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Olfactory receptors in neural regeneration in the central nervous system

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Neural Regeneration Research 2025年第9期20卷 2480-2494页

作者： Rafael Franco Claudia Garrigós Toni Capó Joan Serrano-Marín Rafael Rivas-Santisteban Jaume Lillo molecular Neurobiology laboratory Department of Biochemistry and Molecular BiomedicineFacultat de BiologiaUniversitat de BarcelonaBarcelonaSpain CiberNed Network Center for Biomedical Research in Neurodegenerative Diseases Spanish National Health Institute Carlos ⅢMadridSpain School of Chemistry Universitat de BarcelonaBarcelonaSpain Department of Biochemistry and Physiology School of Pharmacy and Food SciencesUniversitat de BarcelonaBarcelonaSpain laboratory of computational Medicine Biostatistics UnitFaculty of MedicineAutonomous University of BarcelonaCampus BellaterraBarcelonaSpain

Olfactory receptors are crucial for detecting odors and play a vital role in our sense of smell,influencing behaviors from food choices to emotional *** receptors also contribute to our perception of flavor and have potential applications in medical diagnostics and environmental *** ability of the olfactory system to regenerate its sensory neurons provides a unique model to study neural regeneration,a phenomenon largely absent in the central nervous *** gained from how olfactory neurons continuously replace themselves and reestablish functional connections can provide strategies to promote similar regenerative processes in the central nervous system,where damage often results in permanent *** the molecular and cellular mechanisms underpinning olfactory neuron regeneration could pave the way for developing therapeutic approaches to treat spinal co rd injuries and neurodegenerative diseases like Alzheimer's *** ctory receptors are found in almost any cell of eve ry orga n/tissue of the mammalian *** ectopic expression provides insights into the chemical structures that can activate olfactory *** addition to odors,olfactory receptors in ectopic expression may respond to endogenous compounds and molecules produced by mucosal colonizing *** analysis of the function of olfactory receptors in ectopic expression provides valuable information on the signaling pathway engaged upon receptor activation and the receptor's role in proliferation and cell differentiation *** review explo res the ectopic expression of olfa ctory receptors and the role they may play in neural regeneration within the central nervous system,with particular attention to compounds that can activate these receptors to initiate regenerative *** suggests that olfactory receptors could serve as potential therapeutic targets for enhancing neural repair and recovery following central nervous syste

关键词： adenosine receptors adrenergic receptors ectopic expression G proteincoupled receptors glia neurons

molecular dynamics simulation of quartz deformation under slow earthquake background

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Science China Earth Sciences 2025年

作者： Jingxian SUN Qianqian GUO Quanlin HOU College of Earth and Planetary Sciences University of Chinese Academy of Sciences Key laboratory of computational Geodynamics CAS

Slow earthquakes are the primary mechanism of slow energy release, and research on the focal mechanism has been inconclusive. Studies have primarily focused on the friction law based on physical mechanisms and have suggested that slow earthquakes are caused by brittle faults. However, the focal strength and structural characteristics of slow earthquakes in subduction zones provide evidence of plastic deformation. What is the role of plastic deformation in the focal mechanisms of slow earthquakes? Mechanochemical study have shown that mechanical forces can directly affect chemical bonds. In this study,we examine the storage and release of chemical energy during plastic deformation and consider a mechanochemical process in the focal mechanism of slow earthquakes. Combined with the Tersoff potential, molecular dynamics simulation on the shear deformation process of two α-quartz crystals show that the shear modulus of α-quartz is 18 GPa, and that the crystal model primarily exhibits atoms flowing and changing in the direction of chemical bonds during the steady-state flow stage. The molecular potential energy and stress vary in an oscillating up-and-down curve during shear, indicating that chemical energy can be stored and released during plastic deformation. This is consistent with the energy variation during slow earthquakes. Under the initial simple-shear loading condition, α-quartz crystals undergo general shear deformation instead of plane strain and the angle between the longest instantaneous stretching axis （ISA1） and the shearing direction is approximately 30°, not 45°. Both the deformation type and direction of ISA1are contrary to basic deformation theory, which may provide clues for future *** study reveals the process of quartz elastic-plastic shear deformation on an atomic scale. This information is useful for understanding focal mechanisms of slow earthquakes. This study is part of a series of investigations on tectonic stress chemistry.

