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    A Xenograft Model for Venous Malformation

    Xenograft models allow for an in vivo approach to monitor cellular functions within the context of a host microenvironment. Here we describe a protocol to generate a xenograft model of venous malformation (VM)...

    Jillian Goines, Elisa Boscolo in Vascular Morphogenesis (2021)

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    Computational Detection of Plant RNA Editing Events

    手机体育投注平台 Computers are able to systematically exploit RNA-seq data allowing us to efficiently detect RNA editing sites in a genome-wide scale. This chapter introduces a very flexible computational framework for detecti...

    Alejandro A. Edera, M. Virginia Sanchez-Puerta in RNA Editing (2021)

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    Spatial Statistics-Based Image Analysis Methods for the Study of Vascular Morphogenesis

    Several studies are available addressing the mechanisms of vascular morphogenesis in order to unravel how cooperative cell behavior can follow from the underlying, genetically regulated behavior of endothelial...

    Diego Guidolin, Cinzia Tortorella, Domenico Ribatti in Vascular Morphogenesis (2021)

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    Assessment of Vascular Patterning in the Zebrafish

    手机体育投注平台 The zebrafish has emerged as a valuable and important model organism for studying vascular development and vascular biology. Here, we discuss some of the approaches used to study vessels in fish, including los...

    Amber N. Stratman, Brant M. Weinstein in Vascular Morphogenesis (2021)

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    C-to-U RNA Editing: From Computational Detection to Experimental Validation

    手机体育投注平台 The AID/APOBEC family of enzymes are cytidine deaminases that act upon DNA and RNA. Among APOBECs, the best characterized family member to act on RNA is the enzyme APOBEC1. APOBEC1-mediated RNA editing plays a...

    Taga Lerner, Mitchell Kluesner, Rafail Nikolaos Tasakis in RNA Editing (2021)

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    Avians as a Model System of Vascular Development

    For more than 2000 years, the avian embryo has helped scientists understand questions of developmental and cell biology. As early as 350 BC Aristotle described embryonic development inside a chicken egg (Aristotl...

    Rieko Asai, Michael Bressan, Takashi Mikawa in Vascular Morphogenesis (2021)

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    Adenosine-to-Inosine RNA Editing Enzyme ADAR and microRNAs

    手机体育投注平台 RNA is subjected to over 100 different types of chemical modifications inside the cell. These modifications have various effects on its function and expression, resulting in RNA diversity. RNA editing or conve...

    Kang Yuting, Dan Ding, Hisashi Iizasa in RNA Editing (2021)

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    Co-transcriptional Analysis of Self-Cleaving Ribozymes and Their Ligand Dependence

    Self-cleaving ribozymes are RNA molecules that catalyze a site-specific self-scission reaction. Analysis of self-cleavage is a crucial aspect of the biochemical study and understanding of these molecules. Here...

    Luiz F. M. Passalacqua, Andrej Lupták in Ribozymes (2021)

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    Analysis of Lipids in Ceramide-Enriched Membrane Domains

    Ceramide can be generated on cell surfaces by the activity of the acid sphingomyelinase. The unique biophysical properties of ceramide result in the self-formation of small ceramide-enriched membrane domains t...

    Alexander Carpinteiro, Erich Gulbins in Lipid Rafts (2021)

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    Discovering A-to-I RNA Editing Through Chemical Methodology “ICE-seq”

    手机体育投注平台 RNA editing of adenosines to inosines contributes to a wide range of biological processes by regulating gene expression post-transcriptionally. To understand the effect, accurate mapping of inosines is necessa...

    Masayuki Sakurai, Shunpei Okada, Hiroki Ueda, Yuxi Yang in RNA Editing (2021)

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    Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNA

    The epsilon domain of Hepatitis B virus plays a crucial role in encapsidation of viral pregenomic RNA and its partial NMR structure has been determined. However, we recently described a potassium-dependent rib...

    Dibyajnan Chakraborty, Sagarmoy Ghosh in Ribozymes (2021)

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    Biophysical Analysis of Lipid Domains by Fluorescence Microscopy

    手机体育投注平台 The study of the structure and dynamics of in vivo is a challenging task. However, major advances could be achieved through the application of microscopic and spectroscopic techniques coupled with the use of...

    Ana E. Ventura, Tânia C. B. Santos, Joaquim T. Marquês in Lipid Rafts (2021)

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    Characterization and Optimization of a Deoxyribozyme with a Short Left Binding Arm

    Deoxyribozymes capable of catalyzing sequence-specific RNA cleavage have broad applications in biotechnology. In vitro selected RNA-cleaving deoxyribozymes normally contain two substrate-binding arms and a cen...

    Yueyao Wang, Hanyang Yu in Ribozymes (2021)

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    Characterization of Lipid Order and Domain Formation in Model Membranes Using Fluorescence Microscopy and Spectroscopy

    手机体育投注平台 Fluorescence-based techniques have been an integral factor in the study of cellular and model membranes. Fluorescence studies carried out on model membranes have provided valuable structural information and ha...

    Andrew Fuhrer, Amir M. Farnoud in Lipid Rafts (2021)

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    SHAPE Profiling to Probe Group II Intron Conformational Dynamics During Splicing

    Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) is a widely used technique for studying the structure and function of RNA molecules. It characterizes the flexibility of single nucleotides ...

    Timothy Wiryaman, Navtej Toor in Ribozymes (2021)

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    Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots

    Ribozymes are RNAs that catalyze reactions. They occur in nature, and can also be evolved in vitro to catalyze novel reactions. This chapter provides detailed protocols for using inverse folding software to de...

    Mohammad Kayedkhordeh, Ryota Yamagami, Philip C. Bevilacqua, David H. Mathews in Ribozymes (2021)

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    Superresolution Microscopy of Sphingolipids

    This chapter provides a step-by-step protocol to label and visualize sphingolipids by superresolution microscopy with a special focus on single-molecule localization microscopy by dSTORM. We provide information o...

    Jan Schlegel, Markus Sauer in Lipid Rafts (2021)

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    RNA Editing in Human and Mouse Tissues

    Adenosine-to-inosine (A-to-I) RNA editing is a fundamental posttranscriptional mechanism that greatly diversifies the transcriptome in many living organisms, including mammals. Multiple studies have demonstrat...

    Harini Srinivasan, Eng Piew Louis Kok, Meng How Tan in RNA Editing (2021)

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    Isolation and Analysis of Lipid Rafts from Neural Cells and Tissues

    Lipid rafts are membrane areas characterized by the clustering of selected membrane lipids, as the result of their phase separation forming a liquid-ordered phase floating in the lipid-disordered bulk membrane...

    Sara Grassi, Paola Giussani, Laura Mauri, Simona Prioni, Alessandro Prinetti in Lipid Rafts (2021)

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    Design and Evaluation of Guide RNA Transcripts with a 3′-Terminal HDV Ribozyme to Enhance CRISPR-Based Gene Inactivation

    手机体育投注平台 The recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 system, now reclassified as Cas12a, is a DNA-editing platform analogous to the widely used CRISPR-Cas9 system. Th...

    Ben Berkhout, Zongliang Gao, Elena Herrera-Carrillo in Ribozymes (2021)

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