• 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.4278

Past Issues in 2022

Volume: 12 Issue: 1

Biochemistry

Heterologous Expression and High Degree Purification of the Restriction Endonuclease SauUSI Authors:  Vinayak Sadasivam Tumuluri and Kayarat Saikrishnan, date: 01/05/2022, view: 967, Q&A: 0

Mechanisms that target and destroy foreign nucleic acids are major barriers to horizontal gene transfer (HGT) in prokaryotes. Amongst them, restriction-modification (R-M) systems are found in ≥75% of the sequenced genomes in Bacteria and Archaea. Due to their high target sequence specificity and potent nucleolytic activity, R-M systems are used

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A Simple Technique for Direct Immobilization of Target Enzymes from Cell Lysates Based on the SpyTag/SpyCatcher Spontaneous Reaction Authors:  Li-xi Cai, Yuan-qing Lin, Yun-meng Chu, Xiao-pin Chen, Li-xing Liu, Ming Zhang and Guang-ya Zhang, date: 01/05/2022, view: 837, Q&A: 0

Many of the current methods for enzyme purification and immobilization suffer from several drawbacks, such as requiring tedious multistep procedures or long preparation, and being environmentally unfriendly, due to the chemicals and conditions involved. Thus, a simple technique for direct purification and immobilization of target enzymes from cell

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Developmental Biology

Total Nucleic Acid Extraction from Single Zebrafish Embryos for Genotyping and RNA-seq Authors:  Neha Wali, Munise Merteroglu, Richard J. White and Elisabeth M. Busch-Nentwich, date: 01/05/2022, view: 878, Q&A: 0

RNA sequencing allows for the quantification of the transcriptome of embryos to investigate transcriptional responses to various perturbations (e.g., mutations, infections, drug treatments). Previous protocols either lack the option to genotype individual samples, or are laborious and therefore difficult to do at a large scale. We have developed a

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Identification of Protein-RNA Interactions in Mouse Testis Tissue Using fRIP Authors:  Alexis S. Bailey, Pedro J. Batista, Howard Y. Chang and Margaret T. Fuller, date: 01/05/2022, view: 832, Q&A: 0

During development, cells must quickly switch from one cell state to the next to execute precise and timely differentiation. One method to ensure fast transitions in cell states is by controlling gene expression at the post-transcriptional level through action of RNA-binding proteins on mRNAs. The ability to accurately identify the RNA targets of

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Immunology

Static Adhesion Assay for Human Peripheral Blood Mononuclear Cells Authors:  Giulia Vanoni, Camilla Jandus and Sara Trabanelli, date: 01/05/2022, view: 745, Q&A: 0

Blood endothelial cells (ECs) constitute the primary physical barrier to be crossed by circulating leukocytes, once attracted to a site of ongoing inflammation/infection. Upon a pro-inflammatory stimulus, such as tumor necrosis factor (TNF), ECs upregulate adhesion molecule expression to favor the adhesion and, subsequently, the transendothelial

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Evaluating Human Natural Killer Cells Antibody-dependent Cellular Cytotoxicity (ADCC) Using Plate-bound Anti-CD16 Antibodies Author:  Weiru Liu, date: 01/05/2022, view: 627, Q&A: 0

Natural killer (NK) cells are large granular lymphocytes that keep in check the health of neighboring cells through a large array of intrinsically expressed germline-coded receptors. Most importantly, CD16 is a low affinity Fc receptor for IgG that mediates the antibody-dependent cellular cytotoxicity (ADCC) of NK cells, bridging the innate and

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Induction of Acute or Disseminating Bacterial Pneumonia in Mice and Sampling of Infected Organs for Studying the Host Response to Bacterial Pneumonia Authors:  Wanhai Qin, Zhe Liu, Tom van der Poll and Alex F. de Vos, date: 01/05/2022, view: 814, Q&A: 0

Experimental pneumonia models are important tools to study the pathophysiology of lung inflammation caused by microbial infections and the efficacy of (novel) drugs. We have applied a murine model of pneumonia induced by Pseudomonas (P.) aeruginosa infection to study acute host antibacterial defense in lungs, and assess epithelial cell specific

