1.The Refinement and Innovation of The UV Cross-linking and Immunoprecipitation
Jia-Min ZHAO ; Cheng-Jiang LU ; Ming YANG ; Nashun BUHE ; Gang WANG
Progress in Biochemistry and Biophysics 2025;52(4):1036-1052
RNA-binding proteins (RBPs) are ubiquitous components within cells, fulfilling essential functions in a myriad of biological processes. These proteins interact with RNA molecules to regulate gene expression at various levels, including transcription, splicing, transport, localization, translation, and degradation. Understanding the intricate network of RBP-RNA interactions is crucial for deciphering the complex regulatory mechanisms that govern cellular function and organismal development. Ultravidet (UV) cross-linking and immunoprecipitation (CLIP) stands out as a powerful approach designed to map the precise locations where RBPs bind to RNA. By using UV light to create covalent bonds between proteins and RNA, followed by immunoprecipitation to isolate the protein-RNA complexes, researchers can identify the direct targets of specific RBPs. The advent of high-throughput sequencing technologies has revolutionized CLIP, enabling the identification of not only the types but also the exact sequences of RNA bound by RBPs on a genome-wide scale. The evolution of CLIP has led to the development of specialized variants, each with unique features that address specific challenges and expand the scope of what can be studied. High-throughput sequencing CLIP (HITS-CLIP) was one of the first advancements, significantly increasing the throughput and resolution of RNA-protein interaction mapping. Photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) introduced the use of photoactivatable ribonucleosides to enhance cross-linking efficiency and specificity, reducing background noise and improving the detection of low-abundance RNA-protein interactions. Individual-nucleotide resolution CLIP (iCLIP) further refined the technique, achieving unprecedented precision by resolving individual nucleotides involved in RBP binding, which is particularly valuable for studying the fine details of RNA structure and function. Despite the remarkable progress, there remains room for improvement in CLIP technology. Researchers continue to seek methods to increase sensitivity, reduce technical variability, and improve the reproducibility of results. Advances in sample preparation, data analysis algorithms, and computational tools are critical for addressing these challenges. Moreover, the application of CLIP to more diverse biological systems, including non-model organisms and clinical samples, requires the development of tailored protocols and the optimization of existing ones. Looking forward, the field of RNA biology is poised to benefit greatly from ongoing innovations in CLIP technology. The exploration of non-canonical RNA-protein interactions, such as those involving long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), promises to reveal new layers of cellular regulation and may lead to the discovery of novel therapeutic targets. Furthermore, integrating CLIP data with other omics approaches, such as proteomics and metabolomics, will provide a more comprehensive understanding of the dynamic interplay between RNA and its binding partners within the cell. In conclusion, the continuous refinement and expansion of CLIP techniques have not only deepened our knowledge of RNA biology but have also opened up new avenues for investigating the molecular underpinnings of health and disease. As the technology matures, it is expected to play an increasingly pivotal role in both basic and applied research, contributing to the advancement of medical science and biotechnology.
2.Preparation and evaluation of long-acting light-protective nanogel based on fullerenol-cerium oxide composite system
Tianlong ZHANG ; Jia LIU ; Qing ZHAO ; Yue ZHOU ; Ming YANG ; Qianyu LUO
China Pharmacy 2025;36(17):2106-2112
OBJECTIVE To develop a long-acting light-protective nanogel with both physical barrier and chemical clearance functions, and evaluate its performance. METHODS The photoprotective nanogel composed of mussel mucin and sodium hyaluronate was constructed based on a fullerenol-cerium oxide composite nano system, namely fullerenol-cerium oxide nanogel (FCN), and was characterized. The antioxidant capacity of FCN was evaluated using in vitro free radical scavenging experiments; its UV shielding ability was assessed by using an SPF value detector; its biosafety was assessed according to the requirements of the Guidelines for Drug Safety Evaluation; skin adhesion was assessed using small animal 3D live imaging technology; its sun protection ability was assessed through skin sunscreen detection and histopathological observation. RESULTS The average particle sizes of cerium oxide and fullerenol nanoparticles in FCN were about 20 and 10 nm, respectively, and FCN exhibited good UV absorption and free radical scavenging abilities. SPF value of FCN was 58.95±0.82, and the ultraviolet A protection level value was 6.21±0.15. No pathogenic colonies such as Staphylococcus aureus, were detected in the nanogel, and the contents of lead, arsenic, mercury and cadmium all met the standards for pharmaceutical excipients; FCN group did not show any irritating reactions such as erythema, edema, or desquamation; blood biochemical indicators of the FCN group were within the normal reference range. The material clearance rate of mice in the artificial sweat flushing group was less than 30%, while the material clearance rate of mice in the dry cleaning group reached about 92%. The mice in the protective group did not show obvious erythema or ulcer formation throughout the experiment. Histopathology showed that the fibers were arranged in an orderly manner, and the number of collagen fibers was close to that of the control group. CONCLUSIONS The FCN formulation constructed in this study meets the relevant requirements of the Chinese Pharmacopoeia, has good safety and skin compatibility, and achieves dual synergistic protection of UV shielding and free radical scavenging.
