1.Resolution Assessment in Super-resolution Optical Microscopy: Adaptive Methods and Recent Advances
San-Hua FANG ; Jing-Yao CHEN ; Dan YANG ; Li LIU
Progress in Biochemistry and Biophysics 2026;53(4):805-825
Optical microscopy is essential for exploring biological and material structures, with resolution determining the level of observable detail. The advent of super-resolution fluorescence microscopy has broken the diffraction limit, achieving nanoscale resolution. However, traditional assessment methods, such as the Rayleigh criterion and point spread function (PSF) width measurement, rely on empirical judgments and diffraction-limited models, rendering them inadequate for modern super-resolution imaging. This review systematically traces the evolution of resolution assessment methodologies, from classical criteria to advanced strategies tailored for various super-resolution modalities. We first discuss Fourier-based quantitative methods. Fourier ring correlation (FRC) and its 3D counterpart, Fourier shell correlation (FSC), objectively determine resolution by evaluating the statistical correlation of two independent image reconstructions in frequency space. These methods offer robustness against noise and provide a global resolution metric, but they require data independence and are computationally intensive. They have become the prevailing standards in electron and super-resolution microscopy. Subsequently, we examine adaptations for specific super-resolution techniques. For single-molecule localization microscopy (SMLM) techniques such as PALM and STORM, the Fourier image resolution (FIRE) method extends FRC by incorporating a physical model that accounts for localization precision and labeling density. For stimulated emission depletion (STED) microscopy and other nonlinear techniques, assessment strategies differ. While PSF shrinkage measurements using fluorescent beads are useful for system calibration, evaluating the effective resolution directly on biological samples is more practical. This is typically performed via linewidth analysis of known structures (e.g., microtubules) or edge-spread function measurements, capturing the effects of photobleaching and sample-induced aberrations. A major paradigm shift is parameter-free resolution estimation based on decorrelation analysis. This method analyzes the autocorrelation decay of a single image’s Fourier spectrum to identify the cutoff spatial frequency without requiring dual datasets or user-defined thresholds. Its high efficiency and broad applicability have been validated across widefield, confocal, STED, SIM, and SMLM modalities. Optimized rendering strategies for SMLM data further enhance its accuracy, and it is emerging as a tool for real-time optimization of experimental parameters. The review also addresses the “gold standard” of resolution validation using well-defined nanostructures, such as DNA origami and nuclear pore complexes, which provide ground truth for verifying resolution claims and detecting artifacts. In the era of artificial intelligence, deep learning plays a dual role: it powerfully enhances image resolution but also introduces challenges, as models may generate “hallucinations” or false details. This underscores the need for new validation metrics to verify the physical fidelity of AI-generated content. Finally, we outline future directions: developing unified cross-modality standards, enabling real-time dynamic resolution monitoring for live-cell imaging, creating techniques for generating local resolution maps to capture sample heterogeneity, and integrating intelligent error correction to ensure data veracity. By providing a comprehensive overview of resolution assessment progress and challenges, this review aims to equip researchers with the knowledge to select appropriate tools, thereby fostering rigorous quantitative imaging in the life and material sciences.
2.Nontarget Screening and Identification of Novel Per-and Polyfluoroalkyl Substances in Cosmetics Using Ultra-High Performance Liquid Chromatography-High-Resolution Mass Spectrometry
Xin-Ling LI ; Tao YANG ; Wen-Yao LIANG ; Jian-Hua TAN ; Xian-Zhi PENG
Chinese Journal of Analytical Chemistry 2025;53(4):640-651,中插23-中插28
Cosmetics may be an important source of human exposure to per-and polyfluoroalkyl substances(PFASs),posing risks to human health.In this study,a nontarget screening method for PFASs in cosmetics was developed using ultra-high performance liquid chromatography-high-resolution mass spectrometry(UHPLC-Q-Orbitrap HRMS)based on the Kendrick mass defect(KMD).The sample was extracted by ultrasonic assisted extraction prior to being analyzed by UHPLC-Q-Orbitrap HRMS.Acquisition of HRMS data was achieved in both full scan and data-dependent(Full MS/dd MS2)mode.The data collected by HRMS were imported into an in-lab built R script for processing.Samples retained the mass spectra peaks with KMD values in the range of 0.85-1 or 0-0.15 for in-and out-of-library matching;when KMD deviation(δKMD)<0.001 and CF 2 mass error(δMS)<15 ppm,it was considered as a potential PFASs homologues.According to matches of parent ions(MS),fragment ions(MS2)and retention time(RT)with the in-house built PFASs database,the screened and identified potential PFASs were categorized to 5 confidence levels(CL1-CL5).A total of 15 kinds of PFASs homologues with confidence level of CL3 and above were screened from 13 cosmetics products and 8 cosmetic raw materials,including perfluoroalkyl alcohol,hydroperfluoroalkyl sulfonic acid,chloroperfluoroalkyl sulfonic acid,etc.with concentrations ranging from 1.9 ng/g to 98.1 ng/g.The nontarget screening method could be used to screen and identify PFASs homologues feasibly and therefore provided data basis for management and control of PFASs addition in cosmetics.
