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Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit

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Plant Communications 2024年第8期5卷 50-68页

作者： Yuanyuan Cui Yanning Su Jianxin Bian Xue Han Haosong Guo Zhiyuan Yang Yijun Chen Lihui Li Tianyu Li Xing Wang Deng Xiaoqin Liu Peking university Institute of Advanced agricultural sciences Shandong Laboratory for Advanced Agricultural Sciences at WeifangShandong 261325China School of Advanced agricultural sciences Peking UniversityBeijing 100083China

Peanut(Arachis hypogaea L.)is an important leguminous oil and economic crop that produces flowers aboveground and fruits *** fruit-pod development,which significantly affects peanut production,involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different *** investigate the molecular mechanisms that underlie peanut fruitpod development,we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing(snRNA-seq)and single-nucleus assay for transposase-accessible chromatin with sequencing(snATAC-seq)data at the single-cell *** identified distinct cell types,such as meristem,embryo,vascular tissue,cuticular layer,and stele cells within the shell *** specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod ***-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk *** instance,we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells,indicating an essential role for the vascular cells in peg ***,our single-nucleus analysis provides comprehensive and novel information on specific cell types,gene expression,and chromatin accessibility during the early stages of fruit-pod *** information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.

关键词： peanut pod development single-nucleus RNA-seq single-nucleus ATAC-seq in situ RNA hybridization

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Opportunities and Challenges in Advancing Plant Research with Single-cell Omics

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 13-26页

作者： Mohammad Saidur Rhaman Muhammad Ali Wenxiu Ye Bosheng Li Peking university Institute of Advanced agricultural sciences Shandong Laboratory of Advanced Agricultural Sciences in WeifangWeifang 261325China

Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of *** strategies have been employed to study cell types and their developmental progressions,including single-cell sequencing methods which provide high-dimensional catalogs to address biological *** recent years,single-cell sequencing technologies in transcriptomics,epigenomics,proteomics,metabolomics,and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell ***,the application of single-cell technologies to plants is more limited due to the challenges posed by cell *** review outlines the advancements in single-cell omics technologies,their implications in plant systems,future research applications,and the challenges of single-cell omics in plant systems.

关键词： Multi-omics Single-cell transcriptomics Spatial transcriptomics Single-cell epigenomics Single-cell proteomics

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Trichoderma viride F7 improves peanut performances while remediating cadmium-contaminated soil with microplastics

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Pedosphere 2024年第5期34卷 971-980页

作者： Xin SONG Jianpeng JIN Hongliang YIN Tingjuan WANG Haiying ZONG Fangli WANG Jun LIU Xiaoli HUANG Bin WANG Chao CHAI Zhi LI Dongsheng LIU Xuexia WANG Ningning SONG School of Resources and Environment Qingdao Agricultural University Central Laboratory Qingdao Agricultural University Institute of Soil Fertilizer and agricultural Water Saving Xinjiang Academy of Agricultural Sciences Institute of Plant Nutrition and Resources Beijing Agricultural Forestry Academy Sciences

Microplastics(MPs) and cadmium(Cd) in soil have serious negative impacts on plant growth. As a bioremediator, Trichoderma viride may modulate the impacts of MPs and/or Cd on plant growth and heavy metal uptake. In this study, T. viride F7 was used to treat Cd-contaminated soil with and without the presence of polylactic acid MPs to investigate its effects on peanut growth, Cd uptake efficiency, and soil properties. Results showed that F7 increased soil pH,dissolved organic carbon, cation exchange capacity, microbial biomass nitrogen, and microbial biomass carbon, which resulted in increases of 2.10%–19.83% in peanut biomass and mitigated the negative effects of MPs and Cd on peanut growth. Trichoderma viride F7 reduced the soil bioavailable Cd and plant Cd concentrations by 16.68%–34.20% and 5.37%–25.84%, respectively. Regression path analysis showed that F7 could improve peanut performances by altering soil properties and reducing peanut Cd concentrations in MP-Cd-contaminated soil. Soil fungal community analysis indicated that the microbial community was altered via F7 inoculation, which antagonized Fusarium and promoted peanut growth. This study reveals the mechanisms of F7 in mitigating Cd contamination in the soil with the presence of MPs, which provides new ideas for managing MP-heavy metal-contaminated soil and improving soil health.