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Deciphering fungal metabolon coupling tandem inverse-electrondemand Diels-Alder reaction and semipinacol rearrangement for the biosynthesis of spiro polycyclic alkaloids

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Science China Chemistry 2025年第1期68卷 288-296页

作者： Shuai Liu Wen-Qiang Xu Ying-Tong Di Man-Cheng Tang Ding-Kang Chen Ming-Ming Cao Yao-Wen Chang Hong-Yu Tang Chun-Mao Yuan Jun-Bo Yang Zhi-Li Zuo Han Guo Zi-Fei Xu Ying Zeng Yun-Dong Wu Xiao-Jiang Hao Key laboratory of Phytochemistry and Natural Medicines (Chinese Academy of Sciences) Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences Lab of computational Chemistry and Drug Design State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen Bay laboratory State Key laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University State Key laboratory of Functions and Applications of Medicinal Plants Guizhou Medical University molecular Biology Experimental Center Germplasm Bank of Wild Species in Southwest China Kunming Institute of Botany Chinese Academy of Sciences Yunnan Key laboratory for Wild Plant Resources Kunming Institute of Botany Chinese Academy of Sciences Research Unit of Chemical Biology of Natural Anti-Virus Products Chinese Academy of Medical Sciences

In the intricate process of natural product biosynthesis, a metabolon can enhance metabolic flux by associating sequential enzymes. A fungal metabolon, comprising of flavin-dependent monooxygenase Spe F and P450 monooxygenase Spe G, is identified in the biosynthesis of spiro polycyclic alkaloids(+)-notoamide B and its diastereomer(+)-versicolamide B. Using notoamide E as a substance, Spe F/Spe G metabolon can control the stereoselectivity of its 2,3-epoxidation, followed by hydrogen atom ion at C-17 to generate reactive epoxide tau-m A with dienyl iminium unit. Subsequently,(+)-notoamide B and(+)-versicolamide B are produced via tandem nonenzymatic inverse-electron-demand Diels-Alder reaction and semipinacol rearrangement. This provides the first example of metabolon in the biosynthesis of spiro-prenylated indole alkaloids.

关键词： metabolon Diels-Alder reaction semipinacol rearrangement biosynthesis notoamides spiro polycyclic alkaloids

Epigenetics in the modern era of crop improvements

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Science China Life Sciences 2025年

作者： Yan Xue Xiaofeng Cao Xiangsong Chen Xian Deng Xingwang Deng Yong Ding Aiwu Dong Chengguo Duan Xiaofeng Fang Lei Gong Zhizhong Gong Xiaofeng Gu Chongsheng He Hang He Shengbo He Xinjian He Yan He Yuehui He Guifang Jia Danhua Jiang Jianjun Jiang Jinsheng Lai Zhaobo Lang Chenlong Li Qing Li Xingwang Li Bao Liu Bing Liu Xiao Luo Yijun Qi Weiqiang Qian Guodong Ren Qingxin Song Xianwei Song Zhixi Tian Jiawei Wang Yuan Wang Liang Wu Zhe Wu Rui Xia Jun Xiao Lin Xu Zhengyi Xu Wenhao Yan Hongchun Yang Jixian Zhai Yijing Zhang Yusheng Zhao Xuehua Zhong Daoxiu Zhou Ming Zhou Yue Zhou Bo Zhu Jiankang Zhu Qikun Liu College of Life Sciences Institute of Life Science and Green Development Hebei University Biotechnology Research Institute Chinese Academy of Agricultural Sciences College of Biology Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan Engineering and Technology Research Center of Hybrid Rapeseed Hunan University Institute of Advanced Agricultural Sciences School of Advanced Agricultural Sciences Peking University State Key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural University National Institute of Biological Sciences Key laboratory of Seed Innovation Institute of Genetics and Developmental Biology Chinese Academy of Sciences School of Advanced Agricultural Sciences Peking-Tsinghua Center for Life Sciences Peking University Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University Key laboratory of Seed Innovation State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences State Key laboratory of Wheat Improvement Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in Weifang State Key laboratory of Crop Stress Adaptation and Improvement School of Life Sciences Henan University State Key laboratory of Maize Bio-breeding National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University Frontiers Science Center for molecular Design Breeding China Agricultural University Center for Crop Functional genomics and molecular Breeding China Agricultural University Sanya Institute of China Agricultural University Hainan Yazhou Bay Seed laboratory Institute of Advan

