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Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

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Plant Diversity 2024年第5期46卷 575-584页

作者： Yiqing Chen Lina Dong Huiqin Yi Catherine Kidner Ming Kang Key laboratory of national Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China Guangzhou 510650China University of Chinese Academy of Sciences Beijing 100049China Guangxi Key laboratory of Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of BotanyGuangxi Zhang Autonomous Region and the Chinese Academy of SciencesGuilin 541006China Institute of Molecular Plant Sciences University of EdinburghDaniel Rutherford Building Max Born CrescentThe King's BuildingsEdinburgh EH93BFUK Royal Botanic Garden Edinburgh 20a Inverleith RowEdinburgh EH35LRUK State Key laboratory of Plant Diversity and Specialty Crops South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China

Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and ***,these effects are rarely studied in limestone karst ***,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(***,***,*** and ***)and investigated genomic divergence and genetic load for these four *** analyses revealed four distinct clusters corresponding to each species within the ***,there was only limited admixture between *** and *** occurring in overlapping geographic *** species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate *** detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic *** found that isolated populations of *** have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious *** findings underscore the urgency to prioritize conservation efforts for these isolated *** study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of ***,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

关键词： Conservation genomics Karst landscape Demographic history Inbreeding Isolated populations Mutation load

Updated roles of the gut microbiota in exploring shrimp etiology, polymicrobial pathogens, and disease incidence

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Zoological Research 2024年第4期45卷 910-923页

作者： Jin-Bo Xiong Hao-Nan Sha Jiong Chen State Key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products School of Marine SciencesNingbo UniversityNingboZhejiang 315211China Key laboratory of Aquacultural Biotechnology Ministry of EducationSchool of Marine SciencesNingbo UniversityNingboZhejiang 315211China laboratory of Biochemistry and Molecular Biology School of Marine SciencesNingbo UniversityNingboZhejiang 315211China

Litopenaeus vannamei is the most extensively cultured shrimp species globally,recognized for its scale,production,and economic ***,its aquaculture is plagued by frequent disease outbreaks,resulting in rapid and massive *** research often lags behind the emergence of new diseases,leaving the causal agents of some shrimp diseases unidentified and leading to nomenclature based on symptomatic presentations,especially in cases involving co-and polymicrobial *** data on shrimp disease statuses remain *** this review,we summarize current knowledge on shrimp diseases and their effects on the gut ***,we also propose a workflow integrating primary colonizers,“driver”taxa in gut networks from healthy to diseased states,disease-discriminatory taxa,and virulence genes to identify potential polymicrobial *** examine both abiotic and biotic factors(e.g.,external and internal sources and specific-disease effects)that influence shrimp gut microbiota,with an emphasis on the“holobiome”concept and common features of gut microbiota response to diverse *** excluding the effects of confounding factors,we provide a diagnosis model for quantitatively predicting shrimp disease incidence using disease common-discriminatory taxa,irrespective of the causal *** to the conservation of functional genes used in designing specific primers,we propose a practical strategy applying qPCR-assayed abundances of disease common-discriminatory functional *** review updates the roles of the gut microbiota in exploring shrimp etiology,polymicrobial pathogens,and disease incidence,offering a refined perspective for advancing shrimp aquaculture health management.

关键词： Shrimp disease Gut microbiota Polymicrobial pathogens Diagnosis model Disease common-discriminatory taxa Disease prediction

Hot versus cold subduction initiation

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national Science Review 2024年第2期11卷 101-102页

作者： Zhong-Hai Li Key laboratory of Computational Geodynamics College of Earth and Planetary SciencesUniversity of Chinese Academy of Sciences

In the framework of plate tectonics, subduction initiation(SI) indicates the birth of a plate convergent boundary, which is a key point of plate tectonics and Wilson's cycle; however, its dynamic process is not well c... 详细信息

关键词： DRIVEN CRUST

Interactive effects of soils,local environmental conditions and herbivores on secondary chemicals in tallow tree

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Journal of Plant Ecology 2024年第4期17卷 167-180页

作者： Li Xiao Wei Huang Juli Carrillo Jianqing Ding Evan Siemann College of Life and Environmental Science Central South University of Forestry and TechnologyChangsha 410004China national Engineering laboratory of Applied Technology for Forestry&Ecology in Southern China Central South University of Forestry and TechnologyChangsha 410004China CAS Key laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074China Faculty of Land and Food Systems Centre for Sustainable Food SystemsBiodiversity Research CentreUniversity of British ColumbiaVancouver V6T 1Z4Canada State Key laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Biosciences Department Rice UniversityHoustonTX 77005USA

