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Parallel screening and cheminformatics modeling of flavonoid activated aptasensors

Synthetic and Systems Biotechnology 2022年第4期7卷 1148-1158页

作者： Yu Xiu Ni Zhang Pranesha Prabhakaran Sungho Jang Qipeng Yuan Curt MBreneman Gyoo Yeol Jung Wanwipa Vongsangnak Mattheos A.G.Koffas Beijing Key Laboratory of Bioactive Substances and Functional Food Beijing Union UniversityBeijing100029China Department of Chemical and Biological Engineering Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic InstituteTroyNY12180USA State Key Laboratory of Chemical Resource Engineering Beijing University of Chemical TechnologyBeijing100029China Department of Chemistry and Chemical Biology Rensselaer Polytechnic InstituteTroyNY12180USA interdisciplinary graduate programs in bioscience Faculty of ScienceKasetsart UniversityBangkok10900Thailand Omics Center for Agriculture BioresourcesFoodand HealthKasetsart University(OmiKU)BangkokThailand Division of Bioengineering College of Life Sciences and BioengineeringIncheon National University119 Academy-roYeonsu-guIncheon22012South Korea Department of Bioengineering and Nano-Bioengineering Incheon National University119 Academy-roYeonsu-guIncheon22012South Korea Research Center for Bio Materials&Process Development Incheon National University119 Academy-roYeonsu-guIncheon22012South Korea Department of Chemical Engineering Pohang University of Science and Technology77 Cheongam-roNam-guPohangGyeongbuk37673South Korea School of interdisciplinary bioscience and Bioengineering Pohang University of Science and Technology77 Cheongam-roNam-guPohangGyeongbuk37673South Korea Department of Zoology Faculty of ScienceKasetsart UniversityBangkok10900Thailand

A parallel screening of 27 different flavonoids and chalcones was conducted using 6 artificial naringenin-activated riboswitches(M1,M2,M3,O,L and H).A quantitative structure-property relationship approach was applied to understand the physicochemical properties of the flavonoid structures resulting in specificity differences relied on the fluorescence intensity of a green fluorescent protein *** models of riboswitches M1,M2 and O that had good predictive power were constructed with descriptors selected for their high *** electronegativity and hydrophilicity of the flavonoids structures were identified as two properties that increased binding affinity to RNA *** groups at the C-3′and C-4’positions of the flavonoid molecule were strictly required for ligand-activation with riboswitches M1 and *** O and L preferred multi-hydroxylated flavones as *** on the A ring of the flavonoid molecule were not important in the molecular recognition process.O-glycosylated derivatives were not recognized by any of the riboswitches,presumably due to steric *** the challenges of detecting RNA conformational change after ligand binding,the resulting models elucidate important physicochemical features in the ligands for conformational structural studies of artificial aptamer complexes and for design of ligands having higher binding specificity.

关键词： Riboswitch RNA device Flavonoids Structure-property relationships Physicochemical properties

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Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

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药物分析学报:英文版 2023年第7期13卷 691-693页

作者： Dan Li Zhou Fang Qiang Shi Nicholas Zhang Binsheng Gong Weida Tong Ahmet F.Coskun Joshua Xu Division of Bioinformatics and Biostatistics National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Wallace H.Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory UniversityAtlantaGA30332USA Machine Learning graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Division of Systems Biology National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA interdisciplinary Bioengineering graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Parker H.Petit Institute for Bioengineering and bioscience Georgia Institute of TechnologyAtlantaGA30332USA

Reducing the use of animal models in drug development and safety assessment has long been supported by the *** and Drug Administration(FDA).The report by Royal Society for the Prevention of Cruelty to Animals indicates that in 2020,experiments involved the use of over 100 million animals,with the United States leading the list by utilizing 20 million *** ethical considerations associated with animal testing and the costs in terms of time and money,animal models are not always effective in predicting human reactions to drug *** animal testing has been the traditional method for assessing the safety and efficacy of drugs.

