目的:应用计算机系统生物学方法预测茵陈蒿汤的分子靶标,并阐明有效成分群的协同作用机制。方法:采用TCMGeneDIT数据库系统,文本挖掘茵陈蒿、大黄、栀子各自所能影响的基因或蛋白质数据;收集茵陈蒿汤中6,7-二甲基氧香豆素、京尼平苷、...目的:应用计算机系统生物学方法预测茵陈蒿汤的分子靶标,并阐明有效成分群的协同作用机制。方法:采用TCMGeneDIT数据库系统,文本挖掘茵陈蒿、大黄、栀子各自所能影响的基因或蛋白质数据;收集茵陈蒿汤中6,7-二甲基氧香豆素、京尼平苷、红花黄色素A、大黄酸、大黄素等17种血中移行成分,采用Accelrys公司Discovery Studio 2.5版完成分子构建,并上载至PharmMapper服务器进行靶标预测;从BIND、BioGRID、DIP、HPRD、IntAct、MINT等分子相互作用数据库中收集与预测靶标有直接相互作用的蛋白质,进行综合分析。结果:已有的实验证实:4个蛋白质与茵陈蒿汤相关,8个蛋白质与大黄相关,没有蛋白质与栀子相关。大黄酸、大黄素、6,7-二甲基氧香豆素、绿原酸等6种化学成分不但可直接作用于实验证实的靶标,也可像异秦皮啶、檞皮素3-O-葡萄糖苷等8种化学成分一样,通过影响相关靶标而发挥间接的治疗作用。结论:本研究结果可为茵陈蒿汤的后续研究提供有用的线索,促进茵陈蒿汤的分子作用机制研究,本研究策略可为中药复方的系统研究提供参考。展开更多
目的:应用计算机系统生物学方法预测生脉散的分子靶标,并为生脉散的分子机制提供线索。方法:采用TCMGeneDIT数据库系统,文本挖掘人参、麦冬、五味子各自所能影响的基因或蛋白质数据;收集生脉散中五味子醇甲、五味子醇乙、戈米辛D、五味...目的:应用计算机系统生物学方法预测生脉散的分子靶标,并为生脉散的分子机制提供线索。方法:采用TCMGeneDIT数据库系统,文本挖掘人参、麦冬、五味子各自所能影响的基因或蛋白质数据;收集生脉散中五味子醇甲、五味子醇乙、戈米辛D、五味子乙素、γ-五味子素、20(S)-人参皂苷Rh、人参皂苷Rk3等14种血中移行成分,采用Accelrys公司Discovery Studio 2.5版完成分子构建,并上载至PharmMapper服务器进行靶标预测;从BIND,BioGRID,DIP,HPRD,IntAct,MINT等分子相互作用数据库中收集与预测靶标有直接相互作用的蛋白质,进行综合分析。结果:已有的实验发现,五味子有10个血中移行成分,人参只有4个血中移行成分;人参与55个基因相关,五味子与1个基因相关,没有基因与麦冬相关。人参的4种血中移行成分不但可直接作用于实验证实的靶标,还能影响相关靶标发挥广泛的生物学效应。五味子的10种血中移行成分只能通过影响相关靶标而发挥间接的治疗作用。结论:结果可为生脉散的后续研究提供有用的线索,促进生脉散的分子作用机制研究,为中药复方的系统研究提供参考。展开更多
The gastrointestinal (GI) tract is the system of organs within multi-cellular animals that takes in food, digests it to extract energy and nutrients, and expels the remaining waste. The various patterns of GI tract fu...The gastrointestinal (GI) tract is the system of organs within multi-cellular animals that takes in food, digests it to extract energy and nutrients, and expels the remaining waste. The various patterns of GI tract function are generated by the integrated behaviour of multiple tissues and cell types. A thorough study of the GI tract requires understanding of the interactions between cells, tissues and gastrointestinal organs in health and disease. This depends on knowledge, not only of numerous cellular ionic current mechanisms and signal transduction pathways, but also of large scale GI tissue structures and the special distribution of the nervous network. A unique way of coping with this explosion in complexity is mathematical and computational modelling; providing a computational framework for the multilevel modelling and simulation of the human gastrointestinal anatomy and physiology. The aim of this review is to describe the current status of biomechanical modelling work of the GI tract in humans and animals, which can be further used to integrate the physiological, anatomical and medical knowledge of the GI system. Such modelling will aid research and ensure that medical professionals benefit, through the provision of relevant and precise information about the patient's condition and GI remodelling in animal disease models. It will also improve the accuracy and efficiency of medical procedures, which could result in reduced cost for diagnosis and treatment.展开更多