3.Construction,identification and efficiency detection of CX3CR1GFP reporter gene mice
Xin-Xin ZHAO ; Rong HUANG ; Lu-Yun CHEN ; Chun-Mei HUANG ; Jia-Jie TU ; Xin-Ming WANG
Chinese Pharmacological Bulletin 2024;40(12):2392-2398
Aim To construct CX3CR1GFP transgenic mice based on the Cre/Loxp system,and to analyze the expression efficiency of CX3CR1GFP.Methods Targeted vectors were designed using restriction enzyme-based cloning technology to create a linearized targeted vector for transfecting embryonic stem cells(ES).The ES cells with a deletion of the neomycin resistance gene(neo)were then cloned into blastocysts to generate chimeric CX3CR1+/GFPmice.These mice were subsequently bred with wild-type mice(WT),and repeated backcrossing was performed to obtain CX3CR1GFP/GFP mice.DNA and mRNA from WT and CX3CR1GFP mice were extracted and genotyped using agarose gel electrophoresis.The expression level of CX3CR1 in various tis-sues of the mice was detected by RT-qPCR.Western blot analy-sis was used to analyze the expression of GFP protein in periph-eral blood mononuclear cells(PBMC)and various tissues.The labeling efficiency of immune cells in bone marrow was detected by flow cytometry.The expression of GFP in different mouse tis-sues was observed by immunofluorescence.Results The results of agarose gel electrophoresis showed that the transgenic mouse genotype was CX3CR1GFP/GFP homozygote.RT-qPCR and West-ern blot showed that EGFP were targeted to replace CX3CR1 gene,so CX3CR1 expression was very low in CX3CR1GFP mice,while GFP expression was significantly upregulated.Flow cytom-etry and immunofluorescence showed that GFP effectively marked CX3CR1GFP mice,expressed in various tissues and cells with different expression levels.Conclusion This study con-structs and identifies the CX3CR1GFP genetic reporter mice,and GFP is stably expressed in mice,which provides a foundation for further research into the potential mechanisms of CX3CR1 in im-mune regulation.
4.Treatment of massive rotator cuff tears with modified Chinese-way technique
Wen-Yi MING ; Xu-Dong WU ; Hai-Dong DAI ; Zhe-Ming LI ; Lin CHEN ; Hong-Ming LIN ; Jia-Yi ZHAO
China Journal of Orthopaedics and Traumatology 2024;37(9):921-924
Objective To explore clinical effect of modified Chinese-way technique under shoulder arthroscopy in treating massive rotator cuff tears.Methods From January 2019 to June 2022,22 patients with massive rotator cuff tears who underwent arthroscopic rotator cuff repair with improved Chinese-way technique,including 10 males and 12 females,aged from 46 to 76 years old with an average of(64.14±7.45)years old;the courses of disease ranged from 5 to 14 months with an average of(8.32±2.42)months;19 patients were complete repaired,and 3 patients were partial repaired.Visual analogue scale(VAS)and University of California at Los Angeles(UCLA)scale were used to evaluate pain and function of shoulder joint preopera-tively and 1 year postoperatively.Postoperative complications,the integrity of reconstructed tissue structure and the size of sub-acromial space were observed.Results All patients were followed up from 12 to 34 months with an average of(17.14±5.93)months.Re-tear were occurred in 4 patients during MRI follow-up,but clinical symptoms of patients were improved significant-ly and they were satisfied with the treatment,the others were no complications such as incision infection,peripheral nerve in-jury,loosening and falling off of internal fixation anchors.Preoperative and 1 year after operation VAS were(8.05±1.12)and(1.82±1.50),UCLA scores were(7.45±1.65)and(31.41±2.87)respectively,and the difference was statistically significant(P<0.05).Conclusion The modified Chinese-way technique under shoulder arthroscopy for the massive rotator cuff tear could relieve pain obviously and recovery postoperative function well,with satisfactory curative effect.
