CI: 1.6-4.2. men, OR=2.1, 95% CI: 1.3-3.5. women, OR=14.2, 95% CI: 3.0-68.3) and significantly high in women with high GGT(OR=1.8, 95% CI: 2.4-12.6). Conclusion: Risk factors of incident MS were baseline sex, ages, heavy drinking in women, uric acid and GGT in women. These can be utilized as an important index to determine risk factors of incident MS and will be basic data in part of management, education, countermeasure and selection test of the MS.

Association of Single Nucleotide Polymorphism (SNP) in the PGK 2 Gene with Growth Traits in Pigs (돼지 PGK 2 유전자의 단일염기다형성 및 성장 형질과의 연관성 구명)

  • Jang, Hong-Chul;Kim, Sang-Wook;Lim, Da-Jeong;Kim, Jae-Young;Cho, Kyu-Ho;Kim, Myung-Jick;Lee, Ji-Woong;Choi, Bong-Hwan;Kim, Tae-Hun
    • Journal of Animal Science and Technology
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    • v.53 no.1
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    • pp.15-22
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    • 2011
  • The purpose of this study was to analyse of association between growth traits and single nucleotide polymorphisms (SNPs) polymorphism of phosphoglycerate kinase 2 (PGK 2) gene in pigs. The birth weight of piglet influences on weaning weight and survival rate that are import economic traits in pig industry. Also, these growth traits are representative factor to decrease a period getting to marketing weight as well as growth rate in pig. The PGK 2 is an isozyme that catalyzes the first ATP-generating step in the glycolytic pathwayand important enzyme related with energy metabolism. Twenty of SNPs were discoveredby genome structure analysis that compares the sequence on promoter and transcription region of PGK 2 gene in porcine chromosome 7. An association between PGK 2 SNPs and growth traits was analyzed in $F_2$ reciprocal-crossbred population between korean native pig (KNP) and Landrace. Association analysis indicated that polymorphism of the PGK 2 gene promoter region has significant effects on weight at birth (p<0.01) and weight at 3 weeks of age (p<0.0001). These results suggest that PGK 2 gene polymorphism was associated with energy metabolism and physiological function of growth in pig.

Diagnostic Value of Ceruloplasmin in the Diagnosis of Pediatric Wilson's Disease

  • Kim, Jung Ah;Kim, Hyun Jin;Cho, Jin Min;Oh, Seak Hee;Lee, Beom Hee;Kim, Gu-Hwan;Choi, Jin-Ho;Kim, Kyung Mo;Yoo, Han-Wook
    • Pediatric Gastroenterology, Hepatology & Nutrition
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    • v.18 no.3
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    • pp.187-192
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    • 2015
  • Purpose: Measurement of serum ceruloplasmin level is the first step in screening for Wilson's disease (WD). Despite the rarity of WD in the general population, ceruloplasmin levels are routinely measured through hepatitis screening in both adults and children. Herein, we evaluated the diagnostic value of ceruloplasmin for the diagnosis of WD among children with hepatitis. Methods: We retrospectively reviewed data on serum ceruloplasmin levels measured as a serologic marker for patients with hepatitis at Asan Medical Center (Seoul, Korea) between from January 2004 to November 2013. The diagnosis of WD was confirmed by the identification of pathogenic variants in the ATP7B gene. To determine the diagnostic accuracy of ceruloplasmin, receiver operation characteristic (ROC) curves were constructed and the area under curve (AUC) were calculated. Results: Measurements of serum ceruloplasmin were performed in 2,834 children who had hepatitis. Among these, 181 (6.4%) children were diagnosed with WD. The sensitivity, specificity, and accuracy of a ceruloplasmin level of <20 mg/dL in the discrimination of WD were 93.4%, 84.2%, and 84.8%, respectively. In this study, 418 (14.7%) false-positive cases and 12 (0.4%) false-negative cases were noted. Using a ROC curve, a ceruloplasmin level of ${\leq}16.6mg/dL$ showed the highest AUC value (0.956) with a sensitivity of 91.2%, a specificity of 94.9%, and an accuracy of 94.7%. Conclusion: The measurement of serum ceruloplasmin was frequently used for the screening of WD in children, despite a low positive rate. The diagnostic value of ceruloplasmin may be strengthened by adopting a new lower cut-off level.

