Molecular Biology

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    Protocols in Current Issue
    Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer
    Authors:  Regina Wirth, Peng Gao, G. Ulrich Nienhaus, Murat Sunbul and Andres Jäschke, date: 05/05/2020, view: 922, Q&A: 0
    [Abstract] Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be ...
    Viral Double-Stranded RNA Detection by DNase I and Nuclease S1 digestions in Leishmania parasites
    Authors:  Nathalie Isorce and Nicolas Fasel, date: 05/05/2020, view: 315, Q&A: 0
    [Abstract] Many RNA viruses are found in protozoan parasites. They can be responsible for more serious pathology or treatment failure. For the detection of viral double-stranded RNA (dsRNA), sequence-dependent and -independent methods are available, such as quantitative real-time PCR and immunofluorescence, dot blot, ELISA or sequencing. The technique ...
    High-throughput Flow Cytometry Assay to Investigate TDP43 Splicing Function
    Authors:  H. Broder Schmidt and Rajat Rohatgi, date: 04/20/2020, view: 717, Q&A: 0
    [Abstract] Mutations in RNA-binding proteins (RBPs) such as TDP43 are associated with transcriptome-wide splicing defects and cause severe neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The impact of RBP mutations on splicing function is routinely studied using PCR-based bulk measurements. ...
    Circadian Gene Profiling in Laser Capture Microdissected Mouse Club Cells
    Authors:  Zhenguang Zhang and Andrew Loudon, date: 04/20/2020, view: 393, Q&A: 0
    [Abstract] Cell heterogeneity is high in tissues like lung. Research conducted on pure population of cells usually offers more insights than bulk tissues, such as circadian clock work. In this protocol, we provide a detailed work flow on how to do circadian clock study by RNA seq in laser capture micro-dissected mouse lung club cells. The method uses frozen ...
    Real-time Fluorescence Measurement of Enterovirus Uncoating
    Authors:  Visa Ruokolainen, Mira Laajala and Varpu Marjomäki, date: 04/05/2020, view: 320, Q&A: 0
    [Abstract] Viruses need to open, i.e., uncoat, in order to release their genomes for efficient replication and translation. Especially for non-enveloped viruses, such as enteroviruses, the cues leading to uncoating are less well known. The status of the virus has previously been observed mainly by transmission electron microscopy using negative ...
    Single-cell qPCR Assay with Massively Parallel Microfluidic System
    Authors:  Marta Prieto-Vila, Takahiro Ochiya and Yusuke Yamamoto, date: 03/20/2020, view: 500, Q&A: 0
    [Abstract] The single-cell transcriptome is the set of messenger RNA molecules expressed in one cell. It is extremely variable and changes according to external, physical and biochemical conditions. Due to sensitivity shortages, most of genetic studies use bulk samples, providing only the average gene expression. Single-cell technologies have provided a ...
    mRNA Extraction from Gill Tissue for RNA-sequencing
    Authors:  Jukka-Pekka Verta and Felicity Jones, date: 03/05/2020, view: 512, Q&A: 0
    [Abstract] Adaptation is thought to proceed in part through spatial and temporal changes in gene expression. Fish species such as the threespine stickleback are powerful vertebrate models to study the genetic architecture of adaptive changes in gene expression since divergent adaptation to different environments is common, they are abundant and easy to study ...
    RNA Sequencing of Single Myofibers from Mus musculus
    Authors:  Darren M. Blackburn, Felicia Lazure and Vahab D. Soleimani, date: 02/20/2020, view: 1374, Q&A: 0
    [Abstract] Whole transcriptome analysis is a key method in biology that allows researchers to determine the effect a condition has on gene regulation. One difficulty in RNA sequencing of muscle is that traditional methods are performed on the whole muscle, but this captures non-myogenic cells that are part of the muscle. In order to analyze only the ...
    Structural Alignment and Covariation Analysis of RNA Sequences
    Authors:  Nicolas J. Tourasse and Fabien Darfeuille, date: 02/05/2020, view: 674, Q&A: 0
    [Abstract] RNA molecules adopt defined structural conformations that are essential to exert their function. During the course of evolution, the structure of a given RNA can be maintained via compensatory base-pair changes that occur among covarying nucleotides in paired regions. Therefore, for comparative, structural, and evolutionary studies of RNA ...
    Detection of Individual RNA in Fixed Cells and Tissues by Chromogenic ISH
    Authors:  Meng Jiang, Chen Lin and Rongqin Ke, date: 02/05/2020, view: 558, Q&A: 0
    [Abstract] Visualization of RNA molecules in situ helps to better understand the functions of expressed genes. Currently, most conventional in situ hybridization methods for visualization of individual RNAs are based on fluorescence detection. Herein we present a chromogenic in situ hybridization protocol for visualization of ...



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