Molecular Biology

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    Protocols in Current Issue
    VirScan: High-throughput Profiling of Antiviral Antibody Epitopes
    Authors:  Ellen L. Shrock, Christine L. Shrock and Stephen J. Elledge, date: 07/05/2022, view: 33, Q&A: 0
    [Abstract]

    Profiling the specificities of antibodies can reveal a wealth of information about humoral immune responses and the antigens they target. Here, we present a protocol for VirScan, an application of the phage immunoprecipitation sequencing (PhIP-Seq) method for profiling the specificities of human antiviral antibodies. Accompanying this protocol is

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    HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes in vivo
    [Abstract]

    Chromatin immunoprecipitation (ChIP) maps, on a genome-wide scale, transcription factor binding sites, and the distribution of other chromatin-associated proteins and their modifications. As such, it provides valuable insights into mechanisms of gene regulation. However, successful ChIP experiments are dependent on the availability of a

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    ATAC-Seq of a Single Myofiber from Mus musculus
    Authors:  Korin Sahinyan, Darren M. Blackburn and Vahab D. Soleimani, date: 06/20/2022, view: 1225, Q&A: 0
    [Abstract]

    Chromatin accessibility is a key determinant of gene expression that can be altered under different physiological and disease conditions. Skeletal muscle is made up of myofibers that are highly plastic and adaptive. Therefore, assessing the genome-wide chromatin state of myofibers under various conditions is very important to gain insight into the

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    A Modified Fluctuation Assay with a CAN1 Reporter in Yeast
    Authors:  Pengyao Jiang, Anja R. Ollodart and Maitreya J. Dunham, date: 06/05/2022, view: 524, Q&A: 0
    [Abstract]

    Understanding the generation of mutations is fundamental to understanding evolution and genetic disease; however, the rarity of such events makes experimentally identifying them difficult. Mutation accumulation (MA) methods have been widely used. MA lines require serial bottlenecks to fix de novo mutations, followed by whole-genome sequencing.

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    A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples
    Authors:  Linxuan Zhao, Vamsi Krishna Polavarapu, Ram Prakash Yadav, Pengwei Xing and Xingqi Chen, date: 05/20/2022, view: 758, Q&A: 0
    [Abstract]

    The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide

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    A Molecular Cloning and Sanger Sequencing-based Protocol for Detecting Site-specific DNA Methylation
    Authors:  Wei Guo, Anthony Cannon and Damon Lisch, date: 05/05/2022, view: 691, Q&A: 1
    [Abstract]

    DNA methylation is a conserved chemical modification, by which methyl groups are added to the cytosine of DNA molecules. Methylation can influence gene expression without changing the sequence of a particular gene. This epigenetic effect is an intriguing phenomenon that has puzzled biologists for years. By probing the temporal and spatial patterns

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    An Improved EMSA-based Method to Prioritize Candidate cis-REs for Further Functional Validation
    Authors:  Ting Wu and Gang Li, date: 04/20/2022, view: 588, Q&A: 0
    [Abstract]

    Cells are the complex product of gene expression programs that involve the coordinated transcription of thousands of genes controlled by cis-regulatory elements (cis-REs). Therefore, identification of cis-REs is the key to decipher the mechanisms underlying the regulation of gene expression. Here, we describe a simple and time-effective protocol

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    An Optimized Tat/Rev Induced Limiting Dilution Assay for the Characterization of HIV-1 Latent Reservoirs
    [Abstract]

    The administration of antiretroviral therapy (ART) leads to a rapid reduction in plasma viral load in HIV-1 seropositive subjects. However, when ART is suspended, the virus rebounds due to the presence of a latent viral reservoir. Several techniques have been developed to characterize this latent viral reservoir. Of the various assay formats

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    Conditional Human BRD4 Knock-In Transgenic Mouse Genotyping and Protein Isoform Detection
    Authors:  Michael Paul Lewis, Shwu-Yuan Wu and Cheng-Ming Chiang, date: 04/05/2022, view: 576, Q&A: 0
    [Abstract]

    Bromodomain-containing protein 4 (BRD4) is an acetyl-lysine reader protein and transcriptional regulator implicated in chromatin dynamics and cancer development. Several BRD4 isoforms have been detected in humans with the long isoform (BRD4-L, aa 1-1,362) playing a tumor-suppressive role and a major short isoform (BRD4-S, aa 1-722) having

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    A Rapid FRET Real-Time PCR Protocol for Simultaneous Quantitative Detection and Discrimination of Human Plasmodium Parasites
    [Abstract]

    Malaria is the most important parasitic disease worldwide, and accurate diagnosis and treatment without delay are essential for reducing morbidity and mortality, especially in P. falciparum malaria. Real-time PCR is highly sensitive and highly specific, therefore an excellent diagnostic tool for laboratory detection and species-specific

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