Nanjing Agricultural University 11 articles published in JoVE Environment Measuring Bacterial Colonization on Arabidopsis thaliana Roots in Hydroponic Condition Xia Shu1,2, Huatai Li1, Jing Wang3, Shan Wang4, Yunpeng Liu1, Ruifu Zhang1,3 1State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 2State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 3Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 4Jiangsu Engineering and Technology Center for Modern Horticulture, Jiangsu Vocational College of Agriculture and Forestry Colonization of plant growth-promoting rhizobacteria (PGPR) in the rhizosphere is essential for its growth-promoting effect. It is necessary to standardize the method of detection of bacterial rhizosphere colonization. Here, we describe a reproducible method for quantifying bacterial colonization on the root surface. Biochemistry Extracting Venom from the Parasitoid Wasp Trichogramma dendrolimi Using an Artificial Host Hai-yan Wang*1,2, Ze-qi Yu*1,2, Xin-yue Ren1,2, Yuan-xi Li1,2, Zhi-chao Yan1,2,3 1Department of Entomology, Nanjing Agricultural University, 2Key Laboratory of Integrated Pest Management of Crop of East China, Ministry of Agriculture, 3Sanya Institute of Nanjing Agricultural University Here, we present a protocol for extracting venom from Trichogramma dendrolimi using an artificial host created with polyethylene film and amino acid solution. Environment Application of the Intelligent High-Throughput Antimicrobial Sensitivity Testing/Phage Screening System and Lar Index of Antimicrobial Resistance Ming Hu1, Zhengjie Liu1,2, Ziang Song1,3, Lulu Li1, Xiaonan Zhao1, Yanbo Luo1, Qing Zhang1, Yibao Chen1, Xiaohui Xu1, Yahui Dong1, Nataliia Hrabchenko1, Wei Zhang3, Yuqing Liu1 1Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, P.R. China, Key Laboratory of Livestock and Poultry Multi-omics of MARA, 2Department of Genetic and Genomes Biology, University of Leicester, 3College of Veterinary Medicine, Nanjing Agricultural University Here we introduce the principle, structure, and instruction of the intelligent high-throughput antimicrobial sensitivity testing/phage screening system. Its application is illustrated by using Salmonella isolated from poultry in Shandong, China, as an example. The Lar index is calculated, and its significance in evaluating antimicrobial resistance is discussed comprehensively. Biology Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation Xiaoyuan Tao*1,2, Mengtao Gao*3, Siyuan Wang*1, Xueying Guan1,4 1College of Agriculture and Biotechnology, Zhejiang University, 2Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, 3State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 4Hainan Institute of Zhejiang University Cleavage under targets and tagmentation (CUT&Tag) is an efficient chromatin epigenomic profiling strategy. This protocol presents a refined CUT&Tag strategy for the profiling of histone modifications in plants. Biochemistry Plant Sample Preparation for Nucleoside/Nucleotide Content Measurement with An HPLC-MS/MS Changhua Zhu*1, Xiaoye Liu*2, Wenlei Wang1, Xiaoguang Chen3, Shangyu Gao1, Meng Qian1, Na Yang1, Yifeng Xu1, Mingjia Chen1 1College of Life Sciences, Nanjing Agricultural University, 2Department of Criminal Science and Technology, Nanjing Forest Police College, 3Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover A precise and reproducible method for in vivo nucleosides/nucleotides quantification in plants is described here. This method employs an HPLC-MS/MS. Bioengineering A Converging Strategy for the Generation of a Virtually Sequenced cDNA Library from Unreferenced Pacific Oysters Yong M. Lyu1, Yu Q. Li1, Hui B. Song1, Juan Guo1, Ting Wang1, Li Liu1, Gabriel Yedid2, Josef Voglmeir1 1Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 2College of Life Science, Nanjing Agricultural University We describe a strategy for how to use RNA samples from unreferenced Pacific oyster specimens, and evaluate the genetic material by comparison with publicly available genome data to generate a virtually sequenced cDNA library. Environment Preparation of Biomass-based Mesoporous Carbon with Higher Nitrogen-/Oxygen-chelating Adsorption for Cu(II) Through Microwave Pre-Pyrolysis Kunquan Li1, Zeqing Wan1 1College of Engineering, Nanjing Agricultural University Here, we present a protocol to synthesize nitrogen/oxygen dual-doped mesoporous carbon from biomass by chemical activation in different pyrolysis modes followed by modification. We demonstrate that the microwave pyrolysis benefits the subsequent modification process to simultaneously introduce more nitrogen and oxygen functional groups on the carbon. Immunology and Infection Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin Dechun Zhang*1, Xianzhao Kan*2, Sarah Elizabeth Huss3, Lan Jiang2, Li-Qing Chen3, Yibing Hu4 1Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, 2The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, 3Department of Plant Biology, University of Illinois at Urbana-Champaign, 4College of Resources & Environmental Sciences, Nanjing Agricultural University A method of constructing a phylogenetic tree based on sequence homology of SWEETs from eukaryotes and SemiSWEETs from prokaryotes is described. Phylogenetic analysis is a useful tool for explaining the evolutionary relatedness between homologous proteins or genes from different organism groups. Immunology and Infection Intracranial Subarachnoidal Route of Infection for Investigating Roles of Streptococcus suis Biofilms in Meningitis in a Mouse Infection Model Shouming Zhang1,2,3, Xueping Gao1,2,3, Genhui Xiao1,2,3,4, Chengping Lu1,2,3, Huochun Yao1,2,3, Hongjie Fan1,2,3,5, Zongfu Wu1,2,3 1College of Veterinary Medicine, Nanjing Agricultural University, 2Key Lab of Animal Bacteriology, Ministry of Agriculture, 3OIE Reference Lab for Swine Streptococcosis, 4School of Medicine, Tsinghua University, 5Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses Here, we describe the intracranial subarachnoidal route of infection in mice to study roles of biofilms in Streptococcus suis meningitis. This infection model is also suitable for studying the pathogenesis of other bacterial meningitis and the efficacy of new drugs against bacterial meningitis. Biochemistry Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+ Ya-Min Du1, Shen-Li Zheng1, Li Liu1, Josef Voglmeir1, Gabriel Yedid2 1Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 2College of Life Science, Nanjing Agricultural University We describe a simple and rapid method for the preparation and analysis of N-glycans from different cultivars of radish (Raphanus sativus). Biology Determination of Sialic Acids in Liver and Milk Samples of Wild-type and CMAH Knock-out Mice. Cui Cao1, Wen J. Wang1, Ying Y. Huang1, Hong L. Yao1, Louis P. Conway1, Li Liu1, Josef Voglmeir1 1Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University We describe a HPLC-based method for the determination of N-acetylneuraminic acid and N-glycolylenuraminic acid in mouse liver and milk.
