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Jianquan Xu, Yang Liu
Higher-order chromatin organization shaped by epigenetic modifications influence the chromatin environment and subsequently regulate gene expression. Direct visualization of the higher-order chromatin structure at their epigenomic states is of great importance for understanding chromatin compaction and its subsequent effect on gene expression and various cellular processes. With the recent advances in super-resolution microscopy, the higher-order chromatin structure can now be directly visualized in situ down to the scale of ~30 nm...
February 5, 2019: Bio-protocol
Ashley M Cowie, Cheryl L Stucky
Postoperative pain is highly debilitating and hinders recovery. Opioids are the main pain medication used for acute postoperative pain. Given the devastating opioid addiction and overdose epidemic across the US, non-opioid pain therapeutics are desperately needed. In order to develop novel, non-opioid therapies for the treatment of postoperative pain and identify the mechanisms underlying this pain, rodent models of incisional pain have been established. The protocol herein describes in detail how to create a mouse model of postoperative pain that was adapted from established protocols...
January 20, 2019: Bio-protocol
Khoa Tran, Erin M Green
In the presence of oxidative stress, cellular defense systems that can detoxify reactive oxygen species are activated through multiple signaling cascades and transcriptional reprogramming. The budding yeast Saccharomyces cerevisiae has served as an excellent model for genetically-identifying factors important for the response to oxidative stress. Here, we describe two assays for testing yeast gene deletion strains or strains overexpressing a gene of interest for viability following oxidative stress induced by hydrogen peroxide treatment...
January 20, 2019: Bio-protocol
Pragya Goel, Xiling Li, Dion Dickman
Presynaptic boutons at nerve terminals are densely packed with synaptic vesicles, specialized organelles for rapid and regulated neurotransmitter secretion. Upon depolarization of the nerve terminal, synaptic vesicles fuse at specializations called active zones that are localized at discrete compartments in the plasma membrane to initiate synaptic transmission. A small proportion of synaptic vesicles are docked and primed for immediate fusion upon synaptic stimulation, which together comprise the readily releasable pool...
January 5, 2019: Bio-protocol
Farzane Sivandzade, Aditya Bhalerao, Luca Cucullo
In recent years, fluorescent dyes have been frequently used for monitoring mitochondrial membrane potential to evaluate mitochondrial viability and function. However, the reproducibility of the results across laboratories strongly depends upon following well validated and reliable protocols along with the appropriate controls. Herein, we provide a practical user guide for monitoring mitochondrial membrane potential in whole cells using a fluorescent cationic probe. The data analysis of mitochondrial membrane potential we provide is one associated with the impact of xenobiotics such as tobacco smoking on blood-brain barrier endothelial cells including both mouse primary (mBMEC) and a mouse-based endothelial cell line (bEnd3) in a side by side comparison...
January 5, 2019: Bio-protocol
Verena Burtscher, Matej Hotka, Walter Sandtner
In multi-cellular organisms, cells communicate with each other utilizing chemical messengers. For many of these messenger molecules, the membrane is an insurmountable barrier. Yet, they act by binding to surface proteins often triggering a cascade of reactions inside the cell. Accordingly, studying ligand-receptor interactions at the cellular surface is key to understanding important aspects of membrane biology. However, despite a multitude of approaches to study membrane features, there is a need for developing techniques that can measure ligand binding with high temporal resolution and on a single cellular level...
January 5, 2019: Bio-protocol
Nataša Savić, Femke Cas Ringnalda, Christian Berk, Katja Bargsten, Jonathan Hall, Martin Jinek, Gerald Schwank
The CRISPR-Cas9 system is a powerful genome-editing tool that promises application for gene editing therapies. The Cas9 nuclease is directed to the DNA by a programmable single guide (sg)RNA, and introduces a site-specific double-stranded break (DSB). In mammalian cells, DSBs are either repaired by non-homologous end joining (NHEJ), generating small insertion/deletion (indel) mutations, or by homology-directed repair (HDR). If ectopic donor templates are provided, the latter mechanism allows editing with single-nucleotide precision...
January 5, 2019: Bio-protocol
Isabelle Bergiers, Christian Tischer, Özge Vargel Bölükbaşı, Christophe Lancrin
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 the progression of EHT and also to test conditions potentially enhancing or repressing this process. Here, we describe how to quantify the formation of mouse hematopoietic progenitors during EHT in normal conditions or following over-expression of eight essential transcription factors using time-lapse microscopy and image analysis...
January 5, 2019: Bio-protocol
Kailey E Harrell, Emily Koury, Sarit Smolikove
DNA double-strand breaks (DSBs) are toxic lesions that every cell must accurately repair in order to survive. The repair of DSBs is an integral part of a cell life cycle and can lead to lethality if repaired incorrectly. Laser microirradiation is an established technique which has been used in yeast, mammalian cell culture, and Drosophila cell culture to study the regulation of DSB repair. Up to our studies, this method has not been adapted for use in a whole, live, multicellular organism to study this repair in vivo...
December 20, 2018: Bio-protocol
Gaurav Kumar, Subhash B Arya, Amit Tuli
Macrophages are highly phagocytic cells that utilize various pathogen recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs). These PAMPs can be present within the microbe, such as bacterial CpG DNA, and are recognized by Toll-like receptor 9 (TLR9), a PRR present on the endosomal membrane of macrophages. PAMPs can also be present on the surface of microbes, such as Lipopolysaccharide (LPS), which decorates the outer membrane of gram-negative bacteria like Salmonella typhimurium and Escherichia coli ...