关键词： money utilizing testing

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Deep learning acceleration of multiscale superresolution localization photoacoustic imaging

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Light(Science & Applications) 2022年第6期11卷 1166-1177页

作者： Jongbeom Kim Gyuwon Kim Lei Li Pengfei Zhang Jin Young Kim Yeonggeun Kim Hyung Ham Kkim Lihong V.Wang Seungchul Lee Chulhong Kim Departments of Electrical Engineering Mechanical EngineeringConvergence IT Engineeringand Interdisciplinary Bioscience and BioengineeringGraduate School of Artificial IntelligenceMedical Device Innovation CenterPohang University of Science and Technology(POSTECH)77 Cheongam-roNam-guPohangGyeongbuk 37673Republic of Korea Caltech Optical Imaging Laboratory Andrew and Peggy Cherng Department of Medical EngineeringDepartment of Electrical EngineeringCalifornia Institute of Technology1200 E.California Blvd.MC 138-78PasadenaCA 91125USA School of Precision Instruments and Optoelectronics Engineering Tianjin University92 Weijin RoadNankai DistrictTianjin 300072China Opticho 532CHANGeUP GROUND87 Cheongam-roNam-guPohangGyeongsangbuk 37673Republic of Korea

A superresolution imaging approach that localizes very small targets,such as red blood cells or droplets of injected photoacoustic dye,has significantly improved spatial resolution in various biological and medical imaging ***,this superior spatial resolution is achieved by sacrificing temporal resolution because many raw image frames,each containing the localization target,must be superimposed to form a sufficiently sampled high-density superresolution ***,we demonstrate a computational strategy based on deep neural networks(DNNs)to reconstruct high-density superresolution images from far fewer raw image *** localization strategy can be applied for both 3D label-free localization optical-resolution photoacoustic microscopy(OR-PAM)and 2D labeled localization photoacoustic computed tomography(PACT).For the former,the required number of raw volumetric frames is reduced from tens to fewer than *** the latter,the required number of raw 2D frames is reduced by 12 ***,our proposed method has simultaneously improved temporal(via the DNN)and spatial(via the localization method)resolutions in both label-free microscopy and labeled ***-learning powered localization PA imaging can potentially provide a practical tool in preclinical and clinical studies requiring fast temporal and fine spatial resolutions.

关键词： Deep frames networks

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The Phytophthora nucleolar effector Pi23226 targets host ribosome biogenesis to induce necrotrophic cell death

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Plant Communications 2023年第5期4卷 263-276页

作者： Soeui Lee Jaehwan Kim Myung-Shin Kim Cheol Woo Min Sun Tae Kim Sang-Bong Choi Joo Hyun Lee Doil Choi Plant Immunity Research Center Seoul National UniversitySeoul 08826Republic of Korea Plant Genomics and Breeding Institute Department of AgricultureForestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul 08826Republic of Korea interdisciplinary programs in Agricultural Genomics College of Agriculture and Life ScienceSeoul National UniversitySeoul 08826Republic of Korea Department of Plant bioscience Life and Industry Convergence Research InstitutePusan National UniversityMiryang 50463Republic of Korea Division of bioscience and Bioinformatics Myongji UniversityYongin 449-728Republic of Korea

Pathogen effectors target diverse subcellular organelles to manipulate the plant immune *** the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus,the roles of nucleolar-targeted effectors remain *** this study,we showed that Phytophthora infestans infection of Nicotiana benthamiana results in nucleolar inflation during the transition from the biotrophic to the necrotrophic *** *** effectors were localized in the nucleolus:Pi23226 induced cell death in *** and nucleolar inflation similar to that observed in the necrotrophic stage of infection,whereas its homolog Pi23015 and a deletion mutant(Pi23226DC)did not induce cell death or affect nucleolar *** immunoprecipitation and individual-nucleotide-resolution UV crosslinking and immunoprecipitation sequencing analysis indicated that Pi23226 bound to the 30 end of 25S rRNA precursors,resulting in accumulation of unprocessed 27S *** nucleolar stress marker NAC082 was strongly upregulated under Pi23226-expressing ***23226 subsequently inhibited global protein translation in host cells by interacting with ***23226 enhanced *** pathogenicity,indicating that Pi23226-induced ribosome malfunction and cell death were beneficial for pathogenesis in the *** results provide evidence for the molecular mechanism underlying RNA-binding effector activity in host ribosome biogenesis and lead to new insights into the nucleolar action of effectors in pathogenesis.