Systems that exhibit complex behaviours are often found in a particular dynamical con- dition, poised between order and disorder. This observation is at the core of the so-called criticality hypothesis, which states t...Systems that exhibit complex behaviours are often found in a particular dynamical con- dition, poised between order and disorder. This observation is at the core of the so-called criticality hypothesis, which states that systems in a dynamical regime between order and disorder attain the highest level of computational capabilities and achieve an optimal trade-off between robustness and flexibility. Recent results in cellular and evolutionary biology, ueuroscience and computer science have revitalised the interest in the criticality hypothesis, emphasising its role as a viable candidate general law in adaptive complex systems. This paper provides an overview of the works on dynamical criticality that are -- To the best of our knowledge -- Particularly relevant for the criticality hypothesis. The authors review the main contributions concerning dynamics and information processing at the edge of chaos, and illustrate the main achievements in the study of critical dynamics in biological systems. Finally, the authors discuss open questions and propose an agenda for future work.展开更多
Although Yin-Yang Wu-Xing （Yin-Yang and Five-Elements, subsystems of human body） has been the theoretical basis of traditional Chinese medicine （TCM） for more than 5 000 years, it has been primarily analytical or ...Although Yin-Yang Wu-Xing （Yin-Yang and Five-Elements, subsystems of human body） has been the theoretical basis of traditional Chinese medicine （TCM） for more than 5 000 years, it has been primarily analytical or empirical in nature without a formal scientific foundation. Based on bipolar set theory, an equilibrium/non-equilibrium computational model of Yin-Yang Wu-Xing is proposed. The Yin-Yang Wu-Xing dynamical systems are formulated so that equilibrium and non-equilibrium conditions can be established and proved. Computer simulations of equilibrium and non-equilibrium processes show that this new approach can provide diagnostic decision support in TCM. Thus, this equilibrium-based approach provides a unique scientific basis for future research in TCM, Qi （vital energy）, QiGong, Meridians and Collaterals （acupuncture channels） and herbal treatment. On the other hand, it provides a basic Yin-Yang cellular network architecture for modem scientific research in genomics such that regulation mechanisms of the ubiquitous YY1 protein for cell processes can be explained.展开更多
文摘目的:应用计算机系统生物学方法预测茵陈蒿汤的分子靶标,并阐明有效成分群的协同作用机制。方法:采用TCMGeneDIT数据库系统,文本挖掘茵陈蒿、大黄、栀子各自所能影响的基因或蛋白质数据;收集茵陈蒿汤中6,7-二甲基氧香豆素、京尼平苷、红花黄色素A、大黄酸、大黄素等17种血中移行成分,采用Accelrys公司Discovery Studio 2.5版完成分子构建,并上载至PharmMapper服务器进行靶标预测;从BIND、BioGRID、DIP、HPRD、IntAct、MINT等分子相互作用数据库中收集与预测靶标有直接相互作用的蛋白质,进行综合分析。结果:已有的实验证实:4个蛋白质与茵陈蒿汤相关,8个蛋白质与大黄相关,没有蛋白质与栀子相关。大黄酸、大黄素、6,7-二甲基氧香豆素、绿原酸等6种化学成分不但可直接作用于实验证实的靶标,也可像异秦皮啶、檞皮素3-O-葡萄糖苷等8种化学成分一样,通过影响相关靶标而发挥间接的治疗作用。结论:本研究结果可为茵陈蒿汤的后续研究提供有用的线索,促进茵陈蒿汤的分子作用机制研究,本研究策略可为中药复方的系统研究提供参考。
文摘目的:应用计算机系统生物学方法预测生脉散的分子靶标,并为生脉散的分子机制提供线索。方法:采用TCMGeneDIT数据库系统,文本挖掘人参、麦冬、五味子各自所能影响的基因或蛋白质数据;收集生脉散中五味子醇甲、五味子醇乙、戈米辛D、五味子乙素、γ-五味子素、20(S)-人参皂苷Rh、人参皂苷Rk3等14种血中移行成分,采用Accelrys公司Discovery Studio 2.5版完成分子构建,并上载至PharmMapper服务器进行靶标预测;从BIND,BioGRID,DIP,HPRD,IntAct,MINT等分子相互作用数据库中收集与预测靶标有直接相互作用的蛋白质,进行综合分析。结果:已有的实验发现,五味子有10个血中移行成分,人参只有4个血中移行成分;人参与55个基因相关,五味子与1个基因相关,没有基因与麦冬相关。人参的4种血中移行成分不但可直接作用于实验证实的靶标,还能影响相关靶标发挥广泛的生物学效应。五味子的10种血中移行成分只能通过影响相关靶标而发挥间接的治疗作用。结论:结果可为生脉散的后续研究提供有用的线索,促进生脉散的分子作用机制研究,为中药复方的系统研究提供参考。
基金Supported by A grant from US National Institute of Health with No. 1RO1DK072616-01A2Karen Elise Jensen Fond