关键词： bioremediation compound pollution emerging pollutant heavy metal polyethylene soil health

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Nutrition impacts of non-solid cooking fuel adoption on under-five children in developing countries

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Journal of Integrative Agriculture 2024年第2期23卷 397-413页

作者： Yalin Tang Yuhe Guo Gang Xie Chengfang Liu China Center for agricultural Policy School of Advanced Agricultural SciencesPeking UniversityBeijing 100871China agricultural Information Institute Chinese Academy of Agricultural SciencesBeijing 100081China

This paper examines the nutrition impacts of using non-solid cooking fuel on under-five children in developing *** draw on data from more than 1.12 million children in 62 developing countries from the Demographic and Health Surveys(DHS).Results from both fixed effects(FE)and instrumental variable(IV)estimates show that using non-solid cooking fuel significantly improves the nutrition outcomes of under-five *** with their peers from households mainly using solid fuel,children from households mainly using non-solid fuel exhibit a lower probability of experiencing stunting(by 5.9 percentage points)and being underweight(by 1.2 percentage points).Our further investigation provides evidence for several underlying mechanisms,such as improved indoor air quality,induced reduction in children’s respiratory symptoms,benefits on maternal health,and reduction in maternal time spent on fuel collection or *** analyses suggest that the nutrition benefits of using non-solid cooking fuel are more prominent among boys,children above three years old,and those from households of lower socioeconomic status,rural areas,and Southeast Asia.

关键词： non-solid cooking fuel nutrition benefits under-five children developing countries

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Induced magneto-conductivity in a two-nodeWeyl semimetal under Gaussian random disorder

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Chinese Physics B 2024年第9期33卷 566-574页

作者： Chuanxiong Xu Haoping Yu Mei Zhou Xuanting Ji Department of Applied Physics China Agricultural UniversityBeijing 100083China Department of Applied Mechanics China Agricultural UniversityBeijing 100083China School of Physical sciences University of Chinese Academy of SciencesBeijing 100049China

Measuring the magneto-conductivity induced from impurities may help determine the impurity distribution and reveal the structure of a Weyl semimetal *** verify this,we utilize the Gaussian random disorder to simulate charged impurities in a two-node Weyl semimetal model and investigate the impact of charged impurities on magneto-conductivity in Weyl *** first compute the longitudinal magnetic conductivity and find that it is positive and increases proportionally with the parameter governing the Gaussian distribution of charged impurities,suggesting the presence of negative longitudinal *** we consider both the intra-valley and inter-valley scattering processes to calculate the induced transverse magneto-conductivity in the *** findings indicate that both inter-valley and intravalley scattering processes play important roles in the transverse *** locations of Weyl nodes can also be determined by magneto-conductivity *** is possible if the magnetic field strength and the density of charged impurities are ***,the measurement of magnetic conductivity may reveal the distribution of charged impurities in a given sample once the locations of the Weyl nodes have been *** findings can aid in detecting the structure of a Weyl semimetal sample,enhancing comprehension of magnetotransport in Weyl semimetals and promoting the development of valley electronics.

关键词： Weyl semimetal inter-valley scattering magneto-conductivity

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Resilience effects for household food expenditure and dietary diversity in rural western China

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Journal of Integrative Agriculture 2024年第2期23卷 384-396页

作者： Xiao Han Kaiyu Lyu Fengying Nie Yuquan Chen Institute of agricultural Economics and Development Chinese Academy of Agricultural SciencesBeijing 100081China agricultural Information Institute Chinese Academy of Agricultural SciencesBeijing 100081China Academy of Global Food Economics and Policy China Agricultural UniversityBeijing 100083China

A more resilient livelihood is increasingly recognized as an efficient way to improve vulnerable households’food security and optimize their dietary *** study quantifies rural household resilience in western China,identifies the three pillars(absorptive capacity,adaptive capacity,and transformative capacity)contribution to resilience,and then establishes the estimated Resilience Capacity Index(RCI)linked with food security and dietary diversity supported by the multiple indicator multiple cause(MIMIC)*** show that,despite geographical heterogeneity,the RCI consistently increased from 2015 to *** with a higher RCI inheriting better capacity to deal with risk and shocks are significantly and positively correlated with increasing food expenditure and diversifying food *** can be because resilient households will allocate more money to food expenditure instead of saving for livelihood ***,policymakers can provide more incentives for rural households to adopt more dynamic and effective risk management ***,in turn,could yield positive spillover effects by preventing human capital loss associated with dietary-related chronic diseases and mortality.

