Systems Biology

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    Protocols in Current Issue
    Metabolomic and Lipidomic Analysis of Bone Marrow Derived Macrophages
    Authors:  Gretchen L. Seim, Steven V. John and Jing Fan, date: 07/20/2020, view: 284, Q&A: 0
    [Abstract] Macrophages are highly plastic immune cells that are capable of adopting a wide array of functional phenotypes in response to environmental stimuli. The changes in macrophage function are often supported and regulated by changes in cellular metabolism. Capturing a comprehensive picture of metabolism is vital for understanding the role of metabolic ...
    Experiments for in silico evaluation of Optimality of Photosynthetic Nitrogen Distribution and Partitioning in the Canopy: an Example Using Greenhouse Cucumber Plants
    Authors:  Yi-Chen Pao, Tsu-Wei Chen, Dany Pascal Moualeu-Ngangue and Hartmut Stützel, date: 03/20/2020, view: 1049, Q&A: 0
    [Abstract] Acclimation of leaf traits to fluctuating environments is a key mechanism to maximize fitness. One of the most important strategies in acclimation to changing light is to maintain efficient utilization of nitrogen in the photosynthetic apparatus by continuous modifications of between-leaf distribution along the canopy depth and within-leaf ...
    Isolation and Quantification of Metabolite Levels in Murine Tumor Interstitial Fluid by LC/MS
    Authors:  Mark R Sullivan, Caroline A Lewis and Alexander Muir, date: 11/20/2019, view: 2547, Q&A: 0
    [Abstract] Cancer is a disease characterized by altered metabolism, and there has been renewed interest in understanding the metabolism of tumors. Even though nutrient availability is a critical determinant of tumor metabolism, there has been little systematic study of the nutrients directly available to cancer cells in the tumor microenvironment. Previous ...
    Non-aqueous Fractionation (NAF) for Metabolite Analysis in Subcellular Compartments of Arabidopsis Leaf Tissues
    [Abstract] The accurate determination of metabolite distribution in subcellular compartments is still challenging in plant science. Various methodologies, such as fluorescence resonance energy transfer-based technology, nuclear magnetic resonance spectroscopy and protoplast fractionation allow the study of metabolite compartmentation. However, large changes ...
    Use of Gas Chromatography to Quantify Short Chain Fatty Acids in the Serum, Colonic Luminal Content and Feces of Mice
    [Abstract] Short-Chain Fatty Acids (SCFAs) are a product of the fermentation of resistant starches and dietary fibers by the gut microbiota. The most important SCFA are acetate (C2), propionate (C3) and butyrate (C4). These metabolites are formed and absorbed in the colon and then transported through the hepatic vein to the liver. SCFAs are more concentrated ...
    Stable-isotope Labeled Metabolic Analysis in Drosophila melanogaster: From Experimental Setup to Data Analysis
    Authors:  Yuping Cai, Nan Liu and Zheng-Jiang Zhu, date: 09/20/2018, view: 3229, Q&A: 0
    [Abstract] Stable-isotope labeled metabolic analysis is an essential methodology to characterize metabolic regulation during biological processes. However, the method using stable-isotope-labeled tracer (e.g., 13C-glucose) in live animal is only beginning to be developed. Here, we contribute a qualitative metabolic labeling experiment ...
    Extraction and Analysis of Pan-metabolome Polar Metabolites by Ultra Performance Liquid Chromatography–Tandem Mass Spectrometry (UPLC-MS/MS)
    Authors:  Dania M. Malik, Seth Rhoades and Aalim Weljie, date: 02/05/2018, view: 4682, Q&A: 0
    [Abstract] Modern triple quadrupole mass spectrometers provide the ability to detect and quantify a large number of metabolites using tandem mass spectrometry (MS/MS). Liquid chromatography (LC) is advantageous, as it does not require derivatization procedures and a large diversity in physiochemical characteristics of analytes can be accommodated through a ...
    Identification and Quantification of Secondary Metabolites by LC-MS from Plant-associated Pseudomonas aurantiaca and Pseudomonas chlororaphis
    Authors:  Izzah Shahid, Muhammad Rizwan and Samina Mehnaz, date: 01/20/2018, view: 6798, Q&A: 0
    [Abstract] Increased antibiotic resistance of plants and human pathogens and continuous use of chemical fertilizers has pushed microbiologists to explore new microbial sources as potential antagonists. In this study, eight strains of Pseudomonas aurantiaca and Pseudomonas chlororaphis, have been isolated from different plant sources and ...
    Lipidomic Analysis of Caenorhabditis elegans Embryos
    Authors:  Hung-Chi Yang, Cheng-Yu Hung, Yi-Yun Pan, Szecheng J Lo and Daniel Tsun-Yee Chiu, date: 09/20/2017, view: 6123, Q&A: 0
    [Abstract] Metabolomic is an emerging field of system biology. Lipidomic, a branch of metabolomic, aims to characterize lipophilic metabolites in biological systems. Caenorhabditis elegans (C. elegans) is a genetically tractable and versatile animal model for novel discovery of lipid metabolism. In addition, C. elegans embryo is ...
    Metabolite Profiling of Mature Arabidopsis thaliana Seeds Using Gas Chromatography-Mass Spectrometry (GC-MS)
    Authors:  Hagai Cohen, Ifat Matityahu and Rachel Amir, date: 11/05/2016, view: 7669, Q&A: 0
    [Abstract] Metabolite profiling using gas chromatography-mass spectrometry (GC-MS) permits the annotation and quantification of a relatively wide variety of metabolites, covering a wide range of biochemical groups of metabolites. Lisec et al. (2006) established a method for GC-MS profiling in plants. Based on this protocol, we provide here a ...



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