• 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.4334

Past Issues in 2022

Volume: 12 Issue: 4

Biological Engineering

An in vitro Blood-brain Barrier Model to Study the Penetration of Nanoparticles Authors:  Sezin Aday, Wen Li, Jeffrey M. Karp and Nitin Joshi, date: 02/20/2022, view: 2467, Q&A: 0

The blood-brain barrier (BBB), a crucial protection mechanism in the central nervous system (CNS), is a selective barrier comprised of endothelial cells. It hampers the development of therapeutic and diagnostic tools for neurological diseases due to the poor penetration of most of these agents. Rationally engineered nanoparticles (NP) can

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Biophysics

Femtoliter Injection of ESCRT-III Proteins into Adhered Giant Unilamellar Vesicles Authors:  Vasil N. Georgiev, Yunuen Avalos-Padilla, Xavier Fernàndez-Busquets and Rumiana Dimova, date: 02/20/2022, view: 1387, Q&A: 0

The endosomal sorting complex required for transport (ESCRT) machinery mediates membrane fission reactions that exhibit a different topology from that observed in clathrin-coated vesicles. In all of the ESCRT-mediated events, the nascent vesicle buds away from the cytosol. However, ESCRT proteins are able to act upon membranes with different

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Cancer Biology

Spherical Invasion Assay: A Novel Method to Measure Invasion of Cancer Cells Authors:  Stephen D. Richbart, Justin C. Merritt, Emily G. Moles, Kathleen C. Brown, Adeoluwa A. Adeluola, Paul T. Finch, Joshua A. Hess, Maria T. Tirona, Sarah L. Miles, Monica A. Valentovic and Piyali Dasgupta, date: 02/20/2022, view: 1855, Q&A: 0
The invasion of tumor cells into the neighboring blood vessels and lymph nodes is a vital step for distant metastasis. Traditionally, the invasive activity of growth factors (or the anti-invasive activity of drugs) is measured with the Boyden chamber assay. However, this assay has a few disadvantages like poor physiological relevance of transwell ...
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Optimization of Extracellular Flux Assay to Measure Respiration of Anchorage-independent Tumor Cell Spheroids Authors:  Zaineb Javed, Beth L. Worley, Coryn Stump, Sara S. Shimko, LaTaijah C. Crawford, Karthikeyan Mythreye and Nadine Hempel, date: 02/20/2022, view: 1348, Q&A: 0
Three-dimensional (3D) cell culture models are widely used in tumor studies to more accurately reflect cell-cell interactions and tumor growth conditions in vivo. 3D anchorage-independent spheroids derived by culturing cells in ultra-low attachment (ULA) conditions is particularly relevant to ovarian cancer, as such cell clusters are ...
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A Cell-based Screening Method Using an Intracellular Antibody for Discovering Small Molecules Targeting Hard-to-drug Proteins Authors:  Nicolas Bery and Terry H. Rabbitts, date: 02/20/2022, view: 1845, Q&A: 0
Targeting hard-to-drug proteins, such as proteins functioning by protein-protein interactions (PPIs) with small molecules, is difficult because of the lack of well-defined pockets. Fragment or computational-based methods are usually employed for the discovery of such compounds, but no generic method is available to quickly identify small molecules ...
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Cell Biology

NBD-lipid Uptake Assay for Mammalian Cell Lines Authors:  Sara Abad Herrera, Marta Grifell-Junyent and Thomas Günther Pomorski, date: 02/20/2022, view: 1564, Q&A: 0

All eukaryotic cells are equipped with transmembrane lipid transporters, which are key players in membrane lipid asymmetry, vesicular trafficking, and membrane fusion. The link between mutations in these transporters and disease in humans highlights their essential role in cell homeostasis. Yet, many key features of their activities, their

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Computational Biology and Bioinformatics

Tracking Moving Cells in 3D Time Lapse Images Using 3DeeCellTracker Authors:  Chentao Wen and Koutarou D. Kimura, date: 02/20/2022, view: 1256, Q&A: 0

Recent advancements in 3D microscopy have enabled scientists to monitor signals of multiple cells in various animals/organs. However, segmenting and tracking the moving cells in three-dimensional time-lapse images (3D + T images), to extract their dynamic positions and activities, remains a considerable bottleneck in the field. We developed a deep

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Immunology

Restimulation-Induced Cell Death (RICD): Methods for Modeling, Investigating, and Quantifying RICD Sensitivity in Primary Human T Cells via Flow Cytometric Analysis Authors:  Katherine Pohida, Camille M. Lake, Debra Yee and Andrew L. Snow, date: 02/20/2022, view: 1051, Q&A: 0

