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Spatial search weighting information contained in cell velocity distribution

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Chinese Physics B 2024年第2期33卷 522-528页

作者：马一凯李娜陈唯 State Key Laboratory of Surface Physics and Department of Physics Fudan UniversityShanghai 200438China China National Center for Bioinformation Beijing 100101China National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China

Cell migration plays a significant role in physiological and pathological processes.Understanding the characteristics of cell movement is crucial for comprehending biological processes such as cell functionality,cell migration,and cell–cell interactions.One of the fundamental characteristics of cell movement is the specific distribution of cell speed,containing valuable information that still requires comprehensive understanding.This article investigates the distribution of mean velocities along cell trajectories,with a focus on optimizing the efficiency of cell food search in the context of the entire colony.We confirm that the specific velocity distribution in the experiments corresponds to an optimal search efficiency when spatial weighting is considered.The simulation results indicate that the distribution of average velocity does not align with the optimal search efficiency when employing average spatial weighting.However,when considering the distribution of central spatial weighting,the specific velocity distribution in the experiment is shown to correspond to the optimal search efficiency.Our simulations reveal that for any given distribution of average velocity,a specific central spatial weighting can be identified among the possible central spatial weighting that aligns with the optimal search strategy.Additionally,our work presents a method for determining the spatial weights embedded in the velocity distribution of cell movement.Our results have provided new avenues for further investigation of significant topics,such as relationship between cell behavior and environmental conditions throughout their evolutionary history,and how cells achieve collective cooperation through cell-cell communication.

关键词： cell migration foraging efficiency random walk spatial search weight

Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses

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Molecular Plant 2024年第3期17卷 478-495页

作者： Yeling Zhou Yuzhu Wang Dong Zhang Jiansheng Liang institute of Plant and food Science Department of BiologySchool of Life SciencesSouthern University of Science and Technology(SUSTech)Shenzhen 518055China Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes Southern University of Science and Technology(SUSTech)Shenzhen 518055China jiangsu Key Laboratory of Crop Genetics and Physiology/Co-lnnovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009China

ATP-binding cassette(ABC)transporters are integral membrane proteins that have evolved diverse func-tions fulfilled via the transport of various substrates.In Arabidopsis,the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress responses.In this study,we revealed that two Arabidopsis ABCG transporters,ABCG16 and ABCG25,engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester(ABA-GE),respectively.We first revealed that ABCG16 contributes to osmotic stress tolerance via ABA signaling.More specifically,ABCG16 induces cellular ABA efflux in both yeast and plant cells.Using FRET analysis,we showed that ABCG16 forms oblig-atory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA,undergoing notable conformational changes.Furthermore,we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum(ER)membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco cells.The specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhib-itory role of these twoABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER membrane.Our endomembrane-specific analysis of the FRET signals derived from the homo-or heterodimerized ABcG complexes allowed us to link endomembrane-biased dimerization to the transloca-tion of distinct substrates by ABcG transporters,providing a prototypic framework for understanding the omnipotence of ABcG transporters in plant development and stress responses.

关键词： abscisic acid ABCG transporter dimerization endomembrane substrate selectivity

Combined ATAC-seq,RNA-seq,and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

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Zoological Research 2024年第1期45卷 201-214页

作者： Biao Wu Xi Chen Jie Hu Zhen-Yuan Wang Yan Wang Da-You Xu Hao-Bing Guo Chang-Wei Shao Li-Qing Zhou Xiu-Jun Sun Tao Yu Xiao-Mei Wang Yan-Xin Zheng Guang-Yi Fan Zhi-Hong Liu State Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China Laboratory for Marine Fisheries Science and food Production Processes Laoshan LaboratoryQingdaoShandong 266071China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266426China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai 201306China Changdao Enhancement and Experiment Station Chinese Academy of Fishery SciencesYantaiShandong 265800China State Key Laboratory of Agricultural genomics BGI-ShenzhenShenzhenGuangdong 518083China

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.

