Whole-genome sequencing in medicinal plants: current progress and prospect.

Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

Strategy and significance of Chinese medicine combined with medical hydrogel for disease treatment / 中国组织工程研究

BACKGROUND:Medical hydrogels are new functional polymer materials with three-dimensional structural networks and excellent biocompatibility,which have been widely studied in the field of tissue engineering and drug carriers,but the research on the combination of medical hydrogels and Chinese medicine for the treatment of diseases based on tissue engineering is still in the early exploration stage.Therefore,through the analysis of the mechanism of the role of medical hydrogels,the integration of medical hydrogels and Chinese medicine in the research of the joint application of the article,can better provide ideas for scientific researchers,and the joint application of Chinese medicine and medical hydrogels is of great significance. OBJECTIVE:To explore the strategy and significance of Chinese medicine combined with medical hydrogel for disease treatment based on tissue engineering research. METHODS:PubMed and CNKI were used to retrieve articles about the application of Chinese medicine combined with medical hydrogel in tissue engineering from January 2010 to November 2022,with the Chinese and English search terms"hydrogel,traditional Chinese medicine,drug carrier,tissue engineering".After the initial screening of all articles according to the inclusion and exclusion criteria,the 61 articles with high relevance were retained for review. RESULTS AND CONCLUSION:(1)Although the application of Chinese medicine combined with medical hydrogel is involved in intra-articular,intra-tissue organ,soft tissue wounds,tissue engineering,etc.,except for the clinical application of Chinese medicine combined with hydrogel dressing for soft tissue injury,other aspects are still in the experimental stage.(2)The development of Chinese medicine combined with medical hydrogel has great potential and development prospects,but there is a certain difficulty in the manufacture of the gel with high-performance requirements,and it is difficult to master the physical and chemical properties precisely.(3)At present,the comprehensive view of injectable hydrogel with the characteristics of easy to use,its joint use of Chinese medicine can be extended to a wider range,can be used for joint,organ,tissue engineering-related disease treatment.Smart hydrogel has high sensitivity and reversible transformation can also meet the use of the special environment.During the combined use of Chinese medicine,it also needs to understand the mechanism of action of Chinese medicine components.(4)The strategy of combining Chinese medicine with medical hydrogels for disease treatment should start with matching the therapeutic effects of Chinese medicine on organs,tissues and cells combined with appropriate types of medical hydrogels to make up for the shortcomings of traditional Chinese medicine delivery methods and frequent drug delivery.In tissue engineering,hydrogels can be loaded with stem cells after Chinese medicine intervention,or with both Chinese medicine and stem cells for disease treatment.(5)In future research of combined Chinese medicine and medical hydrogel application,we also need to consider:we should ensure that the biological properties of medical hydrogel can be quantified,and grasp the characteristics of hydrogel with different manufacturing processes of different materials to produce the required medical hydrogel that meets the application conditions.In Chinese medicine,we need to comprehensively understand and analyze the therapeutic effects and application mechanisms of known Chinese medicine monomer and Chinese medicine compound extracts,so as to achieve a more perfect combination between Chinese medicine and medical hydrogel under a more clear mechanism.With the continuous improvement of medical science and technology innovation,the medical hydrogel can be innovatively combined with other traditional treatment methods of Chinese medicine,such as acupuncture,massage,cupping and so on,to be used from multiple angles.

