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Direct RNA sequencing in plants:Practical applications and future perspectives

Plant Communications 2024年第11期5卷 54-71页

作者： Xi-Tong Zhu Pablo Sanz-Jimenez Xiao-Tong Ning Muhammad Tahir ul Qamar Ling-Ling Chen State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Integrative Omics and Molecular Modeling Laboratory Department of Bioinformatics and BiotechnologyGovernment College University Faisalabad(GCUF)Faisalabad 38000Pakistan These authors contributed equally to this article

The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions,providing numerous insights into the dynamic changes,evolutionary traces,and elaborate regulation of the plant *** substantial improvement in accuracy and throughput,direct RNA sequencing(DRS)has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts,overcoming many limitations such as read length and PCR bias that are inherent to short-read ***,we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach,covering many aspects of RNA metabolism,including novel isoforms,poly(A)tails,and RNA modification,and we propose a comprehensive workflow for processing of plant DRS *** challenges to the application of DRS in plants,such as the need for machine learning tools tailored to plant transcriptomes,remain to be overcome,and together we outline future biological questions that can be addressed by DRS,such as allele-specific RNA *** technology provides convenient support on which the connection of distinct RNA features is tightly built,sustainably refining our understanding of the biological functions of the plant transcriptome.

关键词： direct RNA sequencing novel isoforms fusion transcripts poly(A)tail RNA modifications

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Structural and dynamic properties of the YTH domain in complex with N^(6)-methyladenosine RNA studied by accelerated molecular dynamics simulations

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Quantitative Biology 2023年第1期11卷 72-81页

作者： Mingwei Li Guanglin Chen Zhiyong Zhang MOE Key Laboratory for Membraneless Organelles&Cellular Dynamics National Science Center for Physical Sciences at MicroscaleDivision of Life Sciences and Medicineand Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefei 230026China Department of Physics University of Science and Technology of ChinaHefei 230026China

Background:N^(6)-methyladenosine(m^(6)A)modifications of mRNA and long non-coding RNA(lncRNAs)are known to play a significant role in regulation of gene expression and organismal *** writer and eraser proteins of this dynamic modification,the YT521-B homology(YTH)domain can recognize the modification involved in numerous cellular *** function of proteins containing YTH domain and its binding mode with N^(6)-methyladenosine RNA has attracted considerable ***,the structural and dynamic characteristics of the YTH domain in complex with m^(6)A RNA is still ***:This work presents results of accelerated molecular dynamics(aMD)simulations at the timescale of *** component analysis(PCA),molecular mechanics generalized Born surface area(MM/GBSA)calculations,contact analysis and contact-based principal component analysis(conPCA)provide new insights into structure and dynamics of the YTH-RNA ***:The aMD simulations indicate that the recognition loop has a larger movement away from the binding pocket in the YTH-A3 RNA than that in the YTH-m^(6)A3 *** aMD trajectories of the apo YTH,there is a significant close-open transition of the recognition loop,that is to say,the apo YTH can take both the closed and open *** have found that the YTH domain binds more favorably to the methylated RNA than the nonmethylated *** per-residue free energy decomposition and conPCA suggest that hydrophobic residues including W380,L383-V385,W431-P434,M437,and M441-L442,may play important roles in favorable binding of the m^(6)A RNA to the YTH domain,which is also supported by aMD simulations of a double mutated system(L383A/M437A).Conclusion:The results are in good agreement with higher structural stability of the YTH-m^(6)A RNA than that of the YTH-A3 *** addition of a methylation group on A3 can enhance its binding to the hydrophobic pocket in the YTH *** simulations support a‘conformational

关键词： RNA methylation YTH-m^(6)A3 RNA principal component analysis(PCA) binding free energy contactbased PCA

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Corrigendum to “Remodeling tumor immunosuppressive microenvironment via a novel bioactive nanovaccines potentiates the efficacy of cancer immunotherapy” [Bioactive Mater. 16 107-119]

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Bioactive Materials 2023年第3期21卷 239-240页

作者： Xiaoxue Xie Yi Feng Hanxi Zhang Qingqing Su Ting Song Geng Yang Ningxi Li Xiaodan Wei Tingting Li Xiang Qin Shun Li Chunhui Wu Xiaojuan Zhang Guixue Wang Yiyao Liu Hong Yang Department of Biophysics School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengdu610054SichuanPR China TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province Hospital of Chengdu University of Traditional Chinese MedicineNo.39 Shi-er-qiao RoadChengdu610072SichuanPR China Key Laboratory of Biorheological Science and Technology Ministry of EducationState and Local Joint Engineering Laboratory for Vascular ImplantsBioengineering College of Chongqing UniversityChongqing400030PR China