关键词： Phytophthora infestans hemibiotroph nucleolar effector cell death ribosome biogenesis translation inhibition

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Prevention of esophageal strictures after endoscopic submucosal dissection

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World Journal of Gastroenterology 2014年第41期20卷 15098-15109页

作者： Shinichiro Kobayashi Nobuo Kanai Takeshi Ohki Ryo Takagi Naoyuki Yamaguchi Hajime Isomoto Yoshiyuki Kasai Takahiro Hosoi Kazuhiko Nakao Susumu Eguchi Masakazu Yamamoto Masayuki Yamato Teruo Okano Institute of Advanced Biomedical Engineering and Science Tokyo Women’s Medical University Department of Surgery Nagasaki University Graduate School of Biomedical Sciences Department of Surgery Institute of GastroenterologyTokyo Women’s Medical University Department of Gastroenterology and Hepatology Nagasaki University Graduate School of Biomedical Sciences graduate School of Advanced Science and Engineering Life Science and Medical BioscienceWaseda University Department of Pharmaceutical Sciences Graduate School of Pharmaceutical SciencesTokyo University of Science

Endoscopic mucosal resection (EMR) and endoscopic submucosal dissection (ESD) have recently been accepted as less invasive methods for treating patients with early esophageal cancers such as squamous cell carcinoma and dysplasia of Barrett’s esophagus. However, the large defects in the esophageal mucosa often cause severe esophageal strictures, which dramatically reduce the patient’s quality of life. Although preventive endoscopic balloon dilatation can reduce dysphagia and the frequency of dilatation, other approaches are necessary to prevent esophageal strictures after ESD. This review describes several strategies for preventing esophageal strictures after ESD, with a particular focus on anti-inflammatory and tissue engineering approaches. The local injection of triamcinolone acetonide and other systemic steroid therapies are frequently used to prevent esophageal strictures after ESD. Tissue engineering approaches for preventing esophageal strictures have recently been applied in basic research studies. Scaffolds with temporary stents have been applied in five cases, and this technique has been shown to be safe and is anticipated to prevent esophageal strictures. Fabricated autologous oral mucosal epithelial cell sheets to cover the defective mucosa similarly to how commercially available skin products fabricated from epidermal cells are used for skin defects or in cases of intractable ulcers. Fabricated autologous oral-mucosal-epithelial cell sheets have already been shown to be safe.

关键词： Endoscopic submucosal dissection Esophageal stricture Systemic steroid therapy Autologous oral mucosal epithelial cell sheet

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Direct acetylation of a conserved threonine of RIN4 by the bacterial effector HopZ5 or AvrBsT activates RPM1-dependent immunity in Arabidopsis

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Molecular Plant 2021年第11期14卷 1951-1960页

作者： Arabidopsis Sera Choi Maxim Prokchorchik Hyeonjung Lee Ravi Gupta Yoonyoung Lee Eui-Hwan Chung Buhyeon Cho Min-Sung Kim Sun Tae Kim Kee Hoon Sohn Department of Life Sciences Pohang University of Science and TechnologyPohang 37673Republic of Korea School of interdisciplinary bioscience and Bioengineering Pohang University of Science and TechnologyPohang 37673Republic of Korea Department of Plant bioscience Life and Industry Convergence Research InstitutePusan National UniversityMiryang 50463Republic of Korea Department of Botany School of Chemical and Life SciencesJamia HamdardHamdard NagarNew Delhi 110062India Division of Biotechnology Korea UniversitySeoul 02841Republic of Korea The Institute of Crop Science and Resource Conservation(INRES) University of BonnNussallee 953115 BonnGermany

