• Title/Summary/Keyword: Network biology

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The Study of Bfa1pE438K Suggests that Bfa1 Control the MitoticExit Network in Different Mechanisms Depending on DifferentCheckpoint-activating Signals

  • Kim, Junwon;Song, Kiwon
    • Molecules and Cells
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    • v.21 no.2
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    • pp.251-260
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    • 2006
  • During mitosis, genomic integrity is maintained by the proper coordination of anaphase entry and mitotic exit via mitotic checkpoints. In budding yeast, mitotic exit is controlled by a regulatory cascade called the mitotic exit network (MEN). The MEN is regulated by a small GTPase, Tem1p, which in turn is controlled by a two-component GAP, Bfa1p-Bub2p. Recent results suggested that phosphorylation of Bfa1p by the polorelated kinase Cdc5p is also required for triggering mitotic exit, since it decreases the GAP activity of Bfa1p-Bub2p. However, the dispensability of GEF Lte1p for mitotic exit has raised questions about regulation of the MEN by the GTPase activity of Tem1p. We isolated a Bfa1p mutant, $Bfa1p^{E438K}$, whose overexpression only partially induced anaphase arrest. The molecular and biochemical functions of $Bfa1p^{E438K}$ are similar to those of wild type Bfa1p, except for decreased GAP activity. Interestingly, in $BFA1^{E438K}$ cells, the MEN could be regulated with nearly wild type kinetics at physiological temperature, as well as in response to various checkpoint-activating signals, but the cells were more sensitive to spindle damage than wild type. These results suggest that the GAP activity of Bfa1p-Bub2p is responsible for the mitotic arrest caused by spindle damage and Bfa1p overproduction. In addition, the viability of cdc5-2 ${\Delta}bfa1 $ cells was not reduced by $BFA1^{E438K}$, suggesting that Cdc5p also regulates Bfa1p to activate mitotic exit by other mechanism(s), besides phosphorylation.

Re-understanding of Technoscience and Nature through Actor-Network Theory (행위자-연결망 이론을 통한 과학과 자연의 재해석)

  • Kim, Sook-Jin
    • Journal of the Korean Geographical Society
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    • v.45 no.4
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    • pp.461-477
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    • 2010
  • Recent environmental issues such as genetically modified organisms, the loss of biodiversity, climate change, and nuclear waste cannot be reduced to a matter of science or society and explained through nature-society dualist approaches because of their complexity and heterogeneity. This paper examines how nature-society dualism has been embedded in science studies and geography and how this dualism can be overcome. Actor-Network Theory as an attempt to overcome this nature-society dualism is appropriate in analysing "strange imbriglio" of biology, politics, technoscience, market, value, ethics and facts that constitute our society by focusing on heterogeneous association, and can contribute to providing a useful framework to solve environmental problems.

Discovery of Herbal Medicine Resources through Network Pharmacology Analysis Predicted to Be Useful for Tourette Syndrome (네트워크 약리학 분석을 통한 뚜렛 증후군에 유용할 것으로 예측되는 한약 자원 탐색)

  • Lee, Byoungho;Cho, Suin
    • Journal of TMJ Balancing Medicine
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    • v.10 no.1
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    • pp.12-20
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    • 2020
  • Objectives: Tourette syndrome (TS) is a disease that occurs evenly in many social classes. Despite the long experience of drug treatment, the preference is low due to various side effects. The aim of this study was to discover herbal medicine resources through network pharmacology analysis predicted to be useful for Tourette syndrome. Methods: We used Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) to identify herbal medicines that can be used for TS by using network pharmacology research methods and to predict the mechanism of action. After evaluating compounds of each identified herb, molecular target proteins and mechanisms of action were analyzed, focusing on compounds that are likely to exhibit clinical activity in consideration of the pharmacokinetic parameters of these individual compounds. Results: Fifty nine ingredients such as atropine, veraguensin, and nuciferin among the compounds contained in 48 types of medicinal herbs such as Daturae Flos (洋金花), Salviae Radix (丹参), and Nelumbinis Plumula (蓮子心) act on the D(2) dopamine receptor, which is a protein involved in the development of TS. It has been found that atropine, veraguensin, and nuciferin are highly likely to exhibit activity by acting on the G protein-coupled receptor signaling pathway. Conclusions: It can be used in conjunction with non-invasive treatment means such as FCST Yinyang Balancing Appliance with herbal therapy to bring about a significant therapeutic effect, and it will be possible to develop a treatment that can replace drug therapy used in Western medicine.

