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Nanjing Agricultural University

17 ARTICLES PUBLISHED IN JoVE

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Biology

A Technique for Serial Collection of Cerebrospinal Fluid from the Cisterna Magna in Mouse
Li Liu 1, Karen Duff 1
1Department of Pathology, Columbia University

Transgenic (Tg) mouse models of AD provide an excellent opportunity to investigate how and why Aβ or tau levels in CSF change as the disease progresses in human patients. Here, we demonstrate a refined cisterna magna puncture technique for serial CSF sampling from the mouse.

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JoVE Journal

Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution
Li Liu 1, Lauren Boldon 1, Melissa Urquhart 1, Xiangyu Wang 1
1Department of Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute

The demonstration of the small and wide angle X-ray scattering (SWAXS) procedure has become instrumental in the study of biological macromolecules. Through the use of the instrumentation and procedures of specific angle methods and preparation, the experimental data from the SWAXS displays the atomic and nano-scale characterization of macromolecules.

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Biology

Determination of Sialic Acids in Liver and Milk Samples of Wild-type and CMAH Knock-out Mice.
Cui Cao 1, Wen J. Wang 1, Ying Y. Huang 1, Hong L. Yao 1, Louis P. Conway 1, Li Liu 1, Josef Voglmeir 1
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.

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JoVE Journal

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Dechun Zhang *1, Xianzhao Kan *2, Sarah Elizabeth Huss 3, Lan Jiang 2, Li-Qing Chen 3, Yibing Hu 4
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.

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Bioengineering

Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array
Yasumasa Mashimo 1,2, Momoko Yoshioka 1, Yumie Tokunaga 1, Christopher Fockenberg 1, Shiho Terada 1, Yoshie Koyama 1, Teiko Shibata-Seki 2, Koki Yoshimoto 1, Risako Sakai 1, Hayase Hakariya 1, Li Liu 1, Toshihiro Akaike 3, Eiry Kobatake 2, Siew-Eng How 4, Motonari Uesugi 1,5, Yong Chen 1,6, Ken-ichiro Kamei 1
1Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, 2Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 3Biomaterials Center for Regenerative Medical Engineering, Foundation for Advancement of International Science, 4Faculty of Science and Natural Resources, Universiti Malaysia Sabah, 5Institute for Chemical Research, Kyoto University, 6Ecole Normale Supérieure

This article describes the detailed methodology to prepare a Multiplexed Artificial Cellular MicroEnvironment (MACME) array for high-throughput manipulation of physical and chemical cues mimicking in vivo cellular microenvironments and to identify the optimal cellular environment for human pluripotent stem cells (hPSCs) with single-cell profiling.

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Immunology and Infection

Intracranial Subarachnoidal Route of Infection for Investigating Roles of Streptococcus suis Biofilms in Meningitis in a Mouse Infection Model
Shouming Zhang 1,2,3, Xueping Gao 1,2,3, Genhui Xiao 1,2,3,4, Chengping Lu 1,2,3, Huochun Yao 1,2,3, Hongjie Fan 1,2,3,5, Zongfu Wu 1,2,3
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.

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Biochemistry

Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+
Ya-Min Du 1, Shen-Li Zheng 1, Li Liu 1, Josef Voglmeir 1, Gabriel Yedid 2
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).

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Environment

Preparation of Biomass-based Mesoporous Carbon with Higher Nitrogen-/Oxygen-chelating Adsorption for Cu(II) Through Microwave Pre-Pyrolysis
Kunquan Li 1, Zeqing Wan 1
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.

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Bioengineering

A Converging Strategy for the Generation of a Virtually Sequenced cDNA Library from Unreferenced Pacific Oysters
Yong M. Lyu 1, Yu Q. Li 1, Hui B. Song 1, Juan Guo 1, Ting Wang 1, Li Liu 1, Gabriel Yedid 2, Josef Voglmeir 1
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.

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Bioengineering

Bioinspired Soft Robot with Incorporated Microelectrodes
Ting Wang 1,2, Bianca Migliori 1,3, Beatrice Miccoli 1,4, Su Ryon Shin 1
1Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 2School of Medicine, Jiangsu University, 3Tech4Health and Neuroscience Institutes, NYU Langone Health, 4Department of Electronics and Telecommunication, Politecnico di Torino

A bioinspired scaffold is fabricated by a soft photolithography technique using mechanically robust and electrically conductive hydrogels. The micropatterned hydrogels provide directional cardiomyocyte cell alignment, resulting in a tailored direction of actuation. Flexible microelectrodes are also integrated into the scaffold to bring electrical controllability for a self-actuating cardiac tissue.

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Biochemistry

Plant Sample Preparation for Nucleoside/Nucleotide Content Measurement with An HPLC-MS/MS
Changhua Zhu *1, Xiaoye Liu *2, Wenlei Wang 1, Xiaoguang Chen 3, Shangyu Gao 1, Meng Qian 1, Na Yang 1, Yifeng Xu 1, Mingjia Chen 1
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.

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Biology

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
Xiaoyuan Tao *1,2, Mengtao Gao *3, Siyuan Wang *1, Xueying Guan 1,4
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.

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Medicine

Interphase Fluorescence in situ Hybridization of Bone Marrow Smears of Multiple Myeloma
Yalan Yu *1, Hui Shen *1, Li Liu 1, Ping Luo 1, Sanyun Wu 1, Jing He 1,2, Xiqin Tong 1, Yufeng Shang 1, Liang Shao 1, Fuling Zhou 1
1Department of Hematology, Zhongnan Hospital of Wuhan University, 2Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology

Here, we present a protocol for improving the success of interphase fluorescence in situ hybridization detection on bone marrow smears from multiple myeloma patients.

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Environment

Application of the Intelligent High-Throughput Antimicrobial Sensitivity Testing/Phage Screening System and Lar Index of Antimicrobial Resistance
Ming Hu 1, Zhengjie Liu 1,2, Ziang Song 1,3, Lulu Li 1, Xiaonan Zhao 1, Yanbo Luo 1, Qing Zhang 1, Yibao Chen 1, Xiaohui Xu 1, Yahui Dong 1, Nataliia Hrabchenko 1, Wei Zhang 3, Yuqing Liu 1
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.

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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 Ren 1,2, Yuan-xi Li 1,2, Zhi-chao Yan 1,2,3
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.

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Environment

Measuring Bacterial Colonization on Arabidopsis thaliana Roots in Hydroponic Condition
Xia Shu 1,2, Huatai Li 1, Jing Wang 3, Shan Wang 4, Yunpeng Liu 1, Ruifu Zhang 1,3
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.

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Biology

An Approach to Constructing Multispecies Biofilm Communities from Rhizosphere Soil
Pan Wang 1, Bin Xia 1, Zhiyuan Chen 1, Jiyu Xie 1, Xinli Sun 1, Qingyun Tian 2, Chun-hui Gao 2, Weibin Xun 1, Nan Zhang 1, Ruifu Zhang 1, Qirong Shen 1, Zhihui Xu 1
1Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key lab of organic-based fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, 2National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University

A rapid and standardized procedure for establishing synergistic multispecies biofilm communities from various rhizosphere soils is presented here. It is a unique protocol designed to probe and simulate the complex rhizosphere soil microbiota.

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