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Selenium-oxidizing Agrobacterium sp.T3F4 decreases arsenic uptake by Brassica rapa *** a native polluted soil

Journal of Environmental Sciences 2024年第4期138卷 506-515页

作者： Lijin An Chunzhi Zhou Lipeng Zhao Ao Wei Yiting Wang Huimin Cui Shixue Zheng State Key laboratory of Agricultural microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China

Toxic arsenic(As)and trace element selenium(Se)are transformed by microorganisms but their complex interactions in soil-plant systems have not been fully *** Asand Se-oxidizing bacterium,Agrobacterium sp.T3F4,was applied to a native seleniferous As-polluted soil to investigate As/Se uptake by the vegetable Brassica rapa *** As-Se interaction as mediated by strain *** Se content in the aboveground plants was significantly enhanced by 34.1%,but the As content was significantly decreased by 20.5% in the T3F4-inoculated pot culture compared to the control(P<0.05).Similar result was shown in treatment with additional 5 mg/kg of Se(IV)in *** addition,the As contents in roots were significantly decreased by more than 35% under T3F4 or Se(IV)treatments(P<0.05).Analysis of As-Se-bacterium interaction in a soil simulation experiment showed that the bioavailability of Se significantly increased and As was immobilized with the addition of the T3F4strain(P<0.05).Furthermore,an As/Se co-exposure hydroponic experiment demonstrated that As uptake and accumulation in plants was reduced by increasing Se(IV)*** 50% growth inhibition concentration(IC50)values for As in plants were increased about one-fold and two-fold under co-exposure with 5 and 10μmol/L Se(IV),*** conclusion,strain T3F4 improves Se uptake but decreases As uptake by plants via oxidation of As and Se,resulting in decrease of soil As bioavailability and As/Se competitive absorption by *** provides a potential bioremediation strategy for Se biofortification and As immobilization in As-polluted soil.

关键词： Selenium oxidation Selenium biofortification Arsenite-oxidizing bacteria Arsenic immobilization Brassica rapa L

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Gut microbial interactions based on network construction and bacterial pairwise cultivation

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Science China(Life Sciences) 2024年第8期67卷 1751-1762页

作者： Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu State Key laboratory of Microbial Technology Shandong UniversityQingdao 266000China State Key laboratory of Microbial Resources and Environmental Microbiology Research Center(EMRC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut ***,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated *** this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon *** samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 *** cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were *** dynamics of bacteria growing on the YCFA agar were used to infer microbial association *** experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise *** co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or *** also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly *** approach provides new insights into the gut microbiome complexity and microbial interactions in association *** work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关键词： human gut microbiome gut microbial pairwise interaction co-culture association network microbial community

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The human-derived novel gut commensal Luoshenia tenuis regulates body weight and food intake in mice

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Food Science and Human Wellness 2024年第2期13卷 830-841页

作者： Yu Jiang Mengxuan Du Lisheng Xie Minzhi Jiang Yaokun Zhang Mingxia Bi Chang Liu Hongwei Liu Shuangjiang Liu State Key laboratory of Microbial Technology Shandong UniversityQingdao 266237China State Key laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Science Hebei UniversityBaoding 071000China State Key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Many studies have revealed that gut microbes modulate host *** this study,we characterized the therapeutic effects of a novel gut commensal Luoshenia tenuis against host metabolic ***,by in silico analysis,we demonstrated that the *** was prevalent in the gut microbiomes of healthy humans but were depleted specifically in obesity *** in vitro cultivation revealed that *** produced short chain fatty acids that were verified to modulate host metabolism and some other volatile metabolites to benefit hosts by anti-inflammation and ***,gavage of the *** significantly decreased the body weight gain and food intake of high-fat diet-feeding C57BL/6J mice,which was in parallel with the changed expression level of genes related to satiety and feeding *** then performed the gavage trial using diet induced obese mice,and it revealed that the administration of *** alleviated significantly the abnormal glucose and lipid metabolisms and reduced the inflammatory *** summary,this study revealed a previously-unknown human gut commensal microbe that benefited host metabolism,and set the stage for the development of novel next-generation probiotic applicable for treatment of obesity and related metabolic disorders.

