• 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.4160

Past Issues in 2021

Volume: 11 Issue: 18

Biochemistry

Methods for the Extraction of Heme Prosthetic Groups from Hemoproteins Authors:  Kat Ellis-Guardiola, Jess Soule and Robert T. Clubb, date: 09/20/2021, view: 852, Q&A: 0

Hemoproteins are widely researched because they contain redox-active heme prosthetic groups (iron + protoporphyrin IX) that enable them to perform a range of vital functions, acting as enzymes, participants in electron transfer reactions, or gas sensing, carrying, and storage proteins. While the heme prosthetic group is almost always essential for

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Comprehensive Identification of Translatable Circular RNAs Using Polysome Profiling Authors:  Yanwen Ye, Zefeng Wang and Yun Yang, date: 09/20/2021, view: 766, Q&A: 0

Circular RNAs (circRNAs), a special type of RNAs without 5’- and 3’-ends, are widely present in eukaryotes and known to function as noncoding RNAs to regulate gene expression, including as miRNA sponges. Recent studies showed that many exonic circRNAs, generated by back-splicing of pre-mRNAs, can be translated in a cap-independent

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Biological Engineering

Anaerobic Expression and Purification of Holo-CCIS, an Artificial Iron-sulfur Protein Authors:  Bhanu P. Jagilinki, Irina Paluy, Vikas Nanda and Dror Noy, date: 09/20/2021, view: 697, Q&A: 0

Iron-sulfur proteins are ubiquitous among all living organisms and are indispensable for almost all metabolic pathways ranging from photosynthesis, respiration, nitrogen, and carbon dioxide cycles. The iron-sulfur clusters primarily serve as electron acceptors and donors and transfer electrons to active sites of various enzymes, thus driving the

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Cell Biology

Isolation of Nasal Brush Cells for Single-cell Preparations Authors:  Saltanat Ualiyeva, Amelia A. Boyd, Nora A. Barrett and Lora G. Bankova, date: 09/20/2021, view: 1200, Q&A: 0

Solitary chemosensory epithelial cells are scattered in most mucosal surfaces. They are referred to as tuft cells in the intestinal mucosa, brush cells in the trachea, and solitary chemosensory and microvillous cells in the nasal mucosa. They are the primary source of IL-25 in the epithelium and are also engaged in acetylcholine generation. We

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Developmental Biology

En masse DNA Electroporation for in vivo Transcriptional Assay in Ascidian Embryos Author:  Sébastien Darras, date: 09/20/2021, view: 748, Q&A: 0

Ascidian embryos are powerful models for functional genomics, in particular, due to the ease of generating a large number of transgenic embryos by electroporation. In addition, the small size of their genome makes them an attractive model for studying cis-regulatory elements that control gene expression during embryonic development. Here, I

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Inter-species Transplantation of Blastocysts between Medaka and Zebrafish Authors:  Jana F. Fuhrmann, Jasmin Onistschenko and Lázaro Centanin, date: 09/20/2021, view: 609, Q&A: 0

Transplantation of blastocysts from a donor to a host blastula constitutes a powerful experimental tool to tackle major developmental biology questions. The technique is widely implemented in diverse biological models including teleost fish, where it is typically used for intra-species blastula transplantations – i.e., labeled blastocysts

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Immunology

Identification and Quantitation of Neutrophil Extracellular Traps in Human Tissue Sections Authors:  Coraline Radermecker, Alexandre Hego, Philippe Delvenne and Thomas Marichal, date: 09/20/2021, view: 806, Q&A: 0

Neutrophils are one of the first innate immune cells recruited to tissues during inflammation. An important function of neutrophils relies on their ability to release extracellular structures, known as Neutrophil Extracellular Traps or NETs, into their environment. Detecting such NETs in humans has often proven challenging for both biological

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Microbiology

Cell-free Translation: Preparation and Validation of Translation-competent Extracts from Saccharomyces cerevisiae Authors:  Brandon M. Trainor, Anton A. Komar, Dimitri G. Pestov and Natalia Shcherbik, date: 09/20/2021, view: 742, Q&A: 0

Cell-free translation is a powerful technique for in vitro protein synthesis. While cell-free translation platforms prepared from bacterial, plant, and mammalian cells are commercially available, yeast-based translation systems remain proprietary knowledge of individual labs. Here, we provide a detailed protocol for simple, fast, and

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Glucose Starvation, Magnesium Ion Starvation, and Bile Stress Assays Authors:  Aryashree Arunima and Mrutyunjay Suar, date: 09/20/2021, view: 421, Q&A: 0

