CHEMICAL ENGINEERING JOURNAL
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2021
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IF 13.273
Minghui Wang,Yuxin Lin,Jianyang Lu,Zhaowei Sun,Ying Deng,Lei Wang,Yongxiang Yi,Jinlong Li,Jie Yang,Genxi Li
The ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted that new diagnosis technologies are crucial for controlling the spread of the disease. Especially in the resources-limit region, conveniently operated detection methods such as “naked-eye” detection are urgently required that no instrument is needed. Herein, we have designed a novel and facile strategy to fabricate covalent organic framework (COF) capsules, which can be utilized to establish a new colorimetric assay for naked-eye detection of SARS-CoV-2 RNA. Specifically, we employ the digestible ZIF-90 as the sacrificial template to prepare the hollow COF capsules for horseradish peroxidase (HRP) encapsulation. The fabricated COF capsules can provide an appropriate microenvironment for the enzyme molecules, which may improve the conformational freedom of enzymes, enhance the mass transfer, and endow the enzyme with high environmental resistance. With such design, the proposed assay exhibits outstanding analytical performance for the detection of SARS-CoV-2 RNA in the linear range from 5 pM to 50 nM with a detection limit of 0.28 pM which can go parallel to qTR-PCR analysis. Our method also possesses excellent selectivity and reproducibility. Moreover, this method can also be served to analyze the clinical samples, and can successfully differentiate COVID-19 patients from healthy people, suggesting the promising potential in clinical diagnosis.
研究领域:
生物化学
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医学诊断
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材料科学
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产品关联
DOI
PubMed
高影响因子
ACS Applied Materials & Interfaces
·
2024
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IF 8.3
Yuxi Wang,Pan Cheng,Tiange Chen,Mingyue Li,Qihao Guo,Qin Cheng,Dong Wang,Ke Liu
Developing monolithic materials for chromatography columns with a novel interconnected porous structure is vital for the enhancement of the separation efficiency of RNA purification processes. Herein, a porous nanofibrous sponge (PNFS) is constructed by freeze molding and freeze-drying a nanofiber dispersion with ethylene vinyl alcohol copolymer nanofibers as the skeleton, chitosan (CS) and polyethylenimine (PEI) as the binders, and glutaraldehyde (GA) as the crosslinking agent. The results show that when the CS content of the dispersion is 1.5 wt %, PNFS demonstrates a high static adsorption capacity of 406.5 mg/g (30.7 mg/m2) and a dynamic adsorption capacity of 382.6 mg/g (28.9 mg/m2) at a flow rate of 1 mm/min. Moreover, PNFS shows a high specific adsorption performance toward RNA in the presence of bovine serum albumin, lecithin, or DNA by adjusting the solution pH value and the method of gradient elution. Besides, PNFS presents exceptional performance in the rapid separation of RNA from HT22 cells without degradation. This result can be attributed to optimized morphology, pore structure, and comprehensive performance of PNFS, benefiting from the synergistic effect of the highly oriented porous structure and CS–PEI interaction derived from the high-density adsorption ligands on the channel walls of PNFS. This work provided an efficient strategy to handle the permeability/adsorptivity trade-off for ion-exchange chromatographic materials.
