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Evolution of the newest diagnostic methods for COVID-19:a Chinese perspective

Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2023年第6期24卷 463-484页

作者： Mingtao LIU Jiali LYU Xianhui ZHENG Zhiman LIANG Baoying LEI Huihuang CHEN Yiyin MAI Huimin HUANG Baoqing SUN Department of clinical laboratory National Center for Respiratory MedicineNational Clinical Research Center for Respiratory DiseaseState Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510140China National Center for Respiratory Medicine National Clinical Research Center of Respiratory DiseaseState Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510140China Guangzhou Medical University Guangzhou 511495China

Coronavirus disease 2019(COVID-19)has continued to spread globally since late 2019,representing a formidable challenge to the world's healthcare systems,wreaking havoc,and spreading rapidly through human *** fever,fatigue,and a persistent dry cough being the hallmark symptoms,this disease threatened to destabilize the delicate balance of our global *** and accurate diagnosis of COVID-19 is a prerequisite for understanding the number of confirmed cases in the world or a region,and an important factor in epidemic assessment and the development of control *** also plays a crucial role in ensuring that patients receive the appropriate medical treatment,leading to optimal patient *** transcription-polymerase chain reaction(RT-PCR)technology is currently the most mature method for detecting viral nucleic acids,but it has many ***,a variety of COVID-19 detection methods,including molecular biological diagnostic,immunodiagnostic,imaging,and artificial intelligence methods have been developed and applied in clinical practice to meet diverse scenarios and *** methods can help clinicians diagnose and treat COVID-19 *** review describes the variety of such methods used in China,providing an important reference in the field of the clinical diagnosis of COVID-19.

关键词： Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) Coronavirus disease 2019(COVID-19) Diagnosis Polymerase chain reaction(PCR) Immunoassay Radiography

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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of clinical laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics institute College of Pharmaceutical SciencesZhejiang University Key laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research institute of Intelligent Computing Zhejiang Lab Shanghai Research institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key laboratory of Precision Diagnosis and Therapy for Major Gynecological diseases Women's HospitalZhejiang University School of Medicine Key laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Novel Species Including Mycobacterium fukienense sp. Is Found from Tuberculosis Patients in Fujian Province, China, Using Phylogenetic Analysis of Mycobacterium chelonae/abscessus Complex

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Biomedical and Environmental Sciences 2013年第11期26卷 894-901页

作者： ZHANG Yuan Yuan LI Yan Bing HUANG Ming Xiang ZHAO Xiu Qin ZHANG Li Shui LIU Wen En WAN Kang Lin State Key laboratory for Infections disease Prevention and Control/National institute for Communicable disease Control and Prevention Chinese Center for Disease Control and Prevention Xiangya Hospital Central South University Fuzhou pulmonary Hospital / clinical Teaching Hospital of Fujian Medical University

Objective To identify the novel species ‘Mycobacterium fukienense＇ sp. nov of Mycobacterium chelonoe/abscessus complex from tuberculosis patients in Fujian Province, China. Methods Five of 27 clinical Mycobucterium isolates （CIs） were previously identified as M. chelonoe/obscessus complex by sequencing the hsp65, rpoB, 165-235 rRNA internal transcribed spacer region （its）, recA and sodA house-keeping genes commonly used to describe the molecular characteristics of Mycobocterium. clinical Mycobecterium isolates were classified according to the gene sequence using a clustering analysis program. Sequence similarity within clusters and diversity between clusters were analyzed. Results The 5 isolates were identified with distinct sequences exhibiting 99.8% homology in the hsp65 gene. However, a complete lack of homology was observed among the sequences of the rpoB, 165-235 rRNA internal tronscribed spacer region （its）, sodA, and recA genes as compared with the M. obscessus. Furthermore, no match for rpoB, sodA, and recA genes was identified among the published sequences. Conclusion The novel species, Mycobacterium fukienense, is identified from tuberculosis patients in Fujian Province, China, which does not belong to any existing subspecies of M. cheloneo/abscessus complex.

关键词： Species identification Mycobacterium chelonae/abscessus complex Mycobacterium fukienense

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Epigenetic regulation of the inflammatory response in stroke

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Neural Regeneration Research 2025年第11期20卷 3045-3062页

作者： Jingyi Liang Fei Yang Zixiao Li Qian Li School of Basic Medical Sciences Capital Medical UniversityBeijingChina Department of Neurobiology School of Basic Medical SciencesCapital Medical UniversityBeijingChina laboratory for clinical Medicine Beijing Key Laboratory of Neural Regeneration and RepairCapital Medical UniversityBeijingChina Department of Neurology Beijing Tiantan HospitalCapital Medical UniversityBeijingChina China National clinical Research Center for Neurological diseases Beijing Tiantan HospitalCapital Medical UniversityBeijingChina National Center for Healthcare Quality Management in Neurological diseases Beijing Tiantan HospitalCapital Medical UniversityBeijingChina Chinese institute for Brain Research BeijingChina Research Unit of Artificial Intelligence in Cerebrovascular disease Chinese Academy of Medical SciencesBeijingChina Beijing Engineering Research Center of Digital Healthcare for Neurological diseases BeijingChina Department of Biochemistry and Molecular Biology School of Basic Medical SciencesCapital Medical UniversityBeijingChina Beijing Key laboratory of Cancer Invasion and Metastasis Research Capital Medical UniversityBeijingChina