When the body mounts an immune response against a foreign pathogen, the adaptive arm of the immune system relies upon clonal expansion of antigen-specific T cell populations to exercise acquired effector and cytotoxic functions to clear it. However, T cell expansion must be modulated to effectively combat the perceived threat without inducing

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Microbiology

Activity-based Crosslinking to Identify Substrates of Thioredoxin-domain Proteins in Malaria Parasites Authors:  David W. Cobb, Grace S. Woods and Vasant Muralidharan, date: 02/20/2022, view: 1042, Q&A: 0
Malaria remains a major public health issue, infecting nearly 220 million people every year. The spread of drug-resistant strains of Plasmodium falciparum around the world threatens the progress made against this disease. Therefore, identifying druggable and essential pathways in P. falciparum parasites remains a major area of ...
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An in vitro Assay of mRNA 3’ end Using the E. coli Cell-free Expression System Authors:  Monford Paul Abishek N and Heon M. Lim, date: 02/20/2022, view: 1247, Q&A: 0

At the end of about 80% of the operon in Escherichia coli, translation termination decouples transcription, leading to Rho-dependent transcription termination (RDT). However, no in vitro or in vivo assay system has proven to be good enough to see the 3’ end of the mRNA generated by RDT. Here, we present a cell-free assay system that

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Molecular Biology

Normalized Ribo-Seq for Quantifying Absolute Global and Specific Changes in Translation Authors:  Katharina Hoerth, Sonja Reitter and Johanna Schott, date: 02/20/2022, view: 876, Q&A: 0
Ribosome profiling (Ribo-Seq) is a highly sensitive method to quantify ribosome occupancies along individual mRNAs on a genome-wide scale. Hereby, ribosome-protected fragments (= footprints) are generated by nuclease digestion, isolated, and sequenced together with the corresponding randomly fragmented input samples, to determine ribosome ...
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Pull-down of Biotinylated RNA and Associated Proteins Authors:  Jagadeesh K. Uppala, Chandrima Ghosh, Grzegorz Sabat and Madhusudan Dey, date: 02/20/2022, view: 1044, Q&A: 0

Mapping networks of RNA-protein interactions in cells is essential for understanding the inner workings of many biological processes, including RNA processing, trafficking, and translation. Current in vivo methods for studying protein-RNA interactions rely mostly on purification of poly(A) transcripts, which represent only ~2–3% of total

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Neuroscience

Anticipatory and Consummatory Responses to Touch and Food Rewards: A Protocol for Human Research Authors:  Emilio Chiappini, Giorgia Silani and Sebastian Korb, date: 02/20/2022, view: 621, Q&A: 0

Understanding the neural basis of reward processing is a major concern, as it holds the key to alleviating symptoms of addiction and poor mental health. However, this goal seems difficult to attain as long as research on reward processing cannot easily be compared across species and reward types, due to methodological differences and the presence

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A Behavioural Assay to Investigate Judgment Bias in Zebrafish Authors:  Felipe Espigares, Raquel R. Martins and Rui F. Oliveira, date: 02/20/2022, view: 775, Q&A: 1

In this protocol, we describe for the first time a judgment bias paradigm to phenotype the way zebrafish assess ambiguous stimuli. We have developed and validated a protocol for a judgment bias test based on a Go/No-go task, and performed using a half radial maze. After a habituation phase, fish are trained to discriminate between two reference

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Immunoprecipation Assay to Quantify the Amount of tRNAs associated with Their Interacting Proteins in Tissue and Cell Culture Authors:  Sarada Das, Amila Zuko, Robin Thompson, Erik Storkebaum and Zoya Ignatova, date: 02/20/2022, view: 1095, Q&A: 1

Transfer RNAs (tRNAs) are highly abundant species and, along their biosynthetic and functional path, they establish interactions with a plethora of proteins. The high number of nucleobase modifications in tRNAs renders conventional RNA quantification approaches unsuitable to study protein-tRNA interactions and their associated functional roles in

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Plant Science

Measuring Endogenous GA and IAA Authors:  Yunping Chen, Zhiwu Dan and Shaoqing Li, date: 02/20/2022, view: 1024, Q&A: 0

Plant hormones regulate many physiological processes that largely influence growth, differentiation, and development. Contents of phytohormones were analyzed using a liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) system. This protocol describes a detailed procedure to extract and quantify indole-3-acetic acid

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