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Developing a novel quantitative parameter for characterizing spatial distribution of fish following exposure to chemicals and wastewater:Behavioral Gini coefficient

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Journal of Environmental sciences 2024年第7期141卷 129-138页

作者： Xuanyue Chen Yuanyuan Li Zhanfen Qin State Key Laboratory of Environmental Chemistry and Ecotoxicology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of sciences Beijing 100049China

While the spatial distribution pattern of fish is increasingly used for toxicological test o chemicals or wastewater,no ideal parameter is available for quantitative assessment of spa tial distribution,especially uneven distribution with multiple ***,to develop a quantitative assessment parameter for spatial distribution,the zebrafish were exposed to ethanol,pentylenetetrazole(PTZ),paraquat dichloride(paraquat)and wastewater,followed by a behavioral test in a narrow *** data was acquired and analyzed by id Tracker and *** comparing the effects of all treatments on behavior parameters we confirmed that the spatial distribution was more easily altered rather than general loco motor parameters,e.g.0.7-70 mg/L PTZ and 5-20 mg/L paraquat being effective for altering spatial distribution but having little effects on general locomotor *** on the heatmap,i.e.,the cumulative proportion of grids and that of frequency in grids,we calcu lated the behavioral Gini coefficient(G_(b))for quantitative assessment of fish spatial distri *** Gini coefficient ranged from zero to 1,with larger values meaning poorer even ness of spatial *** note,G_(b)showed smaller coefficient of variations(CV)with3%-19%between replicate tanks in all treatments than the highest frequency(4%-79%),dis playing well ***,G_(b)addressed the challenge of the complicated heatmap with multiple ***,the behavioral Gini coefficient we established is an idea parameter to quantitatively assess spatial distribution of fish shoal,which is expected to be applied in toxicity testing for chemicals and wastewater and automatic quality monitoring for surface water and aquaculture water.

关键词： Zebrafish Behavioral test Spatial distribution Behavioral Gini coefficient

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How plants sense and respond to osmotic stress

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Journal of Integrative Plant Biology 2024年第3期66卷 394-423页

作者： Bo Yu Dai-Yin Chao Yang Zhao Shanghai center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesThe Chinese Academy of SciencesShanghai 200032China Key Laboratory of Plant Carbon Capture The Chinese Academy of SciencesShanghai 200032China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyThe Chinese Academy of SciencesShanghai 200032China University of Chinese Academy of sciences Beijing 100049China

Drought is one of the most serious abiotic stresses to land *** sense and respond to drought stress to survive under water *** have studied how plants sense drought stress,or osmotic stress caused by drought,ever since Charles Darwin,and gradually obtained clues about osmotic stress sensing and signaling in *** stress is a physical stimulus that triggers many physiological changes at the cellular level,including changes in turgor,cell wall stiffness and integrity,membrane tension,and cell fluid volume,and plants may sense some of these stimuli and trigger downstream *** this review,we emphasized water potential and movements in organisms,compared putative signal inputs in cell wall-containing and cell wall-free organisms,prospected how plants sense changes in turgor,membrane tension,and cell fluid volume under osmotic stress according to advances in plants,animals,yeasts,and bacteria,summarized multilevel biochemical and physiological signal outputs,such as plasma membrane nanodomain formation,membrane water permeability,root hydrotropism,root halotropism,Casparian strip and suberin lamellae,and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple *** also discussed the core scientific questions,provided perspective about the future directions in this field,and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

关键词： cell volume drought membrane tension osmotic stress turgor

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MAVS Antagonizes Human Stem Cell Senescence as a Mitochondrial Stabilizer

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Research 2024年第2期2023卷 239-257页

作者： Cui Wang Kuan Yang Xiaoqian Liu Si Wang Moshi Song Juan Carlos Izpisua Belimonte Jing Qu Guang-Hui Liu Weiqi Zhang CAS Key Laboratory of Genomic and Precision Medicine Beijng Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of sciences Beijing 100049China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China State Key Laboratory of Stem Cell and reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Institute for Stem Cell and Regeneration Chinese Academy of sciences Beijing 100101China Beijing Institute for Stem Cell and Regenerative Medicine Bejing 100101China Advanced Innovation center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Altos Labs Inc.San DiegoCA 94022USA