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades,our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

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Toward understanding the role of genomic repeat elements in neurodegenerative diseases

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Neural Regeneration Research 2025年第3期20卷 646-659页

作者： Zhengyu An Aidi Jiang Jingqi Chen Institute of Science and Technology for Brain-Inspired Intelligence Fudan UniversityShanghaiChina MOE Frontiers Center for Brain Science Fudan UniversityShanghaiChina MOE Key laboratory of computational Neuroscience and Brain-Inspired Intelligence Fudan UniversityShanghaiChina Zhangjiang Fudan International Innovation Center ShanghaiChina

Neurodegenerative diseases cause great medical and economic burdens for both patients and society;however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.

关键词： Alzheimer's disease ataxia deep learning long-read sequencing neurodegeneration neurodegenerative diseases Parkinson's disease repeat element structural variant

New Generations: Sequencing Machines and Their computational Challenges

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Journal of Computer Science & Technology 2010年第1期25卷 3-9页

作者： David C. Schwartz Michael S. Waterman laboratory for molecular and computational genomics Departme4nt of Chemistry and Laboratory of Genetics University of Wisconsin-Madison Department of Biological Sciences University of Southern California Department of Automation Tsinghua University

New generation sequencing systems are changing how molecular biology is practiced. The widely promoted $1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations will be commonplace. What is less appreciated is the explosive demands on computation, both for CPU cycles and storage as well as the need for new computational methods. In this article we will survey some of these developments and demands.

关键词： genome sequencing new generation sequencing read mapping optical mapping sequence assembly Eulerian graphs

Big picture of relativistic molecular quantum mechanics

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National Science Review 2016年第2期3卷 204-221页

作者： Wenjian Liu Beijing National laboratory for molecular Sciences Institute of Theoretical and Computational ChemistryState Key Laboratory of Rare Earth Materials Chemistry and ApplicationsCollege of Chemistry and Molecular Engineeringand Center for Computational Science and EngineeringPeking University

Any quantum mechanical calculation on electronic structure ought to choose first an appropriate Hamiltonian H and then an Ansatz for parameterizing the wave function Ψ,from which the desired energy/property E(X) can finally be ***,the very first question is:what is the most accurate many-electron Hamiltonian H? It is shown that such a Hamiltonian *** quantum electrodynamics(eQED) Hamiltonian,can be obtained naturally by incorporating properly the charge conjugation symmetry when normal ordering the second quantized fermion *** this eQED Hamiltonian as the basis,various approximate relativistic many-electron Hamiltonians can be obtained based entirely on physical *** these Hamiltonians together form a complete and continuous’ Hamiltonian ladder’,from which one can pick up the right one according to the target physics and *** for the many-electron wave function Ψ,the most intriguing questions are as follows,(i) How to do relativistic explicit correlation?(ⅱ) How to handle strong correlation? Both general principles and practical strategies are outlined here to handle these *** the electronic properties E(λ) that sample the electronic wave function nearby the nuclear region,nuclear magnetic resonance(NMR)shielding and nuclear spin-rotation(NSR) coupling constant are especially challenging:they require body-fixed molecular Hamiltonians that treat both the electrons and nuclei as relativistic quantum ***,they have been formulated *** particular,a very robust ’relativistic mapping’between the two properties has been established,which can translate experimentally measured NSR coupling constants to very accurate absolute NMR shielding scales that otherwise cannot be obtained *** the most general and fundamental issues pertinent to all the three components of the quantum mechanical equation HΨ = EΨ(*** H,wave function Ψ,and energy/property E(λ)) have f

