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Understanding channel tropism in traditional Chinese medicine in the context of systems biology

null

《医学前沿（英文）》 2013年第7卷第3期页码 277-279 doi: 10.1007/s11684-013-0273-3

摘要：

Channel tropism is investigated and developed through long-term clinical practice. In recent years, the development of channel tropism theory has attracted increasing attention. This study analyzed channel tropism theory and the problems associated with it. Results showed that this theory and systems biology have a similar holistic viewpoint. Systems biology could provide novel insights and platform in the study of channel tropism. Some problems in channel tropism theory, including pharmacology and action mechanism, were investigated.

关键词： systems biology channel tropism theory traditional Chinese medicine application

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Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

《农业科学与工程前沿（英文）》 2016年第3卷第2期页码 102-112 doi: 10.15302/J-FASE-2016100

摘要： Plants are frequently affected by pathogen infections. To effectively defend against such infections, two major modes of innate immunity have evolved in plants; pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. Although the molecular components as well as the corresponding pathways involved in these two processes have been identified, many aspects of the molecular mechanisms of the plant immune system remain elusive. Recently, the rapid development of omics techniques (e.g., genomics, proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions (PPIs) between plants and pathogens have been carried out and characterized at the network level. In this review, we introduce experimental and computational identification methods of PPIs, popular PPI network analysis approaches, and existing bioinformatics resources/tools related to PPIs. Then, we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions, including pathogen-centric PPI networks, plant-centric PPI networks and interspecies PPI networks between plants and pathogens. We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.

关键词： plant–pathogen interactions systems biology omics plant immunity protein–protein interaction network

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Dendritic cell vaccines in cancer immunotherapy: from biology to translational medicine

Hongmei Xu, Xuetao Cao

《医学前沿（英文）》 2011年第5卷第4期页码 323-332 doi: 10.1007/s11684-011-0172-4

摘要：

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Comparative lipidomic analysis of

Bin QIAO, Hong-Chi TIAN, Ying-Jin YUAN

《化学科学与工程前沿（英文）》 2012年第6卷第4期页码 461-469 doi: 10.1007/s11705-012-1223-3

摘要： Variations in the composition and level of phospholipids (PLs) in yeast cells during industrial ethanol fermentation processes were analyzed. A comparative lipidomic method was used to investigate the changes in total cellular PLs during continuous and fed-batch/batch processes. The phospholipid metabolism in yeast changed during both processes, mainly due to the presence of long-chain poly unsaturated fatty acids (PUFA) that contained phosphatidyglycerol (PG), phosphatidylethanolamine (PE) and phosphatidylserine (PS). The complexity of the media affected the growth of the yeast and the membrane composition. Yeast incorporated lots of exogenous saturated and PUFAs from the feedstock during the fermentations. During the continuous fermentation, there was an increase in PLs with shorter chains as the fermentation progressed and early in process there were more long-chains. During the fed-batch/batch process, the PG species increased as the fermentation progressed. This is probably due to an inositol deficiency in the earlier part of the fermentation.

关键词： lipidomics systems biology phospholipids stirred-tank saccharomyces cerevisiae biorefinery engineering

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Cytokine storm and translating IL-6 biology into effective treatments for COVID-19

《医学前沿（英文）》 doi: 10.1007/s11684-023-1044-4

摘要： As of May 3, 2023, the coronavirus disease 2019 (COVID-19) pandemic has resulted in more than 760 million confirmed cases and over 6.9 million deaths. Several patients have developed pneumonia, which can deteriorate into acute respiratory distress syndrome. The primary etiology may be attributed to cytokine storm, which is triggered by the excessive release of proinflammatory cytokines and subsequently leads to immune dysregulation. Considering that high levels of interleukin-6 (IL-6) have been detected in several highly pathogenic coronavirus-infected diseases, such as severe acute respiratory syndrome in 2002, the Middle East respiratory syndrome in 2012, and COVID-19, the IL-6 pathway has emerged as a key in the pathogenesis of this hyperinflammatory state. Thus, we review the history of cytokine storm and the process of targeting IL-6 signaling to elucidate the pivotal role played by tocilizumab in combating COVID-19.

