Biochemistry

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    Protocols in Current Issue
    Isolation of Tumor Cells Based on Their Distance from Blood Vessels
    Authors:  Saran Kumar, Husni Sharife, Tirzah Kreisel, Libat Bar-Lev, Myriam Grunewald and Eli Keshet, date: 05/20/2020, view: 1351, Q&A: 0
    [Abstract] Differential exposure of tumor cells to microenvironmental cues greatly impacts cell phenotypes, raising a need for position based sorting of tumor cells amenable to multiple OMICs and functional analyses. One such key determinant of tumor heterogeneity in solid tumors is its vasculature. Proximity to blood vessels (BVs) profoundly affects tumor ...
    Negative Ion Mode nanoLC-ESI-MS/MS Analyses of Permethylated Sulfated Glycans
    Authors:  Shin-Yi Yu, Chu-Wen Cheng and Kay-Hooi Khoo, date: 05/20/2020, view: 1006, Q&A: 0
    [Abstract] We have developed enabling techniques for sulfoglycomics based on MALDI-MS mapping and MS/MS sequencing of permethylated sulfated glycans. We then extended further the analytical workflow to C18 reverse phase (RP)-nanoLC-nanoESI-MS/MS analyses of permethylated sulfated glycans in the negative ion mode. The advantages are that extra sulfates on ...
    Permethylation and Microfractionation of Sulfated Glycans for MS Analysis
    Authors:  Shin-Yi Yu, Sergei Snovida and Kay-Hooi Khoo, date: 05/20/2020, view: 1084, Q&A: 0
    [Abstract] Sulfated glycans are barely detectable in routine mass spectrometry (MS)-based glycomic analysis due to ion suppression by the significantly more abundant neutral glycans in the positive ion mode, and sialylated non-sulfated glycans in the negative ion mode, respectively. Nevertheless, the negative charge imparted by sulfate can be advantageous ...
    Single-run HPLC Quantification of Plant Cell Wall Monosaccharides
    [Abstract] The plant cell wall is a complex network of polysaccharides and proteins that provides strength and structural integrity to plant cells, as well as playing a vital role in growth, development, and defense response. Cell wall polysaccharides can be broadly grouped into three categories: cellulose, pectins, and hemicelluloses. Dynamic interactions ...
    Steady-state and Flux-based Trehalose Estimation as an Indicator of Carbon Flow from Gluconeogenesis or Glycolysis
    Authors:  Ritu Gupta and Sunil Laxman, date: 01/05/2020, view: 1512, Q&A: 0
    [Abstract] Trehalose (and glycogen) is a major storage carbohydrate in many cells, including S. cerevisiae. Typically, trehalose (a disaccharide of glucose) is synthesized and stored through gluconeogenesis. However, trehalose can also be made directly from glucose, if glucose-6-phosphate is channeled away from glycolysis or pentose phosphate ...
    Analysis of Monosaccharides from Arabidopsis Seed Mucilage and Whole Seeds Using HPAEC-PAD
    Authors:  Gillian H. Dean, Kresimir Sola, Faride Unda, Shawn D. Mansfield and George W. Haughn, date: 12/20/2019, view: 1693, Q&A: 0
    [Abstract] Arabidopsis seed coat epidermal cells deposit a significant quantity of mucilage, composed of the cell wall components pectin, hemicellulose, and cellulose, into the apoplast during development. When mature seeds are hydrated, mucilage extrudes to form a gelatinous capsule around the seed. Determining the monosaccharide composition of ...
    Purification and HPLC Analysis of Cell Wall Muropeptides from Caulobacter crescentus
    Authors:  Gabriele Stankeviciute and Eric A. Klein, date: 11/05/2019, view: 1522, Q&A: 0
    [Abstract] The peptidoglycan sacculus, or cell wall, is what defines bacterial cell shape. Cell wall composition can be best characterized at the molecular level by digesting the peptidoglycan murein polymer into its muropeptide subunits and quantifying the abundance of muropeptides using high-pressure liquid chromatography. Certain features of the cell wall ...
    A Robust, One-step FRET Assay for Human Heparanase
    Authors:  Jyothi C. Sistla and Umesh R. Desai, date: 09/05/2019, view: 1578, Q&A: 0
    [Abstract] Heparanase, an endo-β-D-glucuronidase, cleaves cell surface and extracellular matrix heparan sulfate (HS) chains at distinct sites and plays important biological roles including modulation of cell growth and metastasis. Although a number of different types of heparanase assays have been reported to date, most are labor intensive, complex ...
    Glucosidase Inhibition to Study Calnexin-assisted Glycoprotein Folding in Cells
    Authors:  Hao Wang and Qingyu Wu, date: 06/05/2019, view: 2066, Q&A: 0
    [Abstract] Calnexin is a chaperone protein that plays a critical role in glycoprotein folding in the endoplasmic reticulum (ER). The function of calnexin depends on its binding to monoglucosylated oligosaccharides on nascent glycoproteins, whereas the generation of monoglucosylated oligosaccharides depends on the activity of α-glucosidases I and II, which ...
    Biofilm Formation Assay in Pseudomonas syringae
    Authors:  Xiaolong Shao, Yingpeng Xie, Yingchao Zhang and Xin Deng, date: 05/20/2019, view: 4633, Q&A: 0
    [Abstract] Pseudomonas syringae is a model plant pathogen that infects more than 50 plant species worldwide, thus leading to significant yield loss. Pseudomonas biofilm always adheres to the surfaces of medical devices or host cells, thereby contributing to infection. Biofilm formation can be visualized on numerous matrixes, including ...



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