关键词： relativistic quantum mechanics quantum electrodynamics relativistic Hamiltonian electron correlation magnetic property

Host-induced gene silencing of multiple pathogenic factors of Sclerotinia sclerotiorum confers resistance to Sclerotinia rot in Brassica napus

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The Crop Journal 2022年第3期10卷 661-671页

作者： Jian Wu Shengliang Yin Li Lin Dongxiao Liu Sichao Ren Wenjing Zhang Wencheng Meng Peipei Chen Qinfu Sun Yujie Fang Cunxu Wei Youping Wang Key laboratory of Plant Functional genomics of the Ministry of Education Yangzhou UniversityYangzhouChina Jiangsu Key laboratory of Crop genomics and molecular Breeding Yangzhou UniversityYangzhouChina

Sclerotinia sclerotiorum is generally considered one of the most economically damaging pathogens in oilseed rape(Brassica napus).Breeding for Sclerotinia resistance is challenging,as no immune germplasm available in *** is desirable to develop new breeding *** the present study,hostinduced gene silencing(HIGS),developed based on RNA interference(RNAi),was applied to protect *** from *** *** pathogenicity genes,the endo-polygalacturonase gene(Ss PG1),cellobiohydrolase gene(Ss CBH),and oxaloacetate acetylhydrolase gene(Ss OAH1),were chosen as HIGS ***-incubation of synthesized double-stranded RNAs(ds RNAs)with *** in liquid medium significantly reduced the transcript levels of the target *** to plant surfaces of ds RNA targeting the three genes conferred effective protection against *** transgenic *** plants expressing small interfering RNAs with sequence identity to Ss PG1,Ss CBH,and Ss OAH1 were *** transgenic *** prevented the expression of *** target genes,slowed pathogenicity-factor accumulation,impeded fungal growth,and suppressed appressorium formation,thereby conferring resistance to *** silencing of Ss PG1,Ss CBH,and Ss OAH1 by stable expression of a chimeric hairpin RNAi construct in *** led to enhanced protection phenotypes(with disease lesion size reduced by 36.8%–43.7%).We conclude that HIGS of pathogenic-factor genes of *** is a promising strategy for controlling Sclerotinia rot in oilseed rape.

关键词： Sclerotinia sclerotiorum Brassica napus SIGS HIGS RNAi

Dissociations of O_2 molecules on ultrathin Pb(111) films:first-principles plane wave calculations

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Chinese Physics B 2012年第1期21卷 380-388页

作者： Hu Zi-Yu Yang Yu Sun Bo Zhang Ping Wang Wen-Chuan Shao Xiao-Hong laboratory of molecular and Materials Simulation Key Laboratory for Nanomaterials of Ministry of EducationBeijing University of Chemical TechnologyBeijing 100029China laboratory of computational Physics Institute of Applied Physics and Computational MathematicsBeijing 100088China

Using first-principles calculations, we systematically study the dissociations of 02 molecules on different ultrathin Pb（lll） films. According to our previous work revealing the molecular adsorption precursor states for O2, we further explore why there are two nearly degenerate adsorption states on Pb（lll） ultrathin films, but no precursor adsorption states existing at all on Mg（0001） and Al（lll） surfaces. The reason is concluded to be the different surface electronic structures. For the O2 dissociation, we consider both the reaction channels from gas-like and molecularly adsorbed O2 molecules. We find that the energy barrier for O2 dissociation from the molecular adsorption precursor states is always smaller than that from O2 gas. The most energetically favorable dissociation process is found to be the same on different Pb（lll） fihns, and the energy barriers are found to be influenced by the quantum size effects of Pb（lll） films.

关键词： first-principles calculation dissociation Pb(lll) quantum size effects