December 20, 2018: Bio-protocol
Steven D Cothren, Joel N Meyer, Jessica H Hartman
In nearly all subfields of biomedical sciences, there are phenotypes that are currently classified by expert visual scoring. In research applications, these classifications require the experimenter to be blinded to the treatment group in order to avoid unintentional bias in scoring. Currently, many labs either use laborious and tedious methods to manually blind the images, require multiple experimenters to gather and score the data blindly or fail to properly blind the data altogether. In this protocol, we present a simple, freely available software that we created that allows the experimenter to blindly score images...
December 5, 2018: Bio-protocol
Yili Zhu, Weimin Tan, Wei-Lih Lee
In this protocol, we describe a simple microscopy-based method to assess the interaction of a microtubule-associated protein (MAP) with microtubules. The interaction between MAP and microtubules is typically assessed by a co-sedimentation assay, which measures the amount of MAP that co-pellets with microtubules by centrifugation, followed by SDS-PAGE analysis of the supernatant and pellet fractions. However, MAPs that form large oligomers tend to pellet on their own during the centrifugation step, making it difficult to assess co-sedimentation...
December 5, 2018: Bio-protocol
Zhiqiang Zeng, Juan C Lopez-Baez, Laura Lleras-Forero, Hannah Brunsdon, Cameron Wyatt, Witold Rybski, Nicholas D Hastie, Stefan Schulte-Merker, E Elizabeth Patton
Zebrafish have become an increasingly important model organism in the field of wound healing and regenerative medicine, due to their high regenerative capacity coupled with high-resolution imaging in living animals. In a recent study, we described multiple physical and chemical methods to induce notochord injury that led to highly specific transcriptional responses in notochord cellular subpopulations. The notochord is a critical embryonic structure that functions to shape and pattern the vertebrae and spinal column...
December 5, 2018: Bio-protocol
Sun-Young Lee, Mina J Bissell
Drug resistance is a major obstacle in cancer treatment: A case in point is the failure of cancer patients to respond to tyrosine kinase inhibitors (TKI) of EGFR, a receptor that is highly expressed in many cancers. Identification of the targets and delineation of mechanisms of drug resistance remain major challenges. Traditional pharmacological assays of drug resistance measure the response of tumor cells using cell proliferation or cell death as readouts. These assays performed using traditional plastic tissue culture plates (2D) do not translate to in vivo realities...
November 20, 2018: Bio-protocol
Cathrin J Czupalla, Hanadie Yousef, Tony Wyss-Coray, Eugene C Butcher
The brain endothelium is a highly specialized vascular structure that maintains the activity and integrity of the central nervous system (CNS). Previous studies have reported that the integrity of the brain endothelium is compromised in a plethora of neuropathologies. Therefore, it is of particular interest to establish a method that enables researchers to investigate and understand the molecular changes in CNS endothelial cells and underlying mechanisms in conjunction with murine models of disease. In the past, approaches to isolate endothelial cells have either involved the use of transgenic reporter mice or suffered from insufficiently pure cell populations and poor yield...
November 20, 2018: Bio-protocol
Agnik Dasgupta, Andrew E Jacob, Jeffrey D Amack
A transient epithelial structure called the left-right organizer (LRO) establishes left-right asymmetry in vertebrate embryos. Developmental defects that alter LRO formation result in left-right patterning errors that often lead to congenital heart malformations. However, little is known about mechanisms that regulate individual cell behaviors during LRO formation. To address this, we developed a Cre- loxP based method to mosaically label precursor cells, called dorsal forerunner cells, that give rise to the zebrafish LRO known as Kupffer's vesicle...
November 20, 2018: Bio-protocol
Mallory R Kakley, Katrina B Velle, Lillian K Fritz-Laylin
The amount of polymerized actin within a cell can vary widely due to natural processes and/or experimentally induced perturbations. We routinely use this protocol to measure relative polymerized actin content between cell populations by staining cells in suspension with fluorescent phalloidin, then measuring total cell fluorescence using flow cytometry. Although developed for human cells, we have easily adapted this method for use with diverse eukaryotic cell types.
November 20, 2018: Bio-protocol
Nazanin Valibeigi, Daniel G McHail, Carmen L Kimball, Theodore C Dumas
To better understand neural codes for spatial navigation and to address cognitive development questions, the neurobiology of postnatal hippocampal development is receiving increased attention. While the Morris Water Maze is the gold standard for assessing hippocampal integrity, potential confounds can be difficult to control for in juvenile rodents (around three weeks of age, when spatial navigation ability first emerges) and this wet maze is not amenable to electrophysiological recording. A dry maze alternative with minimal training, like the Barnes Maze adapted for juvenile rats, can help overcome these obstacles...
November 20, 2018: Bio-protocol
Cindy L Linn, Sarah E Webster, Mark K Webster
Eye drop treatments are typically used to apply drugs to the anterior structures of the eye. Recently, however, studies have demonstrated that eye drops can reach the retina in the back of the eye if pharmacological agents are carried in appropriate vehicles. Here, we introduce an eye drop procedure to deliver a drug (PNU-282987), in combination with BrdU, to stimulate cell cycle re-entry and label dividing cells in the retinas of adult rodents. This procedure avoids potential systemic complications of repeated intraperitoneal injections, as well as the retinal damage that is induced by repeated intravitreal injections...
November 5, 2018: Bio-protocol
Narihito Tatsumoto, Takamasa Miyauchi, Moshe Arditi, Michifumi Yamashita
Sendai virus (SeV) is an enveloped, single-stranded RNA virus of the family Paramyxoviridae . SeV is a useful tool to study its infectious pathomechanism in immunology and the pathomechanism of a murine model of IgA nephropathy. Virus quantification is essential not only to determine the original viral titers for an appropriate application, but also to measure the viral titers in samples from the harvests from experiments. There are mainly a couple of units/titers for Sendai viral quantification: plaque-forming units (PFU) and hemagglutination (HA) titer...
November 5, 2018: Bio-protocol
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