5.Summary of best evidence on medication adherence interventions for patients with multiple chronic conditions
Yudan LIU ; Caiyun ZHANG ; Mingmei GUO ; Yujuan ZHENG ; Ming JIA ; Jiale YANG ; Jianing HOU ; Hua ZHAO
Chinese Journal of Modern Nursing 2024;30(30):4156-4162
Objective:To summarize the best evidence of medication adherence interventions for patients with multiple chronic conditions.Methods:According to the "6S" evidence model, literature on medication adherence in patients with multiple chronic conditions was retrieved from BMJ Best Clinical Practice, UpToDate, Medlive, National Institute for Health and Clinical Excellence, Cochrane Library, Embase, PubMed, Web of Science, China Biology Medicine disc, China National Knowledge Infrastructure, WanFang data and so on. The search period was from establishing the database to August 30, 2023.Results:A total of 16 articles were included, including three guidelines, four expert consensus, seven systematic reviews, and two meta-analyses. Twenty-seven pieces of evidence were summarized from six aspects of compliance assessment, educational intervention, behavioral intervention, optimized treatment program, technical reminder intervention, and social-psychological-emotional intervention.Conclusions:The best evidence of medication adherence interventions for patients with multiple chronic conditions summarized provides a reference for medical and nursing staff to develop medication adherence interventions.
6.Characteristics of gut microbiota dysbiosis in patients with infectious diarrhea
Wen-Peng GU ; Di LYU ; Xiao-Fang ZHOU ; Sen-Quan JIA ; Xiao-Nan ZHAO ; Yong ZHANG ; Yong-Ming ZHOU ; Jian-Wen YIN ; Li HUANG ; Xiao-Qing FU
Chinese Journal of Zoonoses 2024;40(5):408-414
This study investigated the characteristics of gut microbiota imbalance in patients with infectious diarrhea caused by various pathogenic infections,and the role of Bacteroides in maintaining homeostasis in the intestinal environment.The gut microbiota in patients with diarrhea caused by pathogenic infections,such as viral and bacterial infections,was determined through full-length 16S rRNA amplicon sequencing.Patients with diarrhea were grouped and analyzed according to the presence of single bacterial infection,single viral infection,mixed infection,or Clostridioides difficile infection.Bacteroides had the highest absolute number and relative abundance in the gut microbiota in healthy people,whereas patients with infectious diar-rhea showed lower relative abundance of Bacteroides at each phylum/order/family/genus taxonomic level.Alpha diversity anal-ysis indicated no significant differences among groups.NMDS and PCoA indicated formation of distinct clusters in the control group compared with the different infectious diarrhea groups.The diversity of the gut microbiota was higher in the control group than the infectious diarrhea groups.Patients with infec-tious diarrhea caused by different pathogens showed differing predominant gut microbiota.Bifidobacterium predominated in the single viral infection group,Streptococcus predominated in the single bacterial infection group,and Lachnoclostridium predominated in the mixed infection group.Escherichia and Klebsiella were the major gut microbiota in the C.difficile infection group.Meanwhile,the dominant gut microbiota in the healthy population was Bacteroides.COG function prediction revealed that the healthy control group formed a distinct cluster from the different infection groups.The functions of defense mechanisms,cell wall synthesis,protein modification,cellular differentiation,and replication and recombination were signifi-cantly diminished in all infectious diarrhea groups.In general,patients with infectious diarrhea caused by different pathogens showed dysbiosis,with diminished gut microbiota diversity and the emergence of related biomarkers.Our findings indicated that Bacteroides has a key role in maintaining the homeostasis of the human intestinal environment,thus providing new ideas for the subsequent treatment of infectious diarrhea and research in other fields.