Protein Modification Omics： A Novel Approach Investigating Mechanisms of Chinese Medicines / 中国实验方剂学杂志

Traditional Chinese medicine （TCM）， as an invaluable scientific legacy and cultural patrimony of China， encapsulates the cumulative wisdom of millennia from the Chinese civilization. The deeply rooted medical theories and extensive empirical practices of TCM hold an indispensible central role within China's healthcare framework. Facing the challenges of modern medicine and health needs， it is particularly urgent to explore the mechanisms of Chinese medicines. Post-translational modification （PTM）， as a core mechanism to regulate the complex and diverse protein functions， is a bridge between environmental stimuli and physiological responses. Different PTMs can interact with each other to form a complex regulatory network， which is in line with the multi-component and multi-target action of Chinese medicines. In recent years， protein modification omics has emerged as a powerful means to probe into PTMs， and studies have employed protein modification omics to investigate the mechanisms of Chinese medicines. However， the research in this field is still in the initial stage. This article summarizes the basic theory of PTM and the basic research process of protein modification omics， reviews the application status of protein modification omics in the research on the mechanisms of Chinese medicines， and analyzes the existing research limitations. This study aims to explore an innovative research paradigm for analyzing the mechanisms of Chinese medicines from the perspective of PTM and provide a theoretical basis and practical guidance for understanding the mechanisms of Chinese medicines in the future.

Network pharmacology: a bright guiding light on the way to explore the personalized precise medication of traditional Chinese medicine.

Network pharmacology can ascertain the therapeutic mechanism of drugs for treating diseases at the level of biological targets and pathways. The effective mechanism study of traditional Chinese medicine (TCM) characterized by multi-component, multi-targeted, and integrative efficacy, perfectly corresponds to the application of network pharmacology. Currently, network pharmacology has been widely utilized to clarify the mechanism of the physiological activity of TCM. In this review, we comprehensively summarize the application of network pharmacology in TCM to reveal its potential of verifying the phenotype and underlying causes of diseases, realizing the personalized and accurate application of TCM. We searched the literature using "TCM network pharmacology" and "network pharmacology" as keywords from Web of Science, PubMed, Google Scholar, as well as Chinese National Knowledge Infrastructure in the last decade. The origins, development, and application of network pharmacology are closely correlated with the study of TCM which has been applied in China for thousands of years. Network pharmacology and TCM have the same core idea and promote each other. A well-defined research strategy for network pharmacology has been utilized in several aspects of TCM research, including the elucidation of the biological basis of diseases and syndromes, the prediction of TCM targets, the screening of TCM active compounds, and the decipherment of mechanisms of TCM in treating diseases. However, several factors limit its application, such as the selection of databases and algorithms, the unstable quality of the research results, and the lack of standardization. This review aims to provide references and ideas for the research of TCM and to encourage the personalized and precise use of Chinese medicine.

Research strategies and applications of functional metabolomics in anti-depressive mechanisms of traditional Chinese medicine / 药学学报

Depression is a common emotional disorder that seriously affects people's life and health all over the world. The pathogenesis of depression is complex, and traditional Chinese medicine (TCM) for antidepressants has a good therapeutic effect because of its multi-component, multi-pathway, and multi-target action mode. At present, the anti-depressive mechanism of TCM has not been fully clarified, but it is clear that depression is closely related to metabolic health. Therefore, in order to further explore the anti-depressive mechanism of TCM, this paper proposes research strategies on the anti-depressive mechanism of TCM based on functional metabolomics from the perspective of metabolism, the potential biomarkers of depression are analyzed with the help of multi-omics combined analysis technology, and the functional molecules of TCM for antidepressant are studied. Molecular biology techniques are used to accurately capture the molecular interactions between biomarkers of depression and functional compounds, which identify effective drug targets and further elucidate the biochemical functions and related mechanisms involved in depression metabolic disorders. This paper systematically reviews the research strategies and applications of functional metabolomics in the anti-depressive mechanisms of TCM, expounds on the core value of functional metabolomics, and summarizes the current research status and hot issues of TCM for antidepressants in recent years, providing new methods and new ideas for the study of mechanisms of TCM with the help of functional metabolomics.

Challenges and strategies in depression research / 四川精神卫生

Depression constitutes the most common mental disorder with high prevalence rate， and is the leading contributor to the global burden of disease. Many factors are found to influence the development of depression， whereas either reliable biomarkers for the early diagnosis or diagnostic criteria for subtype classification currently exist for depression. Therefore， this paper gives a detailed discussion on the current status and existing challenges of depression research in the context of brain imaging， psychoneuroimmunology and electroencephalography， thus providing a new perspective for research directions and future strategies related to depression.