The authors regret that the published version of the above article contained two errors which were not identified during the proofing ***,Figure 2A and 6C have been *** authors apologize for these errors and state tha... 详细信息

关键词： Cor vaccines immunotherapy

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Evolution of Monkeypox C9L RNA G-Quadruplex Elevates the Translation of Its Only Kelch-like Protein by Accelerating G-Quadruplex Unfolding Kinetics

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CCS Chemistry 2024年第4期6卷 953-963页

作者： Yicong Dai Xucong Teng Difei Hu Qiushuang Zhang Jinghong Li Department of Chemistry Center for Bioanalytical ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua UniversityBeijing 100084 New Cornerstone Science Laboratory Shenzhen 518054 Beijing Life Science Academy Beijing 102209 Center for Bioanalytical Chemistry Hefei National Laboratory of Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefei 230026

Genomic surveillance of monkeypox virus(MPXV)is essential to explore the reason of its unusual *** phylogenomic analysis of the MPXV genome mainly focuses on the effect of amino acid ***,we explore the evolutionary variation of RNA G-quadruplex(RG4)of MPXV and find that the genome evolution of MPXV can also produce new effects through changes in the RG4 *** RG4 is located in MPXV’s only Kelch-like C9L gene,which encodes for an antagonist of the innate immune *** evolution of this virus increases the unfolding kinetic constant of C9L RG4 and promotes the C9 protein level in living ***,all reported MPXV genomes in 2022 carry the C9L-RG4-5 pattern with the highest unfolding kinetic ***,the RG4 ligand,RGB-1,can impede the unfolding of C9L-RG4-5 and thereby reduce the C9 protein *** findings carve out a new path to comprehensively understanding MPXV virology.

关键词： G-quadruplex RNA secondary structure unfolding kinetics monkeypox virus genomic evolution immune evasion

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An investigation on catalytic performance and reaction mechanisms of Fe/OMS-2 for the oxidation of carbon monoxide, ethyl acetate, and toluene

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Journal of Environmental sciences 2022年第2期34卷 258-268页

作者： Ning Dong Mengyue Chen Qing Ye Dan Zhang Hongxing Dai Key Laboratory of Beijing on Regional Air Pollution Control Department of Environmental ScienceSchool of Environmental and Chemical EngineeringFaculty of Environment and LifeBeijing University of TechnologyBeijing 100124China Beijing Key Laboratory for Green Catalysis and Separation Key Laboratory of Beijing on Regional Air Pollution ControlKey Laboratory of Advanced Functional MaterialsEducation Ministry of Chinaand Laboratory of Catalysis Chemistry and NanoscienceDepartment of Environmental Chemical EngineeringSchool of Environmental and Chemical EngineeringFaculty of Environment and LifeBeijing University of TechnologyBeijing 100124China

The octahedral molecular sieve(OMS-2)-supported Fe( xFe/OMS-2: x = 1, 3, 5, and 10) catalysts were prepared using the pre-incorporation method. Physicochemical properties of the as-synthesized materials were characterized by means of various techniques, and their catalytic activities for CO, ethyl acetate, and toluene oxidation were evaluated. Among all of the samples, performed the best, with the reaction temperature required to achieve 90% conversion( T 90%) being 160 ℃ for CO oxidation, 210 ℃ for ethyl acetate oxidation, and 285 ℃ for toluene oxidation. Such a good catalytic performance of 5Fe/OMS-2 was associated with its high(Mn^(3+) + Mn^(2+)) content and adsorbed oxygen species concentration, and good lowtemperature reducibility and lattice oxygen mobility as well as strong interaction between Fe and OMS-2. In addition, catalytic mechanisms of the oxidation of three pollutants over the 5Fe/OMS-2 catalyst were also studied. It was found that CO, ethyl acetate or toluene was first adsorbed, then the related intermediates were formed, and finally the formed intermediates were completely converted into CO_(2) and H_(2)O.