7.Small molecule deoxynyboquinone triggers alkylation and ubiquitination of Keap1 at Cys489 on Kelch domain for Nrf2 activation and inflammatory therapy
Linghu KE-GANG ; Zhang TIAN ; Zhang GUANG-TAO ; Lv PENG ; Zhang WEN-JUN ; Zhao GUAN-DING ; Xiong SHI-HANG ; Ma QIU-SHUO ; Zhao MING-MING ; Chen MEIWAN ; Hu YUAN-JIA ; Zhang CHANG-SHENG ; Yu HUA
Journal of Pharmaceutical Analysis 2024;14(3):401-415
Activation of nuclear factor erythroid 2-related factor 2(Nrf2)by Kelch-like ECH-associated protein 1(Keap1)alkylation plays a central role in anti-inflammatory therapy.However,activators of Nrf2 through alkylation of Keap1-Kelch domain have not been identified.Deoxynyboquinone(DNQ)is a natural small molecule discovered from marine actinomycetes.The current study was designed to investigate the anti-inflammatory effects and molecular mechanisms of DNQ via alkylation of Keap1.DNQ exhibited signif-icant anti-inflammatory properties both in vitro and in vivo.The pharmacophore responsible for the anti-inflammatory properties of DNQ was determined to be the α,β-unsaturated amides moieties by a chemical reaction between DNQ and N-acetylcysteine.DNQ exerted anti-inflammatory effects through activation of Nrf2/ARE pathway.Keap1 was demonstrated to be the direct target of DNQ and bound with DNQ through conjugate addition reaction involving alkylation.The specific alkylation site of DNQ on Keap1 for Nrf2 activation was elucidated with a synthesized probe in conjunction with liquid chromatography-tandem mass spectrometry.DNQ triggered the ubiquitination and subsequent degra-dation of Keap1 by alkylation of the cysteine residue 489(Cys489)on Keap1-Kelch domain,ultimately enabling the activation of Nrf2.Our findings revealed that DNQ exhibited potent anti-inflammatory capacity through α,β-unsaturated amides moieties active group which specifically activated Nrf2 signal pathway via alkylation/ubiquitination of Keap1-Kelch domain,suggesting the potential values of targeting Cys489 on Keap1-Kelch domain by DNQ-like small molecules in inflammatory therapies.
8.Lung protection and mechanism of total flavonoids from Patrina villosa Juss in an experimental model of acute lung injury in rats
Jianbo LI ; Haiying FENG ; Jie ZHANG ; Ming LIU ; Haibo JIA ; Weipeng ZHAO
Chinese Journal of Pathophysiology 2024;40(7):1230-1236
AIM:To investigate the protective effect of total flavonoids from Patrina villosa Juss(PJF)on the lung in an experimental rat model of acute lung injury(ALI),and to elucidate the potential mechanism.METHODS:The ALI rat model was established by instilling 5 mg/kg of lipopolysaccharide(LPS)into the airway.Sixty male SD rats were randomly divided into 4 groups:control,LPS,LPS+low-dose PJF(receiving 100 mg/kg PJF one hour before ALI modeling)and LPS+high-dose PJF(receiving 300 mg/kg PJF one hour before ALI modeling).Each group consisted of 15 animals.Lung tissues and bronchoalveolar lavage fluid(BALF)were collected from all groups 24 h after modeling.For as-sessment of lung tissue morphology,HE staining was performed.The wet/dry weight ratio of the lung tissue was deter-mined using the wet/dry weighing method.Evans blue staining was conducted to assess epithelial barrier permeability in lung tissues.ELISA was used to detect the levels of inflammatory factors tumor necrosis factor-α(TNF-α),interleukin-1β(IL-1β)and IL-6 in the BALF,as well as oxidative stress markers including superoxide dismutase(SOD),myeloperoxi-dase(MPO)and glutathione peroxidase(GSH-Px)activity,and malondialdehyde(MDA)content in the lung tissue.The expression levels of C/EBP homologous protein(CHOP),glucose-regulated protein 78(GRP78)and X-box binding pro-tein 1(XBP1)in the lung tissue were analyzed by Western blotting.RESULTS:Compared with control group,the rats in LPS group exhibited a blurred alveolar structure with a significant infiltration of inflammatory cells.The ALI score and the wet/dry weight ratio of the lung tissue were increased(P<0.05).Concurrently,the levels of IL-6,IL-1β and TNF-α in the BALF,along with MDA content and MPO activity in the lung tissue,were elevated(P<0.05).Additionally,the pro-tein levels of CHOP,GRP78 and XBP1 were up-regulated in the lung tissue(P<0.05),while the SOD and GSH-Px activi-ty was significantly decreased(P<0.05).Compared with LPS group,PJF intervention exerted beneficial effects on the lung tissue morphology with reduced ALI score and lower lung wet/dry weight ratio(P<0.05).Moreover,the levels of IL-6,IL-1β and TNF-α in BALF,as well as MDA content,MPO activity and the protein levels of CHOP,GRP78 and XBP1 in the lung tissue were all significantly decreased(P<0.05),while the SOD and GSH-Px activity was significantly in-creased(P<0.05).The efficacy in high-dose group exceeded that in low-dose group.CONCLUSION:The PJF have pro-tective effect on the lungs of rats with ALI,and its mechanism may be related to the inhibition of inflammation,oxidative stress and endoplasmic reticulum stress.
