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Enhanced Nitrogen and Phosphorus Activation with an Optimized Bacterial Community by Endophytic Fungus Phomopsis liquidambari in Paddy Soil

2014年第七届中国模式真菌研讨会

作者： Lei Sun Xiaowei Yang Feifei Chen Rongpeng Li Xuesong Li Zhenxing Liu Yuyu Gu Xiaoyan Gong 刘中华 Hua Wei Ying Huang Sheng Yuan Jiangsu Key Laboratory for Microbes and functional genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial ResourcesCollege of Life ScienceNanjing Normal University

Fission yeast cells express Rp132-2 highly while Rp132-1 lowly in log phase;in contrast,expression of Rp132-1 raises and reaches a peak level while Rpi32-2 is downregulated to a low basic level when cells enter into stationary *** of Rp132-1 inhibits cell growth while overexpression of Rp132-2 does *** rpl32-2 impairs cell growth more severely than deleting rpl32-1 *** growth impaired by deleting either paralog can be rescued completely by reintroducing rpl32-2,but only partly by *** of Rp132-1inhibits cell division,yielding 4c DNA and multiple septa,while overexpressed Rp132-2 promotes

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Enhanced Nitrogen and Phosphorus Activation with an Optimize...

Liquid laccase production by Phomopsis liquidambari B3accelerated phenolic acids degradation in long-term cropping soil of peanut

中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Mengjun Tang Qiang Zhu Fengmin Zhang Wei Zhang Jie Yuan Kai Sun Fangji Xu Chuanchao Dai Jiangsu Key Laboratory for Microbes and functional genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial ResourcesCollege of Life SciencesNanjing Normal University

The endophytic fungus Phomopsis liquidambari play a key role in habitat adaptation of rice(Oryza sativa L.) with potential multiple ***,our previous published work on this subject remains ***,we performed a soil nutrient(nitrogen and phosphorus) transformation with related functional genes and elucidated how rhizosphere microbiota vary their response to *** interaction throughout the plant’s life cycle under field conditions by Illumina Miseq sequencing platforms in a nutrient-limited paddy *** results showed that *** symbiosis decreased the nitrogen and phosphorus loss by 531.24 mg and 558.12 mg per pot,***,we suggest that the application of *** altered the activation of soil nitrogen and phosphorus functional genes to accelerate nutrient turnover in the rice ***-throughput sequencing with cooccurrence network and species-related network analysis further revealed that *** colonization influenced the patterns of microbiota shift in the rhizosphere,especially during the heading *** led to an optimized microbial community through the promotion and inhibition of indigenous soil microbes with a higher level of available nutrient *** study strongly proposes *** symbiosis as a useful candidate for improving N and P acquisition and utilization.

关键词： rhizosphere microbiota whole developmental stages fungal endophyte network analysis rice soil nutrient

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Liquid laccase production by Phomopsis liquidambari B3accele...

Quantum Dot Nanobeads-Labelled Lateral Flow Immunoassay Strip for Rapid and Sensitive detection of Salmonella Typhimurium Based on Strand Displacement Loop-Mediated Isothermal Amplification

2014年第七届中国模式真菌研讨会

作者：周俊 Li Kang Hong-Wei Wang Teng Yang Chuan-Chao Dai Jiangsu engineering and Technology research center for Industrialization of microbial Resources Jiangsu Key Laboratory for Microbes and Functional GenomicsCollege of Life SciencesNanjing Normal University

Food waste and wheat straw are waste products that pollute the *** if we make full use of them,they will be the resources which improve laccase production by the endophytic fungus Phomopsis liquidambari *** cultured *** B3 in medium containing food waste and wheat straw as the main nitrogen and carbon sources,*** fermentation products with high laccase activity were put into the continuously cropped soil of *** results show that laccase significantly(p<0.05) reduce the accumulation of phenolic acids in soil compare with other *** of denaturing gradient gel electrophoresis(DGGE) profiles show that bacterial and fungal community structure of rhizosphere soil were significantly affected by changes in phenolic acids *** decrease of phenolic acids and increase in dominant microorganisms resulted in the promotion of peanut seeding growth and *** technology provides a new idea for bioremediation of the continuous cropping soil,and helps to realize waste disposal and environment protection.

关键词： Food waste Wheat straw Phomopsis liquidambari B3 Laccase Phenolic acids Continuous cropping obstacle

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engineering 2022年第12期19卷 62-70页

作者： Yuting Shang Shuzhen Cai Qinghua Ye Qingping Wu Yanna Shao Xiaoying Qu Xinran Xiang Baoqing Zhou Yu Ding Moutong Chen Liang Xue Honghui Zhu Jumei Zhang Guangdong Provincial Key Laboratory of microbial Safety and Health&State Key Laboratory of Applied Microbiology Southern China&Institute of Microbiology Guangdong Academy of SciencesGuangzhou 510070China State Key Laboratory of Food Science and Technology&National engineering research center for functional Foods&Synergetic Innovation center of Food Safety&Joint International research Laboratory on Food Safety School of Food Science and TechnologyJiangnan UniversityWuxi 214122China