文摘The gastrointestinal (GI) tract is the system of organs within multi-cellular animals that takes in food, digests it to extract energy and nutrients, and expels the remaining waste. The various patterns of GI tract function are generated by the integrated behaviour of multiple tissues and cell types. A thorough study of the GI tract requires understanding of the interactions between cells, tissues and gastrointestinal organs in health and disease. This depends on knowledge, not only of numerous cellular ionic current mechanisms and signal transduction pathways, but also of large scale GI tissue structures and the special distribution of the nervous network. A unique way of coping with this explosion in complexity is mathematical and computational modelling; providing a computational framework for the multilevel modelling and simulation of the human gastrointestinal anatomy and physiology. The aim of this review is to describe the current status of biomechanical modelling work of the GI tract in humans and animals, which can be further used to integrate the physiological, anatomical and medical knowledge of the GI system. Such modelling will aid research and ensure that medical professionals benefit, through the provision of relevant and precise information about the patient's condition and GI remodelling in animal disease models. It will also improve the accuracy and efficiency of medical procedures, which could result in reduced cost for diagnosis and treatment.
文摘Systems that exhibit complex behaviours are often found in a particular dynamical con- dition, poised between order and disorder. This observation is at the core of the so-called criticality hypothesis, which states that systems in a dynamical regime between order and disorder attain the highest level of computational capabilities and achieve an optimal trade-off between robustness and flexibility. Recent results in cellular and evolutionary biology, ueuroscience and computer science have revitalised the interest in the criticality hypothesis, emphasising its role as a viable candidate general law in adaptive complex systems. This paper provides an overview of the works on dynamical criticality that are -- To the best of our knowledge -- Particularly relevant for the criticality hypothesis. The authors review the main contributions concerning dynamics and information processing at the edge of chaos, and illustrate the main achievements in the study of critical dynamics in biological systems. Finally, the authors discuss open questions and propose an agenda for future work.
文摘Although Yin-Yang Wu-Xing （Yin-Yang and Five-Elements, subsystems of human body） has been the theoretical basis of traditional Chinese medicine （TCM） for more than 5 000 years, it has been primarily analytical or empirical in nature without a formal scientific foundation. Based on bipolar set theory, an equilibrium/non-equilibrium computational model of Yin-Yang Wu-Xing is proposed. The Yin-Yang Wu-Xing dynamical systems are formulated so that equilibrium and non-equilibrium conditions can be established and proved. Computer simulations of equilibrium and non-equilibrium processes show that this new approach can provide diagnostic decision support in TCM. Thus, this equilibrium-based approach provides a unique scientific basis for future research in TCM, Qi （vital energy）, QiGong, Meridians and Collaterals （acupuncture channels） and herbal treatment. On the other hand, it provides a basic Yin-Yang cellular network architecture for modem scientific research in genomics such that regulation mechanisms of the ubiquitous YY1 protein for cell processes can be explained.