关键词： Cryptomelane-type OMS-2 supported iron catalyst CO oxidation Volatile organic compound oxidation Toluene oxidation

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A nitrogen-rich halogen-bonded organic framework (XOF) for efficient iodine capture and security printing

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science China Chemistry 2025年第2期68卷 631-640页

作者： Qi Zhao Penghao Sun Guanfei Gong Yi Chen Lingzhi Luo Yongfei Yin Chunsheng Li Jike Wang Lu Wang Shigui Chen The Institute for Advanced Studies Wuhan UniversityWuhan 430072China Ningxia Vocational Technical College of Industry and Commerce Yinchuan 750100China Key Laboratory of Advanced Electrode Materials for Novel Solar Cells for Petroleum and Chemical Industry of China School of Chemistry and Life SciencesSuzhou University of Science and TechnologySuzhou 215009China

The escalating utilization of nuclear energy and nuclear medicine raises concerns about the environmental impact of radioactive iodine,necessitating the development of effective iodine adsorbents,especially under a real-world scenario with extremely low iodine concentration and elevated ***,we have presented the construction of a nitrogen-abundant two-dimensional(2D)halogen-bonded organic framework,XOF-TNP,characterized by exceptional crystallinity,thermal stability,and nitrogen-rich ***-TNP exhibits strong binding to iodine,thanks to the fact that iodine can be pre-enriched into the framework through N…I *** nitrogen-rich framework and I^(+) synergistically have extremely high binding force to iodine,enabling the rapid and efficient capture of iodine in both vapor and solution phases,with significant *** flow-through adsorption experiments using an XOF-TNP-packed column achieve 99%iodine removal from hexane and aqueous solutions,surpassing traditional activated *** highlights its potential for environmental *** enables the development of a novel rewritable security paper,utilizing its iodine adsorption properties to encrypt and decrypt QR *** research expands the application scope of halogen-bonded organic frameworks,providing insights into the design of materials for environmental remediation and security applications.

关键词： [N…I+…N]halogen bond halogen-bonded organic framework iodine capture security printing supramolecular assembly

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Critical review on anti-fatigue effects of natural dietary products: Present insights and future trends

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Food science and Human Wellness 2025年

作者： Syam P.K.Jeepipalli Nidesha Randeni Bin Du Baojun Xu Food Science and Technology Program， Department of Life Sciences， Beijing Normal-Hong Kong Baptist University Department of Agricultural and Plantation Engineering， Faculty of Engineering Technology， The Open University of Sri Lanka Hebei Key Laboratory of Natural Products Activity Components and Function， Hebei Normal University of Science and Technology

Fatigue impacts both mental and physical health， significantly reducing quality of life and daily productivity. Natural bioactive compounds have emerged as promising agents to combat fatigue due to their multifaceted biological activities and minimal side effects. key mechanisms through which these compounds exert anti-fatigue effects include enhancing energy metabolism， reducing oxidative stress， supporting mitochondrial integrity， modulating the immune response， and regulating neurotransmitter balance. Plant-derived metabolites such as flavonoids， ginsenosides， saponins， and polysaccharides， as well as animal-based peptides and microbial-derived substances， have demonstrated significant potential in alleviating fatigue symptoms in both clinical and preclinical studies. Additionally， fermented products like kefir， fermented rice bran， and yogurt enhance endurance performance， reduce lactate buildup， and improve glycogen storage， further contributing to fatigue mitigation. As consumer interest in natural alternatives grows， future research should prioritize improving the bioavailability， stability， and targeted delivery of these compounds. This review consolidates recent advances in the understanding of anti-fatigue mechanisms of natural products and highlights emerging directions for their development as functional foods and therapeutic agents.

关键词： Anti-fatigue activity plant metabolites animal products microbial products fermented products amino acid

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On-chip ultrasensitive and rapid hydrogen sensing based on plasmon-induced hot electron-molecule interaction

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Light(science & Applications) 2023年第4期12卷 625-635页

作者： Long Wen Zhiwei Sun Qilin Zheng Xianghong Nan Zaizhu Lou Zhong Liu David R.S.Cumming Baojun Li Qin Chen Guangdong Provincial Key Laboratory of Nanophotonic Manipulation Institute of NanophotonicsJinan University511443 GuangzhouChina College of Life Science and Technology Jinan University510632 GuangzhouChina School of Engineering University of GlasgowGlasgow G128QQUK

Hydrogen energy is a zero-carbon replacement for fossil ***,hydrogen is highly flammable and explosive hence timely sensitive leak detection is *** optical sensing techniques rely on complex instruments,while electrical sensing techniques usually operate at high temperatures and biasing *** this paper an on-chip plasmonic-catalytic hydrogen sensing concept with a concentration detection limit down to 1 ppm is presented that is based on a metal-insulator-semiconductor(MIS)nanojunction operating at room temperature and zero *** sensing signal of the device was enhanced by three orders of magnitude at a one-order of magnitude higher response speed compared to alternative non-plasmonic *** excellent performance is attributed to the hydrogen induced interfacial dipole charge layer and the associated plasmonic hot electron modulated photoelectric *** agreements were achieved between experiment and theoretical calculations based on a quantum tunneling *** an on-chip combination of plasmonic optics,photoelectric detection and photocatalysis offers promising strategies for next-generation optical gas sensors that require high sensitivity,low time delay,low cost,high portability and flexibility.

