8 results on '"Yang, Hongjun"'
Search Results
2. Influences of micro-geomorphology on the stoichiometry of C, N and P in Chenier Island soils and plants in the Yellow River Delta, China.
- Author
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Qu, Fanzhu, Meng, Ling, Yu, Junbao, Liu, Jingtao, Sun, Jingkuan, Yang, Hongjun, and Dong, Linshui
- Subjects
GEOMORPHOLOGY ,STOICHIOMETRY ,SOIL profiles ,SOIL formation - Abstract
Studies have indicated that consistent or well-constrained (relatively low variability) carbon:nitrogen:phosphorus (C:N:P) ratios exist in large-scale ecosystems, including both marine and terrestrial ecosystems. Little is known about the C, N and P stoichiometric ratios that exist in the soils and plants of Chenier Island in the Yellow River Delta (YRD). We examined the distribution patterns and relationships of C, N and P stoichiometry in the soils and plants of Chenier Island, as well as the potential influences of the island’s micro-geomorphology. Based on a study of four soil profile categories and Phragmites australis and Suaeda heteroptera plant tissues, our results showed that micro-geomorphology could leave a distinct imprint on the soil and plant elemental stoichiometry of Chenier Island; significant variation in the atomic C:N:P ratios (R
CNP ) existed in soils and plants, indicating that the RCNP values in both the soil and plants are not well constrained at the Chenier Island scale. RCN and RCP in Chenier Island soils were high, whereas the RNP values were comparatively low, indicating that the ecosystems of Chenier Island are nutrient-limited by N and P. However, the RNP values in P. australis and S. heteroptera plant tissues were high, suggesting that the plants of Chenier Island are nutrient-limited by P. Finally, we suggest that soil and plant N:P ratios may be good indicators of the soil and plant nutrient status during soil development and plant growth, which could be a useful reference for restoring the degraded soils of Chenier Island. [ABSTRACT FROM AUTHOR]- Published
- 2017
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3. A Modularity-Based Method Reveals Mixed Modules from Chemical-Gene Heterogeneous Network.
- Author
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Song, Jianglong, Tang, Shihuan, Liu, Xi, Gao, Yibo, Yang, Hongjun, and Lu, Peng
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BIOCHEMICAL genetics ,CHINESE medicine ,TARGETED drug delivery ,INTESTINAL absorption ,MOLECULAR biology - Abstract
For a multicomponent therapy, molecular network is essential to uncover its specific mode of action from a holistic perspective. The molecular system of a Traditional Chinese Medicine (TCM) formula can be represented by a 2-class heterogeneous network (2-HN), which typically includes chemical similarities, chemical-target interactions and gene interactions. An important premise of uncovering the molecular mechanism is to identify mixed modules from complex chemical-gene heterogeneous network of a TCM formula. We thus proposed a novel method (MixMod) based on mixed modularity to detect accurate mixed modules from 2-HNs. At first, we compared MixMod with Clauset-Newman-Moore algorithm (CNM), Markov Cluster algorithm (MCL), Infomap and Louvain on benchmark 2-HNs with known module structure. Results showed that MixMod was superior to other methods when 2-HNs had promiscuous module structure. Then these methods were tested on a real drug-target network, in which 88 disease clusters were regarded as real modules. MixMod could identify the most accurate mixed modules from the drug-target 2-HN (normalized mutual information 0.62 and classification accuracy 0.4524). In the end, MixMod was applied to the 2-HN of Buchang naoxintong capsule (BNC) and detected 49 mixed modules. By using enrichment analysis, we investigated five mixed modules that contained primary constituents of BNC intestinal absorption liquid. As a matter of fact, the findings of in vitro experiments using BNC intestinal absorption liquid were found to highly accord with previous analysis. Therefore, MixMod is an effective method to detect accurate mixed modules from chemical-gene heterogeneous networks and further uncover the molecular mechanism of multicomponent therapies, especially TCM formulae. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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4. A Systems Biology-Based Approach to Uncovering the Molecular Mechanisms Underlying the Effects of Dragon's Blood Tablet in Colitis, Involving the Integration of Chemical Analysis, ADME Prediction, and Network Pharmacology.
