Systems Biology


    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: 492, Q&A: 0

    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

    Method for Analysing Protein Structure of SARS-COV-2 M Protein for Possible Clues Regarding Virion Stability, Longevity and Transmission
    Authors:  Saam Hasan and Muhammad Maqsud Hossain, date: 05/05/2022, view: 53, Q&A: 0

    The Severe Acute Respiratory Syndrome Coronavirus 2 or SARS-CoV-2 has been the causative agent behind the 2020 global pandemic. With the numbers infected rising well above a 2.7 million and confirmed deaths above 122,000 as of 25th April 2020, it

    circFL-seq, A Full-length circRNA Sequencing Method
    Authors:  Zelin Liu and Ence Yang, date: 04/20/2022, view: 787, Q&A: 1

    Due to overlapping sequences with linear cognates, identifying internal sequences of circular RNA (circRNA) remains a challenge. Recently, we have developed a full-length circRNA sequencing method (circFL-seq) and computational pipeline, to profile

    Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing

    In recent years, DNA methylation research has been accelerated by the advent of nanopore sequencers. However, read length has been limited by the constraints of base conversion using the bisulfite method, making analysis of chromatin content

    Enrichment of Tyrosine Phosphorylated Peptides for Quantitative Mass Spectrometry Analysis of RTK Signaling Dynamics
    Authors:  Vidyasiri Vemulapalli, Stephen C. Blacklow, Steven P. Gygi and Alison Erickson, date: 02/05/2022, view: 1107, Q&A: 0

    Cells sense and respond to mitogens by activating a cascade of signaling events, primarily mediated by tyrosine phosphorylation (pY). Because of its key roles in cellular homeostasis, deregulation of this signaling is often linked to oncogenesis. To

    Subcellular RNA-seq for the Analysis of the Dendritic and Somatic Transcriptomes of Single Neurons
    Authors:  Julio D. Perez and Erin M. Schuman, date: 01/05/2022, view: 1368, Q&A: 0

    In neurons, local translation in dendritic and axonal compartments allows for the fast and on-demand modification of the local proteome. As the last few years have witnessed dramatic advancements in our appreciation of the brain’s neuronal

    TGIRT-seq Protocol for the Comprehensive Profiling of Coding and Non-coding RNA Biotypes in Cellular, Extracellular Vesicle, and Plasma RNAs
    Authors:  Hengyi Xu, Ryan M. Nottingham and Alan M. Lambowitz, date: 12/05/2021, view: 1186, Q&A: 0

    High-throughput RNA sequencing (RNA-seq) has extraordinarily advanced our understanding of gene expression and disease etiology, and is a powerful tool for the identification of biomarkers in a wide range of organisms. However, most RNA-seq methods

    Macroscopic Structural and Connectome Mapping of the Mouse Brain Using Diffusion Magnetic Resonance Imaging
    Authors:  Tanzil Mahmud Arefin, Choong Heon Lee, Jordon D. White, Jiangyang Zhang and Arie Kaffman, date: 11/20/2021, view: 1704, Q&A: 0

    Translational work in rodents elucidates basic mechanisms that drive complex behaviors relevant to psychiatric and neurological conditions. Nonetheless, numerous promising studies in rodents later fail in clinical trials, highlighting the need for

    Histone modification ChIP-seq on Arabidopsis thaliana Plantlets
    Authors:  Juan S. Ramirez-Prado, David Latrasse and Moussa Benhamed, date: 11/05/2021, view: 1671, Q&A: 1

    Characterizing the molecular mechanisms regulating gene expression is crucial for understanding the regulatory processes underlying physiological responses to environmental and developmental signals in eukaryotes. The covalent modification of

    Protocols to Induce, Prevent, and Treat Post-traumatic Stress Disorder-like Memory in Mice: Optogenetics and Behavioral Approaches

    One of the cardinal features of post-traumatic stress disorder (PTSD) is a paradoxical memory alteration including both emotional hypermnesia for salient trauma-related cues and amnesia for the surrounding traumatic context. Interestingly, some


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