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Bio-protocol

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https://www.readbyqxmd.com/read/30515449/-ex-vivo-culture-and-lentiviral-transduction-of-benign-prostatic-hyperplasia-bph-samples
#1
Urszula Lucja McClurg, Stuart R McCracken, Lisa Butler, Karl T Riabowol, Olivier Binda
To assess oncogenic potential, classical transformation assays are based on cell line models. However, cell line based models do not reflect the complexity of human tissues. We thus developed an inducible expression system for gene expression in ex vivo human tissues, which maintain native tissue architecture, such as epithelia and stroma. To validate the system, we transduced and expressed known tumor suppressors (p53, p33ING1b), oncoproteins (RasV12, p47ING3), or controls (empty vector, YFP) in ex vivo prostate tissues, then assessed proliferation by immunohistochemistry of markers (H3S10phos )...
November 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30505888/generation-of-stable-expression-mammalian-cell-lines-using-lentivirus
#2
Neha Tandon, Kaushik N Thakkar, Edward L LaGory, Yu Liu, Amato J Giaccia
Lentiviruses are used very widely to generate stable expression mammalian cell lines. They are used for both gene down-regulation (by using shRNA) or for gene up-regulation (by using ORF of gene of interest). The technique of generating stable cell lines using 3rd generation lentivirus is very robust and it typically takes about 1-2 weeks to get stable expression for most mammalian cell lines. The advantage of using the 3rd generation lentivirus are that are very safe and they are replication incompetent.
November 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30505887/eicosanoid-isolation-from-mouse-intestinal-tissue-for-elisa
#3
Isabella Rauch
Activation of inflammasomes in peritoneal macrophages and intestinal epithelial cells (IEC) leads to the release of eicosanoids. To assess the amount of eicosanoids released by IEC, lipids need to be isolated from whole tissue previous to analysis by lipid mass spectrometry or ELISA. This protocol describes how to isolate lipids from intestinal tissue for analysis by PGE2 -ELISA and normalize to tissue protein content.
November 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30474049/kinetic-characterization-of-the-shigella-type-three-secretion-system-atpase-spa47-using-%C3%AE-32-p-atp
#4
Heather B Case, Nicholas E Dickenson
ATPases represent a diverse class of enzymes that utilize ATP hydrolysis to support critical biological functions such as driving ion pumps, providing mechanical work, unfolding/folding proteins, and supporting otherwise thermodynamically unfavorable chemical reactions. We have recently shown that the Shigella protein Spa47 is an ATPase that supports protein secretion through its specialized type three secretion apparatus (T3SA), supporting infection of human host cells. Characterizing ATPases, such as Spa47, requires a means to accurately determine enzyme activity (ATP hydrolysis) as a function of time, reaction conditions, and potential cofactors, regulators, inhibitors, etc ...
November 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30467550/electroporation-of-labeled-antibodies-to-visualize-endogenous-proteins-and-posttranslational-modifications-in-living-metazoan-cell-types
#5
Sascha Conic, Dominique Desplancq, László Tora, Etienne Weiss
The spatiotemporal localization of different intracellular factors in real-time and their detection in live cells are important parameters to understand dynamic protein-based processes. Therefore, there is a demand to perform live-cell imaging and to measure endogenous protein dynamics in single cells. However, fluorescent labeling of endogenous protein in living cells without overexpression of fusion proteins or genetic tagging has not been routinely possible. Here we describe a versatile antibody-based imaging approach (VANIMA) to be able to precisely locate and track endogenous proteins in living cells...
November 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30505886/detection-and-differentiation-of-multiple-viral-rnas-using-branched-dna-fish-coupled-to-confocal-microscopy-and-flow-cytometry
#6
Nicholas van Buuren, Karla Kirkegaard
Due to the exceptionally high mutation rates of RNA-dependent RNA polymerases, infectious RNA viruses generate extensive sequence diversity, leading to some of the lowest barriers to the development of antiviral drug resistance in the microbial world. We have previously discovered that higher barriers to the development of drug resistance can be achieved through dominant suppression of drug-resistant viruses by their drug-susceptible parents. We have explored the existence of dominant drug targets in poliovirus, dengue virus and hepatitis C virus (HCV)...