研究领域:
生物工程
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材料科学
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分子生物学
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DOI
PubMed
高影响因子
PLANT PHYSIOLOGY
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2023
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IF 7.4
Xu Jidi,He Jieqiang,Hu Bichun,Hou Nan,Guo Junxing,Wang Caixia,Li Xuewei,Li Zhongxing,Zhai Jingjing,Zhang Ting,Ma Chuang,Ma Fengwang,Guan Qingmei
Grafting can facilitate better scion performance and is widely used in plants. Numerous studies have studied the involvement of mRNAs, small RNAs, and epigenetic regulations in the grafting process. However, it remains unclear whether the mRNA N6-methyladenosine (m6A) modification participates in the apple (Malus x domestica Borkh.) grafting process. Here, we decoded the landscape of m6A modification profiles in ‘Golden delicious’ (a cultivar, Gd) and Malus prunifolia ‘Fupingqiuzi’ (a unique rootstock with resistance to environmental stresses, Mp), as well as their heterografted and self-grafted plants. Interestingly, global hypermethylation of m6A occurred in both heterografted scion and rootstock compared with their self-grafting controls. Gene Ontology (GO) term enrichment analysis showed that grafting-induced differentially m6A-modified genes were mainly involved in RNA processing, epigenetic regulation, stress response, and development. Differentially m6A-modified genes harboring expression alterations were mainly involved in various stress responses and fatty acid metabolism. Furthermore, grafting-induced mobile mRNAs with m6A and gene expression alterations mainly participated in ABA synthesis and transport (e.g. carotenoid cleavage dioxygenase 1 [CCD1] and ATP-binding cassette G22 [ABCG22]) and abiotic and biotic stress responses, which might contribute to the better performance of heterografted plants. Additionally, the DNA methylome analysis also demonstrated the DNA methylation alterations during grafting. Downregulated expression of m6A methyltransferase gene MdMTA (ortholog of METTL3) in apples induced the global m6A hypomethylation and distinctly activated the expression level of DNA demethylase gene MdROS1 (REPRESSOR OF SILENCING 1) showing the possible association between m6A and 5mC methylation in apples. Our results reveal the m6A modification profiles in the apple grafting process and enhance our understanding of the m6A regulatory mechanism in plant biological processes.
研究领域:
植物生物学
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表观遗传学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
Evidence-based Complementary and Alternative Medicine
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2023
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IF 2.65
Hui Wang,HaiTang Ren
The action mechanism in which circular RNA (circ) SMARCA5 targeted nasopharyngeal carcinoma (NPC) cell proliferation, migration, invasion, and apoptosis via microRNA (miR)-582-3p/phosphatase and tensin homolog (PTEN) axis was explored. The examination was performed via reverse transcription-quantitative polymerase chain reaction (RT-qPCR), discovering that circSMARCA5 was elevated while miR-582-3p was silenced in NPC tissues and cells. E-cadherin and N-cadherin were detected. The results illustrated transfection with si-circSMARCA5 or miR-582-3p-mimic was available to repress cancer cell advancement, and E-cadherin was augmented. Transfection with pcDNA 3.1-circSMARCA5 or miR-582-3p-inhibitor was available to accelerate cancer cell advancement, and N-cadherin was augmented. MiR-582-3p-inhibitor blocked the suppression of si-circSMARCA5 on NPC. The si-PTEN blocked the malignant behavior of pcDNA 3.1-circSMARCA5 against NPC. The binding sites between circSMARCA5 and miR-582-3p and between miR-582-3p and PTEN were verified. Linear analysis results illuminated the expression pattern of circSMARCA5 was opposite to miR-582-3p, while the expression pattern of circSMARCA5 was positively associated with PTEN. In brief, the results of the research clarified circSMARCA5 modulated NPC cells’ vital movement via the miR-582-3p/PTEN molecular axis.
研究领域:
癌症生物学
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分子生物学
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细胞生物学
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产品关联
DOI
PubMed
高影响因子
ACS Applied Materials & Interfaces
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2022
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IF 10.383
Zhiyan Chen,Wen-Tao Wang,Wenchao Wang,Jinsong Huang,Jia-Yu Liao,Su Zeng,Linghui Qian
Owing to its important biological functions, RNA has become a promising molecular biomarker of various diseases. With a dynamic change in its expression level and a relatively low amount within the complicated biological matrix, signal amplification detection based on DNA probes has been put forward, which is helpful for early diagnosis and prognostic prediction. However, conventional methods are confined to cell lysates or dead cells and are not only time-consuming in sample preparation but also inaccessible to the spatial–temporal information of target RNAs. To achieve live-cell imaging of specific RNAs, both the detection sensitivity and intracellular delivery issues should be addressed. Herein, a new cascaded fluorogenic system based on the combination of hybridization chain reactions (HCRs) and proximity-induced bioorthogonal chemistry is developed, in which a bioorthogonal reaction pair (a tetrazine-quenched dye and its complementary dienophile) is brought into spatial proximity upon target RNA triggering the HCR to turn on and amplify the fluorescence in one step, sensitively indicating the cellular distribution of RNA with minimal false positive results caused by unspecific degradation. Facilitated by a biodegradable carrier based on black phosphorus with high loading capacity and excellent biocompatibility, the resulting imaging platform allows wash-free tracking of target RNAs inside living cells.