关键词： Luoshenia tenuis Gut microbe Feeding behavior Obesity Next-generation probiotic

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Cross-linkedα-amylase aggregates on Fe3O4 magnetic nanoparticles modified with polydopamine/polyethyleneimine for efficient hydrolysis of starch

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Particuology 2024年第7期90卷 98-105页

作者： Jiandong Cui Xiuming Tang Qingqing Ma Yuyan Chang Qunli Zhang Shiru Jia State Key laboratory of Food Nutrition and Safety Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin 300457China Key laboratory of Biomass Chemical Engineering of Ministry of Education Zhejiang UniversityHangzhou 310027China

In this workα-amylase was immobilized on magnetic Fe3O4 nanoparticles with polyethylenimine(PEI)/polydopamine(PDA)coating or 3-aminopropyl triethoxysilane(APTES)for the first time via adsorption–precipitation–*** with the freeα-amylase,the resultant magnetic cross-linkedα-amylase aggregates(PEI/PDA-M-CLEAs and N-M-CLEAs)exhibited excellent thermal and storage stability as well as pH *** storage at 25°C for 60 days,freeα-amylase only retained 60%of its initial activity,while PEI/PDA-M-CLEAs and N-M-CLEAs retained 80%and 78%of their initial activities,***,N-M-CLEAs and PEI/PDA-M-CLEAs showed good *** 6 repeated uses,PEI/PDA-M-CLEAs and N-M-CLEAs still maintained 65%and 62%of their initial activities,***,PEI/PDA-M-CLEAs and N-M-CLEAs exhibited higher starch hydrolysis efficiency than freeα-*** maximum dextrose equivalent(DE)values of starch hydrolysis by PEI/PDA-M-CLEAs and N-M-CLEAs reached 29.24%and 28.79%within 90 min,***,the maximum DE values of starch hydrolysis by the freeα-amylase was only 27.89%even in 150 *** magnetic cross-linkedα-amylase aggregates could be introduced as effective biocatalyst for industrial applications in production of maltose syrups.

关键词： α-amylase Magnetic nanoparticles Functional modification Magnetic cross-linked enzyme aggregates Hydrolysis of starch

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Integrated application of synthetic community reduces consumption of herbicide in field Phalaris minor control

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Soil Ecology Letters 2024年第2期6卷 125-136页

作者： Amina Hadayat Zahir Ahmad Zahir Peng Cai Chun-Hui Gao National Key laboratory of Agricultural microbiology College of Resources and EnvironmentHuazhong Agricultural UniversityWuhan430070China Soil microbiology and Biochemistry laboratory Institute of Soil and Environmental SciencesUniversity of AgricultureFaisalabadPakistan

Herbicide-based weeds control impacts wheat crops as *** of Pseudomonas strains reduce the need for high-dose herbicides.100%Axial provides less weed control compared to 75%Axial with C4 *** 75%with C4 SynCom promotes... 详细信息

关键词： weed control synthetic microbial communities Phalaris minor wheat growth promotion synergistic effect

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shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

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Journal of Genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key laboratory of Applied microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

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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

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Naturally occurring PA^(E206K)point mutation in 2009 H1N1 pandemic influenza viruses impairs viral replication at high temperatures

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Virologica Sinica 2024年第1期39卷 71-80页

作者： Mengmeng Cao Qiannan Jia Jinghua Li Lili Zhao Li zhu Yufan Zhang Shan Li Tao Deng National Institute of Pathogen Biology Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing100730China CAS Key laboratory of Pathogen microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing100101China

The emergence of influenza virus A pandemic H1N1 in April 2009 marked the first pandemic of the 21st *** this study,we observed significant differences in the polymerase activities of two clinical 2009 H1N1 influenza A virus isolates from Chinese and Japanese *** comparison of the three main protein subunits(PB2,PB1,and PA)of the viral RNA-dependent RNA polymerase complex and subsequent mutational analysis revealed that a single amino acid substitution(E206K)was responsible for the observed impaired replication *** in vitro experiments showed that presence of PAE206K decreased the replication of influenza A/WSN/33 virus in mammalian cells and a reduction in the virus’s pathogenicity in *** studies revealed that PAE206K is a temperature-sensitive mutant associated with the inability to transport PB1–PA complex to the nucleus at high temperature(39.5℃).Hence,this naturally occurring variant in the PA protein represents an ideal candidate mutation for the development of live attenuated influenza vaccines.

