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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.
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Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions
Authors:  Robert Cooper, Lev Tsimring and Jeff Hasty, date: 08/20/2018, view: 538, 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: 527, 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 ...
Evaluating Working Memory on a T-maze in Male Rats
Authors:  Ahmed M. Hussein, Mekite Bezu and Volker Korz, date: 07/20/2018, view: 666, Q&A: 0
Working memory is short-term memory, so temporal improvement does not reflect the consolidation of a memory trace, rather the functionality of the underlying neuronal circuits and molecular signaling cascades. The administration of drugs–either one-time or through daily injection–can elucidate the underlying mechanisms. The T-maze is especially ...
Fluorescent Labeling of Rat-tail Collagen for 3D Fluorescence Imaging
Author:  Andrew D. D Doyle, date: 07/05/2018, view: 910, Q&A: 0
Rat tail collagen solutions have been used as polymerizable in vitro three-dimensional (3D) extracellular matrix (ECM) gels for single and collective cell migration assays as well as spheroid formation. These 3D hydrogels are a relatively inexpensive, simple to use model system that can mimic the in vivo physical characteristics ...
Quantification of Starch in Guard Cells of Arabidopsis thaliana
Authors:  Sabrina Flütsch, Luca Distefano and Diana Santelia, date: 07/05/2018, view: 918, Q&A: 0
In this protocol, we describe how to quantify starch in guard cells of Arabidopsis thaliana using the fluorophore propidium iodide and confocal laser scanning microscopy. This simple method enables monitoring, with unprecedented resolution, the dynamics of starch in guard cells.
Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots
Authors:  Joseph Edwards, Christian Santos-Medellín and Venkatesan Sundaresan, date: 06/20/2018, view: 1330, Q&A: 0
Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets ...
Implementation of Blue Light Switchable Bacterial Adhesion for Design of Biofilms
Authors:  Fei Chen and Seraphine V. Wegner, date: 06/20/2018, view: 903, Q&A: 0
Control of bacterial adhesions to a substrate with high precision in space and time is important to form a well-defined biofilm. Here, we present a method to engineer bacteria such that they adhere specifically to substrates under blue light through the photoswitchable proteins nMag and pMag. This provides exquisite spatiotemporal remote control ...
Immunohistochemical Identification of Human Skeletal Muscle Macrophages
Macrophages have well-characterized roles in skeletal muscle repair and regeneration. Relatively little is known regarding the role of resident macrophages in skeletal muscle homeostasis, extracellular matrix remodeling, growth, metabolism and adaptation to various stimuli including exercise and training. Despite speculation into macrophage ...
ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803
Authors:  Joaquín Giner-Lamia, Miguel A. Hernández-Prieto and Matthias E. Futschik, date: 06/20/2018, view: 957, Q&A: 0
Nitrogen is an essential nutrient for all living organisms. In cyanobacteria, a group of oxygenic photosynthetic bacteria, nitrogen homeostasis is maintained by an intricate regulatory network around the transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, the sets of genes under its control (i.e. ...
Protocols to Study Declarative Memory Formation in Mice and Humans: Optogenetics and Translational Behavioral Approaches
Declarative memory formation depends on the hippocampus and declines in aging. Two functions of the hippocampus, temporal binding and relational organization (Rawlins and Tsaltas, 1983; Eichenbaum et al., 1992; Cohen et al., 1997), are known to decline in aging (Leal and Yassa, 2015). However, in the literature distinct ...