Mitochondrial dysfunction is a hallmark feature of cellular senescence and organ ***,we asked whether the mitochondrial antiviral signaling protein(MAVS),which is essential for driving antiviral response,also regulates human stem cell *** answer this question,we used CRISPR/Cas9-mediated gene editing and directed differentiation techniques to generate various MAVS-knockout human stem cell *** found that human mesenchymal stem cells(hMSCs)were sensitive to MAVS deficiency,as manifested by accelerated senescence *** uncovered that the role of MAVS in maintaining mitochondrial structural integrity and functional homeostasis depends on its interaction with the guanosine triphosphatase optic atrophy type 1(OPA1).Depletion of MAVS or OPA1 led to the dysfunction of mitochondria and cellular senescence,whereas replenishment of MAVS or OPA1 in MAVS-knockout hMSCs alleviated mitochondrial defects and premature senescence *** together,our data underscore an uncanonical role of MAVS in safeguarding mitochondrial homeostasis and antagonizing human stem cell senescence.

关键词： CRISPR/Cas9 homeostasis Mitochondrial

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Q-BioLiP:A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 151-159页

作者： Hong Wei Wenkai Wang Zhenling Peng Jianyi Yang School of Mathematical sciences Nankai UniversityTianjin 300071China MOE Frontiers Science center for Nonlinear Expectations Research Center for Mathematics and Interdisciplinary SciencesShandong UniversityQingdao 266237China

Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand ***,several known issues occurred with it over the past *** example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand *** major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex *** these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://***/Q-BioLiP/.

关键词： Protein-ligand interaction Quaternary structure Protein-ligand binding site Protein-protein interaction Binding affinity

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Suspended particulate matter promotes epithelial-to-mesenchymal transition in alveolar epithelial cells via TGF-β1-mediated ROS/IL-8/SMAD3 axis

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Journal of Environmental sciences 2024年第7期141卷 139-150页

作者： Shahrzad Molavinia Dian Dayer Mohammad Javad Khodayar Gholamreza Goudarzi Maryam Salehcheh Cellular and Molecular Research center Medical Basic Sciences Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran Department of Toxicology School of PharmacyAhvaz Jundishapur University of Medical SciencesAhvazIran Student Research Committee Ahvaz Jundishapur University of Medical SciencesAhvazIran Toxicology Research center Medical Basic Sciences Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran Air Pollution and Respiratory Diseases Research center Ahvaz Jundishapur University of Medical SciencesAhvazIran Iranian Scientific Association of Clean Air TehranIran

Epidemiological evidence presents that dust storms are related to respiratory diseases,such as pulmonary fibrosis(PF).However,the precise underlying mechanisms of SPM-elicited adverse effects still need to be ***-mesenchymal transition(EMT)process is a characteristic of *** discussed whether suspended particulate matter(SPM)is involved in EMT induction via transforming growth factor-β1(TGF-β1).In this study,a detailed elemental analysis(55 elements),particle size,and morphology were *** investigate the toxicity of SPM,an MTT test was performed to detect cell ***,A549cells were exposed to selected concentrations of SPM(20 and 40μg/mL)for single and repeated *** DCFH-DA assay showed that exposure to SPM could produce reactive oxygen species(ROS).The ELISA assay demonstrated increased levels of interleukin-8(IL-8)and TGF-β1 in the *** blot was used to detect the expression of proteins associated with EMT and the SMAD3-dependent *** of western blot demonstrated that E-cadherin was reduced,whereas p-SMAD3,vimentin,andα-smooth muscle actin were *** findings indicated that SPM triggered EMT by induction of oxidative stress,inflammation,and the TGF-β1/SMAD3 pathway activation.