Salmonella enterica serovar Enteritidis (S. Enteritidis) is a leading causative pathogen for food-borne gastroenteritis. During its course of infection, it confronts myriads of physiological barriers inside the host, such as nutrient deprivation, low micronutrient availability, and toxicity from bile salts, to promote bacterial survival and

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An Inexpensive Imaging Platform to Record and Quantitate Bacterial Swarming Authors:  Weijie Chen, Sridhar Mani and Jay X. Tang, date: 09/20/2021, view: 506, Q&A: 0

Bacterial swarming refers to a rapid spread, with coordinated motion, of flagellated bacteria on a semi-solid surface (Harshey, 2003). There has been extensive study on this particular mode of motility because of its interesting biological and physical relevance, e.g., enhanced antibiotic resistance (Kearns, 2010) and turbulent collective motion

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Intrathoracic Inoculation of Zika Virus in Aedes aegypti Authors:  Irma Sanchez-Vargas, Adeline E. Williams, Alexander W.E. Franz and Ken E. Olson, date: 09/20/2021, view: 341, Q&A: 0

Aedes aegypti mosquitoes are the main vectors of many medically relevant arthropod-borne (arbo) viruses, including Zika (ZIKV), dengue (DENV), and yellow fever (YFV). Vector competence studies with Ae. aegypti often involve challenging mosquitoes with an artificial bloodmeal containing virus and later quantifying viral titer or infectious

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Molecular Biology

Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats Authors:  Jiahui Zhang, Ashkan Fakharzadeh, Feng Pan, Christopher Roland and Celeste Sagui, date: 09/20/2021, view: 471, Q&A: 0

Atypical DNA and RNA secondary structures play a crucial role in simple sequence repeat (SSR) diseases, which are associated with a class of neurological and neuromuscular disorders known as “anticipation diseases,” where the age of disease onset decreases and the severity of the disease is increased as the intergenerational expansion

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Neuroscience

A Co-purification Method for Efficient Production and Src Kinase-mediated Phosphorylation of Aplysia Cortactin Authors:  Sherlene L. Brown, Yuan Ren, Daniel M. Suter and Seema Mattoo, date: 09/20/2021, view: 441, Q&A: 0

Cortactin is an actin-binding protein that regulates processes like cell migration, endocytosis, and tumor cell metastasis. Although cortactin is associated with actin-cytoskeletal dynamics in non-neuronal cells and cell-free systems, the exact mechanisms underlying its fundamental roles in neuronal growth cones are not fully explored. Recent

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Plant Science

Agrobacterium-mediated Transformation of Japonica Rice Using Mature Embryos and Regenerated Transgenic Plants Authors:  Ammar Elakhdar, Masako Fukuda and Takahiko Kubo, date: 09/20/2021, view: 555, Q&A: 0

Identification of novel genes and their functions in rice is a critical step to improve economic traits. Agrobacterium tumefaciens-mediated transformation is a proven method in many laboratories and widely adopted for genetic engineering in rice. However, the efficiency of gene transfer by Agrobacterium in rice is low, particularly among japonica

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Quantitative Analysis of RNA Editing at Specific Sites in Plant Mitochondria or Chloroplasts Using DNA Sequencing Authors:  Yang Yang and Weixing Shan, date: 09/20/2021, view: 397, Q&A: 0

Cytidine-to-uridine (C-to-U) RNA editing is one of the most important post-transcriptional RNA processing in plant mitochondria and chloroplasts. Several techniques have been developed to detect the RNA editing efficiency in plant mitochondria and chloroplasts, such as poisoned primer extension (PPE) assays, high-resolution melting (HRM) analysis,

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Systems Biology

Protocol for RNA-seq Expression Analysis in Yeast Author:  Stefan Bohn, date: 09/20/2021, view: 550, Q&A: 0

Genome-wide sequencing of RNA (RNA-seq) has become an inexpensive tool to gain key insights into cellular and disease mechanisms. Sample preparation and sequencing are streamlined and allow the acquisition of hundreds of gene expression profiles in a few days; however, in particular, data processing, curation, and analysis involve numerous steps

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Assessing the in vitro Binding Specificity of Histone Modification Reader Proteins Using Histone Peptide Arrays Authors:  Mark W. Soo and Arneet L. Saltzman, date: 09/20/2021, view: 346, Q&A: 0

In the field of chromatin biology, a major goal of understanding the roles of histone post-translational modifications is to identify the proteins and domains that recognize these modifications. Synthetic histone peptides containing one or more modifications are a key tool to probe these interactions in pull-down assays with recombinant proteins

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