Rapid,sensitive,point-of-care detection of pathogenic bacteria is important for food *** this study,we developed a novel quantum dot nanobeads-labelled lateral flow immunoassay strip(QBs-labelled LFIAS)combined with strand displacement loop-mediated isothermal amplification(SD-LAMP)for quantitative Salmonella Typhimurium(ST)*** dot nanobeads(QBs)served as fluorescence reporters,providing good detection *** customizable strand displacement(SD)probe was used in LAMP to improve the specificity of the method and prevent by-product *** was based on a sandwich immunoassay.A fluorescence strip reader measured the fluorescence intensity(FI)of the test(T)line and control(C)*** linear detection range of the strip was 10^(2)–10^(8) colony forming units(CFU)·mL^(-1).The visual limit of detection was 10^(3) CFU·mL^(-1),indicating that the system was ten-fold more sensitive than AuNPs-labelled test *** specificity was analyzed in accordance with agarose gel outputs of polymerase chain reaction(PCR)and *** detected ST in foods with an acceptable recovery of 85%–110%.The method is rapid,simple,almost equipment-free,and suitable for bacterial detection in foods and for clinical diagnosis.

关键词： Salmonella Typhimurium Quantum dot nanobeads Lateral flow immunoassay strip Loop-mediated isothermal amplification Strand displacement probe

Liquid biopsies:DNA methylation analyses in circulating cell-free DNA

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Journal of Genetics and genomics 2018年第4期45卷 185-192页

作者： Hu Zeng Bo He Chengqi Yi Jinying Peng State Key Laboratory of Protein and Plant Gene research School of Life SciencesPeking University Peking-Tsinghua center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking University Synthetic and functional Biomolecules center College of Chemistry and Molecular EngineeringPeking University

Analysis of patient＇s materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA（cfDNA） is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. This re？view summarizes the various investigational applications of cfDNA methylation and its oxidized de？rivatives as biomarkers for cancer diagnosis, prenatal diagnosis and organ transplantation *** review also provides a brief overview of the technologies for cfDNA methylation analysis based on next generation sequencing.

关键词： Circulating cell-free DNA DNA methylation Cancer detection Biomarkers Methylation analysis methods

Whole genome engineering by synthesis

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Science China(Life Sciences) 2018年第12期61卷 1515-1527页

作者： Zhouqing Luo Qing Yang Binan Geng Shuangying Jiang Shihui Yang Xiaozheng Li Yizhi Cai Junbiao Dai Shenzhen Key Laboratory of Synthetic genomics and center for Synthetic genomics Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Hubei Collaborative Innovation center for Green Transformation of Bio-resources Environmental Microbial Technology Center of Hubei Province Hubei Key Laboratory of Industrial Biotechnology College of Life Sciences Hubei University College of Life Sciences and Oceanography Shenzhen University College Manchester Institute of Biotechnology University of Manchester

Whole genome engineering is now feasible with the aid of genome editing and synthesis tools. Synthesizing a genome from scratch allows modifications of the genomic structure and function to an extent that was hitherto not possible, which will finally lead to new insights into the basic principles of life and enable valuable applications. With several recent genome synthesis projects as examples, the technical details to synthesize a genome and applications of synthetic genome are addressed in this perspective. A series of ongoing or future synthetic genomics projects, including the different genomes to be synthesized in GPwrite, synthetic minimal genome, massively recoded genome, chimeric genome and synthetic genome with expanded genetic alphabet, are also discussed here with a special focus on theoretical and technical impediments in the design and synthesis process. Synthetic genomics will become a commonplace to engineer pathways and genomes according to arbitrary sets of design principles with the development of high-efficient, low-cost genome synthesis and assembly technologies.

关键词： synthetic biology synthetic genome genome engineering functional genomics genome design

Iron and lead ion adsorption by microbial flocculants in synthetic wastewater and their related carbonate formation

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Journal of Environmental Sciences 2013年第12期25卷 2422-2428页

作者： Minjie Yao Bin Lian Hailiang Dong Jianchao Hao Congqiang Liu State Key Laboratory of Environmental Geochemistry Institute of GeochemistryChinese Academy of Sciences Key Laboratory of Environmental and Applied Microbiology Chengdu Institute of BiologyChinese Academy of Sciences Jiangsu Key Laboratory for Microbes and functional genomics Jiangsu Engineering and Technology Research Center for MicrobiologyCollege of Life ScienceNanjing Normal University State Key Laboratory of Geobiology and Environmental Geology China University of Geosciences Department of Geology and Environmental Earth Science Miami University