Plant pathogenic bacteria deliver effectors into plant cells to suppress immunity and promote pathogen survival;however, these effectors can be recognised by plant disease resistance (R) proteins to activate innate immunity. The bacterial acetyltransferase effectors HopZ5 and AvrBsT trigger immunity in Arabidopsis thaliana genotypes lacking SUPPRESSOR OF AVRBST-ELICITED RESISTANCE 1 (SOBER1). Using an Arabidopsis accession, Tscha-1, that naturally lacks functional SOBER1 but is unable to recognise HopZ5, we demonstrate that RESISTANCE TO P. SYRINGAE PV MACULICOLA 1 (RPM1) and RPM1-INTERACTING PROTEIN 4 (RIN4) are indispensable for HopZ5- or AvrBsT-triggered immunity. Remarkably, T166 of RIN4, the phosphorylation of which is induced by AvrB and AvrRpm1, was directly acetylated by HopZ5 and AvrBsT. Furthermore, we demonstrate that the acetylation of RIN4 T166 is required and sufficient for HopZ5- or AvrBsT-triggered RPM1-dependent defence activation. Finally, we show that SOBER1 interferes with HopZ5- or AvrBsT-triggered immunity by deacetylating RIN4 T166. We have thus elucidated detailed molecular mechanisms underlying the activation and suppression of plant innate immunity triggered by two bacterial acetyltransferases, HopZ5 and AvrBsT from different bacterial pathogens.

关键词： Acetyltransferase effectors Effector-triggered immunity Immunity suppressors NLR Plant deacetylase Plant immunity

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The altered network complexity of resting-state functional brain activity in schizophrenia and bipolar disorder patients

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Brain Science Advances 2023年第2期9卷 78-94页

作者： Yan Niu Nan Zhang Mengni Zhou Lan Yang Jie Sun Xueting Cheng Yanan Li Lefan Guo Jie Xiang Bin Wang College of Information and Computer Taiyuan University of TechnologyTaiyuan 030024ShanxiChina graduate School of interdisciplinary Science and Engineering in Health Systems Okayama UniversityOkayamaJapan Research Center for Medical Artificial Intelligence Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055GuangzhouChina

Schizophrenia(SZ)and bipolar disorder(BD)are two of themost frequent mental *** disorders exhibit similarpsychotic symptoms,making diagnosis challenging and leadingto ***,the network complexity changes drivingspontaneous brain activity in SZ and BD patients are still *** entropy(FE)is a novel way of measuring the dispersion(or spread)of functional connectivities inside the *** FE wasutilized in this study to examine the network complexity of the resting-state fMRI data of SZ and BD patients at three levels,including global,modules,and *** three levels,the FE of SZand BD patients was considerably lower than that of normal control(NC).At the intra-module level,the FE of SZ was substantially higher than that of BD in the cingulo-opercular ***,a strong negative association between FE and clinical measureswas discovered in patient ***,we classified using theFE features and attained an accuracy of 66.7%(BD *** ***)and an accuracy of 75.0%(SZ ***).These findings proposed that network connectivity’s complexity analyses using FE can provideimportant insights for the diagnosis of mental illness.

关键词： functional entropy network complexity schizophrenia bipolar disorder resting-state fMRI

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Field Modeling Method for Identifying Urban Sphere of Influence:A Case Study on Central China

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Chinese Geographical Science 2010年第4期20卷 353-362页

作者： DENG Yu LIU Shenghe WANG Li MA Hanqing WANG Jianghao Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing 100101 China graduate University of the Chinese Academy of Sciences Beijing 100049 China Institute of Policy and Management Chinese Academy of Sciences Beijing 100190 China Center for interdisciplinary Studies of Natural and Social Sciences Chinese Academy of Sciences Beijing 100190 China

With rapid development of urbanization and regional interaction and interdependence, regional urban agglomeration planning becomes more and more important in China, in order to promote integrated development of various cities with close interrelationship. However, it is still arguable academically on how to define the boundary or which cities to be included for the urban agglomeration of a region. This paper aims to shed lights on how to identify urban spheres of influence scientifically by introducing field modeling method and by practicing a case study on 168 cities in Central China. In our field modeling method, the influence intensities of cities were measured by a compre-ensive index and urban spheres of influence were represented spatially by field intensity. Then, their classification and spatial distribution characteristics of study area in 2007 were identified and explored by using GIS and statistical methods. The result showed that： 1） Wuhan is the absolute dominant city in Central China; 2） the provincial capital cities dominate their own provinces and there are no other lower grade agglomeration centers; and 3） the basic types of organization form of urban sphere of influence are single-polar type, agglomeration type, close-related group type and loose-related group type.

