• Volume 12, 2022
  • Volume 11, 2021
  • Volume 10, 2020
  • Volume 9, 2019
  • Volume 8, 2018
  • Volume 7, 2017
  • Volume 6, 2016
  • Volume 5, 2015
  • Volume 4, 2014
  • Volume 3, 2013
  • Volume 2, 2012
  • Volume 1, 2011
Image Credit: BioProtoc.4394

Past Issues in 2022

Volume: 12 Issue: 8

Biochemistry

Bsoft: Image Processing for Structural Biology Author:  J. Bernard Heymann, date: 04/20/2022, view: 1063, Q&A: 0

Bsoft is a software package primarily developed for processing electron micrographs, with the goal of determining the structures of biologically relevant molecules, molecular assemblies, and parts of cells. However, it incorporates many ways to deal with images, from the mundane to very sophisticated algorithms. This article is an introduction

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Biophysics

Characterization of the Elasticity of CD4+ T Cells: An Approach Based on Peak Force Quantitative Nanomechanical Mapping Authors:  Philipp Jung, Xiangda Zhou, Sandra Iden, Bin Qu and Markus Bischoff, date: 04/20/2022, view: 744, Q&A: 0

CD4+ T cells are essential players in orchestrating the specific immune response against intracellular pathogens, and in inhibiting tumor development in an early stage. The activation of T cells is triggered by engagement of T cell receptors (TCRs). Here, CD3 and CD28 molecules are key factors, (co)stimulating signaling pathways essential for

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Single Molecule Tracking Nanoscopy Extended to Two Colors with MTT2col for the Analysis of Cell-Cell Interactions in Leukemia Authors:  Loriane Maillot, Magali Irla and Arnauld Sergé, date: 04/20/2022, view: 690, Q&A: 0

Single molecule tracking (SMT) is a powerful technique to study molecular dynamics, and is particularly adapted to monitor the motion and interactions of cell membrane components. Assessing interactions among two molecular populations is classically performed by several approaches, including dual-color videomicroscopy, which allows monitoring of

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Cancer Biology

Measurement of Cell Intrinsic TGF-β Activation Mediated by the Integrin αvβ8 Authors:  Robert Ian Seed and Stephen Lloyd Nishimura, date: 04/20/2022, view: 1091, Q&A: 0

Transforming growth factor beta (TGF-β) is a multi-functional cytokine that plays a significant role in multiple diseases, including fibrosis and tumor progression. Whilst the biologic effects of TGF-β are well characterized, it is unclear how TGF-β signaling is regulated to impart specific responses within certain cell types. One

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Low-viscosity Matrix Suspension Culture for Human Colorectal Epithelial Organoids and Tumoroids Authors:  Tao Tan, Yumiko Hirokawa, Jordan Clarke, Anuratha Sakthianandeswaren and Oliver M. Sieber, date: 04/20/2022, view: 839, Q&A: 0

Three-dimensional culture of human normal colorectal epithelium and cancer tissue as organoids and tumoroids has transformed the study of diseases of the large intestine. A widely used strategy for generating patient-derived colorectal organoids and tumoroids involves embedding cells in domes of extracellular matrix (ECM). Despite its success,

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Cell Biology

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 ordinary and fusion circRNA at the isoform level. Compared to short-read RNA-seq, rolling circular

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Developmental Biology

Visualization and Purification of Caenorhabditis elegans Germ Granule Proteins Using Proximity Labeling Authors:  Hannah L. Hertz, Ian F. Price and Wen Tang, date: 04/20/2022, view: 1043, Q&A: 0

Membraneless organelles, such as germ granules and stress granules, are liquid-like condensates formed by phase transition. Recently, we and others have adopted proximity-based labeling methods to determine the composition of these membraneless compartments. Here, we describe the use of TurboID—an engineered promiscuous biotin

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RNA Interference Method for Gene Function Analysis in the Japanese Rhinoceros Beetle Trypoxylus dichotomus Authors:  Kazuki Sakura, Shinichi Morita and Teruyuki Niimi, date: 04/20/2022, view: 713, Q&A: 0

In the Japanese rhinoceros beetle Trypoxylus dichotomus, various candidate genes required for a specific phenotype of interest are listed by next-generation sequencing analysis. Their functions were investigated using RNA interference (RNAi) method, the only gene function analysis tool for T. dichotomus developed so far. The summarized procedure

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Isolation of tdTomato Expressing Inter-follicular Epidermal Melanocytes or Keratinocytes from Mouse Tail Skin Authors:  Samuel Pop, Oscar Urtatiz and Catherine D. Van Raamsdonk, date: 04/20/2022, view: 961, Q&A: 0

The epidermis is the outermost layer of the skin. It is made up of mostly keratinocytes along with a small number of melanocytes and Langerhans cells. Melanocytes produce a pigment called melanin, which is transferred to the keratinocytes, and protects these cells from damage from UV radiation, as well as generating hair and skin colours. In this

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Immunology

An Optimized Tat/Rev Induced Limiting Dilution Assay for the Characterization of HIV-1 Latent Reservoirs Authors:  Swarnima Mishra, Yuvrajsinh Gohil, Kavita Mehta, Anish D'silva, Afzal Amanullah, Deepak Selvam, Neelam Pargain, Narendra Nala, G. N. Sanjeeva and Udaykumar Ranga, date: 04/20/2022, view: 376, Q&A: 0

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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Microbiology

Production of Recombinant Hepatitis B virus (HBV) and Detection of HBV in Infected Human Liver Organoids Authors:  Tanvir Hossain, Shahla Romal and Tokameh Mahmoudi, date: 04/20/2022, view: 409, Q&A: 0

The absence of long term, primary untransformed in vitro models that support hepatitis B virus (HBV) infection and replication have hampered HBV pre-clinical research, which was reflected in the absence of a curative therapy until recently. One of the limitations for in vitro HBV research has been the absence of high titer and pure recombinant HBV

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Molecular Biology

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: 456, Q&A: 0

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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Neuroscience

High Throughput Blood-brain Barrier Organoid Generation and Assessment of Receptor-Mediated Antibody Transcytosis Authors:  Elena Kassianidou, Claire Simonneau, Alina Gavrilov and Roberto Villaseñor, date: 04/20/2022, view: 535, Q&A: 0

Targeting receptor-mediated transcytosis (RMT) is a successful strategy for drug delivery of biologic agents across the blood-brain barrier (BBB). The recent development of human BBB organoid models is a major advancement to help characterize the mechanisms of RMT and thus accelerate the design of brain delivery technologies. BBB organoids exhibit

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Plant Science

Apoplastic Expression of CARD1-ecto Domain in Nicotiana benthamiana and Purification from the Apoplastic Fluids Authors:  Nobuaki Ishihama, Anuphon Laohavisit, Kaori Takizawa and Ken Shirasu, date: 04/20/2022, view: 772, Q&A: 0

The protein expression and purification process is an essential initial step for biochemical analysis of a protein of interest. Traditionally, heterologous protein expression systems (such as E. coli, yeast, insect cells, and cell-free) are employed for plant protein expression, although a plant expression system is often desirable for plant

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Application of Cadaverine to Inhibit Biotin Biosynthesis in Plants Authors:  Nicole M. Gibbs, Shih-Heng Su and Patrick H. Masson, date: 04/20/2022, view: 406, Q&A: 0

Biotin is an essential vitamin in plants. However, characterization of biotin deficiency has been limited by embryo lethality in mutants, which can only be rescued by supplementation of biotin. Here, we describe a protocol to characterize biotin deficiency in Arabidopsis thaliana through application of the polyamine cadaverine. Cadaverine

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