关键词： resilience food expenditure dietary diversity China risk management

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Kinetic model of vibration screening for granular materials based on biological neural network

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Particuology 2024年第5期88卷 98-106页

作者： Zhan Zhao Yan Zhang Fang Qin Mingzhi Jin School of agricultural Engineering Jiangsu UniversityZhenjiang212013China Shandong Academy of agricultural Machinery sciences Ji'nan250100China

The kinetic model is the theoretical basis for optimizing the structure and operation performance of vibration screening *** this paper,a biological neurodynamic equation and neural connections were established according to the motion and interaction properties of the material under vibration *** material feeding to the screen and the material passing through apertures were considered as excitatory and inhibitory inputs,respectively,and the generated stable neural activity landscape was used to describe the material distribution on the 2D screen *** dynamic process of material vibration screening was simulated using discrete element method(DEM).By comparing the similarity between the material distribution established using biological neural network(BNN)and that obtained using DEM simulation,the optimum coefficients of BNN model under a certain screening parameter were determined,that is,one relationship between the BNN model coefficients and the screening operation parameters was *** screening parameters were randomly selected,and the corresponding relationships were established as a ***,with straw/grain ratio,aperture diameter,inclination angle,vibration strength in normal and tangential directions as inputs,five independent adaptive neuro-fuzzy inference systems(ANFIS)were established to predict the optimum BNN model coefficients,*** training results indicated that ANFIS models had good stability and *** flexibility and adaptability of the proposed BNN method was demonstrated by modeling material distribution under complex feeding conditions such as multiple regions and non-uniform rate.

关键词： Kinetic model Material distribution Vibration screening Biological neural network DEM simulation Adaptive neuro-fuzzy inference systems

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Fake News Detection Based on Text-Modal Dominance and Fusing Multiple Multi-Model Clues

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Computers, Materials & Continua 2024年第3期78卷 4399-4416页

作者： Li fang Fu Huanxin Peng Changjin Ma Yuhan Liu College of Arts and sciences Northeast Agricultural UniversityHarbin150030China College of Engineering Northeast Agricultural UniversityHarbin150030China

In recent years,how to efficiently and accurately identify multi-model fake news has become more ***,multi-model data provides more evidence but not all are equally ***,social structure information has proven to be effective in fake news detection and how to combine it while reducing the noise information is ***,existing approaches fail to handle these *** paper proposes a multi-model fake news detection framework based on Tex-modal Dominance and fusing Multiple Multi-model Cues(TD-MMC),which utilizes three valuable multi-model clues:text-model importance,text-image complementary,and text-image ***-MMC is dominated by textural content and assisted by image information while using social network information to enhance text *** reduce the irrelevant social structure’s information interference,we use a unidirectional cross-modal attention mechanism to selectively learn the social structure’s features.A cross-modal attention mechanism is adopted to obtain text-image cross-modal features while retaining textual features to reduce the loss of important *** addition,TD-MMC employs a new multi-model loss to improve the model’s generalization *** experiments have been conducted on two public real-world English and Chinese datasets,and the results show that our proposed model outperforms the state-of-the-art methods on classification evaluation metrics.