Although microbial treatments of heavy metal ions in wastewater have been studied, the removal of these metals through incorporation into carbonate minerals has rarely been reported. To investigate the removal of Fe^3＋ and Pb^2＋, two representative metals in wastewater, through the precipitation of carbonate minerals by a microbial flocculant （MBF） produced by Bacillus mucilaginosus. MBF was added to synthetic wastewater containing different Fe^3＋ and Pb^2＋ concentrations, and the extent of flocculation was analyzed. CO2 was bubbled into the mixture of MBF and Fe^3＋/Pb^2＋ to initiate the reaction. The solid substrates were analyzed via X-ray diffraction, transmission electron microscopy and energy dispersive spectroscopy. The results showed that the removal efficiency decreased and the MBF adsorption capacity for metals increased with increasing heavy metal concentration. In the system containing MBF, metals （Fe^3＋ and Pb^2＋）, and CO2, the concentrated metals adsorbed onto the MBF combined with the dissolved CO2, resulting in oversaturation of metal carbonate minerals to form iron carbonate and lead carbonates. These results may be used in designing a method in which microbes can be utilized to combine CO2 with wastewater heavy metals to form carbonates, with the aim of mitigating environmental problems.

关键词： Bacillus mucilaginosus microbial flocculation wastewater treatment carbon dioxide fixation mineral carbonation

The Value and Significance of Metagenomics of Marine Environments

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genomics, Proteomics & Bioinformatics 2015年第5期13卷 271-274页

作者： Fangqing Zhao Vladimir B.Bajic Computational genomics Lab Beijing Institutes of Life ScienceChinese Academy of Sciences Computational Bioscience research center (CBRC) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST)

Microbes have played a fundamental role in the natural his- tory of our planet, and have done so for billions of years. They have adapted to Earth＇s many environments from the mild to the very extreme. Studying their diversity and their way of life is critical for understanding their full impact on the global ecology. Although the field of metagenomics is still young, it has unravelled a wider microbial diversity that had otherwise been completely overlooked by the traditional methods of microbiology. There are three major metagenomic themes：（a） marker metagenomics that surveys microbial community structure by targeting the highly-conserved 16S rRNA gene, （b） functional metagenomics that takes the total environmental DNA, from which it infers the metabolic potential of the microbial community, and （c） identification of novel enzymes.

关键词： The Value and Significance of Metagenomics of Marine Environments

From Receptor-Like Kinases to Calcium Spikes： What Are the Missing Links？

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Molecular Plant 2014年第10期7卷 1501-1504页

作者： Feng Yu[a],, Wang Tian[b], Sheng Luan[b],[c], a Hunan Province Key Laboratory of Plant functional genomics and Developmental Regulation Hunan University Changsha 410082 P.R. Chinab Department of Plant and Microbial Biology University of California Berkeley CA 94720 USAc NJU-NJFU Joint Institute for Plant Molecular Biology School of Life Sciences Nanjing University Nanjing 210093 P.R. China

As sessile organisms, plants have evolved with complex signaling networks to cope with the constantly changing environment. Receptor-like kinases （RLKs） and calcium both play important roles during the early stage of envi- ronmental responses in plants. RLKs are trans-membrane receptor kinases that sense extracellular signals, such as hormones, peptides, and pathogens, and trigger sig- nal transduction pathways leading to cellular responses （Osakabe et al., 2013）.

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Antiviral function of peptidoglycan recognition protein in Spodoptera exigua(Lepidoptera:Noctuidae)

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Insect Science 2023年第4期30卷 1092-1104页

作者： Jie Li Jie Li Zhaohao Jing Qianlong Yu Guiling Zheng Bin Zhang Longsheng Xing Huan Zhang Fanghao Wan Changyou Li Shandong engineering research center for Environment-Friendly Agricultural Pest Management Cllege of Plant Health and MedicineQingdao Agricultural UniversityQingdaoChina Agricultural genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhenChina Institute of Zoology Chinese Academy of SciencesBejingChina

Peptidoglycan recognition proteins(PGRPs)are a class of molecules that play a critical role in insect *** the function of PGRPs is important to improve the efficiency of microbial *** this study,we investigated the role of PGRP-LB(a long type PGRP)in insect immunity against viruses using Spodoptera exigua and Spodoptera exigua multiple nucleopolyhedrovirus(SeMNPV)as an insect-virus *** cloned and identified a PGRP-LB gene from ***;the gene consisted of 7 exons that encoded a polypeptide of 234 amino acids with a signal peptide and a typical amidase *** analysis revealed that the abundance of SePGRP-LB transcripts in the fat body was greater than in other *** of SePGRP-LB resulted in a significant decrease of 49%in the rate of SeMNPV-infected *** addition,the multiplication of SeMNPV was significantly decreased:a decrease of 79%in the production of occlusion-derived virion(ODV),and a maximum decrease of 50%in the production of budded virion(BV).In contrast,silencing of SePGRP-LB expression by RNA interference resulted in a significant 1.65-fold increase in the rate of SeMNPV-infected cells,a significant 0.54-fold increase in ODV production,a maximum 1.57-fold increase in BV production,and the larval survival dropped to 21%.Our findings show that SePGRP-LB has an antiviral function against SeMNPV,and therefore this gene may provide a target for lepidopteran pest control using virus insecticides.

关键词： antiviral long-type peptidoglycan recognition protein gene PGRP-LB Spodoptera exigua multiple nucleopolyhedrovirus Spodoptera exigua