研究领域:
分子生物学
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生物医学工程
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分析化学
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细胞生物学
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产品关联
DOI
PubMed
高影响因子
ACS Applied Bio Materials
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2020
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IF 0
Hua Yang,Yufei Zhang,Xuan Xu,Huanxiang Wang,Ziyun Huang,Ziling Luo,Xiangxi Deng,Qian Xue,Zhihe Qing,Zhen Zou,Ronghua Yang
Visual imaging of long noncoding RNA (lncRNA) MEG3, a newfound regulator of transactivation and tumor growth suppression, is conducive to unlock the secrets of MEG3 in some important biological processes. Here, for the first time, we designed a DNA tetrahedron-based three-dimensional (3D) catcher for imaging cytoplasmic lncRNA MEG3 in living cells. The 3D catcher is composed of a triple-helix-forming dsDNA with capacity to bind the 5′-end GA-rich domain of the lncRNA MEG3 and four hairpin-shaped antisense sequences toward contiguous domain on MEG3. Once ingested by the cell, the 3D catcher quickly captures lncRNA MEG3 via forming a DNA–RNA triple-helix structure and triggering the hybridization-based string disassembly of the catcher. Concomitantly, the quenched hairpin is opened and the fluorescent signal undergoes lighting on conversion. Ascribed to the triple-helix-induced “domino effect,” the disassembly reaction time is greatly shorter than the reaction with the inability to form a triple helix. The 3D catcher allows detection of long-chain targets as long as 129 nucleotide (129 nt) with a detection limit of 0.36 nM and distinguishes endogenous lncRNA MEG3 fragments in living cells between hepatoma cells and normal hepatocytes, which provides a reliable strategy for monitoring endogenous long fragment nucleic acid biomarkers in early clinical lesion diagnoses.
研究领域:
分子生物学
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医学诊断
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遗传学
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DOI
PubMed
Frontiers in Genetics
·
2025
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IF 2.8
Minglu Zhang,Jianbo He,Rao Fu,Guojian Bao,Yijun Lu,Zechuan Zhang,Jiawu Yan,Jialu Ding,Fei Yang,Beicheng Sun
Introduction: Small nucleolar RNA (snoRNA) mediates RNA modifications, including 2′-O-methylation (Nm) and pseudouridine (Ψ), which has been proven to impact tumor progression. However, the role of snoRNA in the epigenetics of tumors remains poorly understood due to the lack of sufficiently effective experimental methods to identify snoRNA targets. Here, we identified SNORD13H, a C/D box snoRNA, as being downregulated in hepatocellular carcinoma (HCC), and its low expression was associated with HCC development.Methods: To elucidate specific roles of SNORD13H in HCC, we used a comprehensive array of methodologies, including flow cytometry, xenograft mouse model, reverse transcription at low dNTP concentration followed by PCR (RTL-P) assay, and surface sensing of translation (SUnSET) assay.Results: In this study, we first demonstrated that reduced SNORD13H serves as a biomarker for HCC, facilitating cellular proliferation. SNORD13H mediates 2′-O-methylations of 18S rRNA and RAS mRNA, thereby enhancing translation efficiency and regulating RAS protein levels in HCC. The diminution of SNORD13H activates the RAS pathway, contributing to the progression of HCC.Discussion: Our study establishes SNORD13H as a dual-function regulator in HCC progression. Furthermore, our findings indicate that SNORD13H is detectable in plasma, highlighting its potential utility in tumor screening.
