• 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.4150

Past Issues in 2021

Volume: 11 Issue: 17

Biochemistry

Kinetic Analysis of a Protein-protein Complex to Determine its Dissociation Constant (KD) and the Effective Concentration (EC50) of an Interplaying Effector Molecule Using Bio-layer Interferometry Authors:  Tim Orthwein, Luciano F. Huergo, Karl Forchhammer and Khaled A. Selim, date: 09/05/2021, view: 986, Q&A: 0

Biolayer interferometry (BLI) is an emerging analytical tool that allows the study of protein complexes in real time to determine protein complex kinetic parameters. This article describes a protocol to determine the KD of a protein complex using a 6×His tagged fusion protein as bait immobilized on the NTA sensor chip of the

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Biophysics

Using Atomic Force Microscopy to Study the Real Time Dynamics of DNA Unwinding by Mitochondrial Twinkle Helicase Authors:  Parminder Kaur, Hai Pan, Matthew J. Longley, William C. Copeland and Hong Wang, date: 09/05/2021, view: 784, Q&A: 0

Understanding the structure and dynamics of DNA-protein interactions during DNA replication is crucial for elucidating the origins of disorders arising from its dysfunction. In this study, we employed Atomic Force Microscopy as a single-molecule imaging tool to examine the mitochondrial DNA helicase Twinkle and its interactions with DNA. We used

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Cell Biology

Cytoduction and Plasmiduction in Yeast Authors:  Jane E. Dorweiler and Anita L. Manogaran, date: 09/05/2021, view: 737, Q&A: 0

Cytoduction, and a related technique referred to as plasmiduction, have facilitated substantial advancements in the field of yeast prion biology by providing a streamlined method of transferring prions from one yeast strain to another. Prions are cytoplasmic elements consisting of aggregated misfolded proteins, and as such, they exhibit

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Developmental Biology

Isolation of Myofibres and Culture of Muscle Stem Cells from Adult Zebrafish Authors:  Massimo Ganassi, Peter S. Zammit and Simon M. Hughes, date: 09/05/2021, view: 1226, Q&A: 0

Skeletal muscles generate force throughout life and require maintenance and repair to ensure efficiency. The population of resident muscle stem cells (MuSCs), termed satellite cells, dwells beneath the basal lamina of adult myofibres and contributes to both muscle growth and regeneration. Upon exposure to activating signals, MuSCs proliferate to

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Immunology

Plasmodium cynomolgi Berok Growth Inhibition Assay by Thiol-reactive Probe Based Flow Cytometric Measurement Authors:  Jessica Jie Ying Ong, Bruce Russell and Jin-Hee Han, date: 09/05/2021, view: 650, Q&A: 0

The relapsing malaria species, Plasmodium vivax, is the most widely distributed and difficult-to-treat cause of human malaria. The merozoites of P. vivax preferentially invade ephemeral human CD71+ reticulocytes (nascent reticulocytes), thereby limiting the development of a robust continuous culture in vitro. Fortunately, P. vivax’s sister

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Isolation and Quantification of Mouse γδT-cells in vitro and in vivo Authors:  Isha Rana, Krithika Badarinath, Ravindra K. Zirmire and Colin Jamora, date: 09/05/2021, view: 806, Q&A: 0

The skin plays an important role in protecting the body from pathogens and chemicals in the external environment. Upon injury, a healing program is rapidly initiated and involves extensive intercellular communication to restore tissue homeostasis. The deregulation of this crosstalk can lead to abnormal healing processes and is the foundation of

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Microscopic Detection of ASC Inflammasomes in Bone Marrow Derived Macrophages Post Stimulation Authors:  Longjun Li, Rudi Mao and Xiaopeng Qi, date: 09/05/2021, view: 681, Q&A: 0

An inflammasome is an intracellular multiprotein complex that plays important roles in host defense and inflammatory responses. Inflammasomes are typically composed of the adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC), cytoplasmic sensor protein, and the effector protein pro-caspase-1. ASC assembly into a protein

