Volume: 8 Issue: 18 —BIO-PROTOCOL

Biochemistry

Retroviral Capsid Core Stability Assay Authors: Tyler Milston Renner, Kasandra Bélanger and Marc-André Langlois, date: 09/20/2018, view: 3127, Q&A: 0

Structural stability of the capsid core is a critical parameter for the productive infection of a cell by a retrovirus. Compromised stability can lead to premature core disassembly, exposure of replication intermediates to cytosolic nucleic acid sensors that can trigger innate antiviral responses, and failure to integrate the proviral genome into ...

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Cancer Biology

Qualitative in vivo Bioluminescence Imaging Authors: Devbarna Sinha, Zalitha Pieterse and Pritinder Kaur, date: 09/20/2018, view: 5484, Q&A: 1

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 ...

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Zebrafish Embryo Xenograft and Metastasis Assay Authors: Ilkka Paatero, Sanni Alve, Silvia Gramolelli, Johanna Ivaska and Päivi M. Ojala, date: 09/20/2018, view: 7163, Q&A: 1

Xenograft models, and in particular the mouse xenograft model, where human cancer cells are transplanted into immunocompromised mice, have been used extensively in cancer studies. Although these models have contributed enormously to our understanding of cancer biology, the zebrafish xenograft model offers several advantages over the mouse model. ...

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Cell Biology

Extracting and Integrating Protein Localization Changes from Multiple Image Screens of Yeast Cells Authors: Alex X Lu, Louis-Francois Handfield and Alan M Moses, date: 09/20/2018, view: 2970, Q&A: 0

The evaluation of protein localization changes in cells under diverse chemical and genetic perturbations is now possible due to the increasing quantity of screens that systematically image thousands of proteins in an organism. Integrating information from different screens provides valuable contextual information about the protein function. For ...

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Developmental Biology

Activation of Fibroblast Contractility via Cell-Cell Interactions and Soluble Signals Authors: Neha Pincha, Dyuti Saha, Tanay Bhatt, Ravindra K. Zirmire and Colin Jamora, date: 09/20/2018, view: 5433, Q&A: 0

The collagen contraction assay is an in vitro, three-dimensional method to determine the factor(s) affecting the contractile behavior of activated cells such as fibroblasts in either physiological or pathological scenarios. The collagen lattices/hydrogels are seeded with fibroblasts to mimic the interactions between these cells and their ...

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Immunology

Platelet Migration and Bacterial Trapping Assay under Flow Authors: Shuxia Fan, Michael Lorenz, Steffen Massberg and Florian Gaertner, date: 09/20/2018, view: 4051, Q&A: 0

Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing ...

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Microbiology

Sendai Virus Propagation Using Chicken Eggs Authors: Narihito Tatsumoto, Moshe Arditi and Michifumi Yamashita, date: 09/20/2018, view: 3737, Q&A: 0

Sendai virus is a member of the family Paramyxoviridae, and an enveloped virus with a negative-stranded RNA genome. Sendai virus is not pathogenic to humans, but for mice and can cause pneumonia in mice. Easy and efficient techniques for propagating Sendai virus are required for studying virus replication, virus-induced innate- and ...

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Extraction and Quantification of Polyphosphate (polyP) from Gram-negative Bacteria Authors: Jan-Ulrik Dahl, Lihan Xie and Ursula Jakob, date: 09/20/2018, view: 3722, Q&A: 0

Polyphosphate (polyP), a universally conserved biomolecule, is composed of up to 1,000 phosphate monomers linked via phosphoanhydride bonds. Reaching levels in bacteria that are in the high nmoles per mg protein range, polyP plays important roles in biofilm formation and colonization, general stress protection and virulence. Various protocols for ...

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High-throughput Microscopic Analysis of Salmonella Invasion of Host Cells Authors: Jakub Voznica, Jost Enninga and Virginie Stévenin, date: 09/20/2018, view: 3583, Q&A: 0

Salmonella is a Gram-negative bacterium causing a gastro-enteric disease called salmonellosis. During the first phase of infection, Salmonella uses its flagella to swim near the surface of the epithelial cells and to target specific site of infection. In order to study the selection criteria that determine which host cells are ...

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Plant Assays for Quantifying Ralstonia solanacearum Virulence Authors: Devanshi Khokhani, Tuan Minh Tran , Tiffany M. Lowe-Power and Caitilyn Allen, date: 09/20/2018, view: 4197, Q&A: 0

Virulence assays are powerful tools to study microbial pathogenesis in vivo. Good assays track disease development and, coupled with targeted mutagenesis, can identify pathogen virulence factors. Disease development in plants is extremely sensitive to environmental factors such as temperature, atmospheric humidity, and soil water level, ...

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Molecular Biology

Identifying Protein Interactions with Histone Peptides Using Bio-layer Interferometry Authors: Bingbing Ren, Ahmed Mahmoud Mohammed Sayed, Hwei Ling Tan, Yu Keung Mok and Ee Sin Chen, date: 09/20/2018, view: 4494, Q&A: 0

Histone post-translational modifications (PTMs) regulate numerous cellular processes, including gene transcription, cell division, and DNA damage repair. Most histone PTMs affect the recruitment or exclusion of reader proteins from chromatin. Here, we present a protocol to measure affinity and interaction kinetics between histone peptides and the ...