研究领域:
分子生物学
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癌症研究
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遗传学
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表观遗传学
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RNA修饰
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产品关联
DOI
PubMed
高影响因子
ACS Synthetic Biology
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2024
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IF 3.7
Qing Wang,Jiajia You,Yichen Li,Jie Zhang,Yi Wang,Meijuan Xu,Zhiming Rao
In vivo targeted mutagenesis technologies are the basis for the continuous directed evolution of specific proteins. Here, an efficient mutagenesis system (CgMutaT7) for continuous evolution of the targeted gene in Corynebacterium glutamicum was developed. First, cytosine deaminase and uracil-DNA glycosylase inhibitor were sequentially fused to T7 RNA polymerase using flexible linkers to build the CgMutaT7 system, which introduces mutations in targeted regions controlled by the T7 promoter. After a series of optimizations, the resulting targeted mutagenesis system (CgMutaT74) can increase the mutant frequency of the target gene by 1.12 × 104-fold, with low off-target mutant frequency. Subsequently, high-throughput sequencing further revealed that the CgMutaT74 system performs efficient and uniform C → T transitions in at least a 1.8 kb DNA region. Finally, the xylose isomerase was successfully continuously evolved by CgMutaT74 to improve the xylose utilization, indicating that the CgMutaT7 system has great potential for applications in the continuous evolution of protein function and expression components.
研究领域:
合成生物学
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分子遗传学
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产品关联
DOI
PubMed
高影响因子
Oncology Letters
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2020
·Vol. 20
·期 4
·1-1
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IF 2.311
Peng He,Guoguang Xiong,Wei Guo,Guanjun Jiang,Yun Li,Hao Li
Long non‑coding RNA colon cancer associated transcript 2 (CCAT2) is dysregulated in a number of different types of human cancer, and affects cancer progression via the Wnt/β‑catenin signaling pathway. However, the roles of CCAT2 and the Wnt/β‑catenin signaling pathway in prostate cancer (PCa) are not completely understood. The present study aimed to investigate the potential mechanism of CCAT2 in PCa. In the present study, the reverse transcription‑quantitative PCR (RT‑qPCR) results indicated that CCAT2 expression was significantly upregulated in PCa tissues, and DU145 and PC3 cell lines compared with normal prostate tissues and the epithelial RWPE‑1 cell line, respectively. Functional assays indicated that CCAT2 downregulation inhibited DU145 and PC3 cell proliferation, cell cycle, migration and invasion. In addition, the luciferase reporter assay, RT‑qPCR and western blotting results indicated that CCAT2 regulated transcription factor 7 like 2 (TCF7L2) expression by binding to microRNA‑217. Further western blotting and TOPFlash assays indicated that CCAT2‑knockdown inhibited the Wnt/β‑catenin signaling pathway in DU145 and PC3 cell lines by inhibiting the expression of TCF7L2. However, CCAT2‑knockdown‑mediated effects were reversed by the Wnt/β‑catenin signaling pathway activator lithium chloride (LiCl). Further cell experiments suggested that LiCl treatment reversed CCAT2‑knockdown‑mediated inhibition of PCa cell proliferation, cell cycle, epithelial‑mesenchymal transition, migration and invasion. Overall, the results indicated that CCAT2 regulated PCa via the Wnt/β‑catenin signaling pathway; therefore, CCAT2 may exhibit key role during the progression of PCa and may serve as a therapeutic target for the disease.