关键词： Fake news detection cross-modal attention mechanism multi-modal fusion social network transfer learning

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Decreased soil pH weakens the positive rhizosphere effect on denitrification capacity

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Pedosphere 2024年第5期34卷 905-915页

作者： Jun WANG Zongxiang ZHANG Fei LIANG Zhao CHE Yongkang WEN Manyu ZHANG Wenjun JIN Zhaorong DONG He SONG College of Agronomy Anhui Agricultural University Key Laboratory of Arable Land Quality Monitoring and Evaluation Ministry of Agriculture and Rural Affairs Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences (CAAS) College of Resources and Environmental sciences China Agricultural University

The stimulating effect of rhizosphere on denitrification is considered to be an unavoidable loss of soil nitrogen（N） and detrimental to crop N use efficiency,which is regulated by crop growth and soil properties. Soil acidification, occurring rapidly in many intensive farming lands, affects both crop growth and soil properties, thereby altering rhizosphere effect on denitrification. However, the mechanism by which soil acidification regulates rhizosphere denitrification still remains unclear. Here, we determined the denitrification capacity（DC） and associated community compositions of nirK-and nirS-type denitrifiers in maize rhizosphere and bulk soils at four acidity gradients（pH = 6.8, 6.1, 5.2, and 4.2）. Results showed that the stimulating effect of rhizosphere on DC strongly depended on soil pH. Compared to bulk soil, rhizosphere soil had significantly higher DC at pH 5.2, but not at pH of 4.2. With increasing soil acidity, the stimulation of rhizosphere on DC（calculated as the difference in DC between rhizosphere and bulk soils） decreased from 8.01 to 0.01 mg N ***, soil acidification significantly reduced the differences in dissolved organic carbon（DOC） and abundance of key nirK-type denitrifier taxa between rhizosphere and bulk soils, both of which were positively related to the stimulation of rhizosphere on DC. These findings demonstrated that soil acidification could weaken the positive rhizosphere effect on denitrification via regulated C availability and associated nirK-type denitrifier community, potentially reducing N loss risk in rhizosphere soil. The independent role of soil p H should be fully considered when modelling N behaviour in plant-soil systems.

关键词： bacterial abundance denitrifier community dissolved organic carbon operational taxonomic unit soil acidification

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Spatiotemporal evolution and assembly processes of ammonia-oxidizing prokaryotic communities in 1 000-year-old coastal reclaimed soils

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Pedosphere 2024年第4期34卷 709-725页

作者： Sarfraz HUSSAIN Yifan YIN Senlin LIU Shanshan YAN Dongjie CHEN Hui CAO Feng WANG Key Laboratory of agricultural Environmental Microbiology Ministry of Agriculture and Rural AffairsCollege of Life SciencesNanjing Agricultural UniversityNanjing 210095China Institute of Eco-Environmental sciences Ningbo Academy of Agricultural SciencesNingbo 315040China

Coastal marshes are transitional areas between terrestrial and aquatic *** are sensitive to climate change and anthropogenic *** recent decades,the reclamation of coastal marshes has greatly increased,and its effects on microbial communities in coastal marshes have been studied with great *** of these studies have explained the short-term spatiotemporal variation in soil microbial community ***,the impact of reclamation on the community composition and assembly processes of functional microbes(e.g.,ammonia-oxidizing prokaryotes)is often *** this study,using quantitative polymerase chain reaction and the Ion S5™XL sequencing platform,we investigated the spatiotemporal dynamics,assembly processes,and diversity patterns of ammonia-oxidizing prokaryotes in 1000-year-old reclaimed coastal salt *** taxonomic and phylogenetic diversity and composition of ammonia oxidizers showed apparent spatiotemporal variations with soil *** null modelling-based analysis showed that across all sites,the archaeal ammonia-oxidizing community was assembled by a deterministic process(84.71%),and deterministic processes were also dominant(55.2%)for ammonia-oxidizing bacterial communities except for communities at 60 years of *** assembly process and nitrification activity in reclaimed soils were positively *** abundance of the amoA gene and changes in ammonia-oxidizing archaeal and bacterial diversities significantly affected the nitrification activity in reclaimed *** findings suggest that long-term coastal salt marsh reclamation affects nitrification by modulating the activities of ammonia-oxidizing microorganisms and regulating their community structures and assembly *** results provide a better understanding of the effects of long-term land reclamation on soil nitrogen-cycling microbial communities.

关键词： ammonia oxidizer beta nearest taxon index coastal salt marshes community assembly deterministic process nitrification rate stochastic process

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