关键词： Particulate matter TGF-β1 Oxidative stress Epithelial-mesenchymal transition Pulmonary fibrosis Cells

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Experimental constraints on the formation of oxychlorine species by UV irradiation and mechanical pulverization on the lunar surface

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Acta Geochimica 2024年第4期43卷 625-637页

作者： Jiamei Li Yu-Yan Sara Zhao He Cui Shuai-Yi Qu Yanhua Peng Yuhong Yang Xiongyao Li Research center for Planetary Science College of Earth and Planetary SciencesChengdu University of TechnologyChengdu 610059China center for Excellence in Comparative Planetology Chinese Academy of SciencesHefei 230026China College of Life sciences Wuchang University of TechnologyWuhan 430204China Technical center of Qingdao Customs Qingdao 266114China Institute of Geology and Geophysics Chinese Academy of SciencesBeijing 100029China University of Chinese Academy of sciences Beijing 100049China Nanning College of Technology Guilin 541006China center for Lunar and Planetary sciences Institute of GeochemistryChinese Academy of SciencesGuiyang 550081China

Perchlorate and chlorate are present in various extraterrestrial celestial bodies throughout the solar system,such as Mars,the moon,and *** date,the origin mechanisms of perchlorate and chlorate on the Martian surface have been well-established;however,relatively little attention has been cast to airless ***,we experimentally investigated the potential oxidation mechanisms of chloride to chlorate and perchlorate,such as ultraviolet irradiation under H_(2)O-and O_(2)-free conditions and mechanical pulverization *** minerals,olivine,pyroxene,ilmenite,magnetite,TiO_(2)and anhydrous ferric sulfate,and lunar regolith simulants(low Ti,CLRS-1;high-Ti,CLRS-2)and their metallic iron(Fe^( 0))bearing counterparts were *** found that pulverization of dry matrix material-halite mixtures,even in the presence of O_(2),does not necessarily lead to perchlorate and chlorate formation without involving *** photocatalytic and H_(2)O and O_(2)-free conditions,olivine and pyroxene can produce oxychlorine(ClO_(x)^(−))species,although the yields were orders of magnitude lower than those under Martian-relevant ***-Fe^(0)particles in the lunar regolith and the common photocatalyst TiO_(2)can facilitate the ClO_(x)^(−)formation,but their yields were lower than those with *** oxides ilmenite and magnetite did not efficiently contribute to ClO_(x)^(−)*** results highlight the critical role of H_(2)O in the oxidation chloride to chlorate and perchlorate,and provide essential insights into the environmental influence on the formation of oxychlorine species on different celestial bodies.

关键词： Perchlorate Chlorate Lunar regolith Metallic Fe Airless bodies

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Inhibition mechanisms of CRISPR-Cas9 by AcrⅡA25.1 and AcrⅡA32

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Science China(Life sciences) 2024年第9期67卷 1781-1791页

作者： Jianlin Zheng Yuwei Zhu Tengjin Huang Wenbo Gao Jiale He Zhiwei Huang HIT center for Life sciences School of Life Science and TechnologyHarbin Institute of TechnologyHarbin 150080China Westlake center for Genome Editing Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou 310024China

In the ongoing arms race between bacteria and bacteriophages,bacteriophages have evolved anti-CRISPR proteins to counteract bacterial CRISPR-Cas ***,AcrⅡA25.1 and AcrⅡA32 have been found to effectively inhibit the activity of Spy Cas9 both in bacterial and human ***,their molecular mechanisms remain ***,we report the cryo-electron microscopy structures of ternary complexes formed by AcrⅡA25.1 and AcrⅡA32 bound to Spy Cas9-sg *** structural analysis and biochemical experiments,we revealed that AcrⅡA25.1 and AcrⅡA32 recognize a novel,previously-unidentified anti-CRISPR binding site on Spy *** found that both AcrⅡA25.1 and AcrⅡA32 directly interact with the WED domain,where they spatially obstruct conformational changes of the WED and PI domains,thereby inhibiting Spy Cas9 from recognizing protospacer adjacent motif(PAM)and unwinding double-stranded *** addition,they may inhibit nuclease activity by blocking the dynamic conformational changes of the Spy Cas9 surveillance *** summary,our data elucidate the inhibition mechanisms of two new anti-CRISPR proteins,provide new strategies for the modulation of Spy Cas9 activity,and expand our understanding of the diversity of anti-CRISPR protein inhibition mechanisms.

