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Proximity ligation assay

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https://www.readbyqxmd.com/read/28094900/high-throughput-precision-measurement-of-subcellular-localization-in-single-cells
#1
Tyler J Burns, Andreas P Frei, Pier F Gherardini, Felice A Bava, Jake E Batchelder, Yuki Yoshiyasu, Julie M Yu, Amanda R Groziak, Samuel C Kimmey, Veronica D Gonzalez, Wendy J Fantl, Garry P Nolan
To quantify visual and spatial information in single cells with a throughput of thousands of cells per second, we developed Subcellular Localization Assay (SLA). This adaptation of Proximity Ligation Assay expands the capabilities of flow cytometry to include data relating to localization of proteins to and within organelles. We used SLA to detect the nuclear import of transcription factors across cell subsets in complex samples. We further measured intranuclear re-localization of target proteins across the cell cycle and upon DNA damage induction...
January 17, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28092041/in-solution-sh2-domain-binding-assay-based-on-proximity-ligation
#2
Kazuya Machida
Protein-protein interactions mediated by SH2 domains confer specificity in tyrosine kinase pathways. Traditional assays for assessing interactions between an SH2 domain and its interacting protein such as far-Western and pull-down are inherently low throughput. We developed SH2-PLA, an in-solution SH2 domain binding assay, that takes advantage of the speed and sensitivity of proximity ligation and real-time PCR. SH2-PLA allows for rapid assessment of SH2 domain binding to a target protein using only a few microliters of cell lysate, thereby making it an attractive new tool to study tyrosine kinase signaling...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28078581/proximity-ligation-assay-pla-to-evaluate-disc-and-misc-composition
#3
Melissa Thomas, Patrick Legembre
Distribution of the death receptor CD95 into lipid rafts (aggregation) and/or its internalization may contribute to the implementation of the apoptotic signal at the detriment of the non-apoptotic signaling pathway [1-6]. Also CD95 can form different protein complexes via dynamic protein-protein interactions (PPIs) according to its interaction with soluble or transmembrane CD95L. Therefore, spatiotemporal identification of these PPIs is pivotal to anticipate the signaling pathway implemented in cells stimulated with different forms of CD95L...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28077698/detection-of-antigenic-variants-of-swine-subtype-h3-influenza-a-viruses-from-clinical-samples
#4
Brigitte E Martin, Andrew S Bowman, Lei Li, Jacqueline M Nolting, David R Smith, Larry A Hanson, Xiu-Feng Wan
A large population of genetically and antigenically diverse influenza A viruses (IAVs) are circulating among the swine population, playing an important role in influenza ecology. Swine IAVs not only cause outbreaks among swine, but they can also be transmitted to humans, causing sporadic infections and even pandemic outbreaks. Antigenic characterization of swine IAVs are key to understanding the natural history of these viruses in swine and to selecting strains for effective vaccines. However, influenza outbreaks generally spread rapidly among swine, and the conventional methods for antigenic characterization require virus propagation, a time-consuming process that can significantly reduce the effectiveness of vaccination programs...
January 11, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28077322/a-protein-kinase-a-ezrin-complex-regulates-connexin-43-gap-junction-communication-in-liver-epithelial-cells
#5
Aleksandra Dukic, Linda Hofstad Haugen, Guillaume Pidoux, Edward Leithe, Oddmund Bakke, Kjetil Taskén
Communication between adjacent cells can occur via gap junctions (GJ) composed of connexin (Cx) hexamers that allow passage of small molecules. One of the most widely and highly expressed Cxs in human tissues is Cx43, shown to be regulated through phosphorylation by several kinases including PKA. Ezrin is a membrane associated protein that can serve as an A kinase anchoring protein (AKAP) and hold an anchored pool of PKA. Here, we used the liver epithelial cell line IAR20, which expresses Cx43 as the predominant GJ protein, to test the hypothesis that Ezrin may associate with Cx43 in cell types that form stable GJs and serve as an AKAP...