- Author
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Xu, Haiyu, Zhang, Yanqiong, Lei, Yun, Gao, Xiumei, Zhai, Huaqiang, Lin, Na, Tang, Shihuan, Liang, Rixin, Ma, Yan, Li, Defeng, Zhang, Yi, Zhu, Guangrong, Yang, Hongjun, and Huang, Luqi
- Subjects
COLITIS ,DRAGON'S blood ,SYSTEMS biology ,ANALYTICAL chemistry ,PHARMACOLOGY ,CHINESE medicine ,DRUG metabolism - Abstract
Traditional Chinese medicine (TCM) is one of the oldest East Asian medical systems. The present study adopted a systems biology-based approach to provide new insights relating to the active constituents and molecular mechanisms underlying the effects of dragon's blood (DB) tablets for the treatment of colitis. This study integrated chemical analysis, prediction of absorption, distribution, metabolism, and excretion (ADME), and network pharmacology. Firstly, a rapid, reliable, and accurate ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry method was employed to identify 48 components of DB tablets. In silico prediction of the passive absorption of these compounds, based on Caco-2 cell permeability, and their P450 metabolism enabled the identification of 22 potentially absorbed components and 8 metabolites. Finally, networks were constructed to analyze interactions between these DB components/metabolites absorbed and their putative targets, and between the putative DB targets and known therapeutic targets for colitis. This study provided a great opportunity to deepen the understanding of the complex pharmacological mechanisms underlying the effects of DB in colitis treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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5. Study on the Absorbed Fingerprint-Efficacy of Yuanhu Zhitong Tablet Based on Chemical Analysis, Vasorelaxation Evaluation and Data Mining.
- Author
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Xu, Haiyu, Li, Ke, Chen, Yanjun, Zhang, Yingchun, Tang, Shihuan, Wang, Shanshan, Shen, Dan, Wang, Xuguang, Lei, Yun, Li, Defeng, Zhang, Yi, Jin, Lan, Yang, Hongjun, and Huang, Luqi
- Subjects
DRUG tablets ,DRUG efficacy ,ANALYTICAL chemistry ,DATA mining ,HERBAL medicine ,IN vitro studies - Abstract
Yuanhu Zhitong Tablet (YZT) is an example of a typical and relatively simple clinical herb formula that is widely used in clinics. It is generally believed that YZT play a therapeutical effect in vivo by the synergism of multiple constituents. Thus, it is necessary to build the relationship between the absorbed fingerprints and bioactivity so as to ensure the quality, safety and efficacy. In this study, a new combinative method, an intestinal absorption test coupled with a vasorelaxation bioactivity experiment in vitro, was a simple, sensitive, and feasible technique to study on the absorbed fingerprint-efficacy of YZT based on chemical analysis, vasorelaxation evaluation and data mining. As part of this method, an everted intestinal sac method was performed to determine the intestinal absorption of YZT solutions. YZT were dissolved in solution (n = 12), and the portion of the solution that was absorbed into intestinal sacs was analyzed using rapid-resolution liquid chromatography coupled with quadruple time-of-flight mass spectrometry (RRLC-Q-TOF/MS). Semi-quantitative analysis indicated the presence of 34 compounds. The effect of the intestinally absorbed solution on vasorelaxation of rat aortic rings with endothelium attached was then evaluated in vitro. The results showed that samples grouped by HCA from chemical profiles have similar bioactivity while samples in different groups displayed very different. Moreover, it established a relationship between the absorbed fingerprints and their bioactivity to identify important components by grey relational analysis, which could predict bioactive values based on chemical profiles and provide an evidence for the quantification of multi-constituents. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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6. An Effective Solution to Discover Synergistic Drugs for Anti-Cerebral Ischemia from Traditional Chinese Medicinal Formulae.
- Author
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Li, Shaojing, Wu, Chuanhong, Chen, Jianxin, Lu, Peng, Chen, Chang, Fu, Meihong, Fang, Jing, Gao, Jian, Zhu, Li, Liang, Rixin, Shen, Xin, and Yang, Hongjun
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CEREBRAL ischemia treatment ,PHARMACEUTICAL industry ,CHINESE medicine ,BRAIN disease treatment ,CEREBRAL arterial diseases ,ARTERIAL occlusions ,PARTICLE swarm optimization - Abstract
Recently, the pharmaceutical industry has shifted to pursuing combination therapies that comprise more than one active ingredient. Interestingly, combination therapies have been used for more than 2500 years in traditional Chinese medicine (TCM). Understanding optimal proportions and synergistic mechanisms of multi-component drugs are critical for developing novel strategies to combat complex diseases. A new multi-objective optimization algorithm based on least angle regression-partial least squares was proposed to construct the predictive model to evaluate the synergistic effect of the three components of a novel combination drug Yi-qi-jie-du formula (YJ), which came from clinical TCM prescription for the treatment of encephalopathy. Optimal proportion of the three components, ginsenosides (G), berberine (B) and jasminoidin (J) was determined via particle swarm optimum. Furthermore, the combination mechanisms were interpreted using PLS VIP and principal components analysis. The results showed that YJ had optimal proportion 3(G): 2(B): 0.5(J), and it yielded synergy in the treatment of rats impaired by middle cerebral artery occlusion induced focal cerebral ischemia. YJ with optimal proportion had good pharmacological effects on acute ischemic stroke. The mechanisms study demonstrated that the combination of G, B and J could exhibit the strongest synergistic effect. J might play an indispensable role in the formula, especially when combined with B for the acute stage of stroke. All these data in this study suggested that in the treatment of acute ischemic stroke, besides restoring blood supply and protecting easily damaged cells in the area of the ischemic penumbra as early as possible, we should pay more attention to the removal of the toxic metabolites at the same time. Mathematical system modeling may be an essential tool for the analysis of the complex pharmacological effects of multi-component drug. The powerful mathematical analysis method could greatly improve the efficiency in finding new combination drug from TCM. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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7. A system-level investigation into the mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for cardiovascular disease treatment.
