Molecular Biology

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    Protocols in Current Issue
    Ribonucleoprotein Immunoprecipitation (RIP) Analysis
    Authors:  Jennifer L. Martindale, Myriam Gorospe and Maria L. Idda, date: 01/20/2020, view: 240, Q&A: 0
    [Abstract] RNAs and RNA-binding proteins (RBPs) can interact dynamically in ribonucleoprotein (RNP) complexes that play important roles in controlling gene expression programs. One of the powerful ways to investigate changes in the association of RNAs with an RBP of interest is by immunoprecipitation (IP) analysis of native RNPs. RIP (RNP ...
    RNA Interactome Identification via RNA-BioID in Mouse Embryonic Fibroblasts
    Authors:  Joyita Mukherjee, Mirita Franz-Wachtel, Boris Maček and Ralf-Peter Jansen, date: 01/05/2020, view: 252, Q&A: 0
    [Abstract] Cytoplasmic localization of mRNAs is common to all organisms and serves the spatial expression of genes. Cis-acting RNA signals (mostly found in the mRNA’s 3'-UTR), called zipcodes recruit trans-acting RNA-binding proteins that facilitate the localization of the mRNA. UV-cross-linking or affinity purification has been applied to identify such ...
    Laser Capture Micro-dissection (LCM) of Neonatal Mouse Forebrain for RNA Isolation
    Authors:  Achira Roy, Mei Deng, Kimberly A. Aldinger, Ian A. GLass and Kathleen J. Millen, date: 01/05/2020, view: 307, Q&A: 0
    [Abstract] Precise and reproducible isolation of desired cell types or layers from heterogeneous tissues is crucial to analyze specific gene profiles and molecular interactions in vivo. Forebrain is the core site of higher functions, like cognition and memory consolidation. It is composed of heterogeneous and distinct cell types, interconnected to ...
    Protocol for Ribosome Profiling in Bacteria
    Authors:  Fuad Mohammad and Allen R. Buskirk, date: 12/20/2019, view: 644, Q&A: 0
    [Abstract] Ribosome profiling provides information on the position of ribosomes on mRNA on a genomic scale. Although this information is often used to detect changes in gene expression under different conditions, it also has great potential for yielding insight into the mechanism and regulation of protein synthesis itself. First developed in yeast, ribosome ...
    Labeling and Isolation of Fluorouracil Tagged RNA by Cytosine Deaminase Expression
    Authors:  Harihar Basnet and Joan Massague, date: 11/20/2019, view: 449, Q&A: 0
    [Abstract] Tissues are comprised of different cell types whose interactions elicit distinct gene expression patterns that regulate tissue formation, regeneration, homeostasis and repair. Analysis of these gene expression patterns require methods that can capture as closely as possible the transcriptomes of cells of interest in their tissue microenvironment. ...
    A Mismatch-tolerant RT-LAMP Method for Molecular Diagnosis of Highly Variable Viruses
    Authors:  Yingxue Li, Yi Zhou, Yingying Ma, Rong Xu, Xia Jin and Chiyu Zhang, date: 11/05/2019, view: 357, Q&A: 0
    [Abstract] Loop-mediated isothermal amplification (LAMP) has been widely used in the detection of pathogens. However, there are usually numerous variants in one viral pathogen and primers employed in LAMP can hardly match all these variants. The mismatches between the primers and the viral genomes, especially those at the 3′-end of the primers, hinder LAMP ...
    Simple Synthesis of Functionalized Paramagnetic Beads for Nucleic Acid Purification and Manipulation
    [Abstract] The purification of nucleic acids is one of the most common procedures employed in modern molecular biology laboratories. Typically, commercial column-based protocols are utilized to isolate DNA or RNA from various sources. However, these methods not only require specialized equipment, but are also extremely expensive for high-throughput ...
    Isolation and Transcriptomic Profiling of Single Myofibers from Mice
    [Abstract] Skeletal muscle is composed of different cells and myofiber types, with distinct metabolic and structural features. Generally, transcriptomic analysis of skeletal muscle is performed using whole muscle, resulting in average information as all cells composing the organ contribute to the expression value detected for each gene with the loss of ...
    Yeast Single-cell RNA-seq, Cell by Cell and Step by Step
    [Abstract] Single-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome. Research with microorganisms such as yeast ...
    A Widely Applicable Urea-based Fluorescent/Colorimetric mRNA in situ Hybridization Protocol
    Author:  Chiara Sinigaglia, date: 09/05/2019, view: 1124, Q&A: 0
    [Abstract] In situ hybridization methods are routinely employed to detect nucleic acid sequences, allowing to localize gene expression or to study chromosomal organization in their native context. These methods rely on the pairwise binding of a labeled probe to the target endogenous nucleic acid sequence–the hybridization step, followed by detection ...



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