Editors' Choice
Editors' Choice corresponds to recently published bio-protocols (past one year) that chosen by Bio-protocol Associate Editors based on the protocols' quality, novelty, or potential impact.
Fields
  • Biochemistry
  • Cancer Biology
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  • Developmental Biology
  • Immunology
  • Microbiology
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  • Neuroscience
  • Plant Science
  • Stem Cell
  • Systems Biology
Organisms
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Quantification of Mouse Hematopoietic Progenitors’ Formation Using Time-lapse Microscopy and Image Analysis
In vitro differentiation of mouse embryonic stem cells (mESCs) towards blood cells constitutes a well-established system to study the endothelial-to-hematopoietic transition (EHT) at the onset of blood development. Assessing the emergence of small non-adherent round blood cells in the culture without disturbing it is essential to evaluate ...
Genome-wide Estimation of Evolutionary Distance and Phylogenetic Analysis of Homologous Genes
Authors:  Meixia Zhao, Biao Zhang, Jianxin Ma and Damon Lisch, date: 12/05/2018, view: 822, Q&A: 0
Homologous genes, including paralogs and orthologs, are genes that share sequence homologies within or between different species. Homologous genes originate from a common origin through speciation, genetic duplication or horizontal gene transfer. Estimation of the sequence divergence of homologous genes help us to understand divergence time, which ...
Separation and Visualization of Low Abundant Ubiquitylated Forms
Authors:  Ramona Schuster, Tânia Simões, Fabian den Brave and Mafalda Escobar-Henriques, date: 11/20/2018, view: 913, Q&A: 0
In this protocol we describe the separation and visualization of ubiquitylated forms of the yeast mitofusin Fzo1 by Western blot. To this aim, we express HA-tagged Fzo1 in Saccharomyces cerevisiae, break the cells to extract a membrane-enriched fraction, solubilize the membranes using detergent and then specifically immunoprecipitate the ...
Optical Clearing and Index Matching of Tissue Samples for High-resolution Fluorescence Imaging Using SeeDB2
Authors:  Meng-Tsen Ke and Takeshi Imai, date: 10/20/2018, view: 1666, Q&A: 1
Tissue clearing techniques are useful for large-scale three-dimensional fluorescence imaging of thick tissues. However, high-resolution imaging deep inside tissues has been challenging, as it is extremely sensitive to light scattering and spherical aberrations. Here, we present a water-based optical clearing and mounting media, SeeDB2, which is ...
Measurement of Dopamine Using Fast Scan Cyclic Voltammetry in Rodent Brain Slices
Authors:  Madelyn I. Mauterer, Paige M. Estave, Katherine M. Holleran and Sara R. Jones, date: 10/05/2018, view: 1233, Q&A: 0
Fast scan cyclic voltammetry (FSCV) is an electrochemical technique that allows sub-second detection of oxidizable chemical species, including monoamine neurotransmitters such as dopamine, norepinephrine, and serotonin. This technique has been used to record the physiological dynamics of these neurotransmitters in brain tissue, including their ...
Qualitative in vivo Bioluminescence Imaging
Authors:  Devbarna Sinha, Zalitha Pieterse and Pritinder Kaur, date: 09/20/2018, view: 1205, Q&A: 0
Bioluminescence imaging (BLI) technology is an advanced method of carrying out molecular imaging on live laboratory animals in vivo. This powerful technique is widely-used in studying a variety of biological processes, and it has been an ideal tool in exploring tumor growth and metastatic spread in real-time. This technique ensures the ...
In planta Transcriptome Analysis of Pseudomonas syringae
Authors:  Tatsuya Nobori and Kenichi Tsuda, date: 09/05/2018, view: 1753, Q&A: 0
Profiling bacterial transcriptome in planta is challenging due to the low abundance of bacterial RNA in infected plant tissues. Here, we describe a protocol to profile transcriptome of a foliar bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, in the leaves of Arabidopsis thaliana at an early stage of ...
Dual Fluorescence Reporter Based Analytical Flow Cytometry for miRNA Induced Regulation in Mammalian Cells
Authors:  Nicolas Lemus-Diaz, Liezel Tamon and Jens Gruber, date: 09/05/2018, view: 2261, Q&A: 0
MicroRNA-induced gene regulation is a growing field in basic and translational research. Examining this regulation directly in cells is necessary to validate high-throughput data originated from RNA sequencing technologies. For this several studies employ luciferase-based reporters that usually measure the whole cell population, which comes with ...
Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions
Authors:  Robert Cooper, Lev Tsimring and Jeff Hasty, date: 08/20/2018, view: 1359, Q&A: 0
Bacteria in nature live in complex communities with multiple cell types and spatially-dependent interactions. Studying cells in well-mixed environments such as shaking culture tubes or flasks cannot capture these spatial dynamics, but cells growing in full-fledged biofilms are difficult to observe in real time. We present here a protocol for ...
Tethered Chromosome Conformation Capture Sequencing in Triticeae: A Valuable Tool for Genome Assembly
Authors:  Axel Himmelbach, Ines Walde, Martin Mascher and Nils Stein, date: 08/05/2018, view: 1365, Q&A: 0
Chromosome conformation capture sequencing (Hi-C) is a powerful method to comprehensively interrogate the three-dimensional positioning of chromatin in the nucleus. The development of Hi-C can be traced back to successive increases in the resolution and throughput of chromosome conformation capture (3C) (Dekker et al., 2002). The basic ...



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