关键词： Central China urban sphere of influence urban influence index field intensity urban influence intensity

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iNID： An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis

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Molecular Plant 2014年第5期7卷 792-813页

作者： Daeseok Choi Jaemyung Choi Byeongsoo Kang Seungchul Lee Young-hyun Cho Ildoo Hwang Daehee Hwang School of interdisciplinary bioscience and Bioengineering POSTECH 790-784 Pohang Republic of Korea Department of Life Sciences POSTECH 790-784 Pohang Republic of Korea Department of New Biology DGIST Daegu 711-873 Republic of Korea Division of Integrative biosciences and Biotechnologies POSTECH 790-784 Pohang Republic of Korea Center for Systems Biology of Plant Senescence and-Life History Institute for BasicScience DGIST Daegu 711-873 Republic of Korea

Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors （IEFs）. However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling （iNID） in Arabidopsis. iNID provides a comprehensive resource of （1） transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and （2） protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of （1） phytohormones and light and （2） phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid （BR）-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.

关键词： transcriptome analysis network analysis signal interplays development Arabidopsis.

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Hetero-bimetallic transition metal-substituted Krebs-type polyoxometalate with N-chelating ligand as anticancer agents

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钨科技(英文) 2023年第2期5卷 225-234页

作者： Han-Zhi Zhang Hong-Xia Zhao Wen-Hui Chang Xin-Yuan Liu Peng Chen Ai-Qin Yu Aadil Nabi Chishti Yu-Zhen Zhang Lu-Bin Ni Xi-Qing Wang Yong-Ge Wei School of Chemistry and Chemical Engineering Yangzhou UniversityYangzhou 225002China College of bioscience and Biotechnology Yangzhou UniversityYangzhou 225009China School of Chemistry and Chemical Engineering Guangxi Minzu UniversityNo.158Daxue West RoadNanning 530006China Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education Department of ChemistryTsinghua UniversityBeijing 100084China

A novel hetero-bimetallic transition metal(Sb^(Ⅴ)/Mn^(Ⅱ))-substituted Krebs-type polyoxometalate(POM)with N-chelating ligand H_(4)Na_(4)[Mn_(4)(H_(2)O)_(4)(trz)_(2)(SbO_(2))_(2)(SbW_(9)O_(33))_(2)]-20H_(2)O(Sb_(2)Mn_(2))(1)(trz=1,2,4-triazole)built from trilacunary Keggin POM unitα-B-[SbW_(9)O_(33)]^(9-){SbW_(9)]has been synthesized and characterized by single-crystal/powder X-ray diffraction and a wide range of analytical methods,including powder X-ray diffraction,Fourier transform infrared spectroscopy,Raman,ultraviolet-visible spectroscopy,electrospray ionization-mass spectroscopy,and thermogravimetric *** further investigate the antitumor activity of the(Sb_(2)Mn_(2))(1)in human gastric cancer Human Gastric Adenocarcinoma Cells and Human Gastric Cancer Cell lines,in vitro cytotoxicity assay and flow cytometry analysis was *** results indicated that the IC_(50) values of(Sb_(2)Mn_(2))(1)on Human Gastric Adenocarcinoma(AGS)and Human Gastric Cancer(BGC-823)Cell Lines were 1.86±0.05μmol·L^(-1) and 14.61±0.55μmol·L^(-1),respectively.(Sb_(2)Mn_(2))(1)also exhibited high cytotoxicity on Human Gastric Cancer Cells and could induce cell apoptosis by inhibiting S and G_(2)/M cell ***,the result not only shows that this new POM-based inorganic-organic hybrid compound has high selectivity and low toxicity,but also provides an effective method for the development of potential transition metal-substituted POMs based antitumor drugs.

关键词： Polyoxometalate Inorganic-organic hybrid material-In vitro cytotoxicity Anticancer agent

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