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Soybean(Glycine max)rhizosphere organic phosphorus recycling relies on acid phosphatase activity and specific phosphorusmineralizing-related bacteria in phosphate deficient acidic soils

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Journal of Integrative Agriculture 2024年第5期23卷 1685-1702页

作者： Qianqian Chen Qian Zhao Baoxing Xie Xing Lu Qi Guo Guoxuan Liu Ming Zhou Jihui Tian Weiguo Lu Kang Chen Jiang Tian Cuiyue Liang root Biology Center State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of Natural Resources and EnvironmentSouth China Agricultural UniversityGuangzhou 510642China College of Natural Resources and Environment South China Agricultural UniversityGuangzhou 510642China Henan Academy of Crops Molecular Breeding Henan Academy of Agricultural SciencesZhengzhou 450002China

Bacteria play critical roles in regulating soil phosphorus(P) cycling. The effects of interactions between crops and soil P-availability on bacterial communities and the feedback regulation of soil P cycling by the bacterial community modifications are poorly understood. Here, six soybean(Glycine max) genotypes with differences in P efficiency were cultivated in acidic soils with long-term sufficient or deficient P-fertilizer treatments. The acid phosphatase(AcP) activities, organic-P concentrations and associated bacterial community compositions were determined in bulk and rhizosphere soils. The results showed that both soybean plant P content and the soil AcP activity were negatively correlated with soil organic-P concentration in P-deficient acidic soils. Soil P-availability affected the ɑ-diversity of bacteria in both bulk and rhizosphere soils. However, soybean had a stronger effect on the bacterial community composition, as reflected by the similar biomarker bacteria in the rhizosphere soils in both P-treatments. The relative abundance of biomarker bacteria Proteobacteria was strongly correlated with soil organic-P concentration and AcP activity in low-P treatments. Further high-throughput sequencing of the phoC gene revealed an obvious shift in Proteobacteria groups between bulk soils and rhizosphere soils, which was emphasized by the higher relative abundances of Cupriavidus and Klebsiella, and lower relative abundance of Xanthomonas in rhizosphere soils. Among them, Cupriavidus was the dominant phoC bacterial genus, and it was negatively correlated with the soil organic-P concentration. These findings suggest that soybean growth relies on organic-P mineralization in P-deficient acidic soils, which might be partially achieved by recruiting specific phoCharboring bacteria, such as Cupriavidus.

关键词： organic phosphorus acid phosphatase soybean bacterial community phoC-harboring bacteria rhizosphere

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

New Opportunities for Neutrons in Environmental and Biological Sciences

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Frontiers of Environmental Science & Engineering 2024年第7期18卷 179-186页

作者： Alexander Johs Shuo Qian Leighton Coates Brian H.Davison James G.Elkins Xin Gu Jennifer Morrell-Falvey Hugh O'Neill Jeffrey M.Warren Eric M.Pierce Kenneth Herwig Oak Ridge national Laboratory Oak RidgeTN37831USA

The use of neutron methods in environmental and biological sciences is rapidly emerging and accelerating with the development of new instruments at neutron user *** article,based on a workshop held at Oak Ridge national Laboratory(ORNL),offers insights into the application of neutron techniques in environmental and biological *** highlight recent advances and identify key challenges and potential future research *** include soil and rhizosphere processes,root water dynamics,plant-microbe interactions,structure and dynamics of biological systems,applications in synthetic biology and enzyme engineering,next-generation bioproducts,biomaterials and bioenergy,nanoscale structure,and fluid dynamics of porous materials in *** provide an outlook on emerging opportunities with an emphasis on new capabilities that will be enabled at the Spallation Neutron Source Second Target Station currently under design at *** mission of scientific neutron user facilities worldwide is to enable science using state-of-the-art neutron *** aim to encourage researchers in the environmental and biological research community to explore the unique capability afforded by neutrons at these facilities.

关键词： Neutrons Environment Biology Neutron imaging Neutron scattering Second Target Station(STS)

Natural variation in maize gene ZmSBR1 confers seedling resistance to Fusarium verticillioides

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The Crop Journal 2024年第3期12卷 836-844页

作者： Yunxia Song Peipei Ma Jingyang Gao Chaopei Dong Zhao Wang Yifan Luan Jiafa Chen Doudou Sun Pei Jing Xuecai Zhang Weibin Song Zijian Zhou Jianyu Wu College of Agronomy Henan Agricultural UniversityZhengzhou 450002HenanChina College of Life Sciences Henan Agricultural UniversityZhengzhou 450002HenanChina Global Maize program International Maize and Wheat Improvement Center(CIMMYT)Apdo 6-64106600 MexicoDFMexico national Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Maize seedling blight caused by Fusarium verticillioides is a widely occurring maize disease,but the genetics and mechanisms of resistance are not well *** this study,GWAS performed by MLM and 3VmrMLM identified 40 and 20 QTNs,associated with seedling blight *** methods identified 49 and 36 genes,*** verification of candidate gene ZmSBR1 identified by both methods showed that the resistance of a mutant line to seedling blight decreased by 0.37 grade points after inoculation with ***,compared with the *** length of the stem rot lesion caused by *** increased by 86%in mutant seedlings,and the relative length of the adult plant stalk rot increased by 35%in mutant plants compared to the wild type after inoculation with Fusarium *** analysis showed that expression of defense-related genes after inoculation was down-regulated in the mutant compared to the wild type,synthesis of secondary metabolites associated with resistance was reduced,and the immune response triggered by PAMP decreased,resulting in decreased resistance of mutant maize *** gene association analysis showed that most maize inbred lines carried the susceptible haplotype.A functional PCR marker was *** results demonstrated that ZmSBR1 conferred resistance to multiple Fusarium diseases at the seedling and adult growth stages and had important application value in breeding.

