• 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.3814

Biochemistry

Generation of Giant Unilamellar Vesicles (GUVs) Using Polyacrylamide Gels Authors:  Eric Parigoris, Daniel L. Dunkelmann and Unai Silvan, date: 11/05/2020, view: 776, Q&A: 0
Giant unilamellar vesicles (GUVs) are a widely used model system for a range of applications including membrane biophysics, drug delivery, and the study of actin dynamics. While several protocols have been developed for their generation in recent years, the use of these techniques involving charged lipid types and buffers of physiological ionic ...
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Developmental Biology

Advances in Proximity Ligation in situ Hybridization (PLISH) Authors:  Monica Nagendran, Adam M Andruska, Pehr B Harbury and Tushar J Desai, date: 11/05/2020, view: 699, Q&A: 0
Understanding tissues in the context of development, maintenance and disease requires determining the molecular profiles of individual cells within their native in vivo spatial context. We developed a Proximity Ligation in situ Hybridization technology (PLISH) that enables quantitative measurement of single cell gene expression ...
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DigiTAG–a RNA Sequencing Approach to Analyze Transcriptomes of Rare Cell Populations in Drosophila melanogaster Authors:  Lisa Landskron, Francois Bonnay, Thomas R. Burkard and Jürgen A. Knoblich, date: 11/05/2020, view: 523, Q&A: 0

Cell-type specific transcriptional programs underlie the development and maintenance of organs. Not only distinct cell types within a tissue, even cells with supposedly identical cell fates show a high degree of transcriptional heterogeneity. Inevitable, low cell numbers are a major hurdle to study transcriptomes of pure cell populations. Here we

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Immunology

Super-resolution Imaging of the T cell Central Supramolecular Signaling Cluster Using Stimulated Emission Depletion Microscopy Authors:  Sin Lih Tan, Dominic Alibhai, Stephen J. Cross, Harry Thompson and Christoph Wülfing, date: 11/05/2020, view: 426, Q&A: 0

Supramolecular signaling assemblies are of interest for their unique signaling properties. A µm scale signaling assembly, the central supramolecular signaling cluster (cSMAC), forms at the center interface of T cells activated by antigen presenting cells (APC). The adaptor protein linker for activation of T cells (LAT) is a key cSMAC component.

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Microbiology

Isolation and CryoTEM of Phages Infecting Bacterial Wine Spoilers Authors:  Amel Chaïb, Marion Decossas, Cécile Philippe, Olivier Claisse, Olivier Lambert and Claire Le Marrec, date: 11/05/2020, view: 398, Q&A: 0

With the objective to isolate phages infecting wine bacterial spoilers, we designed a method for the isolation and purification of phages infecting grape-associated bacteria. The method proved successful to isolate GC1 tectivirus infecting the acetic acid bacterium Gluconobacter cerinus. The isolated phage represents a new genus within the

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Candida albicans Culture, Cell Harvesting, and Total RNA Extraction Authors:  Max V. Cravener and Aaron P. Mitchell, date: 11/05/2020, view: 510, Q&A: 0

Transcriptional analysis has become a cornerstone of biological research, and with the advent of cheaper and more efficient sequencing technology over the last decade, there exists a need for high-yield and efficient RNA extraction techniques. Fungi such as the human pathogen Candida albicans present a unique obstacle to RNA purification in the

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Colorimetric RT-LAMP Methods to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Authors:  Gun-Soo Park, Seung-Hwa Baek, Keunbon Ku, Seong Jun Kim, Seung Il Kim, Bum-Tae Kim and Jin-Soo Maeng, date: 11/05/2020, view: 615, Q&A: 0
Standard diagnostic methods of Coronavirus Disease 2019 (COVID-19) rely on RT-qPCR technique which have limited point-of-care test (POCT) potential due to necessity of dedicated equipment and specialized personnel. LAMP, an isothermal nucleic acid amplification test (NAAT), is a promising technique that may substitute RT-qPCR for POCT of genomic ...
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Murine Acute Pneumonia Model of Pseudomonas aeruginosa Lung Infection Authors:  Xiaolei Pan and Weihui Wu, date: 11/05/2020, view: 402, Q&A: 0
Animal infection models play significant roles in studying bacterial pathogenic mechanisms, host pathogen interaction as well as evaluating drug and vaccine efficacies. We have been utilizing an acute pneumonia model to study bacterial colonization in lungs and assess virulence to the host by determination of bacterial loads and survival assays, ...
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In vitro Glutamylation Inhibition of Ubiquitin Modification and Phosphoribosyl-Ubiquitin Ligation Mediated by Legionella pneumophila Effectors Authors:  Alan G. Sulpizio, Marena E. Minelli and Yuxin Mao, date: 11/05/2020, view: 248, Q&A: 0

Glutamylation is a posttranslational modification where the amino group of a free glutamate amino acid is conjugated to the carboxyl group of a glutamate side chain within a target protein. SidJ is a Legionella kinase-like protein that has recently been identified to perform protein polyglutamylation of the Legionella SdeA Phosphoribosyl-Ubiquitin

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Construction and Validation of A Low-cost, Small-scale, Multiplex Continuous Culturing System for Microorganisms Authors:  Lilit Tonoyan, Freddy Guihéneuf, Ruari Friel and Vincent O’Flaherty, date: 11/05/2020, view: 451, Q&A: 0

This protocol details the construction of a simple, low-cost, small-scale, multiplex chemostat system designed for the continuous cultivation of microorganisms in suspension (i.e., bacteria, yeast, microalgae). The continuous culture device can operate at a working volume of 25 ml and allows the run of 8 chemostats in parallel by a single person.

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Molecular Biology

Long-distance Transport in Bacterial Swarms Revealed by Single Nanoparticle Tracking Authors:  Jingjing Feng and Yan He, date: 11/05/2020, view: 306, Q&A: 0

During swarming, high density flagella-driven bacteria migrate collectively in a swirling pattern on wet agar surfaces, immersed in a thin viscous fluid layer called “swarm fluid”. Though the fluid environment has essential role in the emergence of swarming behavior, the microscopic mechanisms of it in mediating the cooperation of

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Determination of Microtubule Lattice Parameters from Cryo-electron Microscope Images Using TubuleJ Authors:  Siou Ku, Cédric Messaoudi, Charlotte Guyomar, Charles Kervrann and Denis Chrétien, date: 11/05/2020, view: 379, Q&A: 0

The α-β tubulin heterodimer undergoes subtle conformational changes during microtubule assembly. These can be modulated by external factors, whose effects on microtubule structure can be characterized on 2D views obtained by cryo-electron microscopy. Analysis of microtubule images is facilitated if they are straight enough to interpret

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Plant Science

K+ Release Assay and K+ Measurement in Oocyte Assay Author:  Hong Li, date: 11/05/2020, view: 548, Q&A: 0
The Xenopus oocyte is a powerful system for the exogenous expression and functional characterization of plant membrane transport proteins. Until now, a number of potassium transporters and channels have been identified in oocytes expression system by the two-electrode voltage clamp technology. It is difficult to characterize K+ ...
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Systems Biology

Reference-free Association Mapping from Sequencing Reads Using k-mers Authors:  Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, Lior Pachter and Atif Rahman, date: 11/05/2020, view: 438, Q&A: 0
Association mapping is the process of linking phenotypes with genotypes. In genome wide association studies (GWAS), individuals are first genotyped using microarrays or by aligning sequenced reads to reference genomes. However, both these approaches rely on reference genomes which limits their application to organisms with no or incomplete ...
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