• 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.3954

Past Issues in 2021

Volume: 11 Issue: 6

Biochemistry

Monitoring Real-time Temperature Dynamics of a Short RNA Hairpin Using Förster Resonance Energy Transfer and Circular Dichroism Authors:  Martin Balcerowicz, Marco Di Antonio and Betty Y. W. Chung, date: 03/20/2021, view: 2190, Q&A: 0

RNA secondary structures are highly dynamic and subject to prompt changes in response to the environment. Temperature in particular has a strong impact on RNA structural conformation, and temperature-sensitive RNA hairpin structures have been exploited by multiple organisms to modify the rate of translation in response to temperature changes.

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Biological Engineering

Multilayered Fabrication Assembly Technique to Engineer a Corneal Stromal Equivalent Authors:  Julia Fernández-Pérez, Peter W. Madden and Mark Ahearne, date: 03/20/2021, view: 1112, Q&A: 0

Tissue engineering has emerged as a strategy to combat the donor shortage of human corneas for transplantation. Synthetic corneal substitutes are currently unable to support the normal phenotype of human cells and so decellularized animal corneas have been deployed to more closely provide the topographical and biochemical cues to promote cell

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Cancer Biology

Intestinal Co-culture System to Study TGR5 Agonism and Gut Restriction Authors:  Snehal N. Chaudhari and A. Sloan Devlin, date: 03/20/2021, view: 1996, Q&A: 1

The activation of the Takeda G-protein receptor 5 (TGR5, also known as the G protein-coupled bile acid receptor 1, GPBAR1) in enteroendocrine L-cells results in secretion of the anti-diabetic hormone Glucagon-Like Peptide 1 (GLP-1) into systemic circulation. Consequently, recent research has focused on identification and development of TGR5

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Preparation of an Orthotopic, Syngeneic Model of Lung Adenocarcinoma and the Testing of the Antitumor Efficacy of Poly(2-oxazoline) Formulation of Chemo-and Immunotherapeutic Agents Authors:  Natasha Vinod, Duhyeong Hwang, Salma H. Azam, Amanda E. D. Van Swearingen, Elizabeth Wayne, Sloane Christian Fussell, Marina Sokolsky-Papkov, Chad V. Pecot and Alexander V. Kabanov, date: 03/20/2021, view: 2902, Q&A: 0

Tumor xenograft models developed by transplanting human tissues or cells into immune-deficient mice are widely used to study human cancer response to drug candidates. However, immune-deficient mice are unfit for investigating the effect of immunotherapeutic agents on the host immune response to cancer (Morgan, 2012). Here, we describe the

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Preparation and Characterization of Poly(2-oxazoline) Micelles for the Solubilization and Delivery of Water Insoluble Drugs Authors:  Natasha Vinod, Duhyeong Hwang, Salma H. Azam, Amanda E. D. Van Swearingen, Elizabeth Wayne, Sloane Christian Fussell, Marina Sokolsky-Papkov, Chad V. Pecot and Alexander V. Kabanov, date: 03/20/2021, view: 2946, Q&A: 0

Many new drug development candidates are highly lipophilic compounds with low water solubility. This constitutes a formidable challenge for the use of such compounds for cancer therapy, where high doses and intravenous injections are needed (Di et al., 2012). Here, we present a poly(2-oxazoline) polymer (POx)-based nanoformulation strategy to

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Cell Biology

Retention Using Selective Hooks (RUSH) Cargo Sorting Assay for Live-cell Vesicle Tracking in the Secretory Pathway Using HeLa Cells Authors:  Mehrshad Pakdel, Natalia Pacheco-Fernandez and Julia von Blume, date: 03/20/2021, view: 1194, Q&A: 0

More than 30% of the total amount of proteins synthesized in mammalian cells follow the secretory pathway in order to mature and be properly sorted to their final destinations. Among several methodologies that describe live-cell monitoring of vesicles, the Retention Using Selective Hooks (RUSH) system is a powerful one that allows to visualize

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Immunology

Murine Monocyte and Macrophage Culture Authors:  Simone M. Haag and Aditya Murthy, date: 03/20/2021, view: 3350, Q&A: 0

Myeloid progenitors in the bone marrow generate monocytes, macrophages, granulocytes and most dendritic cells. Even though these innate immune cells are part of the same lineage, each cell type plays a specific and critical role in tissue development, host defense and the generation of adaptive immunity. Protocols have been developed in the past

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Liposomal Clodronate-mediated Macrophage Depletion in the Zebrafish Model Authors:  Linlin Yang, Alison M. Rojas and Celia E. Shiau, date: 03/20/2021, view: 2133, Q&A: 0

The ability to conduct in vivo macrophage-specific depletion remains an effective means to uncover functions of macrophages in a wide range of physiological contexts. Compared to the murine model, zebrafish offer superior imaging capabilities due to their optical transparency starting from a single-cell stage to throughout larval development.