Classification-based strategies to simplify complex traditional Chinese medicine (TCM) researches through liquid chromatography-mass spectrometry in the last decade (2011-2020): Theory, technical route and difficulty.

The difficulty of traditional Chinese medicine (TCM) researches lies in the complexity of components, metabolites, and bioactivities. For a long time, there has been a lack of connections among the three parts, which is not conducive to the systematic elucidation of TCM effectiveness. To overcome this problem, a classification-based methodology for simplifying TCM researches was refined from literature in the past 10 years (2011-2020). The theoretical basis of this methodology is set theory, and its core concept is classification. Its starting point is that "although TCM may contain hundreds of compounds, the vast majority of these compounds are structurally similar". The methodology is composed by research strategies for components, metabolites and bioactivities of TCM, which are the three main parts of the review. Technical route, key steps and difficulty are introduced in each part. Two perspectives are highlighted in this review: set theory is a theoretical basis for all strategies from a conceptual perspective, and liquid chromatography-mass spectrometry (LC-MS) is a common tool for all strategies from a technical perspective. The significance of these strategies is to simplify complex TCM researches, integrate isolated TCM researches, and build a bridge between traditional medicines and modern medicines. Potential research hotspots in the future, such as discovery of bioactive ingredients from TCM metabolites, are also discussed. The classification-based methodology is a summary of research experience in the past 10 years. We believe it will definitely provide support and reference for the following TCM researches.

[Metabonomics research strategy based on microdialysis technique].

Metabonomics is the branch of systems biology. It has been widely used in the fields of diagnostic markers discovery, disease prognosis, drug action mechanism, drug efficacy and toxicity evaluation, traditional Chinese medicine syndromes differentiation. There are shortcomings in the conventional metabonomics research. Microdialysis technology is a new type of biosampling technology, and metabonomics research based on microdialysis technology is in the ascendant. In view of the particularity of microdialysis technology and its great differences from traditional sampling and pretreatment methods, the metabonomics process based on microdialysis technology has certain similarities with traditional metabonomics research, and its basic process has some particularity. Advantages and basic strategies of metabonomics research by microdialysis technology are systematically summarized for researchers' reference.

Metabonomics research strategy based on microdialysis technique / 中国中药杂志

Metabonomics is the branch of systems biology. It has been widely used in the fields of diagnostic markers discovery, disease prognosis, drug action mechanism, drug efficacy and toxicity evaluation, traditional Chinese medicine syndromes differentiation. There are shortcomings in the conventional metabonomics research. Microdialysis technology is a new type of biosampling technology, and metabonomics research based on microdialysis technology is in the ascendant. In view of the particularity of microdialysis technology and its great differences from traditional sampling and pretreatment methods, the metabonomics process based on microdialysis technology has certain similarities with traditional metabonomics research, and its basic process has some particularity. Advantages and basic strategies of metabonomics research by microdialysis technology are systematically summarized for researchers' reference.

[Opportunities and challenges in development of compound preparations of traditional Chinese medicine: problems and countermeasures in research of ancient classical prescriptions].