3.Analysis of Nitrofuran Metabolites in Meat by Solid-Phase Extraction of Porous Organic Polymer Combined with Liquid Chromatography-Tandem Mass Spectrometry
Yao CHEN ; Ying-Jiao DONG ; Jia-Yi LI ; Rui-Jie WANG ; Zhi-Kai HONG ; Guan-Hua WANG
Chinese Journal of Analytical Chemistry 2025;53(5):804-813
In this work,with tris(4-aminophenyl)amine(TAPA)and 1,3,5-tris(4-formylphenyl)benzene(TFPB)as monomers,an imine-type porous organic polymer,TAPA-TFPB,was synthesized using a simple method under the catalysis of acetic acid.The material TAPA-TFPB was used as solid-phase extraction adsorbent and combined with ultra-performance liquid chromatography/quadrupole time-of-flight-tandem mass spectrometry(UHPLC-QTOF-MS)to establish a detection method for four kinds of nitrofuran metabolites(NFMs)residues in meat samples.The parameters of the adsorbent dosage,the pH value and volume of sample,and the type and volume of washing and eluent solvents were optimized,respectively.Under the optimal extraction conditions,low detection limits(0.11-1.60 μg/kg)were achieved for four kinds of NFMs.At three different spiked levels,the intra-day and inter-day precisions(Relative standard deviations)were 2.8% -10.9% and 4.3% -16.2%,respectively,and the spiked recoveries were 72.0% -107.2%.The results showed that the method chould be used for efficient extraction and analysis of trace NFMs residues in meat samples,indicating that TAPA-TFPB was a kind of promising SPE adsorbent.
4.Construction and Application of"On-Off-On"Fluorescence Sensor for Chlorpromazine Hydrochloride Based on Near Infrared Carbon Quantum Dots
Yu LIN ; Feng TAN ; Yu-Hua SHEN ; Li-Qin ZHU ; Pei-Yao YAN ; Jin-Tao PAN ; Kai-Shun LIU
Chinese Journal of Analytical Chemistry 2025;53(6):934-943
In this work,near infrared carbon quantum dots(NIR-CDs)were synthesized by hydrothermal method using biomass material Clausena lansium leaves.The synthesized NIR-CDs emitted maximum fluorescence signal at 677 nm,which was independent of excitation wavelength.The characterization results showed that there were abundant groups on the surface of NIR-CDs.Pd2+could form non-fluorescent compounds with the surface groups of NIR-CDs,resulting in fluorescence quenching(Fluorescence signal was denoted as F0).Because chlorpromazine hydrochloride(CPZ)parent nucleus contained unoxidized S atom,CPZ could form stable colored complex with Pd2+under acidic conditions.In the presence of CPZ,Pd2+dissociated from the surface of NIR-CDs and bonded with CPZ,so that the fluorescence signal could be restored(Fluorescence signal was denoted as F).An"on-off-on"fluorescence sensor was thus constructed.The fluorescence signal recovery value of NIR-CDs(△F=F-F0)showed a good linear relationship with the concentration of CPZ in the range of 5.68-28.43 μg/mL,and the detection limit(3σ)was 0.078 μg/mL.The sensor was applied to determination of CPZ in pharmaceutical preparations,and the recoveries were 94%-106%.The developed fluorescence sensor was expected to be used in quality control of actual pharmaceutical preparations.
5.Construction of a Competency Evaluation Model for Forensic Practitioners
Jing-Chun BAO ; Jing-Jing ZHAO ; Jiao-Yong LI ; Jing-Hua MENG ; Xiao-Long WANG ; Xiao-Ni ZHAN ; Jun YAO ; Xu WU
Journal of Forensic Medicine 2025;41(4):371-379
Objective To construct a competency evaluation model for forensic practitioners,providing a reference for their training and assessment.Methods Based on the iceberg and onion models of com-petency,and with reference to Spencer's Competency Dictionary,literature research was conducted and focus group interviews were employed to preliminarily construct core indices and measurement items for evaluating the competency of forensic practitioners.The Delphi method was applied for two rounds of expert consultation to further refine the competency evaluation index system.The analytic hierarchy process(AHP)was used to calculate the weights of the indices.Results A competency evaluation model for forensic practitioners was constructed,consisting of 7 core indices,encompassing forensic skills,identification service capabilities,and the ability to apply relevant legal knowledge and 49 mea-surement items.The weights of the core indices and measurement items were determined.Conclusion The constructed competency evaluation model for forensic practitioners is scientifically sound and inno-vative,and has unique characteristics of forensic medicine compared with other medical models.
