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Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

mLife 2024年第2期3卷 277-290页

作者： Pan Zhang Biliang Zhang Yuan-Yuan Ji Jian Jiao Ziding Zhang Chang-Fu Tian State key laboratory of Plant Environmental Resilience and College of Biological SciencesChina Agricultural UniversityBeijingChina MOA key laboratory of Soil Microbiology and Rhizobium Research CenterChina Agricultural UniversityBeijingChina Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina State key laboratory of Livestock and Poultry Biotechnology Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function,while accessory genes are dispensable,particularly in nutrient-rich ***,this assumption is seldom tested genetically within the pangenome *** this study,we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open *** evaluate the robustness of fitness category assignment,Tn-seq data for three independent mutant libraries per strain were analyzed by three methods,which indicates that the Hidden Markov Model(HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size,outperforming the Bayesian and Monte Carlo simulation-based ***,the HMM method was used to classify the fitness *** genes,categorized as essential(ES),advantage(GA),and disadvantage(GD)genes for growth,are enriched in core genes,while nonessential genes(NE)are over-represented in accessory *** ES/GA genes showed a lower fitness effect than core ES/GA *** degrees in the cofitness network decrease in the order of ES,GD,and GA/*** addition to accessory genes,1599 out of 3284 core genes display differential essentiality across test *** the pangenome core,both shared quasi-essential(ES and GA)and strain-dependent fitness genes are enriched in similar functional *** analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.

关键词： cofitnessnetwork pangenome Tn-seq

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Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice

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Journal of Genetics and Genomics 2024年第6期51卷 583-593页

作者： Chaolong Wang Xiaowen Yu Jian Wang Zhigang Zhao Jianmin Wan State key laboratory for Crop Genetics&Germplasm Enhancement and Utlization Nanjing Agricultural UniversityZhongshan Biological Breeding LaboratoryNanjingJiangsu210095China State key laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Heterosis,also known as hybrid vigor,is commonly observed in rice *** hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive ***,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific *** review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this ***,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive ***,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in *** on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.

关键词： Hybrid vigor Reproductive isolation Hybrid ricebreeding

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Brain circuits for retching-like behavior

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National Science Review 2024年第1期11卷 145-160页

作者： Lifang Huo Zhimin Ye Meiling Liu Ziqing He Meizhu Huang Dapeng Li Qian Wu Qian Wang Xiaoqun Wang Peng Cao Ji Dong Congping Shang School of Basic Medical Sciences Guangzhou National Laboratory The Fifth Afflliated Hospital Guangzhou Medical University Bioland laboratory (Guangzhou Regenerative Medicine and Health Guangdong laboratory) Department of Neurobiology School of Basic Medical Sciences Beijing Key Laboratory of Neural Regeneration and Repair Advanced Innovation Center for Human Brain Protection Capital Medical University State key laboratory of Cognitive Neuroscience and Learning IDG/McGovern Institute for Brain Research Beijing Normal University Changping Life Science laboratory National Institute of biological Sciences

Nausea and vomiting are important defensive responses to cope with pathogens and toxins that invade the body. The nucleus of the solitary tract(NTS) is important for initiating these responses. However, the molecular heterogeneities and cellular diversities of the NTS occlude a better understanding of these defensive responses. Here, we constructed the single-nucleus transcriptomic atlas of NTS cells and found multiple populations of NTS neurons that may be involved in these defensive responses. Among these, we identified Calbindin1-positive(Calb1+) NTS neurons that are molecularly distinct from Tac1+*** Calb1+neurons are critical for nausea and retching induced by cereulide; an emetic toxin secreted by Bacillus Cereus. Strikingly, we found that cereulide can directly modulate vagal sensory neurons that innervate Calb1+NTS neurons, a novel mechanism distinct from that for nausea and retching induced by Staphylococcal enterotoxin A. Together, our transcriptomic atlas of NTS neurons and the functional analyses revealed the neural mechanism for cereulide-induced retching-like behavior. These results demonstrate the molecular and cellular complexities in the brain that underlie defensive responses to the diversities of pathogens and toxins.

关键词： vomiting nausea nucleus of the solitary tract Calbindin1 neural circuits

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Chemico-biological conversion of carbon dioxide

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Journal of Energy Chemistry 2024年第2期89卷 371-387,I0009页

作者： Liangwei Hu Junzhu Yang Qi Xia Jin Zhang Hongxin Zhao Yuan Lu Zhejiang Province key laboratory of Plant Secondary Metabolism and Regulation College of Life Sciences and MedicineZhejiang Sci-Tech UniversityHangzhou 310018ZhejiangChina key laboratory of Industrial Biocatalysis Ministry of EducationTsinghua UniversityBeijing 100084China Department of Chemical Engineering Tsinghua UniversityBeijing 100084China College of biological and Chemical Engineering Jiaxing UniversityJiaxing 314000ZhejiangChina