Porphyromonas gingivalis exacerbates the progression of fatty liver disease via CD36-PPARγ pathway

  • Ahn, Ji-Su;Yang, Ji Won;Oh, Su-Jeong;Shin, Ye Young;Kang, Min-Jung;Park, Hae Ryoun;Seo, Yoojin;Kim, Hyung-Sik
    • BMB Reports
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    • v.54 no.6
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    • pp.323-328
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    • 2021
  • Periodontal diseases have been reported to have a multidirectional association with metabolic disorders. We sought to investigate the correlation between periodontitis and diabetes or fatty liver disease using HFD-fed obese mice inoculated with P. gingivalis. Body weight, alveolar bone loss, serological biochemistry, and glucose level were determined to evaluate the pathophysiology of periodontitis and diabetes. For the evaluation of fatty liver disease, hepatic nonalcoholic steatohepatitis (NASH) was assessed by scoring steatosis, inflammation, hepatocyte ballooning and the crucial signaling pathways involved in liver metabolism were analyzed. The C-reactive protein (CRP) level and NASH score in P. gingivalis-infected obese mice were significantly elevated. Particularly, the extensive lobular inflammation was observed in the liver of obese mice infected with P. gingivalis. Moreover, the expression of metabolic regulatory factors, including peroxisome proliferator-activated receptor γ (Pparγ) and the fatty acid transporter Cd36, was up-regulated in the liver of P. gingivalis-infected obese mice. However, inoculation of P. gingivalis had no significant influence on glucose homeostasis, insulin resistance, and hepatic mTOR/AMPK signaling. In conclusion, our results indicate that P. gingivalis can induce the progression of fatty liver disease in HFD-fed mice through the upregulation of CD36-PPARγ axis.

Identification of Hub Genes in the Pathogenesis of Ischemic Stroke Based on Bioinformatics Analysis

  • Yang, Xitong;Yan, Shanquan;Wang, Pengyu;Wang, Guangming
    • Journal of Korean Neurosurgical Society
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    • v.65 no.5
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    • pp.697-709
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    • 2022
  • Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

Pseudomonas oleovorans Strain KBPF-004 Culture Supernatants Reduced Seed Transmission of Cucumber green mottle mosaic virus and Pepper mild mottle virus, and Remodeled Aggregation of 126 kDa and Subcellular Localization of Movement Protein of Pepper mild mottle virus

  • Kim, Nam-Gyu;Seo, Eun-Young;Han, Sang-Hyuk;Gong, Jun-Su;Park, Cheol-Nam;Park, Ho-Seop;Domier, Leslie L;Hammond, John;Lim, Hyoun-Sub
    • The Plant Pathology Journal
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    • v.33 no.4
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    • pp.393-401
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    • 2017
  • Efforts to control viral diseases in crop production include several types of physical or chemical treatments; antiviral extracts of a number of plants have also been examined to inhibit plant viral infection. However, treatments utilizing naturally selected microorganisms with activity against plant viruses are poorly documented. Here we report isolation of a soil inhabiting bacterium, Pseudomonas oleovorans strain KBPF-004 (developmental code KNF2016) which showed antiviral activity against mechanical transmission of tobamoviruses. Antiviral activity was also evaluated in seed transmission of two tobamoviruses, Pepper mild mottle virus (PMMoV) and Cucumber green mottle mosaic virus (CGMMV), by treatment of seed collected from infected pepper and watermelon, respectively. Pepper and watermelon seeds were treated with culture supernatant of P. oleovorans strain KBPF-004 or control strain ATCC 8062 before planting. Seeds germinated after treatment with water or ATCC 8062 yielded about 60% CGMMV or PMMoV positive plants, whereas < 20% of KBPF-004-treated seeds were virus-infected, a significantly reduced seed transmission rate. Furthermore, supernatant of P. oleovorans strain KBPF-004 remodeled aggregation of PMMoV 126 kDa protein and subcellular localization of movement protein in Nicotiana benthamiana, diminishing aggregation of the 126 kDa protein and essentially abolishing association of the movement protein with the microtubule network. In leaves agroinfiltrated with constructs expressing the coat protein (CP) of either PMMoV or CGMMV, less full-size CP was detected in the presence of supernatant of P. oleovorans strain KBPF-004. These changes may contribute to the antiviral effects of P. oleovorans strain KBPF-004.