Plants produce secondary chemicals that may vary along with latitude due to changing abiotic and biotic stress gradients and local environmental *** apart the individual and combined effects of these different abiotic,such as soil nutrients,and biotic factors,such as soil biota and herbivores,on secondary chemicals is critical for understanding plant responses to changing *** conducted an experiment at different latitudes in China,using tallow tree(Triadica sebifera)seedlings sourced from a population at 31°*** seedlings were cultivated in gardens located at low,middle and high latitudes,with either local soil or soil from the original seed collection site(origin soil).The seedlings were exposed to natural levels of aboveground herbivores or had them *** secondary chemicals(both foliar and root),aboveground herbivores and soil characteristics were *** showed that most leaf and root secondary metabolites depended on the interaction of the experimental site and soil *** and root phenolic and tannin concentrations were higher at the middle latitude site,especially in the origin *** and foliar flavonoid concentrations increased when aboveground herbivores were *** communities depended strongly on soil *** different responses of tannins versus flavonoids suggest that these two chemical classes differ in their responses to the varying abiotic and biotic factors in these sites along *** together,our results emphasize the importance of considering the interactive effects of local environmental conditions,soil properties and herbivory in regulating plant chemical defenses.

关键词： phenolics tannins flavonoids abiotic factors soil characteristics Triadica sebifera

Investigating Sulfur Chemistry in the HD163296 Disk

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Research in Astronomy and Astrophysics 2024年第7期24卷 215-225页

作者： Rong Ma Donghui Quan Yan Zhou Jarken Esimbek Dalei Li Xiaohu Li Xia Zhang Juan Tuo Yanan Feng Xinjiang Astronomical Observatory Chinese Academy of SciencesUrumqi 830011China University of Chinese Academy of Sciences Beijing 100049China Research Center for Intelligent Computing Platforms Zhejiang LaboratoryHangzhou 311100China BinZhou University Binzhou 256600China Key laboratory of Radio Astronomy Chinese Academy of SciencesUrumqi 830011China Xinjiang Key laboratory of Radio Astrophysics Urumqi 830011China

Sulfur chemistry in the formation process of low-mass stars and planets remains poorly *** protoplanetary disks are the birthplace of planets and its distinctive environment provides an intriguing platform for investigating models of sulfur *** analyzed the Atacama Large Millimeter/submillimeter Array observations of CS 7-6 transitions in the HD 163296 disk and performed astrochemical modeling to explore its sulfur *** simulated the distribution of sulfur-containing molecules and compared it with observationally deduced fractional column *** have found that the simulated column density of CS is consistent with the observationally deduced fractional column densities,while the simulated column density of C_(2)S is lower than the observationally deduced upper limits on column *** results indicate that we have a good understanding of the chemical properties of CS and C_(2)S in the *** also investigated the influence of the C/O ratio on sulfur-containing molecules and found that the column densities of SO,SO_(2),and H_2S near the centra star are dependent on the C/O ***,we found that the N[CS]/N[SO]ratio can serve as a promising indicator of the disk’s C/O ratio in HD ***,the disk of HD 163296 provides a favorable environmen for the detection of sulfur-containing molecules.

关键词： Protoplanetary Disks-Astrochemistry-Molecular Processes

A novel low molecular weight compound polysaccharides from Chinese herbal medicines: purification， characterization and anti-tumor activities in vitro and in vivo

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Food Science and Human Wellness 2024年

作者： Xu Yang Dongli Cao Haiyu Ji Huijing Xu Mengjie Xu Anjun Liu Key laboratory of Food Nutrition and Safety， Ministry of Education， School of Food Science and Engineering， Tianjin University of Science and Technology national Center of Inspection and Testing for Processed Food Quality， Tianjin Institute for Food Safety Inspection Technology

A novel low molecular weight polysaccharide (LMW-CPS) was identified from a specific combination of Chinese herb ingredients. The monosaccharide composition of LMW-CPS was consisted of single arabinose， which had an α-L-furanose configuration with an average molecular weight of 2.06 kDa. NMR spectra and monosaccharide constitution analyses revealed that it had a backbone of →5)-α-L-Araf-(1→ with α-L-Araf-(1→ as the terminal residue. In vitro experiments found that it could lead to apoptosis and inhibit hepatocellular carcinoma cell proliferation by arresting them in the S phase. In vivo experiments showed that it protected immune organs such as the thymus and spleen， enhanced immune cell activities， stimulated cytokine release， augmented the abundance of CD8， CD3， CD4， and CD19 positive lymphocytes， and markedly impeded solid hepatocellular carcinoma progression in mice. H&E staining and cell cycle examination also indicated that LMW-CPS arrested hepatocellular carcinoma cells at the S phase to induce apoptosis. These findings indicated its promising potential for the treatment of hepatocellular carcinoma.

