In this paper， the name， origin， producing area， harvesting， processing and functional indications of Arcae Concha were systematically combed and verified by consulting the ancient and modern literature， in order to provide a basis for the development of famous classical formulas containing Arcae Concha. Arcae Concha was first recorded in the name of Han in Bencao Shiyi， but later， due to the influence of LI Shizhen's error of combining Han item with Kuiha in the Ming dynasty， there were aliases such as Kuilu and Fulao， and Yizong Bidu began to include Walengzi as its correct name and has been used ever since. The textual descriptions and illustrations of the medicinal materials of Arcae Concha contained in the materia medica of the past generations were consistent with the modern Arca inflata， A. subcrenata and A. granosa. In ancient times， there were medicinal records of two parts of shell and meat， but now the shell is used as medicine， and the meat is mostly edible. In ancient times， Zhejiang， Shandong， Guangdong and Guangxi were the main producing areas， and Zhejiang was the best. It is now believed that A. inflata is mostly distributed in the northern part of the Huanghai Sea， A. granosa is mostly distributed in the coastal areas south of Shandong Peninsula in China， and A. subcrenata is widely distributed in the coastal areas of China. Its quality is better in a complete， white， no residual meat and sand. In ancient times， there was no clear harvesting period， and the processing was mainly based on vinegar quenching after calcination or powdering of calcined shell， but now the harvesting period is autumn and winter. After harvesting， it is directly washed and crushed for raw use or processed by calcined method. The records of the medicinal materials in the past dynasties on the properties of Arcae Concha were mainly warm， sweet， salty and mild， and it is now believed that Arcae Concha is salty in taste and mild in nature. In ancient times， it was believed that Arcae Concha were mainly used for coldness in the heart and abdomen， coldness in the waist and spine， benefiting the five internal organs， strengthening the stomach. Nowadays， it is believed that Arcae Concha can eliminate phlegm and remove blood stasis， soften the hardness and dissipate the lumps， produce acid and relieve pain. It can be used in the treatment of stubborn phlegm， gall tumor， scrofula and other symptoms. In conclusion， it is suggested that for the famous classical formulas containing Arcae Concha， the corresponding methods should be selected according to the processing requirements of the drug in the formulas， while those without processing requirements can be determined according to the functional position of the products.

This article systematically reviews and verifies the medicinal materials of Dioscoreae Hypoglaucae Rhizoma（DHR）， Dioscoreae Spongiosae Rhizoma（DSR）， Smilacis Chinae Rhizoma（SCR） and Smilacis Glabrae Rhizoma（SGR） from the aspects of name， origin， producing area， quality， harvesting， processing and efficacy by consulting historical literature， in order to provide reference for the development and utilization of famous classical formulas containing the four medicinal materials. DHR， DSR， SCR and SGR have a long history of application as medicinal materials. However， due to their similar growth environment and medicinal properties， as well as their functions of promoting dampness， dispelling wind and removing numbness， there have been instances of homonymous foreign objects and homonymous synonyms throughout history， resulting in confusion of the origin. Therefore， it is necessary to conduct comparative analysis and systematic research for clarifying the historical development and changes of the four， in order to provide a basis for safe and effective medication. According to research， Bixie was first recorded in Shennong Bencaojing and has been historically known as Baizhi， Chijie， Zhumu， and other aliases. From ancient times to the mid-20th century， there has always been a situation where the rhizomes of Dioscorea plants and Smilax plants， and even the rhizomes of Heterosmilax plants， were mixed together to be used as medicinal herbs for Bixie. However， since the Tang dynasty， it has been clearly advocated that the rhizomes of Dioscorea plants have excellent quality and have been the mainstream throughout history. The 2020 edition of Chinese Pharmacopoeia categorized it into two types of medicinal herbs（DHR and DSR）. Among them， the origin of DHR is the dry rhizomes of Dioscorea hypoglauca， and the origins of DSR are the dry rhizomes of D. spongiosa and D. futschauensis. In ancient times， due to different types， the corresponding production areas of DHR and DSR were also different. Nowadays， They are mainly produced in the southern region of the Yangtze River. Since the Tang dynasty， the quality of Bixie has been characterized by its white color and soft nature. In modern times， it has been summarized that those with white color， large and thin pieces， powdery texture， tough and elastic texture， and neat and unbreakable are the best. The harvesting times of DHR and DSR are in spring or autumn， with the best quality harvested in autumn. The mainstream processing methods of them are slicing and then using the raw products or wine-processed products. SCR was first recorded in Mingyi Bielu and has been known as Jinganggen， Tielingjiao， Tieshuazi， and other aliases in history. The mainstream source is the dry rhizomes of Smilax china in the past dynasties， with the best quality being those that are tough and rich in powder. The harvesting time is from the late autumn to the following spring， and the main processing method throughout history has been slicing for raw use. SGR was first recorded under the item of Yuyuliang in Variorum of Shennong's Classic of Materia Medica. It was listed as an independent medicinal material from Bencao Gangmu. In history， there were such aliases as Cao Yuyuliang， Lengfantuan， Xianyiliang， Tubixie， etc. The main source of the past dynasties was dry rhizomes of S. glabra. In history， there have also been instances of multiple plants belonging to the same genus， and even cases of mixing the rhizomes of plants in the genus Heterosmilax. It is mainly produced in Guangdong， Hunan， Hubei， Zhejiang， Sichuan， Anhui and other regions， its quality has been summarized as large in size， powdery in texture， with few veins， and light brown in cross-section since modern times. The harvesting time is in spring or autumn， and the main processing method throughout history has been slicing for raw use. DHR， DSR， SCR and SGR all have the effects of promoting dampness， dispelling wind， relieving rheumatism and detoxifying. However， their detoxification abilities are ranked as follows：SGR>SCR>Bixie（DHR and DSR）. Especially for the treatment of limb spasms， arthralgia and myalgia， scrofula， and scabies caused by syphilis and mercury poisoning， SGR has a unique effect. Based on the research results， DHR is recommended to develop the famous classical formulas containing Bixie as the first choice for medicinal herbs. It should be harvested in autumn， sliced thinly while fresh， and processed according to the requirements of the famous classical formulas， without any requirements for raw use. Selecting the rhizomes of S. china， harvested in late autumn， and thinly sliced while fresh. If there are no special processing requirements in the formulas， use it raw. Selecting the rhizomes of S. glabra， it is harvested in autumn and thinly sliced while fresh. If there are no special processing requirements in the formulas， raw products can be used.