关键词： Crassostrea ariakensis Glycogen Transcriptome ATAC GWAS

Design and test of the plant-correcting reel for harvesting lodging garlic plants

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International Journal of Agricultural and Biological Engineering 2024年第1期17卷 59-68页

作者： Yuhua Li Chao Li Lupeng Liu Kai Zhou Jialin Hou College of Mechanical and Electronic Engineering Shandong Agricultural UniversityTai’an 271018ShandongChina College of Biosystems Engineering&food Science Zhejiang UniversityHangzhou 310058China

Crops are prone to lodging with the decline of stem moisture and the intervention of other factors in the mature harvest period,such as garlic,which is difficult to harvest mechanically.To solve this problem,the plant-correcting reel for harvesting lodging garlic plants,bumped and deformed with plants many times to pull and lift them into a conveyor,is proposed in this study.We analyzed the motion trajectory equation and key influencing factors of the reel and defined the lifting and plant-correcting stages as three processes of contact,stirring and release.For example,the contact deformation model and system energy equations were established in the contact process.Besides,in the stirring process,the garlic plant-correcting conditions were established through the dynamic simulation test analysis of garlic seedling trajectories and the deflection model of garlic stem was constructed.Furthermore,in the release process,the expressions of rubber bars rotation and garlic plant offset bending curvature were constructed and the optimal number and distribution form of bars were determined.Meanwhile,the mechanism and key operating parameters of the auxiliary lifting mechanism of the divider were established.Through the single-factor test,the influence of reel speed,forward speed and reel height on the success feeding rate was analyzed under different bars distribution forms;Through multi-factor experiments,the interaction contour map of various factors was constructed.When reel speed,forward speed and reel height were 3 rad/s,3.5 m/s,and 540 mm,the feeding success rate was 98.73%.The optimization factors were tested and verified,which met the operational requirements of a high feeding success rate and low loss rate of garlic harvest.This study combines laboratory virtual as well as field experiments and analyzes of trajectory of bars,contact deformation and deflection model of garlic plant,and reel rotation and garlic plant offset bending curvature to solve the problem of garlic lodging mechanized harvest and yield reduct

关键词： feeding success rate lodging garlic harvesting reel plant model field test

Trehalose:A sugar molecule involved in temperature stress management in plants

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The Crop Journal 2024年第1期12卷 1-16页

作者： Ali Raza Savita Bhardwaj Md Atikur Rahman Pedro García-Caparrós Madiha Habib Faisal Saeed Sidra Charagh Christine H.Foyer Kadambot H.M.Siddique Rajeev K.Varshney College of Agriculture Fujian Agriculture and Forestry University(FAFU)Fuzhou 350002FujianChina Department of Botany School of Bioengineering and BiosciencesLovely Professional UniversityPhagwara 144411India Department of Botany MCM DAV CollegeKangraHimachal Pradesh 176001India Grassland and Forage Division National Institute of Animal ScienceRural Development AdministrationCheonan 31000Republic of Korea Agronomy Department of Superior School Engineering University of AlmeríaAlmeríaSpain National Institute for genomics and Advanced Biotechnology National Agricultural Research CentrePark Rd.Islamabad 45500Pakistan Agriculture Health and Environment DepartmentNatural Resources InstituteFaculty of Engineering&ScienceUniversity of GreenwichKent ME44TBUK State Key Laboratory of Rice Biology China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhouZhejiangChina School of Biosciences College of Life and Environmental SciencesUniversity of BirminghamEdgbaston B152TTUK The UWA Institute of Agriculture The University of Western AustraliaCrawleyPerth 6009Australia WA State Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWA 6150Australia

Trehalose(Tre)is a non-reducing disaccharide found in many species,including bacteria,fungi,invertebrates,yeast,and even plants,where it acts as an osmoprotectant,energy source,or protein/membrane protector.Despite relatively small amounts in plants,Tre concentrations increase following exposure to abiotic stressors.Trehalose-6-phosphate,a precursor of Tre,has regulatory functions in sugar metabolism,crop production,and stress tolerance.Among the various abiotic stresses,temperature extremes(heat or cold stress)are anticipated to impact crop production worldwide due to ongoing climate changes.Applying small amounts of Tre can mitigate negative physiological,metabolic,and molecular responses triggered by temperature stress.Trehalose also interacts with other sugars,osmoprotectants,amino acids,and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation.Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance.Genome-wide studies of Tre-encoding genes suggest roles in plant growth,development,and stress tolerance.This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism,crosstalk,and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species.We consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture.