As an outstanding representative of traditional Chinese medicine( TCM),ancient classical prescriptions carry the profound accumulation of the splendid civilization of Chinese medicine for thousands of years. It is the best part of the great treasure-house of Chinese medicine after thousands of years' training of TCM theory. It condenses the wisdom of all generations of doctors,and as the summary of clinical experience,it is the most brilliant pearl in the treasure house of TCM. The in-depth research and development of ancient classic prescriptions is a golden key to excavate the treasure house of TCM,which not only conforms to the development trend of TCM industry,but also brings unprecedented opportunities and challenges for the inheritance and innovation of contemporary Chinese herbal compound preparations. However,as a " new member" in the national drug research and development system,classic prescriptions have no specific implementation rules although the guidance is given by macro policies,and there is no successful case of research and development according to the registration requirements. Therefore,unified consensus and standards have not yet been formed for some key issues in the process of the development of the classic prescriptions,and much work is still in the exploration stage,so it is necessary to conduct in-depth research and discussion on these issues. In this paper,the problems in the research process of classical prescriptions were summarized,such as the resources of medicinal materials,the processing of decoction pieces,the prescription dosage,the molding technology and the quality evaluation,and the research strategy was put forward after analysis,hoping to provide a reference for the research and development of classical prescriptions.

Opportunities and challenges in development of compound preparations of traditional Chinese medicine: problems and countermeasures in research of ancient classical prescriptions / 中国中药杂志

As an outstanding representative of traditional Chinese medicine( TCM),ancient classical prescriptions carry the profound accumulation of the splendid civilization of Chinese medicine for thousands of years. It is the best part of the great treasure-house of Chinese medicine after thousands of years' training of TCM theory. It condenses the wisdom of all generations of doctors,and as the summary of clinical experience,it is the most brilliant pearl in the treasure house of TCM. The in-depth research and development of ancient classic prescriptions is a golden key to excavate the treasure house of TCM,which not only conforms to the development trend of TCM industry,but also brings unprecedented opportunities and challenges for the inheritance and innovation of contemporary Chinese herbal compound preparations. However,as a " new member" in the national drug research and development system,classic prescriptions have no specific implementation rules although the guidance is given by macro policies,and there is no successful case of research and development according to the registration requirements. Therefore,unified consensus and standards have not yet been formed for some key issues in the process of the development of the classic prescriptions,and much work is still in the exploration stage,so it is necessary to conduct in-depth research and discussion on these issues. In this paper,the problems in the research process of classical prescriptions were summarized,such as the resources of medicinal materials,the processing of decoction pieces,the prescription dosage,the molding technology and the quality evaluation,and the research strategy was put forward after analysis,hoping to provide a reference for the research and development of classical prescriptions.

[Study and thought on the safety of traditional Chinese medicines under Healthy China strategy].

As the Healthy China planning has been implemented, traditional Chinese medicine (TCM) has witnessed unprecedented developmental opportunities. However, the safety of TCM has always been like The Sword of Damocles in TCM area, endangering the healthy and sustainable development of TCM. In order to solve the problem of TCM safety in China as soon as possible, the author puts forward that the situation and issues of TCM safety should be considered with the change of the times. At the same time, it is suggested that the research on TCM safety should be listed as the most important project in TCM science and technology field. The safety evaluation and risk control system in line with China national situation and TCM characteristics should be established as soon as possible. The research strategy of TCM safety should be innovated from "five changes". The transition of adverse drug reactions of TCM from "still not clear" to "basically clear" should be tried to realize, which allow TCM inherited from our ancestors to make a greater contribution to human's health.

Innovation Strategy in the Modern Chinese Medicine Based on Scientific Representation of Classic Herbs Dosage Forms / 世界科学技术-中医药现代化

Excavating and characterizing the dosage forms characteristics of classic Chinese medicine preparations is the basis for the innovation of modern preparations of Chinese medicine. Through the combing statistics of the National Natural Science Foundation of China (NSFC) on the establishment of traditional Chinese medicine preparations, the research literature on Chinese medicine preparations at home and abroad, and the registration of new Chinese medicines in the past ten years, this paper finds that the research projects of classic Chinese medicines have been greatly reduced. The market share of traditional Chinese medicine classics has shrunk year by year. The modern preparation produced in the "preparation of traditional Chinese medicine by western medicine technology" mode dominates the market. However, because of its "degraded" effect, it is less competitive. Therefore, with the wave of classic dosage forms research promoted by national policies, accelerating the study of classical Chinese medicine preparations will not only promote the development of pharmaceutical discipline of traditional Chinese medicine, enhance the classic medical culture literacy, but also promote the protection and inheritance of classic medicine.

