• 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.3836

Biochemistry

Native Co-immunoprecipitation Assay to Identify Interacting Partners of Chromatin-associated Proteins in Mammalian Cells Authors:  Afzal Husain, Nasim A. Begum, Maki Kobayashi and Tasuku Honjo, date: 12/05/2020, view: 1938, Q&A: 0

Protein-protein interactions play key roles in nuclear processes including transcription, replication, DNA damage repair, and recombination. Co-immunoprecipitation (Co-IP) followed by western blot or mass spectrometry is an invaluable approach to identify protein-protein interactions. One of the challenges in the Co-IP of a protein localized to

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Biophysics

Mechanical Characterization of Glandular Acini Using a Micro-indentation Instrument Authors:  Christopher S. O’Bryan, Qiao Zhang, Tanmay P. Lele and Thomas E. Angelini, date: 12/05/2020, view: 1038, Q&A: 0

The linker of nucleoskeleton and cytoskeleton (LINC) complex is responsible for tethering the nucleus to the cytoskeleton, providing a pathway for the cell’s nucleus to sense mechanical signals from the environment. Recently, we explored the role of the LINC complex in the development of glandular epithelial acini, such as those found in

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Cancer Biology

A 3D Skin Melanoma Spheroid-Based Model to Assess Tumor-Immune Cell Interactions Authors:  Marek Wagner and Shigeo Koyasu, date: 12/05/2020, view: 1277, Q&A: 0
Three-dimensional (3D) tumor spheroids have the potential to bridge the gap between two-dimensional (2D) monolayer tumor cell cultures and solid tumors with which they share a significant degree of similarity. However, the progression of solid tumors is often influenced by the dynamic and reciprocal interactions between tumor and immune cells. ...
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Developmental Biology

Treadmill Running of Mouse as a Model for Studying Influence of Maternal Exercise on Offspring Authors:  Song Ah Chae, Jun Seok Son, Mei-Jun Zhu, Jeanene M. de Avila and Min Du, date: 12/05/2020, view: 1208, Q&A: 0

Epidemiological studies robustly show the beneficial effects of maternal exercise in reducing maternal birth complications and improving neonatal outcomes, though underlying mechanisms remain poorly understood. To facilitate mechanistic exploration, a protocol for maternal exercise of mice is established, with the regimen following the exercise

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Immunology

Analysis of B Cell Migration by Intravital Microscopy Authors:  Michael Schnoor, Leopoldo Santos-Argumedo, Daniel Alberto Girón-Pérez and Eduardo Vadillo, date: 12/05/2020, view: 1192, Q&A: 0

During immune responses, B cells home to lymph nodes (LN), where they encounter antigens. Homing starts with capture and L-selectin-dependent rolling on the activated endothelium of high endothelial venules (HEV). After recognition of chemokines presented on HEV, activation of B cell integrins occurs mediating firm arrest. Subsequently, B cells

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Protocol for Isolation, Stimulation and Functional Profiling of Primary and iPSC-derived Human NK Cells Authors:  Janine E. Melsen, Maria Themeli, Monique M. van Ostaijen-ten Dam, Els van Beelen, Gertjan Lugthart, Rob C. Hoeben, Marco W. Schilham and Harald M. Mikkers, date: 12/05/2020, view: 1232, Q&A: 0

Natural killer (NK) cells are innate immune cells, characterized by their cytotoxic capacity, and chemokine and cytokine secretion upon activation. Human NK cells are identified by CD56 expression. Circulating NK cells can be further subdivided into the CD56bright (~10%) and CD56dim NK cell subsets (~90%). NK cell-like cells can also be derived

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Microbiology

Ribosome Purification from an α-proteobacterium and rRNA Analysis by Northern Blot Authors:  Liang Yin and Caroline S. Harwood, date: 12/05/2020, view: 816, Q&A: 0
Ribosomes are an integral part of cellular life. They are complex molecular machines consisting of multiple ribosomal proteins and RNAs. To study different aspects of ribosome composition, many methods have been developed over the decades. Here, we describe how to purify ribosomes from the α-proteobacterium Rhodopseudomonas palustris ...
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Combining Gel Retardation and Footprinting to Determine Protein-DNA Interactions of Specific and/or Less Stable Complexes Authors:  Meng-Lun Hsieh, Alice Boulanger, Leslie G. Knipling and Deborah M. Hinton, date: 12/05/2020, view: 851, Q&A: 0

