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    Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Endosome and Lysosome Isolation from Eukaryotic Cell

    Here, we report our step-by-step protocol for superparamagnetic nanoparticle (SPMNP)-based endosome and lysosome isolation from HeLa. Briefly, we synthesized SPMNP 1.0 with iron oxide (Fe3O4) core using thermal d...

    Deepak B. Thimiri Govinda Raj, Niamat Ali Khan, Srisaran Venkatachalam, Dinh Toi Chu (2019)

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    Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Plasma Membrane Isolation from Eukaryotic Cell

    Here, we elaborate our detailed protocol for synthesis, functionalization, and application of superparamagnetic nanoparticle (SPMNP) for plasma membrane and lysosome isolation. We used standard thermal decompo...

    Deepak B. Thimiri Govinda Raj, Niamat Ali Khan, Srisaran Venkatachalam, Dinh Toi Chu (2019)

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    Fabrication and Electrospinning of 3D Biodegradable Poly-l-Lactic Acid (PLLA) Nanofibers for Clinical Application

    Poly-l-lactic acid (PLLA) is a biodegradable synthetic polyester synthesized by polymerization or polycondensation. PLLA hydrolytically degrades into lactic acid, a biocompatible metabolic by-product, making it s...

    Balasundari Ramesh, Kotturathu Mammen Cherian, Adegbenro Omotuyi John Fakoya (2019)

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    Simultaneous Isolation of Stem and Niche Cells of Skeletal Muscle: Applicability for Aging Studies

    The maintenance of adult stem cells in their normal quiescent state depends on intrinsic factors and extrinsic signals originating from their microenvironment (also known as the stem cell niche). In skeletal m...

    Eusebio Perdiguero, Victoria Moiseeva, Pura Muñoz-Cánoves (2019)

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    Total Nitrogen Determination by a Spectrophotometric Method

    Being able to measure total nitrogen (TN) is important for following the nitrogen budget. In this chapter, we present the spectrophotometric method we use for determining TN. The method relies on oxidation and...

    Jaana Koistinen, Mervi Sjöblom, Kristian Spilling (2019)

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    3D-Embedded Cell Cultures to Study Tendon Biology

    Tendons harbor various cell populations, including cells displaying classical adult mesenchymal stromal cell criteria. Previous studies have shown that a tenogenic phenotype is more effectively maintained in a...

    Renate Gehwolf, Gabriel Spitzer, Andrea Wagner, Christine Lehner, Nadja Weissenbacher (2019)

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    Representation of Proteins with Posttranslational Modifications in the HL7 SPL Standard

    The Health Level Seven (HL7) Structured Product Labeling (SPL) is an ANSI-accredited data exchange standard, which was adopted by the US Food and Drug Administration (FDA) for the exchange of health and regula...

    Yulia Borodina, Gunther Schadow (2019)

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    Analysis of Hematopoietic Niche in the Mouse Embryo

    The development, differentiation, and maturation of hematopoietic cells are regulated by the intrinsic and extrinsic regulation. Intrinsic activity is affected by cell autonomous gene expression and extrinsic ...

    Keai Sinn Tan, Nathalie Brouard, Daisuke Sugiyama (2019)

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    Metabolic Engineering of Microalgae for Biofuel Production

    Microalgae are considered as promising cell factories for the production of various types of biofuels, including bioethanol, biodiesel, and biohydrogen by using carbon dioxide and sunlight. In spite of unique ...

    Mohammad Pooya Naghshbandi, Meisam Tabatabaei, Mortaza Aghbashlo, Muhammad Nauman Aftab (2019)

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    Programmatic Retrieval of Small Molecule Information from PubChem Using PUG-REST

    PubChem ( is an open archive which contains information on small molecules as well as other chemical entities such as lipids, carb...

    Sunghwan Kim, Paul A. Thiessen, Evan E. Bolton (2019)

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    Predicting Tumor Growth and Ligand Dependence from mRNA by Combining Machine Learning with Mechanistic Modeling

    For successful treatment of cancer patients, it is crucial to identify subgroups that respond to certain types of targeted therapy. A key element for tumor growth is the abundance of receptors and binding of g...

    Helge Hass, Andreas Raue (2019)

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    Image-based Identification of Chemical Compounds Capable of Trapping FOXO in the Cell Nucleus

    Forkhead box O (FOXO) factors are tumor suppressor proteins commonly inactivated in human tumors. Furthermore, genetic variation within the FOXO3a gene is consistently associated with human longevity. FOXO pro...

    Susana Machado, Catarina Raposo, Bibiana I. Ferreira in FOXO Transcription Factors (2019)

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    High-Resolution Mapping of N 6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq)

    N 6-Methyladenosine, an abundant chemical modification in mRNA, plays crucial roles in regulating gene expression and biological processes. Research on m6A and its functions has progressed rapidly in the past fe...

    Phillip J. Hsu, Chuan He in Epitranscriptomics (2019)

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    Transgene Recombineering in Bacterial Artificial Chromosomes

    Bacterial Artificial Chromosome (BAC) libraries are a valuable research resource. Any one of the clones in these libraries can carry hundreds of thousands of base pairs of genetic information. Often the entire...

    Michael G. Zeidler, Thomas L. Saunders in Microinjection (2019)

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    Live Cell Imaging of Hepatitis C Virus Trafficking in Hepatocytes

    Standard fixed cell confocal microscopy is inherently limited in visualizing dynamic processes involving two- and three-dimensional movement. To overcome these limitations, live cell imaging approaches have be...

    Yasmine Baktash, Glenn Randall in Hepatitis C Virus Protocols (2019)

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    A Protocol to Study T-Cell Signaling in an Immune Synapse by Microscopy

    The immune synapse is a complex cellular structure that enables cell–cell communications between immune cells, mainly at the interface of an effector T-cell and an antigen-presenting cell (APC) that expresses ...

    Mobashar Hussain Urf Turabe Fazil, Pankaj Kumar, Navin Kumar Verma in T-Cell Motility (2019)

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    Monitoring of Interferon Response Triggered by Cells Infected by Hepatitis C Virus or Other Viruses Upon Cell–Cell Contact

    Plasmacytoid dendritic cells (pDCs) constitute a unique DC subset specialized in rapid and massive secretion of cytokines, including type I interferon (i.e., IFNα and IFNβ), known to be pivotal for both innate...

    Séverin Coléon, Sonia Assil, Marlène Dreux in Hepatitis C Virus Protocols (2019)

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    Single-Cell Library Preparation of iPSC-Derived Neural Stem Cells

    Single-cell RNA-seq technology allows for the identification of heterogeneous cell populations, measures stochastic gene expressions, and identifies highly variable genes. Thus, with this technology it is poss...

    Jeffrey Kim, Marcel M. Daadi in Neural Stem Cells (2019)

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    Chemical Synthesis of an Asymmetric Mimic of the Nitrogenase Active Site

    The synthetic inorganic chemistry of metal–sulfur (M-S, M = metals) clusters has played an important, complementary role to the biochemical analyses of nitrogenase toward a better understanding of the enzyme a...

    Kazuki Tanifuji, Yasuhiro Ohki in Metalloproteins (2019)

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    An In Vitro Three-Dimensional Organotypic Model to Analyze Peripancreatic Fat Invasion in Pancreatic Cancer: A Culture System Based on Collagen Gel Embedding

    Three-dimensional culture systems reflect biological environments better than conventional two-dimensional culture. Additionally, three-dimensional culture is a strong experimental tool to analyze direct inter...

    Takashi Okumura, Kenoki Ohuchida, Masafumi Nakamura in Pancreatic Cancer (2019)

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