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Multilevel complexity of calcium signaling:Modeling angiogenesis

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World Journal of Biological Chemistry 2012年第6期3卷 121-126页

作者： Luca Munaron Marco Scianna department of Life Sciences and Systems Biology Centre for Nanostructured Interfaces and SurfacesCentre for Complex Systems in Molecular Biology and MedicineUniversity of Torino10123 TorinoItaly department of Mathematics Politecnico Di Torino10123 TorinoItaly Institute for Cancer Research and Treatment Strada Provinciale 14210060 CandioloItaly

Intracellular calcium signaling is a universal,evolutionary conserved and versatile regulator of cell *** complexity of calcium signaling and related cell machinery can be investigated by the use of experimental strategies,as well as by computational *** endothelium is a fascinating model to study the specific properties and roles of calcium signals at multiple biological *** the past 20 years,live cell imaging,patch clamp and other techniques have allowed us to detect and interfere with calcium signaling in endothelial cells(ECs),providing a huge amount of information on the regulation of vascularization(angiogenesis) in normal and tumoral *** data range from the spatiotemporal dynamics of calcium within different cell microcompartments to those in entire multicellular and organized EC *** experimental strategies,in silico endothelial models,specifically designed for simulating calcium signaling,are contributing to our knowledge of vascular physiol-ogy and *** help to investigate and predict the quantitative features of proangiogenic events moving through subcellular,cellular and supracellular *** review focuses on some recent developments of computational approaches for proangiogenic endothelial calcium *** particular,we discuss the creation of hybrid simulation environments,which combine and integrate discrete Cellular Potts *** are able to capture the phenomenological mechanisms of cell morphological reorganization,migration,and intercellular adhesion,with single-cell spatiotemporal models,based on reaction-diffusion equations that describe the agonist-induced intracellular calcium events.

关键词： Calcium signaling Angiogenesis Modeling Cell signaling Endothelial cells

A novel angiography-based computational modelling for assessing the dynamic stress and quantitative fatigue fracture risk of the coronary stents immediately after implantation: Effects of stent materials, designs and target vessel motions

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medicine in Novel Technology and Devices 2022年第2期14卷 31-38页

作者： Xinlei Wu Mattia Lunardi Ahmed Elkoumy Jiayue Huang Jing Kan Shaoliang Chen Shengxian Tu Shanghai Med-X Engineering Research Center Shanghai Jiao Tong UniversityShanghaiChina Institute of Cardiovascular Development and Translational medicine The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina department of Cardiology National University of IrelandGalway(NUIG)GalwayIreland Division of Cardiology Nanjing First HospitalNanjing Medical UniversityNanjingChina Med-X Research Institute Shanghai Jiao Tong UniversityShanghaiChina

Fluctuating stress on the implanted coronary stents within cardiac cycle is an important mechanism of fatigue fracture,which is associated with in-stent restenosis and stent *** developed a novel computational modelling to calculate the dynamic stress of stents based on the time sequence angiography immediately after *** groups of patient-specific cases(one same stent design treated in 4 different coronary arteries and one same artery actually/virtually implanted one stent with 3 different designs)were performed the dynamic stress analysis by this computational modelling and subsequently assessed the fatigue fracture risk by Goodman *** motion of target arteries significantly impacts on distribution of the stress and the risk of stent fracture,particularly in the site of hinge *** the location of stent stress concentration in the obtuse marginal artery and the“unsafe”region in the inverse fatigue safety factor contour co-registered with the position of complete transverse fracture 13 months later after *** stents with different designs had the same location of highest stress concentration at the hinge motion site of the actually/virtually treated *** strength stent materials are significantly lower the risk of stent fracture rather than stent *** new computational modelling might be a useful tool in assessment of fracture risk of the implanted stent and in optimizing new design of dedicated stent treated specific coronary arteries and mechanical properties in vivo of bioresorbable scaffold during degradation process.

关键词： Coronary angiography Dynamic stress Superficial wall strain Fatigue analysis Cardiac cycle Cardiovascular biomechanics

Emodin prevents senescence of retinal pigment epithelium via FOXO1

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Emodin prevents senescence of retinal pigment epithelium via...

computational pharmacokinetics and in vitro-in vivo correlation of anti-diabetic synergistic phyto-composite blend

2017中国营养医学发展论坛暨全军营养医学大会

作者： Nan Yu Xianghong Hou Hanqiang Liu 于芳 department of Ophthalmology He Ping hospital Changzhi Medical College department of Nutrition and Food Hygiene Fourth Military Medical University 第四军医大学营养与食品卫生学教研室