Stroke is classified as ischemic or hemorrhagic,and there are few effective treatments for either *** mechanisms play a critical role in secondary brain injury following a stroke,which manifests as cytokine release,blood–brain barrier disruption,neuronal cell death,and ultimately behavioral *** the inflammatory response has been shown to mitigate this cascade of events in experimental stroke ***,in clinical trials of anti-inflammatory agents,longterm immunosuppression has not demonstrated significant clinical benefits for *** may be attributable to the dichotomous roles of inflammation in both tissue injury and repair,as well as the complex pathophysiologic inflammatory processes in *** acute harmful inflammatory responses or inducing a phenotypic shift from a pro-inflammatory to an anti-inflammatory state at specific time points after a stroke are alternative and promising therapeutic *** agents that can modulate inflammation requires a detailed understanding of the inflammatory processes of ***,epigenetic reprogramming plays a crucial role in modulating post-stroke inflammation and can potentially be exploited for stroke *** this review,we summarize current findings on the epigenetic regulation of the inflammatory response in stroke,focusing on key signaling pathways including nuclear factor-kappa B,Janus kinase/signal transducer and activator of transcription,and mitogen-activated protein kinase as well as inflammasome *** also discuss promising molecular targets for stroke *** evidence to date indicates that therapeutic targeting of the epigenetic regulation of inflammation can shift the balance from inflammation-induced tissue injury to repair following stroke,leading to improved post-stroke outcomes.

关键词： DNA methylation histone modification intracerebral hemorrhage ischemic stroke neuroinflammation neuroprotection non-coding RNA RNA methylation subarachnoid hemorrhage treatment

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From hepatitis A to E:A critical review of viral hepatitis

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World Journal of Gastroenterology 2021年第16期27卷 1691-1715页

作者： Daniel Castaneda Adalberto Jose Gonzalez Mohammad Alomari Kanwarpreet Tandon Xaralambos Bobby Zervos digestive disease institute Cleveland Clinic FloridaWestonFL 33331United States Transplant Department Cleveland Clinic FloridaWestonFL 33331United States

Viral infections affecting the liver have had an important impact on humanity,as they have led to significant morbidity and mortality in patients with acute and chronic *** an unknown etiology,the discovery of the viral agents triggered interest of the scientific community to establish the pathogenesis and diagnostic modalities to identify the affected *** the rapid scientific and technological advances in the last centuries,controlling and even curing the infections became a possibility,with a large focus on preventive medicine through ***,a comprehensive understanding of hepatitis A,B,C,D and E is required by primary care physicians and gastroenterologists to provide care to these *** review article describes the epidemiology,pathogenesis,clinical presentation,diagnostic tools and current medication regimens,with a focus on upcoming treatment options and the role of liver transplantation.

关键词： Hepatitis A Hepatitis B Hepatitis C Hepatitis D Hepatitis E Treatment

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Immunomodulating effects of antibiotics used in the prophylaxis of bacterial infections in advanced cirrhosis

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World Journal of Gastroenterology 2015年第41期21卷 11493-11501页

作者： Pedro Zapater José Manuel González-Navajas José Such Rubén Francés CIBERehd Hospital General Universitario de Alicante digestive disease institute Cleveland Clinic Abu Dhabi Departamento Medicina Clínica Universidad Miguel Hernández

The use of norfloxacin either as primary or secondary prophylaxis of bacterial infections in advanced cirrhosis has improved patient's survival. This may be explained not only due to a significant decrease in the number of infections, but also because of a direct immunomodulatory effect. Selective intestinal decontamination with norfloxacin reduces translocation of either viable bacteria or bacteria-driven products from the intestinal lumen. In addition, norfloxacin directly modulates the systemic inflammatory response. The proinflammatory cytokine profile secreted by neutrophils from these patients shows a close, significant, and inverse correlation with serum norfloxacin levels. Similar effects have been described with other quinolones in different clinical conditions. Although the underlying mechanisms are not well defined for most of the antibiotics, the pathways triggered for norfloxacin to induce such immunomodulatory effects involve the down-regulation of pro-inflammatory inducible nitric oxide synthase, cyclooxygenase-2, and NF-κB and the up-regulation of heme-oxygenase 1 and IL-10 expression. The knowledge of these immunomodulatory effects, additional to their bactericidal role, improves our comprehension of the interaction between antibiotics and the cellular host response and offer new possibilities for the development of new therapeutic strategies to manage and prevent bacterial infections in cirrhosis.