A Study on Living Space with the Internet Information Appliances (인터넷 정보가전을 활용한 주거공간 연구)

  • 전흥수;김주연
    • Korean Institute of Interior Design Journal
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    • no.28
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    • pp.44-50
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    • 2001
  • This study propose the new concept of residence by analyzing the change of residence through the characteristic of popularity and degree of development of technology on home network information appliance for intelligent home. Accordingly, Cyber village represented as home automation and extend to information of society. it encourage need of information and multimedia of home. It expect home information infrastructure for accepting informations, which make smart home to linked home-working home-learning home-treatment. home-shopping and home-banking. The system of intelligent home is the intelligence of human-biology in the side of environmental friendly and multi-function. it distinguish the system of security, controlling system of inside environment, supporting system of house-working, automatic controlling, house working. Future house require to meet demand of young generation, such as small residental space, the multi-functional space, the flexible space, making mood for dual income couple and of single as intelligent home. Accordingly, basic purpose which are pleasantness, the safe and the convenience the mobile multi-function as well as networking with controlling of temperature, security, health-test, home-entertainment, home-office and consider environment together.

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Post-transcriptional Regulation of NK Cell Activation

  • Kim, Tae-Don;Park, Ju-Yeong;Choi, In-Pyo
    • IMMUNE NETWORK
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    • v.9 no.4
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    • pp.115-121
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    • 2009
  • Natural killer (NK) cells play key roles in innate and adaptive immune defenses. NK cell responses are mediated by two major mechanisms: the direct cytolysis of target cells, and immune regulation by production of various cytokines. Many previous reports show that the complex NK cell activation process requires de novo gene expression regulated at both transcriptional and post-transcriptional levels. Specialized un-translated regions (UTR) of mRNAs are the main mechanisms of post-transcriptional regulation. Analysis of posttranscriptional regulation is needed to clearly understand NK cell biology and, furthermore, harness the power of NK cells for therapeutic aims. This review summarizes the current understanding of mRNA metabolism during NK cell activation, focusing primarily on post-transcriptional regulation.

T cell costimulation by CD28, CTLA-4, and ICOS

  • Lee, Kyung-Mi
    • IMMUNE NETWORK
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    • v.1 no.2
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    • pp.95-103
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    • 2001
  • T cells play a central role in the initiation and regulation of the immune response to foreign antigens. Full activation of T cells requires the engagement of T cell receptor complex (TCR) and the binding of a second costimulatory receptor to its ligand expressed on antigen presenting cells (APC). Among the molecules known to provide costimulatory function, CD28 has been the most dominant and potent costimulatory molecule. However, the function of CD28 is becoming more complex due to the recent discovery of its structural homologue, CTLA-4 and ICOS. This review summarizes the biology and physiologic function of each of these receptors, and further focuses on the biochemical mechanism underlying the function of these receptors. Complete understanding of the CD28/CTLA-4/ICOS costimulatory pathway will provide the basis for developing new therapeutic approaches for immunological dieseases.

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Regulatory T Cell Therapy for Autoimmune Disease

  • Ha, Tai-You
    • IMMUNE NETWORK
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    • v.8 no.4
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    • pp.107-123
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    • 2008
  • It has now been well documented in a variety of models that T regulatory T cells (Treg cells) play a pivotal role in the maintenance of self-tolerance, T cell homeostasis, tumor, allergy, autoimmunity, allograft transplantation and control of microbial infection. Recently, Treg cell are isolated and can be expanded in vitro and in vivo, and their role is the subject of intensive investigation, particularly on the possible Treg cell therapy for various immune-mediated diseases. A growing body of evidence has demonstrated that Treg cells can prevent or even cure a wide range of diseases, including tumor, allergic and autoimmune diseases, transplant rejection, graft-versus-host disease. Currently, a large body of data in the literature has been emerging and provided evidence that clear understanding of Treg cell work will present definite opportunities for successful Treg cell immunotherapy for the treatment of a broad spectrum of diseases. In this Review, I briefly discuss the biology of Treg cells, and summarize efforts to exploit Treg cell therapy for autoimmune diseases. This article also explores recent observations on pharmaceutical agents that abrogate or enhance the function of Treg cells for manipulation of Treg cells for therapeutic purpose.