关键词： Seedling blight Stalk rot Multiple disease resistance

Methane Emission from Rice Fields:Necessity for Molecular Approach for Mitigation

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Rice science 2024年第2期31卷 159-178页

作者： Sujeevan RAJENDRAN Hyeonseo PARK Jiyoung KIM Soon Ju PARK Dongjin SHIN Jong-Hee LEE Young Hun SONG Nam-Chon PAEK Chul Min KIM Department of Horticulture Industry Wonkwang UniversityIksan 54538Korea Plant Molecular Biology and Biotechnology Research Center Gyeongsang National UniversityJinju 52828Korea Department of Southern Area Crop Science National Institute of Crop ScienceMiryang 50424Korea Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Korea Department of Plant Science Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Korea

Anthropogenic methane emissions are a leading cause of the increase in global averagetemperatures,often referred to as global *** soils play a significant role in methaneproduction,where the anaerobic conditions promote the production of methane by *** fields contribute a considerable portion of agricultural methane emissions,as riceplants provide both factors that enhance and limit methane *** plants harbor both methaneproducingand methane-oxidizing *** from rice roots provide source for methaneproduction,while oxygen delivered from the root aerenchyma enhances methane *** haveshown that the diversity of these microorganisms depends on rice cultivars with some genes characterizedas harboring specific groups of microorganisms related to methane ***,there is still aneed for research to determine the balance between methane production and oxidation,as rice plantspossess the ability to regulate net methane *** agronomical practices,such as fertilizerand water management,have been employed to mitigate methane ***,studiescorrelating agronomic and chemical management of methane with productivity are ***,evidences for breeding low-methane-emitting rice varieties are scattered largely due to the absence ofcoordinated breeding *** has indicated that phenotypic characteristics,such as rootbiomass,shoot architecture,and aerenchyma,are highly correlated with methane *** reviewdiscusses available studies that involve the correlation between plant characteristics and *** emphasizes the necessity and importance of breeding low-methane-emitting rice varieties inaddition to existing agronomic,biological,and chemical *** review also delves into the idealphenotypic and physiological characteristics of low-methane-emitting rice and potential breeding techniques,drawing from studies conducted

关键词： methane emission rice breeding aerenchyma greenhouse gas radial oxygen loss

Unveiling protein corona composition:predicting with resampling embedding and machine learning

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Regenerative Biomaterials 2024年第1期3卷 27-33页

作者： Rong Liao Yan Zhuang Xiangfeng Li Ke Chen Xingming Wang Cong Feng Guangfu Yin Xiangdong Zhu Jiangli Lin Xingdong Zhang College of Biomedical Engineering National Engineering Research Centre for BiomaterialsSichuan UniversityChengdu610065China

Biomaterials with surface nanostructures effectively enhance protein secretion and stimulate tissue *** nanoparticles(NPs)enter the living system,they quickly interact with proteins in the body fluid,forming the protein corona(PC).The accurate prediction of the PC composition is critical for analyzing the osteoinductivity of biomaterials and guiding the reverse design of ***,achieving accurate predictions remains a significant *** several machine learning(ML)models like Random Forest(RF)have been used for PC prediction,they often fail to consider the extreme values in the abundance region of PC absorption and struggle to improve accuracy due to the imbalanced data *** this study,resampling embedding was introduced to resolve the issue of imbalanced distribution in PC *** ML models were evaluated,and RF model was finally used for prediction,and good correlation coefficient(R^(2))and root-mean-square deviation(RMSE)values were *** ablation experiments demonstrated that the proposed method achieved an R^(2) of 0.68,indicating an improvement of approximately 10%,and an RMSE of 0.90,representing a reduction of approximately 10%.Furthermore,through the verification of label-free quantification of four NPs:hydroxyapatite(HA),titanium dioxide(TiO_(2)),silicon dioxide(SiO_(2))and silver(Ag),and we achieved a prediction performance with an R^(2) value>0.70 using Random ***,the feature analysis revealed that the composition of the PC is most significantly influenced by the incubation plasma concentration,PDI and surface modification.