DNA footprinting is a classic technique to investigate protein-DNA interactions. However, traditional footprinting protocols can be unsuccessful or difficult to interpret if the binding of the protein to the DNA is weak, the protein has a fast off-rate, or if several different protein-DNA complexes are formed. Our protocol differs from traditional

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Expression and Purification of Recombinant Skd3 (Human ClpB) Protein and Tobacco Etch Virus (TEV) Protease from Escherichia coli Authors:  Ryan R. Cupo and James Shorter, date: 12/05/2020, view: 1422, Q&A: 0

Skd3 (encoded by human CLPB) is a mitochondrial AAA+ protein comprised of an N-terminal ankyrin-repeat domain and a C-terminal HCLR-clade nucleotide-binding domain. The function of Skd3 has long remained unknown due to challenges in purifying the protein to high quality and near homogeneity. Recently we described Skd3 as a human mitochondrial

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Molecular Biology

Charging State Analysis of Transfer RNA from an α-proteobacterium Authors:  Liang Yin and Caroline S. Harwood, date: 12/05/2020, view: 832, Q&A: 0
Transfer RNA (tRNA) is an essential link between the genetic code and proteins. During the process of translation, tRNA is charged with its cognate amino acid and delivers it to the ribosome, thus serving as a substrate of protein synthesis. To analyze the charging state of a particular tRNA, total RNA is purified and analyzed on an acid-urea gel. ...
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Neuroscience

Using the Parafilm-assisted Microdissection (PAM) Method to Sample Rodent Nucleus Accumbens Authors:  Marco Pagliusi Jr., Arthur F. Brandão, Gabriel G. Zanetti, Ivan J. M. Bonet, Cesar R. Sartori and Andre S. Vieira, date: 12/05/2020, view: 831, Q&A: 0
Microdissection techniques are very important for anatomical and functional studies focused on neuroscience, where it is often necessary microdissect specific brain areas to perform molecular or anatomical analyses. The parafilm®-assisted microdissection (PAM) was previously described and involves the microdissection of tissue ...
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Headpost Surgery for in vivo Electrophysiological Recording in the Mouse Inferior Colliculus during Locomotion Authors:  Yoonsun Yang and Gunsoo Kim, date: 12/05/2020, view: 907, Q&A: 0

The inferior colliculus (IC) is a critical midbrain integration center for auditory and non-auditory information. Although much is known about the response properties of the IC neurons to auditory stimuli, how the IC neural circuits function during movement such as locomotion remains poorly understood. Mice offer a valuable model in this respect,

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Use of Optogenetic Amyloid-β to Monitor Protein Aggregation in Drosophila melanogaster, Danio rerio and Caenorhabditis elegans Authors:  Prameet Kaur, Caroline Kibat, Emelyne Teo, Jan Gruber, Ajay Mathuru and Nicholas S. Tolwinski, date: 12/05/2020, view: 1536, Q&A: 0

Alzheimer’s Disease (AD) has long been associated with accumulation of extracellular amyloid plaques (Aβ) originating from the Amyloid Precursor Protein. Plaques have, however, been discovered in healthy individuals and not all AD brains show plaques, suggesting that extracellular Aβ aggregates may play a smaller role than

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Plant Science

Chromatin Immunoprecipitation (ChIP) to Assess Histone Marks in Auxin-treated Arabidopsis thaliana Inflorescence Tissue Authors:  André Kuhn and Lars Østergaard, date: 12/05/2020, view: 1335, Q&A: 0
Chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) or high-throughput sequencing (ChIP-seq) has become the gold standard for the identification of binding sites of DNA binding proteins and the localization of histone modification on a locus-specific or genome-wide scale, respectively. ChIP experiments can be divided into seven ...
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Pipecolic Acid Quantification Using Gas Chromatography-coupled Mass Spectrometry Authors:  Keshun Yu, Huazhen Liu and Pradeep Kachroo, date: 12/05/2020, view: 1202, Q&A: 0

Pipecolic acid (Pip), a non-proteinacious product of lysine catabolism, is an important regulator of immunity in plants and humans alike. For instance, Pip accumulation is associated with the genetic disorder Zellweger syndrome, chronic liver diseases, and pyridoxine-dependent epilepsy in humans. In plants, Pip accumulates upon pathogen infection

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