October 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30505885/transcytosis-assay-for-transport-of-glycosphingolipids-across-mdck-ii-cells
#7
Maria Daniela Garcia-Castillo, Wayne I Lencer, Daniel J-F Chinnapen
Absorption and secretion of peptide and protein cargoes across single-cell thick mucosal and endothelial barriers occurs by active endocytic and vesicular trafficking that connects one side of the epithelial or endothelial cell (the lumen) with the other (the serosa or blood). Assays that assess this pathway must robustly control for non-specific and passive solute flux through weak or damaged intercellular junctions that seal the epithelial or endothelial cells together. Here we describe an in vitro cell culture Transwell assay for transcytosis of therapeutic peptides linked covalently to various species of the glycosphingolipid GM1...
October 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30505884/behavioral-evaluation-of-seeking-and-preference-of-alcohol-in-mice-subjected-to-stress
#8
Ana Canseco-Alba, Norman Schanz, Hiroki Ishiguro, Qing-Rong Liu, Emmanuel S Onaivi
The alcohol preference model is one of the most widely used animal models relevant to alcoholism. Stressors increase alcohol consumption. Here we present a protocol for a rapid and useful tool to test alcohol preference and stress-induced alcohol consumption in mice. In this model, animals are given two bottles, one with a diluted solution of ethanol in water, and the other with tap water. Consumption from each bottle is monitored over a 24-h period over several days to assess the animal's relative preference for the ethanol solution over water...
October 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30467549/nuclear-cytoplasmic-fractionation-of-proteins-from-caenorhabditis-elegans
#9
Alejandro Mata-Cabana, Olga Sin, Renée I Seinstra, Ellen A A Nollen
C. elegans is widely used to investigate biological processes related to health and disease. To study protein localization, fluorescently-tagged proteins can be used in vivo or immunohistochemistry can be performed in whole worms. Here, we describe a technique to localize a protein of interest at a subcellular level in C. elegans lysates, which can give insight into the location, function and/or toxicity of proteins.
October 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30406158/testing-for-assortative-mating-by-diet-in-drosophila-melanogaster
#10
Philip T Leftwich, Tracey Chapman
Experimental studies of the evolution of reproductive isolation in real time are a powerful way to reveal the way that fundamental processes, such as mate choice, initiate divergence. Mate choice, while frequently described in females, can occur in either sex, and can be affected by the genetics or environment of an individual. Here we describe simple protocols for assessing mating outcomes in fruit flies, which in this context can be used to assess reproductive isolation derived from rearing on different diets over multiple generations...
October 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30505883/a-method-for-sumo-modification-of-proteins-in-vitro
#11
Christine C Lee, Bing Li, Hongtao Yu, Michael J Matunis
The Small Ubiquitin-related Modifier (SUMO) is a protein that is post-translationally added to and reversibly removed from other proteins in eukaryotic cells. SUMO and enzymes of the SUMO pathway are well conserved from yeast to humans and SUMO modification regulates a variety of essential cellular processes including transcription, chromatin remodeling, DNA damage repair, and cell cycle progression. One of the challenges in studying SUMO modification in vivo is the relatively low steady-state level of a SUMO-modified protein due in part to the activity of SUMO deconjugating enzymes known as SUMO Isopeptidases or SENPs...
October 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30450365/filter-retardation-assay-for-detecting-and-quantifying-polyglutamine-aggregates-using-caenorhabditis-elegans-lysates
#12
Olga Sin, Alejandro Mata-Cabana, Renée I Seinstra, Ellen A A Nollen
Protein aggregation is a hallmark of several neurodegenerative diseases and is associated with impaired protein homeostasis. This imbalance is caused by the loss of the protein's native conformation, which ultimately results in its aggregation or abnormal localization within the cell. Using a C. elegans model of polyglutamine diseases, we describe in detail the filter retardation assay, a method that captures protein aggregates in a cellulose acetate membrane and allows its detection and quantification by immunoblotting...