The unabated carbon dioxide(CO_(2))emission into the atmosphere has exacerbated global climate change,resulting in extreme weather events,biodiversity loss,and an intensified greenhouse *** address these challenges and work toward carbon(C)neutrality and reduced CO_(2)emissions,the capture and utilization of CO_(2)have become imperative in both scientific research and *** cutting-edge approach to achieving efficient catalytic performance involves integrating green bioconversion and chemical *** innovative strategy offers several advantages,including environmental friendliness,high efficiency,and *** study provides a comprehensive review of existing technical routes for carbon sequestration(CS)and introduces two novel CS pathways:the electrochemicalbiological hybrid and artificial photosynthesis *** also thoroughly examines the synthesis of valuable Cnproducts from the two CS systems employing different catalysts and *** both systems heavily rely on electron transfer,direct and mediated electron transfer has been discussed and summarized in ***,this study explores the conditions suitable for different catalysts and assesses the strengths and weaknesses of *** also explored the biocompatibility of the electrode materials and developed novel *** materials were specifically engineered to combine with enzymes or microbial cells to solve the biocompatibility problem,while improving the electron transfer efficiency of ***,this review summarizes the relevant systems developed in recent years for manufacturing different products,along with their respective production efficiencies,providing a solid database for development in this *** novel chemical-biological combination proposed herein holds great promise for the future conversion of CO_(2)into advanced organic ***,it offers exciting prospects for utilizing CO_(2)in synthesizing

关键词： Carbon dioxide Bioelectric synthesis Artificial photosynthesis Synthetic product

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Designing salt stress-resilient crops:Current progress and future challenges

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Journal of Integrative Plant Biology 2024年第3期66卷 303-329页

作者： Xiaoyan Liang Jianfang Li Yongqing Yang Caifu Jiang Yan Guo State key laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100094China State key laboratory of Nutrient Use and Management College of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100194China Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100094China Frontiers Science Center for Molecular Design Breeding China Agricultural UniversityBeijing 100193China

Excess soil salinity affects large regions of land and is a major hindrance to crop production ***,understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical *** recent decades,studies have characterized hundreds of genes associated with plant responses to salt stress in different plant *** studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant *** review summarizes our current knowledge of plant salt tolerance,emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance,salt-ion transport and compartmentalization,oxidative stress tolerance,alkaline stress tolerance,and the trade-off between growth and salt *** also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient *** focus on the model plant Arabidopsis(Arabidopsis thaliana)and the four most-studied crops:rice(Oryza sativa),wheat(Triticum aestivum),maize(Zea mays),and soybean(Glycine max).

关键词： molecular design breeding salt stress-resilient crop salt tolerance

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Unveiling the distinctive traits of functional rye centromeres:minisatellites,retrotransposons,and R-loop formation

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Science China(Life Sciences) 2024年第9期67卷 1989-2002页

作者： Chang Liu Shulan Fu Congyang Yi Yang Liu Yuhong Huang Xianrui Guo Kaibiao Zhang Qian Liu James A.Birchler Fangpu Han State key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China key laboratory for Plant Genetics and Breeding Sichuan Agricultural UniversityChengdu 611130China Division of biological Science University of MissouriColumbia 65211-7400USA

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle *** their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across *** functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains *** this study,we comprehensively characterized the sequence composition and organization of rye *** findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed *** systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 *** minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in ***,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in ***,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere *** work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye *** knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.

关键词： centromere LTR-RTs minisatellite rye R-loop

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Cesium removal from radioactive wastewater by adsorption and membrane technology

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Frontiers of Environmental Science & Engineering 2024年第3期18卷 161-175页

作者： Shuting Zhuang Jianlong Wang School of Environment&Natural Resources Renmin University of ChinaBeijing 100872China laboratory of Environmental Technology INETTsinghua UniversityBeijing 100084China beijing key laboratory of Radioactive Waste Treatment INETTsinghua UniversityBeijing 100084China

Radiocesium is frequently present in radioactive wastewater,while its removal is still a challenge due to its small hydrated radius,high diffusion coefficient,and similar chemical behavior to other alkali metal elements with high background *** review summarized and analyzed the recent advances in the removal of Cs+from aqueous solutions,with a particular focus on adsorption and membrane separation *** inorganic,organic,and biological adsorbents have undergone assessments to determine their efficacy in the removal of cesium ***,membrane-based separation techniques,including reverse osmosis,forward osmosis,and membrane distillation,have also shown promise in effectively separating cesium ions from radioactive ***,this review summarized the main approaches,including Kurion/SARRY system+desalination system and advanced liquid processing system,implemented after the Fukushima Daiichi nuclear power plant accident in Japan to remove radionuclides from contaminated *** technology and membrane separation technology play a vital role in treatment of contaminated water.