Aim: Age-related macular degeneration(AMD) is the leading cause of irreversible blindness in developed countries. Senescence of retinal pigment epithelium(RPE) plays a critical role in age-related eye diseases, such as AMD. However, no effective clinical drugs have been applied to prevent or delay RPE senescence. Emodin is an active component of Chinese medicine rhubarb. Our study was performed to determine if Emodin participated in RPE senescence. Methods: Oxidative stress-induced premature senescence models were established in primary RPE cells and human ARPE-19 cells upon HO ortert-BHP treatment. Senescence-associated β-galactosidase(SA β-gal) staining and LDH viability assay were performed to determine senescent RPE cells. Immunofluorescence staining was used to detect protein sub-cellular localization. Luciferase reporter assay and RNA-IP were applied to demonstrate the association between micro RNA and its target. Results: We found that Emodin significantly inhibited HO-and tert-BHP-induced RPE senescence. Emodin apparently decreased p21/FOXO1 but not p53 signaling pathway. FOXO1 expression was dramatically suppressed by Emodin. FOXO1 cellular localization and its transcriptional level were not altered by Emodin. However, Emodin apparently inhibited FOXO1 3’UTR activity. bioinformatics analysis found that FOXO1 3’UTR included one potential mi R-273 target site conserved in humans and mice. Luciferase repoter assay and RNA-IP demonstrated that mi R-273 was responsible for the inhibitory effect of Emodin on FOXO1. Importantly, Emodin inhibited RPE senescence was apparently diminished upon FOXO1 overexpression in ARPE-19 cells. Conclusions: Our study, for the first time, demonstrated that Emodin prevented oxidative stress-induced RPE senescence, strongly suggesting that Emodin may be exploited clinically to prevent or inhibit age-associated eye diseases.

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World Journal of Diabetes 2015年第11期6卷 1179-1185页

作者： Baishakhi De Koushik Bhandari Nishant Chakravorty Ranjan Mukherjee Rohit Gundamaraju Rajeev K Singla Prakash Katakam Shanta K Adiki Biswajoy Ghosh Analava Mitra School of Medical Science and Technology IIT Kharagpur 721302 India department of Medical Microbiology Faculty of Medicine University of Malaya Division of Biotechnology Netaji Subhas Institute of Technology Faculty of Pharmacy University of Zawiya Nirmala College of Pharmacy

Despite tremendous strides in modern medicine stringent control over insulin resistance or restoration of normoglycemia has not yet been *** the growth of molecular biology,omics technologies,docking studies,and in silico pharmacology,modulators of enzymes and receptors affecting the molecular pathogenesis of the disease are being considered as the latest targets for anti-diabetic *** molecular targets are now being developed basing on the up or down regulation of different signaling pathways affecting the *** antidiabetic therapy is in vogue both with classical and non-classical medicinal *** its chemoprofiling,structural and pharmacokinetic validation awaits providing recognition to such formulations for international *** health research with its focus on benchside product development and its sequential transition to patient bedside puts the pharma RDs to a challenge to develop bio-waiver *** simulation models and establishment of in vitro-in vivo correlation can help to replace in vivo bioavailability studies and provide means of quality control for scale up and post approval *** attempts to bring different shades highlighting phyto-synergy,molecular targeting of antidiabetic agents via different signaling pathways and bio-waiver studies under a single umbrella.

关键词： In silico pharmacology Phytosynergistic Anti-diabe

The Mechanisms of Luteolin in Treating COVID-19 Based on bioinformatics Analysis and Molecular Docking

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Infectious Diseases & Immunity 2023年第2期3卷 97-100页

作者： Hechen Rong Yu Zeng Nan Zheng Yiwei Wang Zhonghong Guo Kun Wang Xiaoping Huang department of Infectious diseases the First Affiliated Hospital of Soochow UniversitySuzhouJiangsu 215006China department of Thyroid and Neck Tumor Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin’s Clinical Research Center for CancerTianjin 300060China.

Luteolin is a natural flavonoid that has a variety of pharmacological activities, such as anti-inflammatory, anti-allergic, anti-bacterial, anti-viral, apoptosis inhibition, cell autophagy regulation, and anti-tumor activity. It is one of the main ingredients of an expert-recommended herbal formula for the prevention and treatment of coronavirus disease 2019 (COVID-19). This suggests that luteolin has strong pharmacological effects on the prevention and treatment of COVID-19. The aims of this study were to identify the molecular targets of luteolin and to infer the possible mechanisms by which it exerts its pharmacological effects. The GSE159787 data set was obtained from the Gene Expression Omnibus online database, and differentially expressed genes were analyzed. There were 22 upregulated differentially expressed genes enriched in the COVID-19 signaling pathway, suggesting that the upregulation of these genes may be closely related to the occurrence of COVID-19. Molecular docking results showed that luteolin had strong binding efficiency to 20 of these 22 key genes. Six of these genes (CFB, EIF2AK2, OAS1, MAPK11, OAS3, and STAT1) showed strong binding activity. Luteolin can regulate the COVID-19 signaling pathway by combining with these targets, which may have a therapeutic effect on COVID-19.