关键词： Abiotic stress Gene expression Genetic engineering Osmolyte Trehalose-6-phosphate

The CropGPT project:Call for a global,coordinated effort in precision design breeding driven by Al using biological big data

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Molecular Plant 2024年第2期17卷 215-218页

作者： Wanchao Zhu Rui Han Xiaoyang Shang Tao Zhou Chengyong Liang Xiaomeng Qin Hong Chen Zaiwen Feng Hongwei Zhang Xingming Fan Weifu Li Lin Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region College of AgronomyNorthwest A&F UniversityYanglingShaanxi712100China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China institute of food Crops Sciences Yunnan Academy of Agricultural Sciences2238 Beijing RoadKunmingYunnan 650200China Hubei Hongshan Laboratory Wuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Since the beginning of humanity,people have been seeking practical solutions to meet their most basic need:food.The advent of agriculture greatly increased the food supply and led to a rapid increase in the human population.Enhanced food production via agriculture can be attributed to both improved crop management practices and crop breeding through genetics.Plant(crop)breeding has been categorized into four major stages based on the techniques employed(Wallace et al.,2018).

关键词： breeding seeking Wallace

A commentary of“Mechanism of alkaline tolerance and application in crop improvement”:Top 10 Chinese Scientific Advances of 2023,China

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Fundamental Research 2024年第3期4卷 697-698页

作者： Yujuan Zhu Sanwen Huang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China State Key Laboratory of Tropical Crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China

As global warming accelerates,soil degradation,exacerbated by extreme weather,has become a significant environmental issue worldwide.China,in particular,is grappling with a yearly reduction in arable land due to soil degradation,acidification,and salinization,posing potential threats to food security.The country has a vast area of saline-alkaline land,over half of which are high-pH soda saline soils.These lands often experience simultaneous salt and alkali stress,severely inhibiting plant growth and crop yield.Therefore,finding ways to utilize this marginal and saline-alkaline land for food production is a critical scientific challenge.In this context,Chinese scientists have achieved a breakthrough towards harnessing saline-alkaline land.

关键词： alkaline utilize breakthrough

Differential roles of seed and sprout regeneration in forest diversity and productivity after disturbance

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Forest Ecosystems 2024年第3期11卷 371-380页

作者： Marek Mejstrík Martin Svatek Martina Pollastrini Martin Sramek Radim Matula Department of Forest Ecology Faculty of Forestry and Wood SciencesCzech University of Life Sciences PragueKamýcka 12916500PragueCzech Republic Department of Forest Botany Dendrology and GeobiocoenologyFaculty of Forestry and Wood TechnologyMendel University in BrnoZemedelska 361300BrnoCzech Republic Department of Agriculture FoodEnvironment and ForestryUniversity of FirenzePiazzale Delle Cascine 2850144FirenzeItaly

Natural regeneration after disturbances is a key phase of forest development,which determines the trajectory of successional changes in tree species composition and diversity.Regenerating trees can originate from either seeds or sprouts produced by disturbed trees with sprouting ability.Although both regeneration strategies often develop and co-occur after a disturbance,they tend to affect forest development differently due to significant functional differences.However,the origin of tree regeneration is rarely distinguished in post-disturbance forest surveys and ecological studies,and the differential roles of seed and sprout regeneration in forest productivity and diversity remain poorly understood.To address these research gaps,we explored the role of sprout and seed regeneration in the formation of woody species diversity and above-ground biomass(AGB)productivity in early-stage forest development.Data were collected in two experimental forest stands in the Czech Republic,where trees were cut with varying intensities with the density of residual(uncut)trees ranging from 0 to 275 trees per hectare.All trees were mapped and their sizes were measured before cutting and then,either as a stump with sprouts or a residual tree,remeasured 11 years later.In addition,all tree saplings were mapped and measured 11 years after logging,and their origin(sprout or seed)was identified.To assess abundances and productivity,we estimated AGB of all2,685 sprouting stumps of 19 woody species and 504 generative(i.e.,seed origin)individuals of 16 woody species,using allometric equations.Mixed-effects models were used to analyze the effects of each regeneration strategy on woody species diversity and the total AGB under varying densities of residual trees.Nonmetric multidimensional scaling was used to evaluate the effect of regeneration strategies on species composition.AGB and diversity of sprouts were significantly higher than those of seed regeneration.Sprouts formed on average97.1%of the total regeneration AGB in H ady and 98.6%in

关键词： Resprouting Seeding Residual trees Tree diversity Above-ground biomass

A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

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Horticultural Plant Journal 2024年第3期10卷 911-930页

作者： Yishan Feng Zhenyi Wang Qimeng Xiao Jia Teng Jianyu Wang Zijian Yu Jiaqi Wang Qiang Xu Yan Zhang Shaoqi Shen Shoutong Bao Yu Li Zimo Yan Yue Ding Zihan Liu Yuxian Li Tianyu Lei Min Yuan Xiu-Qing Li Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

关键词： Nyssaceae Polyploidization Multigenome alignment Evolutionary rate Autotetraploidization Karyotype evolution