关键词： hydrogen interaction hence

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siRNA-functionalized lanthanide nanoparticle enables efficient endosomal escape and cancer treatment

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Nano Research 2022年第10期15卷 9160-9168页

作者： Chanchan Yu Kun Li Lin Xu Bo Li Chunhui Li Shuai Guo Ziyue Li Yuquan Zhang Abid Hussain Hong Tan Mengyu Zhang Yongxiang Zhao Yuanyu Huang Xing-Jie Liang School of Life Science Advanced Research Institute of Multidisciplinary ScienceSchool of Medical Technology(Institute of Engineering Medicine)Key Laboratory of Molecular Medicine and BiotherapyKey Laboratory of Medical Molecule Science and Pharmaceutics EngineeringBeijing Institute of TechnologyBeijing 100081China CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety CAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology of ChinaBeijing 100190China National Center for International Research of Biological Targeting Diagnosis and Therapy Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy ResearchGuangxi Medical UniversityNanning 530021China

Attaching DNA/RNA to nanomaterials is the basis for nucleic acid-based assembly and drug ***,we report that small interfering RNA(siRNA)effectively coordinates with ligand-free lanthanide nanoparticles(NaGdF4 NPs),and forms siRNA/NaGdF4 spherical nucleic acids(SNA).The coordination is primarily attributed to the interaction between Gd and phosphate backbone of the ***,an efficient encapsulation and rapid endosomal escape of siRNA from the endosome/lysosome were achieved,due to its flexible ability to bound to phospholipid head of endosomal membrane,thereby disrupting the membrane *** to the dual properties of NaGdF4 NPs,siRNA loading,and endosomal escape,siRNA targeting programmed cell death-ligand 1(siPD-L1)/NaGdF4 SNA triggers significant gene silencing in vitro and in vivo,and effectively represses the tumor growth in both CT26 tumor model and 4T1 orthotopic murine model.

关键词： coordination chemistry nuclei acid lanthanide nanomaterials small interfering RNA(siRNA)delivery endosome escape

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Lipase-activated glycopeptide nano-assemblies as an antibiotic nano-adjuvant to inhibit Pseudomonas aeruginosa biofilm and enhance antibacterial activity

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science China Chemistry 2022年第12期65卷 2538-2547页

作者： Yifei Song Jingkai Zhang Yue Fei Zhangjian Huang Xiaoxuan Liu Li-Li Li CAS Center for Excellence in Nanoscience CAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyNational Center for Nanoscience and Technology(NCNST)Beijing100190China College of Life Science and Technology Beijing University of Chemical TechnologyBeijing100029China State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases Center of Drug DiscoveryCenter of Advanced Pharmaceutics and BiomaterialsChina Pharmaceutical UniversityNanjing210009China

Bacterial infections,especially those caused by biofilms,pose a serious threat to public *** this work,we propose a glycopeptide-based antibiotic nano-adjuvant(GalAc-2) that can synergistically enhance the antibacterial activity of antibiotics through its biofilm inhibition *** glycopeptide nanoparticles can be specifically activated by bacterial infection overexpressed lipase and sequentially enlarged by glycosyl exposure on the *** stability and bonding affinity of the nanoparticles were enhanced through the increase in β-sheet *** bacterial growth inhibition rate of the mixture of levofloxacin(LEV) and GalAc-2 at 0.54 μg/m L was over sevenfold higher than that of LEV alone because of the electrostatic and multivalence Lec A interactions that inhibited biofilm formation on the bacterial ***,the mixture of the antibiotic with GalAc-2 significantly inhibited the abscess exposed to skin infection and significantly reduced the infiltration of immune *** believe that GalAc-2 can be further used to enhance broad-spectrum antibiotic sensitization and prolong the lifetime of antibiotics.

关键词： glycopeptide self-assembly antibiotic nano-adjuvant bacteria biofilm

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