Pharmacotranscriptomic profiles, which capture drug-induced changes in gene expression, offer vast potential for computational drug discovery and are widely used in modern medicine. However, current computational approaches neglected the associations within gene‒gene functional networks and unrevealed the systematic relationship between drug efficacy and the reversal effect. Here, we developed a new genome-scale functional module (GSFM) transformation framework to quantitatively evaluate drug efficacy for in silico drug discovery. GSFM employs four biologically interpretable quantifiers: GSFM_Up, GSFM_Down, GSFM_ssGSEA, and GSFM_TF to comprehensively evaluate the multi-dimension activities of each functional module (FM) at gene-level, pathway-level, and transcriptional regulatory network-level. Through a data transformation strategy, GSFM effectively converts noisy and potentially unreliable gene expression data into a more dependable FM active matrix, significantly outperforming other methods in terms of both robustness and accuracy. Besides, we found a positive correlation between RS_GSFM and drug efficacy, suggesting that RS_GSFM could serve as representative measure of drug efficacy. Furthermore, we identified WYE-354, perhexiline, and NTNCB as candidate therapeutic agents for the treatment of breast-invasive carcinoma, lung adenocarcinoma, and castration-resistant prostate cancer, respectively. The results from in vitro and in vivo experiments have validated that all identified compounds exhibit potent anti-tumor effects, providing proof-of-concept for our computational approach.

In clinical practice, antibiotics have historically been utilized for the treatment of pathogenic bacteria. However, the gradual emergence of antibiotic resistance among bacterial strains has posed a significant challenge to this approach. In 2022, Escherichia coli, a Gram-negative bacterium renowned for its widespread pathogenicity and high virulence, emerged as the predominant pathogenic bacterium in China. The rapid emergence of antibiotic-resistant E. coli strains has rendered antibiotics insufficient to fight E. coli infections. Traditional Chinese medicine (TCM) has made remarkable contributions to the health of Chinese people for thousands of years, and its significant therapeutic effects have been proven in clinical practice. In this paper, we provide a comprehensive review of the advances and mechanisms of TCM and its active ingredients against antibiotic-resistant E. coli infections. First of all, this review introduces the classification, antibiotic resistance characteristics and mechanisms of E. coli. Then, the TCM formulas and extracts are listed along with their active ingredients against E. coli, including extraction solution, minimum inhibitory concentration (MIC), and the antibacterial mechanisms. In addition, there is growing evidence supporting the synergistic therapeutic strategy of combining TCM with antibiotics for the treatment of antibiotic-resistant E. coli infections, and we provide a summary of this evidence and its underlying mechanisms. In conclusion, we present a comprehensive review of TCM and highlight its potential and advantages in the prevention and treatment of E. coli infections. We hold the opinion that TCM will play an important role in global health, pharmaceutical development, and livestock farming in the future.

