• 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.3947

Past Issues in 2021

Volume: 11 Issue: 5

Biochemistry

Simultaneous Imaging of Single Protein Size, Charge, and Binding Using A Protein Oscillation Approach Authors:  Guangzhong Ma, Zijian Wan and Shaopeng Wang, date: 03/05/2021, view: 2445, Q&A: 0

Electrophoresis and Western blot are important tools in protein research for detection and identification of proteins. These traditional techniques separate the proteins based on size and charge differences and identify the proteins by antibody binding. Over the past decade, the emergence of single-molecule techniques has shown great potential in

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Identification of Intrinsic RNA Binding Specificity of Purified Proteins by in vitro RNA Immunoprecipitation (vitRIP) Authors:  Marisa Müller, Tamas Schauer and Peter B. Becker, date: 03/05/2021, view: 1325, Q&A: 0

RNA-protein interactions are often mediated by dedicated canonical RNA binding domains. However, interactions through non-canonical domains with unknown specificity are increasingly observed, raising the question how RNA targets are recognized. Knowledge of the intrinsic RNA binding specificity contributes to the understanding of target

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Biophysics

Automated Analysis of Cerebrospinal Fluid Flow and Motile Cilia Properties in The Central Canal of Zebrafish Embryos Authors:  Olivier Thouvenin, Yasmine Cantaut-Belarif, Ludovic Keiser, François Gallaire and Claire Wyart, date: 03/05/2021, view: 3459, Q&A: 0

Circulation of cerebrospinal fluid (CSF) plays an important role during development. In zebrafish embryo, the flow of CSF has been found to be bidirectional in the central canal of the spinal cord. In order to compare conditions and genetic mutants across each other, we recently automated the quantification of the velocity profile of exogenous

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Characterize the Interaction of the DNA Helicase PriA with the Stalled DNA Replication Fork Using Atomic Force Microscopy Authors:  Yaqing Wang, Zhiqiang Sun, Piero R. Bianco and Yuri L. Lyubchenko, date: 03/05/2021, view: 2279, Q&A: 0

In bacteria, the restart of stalled DNA replication forks requires the DNA helicase PriA. PriA can recognize and remodel abandoned DNA replication forks, unwind DNA in the 3'-to-5' direction, and facilitate the loading of the helicase DnaB onto the DNA to restart replication. ssDNA-binding protein (SSB) is typically present at the abandoned forks,

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Cancer Biology

Strategy of Isolating ‘Primed’ Tumor Initiating Cells Based on Mitochondrial Transmembrane Potential Authors:  Brian Spurlock, Vidya Sagar Hanumanthu and Kasturi Mitra, date: 03/05/2021, view: 2444, Q&A: 0

Various stem cells have been found to be dependent on mitochondrial energetics. The role of mitochondria in regulating the self-renewal of normal stem cells and stem-like tumor initiating cells (TICs) is increasingly being appreciated. We proposed that TIC populations have a sub population of cells that are “primed” by mitochondria for

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Cell Biology

Retention Using Selective Hooks (RUSH) Cargo Sorting Assay for Protein Vesicle Tracking in HeLa Cells Authors:  Natalia Pacheco-Fernandez, Mehrshad Pakdel and Julia von Blume, date: 03/05/2021, view: 1809, Q&A: 0

Monitoring vesicle trafficking is an excellent tool for the evaluation of protein dynamics in living cells. Such study is key for the understanding of protein sorting and secretion. Recent developments in microscopy, as well as new methodologies developed to study synchronized trafficking of proteins, allowed a better understanding of signaling,

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Live Intravital Intestine with Blood Flow Visualization in Neonatal Mice Using Two-photon Laser Scanning Microscopy Authors:  Yuhki Koike, Bo Li, Yong Chen, Niloofar Ganji, Mashriq Alganabi, Hiromu Miyake, Carol Lee, Alison Hock, Richard Wu, Keiichi Uchida, Mikihiro Inoue, Paul Delgado-Olguin and Agostino Pierro, date: 03/05/2021, view: 3537, Q&A: 0

This protocol describes a novel technique to investigate the microcirculation dynamics underlying the pathology in the small intestine of neonatal mice using two-photon laser-scanning microscopy (TPLSM). Recent technological advances in multi-photon microscopy allow intravital analysis of different organs such as the liver, brain and intestine.

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Microbiology

Assay for Assessing Mucin Binding to Bacteria and Bacterial Proteins Authors:  Lubov S. Grigoryeva, Saima Rehman, Richard C. White, James A. Garnett and Nicholas P. Cianciotto, date: 03/05/2021, view: 1324, Q&A: 0

Legionella pneumophila, a Gram-negative bacterium and the causative agent of Legionnaires’ disease, exports over 300 effector proteins/virulence factors, through its type II (T2SS) and type IV secretion systems (T4SS). One such T2SS virulence factor, ChiA, not only functions as a chitinase, but also as a novel mucinase, which we believe aids

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Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome Authors:  Shuntai Zhou, Collin S. Hill, Michael U. Clark, Timothy P. Sheahan, Ralph Baric and Ronald Swanstrom, date: 03/05/2021, view: 3009, Q&A: 0

Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses.