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Odorant receptor orthologues from moths display conserved responses to cis-jasmone

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Insect Science 2024年第4期31卷 1107-1120页

作者： Xiao-Qing Hou Zhongqiang Jia Dan-Dan Zhang Guirong Wang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureSynthetic Biology Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong ProvinceChina State Key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina Department of Biology Lund UniversityLundSweden

In insects,the odorant receptor(OR)multigene family evolves by the birth-and-death evolutionary model,according to which the OR repertoire of each species has undergone specific gene gains and losses depending on their chemical environment,resulting in taxon-specific OR lineage radiations with different sizes in the phylogenetic *** the general divergence in the gene family across different insect orders,the ORs in moths seem to be genetically conserved across species,clustered into 23 major clades containing multiple orthologous groups with single-copy gene from each *** hypothesized that ORs in these orthologous groups are tuned to ecologically important compounds and functionally ***-Jasmone is one of the compounds that not only primes the plant defense of neighboring receiver plants,but also functions as a behavior regulator to various *** test our hypothesis,using Xenopus oocyte recordings,we functionally assayed the orthologues of BmorOR56,which has been characterized as a specific receptor for *** results showed highly conserved response specificity of the BmorOR56 orthologues,with all receptors within this group exclusively responding to *** is supported by the dN/dS analysis,showing that strong purifying selection is acting on this ***,molecular docking showed that the ligand binding pockets of BmorOR56 orthologues to cis-jasmone are *** together,our results suggest the high conservation of OR for ecologically important compounds across Heterocera.

关键词： cis-jasmone evolutionary conservation functional characterization molec-ular docking moths purifying selection

Discrete Boltzmann model with split collision for nonequilibrium reactive flows

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Communications in Theoretical Physics 2024年第8期76卷 164-186页

作者： Chuandong Lin Kai H Luo Huilin Lai Sino-French Institute of Nuclear Engineering and Technology Sun Yat-sen UniversityZhuhai 519082China Key laboratory for Thermal Science and Power Engineering of Ministry of Education Department of Energy and Power EngineeringTsinghua UniversityBeijing 100084China Department of Mechanical Engineering National University of Singapore10 Kent Ridge Crescent119260Singapore Department of Mechanical Engineering University College LondonTorrington PlaceLondon WC1E 7JEUnited Kingdom School of Mathematics and Statistics Key Laboratory of Analytical Mathematics and Applications(Ministry of Education)Fujian Key Laboratory of Analytical Mathematics and Applications(FJKLAMA)Center for Applied Mathematics of Fujian Province(FJNU)Fujian Normal University350117 FuzhouChina

A multi-relaxation-time discrete Boltzmann model(DBM) with split collision is proposed for both subsonic and supersonic compressible reacting flows, where chemical reactions take place among various components. The physical model is based on a unified set of discrete Boltzmann equations that describes the evolution of each chemical species with adjustable acceleration, specific heat ratio, and Prandtl number. On the right-hand side of discrete Boltzmann equations, the collision,force, and reaction terms denote the change rates of distribution functions due to self-and crosscollisions, external forces, and chemical reactions, respectively. The source terms can be calculated in three ways, among which the matrix inversion method possesses the highest physical accuracy and computational efficiency. Through Chapman-Enskog analysis, it is proved that the DBM is consistent with the reactive Navier-Stokes equations, Fick's law and the Stefan-Maxwell diffusion equation in the hydrodynamic limit. Compared with the one-step-relaxation model, the split collision model offers a detailed and precise description of hydrodynamic, thermodynamic, and chemical nonequilibrium effects. Finally, the model is validated by six benchmarks, including multicomponent diffusion, mixture in the force field, Kelvin-Helmholtz instability, flame at constant pressure, opposing chemical reaction, and steady detonation.

关键词： discrete Boltzmann method reactive flow detonation nonequilibrium effect

Copper-catalyzed asymmetric dearomatizing amination of 2-naphthols:Csp^(2)–N coupling via 1,3-reductive elimination

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Science China Chemistry 2024年第8期67卷 2694-2700页

作者： Aying Yihuo Maoping Pu Zheng Tan Jibang Liao Jiuqi Tan Qi-Lin Zhou Xiaohua Liu Xiaoming Feng Key laboratory of Green Chemistry&Technology Ministry of EducationCollege of ChemistrySichuan UniversityChengdu 610064China Key laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Frontiers Science Centerfor New Organic MatterNankai UniversityTianjin300071China

An efficient catalytic asymmetric dearomatizing amination of 2-naphthols and phenols catalyzed by N,N′-dioxide-copper(I)complex as a chiral catalyst was presented.A variety of optically activeβ-naphthalenone compounds with a nitrogen-containing quaternary carbon stereocenter were obtained with high yield and enantioselectivity under mild reaction *** studies indicated that this Csp^(2)–N dearomatizing coupling proceeds via 1,3-reductive elimination of phenolate-Cu~Ⅲ-amino intermediate in five-membered ring transition *** origin of enantioselectivity has also been elucidated based on density functional theory calculations.

关键词： asymmetric catalysis amination dearomatization copper catalysis coupling reaction