关键词： Cirrhosis Prophylaxis Cytokines Bacterial DNA Norf

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Integrative Medicine on Optimizing Clopidogrel and Aspirin Therapy

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Chinese Journal of Integrative Medicine 2019年第5期25卷 395-400页

作者： CHEN Hui Department of Internal Medicine Fujian Provincial Cardiovascular Disease Institutethe Shengli Clinical Medical College of Fujian Medical UniversityFuzhou(350001)China

This article reviews the available published data on optimizing clopidogrel and aspirin therapy using translational and integrative medicine. Translational and evidence-based medical studies show that the CYP2 C19 gene mutation(CYP2 C19*2 and CYP2 C19*3) could affect > 50% of the Chinese population, and that this mutation is closely associated with clopidogrel resistance and an increased risk of major adverse cardiovascular events, particularly stent thrombosis in patients following percutaneous coronary intervention(PCI). Adjusted-dose warfarin and aspirin reduce stroke in patients with atrial fibrillation(AF), and warfarin is substantially more efficacious than aspirin. However, a poor compliance is a big problem in warfarin use especially in China. The genetic variants of vitamin K expoxide reductase might account for the universally lower warfarin dosage used in Chinese population. The available evidence indicates that the integrating mainstream treatments(e.g., clopidogrel, CYP2 C19 genotyping) and non-mainstream medicines [e.g., Chinese medicines,Naoxintong Capsule(脑心通胶囊, NXT)] to treat CYP2 C19 gene mutation patients following PCI can be *** combined NXT and the adjusted-dose warfarin was equally effective in elderly patients with non-valvular AF in prevention of ischemic stroke.

关键词： integrative medicine clopidogrel aspirin optimizing therapy Chinese medicine

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Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures

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Neural Regeneration Research 2025年第1期20卷 265-276页

作者： Yao Yuan Lingqi Yu Xudong Zhuang Dongjing Wen Jin He Jingmei Hong Jiayu Xie Shengan Ling Xiaoyue Du Wenfeng Chen Xinrui Wang institute of Life Sciences College of Biological Science and EngineeringFuzhou UniversityFuzhouFujian ProvinceChina NHC Key laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate(Fujian Maternity and Child Health Hospital) FuzhouFujian ProvinceChina Medical Research Center Fujian Maternity and Child Health HospitalCollege of Clinical Medicine for Obstetrics&Gynecology and PediatricsFujian Medical UniversityFuzhouFujian ProvinceChina Department of Neurology and institute of Neurology of The First Affiliated Hospital Institute of Neuroscienceand Fujian Key Laboratory of Molecular NeurologyFujian Medical UniversityFuzhouFujian ProvinceChina

Certain amino acids changes in the human Na^(+)/K^(+)-ATPase pump,ATPase Na^(+)/K^(+)transporting subunit alpha 1(ATP1A1),cause Charcot-Marie-Tooth disease type 2(CMT2)disease and refractory *** develop in vivo models to study the role of Na^(+)/K^(+)-ATPase in these diseases,we modified the Drosophila gene homolog,Atpα,to mimic the human ATP1A1 gene mutations that cause *** located within the helical linker region of human ATP1A1(I592T,A597T,P600T,and D601F)were simultaneously introduced into endogenous Drosophila Atpαby CRISPR/Cas9-mediated genome editing,generating the Atpα^(TTTF)*** addition,the same strategy was used to generate the corresponding single point mutations in flies(Atpα^(I571T),Atpα^(A576T),Atpα^(P579T),and Atpα^(D580F)).Moreover,a deletion mutation(Atpα^(mut))that causes premature termination of translation was generated as a positive *** these alleles,we found two that could be maintained as homozygotes(Atpα^(I571T)and Atpα^(P579T)).Three alleles(Atpα^(A576T),Atpα^(P579)and Atpα^(D580F))can form heterozygotes with the Atpαmut *** found that the Atpαallele carrying these CMT2-associated mutations showed differential phenotypes in *** heterozygous for Atpα^(TTTF)mutations have motor performance defects,a reduced lifespan,seizures,and an abnormal neuronal *** Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.