6.Thoughts and practices on research and development of new traditional Chinese medicine drugs under "three combined" evaluation evidence system.
Yu-Qiao LU ; Yao LU ; Geng LI ; Tang-You MAO ; Ji-Hua GUO ; Yong ZHU ; Xue WANG ; Xiao-Xiao ZHANG
China Journal of Chinese Materia Medica 2025;50(7):1994-2000
In recent years, the reform of the registration, evaluation, and approval system for traditional Chinese medicine(TCM) has been promoted at the national level, with establishment of an evaluation evidence system for TCM registration that combines TCM theory, human use experience, and clinical trials(known as the "three-combined" evaluation evidence system). This system, which aligns with the characteristics of TCM clinical practice and the laws of TCM research and development, recognizes the unique value of human use experience in medicine and returns to the essence of medicine as an applied science, thus receiving widespread recognition from both academia and industry. However, it meanwhile poses new and higher challenges. This article delves into the value and challenges faced by the "three-combined" evaluation evidence system from three perspectives: registration management, medical institutions, and the TCM industry. Furthermore, it discusses how the China Association of Chinese Medicine, leveraging its academic platform advantages and leading roles, has made exploratory and practical efforts to facilitate the research and development of new TCM drugs and the implementation of the "three-combined" evaluation evidence system.
Drugs, Chinese Herbal/standards*
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Humans
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Medicine, Chinese Traditional/standards*
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China
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Drug Development
7.Identification of Lonicera japonica TPS gene family and expression analysis under aphid damage.
Gang WANG ; Yuan CUI ; Qi-Dong LI ; Lu-Yao HUANG ; Zhen-Hua LIU ; Jia LI
China Journal of Chinese Materia Medica 2025;50(8):2116-2129
This study explores the basic characteristics and potential functions of the terpene synthase(TPS) gene family members in Lonicera japonica. The L. japonica TPS(LjTPS) gene family was identified and functionally analyzed using bioinformatics methods. The results showed that a total of 70 members of the LjTPS gene family were identified in L. japonica, with protein lengths ranging from 130 to 1 437 amino acids. Most of these proteins were hydrophilic, and they were unevenly distributed across nine chromosomes. Phylogenetic analysis showed that the LjTPS gene family members were divided into six subfamilies, mainly consisting of members from the TPS-a, TPS-b, and TPS-e subfamilies. Promoter cis-acting element analysis showed that LjTPS members contained a large number of stress-responsive cis-acting elements. Aphid inoculation experiments showed that key enzyme genes in the MVA pathway for terpenoid backbone synthesis in L. japonica, such as HMGS, HMGR, MK, MPD, and the key enzyme gene in the DXP pathway, DXS, exhibited an initial increase followed by a decrease under aphid stress. The qRT-PCR analysis showed that the expression levels of the α-farnesene synthase genes LjTPS34 and LjTPS39 were down-regulated, while the expression levels of(E)-β-caryophyllene synthase genes LjTPS15 and LjTPS17 were up-regulated 12 h before aphid feeding, then began to decline. Farnesyl pyrophosphate synthase(FPS), which interacted with these genes, also displayed a pattern of increasing followed by decreasing expression. The expression of linalool synthase genes LjTPS12 and LjTPS33 was significantly up-regulated after 72 h of aphid feeding(P<0.000 1), reaching 24.39 and 22.64 times the initial expression, respectively. This pattern was in close alignment with the trend of linalool content in L. japonica. This study provides a theoretical foundation for future research on the interaction between L. japonica and pests, as well as on the functional roles of the LjTPS gene family.
Animals
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Aphids/physiology*
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Alkyl and Aryl Transferases/chemistry*
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Lonicera/parasitology*
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Phylogeny
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Plant Proteins/chemistry*
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Gene Expression Regulation, Plant
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Multigene Family
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Terpenes/metabolism*
8.Identification of characteristics, supply channels, and imperial court processing of Arecae Semen in the Qing court.
Feng-Yuan LI ; Hua-Sheng PENG ; Xue-Ling GUAN ; Yan JIN ; Ting YAO ; Yuan YUAN ; Lu-Qi HUANG
China Journal of Chinese Materia Medica 2025;50(11):2924-2930
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
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Drugs, Chinese Herbal/history*
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Humans
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Medicine, Chinese Traditional/history*
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History, 19th Century
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History, Ancient
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History, 17th Century
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History, 18th Century
9.Tracing origin of "Qinggong Maidong" production area based on analysis of literature and historical materials and identification of characteristics of Qinggong medicinal materials and cultural relics.