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Microbiology

Isolation and Characterization of Membrane Vesicles from Lactobacillus Species Authors:  Julie C. Caruana, Scott N. Dean and Scott A. Walper, date: 09/05/2021, view: 790, Q&A: 0

Throughout their life cycle, bacteria shed portions of their outermost membrane comprised of proteins, lipids, and a diversity of other biomolecules. These biological nanoparticles have been shown to have a range of highly diverse biological activities, including pathogenesis, community regulation, and cellular defense (among others). In recent

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Molecular Biology

Direct-TRI: High-throughput RNA-extracting Method for all Stages of Zebrafish Development Authors:  Kota Ujibe, Kanako Nishimura, Makoto Kashima and Hiromi Hirata, date: 09/05/2021, view: 468, Q&A: 0

Recent popularization of next-generation sequencing enables conducting easy transcriptome analysis. Nevertheless, substantial RNA isolation work prior to RNA sequencing, as well as the high cost involved, still makes the routine use of large-scale transcriptome analysis difficult. For example, conventional phenol-chloroform RNA extraction cannot

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In vitro Cleavage and Electrophoretic Mobility Shift Assays for Very Fast CRISPR Authors:  Roger S. Zou, Yang Liu and Taekjip Ha, date: 09/05/2021, view: 711, Q&A: 0

CRISPR-Cas9 has transformed biomedical research and medicine through convenient and targeted manipulation of DNA. Time- and spatially-resolved control over Cas9 activity through the recently developed very fast CRISPR (vfCRISPR) system have facilitated comprehensive studies of DNA damage and repair. Understanding the fundamental principles of Cas9

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Preparation and Characterization of Internally Modified DNA Templates for Chemical Transcription Roadblocking Author:  Eric J. Strobel, date: 09/05/2021, view: 394, Q&A: 0

Site-specific transcription arrest is the basis of emerging technologies that assess nascent RNA structure and function. Cotranscriptionally folded RNA can be displayed from an arrested RNA polymerase (RNAP) for biochemical manipulations by halting transcription elongation at a defined DNA template position. Most transcription

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Neuroscience

Measurement of LRRK2 Kinase Activity by Proximity Ligation Assay Authors:  Matthew T. Keeney, Eric K. Hoffman, J. Timothy Greenamyre and Roberto Di Maio, date: 09/05/2021, view: 487, Q&A: 0

Missense mutations in leucine rich-repeat kinase 2 (LRRK2) cause forms of familial Parkinson’s disease and have been linked to ‘idiopathic’ Parkinson’s disease. Assessment of LRRK2 kinase activity has been very challenging due to its size, complex structure, and relatively low abundance. A standard in the field to assess

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Plant Science

U2.3 Precursor Small Nuclear RNA in vitro Processing Assay Authors:  Chan Lin, Yujie Feng, Xueyan Peng, Jiaming Wu, Weili Wang and Yunfeng Liu, date: 09/05/2021, view: 306, Q&A: 0

Small nuclear RNAs (snRNAs) are vital for eukaryotic cell activities and play important roles in pre-mRNA splicing. The molecular mechanism underlying the transcription of snRNA, regulated via upstream/downstream cis-elements and relevant trans-elements, has been investigated in detail using cell-free extracts. However, the processing of precursor

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Solubilization Method for Isolation of Photosynthetic Mega- and Super-complexes from Conifer Thylakoids Authors:  Pushan Bag, Wolfgang P. Schröder, Stefan Jansson and Domenica Farci, date: 09/05/2021, view: 496, Q&A: 0

Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of

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Stem Cell

In situ Hybridization of miRNAs in Human Embryonic Kidney and Human Pluripotent Stem Cell-derived Kidney Organoids Authors:  Filipa M. Lopes, Susan J. Kimber and Ioannis Bantounas, date: 09/05/2021, view: 407, Q&A: 0

MicroRNAs are small RNAs that negatively regulate gene expression and play an important role in fine-tuning molecular pathways during development. There is increasing interest in studying their function in the kidney, but the majority of studies to date use kidney cell lines and assess the total amounts of miRNAs of interest either by qPCR or by

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