Mechanism of Resistance and Epithelial to Mesenchymal Transition of BRAF(V600E) Mutation Thyroid Anaplastic Cancer to BRAF(V600E) Inhibition Through Feedback Activation of EGFR (BRAF(V600E) 돌연변이 갑상선 역형성암에서 BRAF(V600E) 억제에 의한 EGFR 발현 증가가 표적치료에 대한 저항성발현과 상피-간질세포이행과정에 미치는 영향분석)

  • Byeon, Hyung Kwon;Na, Hwi Jung;Yang, Yeon Ju;Park, Jae Hong;Kwon, Hyeong Ju;Chang, Jae Won;Ban, Myung Jin;Kim, Won Shik;Shin, Dong Yeob;Lee, Eun Jig;Koh, Yoon Woo;Choi, Eun Chang
    • Korean Journal of Head & Neck Oncology
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    • v.30 no.2
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    • pp.53-61
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    • 2014
  • Background and Objectives : Anaplastic thyroid carcinoma(ATC) is a rare but highly aggressive thyroid malignancy that is associated with an extremely poor survival despite the best multidisciplinary care. BRAF(V600E) mutation is detected in about a quarter of ATC, but unlike its high treatment response to selective BRAF inhibitor (PLX4032) in metastatic melanoma, the treatment response of ATC is reported to be low. The purpose of this study is to investigate the innate resistance mechanism responsible for this low treatment response to BRAF inhibitor and its effect on epithelial-mesenchymal transition(EMT). Materials and Methods : Two ATP cell lines, 8505C and FRO were selected and treated with PLX4032 and its drug sensitivity and effects on cell migration and EMT were examined and compared. Further investigation on the changes in signals responsible for the different treatment response to PLX4032 was carried out and the same experiment was performed on both orthotopic and ectopic xenograft mouse models. Results : FRO cell line was more sensitive to PLX4032 treatment compared to 8505C cell line. The resistance to BRAF inhibition in 8505C was due to increased expression of EGFR. Effective inhibition of both EGFR and p-AKT was achieved after dual treatment with BRAF inhibitor(PLX4032) and EGFR inhibitor(Erlotinib). Similar results were confirmed on in vivo study. Conclusion : EGFR-mediated reactivation of the PI3K/AKT pathway and MAPK pathway contributes to the relative insensitivity of BRAF(V600E) mutant ATC cells to PLX4032. Dual inhibition of BRAF and EGFR leads to sustained treatment response including cell invasiveness.

Overexpression of Rcan1-1L Inhibits Hypoxia-Induced Cell Apoptosis through Induction of Mitophagy

  • Sun, Lijun;Hao, Yuewen;An, Rui;Li, Haixun;Xi, Cong;Shen, Guohong
    • Molecules and Cells
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    • v.37 no.11
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    • pp.785-794
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    • 2014
  • Mitophagy, a cellular process that selectively targets dysfunctional mitochondria for degradation, is currently a hot topic in research into the pathogenesis and treatment of many human diseases. Considering that hypoxia causes mitochondrial dysfunction, which results in cell death, we speculated that selective activation of mitophagy might promote cell survival under hypoxic conditions. In the present study, we introduced the Regulator of calcineurin 1-1L (Rcan1-1L) to initiate the mitophagy pathway and aimed to evaluate the effect of Rcan1-1L-induced mitophagy on cell survival under hypoxic conditions. Recombinant adenovirus vectors carrying Rcan1-1L were transfected into human umbilical vein endothelial cells and human adult cardiac myocytes. Using the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide MTT assay and Trypan blue exclusion assay, Rcan1-1L overexpression was found to markedly reverse cell growth inhibition induced by hypoxia. Additionally, Rcan1-1L overexpression inhibited cell apoptosis under hypoxic conditions, as detected by annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) apoptosis assay. Meanwhile, the mitochondria-mediated cell apoptotic pathway was inhibited by Rcan1-1L. In contrast, knockdown of Rcan1-1L accelerated hypoxia-induced cell apoptosis. Moreover, Rcan1-1L overexpression significantly reduced mitochondrial mass, decreased depolarized mitochondria, and downregulated ATP and reactive oxygen species production. We further delineated that the loss of mitochondrial mass was due to the activation of mitophagy induced by Rcan1-1L. Rcan1-1L overexpression activated autophagy flux and promoted translocation of the specific mitophagy receptor Parkin into mitochondria from the cytosol, whereas inhibition of autophagy flux resulted in the accumulation of Parkin-loaded mitochondria. Finally, we demonstrated that mitochondrial 1permeability transition pore opening was significantly increased by Rcan1-1L overexpression, which suggested that Rcan1-1L might evoke mitophagy through regulating mitochondrial permeability transition pores. Taken together, we provide evidence that Rcan1-1L overexpression induces mitophagy, which in turn contributes to cell survival under hypoxic conditions, revealing for the first time that Rcan1-1L-induced mitophagy may be used for cardioprotection.