关键词： SARS-CoV-2 COVID-19 cytokine storm interleukin-6 tocilizumab

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Designer enzyme for green materials innovation: Lactate-polymerizing enzyme as a key catalyst

Seiichi Taguchi

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 139-142 doi: 10.1007/s11705-017-1636-0

摘要： Establishment of the regeneratable whole-cell catalyst platform for the?production of biobased polymeric materials is a?typical topic of synthetic biology. In this commentary, discovery story of a “lactate-polymerizing enzyme” (LPE)?and LPE-based?achievements for creating a new variety of polyesters with incorporated unnatural monomers are presented. Besides the importance of microbial platform itself is discussed referring to the “ballooning”- .

关键词： synthetic biology enzyme evolutionary engineering polyhydroxyalkanoate

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Correlation between cold and hot pattern in traditional Chinese medicine and gene expression profiles in rheumatoid arthritis

Miao Jiang, Cheng Xiao, Gao Chen, Cheng Lu, Qinglin Zha, Xiaoping Yan, Weiping Kong, Shijie Xu, Dahong Ju, Pu Xu, Youwen Zou, Aiping Lu

《医学前沿（英文）》 2011年第5卷第2期页码 219-228 doi: 10.1007/s11684-011-0133-y

摘要： Clinical manifestations of rheumatoid arthritis (RA) are diversified, and based on the manifestations, the patients with RA could be classified into different patterns under traditional Chinese medicine. These patterns decide the selection of herbal prescription, and thus they can help find a subset of rheumatoid arthritis patients for a type of therapy. In the present study, we combine genome-wide expression analysis with methods of systems biology to identify the functional gene networks for the sets of clinical symptoms that comprise the major information for pattern classification. Clinical manifestations in rheumatoid arthritis were clustered with factor analysis, and two factors (similar to cold and hot patterns in traditional Chinese medicine) were found. Microarray technology was used to reveal gene expression profiles in CD4 T cells from 21 rheumatoid arthritis patients. Protein-protein interaction information for these genes from databases and literature data was searched. The highly-connected regions were detected to infer significant complexes or pathways in this protein-protein interaction network. The significant pathways and function were extracted from these subnetworks using the Biological Network Gene Ontology tool. The genes significantly related to hot and cold patterns were identified by correlations analysis. MAPK signalling pathway, Wnt signaling pathway, and insulin signaling pathway were found to be related to hot pattern. Purine metabolism was related to both hot and cold patterns. Alanine, aspartate, and tyrosine metabolism were related to cold pattern, and histindine metabolism and lysine degradation were related to hot pattern. The results suggest that cold and hot patterns in traditional Chinese medicine were related to different pathways, and the network analysis might be used for identifying the pattern classification in other diseases.

关键词： gene expression profile pathway rheumatoid arthritis traditional Chinese medicine systems biology

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MicroRNAs and lung cancers: from pathogenesis to clinical implications

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《医学前沿（英文）》 2012年第6卷第2期页码 134-155 doi: 10.1007/s11684-012-0188-4

摘要：

Lung cancer is the leading cause of cancer-related deaths in the US and worldwide. Better understanding of the disease is warranted for improvement in clinical management. Here we summarize the functions of small-RNA-based, posttranscriptional gene regulators, i.e. microRNAs, in the pathogenesis of lung cancers. We discuss the microRNAs that play oncogenic as well as tumor suppressive roles. We also touch on the value of microRNAs as markers for diagnosis, prognosis and the promising field of microRNA-based novel therapies for lung cancers.

关键词： lung biology lung cancer microRNA

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Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 37-45 doi: 10.1007/s11705-017-1618-2

摘要： The ability to go from a digitized DNA sequence to a predictable biological function is central to synthetic biology. Genome engineering tools facilitate rewriting and implementation of engineered DNA sequences. Recent development of new programmable tools to reengineer genomes has spurred myriad advances in synthetic biology. Tools such as clustered regularly interspace short palindromic repeats enable RNA-guided rational redesign of organisms and implementation of synthetic gene systems. New directed evolution methods generate organisms with radically restructured genomes. These restructured organisms have useful new phenotypes for biotechnology, such as bacteriophage resistance and increased genetic stability. Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms, such as J. Craig Venter Institute (JCVI)-syn 3.0. Here we summarize the recent advances in programmable genome engineering tools.