Study and thought on the safety of traditional Chinese medicines under Healthy China strategy / 中国中药杂志

As the Healthy China planning has been implemented, traditional Chinese medicine (TCM) has witnessed unprecedented developmental opportunities. However, the safety of TCM has always been like The Sword of Damocles in TCM area, endangering the healthy and sustainable development of TCM. In order to solve the problem of TCM safety in China as soon as possible, the author puts forward that the situation and issues of TCM safety should be considered with the change of the times. At the same time, it is suggested that the research on TCM safety should be listed as the most important project in TCM science and technology field. The safety evaluation and risk control system in line with China national situation and TCM characteristics should be established as soon as possible. The research strategy of TCM safety should be innovated from "five changes". The transition of adverse drug reactions of TCM from "still not clear" to "basically clear" should be tried to realize, which allow TCM inherited from our ancestors to make a greater contribution to human's health.

[Referencing and inosculating--discussion on modern research strategy for ethnomedicines].

This article reviewed the current situation of ethnomedicines in China, and propos that the important research on ethnomedicine is to focus on the theoretical and empirical characteristics of ethnomedicine and the special features in the processes of collecting,processing and clinical application of ethnomedicine, which will be benefit to find the research principles and methods with the characteristics of ethnomedicine. These principles include making clear of the effective substances and mechanisms, and theoretical and empirical characteristics of ethnomedicine. The three methods in the new drug discovery technology system for ethnomedicine are to solve the difference in varieties of traditional medical systems depending on finding the similarities of them, to find the conjunction in varieties of traditional medical systems through the key-herbs, and to find medicinal sources in varieties of traditional medical systems according to pharmaphylogeny.

Research strategies on orientated effective components of multi-effect Chinese materia medica / 中草药

Multi-effect is a universal phenomenon for Chinese materia medica (CMM). However, only part of the chemical ingredients of CMM show effectiveness in a given formulas for the specific disease, which were recognized as the orientated effective components. In this paper, a strategy on the identification of orientated effective components from multi-effect CMM has been put forward, aiming at the discovery of the orientated material basis for CMM and their mechanisms. Based on these two prerequisites, "compatibility of prescriptions" and "different diseases" or "multiple effects", this strategy is carried out to identify and verify the orientated components of CMM in different syndromes by reverse analysis in vivo, compound compatibility or decomposed recipe analysis and comparative analysis methods, which combined the two key techniques of metabolomics and structure elucidation. Taking Astragali Radix, a Shanxi authentic herb, as an example, a scientific method was constructed for the study of oriented effective components of multi-effect CMM. The results will be expected to explain the compatibility of prescriptions from the molecular level, specify the direction for the quality control of CMM based on efficacy, provide the research basis for the selection of appropriate raw materials for clinical application and Chinese patent medicine production, and provide the foundation for multi-fractions CMM discovery.

Prospect and Progress of the Research on the Technology of Metabolism in Acupuncture and Moxibustion / 浙江中医药大学学报

Objective] Metabolomics is a genomics research methods, has good prospects in the study of mechanisms of acupuncture. In this paper, the progress of the research on the mechanism of the action of metabolism in the mechanism of acupuncture and moxibustion were reviewed. [Methods] Retrieve acupuncture mechanism studies,which use metabolic technology in nearly 15 years, and to summarize. [Results]Nearly 15 years metabolomics research techniques and tools developed rapidly. But the acupuncture metabomoic studies were still based on the research of animal experiments mainly, relative clinical research less. [Conclusion] With the deepening development of metabolomics studies, the metabolic characteristics of various diseases will gradually clear. Acupuncture clinical mechanisms research combined with metabolomics technology will have broader prospects. But the research strategy of metabololic technology on acupuncture clinical efficacy is yet to be further explored and improved.