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Medicine

Chronic Daily House Dust Mite Exposure in Mice is an Effective Model to Quantify the Effect of Pharmacologic Agents on Discrete Stages of Artery Remodeling in Pulmonary Hypertension Authors:  Lea C. Steffes and Maya E. Kumar, date: 01/05/2022, view: 831, Q&A: 0

Pulmonary hypertension (PH) is a heterogenous and incurable disease marked by varying degrees of pulmonary vascular remodeling. This vascular remodeling, which includes thickening of the smooth muscle layer (an early finding) and formation of occlusive neointimal lesions (a late finding) in the pulmonary arteries, is a major driver of morbidity

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Microbiology

Isolation of Mitochondria from Ustilago maydis Protoplasts Authors:  Juan Pablo Pardo, Guadalupe Guerra-Sánchez, Oscar Flores-Herrera and Lucero Romero-Aguilar, date: 01/05/2022, view: 382, Q&A: 0

Ustilago maydis, a basidiomycete that infects Zea mays, is one of the top ten fungal models for studying DNA repair, signal transduction pathways, and dimorphic transitions, among other processes. From a metabolic point of view, U. maydis lacks fermentative capacity, pointing to mitochondria as a key player in central metabolism. Oxidative

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Real-Time Analysis of Mitochondrial Electron Transport Chain Function in Toxoplasma gondii Parasites Using a Seahorse XFe96 Extracellular Flux Analyzer Authors:  Jenni A. Hayward, Esther Rajendran, F. Victor Makota, Brad J. Bassett, Michael Devoy, Teresa Neeman and Giel G. van Dooren, date: 01/05/2022, view: 414, Q&A: 0

The mitochondrial electron transport chain (ETC) performs several critical biological functions, including maintaining mitochondrial membrane potential, serving as an electron sink for important metabolic pathways, and contributing to the generation of ATP via oxidative phosphorylation. The ETC is important for the survival of many eukaryotic

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Molecular Biology

An Aptamer-based mRNA Affinity Purification Procedure (RaPID) for the Identification of Associated RNAs (RaPID-seq) and Proteins (RaPID-MS) in Yeast Authors:  Rohini R. Nair, Gal Haimovich and Jeffrey E. Gerst, date: 01/05/2022, view: 489, Q&A: 0

RNA-RNA and RNA-protein interactions are involved in the regulation of gene expression. Here, we describe an updated and extended version of our RNA purification and protein identification (RaPID) protocol for the pulldown of aptamer-tagged mRNAs by affinity purification. The method takes advantage of the high affinity interaction between the MS2

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Neuroscience

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: 551, 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 diversity, it is increasingly relevant to understand how local translation is regulated according to

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Patch-clamp Recordings and Single Fiber Labeling from Spiral Ganglion Somata in Acutely Prepared Semi-intact Cochleae from Neonatal Rats Authors:  Alexander L. Markowitz, Megana R. Iyer and Radha Kalluri, date: 01/05/2022, view: 772, Q&A: 0

Spiral ganglion neurons (SGN) are the primary neuronal pathway for transmitting sensory information from the inner ear to the brainstem. Recent studies have revealed significant biophysical and molecular diversity indicating that auditory neurons are comprised of sub-groups whose intrinsic properties contribute to their diverse functions. Previous

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Stem Cell

Live-cell Imaging and Analysis of Germline Stem Cell Mitosis in Caenorhabditis elegans Authors:  Réda M. Zellag, Yifan Zhao and Abigail R. Gerhold, date: 01/05/2022, view: 548, Q&A: 0

Model organisms offer the opportunity to decipher the dynamic and complex behavior of stem cells in their native environment; however, imaging stem cells in situ remains technically challenging. C. elegans germline stem cells (GSCs) are distinctly accessible for in situ live imaging but relatively few studies have taken advantage of this

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An in vitro Mechanical Damage Model of Isolated Myofibers in a Floating Culture Condition Authors:  Yoshifumi Tsuchiya and Yusuke Ono, date: 01/05/2022, view: 399, Q&A: 0

Muscle stem cells (satellite cells), located on the surface of myofibers, are rapidly activated from a quiescent state following skeletal muscle injury. Although satellite cell activation is an initial step in muscle regeneration, the stimulation of satellite cell activation by muscle injury remains to be elucidated. We recently established an in

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