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Candida Biofilm Formation Assay on Essential Oil Coated Silicone Rubber Authors:  Gulcan Sahal, Herman J. Woerdenbag, Wouter L. J. Hinrichs, Anita Visser, Henny C. van der Mei and Isil Seyis Bilkay, date: 03/05/2021, view: 923, Q&A: 0

Development of biofilm associated candidemia for patients with implanted biomaterials causes an urgency to develop antimicrobial and biofilm inhibitive coatings in the management of recalcitrant Candida infections. Recently, there is an increase in the number of patients with biofilm formation and resistance to antifungal therapy. Therefore, there

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Generation and Implementation of Reporter BHK-21 Cells for Live Imaging of Flavivirus Infection Authors:  Jorge L. Arias-Arias and Rodrigo Mora-Rodríguez, date: 03/05/2021, view: 876, Q&A: 0

The genus Flavivirus within the family Flaviviridae includes many viral species of medical importance, such as yellow fever virus (YFV), Zika virus (ZIKV), and dengue virus (DENV), among others. Presently, the identification of flavivirus-infected cells is based on either the immunolabeling of viral proteins, the application of recombinant

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Molecular Biology

Trypanosomatid, fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE) Authors:  Wolf-Matthias Leeder, Elisabeth Kruse and H. Ulrich Göringer, date: 03/05/2021, view: 1632, Q&A: 0

Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is

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Defined Mutant Library Sequencing (DML-Seq) for Identification of Conditional Essential Genes Authors:  Shuai Shao, Lifan Wei, Feng Xia, Yuanxing Zhang and Qiyao Wang, date: 03/05/2021, view: 1732, Q&A: 0

Transposon insertion sequencing (TIS) is an emerging technique which utilizes a massive transposon mutant library to screen specific phenotype and determine the conditional essential genetic requirements for bacterial fitness under distinct conditions combined with high-throughput parallel sequencing technology. Compared with a massive mutant

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Neuroscience

Generation of Mouse Primary Hypothalamic Neuronal Cultures for Circadian Bioluminescence Assays Authors:  Cosima X. Schmidt, Anthony H. Tsang and Henrik Oster, date: 03/05/2021, view: 806, Q&A: 0

An endogenous circadian clock system enables organisms to adapt to time-of-day dependent environmental changes. In consequence, most physiological processes exhibit daily rhythms of, e.g., energy metabolism, immune function, sleep, or hormone production. Hypothalamic circadian clocks have been identified to play a particular role in coordinating

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Dissociating Behavior and Spatial Working Memory Demands Using an H Maze Authors:  Hannah S. Wirtshafter, Moqing Quan and Matthew A. Wilson, date: 03/05/2021, view: 969, Q&A: 0

The development of mazes for animal experiments has allowed for the investigation of cognitive maps and place cells, spatial working memory, naturalistic navigation, perseverance, exploration, and choice and motivated behavior. However, many mazes, such as the T maze, currently developed to test learning and memory, do not distinguish temporally

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Transcardiac Perfusion of the Mouse for Brain Tissue Dissection and Fixation Authors:  Jinyun Wu, Yuqi Cai, Xiaoyang Wu, Yue Ying, Yilin Tai and Miao He, date: 03/05/2021, view: 2760, Q&A: 0
Transcardiac perfusion with saline followed by 4% paraformaldehyde (PFA) is widely used to clear blood and preserve brain for immunostaining or in situ hybridization. PFA breaks into formaldehyde in solution, which cross-link protein and DNA molecules to preserve tissue and cell structure. Here we provide a step by step guide for ...
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Plant Science

Chromatographic Analysis for Targeted Metabolomics of Antioxidant and Flavor-Related Metabolites in Tomato Authors:  Nergiz Gürbüz Çolak, Neslihan Tek Eken, Anne Frary and Sami Doğanlar, date: 03/05/2021, view: 1997, Q&A: 0

Targeted metabolomics is a useful approach to evaluate crop breeding studies. Antioxidant and flavor-related traits are of increasing interest and are considered quality traits in tomato breeding. The present study presents chromatographic methods to study antioxidants (carotenoids, vitamin C, vitamin E, phenolic compounds, and glutathione) and

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Stem Cell

Generation of Human iPSC-derived Neural Progenitor Cells (NPCs) as Drug Discovery Model for Neurological and Mitochondrial Disorders Authors:  Annika Zink, Pawel Lisowski and Alessandro Prigione, date: 03/05/2021, view: 2220, Q&A: 1

The high attrition rate in drug development processes calls for additional human-based model systems. However, in the context of brain disorders, sampling live neuronal cells for compound testing is not applicable. The use of human induced pluripotent stem cells (iPSCs) has revolutionized the field of neuronal disease modeling and drug discovery.

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