October 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30417032/fluorescence-titrations-to-determine-the-binding-affinity-of-cyclic-nucleotides-to-sthk-ion-channels
#13
Philipp A M Schmidpeter, Crina M Nimigean
The cyclic-nucleotide modulated ion channel family includes cyclic nucleotide-gated (CNG) and hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels, which play essential roles in visual and olfactory signaling and the heart pacemaking activity. Functionally, these channels have been extensively characterized by electrophysiological techniques from protein heterologously expressed in Xenopus oocytes and mammalian cells. On the other hand, expression and purification of these proteins for biophysical and structural analyses in vitro is problematic and expensive and, accordingly, only limited information on the purified channels is available in the literature...
October 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30406157/an-image-analysis-pipeline-to-quantify-emerging-cracks-in-materials-or-adhesion-defects-in-living-tissues
#14
Stéphane Verger, Guillaume Cerutti, Olivier Hamant
Microcracks in materials reflect their mechanical properties. The quantification of the number or orientation of such cracks is thus essential in many fields, including engineering and geology. In biology, cracks in soft tissues can reflect adhesion defects, and the analysis of their pattern can help to deduce the magnitude and orientation of tensions in organs and tissues. Here, we describe a semi-automatic method amenable to analyze cell separations occurring in the epidermis of Arabidopsis thaliana seedlings...
October 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30345328/preparation-of-sequencing-rna-libraries-through-chemical-cross-linking-coupled-to-affinity-purification-cclap-in-saccharomyces-cerevisiae
#15
Congwei Wang, Julie Weidner, Anne Spang
Ribonucleoprotein particles (mRNPs) are complexes consisting of mRNAs and RNA-binding proteins (RBPs) which control mRNA transcription localization, turnover, and translation. Some mRNAs within the mRNPs have been shown to undergo degradation or storage. Those transcripts can lack general mRNA elements, like the poly(A) tail or 5' cap structure, which prevent their identification through the application of widely-used approaches like oligo(dT) purification. Here, we describe a modified cross-linking affinity purification protocol (cCLAP) based on existing cross-linking and immunoprecipitation (CLIP) methods to isolate mRNAs which could be deadenylated, decapped and/or partially degraded in mRNPs, opening the possibility to detect different types of non-coding RNAs (ncRNAs)...
October 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30417031/artificial-inhalation-protocol-in-adult-mice
#16
Thomas P Eiting, Matt Wachowiak
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 animals must breathe regularly, and the act of breathing itself also controls odorant presentation. However, using an artificial inhalation preparation allows us to decouple breathing from olfaction...
September 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30406156/6-hydroxydopamine-6-ohda-oxidative-stress-assay-for-observing-dopaminergic-neuron-loss-in-caenorhabditis-elegans
#17
Sarah-Lena Offenburger, Anton Gartner
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 as well. Dopaminergic neurons are progressively lost in Parkinson's disease and an important risk factor to develop this disease appears to be oxidative stress, the increased occurrence of highly reactive oxygen species...
September 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30370318/sendai-virus-propagation-using-chicken-eggs
#18
Narihito Tatsumoto, Moshe Arditi, Michifumi Yamashita
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 adaptive-immunity, Sendai-virus-based virotherapy and IgA nephropathy. Here, we describe a protocol for Sendai virus propagation using chicken eggs. This traditional protocol enables us to generate a large amount of virus enough for animal experiments as well as cell culture experiments in a relatively inexpensive way...
September 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30345327/high-throughput-microscopic-analysis-of-salmonella-invasion-of-host-cells
#19
Jakub Voznica, Jost Enninga, Virginie Stévenin
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 targeted by the pathogen, and to analyze the relation between infecting Salmonella ( i.e. , cooperation or competition), we have established a high-throughput microscopic assay of HeLa cells sequentially infected with fluorescent bacteria...
September 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/30283811/pentylenetetrazole-ptz-induced-convulsion-assay-to-determine-gabaergic-defects-in-caenorhabditis-elegans
#20
Shruti Thapliyal, Kavita Babu
Pentylenetetrazole (PTZ) is a GABAA receptor antagonist and is used to monitor presynaptic defects in the release of the inhibitory neurotransmitter GABA. PTZ is a competitive inhibitor of GABA, and prevents binding of GABA on the GABAA receptors present on the surface of muscle. In the absence of GABA binding, the excitatory to inhibitory signal ratio increases resulting in a convulsive phenotype. This assay provides a fast and reliable method to detect presynaptic defects in GABAergic synaptic transmission...
September 5, 2018: Bio-protocol
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