关键词： anti-CRISPR cryo-EM Spy Cas9 AcrⅡA25.1 AcrⅡA32 inhibiton

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Male reproductive function before and after the adjustment of the COVID-19 prevention policy:a multicenter study in China

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Asian Journal of Andrology 2024年第3期26卷 308-314页

作者： Jian-Zheng Li Han Wu Li Wang Yun-Shan Wang Feng Kong Long-Qiao Cao Ming Liang Xiong Wang Ming-Zhen Yuan Shandong Provincial Hospital Affiliated to Shandong First Medical University Jinan 250000China Institute of Women Children and Reproductive HealthShandong UniversityJinan 250012China Engineering Laboratory of Urinary Organ and Functional Reconstruction of Shandong Province Jinan 250000China The First People’sHospital of Jining Jining 272000China Department of reproductive Medicine The Second Affiliated Hospital of Shandong University of Traditional Chinese MedicineJinan 250000China reproductive Medicine center Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantai 264000China

At the end of 2022,the adjustment of the coronavirus disease 2019(COVID-19)pandemic control policy in China resulted in alarge-scale increase in public *** compare the fertility parameters of male patients before and after the adjustments ofthe COVID-19 pandemic control policy in China,we collected data on patients’medical histories and laboratory examinations ontheir first visits between June 2022 and March 2023 in five different *** were divided into five groups according tothe timeline of the policy *** data we collected from male patients included semen quality and serum reproductivehormone levels,and intergroup comparisons were made using the Mann–Whitney U and Chi-square *** total,16784 casesunderwent regular semen analysis,11180 had sperm morphology assessments,and 7200 had reproductive hormone *** showed declining trends in semen volume,sperm motility,and the progressive sperm motility rate after the policy *** comparison revealed an initial decrease and gradual recovery in progressive motility *** morphology analysisshowed increased neck and tail abnormalities after the policy *** significant change in hormone levels was *** the adjustment of the COVID-19 prevention policy in China,a decline in sperm motility and morphology was *** trend may gradually recover over 2 *** the policy adjustment,reproductive hormone levels were relatively stablethroughout,except for an increase in luteinizing hormone(LH).These changes in semen parameters suggest that the policyadjustment had a short-to medium-term impact on male reproductive function.

关键词： COVID-19 multicenter study reproduction SARS-CoV-2 semen analysis

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Modern phenomics to empower holistic crop science, agronomy, and breeding research

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Journal of Genetics and Genomics 2024年第8期51卷 790-800页

作者： Ni Jiang Xin-Guang Zhu Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China center of Excellence for Molecular Plant sciences Chinese Academy of SciencesShanghai 200032China

Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional *** modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal *** multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop *** challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.

关键词： Crop phenomics High-throughput phenotyping Traits Crop designer breeding Agronomy

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Markovian Quadratic BSDEs with an Unbounded Sub-quadratic Growth

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Chinese Annals of Mathematics,Series B 2024年第3期45卷 441-462页

作者： Jingnan JU Shanjian TANG Shanghai center for Mathematical sciences Fudan UniversityShanghai 200433China Department of Finance and Control sciences School of Mathematical SciencesFudan UniversityShanghai 200433China

This paper is devoted to the solvability of Markovian quadratic backward stochastic differential equations(BSDEs for short)with bounded terminal *** generator is allowed to have an unbounded sub-quadratic growth in the second unknown variable *** existence and uniqueness results are given to these *** an application,an existence result is given to a system of coupled forward-backward stochastic differential equations with measurable coefficients.

关键词： Markovian BSDE Quadratic growth Unbounded sub-quadratic term coeficients Coupled FBSDE

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