Diterpenoid ferruginol is a key intermediate in biosynthesis of active ingredients such as tanshinone and carnosic acid.However, the traditional process of obtaining ferruginol from plants is often cumbersome and inefficient. In recent years, the increasingly developing gene editing technology has been gradually applied to the heterologous production of natural products, but the production of ferruginol in microbe is still very low, which has become an obstacle to the efficient biosynthesis of downstream chemicals, such as tanshinone. In this study, miltiradiene was produced by integrating the shortened diterpene synthase fusion protein,and the key genes in the MVA pathway were overexpressed to improve the yield of miltiradiene. Under the shake flask fermentation condition, the yield of miltiradiene reached about(113. 12±17. 4)mg·L~(-1). Subsequently, this study integrated the ferruginol synthase Sm CYP76AH1 and Sm CPR1 to reconstruct the ferruginol pathway and thereby realized the heterologous synthesis of ferruginol in Saccharomyces cerevisiae. The study selected the best ferruginol synthase(Il CYP76AH46) from different plants and optimized the expression of pathway genes through redox partner engineering to increase the yield of ferruginol. By increasing the copy number of diterpene synthase, CYP450, and CPR, the yield of ferruginol reached(370. 39± 21. 65) mg·L~(-1) in the shake flask, which was increased by 21. 57-fold compared with that when the initial ferruginol strain JMLT05 was used. Finally, 1 083. 51 mg·L~(-1) ferruginol was obtained by fed-batch fermentation, which is the highest yield of ferruginol from biosynthesis so far. This study provides not only research ideas for other metabolic engineering but also a platform for the construction of cell factories for downstream products.
Saccharomyces cerevisiae/genetics* ; Diterpenes/metabolism* ; Metabolic Engineering ; Fermentation ; Abietanes

Traditional Chinese medicine(TCM) resources are an important foundation for the theory and practice of TCM. Rare and endangered TCM, as a significant component of these resources, plays an essential role. Conducting research on substitutes for rare and endangered TCM resources is of great significance for alleviating resource shortages, promoting the sustainable utilization of TCM, and advancing TCM modernization. This paper reviews the conservation achievements of rare and endangered Chinese medicinal materials in China and organizes the substitution methods for these materials. Currently, the main substitution approaches include introduction and domestication, tissue culture, varietal replacement, and artificial synthesis. Furthermore, this paper proposes the following approaches for researching the application scenarios of rare and endangered medicinal materials, i.e., tracing the historical context of their use to clarify foundational principles; verifying disease classifications to strengthen the clinical application scenarios of these materials; analyzing the evolution patterns of prescription formulations to strengthen the mining of the compatibility application scenarios of rare and endangered medicinal materials; scientifically evaluating to strengthen the application scenario research and development of endangered Chinese patent medicine industry. These efforts aim to promote the scientific substitution and sustainable utilization of rare and endangered medicinal materials and their substitutes.
Drugs, Chinese Herbal/chemistry* ; Humans ; Medicine, Chinese Traditional ; China ; Plants, Medicinal/growth & development* ; Endangered Species ; Conservation of Natural Resources ; Animals

Amber and subfossil resins are subjects of interdisciplinary research across multiple fields. However, due to their diverse origins and complex compositions, different disciplines vary in their definitions and functional interpretations. In traditional Chinese medicine(TCM), amber has been utilized as a medicinal material since ancient time, with extensive historical documentation. However, its classification, provenance, and nomenclature remain ambiguous, and authentic medicinal amber artifacts are exceedingly rare. This study employed Fourier-transform infrared spectroscopy(FTIR) to characterize amber and subfossil resins from various geological sources and commercially "medicinal amber". Additionally, historical literature and market surveys were analyzed to explore their provenance, composition, and functional attributes. The results indicate that amber and subfossil resins from different sources and with different compositions exhibit distinct fingerprint characteristics in the FTIR spectral range of 1 800-700 cm~(-1). "Medicinal amber" available in the market primarily consists of subfossil or modern resins, significantly differing in composition and structure from geological amber. This study highlights the importance of interdisciplinary research on amber identification and resource management. It is essential to establish a systematic database of amber and subfossil resin characteristics and integrate modern analytical techniques to enhance research on their composition, pharmacological mechanisms, and potential therapeutic effects, thereby promoting the standardized utilization of amber resources and advancing the modernization of TCM.
Amber/history* ; Archaeology ; Spectroscopy, Fourier Transform Infrared ; Medicine, Chinese Traditional