- Author
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Li X, Xu X, Wang J, Yu H, Wang X, Yang H, Xu H, Tang S, Li Y, Yang L, Huang L, Wang Y, and Yang S
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- Administration, Oral, Biological Availability, Cardiovascular Diseases metabolism, Computer Simulation, Databases, Factual, Drugs, Chinese Herbal pharmacology, Humans, Medicine, Chinese Traditional, Metabolic Networks and Pathways, Molecular Docking Simulation, Molecular Dynamics Simulation, Pharmacogenetics, Phenanthrolines pharmacology, Signal Transduction, Systems Biology, Thermodynamics, Cardiovascular Diseases drug therapy, Drugs, Chinese Herbal chemistry, Models, Biological, Phenanthrolines chemistry, Salvia miltiorrhiza chemistry
- Abstract
Compound Danshen Formula (CDF) is a widely used Traditional Chinese Medicine (TCM) which has been extensively applied in clinical treatment of cardiovascular diseases (CVDs). However, the underlying mechanism of clinical administrating CDF on CVDs is not clear. In this study, the pharmacological effect of CDF on CVDs was analyzed at a systemic point of view. A systems-pharmacological model based on chemical, chemogenomics and pharmacological data is developed via network reconstruction approach. By using this model, we performed a high-throughput in silico screen and obtained a group of compounds from CDF which possess desirable pharmacodynamical and pharmacological characteristics. These compounds and the corresponding protein targets are further used to search against biological databases, such as the compound-target associations, compound-pathway connections and disease-target interactions for reconstructing the biologically meaningful networks for a TCM formula. This study not only made a contribution to a better understanding of the mechanisms of CDF, but also proposed a strategy to develop novel TCM candidates at a network pharmacology level.
- Published
- 2012
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8. Identification of short hairpin RNA targeting foot-and-mouth disease virus with transgenic bovine fetal epithelium cells.
- Author
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Wang H, Wu J, Liu X, He H, Ding F, Yang H, Cheng L, Liu W, Zhong J, Dai Y, Li G, He C, Yu L, and Li J
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- Animals, Animals, Genetically Modified, Cattle, Cricetinae, Foot-and-Mouth Disease prevention & control, HEK293 Cells, Humans, Lentivirus genetics, Male, Oocytes metabolism, RNA Interference, Tongue metabolism, Virus Replication, Epithelial Cells cytology, Foot-and-Mouth Disease virology, Foot-and-Mouth Disease Virus genetics, RNA, Small Interfering genetics
- Abstract
Background: Although it is known that RNA interference (RNAi) targeting viral genes protects experimental animals, such as mice, from the challenge of Foot-and-mouth disease virus (FMDV), it has not been previously investigated whether shRNAs targeting FMDV in transgenic dairy cattle or primary transgenic bovine epithelium cells will confer resistance against FMDV challenge., Principal Finding: Here we constructed three recombinant lentiviral vectors containing shRNA against VP2 (RNAi-VP2), VP3 (RNAi-VP3), or VP4 (RNAi-VP4) of FMDV, and found that all of them strongly suppressed the transient expression of a FLAG-tagged viral gene fusion protein in 293T cells. In BHK-21 cells, RNAi-VP4 was found to be more potent in inhibition of viral replication than the others with over 98% inhibition of viral replication. Therefore, recombinant lentiviral vector RNAi-VP4 was transfected into bovine fetal fibroblast cells to generate transgenic nuclear donor cells. With subsequent somatic cell cloning, we generated forty transgenic blastocysts, and then transferred them to 20 synchronized recipient cows. Three transgenic bovine fetuses were obtained after pregnant period of 4 months, and integration into chromosome in cloned fetuses was confirmed by Southern hybridization. The primary tongue epithelium cells of transgenic fetuses were isolated and inoculated with 100 TCID(50) of FMDV, and it was observed that shRNA significantly suppressed viral RNA synthesis and inhibited over 91% of viral replication after inoculation of FMDV for 48 h., Conclusion: RNAi-VP4 targeting viral VP4 gene appears to prevent primary epithelium cells of transgenic bovine fetus from FMDV infection, and it could be a candidate shRNA used for cultivation of transgenic cattle against FMDV.
- Published
- 2012
- Full Text
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