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Neuroscience

Classic Labyrinth Test for Neurobehavioral Evaluation in Wistar Rats Author: Salim Gasmi, date: 09/20/2018, view: 3766, Q&A: 0

The Classic Labyrinth Test (CLT) is a simple way to evaluate behaviors in rodents such as learning ability, memory, and anxiety. The protocol presented here describes the procedure for use with rats, but the protocol can also be adapted for use in mice if a smaller device is used. In short, the CLT uses a square-shaped maze with a starting point ...

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A Behavioral Assay to Examine the Effects of Kavalactones on Caenorhabditis elegans Neuromuscular Excitability Authors: Bwarenaba B. Kautu, Jessie Chappel, Kellie Steele, Juliana Phillips and M. Shawn Mengarelli, date: 09/20/2018, view: 3021, Q&A: 0

Kavalactones are a class of lactone compounds found in Kava, a traditional beverage from the South Pacific Islands that is derived from the root of Piper methysticum. When consumed, these compounds produce sedative and anxiolytic effects, suggesting their potent actions on the nervous system. Here, we provide a protocol to examine the ...

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Assessing Classical Olfactory Fear Conditioning by Behavioral Freezing in Mice Authors: Jordan M. Ross and Max L. Fletcher, date: 09/20/2018, view: 3125, Q&A: 0

Classical fear conditioning typically involves pairing a discrete cue with a foot shock. Quantifying behavioral freezing to the learned cue is a crucial assay for neuroscience studies focused on learning and memory. Many paradigms utilize discrete stimuli such as tones; however, given mice are odor-driven animals and the wide variety of odorants ...

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Behavioral Evaluation of Odor Memory in Mice Authors: Afif J. Aqrabawi and Jun Chul Kim, date: 09/20/2018, view: 3216, Q&A: 0

Behavioural tests based on the spontaneous recognition paradigm have been used extensively for examining the memory capacity of rodents. By exploiting their innate preference to investigate novel stimuli, inferences can be drawn about the perceived familiarity of encountered objects. Olfaction is the dominant sense used by mice to navigate their ...

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Artificial Inhalation Protocol in Adult Mice Authors: Thomas P. Eiting and Matt Wachowiak, date: 09/20/2018, view: 3048, Q&A: 0

Research in the area of in vivo olfactory physiology benefits from having direct access to the nasal airways through which odorants can be presented. Ordinarily, the passage of odorants through the airways is controlled by respiratory rhythm. This fact makes it difficult to control the timing and strength of an olfactory stimulus, since ...

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6-hydroxydopamine (6-OHDA) Oxidative Stress Assay for Observing Dopaminergic Neuron Loss in Caenorhabditis elegans Authors: Sarah-Lena Offenburger and Anton Gartner, date: 09/20/2018, view: 3988, Q&A: 0

The nematode Caenorhabditis elegans is a powerful genetic model that can be used to investigate neuronal death. Research using C. elegans has been crucial to characterize cell death programmes that are conserved in mammals. Many neuronal signaling components, such as those mediating dopaminergic neurotransmission, are preserved ...

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Plant Science

Fabrication and Use of the Dual-Flow-RootChip for the Imaging of Arabidopsis Roots in Asymmetric Microenvironments Authors: Claire E. Stanley, Jagriti Shrivastava, Rik Brugman, Elisa Heinzelmann, Viktoria Frajs, Andreas Bühler, Dirk van Swaay and Guido Grossmann, date: 09/20/2018, view: 5306, Q&A: 0

This protocol provides a detailed description of how to fabricate and use the dual-flow-RootChip (dfRootChip), a novel microfluidic platform for investigating root nutrition, root-microbe interactions and signaling and development in controlled asymmetric conditions. The dfRootChip was developed primarily to investigate how plants roots interact ...

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GC-MS-Based Analysis of Methanol: Chloroform-extracted Fatty Acids from Plant Tissues Authors: Manish Kumar Patel, Shubhashis Das and Jitendra Kumar Thakur, date: 09/20/2018, view: 8732, Q&A: 0

Fatty acids (FAs) are carboxylic acids with long aliphatic chains that may be straight, branched and saturated or unsaturated. Most of the naturally occurring plant FAs contains an even number of carbon (C4-C24). FAs are used in food and pharmacological industries due to their nutritional importance. In addition, FAs are considered as a promising ...

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Live Confocal Imaging of Brachypodium Spikelet Meristems Author: Devin Lee O'Connor, date: 09/20/2018, view: 3532, Q&A: 0

Live confocal imaging of fluorescent reporters and stains in plant meristems provides valuable measurements of gene expression, protein dynamics, cell polarity, cell division, and growth. The spikelet meristem in the grass Brachypodium distachyon (Brachypodium) is well suited to live imaging because of the ease of dissection, small ...

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Systems Biology

Stable-isotope Labeled Metabolic Analysis in Drosophila melanogaster: From Experimental Setup to Data Analysis Authors: Yuping Cai, Nan Liu and Zheng-Jiang Zhu, date: 09/20/2018, view: 3888, Q&A: 0

Stable-isotope labeled metabolic analysis is an essential methodology to characterize metabolic regulation during biological processes. However, the method using stable-isotope-labeled tracer (e.g., ¹³C-glucose) in live animal is only beginning to be developed. Here, we contribute a qualitative metabolic labeling experiment ...

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Past Issues in 2018

Volume: 8 Issue: 18

Biochemistry

Cancer Biology

Cell Biology

Developmental Biology

Immunology

Microbiology

Molecular Biology

Neuroscience

Plant Science

Systems Biology