关键词： nanoparticles protein corona machine learming resampling technique feature analysis

Dynamic modulation of nodulation factor receptor levels by phosphorylation-mediated functional switch of a RING-type E3 ligase during legume nodulation

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Molecular Plant 2024年第7期17卷 1090-1109页

作者： Hao Li Yajuan Ou Jidan Zhang Kui Huang Ping Wu Xiaoli Guo Hui Zhu Yangrong Cao national Key Lab of Agricultural Microbiology Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China national Key Lab of Agricultural Microbiology College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China

The precise control of receptor levels is crucial for initiating cellular signaling transduction in response to specific ligands;however,such mechanisms regulating nodulation factor(NF)receptor(NFR)-mediated perception of NFs to establish symbiosis remain *** this study,we unveil the pivotal role of the NFR-interacting RING-type E3 ligase 1(NIRE1)in regulating NFR1/NFR5 homeostasis to optimize rhizobial infection and nodule development in Lotus *** demonstrated that NiRE1 has a dual function in this regulatory *** associates with both NFR1 and NFR5,facilitating their degradation through K48-linked polyubiquitination before rhizobial ***,following rhizobial inoculation,NFR1 phosphorylates NIRE1ata conserved residue,Tyr-109,inducing a functional switch in NIRE1,which enables NIRE1tomediateK63-linkedpolyubiquitination,thereby stabilizing NFR1/NFR5 in infected root *** introduction of phospho-dead NIRE1Y1osF leads to delayed nodule development,underscoring the significance of phosphorylation at Tyr-1o9 in orchestrating symbiotic ***,expression of the phospho-mimic NIRE1Y0E results in the formation of spontaneous nodules in ***,further emphasizing the critical role of the phosphorylation-dependent functional switch in *** summary,these findings uncover a fine-tuned symbiotic mechanism that a single E3 ligase could undergo a phosphorylationdependent functional switch to dynamically and precisely regulate NF receptor protein levels.

关键词： nodule symbiosis nodulation factor receptors E3 ligase ubiquitination phosphorylation protein degradation protein stabilization Lotus japonicus

Mechanistic modeling of copper corrosions in data center environments

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Building Simulation 2024年第3期17卷 483-492页

作者： Rui Zhang Jianshun Zhang Roger Schmidt Jeremy L.Gilbert Department of Mechanical and Aerospace Engineering College of Engineering and Computer ScienceSyracuse UniversitySyracuseNY13244USA Buildings and Transportation Science Division Oak Ridge National LaboratoryOak RidgeTN37830USA SyracuseCoE-New York Center of Excellence in Environmental and Energy Systems Syracuse University727 E.Washington StreetSyracuseNY13244USA Department of Bioengineering Clemson UniversityClemson-Medical University of South Carolina Bioengineering ProgramCharlestonSC29425USA

Air-side economizers are increasingly used to take advantage of“free-cooling”in data centers with the intent of reducing the carbon footprint of ***,they can introduce outdoor pollutants to indoor environment of data centers and cause corrosion damage to the information technology *** evaluate the reliability of information technology equipment under various thermal and air-pollution conditions,a mechanistic model based on multi-ion transport and chemical reactions was *** model was used to predict Cu corrosion caused by Cl_(2)-containing pollutant *** also accounted for the effects of temperature(25℃and 28℃),relative humidity(50%,75%,and 95%),and *** also identified higher air temperature as a corrosion barrier and higher relative humidity as a corrosion accelerator,which agreed well with the experimental *** average root mean square error of the prediction was 13.7Å.The model can be used to evaluate the thermal guideline for data centers design and operation when Cl_(2)is present based on pre-established acceptable risk of corrosion in data centers’environment.

关键词： chloride pollutant mixture copper corrosion model data center temperature relative humidity synergistic effect

Dual-assisted high-precision tracking technique for wideband multiplexed signals in new generation GNSS

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Satellite Navigation 2024年第1期5卷 52-73页

作者： Yunhan Qi Zheng Yao Mingquan Lu Department of Electronic Engineering Tsinghua UniversityBeijing100084China Beijing national Research Center for Information Science and Technology Beijing100084China

With the evolution of Global Navigation Satellite System(GNSS),new generation GNSS signals have adopted the dual-frequency multiplexing modulation techniques,which jointly modulate multiple signals located on multiple sub-frequencies into a Wideband Multiplexed Signal(WMS).Although WMSs were proposed initially to reduce the complexity of satellite transmitters and improve the transmission efficiency of signals,their multi-component structures and wide root mean square bandwidths introduced by high-frequency subcarriers also provide the possibility to improve the GNSS ranging ***,this paper proposes a Dual-assisted Multi-component Tracking(DMT)technique,which can not only fully use high-frequency subcarriers in WMSs,but also effectively track carrier,subcarrier,and code by jointly utilizing all components in *** this paper,the tracking and ranging performances of DMT are comprehensively analyzed theoretically and by simulation and real *** results show that compared with existing WMS tracking methods,DMT can achieve tracking results with lower tracking jitters and ranging results with higher precision,providing a highly advantageous solution for new generation GNSS signal processing.

关键词： Wideband multiplexed signal Dual-assisted Multi-component High precision tracking