关键词： Cesium Adsorption Membrane separation Advanced liquid processing system Fukushima nuclear accident

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Universal synthesis of metallophthalocyanine covalent organic frameworks as ultra-sensitive multifaceted electrochemical sensor

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Science China Chemistry 2024年第6期67卷 2092-2101页

作者： Qi Liu Qiqi Sun Yuming Zhang Hao Li Wenmiao Chen Yuexing Zhang Sirong Yu Yanli Chen Jianzhuang Jiang School of Materials Science and Engineering China University of Petroleum(East China)Qingdao266580China beijing key laboratory for Science and Application of Functional Molecular and Crystalline Materials School of Chemistry and Biological EngineeringUniversity of Science and Technology BeijingBeijing100083China College of Chemistry and Chemical Engineering Dezhou UniversityDezhou253023China

The universal synthesis of highly stable covalent organic frameworks(COFs)for ultra-sensitive and multi-component electrochemical detection in different scenarios remains a great ***,a series of metallophthalocyanine-based twodimensional(2D)dioxin(DXI)-linked metalophthalocyanine(MPc)-n DXI-COFs(M=Ni,Zn;n=1,2)are afforded in high yield(80%-96%)by a facile trace-quinoline assisted one-pot condensation of tetracarbonitrile *** X-ray diffraction and electron microscopy investigations disclose their lamellar texture 2D network with AA stacking *** and calculation results elucidate that the 2DXI-linked MPc-2DXI-COFs provide the stronger built-in electronic field and more electrostatic/hydrogen bonding adsorption sites than DXI-linked MPc-DXI-COFs,and the lower electrode reaction Gibbs free energy and stronger adsorption of analytes at Ni Pc than Zn Pc unit,which grants Ni Pc-2DXI-COF excellent sensing properties for various analytes including neurotransmitters,organic pollutants,and heavy metal ions,with high sensitivity and low detection limit of 0.53 to 25.66 *** in binary and ternary systems and even in real-world conditions,simultaneous multi-component detection could be achieved.

关键词： covalent organic framework metallophthalocyanine 2D materials electrochemical sensors multi-component detection

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Single-cell characterization of major components of plant cell walls in situ by Raman spectroscopy

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Science China(Life Sciences) 2024年第8期67卷 1772-1774页

作者： Yujian Li Weiwei Shen Xi Zhang Yaning Cui Yuanyuan Zhao Yayu Guo Xiaojuan Li Shuizhong Wang Guoyong Song Pu Wang Jianfeng Ma Jinxing Lin State key laboratory of Efficient Production of Forest Resources College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Institute of Tree Development and Genome Editing Beijing Forestry UniversityBeijing 100083China National Engineering Research Center of Tree Breeding and Ecological Restoration College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China beijing key laboratory of Lignocellulosic Chemistry Engineering Research Center of Forestry Biomass Materials and EnergyMinistry of EducationBeijing Forestry UniversityBeijing 100083China beijing Advanced Innovation Center for Biomedical Engineering School of Biological Science and Medical EngineeringBeihang UniversityBeijing 100191China key lab of Bamboo and Rattan Science&Technology International Center for Bamboo and RattanBeijing 100102China

Dear Editor,Plant cell walls are complex and dynamic structures that are mainly composed of polysaccharide polymers such as cellulose,hemicellulose,and pectin,in addition to substantial amounts of the non-saccharide polymer lignin(McFarlane et al.,2014;German et al.,2023).The components of cell walls are interconnected in various ways to form a complex,multilayered network structure(Wen et al.,2023).

关键词： walls cellulose characterization

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Graphdiyne oxide substrate-enhanced peroxidase-mimicking performance of Ru nanoparticles with physiological pH preference

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Nano Research 2024年第3期17卷 1123-1131页

作者： Cong Xu Wenjie Ma Haozhi Wang Leihou Shao Weiqi Li Ping Yu Lanqun Mao beijing National laboratory for Molecular Science Key Laboratory of Analytical Chemistry for Living BiosystemsInstitute of ChemistryChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China State key laboratory of Marine Resource Utilization in South China Sea School of Materials Science and EngineeringHainan UniversityHaikou 570228China College of Chemistry Beijing Normal UniversityBeijing 100875China

Modulating electronic structure of metal nanoparticles via metal–support interaction has attracted intense interest in the field of catalytic ***,the roles of supporting substrates in regulating catalytic properties of nanozymes remain *** this study,we find that the use of graphdiyne oxide(GDYO)as the substrate for self-terminating growth of Ru nanoparticles(Ru@GDYO)endows the peroxidase-like activity of Ru nanoparticles with intrinsic physiological pH preference and natural horseradish peroxidase(HRP)comparable *** nanoparticles electrolessly deposited onto GDYO possess a partially oxidized electronic structure owing to limited charge transfer between Ru and GDYO,contributing to the intrinsic physiological pH preference of the peroxidase-mimicking *** importantly,the substrate GDYO plays an influential factor in enhancing catalytic activity,that is,the activity of Ru@GDYO is much higher than that of Ru nanoparticles deposited on other carbon substrates including graphene oxides and *** demonstrate the application of Ru@GDYO nanozyme in neutral solutions,we employ Ru@GDYO with nicotinamide adenine dinucleotide(NAD+)-dependent dehydrogenases in physiological conditions to realize a sustainable cascade reaction by means of forming continuous NAD^(+)/dihydronicotiamide adenine dinucleotide(NADH)*** finding represents a promising perspective on designing high-performance peroxidase-mimicking nanozymes with broader applicability,raising fundamental understanding of structure–activity relationship,and investigating new applications of nanozymes in biological systems.

关键词： nanozyme graphdiyne reactive oxygen species electroless deposition metal–support interaction

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