关键词： CRISPR genome engineering synthetic biology rational design

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Current status and prospects of reliability systems engineering in China

《工程管理前沿（英文）》 2021年第8卷第4期页码 492-502 doi: 10.1007/s42524-021-0172-2

摘要： This study provides a systematic overview of the advent and evolution of reliability systems engineering (RSE) in China, and the latest RSE development, that is, model-based RSE (MBRSE), is emphatically introduced. The establishment of the system architecture and conceptual models of MBRSE is first described. The fundamental theory and methodology of MBRSE are then elaborated, with a V-model as the core of this approach. The development of various MBRSE platforms and the effectiveness of their implementation over the past 30 years are presented. The prospective trends in the development of RSE in China are outlined.

关键词： reliability effectiveness model-based systems engineering reliability systems engineering

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Floating production storage and offloading systems’ cost and motion performance: A systems thinking application

Rini NISHANTH, Andrew WHYTE, V. John KURIAN

《工程管理前沿（英文）》 2018年第5卷第3期页码 357-368 doi: 10.15302/J-FEM-2018022

摘要：

Floating production storage and offloading (FPSO) units increasingly represent a practical and economic means for deep-water oil extraction and production. Systems thinking gives a unique opportunity to seek a balance between FPSO technical performance(s), with whole-cost; stakeholder decision-making is charged to align different fit-for-use design specification options’ that address technical-motion(s), with respective life-cycle cost analyses (LCCA). Soft system methodology allows situation based analyses over set periods-of-time by diagnosing the problem-at-hand; namely, assessing the antecedents of life-cycle cost relative to FPSO sub-component design alternatives. Alternative mooring- component comparisons for either new-build hulls or refurbished hulls represent an initial necessary consideration to facilitate extraction, production and storage of deep-water oil reserves. Coupled dynamic analysis has been performed to generate FPSO motion in six degrees of freedom using SESAM DeepC, while life-cycle cost analysis (LCAA) studies give net-present-value comparisons reflective of market conditions. A parametric study has been conducted by varying wave heights from 4 – 8 m to understand FPSO motion behavior in the presence of wind and current, as well as comparing the motions of turreted versus spread mooring design alternatives. LCCA data has been generated to compare the cost of such different mooring options/hull conditions over 10 and 25-year periods. Systems thinking has been used to explain the interaction of problem variables; resultantly this paper is able to identify explicit factors affecting the choice of FPSO configurations in terms of motion and whole-cost, toward assisting significantly with the front-end engineering design (FEED) phase of fit-for-purpose configured FPSOs, in waters off Malaysia and Australia.

关键词： FPSO LCCA spread/turret-mooring DeepC cost motion soft-systems

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TRANSFORMING CHINESE FOOD AND AGRICULTURE: A SYSTEMS PERSPECTIVE

《农业科学与工程前沿（英文）》 2023年第10卷第1期页码 4-15 doi: 10.15302/J-FASE-2023493

摘要：

● The goals of Chinese food and agriculture have shifted from grain self-sufficiency to diversified goals, including protecting natural resources, reducing pollution and greenhouse gas emissions, and improving food safety and nutrition.

关键词： food systems food security nutrition climate change

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Recent advances in fruit crop genomics

Qiang XU,Chaoyang LIU,Manosh Kumar BISWAS,Zhiyong PAN,Xiuxin DENG

《农业科学与工程前沿（英文）》 2014年第1卷第1期页码 21-27 doi: 10.15302/J-FASE-2014002

摘要： In recent years, dramatic progress has been made in the genomics of fruit crops. The publication of a dozen fruit crop genomes represents a milestone for both functional genomics and breeding programs in fruit crops. Rapid advances in high-throughput sequencing technology have revolutionized the manner and scale of genomics in fruit crops. Research on fruit crops is encompassing a wide range of biological questions which are unique and cannot be addressed in a model plant such as . This review summarizes recent achievements of research on the genome, transcriptome, proteome, miRNAs and epigenome of fruit crops.

关键词： fruit crops fruit biology gene function genomics