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Quantitative Measurement of Mucolytic Enzymes in Fecal Samples Authors:  Shahanshah Khan and Hasan Zaki, date: 03/20/2021, view: 1891, Q&A: 0

The mucus layer in the gastrointestinal tract covers the apical surface of intestinal epithelial cells, protecting the mucosal tissue from enteric pathogen and commensal microorganisms. The mucus is primarily composed of glycosylated protein called mucins, which are produced by goblet cells, a type of columnar epithelial cells in the intestinal

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An Image-based Dynamic High-throughput Analysis of Adherent Cell Migration Authors:  Meng Sun, Bence Rethi, Akilan Krishnamurthy, Vijay Joshua, Heidi Wähämaa, Sergiu-Bogdan Catrina and Anca Catrina, date: 03/20/2021, view: 2694, Q&A: 0

In this protocol, we describe a method to monitor cell migration by live-cell imaging of adherent cells. Scratching assay is a common method to investigate cell migration or wound healing capacity. However, achieving homogenous scratching, finding the optimal time window for end-point analysis and performing an objective image analysis imply, even

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Microbiology

A Spectrofluorophotometrical Method Based on Fura-2-AM Probe to Determine Cytosolic Ca2+ Level in Pseudomonas syringae Complex Bacterial Cells Authors:  Simone Trabalza, Roberto Buonaurio, Alberto M. Del Pino, Carlo A. Palmerini, Harrold A. van den Burg and Chiaraluce Moretti, date: 03/20/2021, view: 2282, Q&A: 0

Calcium signaling is an emerging mechanism by which bacteria respond to environmental cues. To measure the intracellular free-calcium concentration in bacterial cells, [Ca2+]i, a simple spectrofluorometric method based on the chemical probe Fura 2-acetoxy methyl ester (Fura 2-AM) is here presented using Pseudomonad bacterial cells. This is an

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Detection and Quantification of African Swine Fever Virus in MA-104 Cells Authors:  Ayushi Rai, Sarah Pruitt, Elizabeth Ramirez-Medina, Elizabeth A. Vuono, Ediane Silva, Lauro Velazquez-Salinas, Consuelo Carrillo, Manuel V. Borca and Douglas P. Gladue, date: 03/20/2021, view: 1449, Q&A: 0

Detection of live African swine fever virus (ASFV) has historically relied on the use of primary swine macrophages (PSM). PSM do not replicate and have to be isolated fresh from donor swine. We previously identified that a MA-104 cells (ATCC #CRL-2378.1), a commercially available cell line isolated from African green monkey (Cercopithecus

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Molecular Biology

Real-time Base Excision Repair Assay to Measure the Activity of the 8-oxoguanine DNA Glycosylase 1 in Isolated Mitochondria of Human Skin Fibroblasts Authors:  Daniel Schniertshauer, Daniel Gebhard and Jörg Bergemann, date: 03/20/2021, view: 1676, Q&A: 0

7,8-dihydro-8-oxoguanine (8-oxoG) is one of the most common and mutagenic oxidative DNA damages induced by reactive oxygen species (ROS). Since ROS is mainly produced in the inner membranes of the mitochondria, these organelles and especially the mitochondrial DNA (mtDNA) contained therein are particularly affected by this damage. Insufficient

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Colorimetric RT-LAMP and LAMP-sequencing for Detecting SARS-CoV-2 RNA in Clinical Samples Authors:  Konrad Herbst, Matthias Meurer, Daniel Kirrmaier, Simon Anders, Michael Knop and Viet Loan Dao Thi, date: 03/20/2021, view: 2628, Q&A: 0

During pandemics, such as the one caused by SARS-CoV-2 coronavirus, simple methods to rapidly test large numbers of people are needed. As a faster and less resource-demanding alternative to detect viral RNA by conventional qPCR, we used reverse transcription loop-mediated isothermal amplification (RT-LAMP). We previously established colorimetric

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Neuroscience

Ligand and Carbohydrate Engagement (LACE) Assay and Fluorescence Quantification on Murine Neural Tissue Authors:  James M. Clegg and Thomas Pratt, date: 03/20/2021, view: 2085, Q&A: 0

The interaction between cell surface heparan sulphate and diffusible ligands such as FGFs is of vital importance for downstream signaling, however, there are few techniques that can be used to investigate this binding event. The ligand and carbohydrate engagement (LACE) assay is a powerful tool which can be used to probe the molecular interaction

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Investigate Synaptic Vesicles Mobility in Neuronal Culture Axons by FRAP Imaging Authors:  Xiao Min Zhang, Fabrice P. Cordelieres and Etienne Herzog, date: 03/20/2021, view: 1998, Q&A: 0

Synaptic vesicles (SVs) are clustered in the presynaptic terminals and consistently trafficking along axons. Based on their release features, SVs are classified into different “pools”. Imaging of SVs that are traveling among multiple presynaptic terminals has helped define a new pool named “SV super-pool”. Here we describe

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A Time Duration Discrimination Task for the Study of Elapsed Time Processing in Rats Authors:  Sarah Tenney, Eleftheria Vogiatzoglou, Deena Chohan, Annette Vo, Thomas Hunt, Kayla Cayanan, Jena B. Hales and Marta Sabariego, date: 03/20/2021, view: 1030, Q&A: 0

Space and time are both essential features of episodic memory. However, while spatial tasks have been used effectively to study the behavioral relevance of place cells, the behavioral paradigms utilized for the study of time cells have not used time duration as a variable that animals need to be aware of to solve the task. In order to evaluate how

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