研究领域:
肿瘤学
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分子生物学
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细胞生物学
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癌症遗传学
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DOI
PubMed
高影响因子
ACS Applied Bio Materials
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2019
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IF 0
Zaizai Dong,Chuanhao Tang,Zhen Zhang,Wei Zhou,Rong Zhao,Lina Wang,Jiachao Xu,Yayun Wu,Jiang Wu,Xing Zhang,Li Xu,Libo Zhao,Xiaohong Fang
Exosomes, which are 30–150 nm extracellular vesicles containing a variety of biomolecules (i.e., proteins, RNA, DNA, and lipids), have emerged as important analytes in liquid biopsy. Although exosome detection offers a valuable chance to understand disease status in a multidimensional manner, comprehensive analysis of different exosomal biomolecules with limited specimens remains a challenge. Herein, we introduced an aptamer-based PCR (polymerase chain reaction) platform and realized highly sensitive detection of CD63 protein positive exosomes as low as 50 particles/μL. More importantly, simultaneous analysis of exosomal RNA and surface protein is available using this method. In a proof of concept experiment, simultaneous detection of two immunotherapy-related biomarkers, programmed death-ligand 1 (PD-L1) protein and indoleamine 2,3-dioxygenase 1 (IDO1) mRNA, was demonstrated with clinical samples. Our method provides a strategy for the comprehensive analysis of exosomes, with the advantages of high sensitivity and practicability.
研究领域:
生物技术
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分子生物学
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癌症研究
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医学诊断
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DOI
PubMed
Journal of Materials Chemistry B
·
2023
·Vol. 11
·期 7
·1478-1485
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IF 7
Chengjie Duan,Yan Chen,Zhiqiang Hou,Dayong Li,Jin Jiao,Weihao Sun,Yang Xiang
Heteromultivalent scaffolds with different repeated monomers have great potential in biomedicine, but convenient construction strategies for integrating various functional modules to achieve multiple biological functions are still lacking. Here, taking advantage of the heteromultivalent effect of dendritic nucleic acids and the specific biochemical properties of microRNAs (miRNAs), we assembled novel heteromultivalent nucleic acid scaffolds by biomimetic co-assembly of DNA–RNA building blocks. In our approach, two miRNAs were used to initiate and maintain dendritic structures in an interdependent manner; so, the heteromultivalent nanostructure can only form in the presence of both miRNAs. The proposed nanostructure can be used for one-step analysis of two miRNAs in an AND logic format. Taking miR-18b-5p and miR-342-3p which are associated with Alzheimer's disease as an example, a FRET sensing system was fabricated for the simultaneous analysis of two miRNAs within one hour at picomolar concentration. Further studies show that the designed device may have the potential to distinguish between AD patients and the healthy population by analysis of two miRNAs in CSF (cerebrospinal fluid) samples, suggesting its possible applicability in clinics.
研究领域:
生物技术
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纳米技术
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分子生物学
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医学诊断
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产品关联
DOI
PubMed
高影响因子
Frontiers in Cell and Developmental Biology
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2022
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IF 6.081
Zhou Tong,Chen Guobin,Chen Meng,Wang Yubin,Zou Guiwei,Liang Hongwei
Sex dimorphism is a key feature of Chinese soft-shelled turtle (Pelodiscus sinensis). The males (M) have higher econosmic value than females (F) due to wider calipash and faster growth. Exogenous hormones like estradiol and methyltestosterone can induce sexual reversal to form new phenotypes (pseudo-female, PF; pseudo-male, PM) without changing the genotype. The possibility of inducing sexual reversal is particularly important in aquaculture breeding, but the underlying biological mechanisms remain unclear. Here we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in P. sinensis. Nanopore sequencing of the four gender types (M, F, PF, and PM) showed that the distribution of read length and gene expression was more similar between same-sex phenotypes than same-sex genotypes. Compared to turtles with an M phenotype, alternative splicing was more pronounced in F turtles, especially at alternative 3′ splice sites, alternative 5′ splice sites, and alternative first exons. Furthermore, the two RNA methylation modifications m5C and m6A were differentially distributed across gender phenotypes, with the M type having more modification sites in coding sequence regions, but fewer modification sites in 3′UTR regions. Quantitative analysis of enriched m6A RNAs revealed that the N6-methylated levels of Odf2, Pacs2, and Ak1 were significantly higher in M phenotype individuals, while the N6-methylated levels of Ube2o were reduced after sexual reversal from both M and F phenotypes. Taken together, these findings reveal an important role of epigenetics during sexual reversal in Chinese soft-shelled turtles.
研究领域:
发育生物学
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分子生物学
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水产养殖学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）