9.Neurodevelopment and cerebral blood flow in children aged 2-6 years with autism spectrum disorder
Jia-Bao YIN ; Gan-Yu WANG ; Gui-Qin DUAN ; Wen-Hao NIE ; Ming-Fang ZHAO ; Ting-Ting JIN
Chinese Journal of Contemporary Pediatrics 2024;26(6):599-604
Objective To investigate the neurodevelopmental characteristics of children with autism spectrum disorder(ASD),analyze the correlation between neurodevelopmental indicators and cerebral blood flow(CBF),and explore the potential mechanisms of neurodevelopment in ASD children.Methods A retrospective study was conducted on 145 children aged 2-6 years with newly-diagnosed ASD.Scores from the Gesell Developmental Diagnosis Scale and the Autism Behavior Checklist(ABC)and CBF results were collected to compare gender differences in the development of children with ASD and analyze the correlation between CBF and neurodevelopmental indicators.Results Fine motor and personal-social development quotient in boys with ASD were lower than those in girls with ASD(P<0.05).Gross motor development quotient in ASD children was negatively correlated with CBF in the left frontal lobe(r=-0.200,P=0.016),right frontal lobe(r=-0.279,P=0.001),left parietal lobe(r=-0.208,P=0.012),and right parietal lobe(r=-0.187,P=0.025).The total ABC score was positively correlated with CBF in the left amygdala(r=0.295,P<0.001).Conclusions Early intervention training should pay attention to gender and developmental structural characteristics for precise intervention in ASD children.CBF has the potential to become a biological marker for assessing the severity of ASD.
10.The diagnostic value of artificial intelligence B-ultrasound image computer-aided diagnosis system in adult goiter
Zexu ZHANG ; Zongyu YUE ; Honglei XIE ; Yue SU ; Haowen PAN ; Jia LI ; Wenjing CHE ; Xin HOU ; Meng ZHAO ; Lanchun LIU ; Dandan LI ; Xian XU ; Weidong LI ; Fangang MENG ; Lijun FAN ; Lixiang LIU ; Ming LI ; Peng LIU
Chinese Journal of Endemiology 2024;43(11):922-927
Objective:To study the diagnostic value of artificial intelligence B-ultrasound image computer-aided diagnosis system (hereinafter referred to as intelligent ultrasound system) in adult goiter.Methods:In June 2022 and March 2023, two phases of thyroid disease survey were carried out in 4 cities in Anhui Province. One village was selected in each city, and 250 adults were selected as survey subjects in each village. Adult bilateral thyroid area was scanned by both intelligent ultrasound system and conventional ultrasound scanning equipment, and the effectiveness of intelligent ultrasound system in the diagnosis of goiter was analyzed based on the results of conventional ultrasound examination. Receiver operating characteristic (ROC) curve was drawn, and Kappa test was used to analyze the consistency between intelligent ultrasound system and conventional ultrasound examination in the diagnosis of goiter. At the same time, Spearman correlation analysis and Bland-Altman method were used to evaluate the consistency of the two methods in measuring thyroid volume.Results:After screening and removing outliers and missing values, a total of 910 adults were included, including 253 males (27.80%) and 657 females (72.20%). The age was (45.92 ± 10.20) years old, ranging from 18 to 60 years old. The sensitivity, specificity, and accuracy of the intelligent ultrasound system for diagnosing adult goiter were 80.00%, 99.67%, and 99.56%, respectively. The area under the ROC curve (AUC) was 0.996, which was consistent with the results of conventional ultrasound examination for diagnosing goiter ( κ = 0.67, P < 0.001). After controlling for variables such as gender, thyroid function, and thyroid nodules, the intelligent ultrasound system showed good consistency with conventional ultrasound examination in the diagnosis of goiter in females, adults with thyroid dysfunction, and adults without thyroid nodules ( κ = 0.66, 0.80, 0.80, P < 0.001). The consistency in the diagnosis of goiter in adults with thyroid nodules was moderate ( κ = 0.56, P < 0.001). Spearman correlation analysis showed a highly positive correlation between the measurement results of adult thyroid volume by intelligent ultrasound system and conventional ultrasound examination ( r = 0.88, P < 0.001). The Bland-Altman method results showed that only 4.62% (42/910) of points in adults were outside the 95% consistency limit, indicating good consistency between intelligent ultrasound system and conventional ultrasound examination in measuring thyroid volume (< 5%). The proportion of points outside the 95% consistency limit in males, adults with thyroid dysfunction, and adults with thyroid nodules was 6.72% (17/253), 5.83% (12/206), and 6.45% (12/186), respectively. Conclusions:The intelligent ultrasound system has certain diagnostic value for adult goiter and has good consistency with conventional ultrasound examination for thyroid volume measurement. However, the accuracy of diagnosis for males and adults with thyroid nodules still needs to be improved.

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