Ao-Yu REN ; Ting YAO ; Feng-Yuan LI ; Hua-Sheng PENG
China Journal of Chinese Materia Medica 2025;50(11):2931-2937
Maidong products are categorized into "Hang Maidong" and "Chuan Maidong". Since the Ming and Qing Dynasties, "Hang Maidong" has been regarded as having superior quality, but currently, it remains in name only in the market. This article reviewed historical materia medica and local chronicles from the Ming and Qing Dynasties and analyzed the historical evolution of Maidong production areas. The history of Maidong production in Zhejiang can be traced back to the Song Dynasty, and cultivation had already developed by at least the Ming Dynasty. During the Ming and Qing Dynasties, it was consistently used as a tribute. Ming Dynasty chronicles record "Chuan Maidong", which had already been cultivated on a large scale by the Qing Dynasty. "Hang Maidong" and "Chuan Maidong" share the same origin, with the former identifiable by the "gourd waist" shape of its tuberous root. Based on this, it can be inferred that the "Maimendong" herb illustrated in the Origins of Materia Medica(Ben Cao Yuan Shi) and the Maidong stored in the Qing Palace Imperial Pharmacy were both "Hang Maidong". The protection and development of the authentic "Hang Maidong" medicinal herb are urgently needed.
China
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Drugs, Chinese Herbal/history*
;
History, 17th Century
;
History, Ancient
;
Medicine, Chinese Traditional/history*
;
History, Medieval
;
History, 16th Century
;
History, 18th Century
;
History, 15th Century
;
Plants, Medicinal/chemistry*
;
History, 19th Century
;
History, 20th Century
;
Humans
;
Materia Medica/history*
;
History, 21st Century
10.Analysis of T7 RNA Polymerase: From Structure-function Relationship to dsRNA Challenge and Biotechnological Applications
Wei-Chen NING ; Yu HUA ; Hui-Ling YOU ; Qiu-Shi LI ; Yao WU ; Yun-Long LIU ; Zhen-Xin HU
Progress in Biochemistry and Biophysics 2025;52(9):2280-2294
T7 RNA polymerase (T7 RNAP) is one of the simplest known RNA polymerases. Its unique structural features make it a critical model for studying the mechanisms of RNA synthesis. This review systematically examines the static crystal structure of T7 RNAP, beginning with an in-depth examination of its characteristic “thumb”, “palm”, and “finger” domains, which form the classic “right-hand-like” architecture. By detailing these structural elements, this review establishes a foundation for understanding the overall organization of T7 RNAP. This review systematically maps the functional roles of secondary structural elements and their subdomains in transcriptional catalysis, progressively elucidating the fundamental relationships between structure and function. Further, the intrinsic flexibility of T7 RNAP and its applications in research are also discussed. Additionally, the review presents the structural diagrams of the enzyme at different stages of the transcription process, and through these diagrams, it provides a detailed description of the complete transcription process of T7 RNAP. By integrating structural dynamics and kinetics analyses, the review constructs a comprehensive framework that bridges static structure to dynamic processes. Despite its advantages, T7 RNAP has a notable limitation: it generates double-stranded RNA (dsRNA) as a byproduct. The presence of dsRNA not only compromises the purity of mRNA products but also elicits nonspecific immune responses, which pose significant challenges for biotechnological and therapeutic applications. The review provides a detailed exploration of the mechanisms underlying dsRNA formation during T7 RNAP catalysis, reviews current strategies to mitigate this issue, and highlights recent progress in the field. A key focus is the semi-rational design of T7 RNAP mutants engineered to minimize dsRNA generation and enhance catalytic performance. Beyond its role in transcription, T7 RNAP exhibits rapid development and extensive application in fields, including gene editing, biosensing, and mRNA vaccines. This review systematically examines the structure-function relationships of T7 RNAP, elucidates the mechanisms of dsRNA formation, and discusses engineering strategies to optimize its performance. It further explores the engineering optimization and functional expansion of T7 RNAP. Furthermore, this review also addresses the pressing issues that currently need resolution, discusses the major challenges in the practical application of T7 RNAP, and provides an outlook on potential future research directions. In summary, this review provides a comprehensive analysis of T7 RNAP, ranging from its structural architecture to cutting-edge applications. We systematically examine: (1) the characteristic right-hand domains (thumb, palm, fingers) that define its minimalistic structure; (2) the structure-function relationships underlying transcriptional catalysis; and (3) the dynamic transitions during the complete transcription cycle. While highlighting T7 RNAP’s versatility in gene editing, biosensing, and mRNA vaccine production, we critically address its major limitation—dsRNA byproduct formation—and evaluate engineering solutions including semi-rationally designed mutants. By synthesizing current knowledge and identifying key challenges, this work aims to provide novel insights for the development and application of T7 RNAP and to foster further thought and progress in related fields.

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