关键词： ATP1A1 Atpα bang-sensitive paralysis Charcot-Marie-Tooth disease type 2 CRISPR/Cas9 homology-directed repair Na^(+)/K^(+)-ATPase point mutation seizures sodium pump

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Potential role of novel hepatocellular carcinoma-associated gene IDD01 in promoting tumorigenesis of HepG2 cell line

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Chinese Medical Journal 2006年第20期119卷 1709-1714页

作者： CHEN Xiang-yu LI Jian-sheng MA Jun DUAN Fang-ling ZHONG Peng Department of digestive disease Institute of Clinical Medical Research of Henan Province First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 China institute of digestive disease Zhengzhou University Zhengzhou 450003 China Faculty of Pharmacy Engineering College of Life Sciences JilinUniversity Changchun 130012 China

Background We have used suppression subtractive hybridization to construct a subtracted cDNA library of hepatocellular carcinoma （HCC） and isolated a panel of differential expression sequence tag （ESTs）. By using bioinformatics and rapid amplification of cDNA ends （RACE）, we found a novel HCC-associated gene IDD01. To further investigate its function, a recombinant eukaryotic vector pEGFP/ORF was constructed and transfected into the HepG2 cell line.Methods The open reading frame （ORF） of IDD01 was amplified by RT-PCR, digested with Bamh Ⅰ and Hind Ⅲ, and subcloned into the pEGFP-C1 vector. The ligation reaction was conducted with T4 DNA ligase, and the recombinant vector was named pEGFP/ORF. Untransfer control （control group）, pEGFP-C1 （HepG2/C1 group） and pEGFP/ORF （HepG2/ORF group） transfer groups were designed. Gene transfer was conducted with lipofectamine. To obtain stable transfection in HepG2 cells, selection was initiated with 500 μg/ml G418. Cellular IDD01 mRNA levels were assayed by semi-quantitative RT-PCR. The MTT colorimetric method and flow cytometry were used to determine the cell proliferation. The tumorigenic potential of transformed cells was determined from their ability to grow as anchorage-independent colonies on soft agar. Transient transfections were performed to observe subcellular location of GFP-IDD01 fusion protein.Results A 778 bp specific band of ORF was obtained by RT-PCR, and the positive clone of recombinant plasmid pEGFP/ORF （5.5 Kb） was identified by restriction endonuclease cleavage and sequence. The brightness ratio of IDD01 mRNA was not obvious between control and pEGFP/C1 groups, whereas the ratio of pEGFP/ORF was higher than that in the other two groups. After culture for 24-72 hours, the A490 values in pEGFP/ORF were higher than those in the other two groups （P〈0.01）. On histograms of flow cytometry, the S phase ratio of HepG2/ORF cells was significantly higher than that of the control and HepG2/C1 groups. The HepG2/ORF ce

关键词： hepatocellular carcinoma gene expression plasmids IDD01 gene

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Association of serum complement C1q with cardiovascular outcomes among patients with acute coronary syndrome undergoing percutaneous coronary intervention

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Journal of Geriatric Cardiology 2022年第12期19卷 949-959,1007-1010页

作者： Qiu-Xuan LI Xiao-Teng MA Qiao-Yu SHAO Zhi-Qiang YANG Jing LIANG Li-Xia YANG Dong-Mei SHI Yu-Jie ZHOU Zhi-Jian WANG Department of Cardiology Beijing Anzhen HospitalCapital Medical UniversityBeijing Institute of Heart Lung and Blood Vessel DiseaseBeijing Key Laboratory of Precision Medicine of Coronary Atherosclerotic DiseaseClinical Center for Coronary Heart DiseaseCapital Medical UniversityBeijingChina

OBJECTIVE To determine the association of serum complement C1q levels with cardiovascular outcomes among patients with acute coronary syndrome(ACS)undergoing percutaneous coronary intervention(PCI),and evaluate the value of C1q modified by high-sensitivity C-reactive protein(hs-CRP)levels as an independent *** As a single-center prospective observational study,we analyzed 1701 patients who had received primary or elective PCI for ACS at Beijing Anzhen Hospital,Capital Medical University,Beijing,China between June 1,2016 and November 30,*** associations of C1q modified by hs-CRP with major adverse cardiovascular events(MACE)were determined in survival *** Patients with the lowest C1q tertile had the highest cumulative risk of MACE(log-rank P=0.007).In fully adjusted Cox regression models,stratifying the total population according to hs-CRP dichotomy,C1q was significantly associated with MACE in patients with hs-CRP levels less than 2 mg/L but not in those with 2 mg/L or more(P_(interaction)=0.02).In patients with hs-CRP levels less than 2 mg/L,with the lowest C1q tertile as reference,the risk of MACE was reduced by 40.0%in the middle C1q tertile[hazard ratio(HR)=0.600,95%CI:0.423–0.852,P=0.004]and by 43.9%in the highest C1q tertile(HR=0.561,95%CI:0.375–0.840,P=0.005).CONCLUSIONS Serum complement C1q is significantly associated with cardiovascular outcomes in patients with ACS undergoing PCI,only when hs-CRP levels are less than 2 mg/*** finding implicates the usefulness of C1q for the risk stratification in ACS patients with reduced systemic inflammation.

关键词： C1q patients coronary

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