关键词： COVID-19 Traditional Chinese medicine Luteolin Differentially expressed genes bioinformatics analysis Molecular docking

星形胶质细胞纳米级形态在三联突触对Ca^(2+)信号的控制

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神经损伤与功能重建 2022年第10期17卷 620-620页

作者： Audrey Denizot Misa Arizono U Valentin Nägerl Hugues Berry Erik De Schutter 杜一星(编译) computational Neuroscience Unit Okinawa Institute of Science and TechnologyOnna-SonJapan Interdisciplinary Institute for Neuroscience Universitéde BordeauxBordeauxFrance Interdisciplinary Institute for Neuroscience CNRS UMR 5297BordeauxFrance department of Pharmacology Kyoto University Graduate School of MedicineKyotoJapan LIRIS UMR5205 CNRSUniv LyonVilleurbanneFrance INRIA VilleurbanneFrance. 不详

星形胶质细胞中的大部分Ca^(2+)活性在空间上仅限于微区,并发生在形成复杂解剖网状结构的细小突起中,即所谓的海绵状结构域。越来越多的文献表明,这些星形细胞Ca^(2+)信号可以影响神经元突触的活动,从而调节通过神经元回路的信息流。局... 详细信息

星形胶质细胞中的大部分Ca^(2+)活性在空间上仅限于微区,并发生在形成复杂解剖网状结构的细小突起中,即所谓的海绵状结构域。越来越多的文献表明,这些星形细胞Ca^(2+)信号可以影响神经元突触的活动,从而调节通过神经元回路的信息流。局限于获取所涉及的小空间尺度方面存在技术困难,关于星形胶质细胞形态对Ca^(2+)微区活性的作用仍然知之甚少。本研究使用计算机技术和基于最近的超分辨率显微镜数据的细小突起的理想化3D几何形状来研究星形胶质细胞纳米级形态与局部Ca^(2+)活性之间的关联机制。模拟表明,星形细胞突起的纳米形态强有力地塑造了Ca^(2+)信号的时空特性并促进了局部Ca^(2+)活性。该模型预测,这种效应在星形胶质细胞肿胀时会减弱,这是脑部疾病的标志,并在低渗透条件下通过实验证实了这一点。该模型还预测,在重复的神经递质释放事件后,肿胀会阻碍星形胶质细胞的信号传播。总而言之,三联突触中星形胶质细胞的突起与突触前和突触后结构密切接触;本研究强调了星形胶质细胞在纳米尺度上的复杂形态及其在病理条件下的重塑对所谓的三联突触的神经元-星形胶质细胞通讯的影响。

关键词：钙微区计算神经科学细胞内信号传导纳米形态反应-扩散模拟

Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED)

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Science China(Life Sciences) 2007年第5期50卷 706-716页

Only from the primary structures of peptides, a new set of descriptors called the molecular electro-negativity edge-distance vector (VMED) was proposed and applied to describing and characterizing the molecular structures of oligopeptides and polypeptides, based on the electronegativity of each atom or electronic charge index (ECI) of atomic clusters and the bonding distance between atom-pairs. Here, the molecular structures of antigenic polypeptides were well expressed in order to propose the auto-mated technique for the computerized identification of helper T lymphocyte (Th) epitopes. Furthermore, a modified MED vector was proposed from the primary structures of polypeptides, based on the ECI and the relative bonding distance of the fundamental skeleton groups. The side-chains of each amino acid were here treated as a pseudo-atom. The developed VMED was easy to calculate and able to work. Some quantitative model was established for 28 immunogenic or antigenic polypeptides (AGPP) with 14 (1― 14) Ad and 14 other restricted activities assigned as "1"(+) and "0"(-), respectively. The latter comprised 6 Ab(15-20), 3 Ak(21-23), 2 Ek(24-26), 2 H-2k(27 and 28) restricted sequences. Good results were obtained with 90% correct classification (only 2 wrong ones for 20 training samples) and 100% correct prediction(none wrong for 8 testing samples); while con-trastively 100% correct classification (none wrong for 20 training samples) and 88% correct classification (1 wrong for 8 testing samples). Both stochastic samplings and cross valida-tions were performed to demonstrate good performance. The described method may also be suitable for estimation and prediction of classes I and II for major histocompatibility an-tigen (MHC) epitope of human. It will be useful in immune identification and recognition of pro-teins and genes and in the design and devel-opment of subunit vaccines. Several quantitative structure activity relationship (QSAR) models were developed for various oligop