关键词： H1N1 Influenza A virus Polymerase acidic protein Point mutation Viral replication

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Improved observation of colonized roots reveals the regulation of arbuscule development and senescence by drought stress in the arbuscular mycorrhizae of citrus

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Horticultural Plant Journal 2024年第2期10卷 425-436页

作者： Xilong Yin Wei Zhang Zengwei Feng Guangda Feng Honghui Zhu Qing Yao College of Horticulture South China Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China)Ministry of Agriculture and Rural AffairsGuangdong Province Key Laboratory of Microbial Signals and Disease ControlGuangzhouGuangdong 510642China Key laboratory of Agricultural Microbiomics and Precision Application Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationKey Laboratory of Agricultural MicrobiomicsState Key Laboratory of Applied Microbiology Southern ChinaGuangdong Microbial Culture Collection Center(GDMCC)Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

Citrus is the typical mycorrhizal fruit tree species establishing symbiosis with arbuscular mycorrhizal (AM) fungi. However, arbuscule development and senescence in colonized citrus roots, especially in response to drought stress, remain unclear, which is mainly due to the difficulty in clearing and staining lignified roots with the conventional method. Here, we improved the observation of colonized roots of citrus plants with the sectioning method, which enabled the clear observation of AM fungal structures. Furthermore, we investigated the effects of one week of drought stress on arbuscule development and senescence with the sectioning method. Microscopy observations indicated that drought stress significantly decreased mycorrhizal colonization (F%and M%) although it did not affect plant growth performance. Fluorescence probes (WGA 488 and/or Nile red) revealed that drought stress inhibited arbuscule development by increasing the percentage of arbuscules at the early stage and decreasing the percentages of arbuscules at the midterm and mature stages. Meanwhile, drought stress accelerated arbuscule senescence, which was characterized by the increased accumulation of neutral lipids. Overall, the sectioning method developed in this study enables the in-depth investigation of arbuscule status, and drought stress can inhibit arbuscule development but accelerate arbuscule senescence in the colonized roots of citrus plants. This study paves the way to elaborately dissecting the arbuscule dynamics in the roots of fruit tree species in response to diverse abiotic stresses.

关键词： Arbuscular mycorrhizae Citrus Drought stress Arbuscule development Arbuscule senescence Fruit tree species

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Ancient dormant virus remnant ERVW-1 drives ferroptosis via degradation of GPX4 and SLC3A2 in schizophrenia

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Virologica Sinica 2024年第1期39卷 31-43页

作者： Dongyan Zhang Xiulin Wu Xing Xue Wenshi Li Ping Zhou Zhao Lv Kexin Zhao Fan Zhu State Key laboratory of Virology and Department of Medical microbiology School of Basic Medical SciencesWuhan UniversityWuhan430071China Hubei Province Key laboratory of Allergy&Immunology Wuhan UniversityWuhan430071China

Human endogenous retroviruses(HERVs)are remnants of retroviral infections in human germline cells from millions of years *** these,ERVW-1(also known as HERV-W-ENV,ERVWE1,or ENVW)encodes the envelope protein of the HERV-W family,which contributes to the pathophysiology of ***,neuropathological studies have revealed cell death and disruption of iron homeostasis in the brains of individuals with ***,our bioinformatics analysis showed that differentially expressed genes in the human prefrontal cortex RNA microarray dataset(GSE53987)were mainly related to ferroptosis and its associated *** data demonstrated significantly lower expression levels of ferroptosis-related genes,particularly Glutathione peroxidase 4(GPX4)and solute carrier family 3 member 2(SLC3A2),in schizophrenia patients compared to normal *** in-depth analyses revealed a significant negative correlation between ERVW-1 expression and the levels of GPX4/SLC3A2 in *** indicated that ERVW-1 increased iron levels,malondialdehyde(MDA),and transferrin receptor protein 1(TFR1)expression while decreasing glutathione(GSH)levels and triggering the loss of mitochondrial membrane potential,suggesting that ERVW-1 can induce *** research has shown that ERVW-1 reduced the expression of GPX4 and SLC3A2 by inhibiting their promoter ***,Ferrostatin-1(Fer-1),the ferroptosis inhibitor,reversed the iron accumulation and mitochondrial membrane potential loss,as well as restored the expressions of ferroptosis markers GSH,MDA,and TFR1 induced by *** conclusion,ERVW-1 could promote ferroptosis by downregulating the expression of GPX4 and SLC3A2,revealing a novel mechanism by which ERVW-1 contributes to neuronal cell death in schizophrenia.

关键词： ERVW-1 Glutathione peroxidase 4(GPX4) Solute carrier family 3 member 2(SLC3A2) Ferroptosis Schizophrenia

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