Qing court records show that Arecae Semen was extensively applied. The royal medical records of the Qing Dynasty document nine types of Arecae Semen, with the Palace Museum preserving seven kinds, totaling twelve cultural relics. Historical documents and physical artifacts corroborate each other, providing evidence for the study of the supply channels and court processing of Arecae Semen in the Qing court. According to relevant Qing court archival records, the sources of Arecae Semen used in the imperial court were diverse, including tributes from foreign countries such as Vietnam and Gurkha, annual tributes from local governments in Guangdong, gifts from close aides, and commodities purchased by the Imperial Household Department from civilian shops. The imperial physicians of the Qing court placed great emphasis on the specifications of Arecae Semen slices and were extremely meticulous about their processing. The variety of Arecae Semen slices used in the Qing palace exceeded those recorded in the botanical texts of the era. Compared with the commonly used processing methods for Arecae Semen in the Qing Dynasty, the imperial physicians adjusted the properties and efficacy of the herbs through different processing techniques, based on the patient's condition, constitution, and other factors, in order to meet the clinical treatment needs of the court. The slicing of Arecae Semen in the Qing court required strict control of thickness, with an average thickness of 0.44 mm, which is significantly thinner than the Arecae Semen slices found in today's markets. The texture was softer, making them easier to chew and absorb. Both the Qing court Arecae Semen slices and the Muxiang Binglang Pills focused on the use of authentic medicinal materials, ensuring the quality of the medicine and enhancing the efficacy of Arecae Semen through meticulous selection and preparation.
China ; Drugs, Chinese Herbal/history* ; Humans ; Medicine, Chinese Traditional/history* ; History, 19th Century ; History, Ancient ; History, 17th Century ; History, 18th Century

Traditionally, Dao-di herbs refer to high-quality traditional Chinese medicine(TCM) produced in specific geographical regions. The development of their assessment theory holds profound significance for ensuring the stability of clinical efficacy and advancing the heritage and modernization of TCM. The concept of assessing Dao-di herbs originated in the Eastern Han Dynasty. Through millennia of inheritance and evolving cognitive frameworks, the assessment system has progressed from the traditional "appearance-based quality assessment" rooted in material phenomenology to the modern "excellent shape, high quality, and superior effect" theory guided by scientific quantification. This evolution epitomizes the innovative integration of traditional wisdom and modern technology. The formation of the "excellent shape and high quality" characteristics in Dao-di herbs involves intricate multi-level biological processes. Molecular biology techniques alone exhibit limitations in this complex system. A paradigm shift from reductionism to systems theory is required, and multidisciplinary approaches should be integrated, including molecular biology, cell biology, biophysics, and systems biology. Future research should prioritize exploring cellular-level features, deciphering relationships between microstructure and function, and investigating how environmental conditions regulate these traits to form the "excellent shape and high quality" attributes. This study systematically reviews the developmental trajectory of Dao-di herbs theory and proposes a biomechanics-driven research framework incorporating cellular developmental principles, aiming to refine the "excellent shape, high quality, and superior effect" theory. Moving forward, research should align with clinical precision medicine demands, leveraging artificial intelligence(AI) to synergize "wet" experiments(elucidation of molecular mechanisms) with "dry" experiments(AI modeling). Data-driven approaches will advance the standardization of Dao-di herbs.
Drugs, Chinese Herbal/standards* ; Medicine, Chinese Traditional/methods* ; Humans ; China ; Plants, Medicinal/chemistry*

Ginkgo biloba, an ancient relict plant, holds a lengthy medicinal tradition in China. The leaves and seeds of this remarkable species contain flavonoids, a class of active compounds that offer a multitude of pharmacological advantages. The understanding of the synthesis process of these flavonoids can be deepened substantially by elucidating their biosynthetic pathway and metabolic regulation mechanisms. This can thereby provide a foundation for achieving precise regulation of flavonoid biosynthesis, which is of great significance for improving the production efficiency and quality of flavonoids in G. biloba. This review comprehensively summarizes research advancements in metabolomics, genomics, and transcriptomics of flavonoids in G. biloba, aiming to establish a thorough academic framework. It examines key enzymes in the biosynthetic pathway of flavonoids in G. biloba and their functions, highlighting their crucial roles in flavonoid production. Additionally, it outlines transcriptional regulation mechanisms associated with flavonoid in G. biloba biosynthesis, focusing on transcription factors responsive to environmental cues and their regulatory networks that modulate flavonoid gene expression. These insights offer a theoretical foundation for precise control of G. biloba flavonoid production. By amalgamating these diverse research findings, this review aims to establish a robust theoretical groundwork for future studies on biosynthesis and efficient utilization of flavonoids in G. biloba.
Ginkgo biloba/chemistry* ; Flavonoids/biosynthesis* ; Gene Expression Regulation, Plant ; Plant Proteins/genetics* ; Biosynthetic Pathways