关键词： molecular electronegativity distance-edge vector (VMED), antigenic polypeptide (AGPP) sequences, bioactive oligopeptide (BAOP) chains, quantitative sequence-activity models (QSAM), theoretically computational descriptors (TCD)

Screening of NKX2-5,GATA4,ZIC3 gene mutations in sporadic congenital simple heart disease in Hainan Province

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Journal of Hainan Medical University 2022年第19期28卷 32-36页

作者： LI Qing-Man GUO Feng LING Yi LI Hui-hui LIU Fang-fang LIU Hui WEN Zhuang-fei SUN Wei-wei LIU Yi-heng ZHANG Hai-ying Hainan Medical University Key Laboratory for Research and Transformation of Tropical Brain Science Haikou 571199China department of Obstetrics and Gynecology The First Affiliated Hospital of Hainan Medical CollegeHaikou 570102China department of Laboratory The First Hospital of Nanping CityFujian ProvinceNanping 353006China Children's Rehabilitation department Haikou Hospital of the Maternal and Child HealthHaikou 570102China department of Pediatrics Haikou People’s HospitalHaikou 570208China department of Orthopedics Haikou Affiliated Hospital of Central South University Xiangya School of MedicineHaikou 570208China

Objective:Congenital heart disease(CHD)is caused by abnormal cardiac development,which is the most common congenital malformation at home and ***2-5,GATA4 and ZIC3 have been shown to be associated with *** experiment explored the relationship between NKX2-5,GATA4 and ZIC3 gene mutations and sporadic CHD in Hainan ***:To collect 210 sporadic CHD patients in Hainan,the DNA of patients was extracted from blood,and the target gene fragments were *** high-resolution melting(HRM)and DNA sequencing technology,and we analyzed the sequences of NKX2-5,GATA4 and ZIC3 ***:NKX2-5,GATA4 and ZIC3 genes were sequenced in 210 CHD patients,and seven gene mutations were found,including NKX2-5 heterozygous missense mutation(c.178G>T)and three heterozygous mutations in GATA4(c.677C>T,c.928A>G,c.1123G>A),three heterozygous mutations in ZIC3(c.19G>C,c.1255C>G,c.1348C>T),in which NKX2-5(c.178G>T),GATA4(c.1123G>A),and ZIC3(c.1255C>G,c.1348C>T)are new mutation *** gene mutations were predicted to be pathogenic mutations by bioinformatics ***:Conclusion:Seven gene mutations were found in 210 patients,and it was the first report that the gene mutations of NKX2-5,GATA4 and ZIC3 in Hainan Province associated with the pathogenesis of CHD.

关键词： Congenital heart disease Gene mutation NKX2-5 GATA4 ZIC3

The therapeutic mechanism of black soybean in atherosclerosis based on network pharmacology

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Food Therapy and Health Care 2019年第4期1卷 130-139页

作者： Yi-Xin Jiang Ming-Han Zhao Qing-Feng Wang Biological Engineering department Liaoning Vocational College of EconomicsShenyang 110122China College of Life Science and Engineering Shenyang University Shenyang 110044China Basic Medical College Liaoning University of Traditional Chinese MedicineShenyang 110032China

Objective:To investigate the cardiovascular mechanism of black soybean,the biological characteristics of black soybean were studied by bioinformatics,and the mechanism of its treatment for atherosclerosis was further ***:Firstly,the basic data sets of effective components and corresponding targets of black beans were constructed,and then mapped to the AS background network obtained from DisGeNET database and CTD ***,the potential targets of black beans acting on AS were *** constructing the protein-protein interaction(PPI)network,the topological characteristics of these targets were *** and GO were enriched to obtain the potential mechanism of black soybean acting on ***:There were 12 bioactive components reported in black *** them,beta-sitosterol,stigmasterol and N-(4-hydroxyphenylethyl)ACTINIDINE were the three most active *** are 19 targets of black soybeans acting on PPI network of AS *** them,ADRB2 and PTGS2 are important targets for black soybeans to alleviate *** therapeutic pathways include arachidonic acid metabolism and serotonin ***:Black soybean can play a therapeutic role in AS through multi-target and *** application of network pharmacology can quickly clarify the characteristics of functional foods and identify their potential targets and mechanisms for disease treatment.

关键词： Black bean Cardiovascular disease Network pharmacology Mechanism of action