January 7, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28069442/novel-signaling-of-dynorphin-at-%C3%AE%C2%BA-opioid-receptor-bradykinin-b2-receptor-heterodimers
#6
Bingyuan Ji, Haiqing Liu, Rumin Zhang, Yunlu Jiang, Chunmei Wang, Sheng Li, Jing Chen, Bo Bai
The κ-opioid receptor (KOR) and bradykinin B2 receptor (B2R) are involved in a variety of important physiological processes and share many similar characteristics in terms of their distribution and functions in the nervous system. We first demonstrated the endogenous expression of KOR and B2R in human SH-SY5Y cells and their co-localization on the membrane of human embryonic kidney 293 (HEK293) cells. Bioluminescence and fluorescence resonance energy transfer and the proximity ligation assay were exploited to demonstrate the formation of functional KOR and B2R heteromers in transfected cells...
January 7, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28065322/visualization-of-cleavage-furrow-proteins-in-fixed-dividing-spermatocytes
#7
A Frappaolo, S Sechi, G Belloni, R Piergentili, M G Giansanti
Cytokinesis separates the cytoplasmic organelles and the duplicated genome into two daughter cells at the end of cell division. In animal cell cytokinesis, assembly and constriction of the contractile apparatus must be finely coordinated with plasma membrane remodeling and vesicle trafficking at the cleavage furrow. Accurate control of these events during cell cleavage is a fundamental task in all organisms and is also essential for maintaining ploidy and preventing neoplastic transformation. Drosophila male meiosis provides a well-suited cell system for exploring the molecular mechanisms underlying cytokinesis, combining the powerful tools of Drosophila genetics with unique cytological characteristics...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28060261/study-of-endoplasmic-reticulum-and-mitochondria-interactions-by-in-situ-proximity-ligation-assay-in-fixed-cells
#8
Emily Tubbs, Jennifer Rieusset
Structural interactions between the endoplasmic reticular (ER) and mitochondrial membranes, in domains known as mitochondria-associated membranes (MAM), are crucial hubs for cellular signaling and cell fate. Particularly, these inter-organelle contact sites allow the transfer of calcium from the ER to mitochondria through the voltage-dependent anion channel (VDAC)/glucose-regulated protein 75 (GRP75)/inositol 1,4,5-triphosphate receptor (IP3R) calcium channeling complex. While this subcellular compartment is under intense investigation in both physiological and pathological conditions, no simple and sensitive method exists to quantify the endogenous amount of ER-mitochondria contact in cells...
December 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28050800/micro-rna-204-participates-in-tmprss2-erg-regulation-and-androgen-receptor-reprogramming-in-prostate-cancer
#9
Krassimira Todorova, Metodi V Metodiev, Gergana Metodieva, Milcho Mincheff, Nelson Fernández, Soren Hayrabedyan
Cancer progression is driven by genome instability incurred rearrangements such as transmembrane protease, serine 2 (TMPRSS2)/v-ets erythroblastosis virus E26 oncogene (ERG) that could possibly turn some of the tumor suppressor micro-RNAs into pro-oncogenic ones. Previously, we found dualistic miR-204 effects, acting either as a tumor suppressor or as an oncomiR in ERG fusion-dependent manner. Here, we provided further evidence for an important role of miR-204 for TMPRSS2/ERG and androgen receptor (AR) signaling modulation and fine tuning that prevents TMPRSS2/ERG overexpression in prostate cancer...
January 3, 2017: Hormones & Cancer
https://www.readbyqxmd.com/read/28039357/key-survival-factor-mcl-1-correlates-with-sensitivity-to-combined-bcl-2-bcl-xl-blockade
#10
Michelle Williams, Linus Lee, Donna J Hicks, Meghan M Joly, David Elion, Bushra Rahman, Courtney McKernan, Violeta Sanchez, Justin M Balko, Thomas Stricker, Monica Valeria Estrada, Rebecca S Cook
: An estimated 40,000 deaths will be attributed to breast cancer in 2016, underscoring the need for improved therapies. Evading cell death is a major hallmark of cancer, driving tumor progression and therapeutic resistance. To evade apoptosis, cancers use anti-apoptotic Bcl-2 proteins to bind to and neutralize apoptotic activators, such as Bim. Investigation of anti-apoptotic Bcl-2 family members in clinical breast cancer datasets, revealed greater expression and more frequent gene amplification of MCL1 as compared to BCL2 or BCL2L1 (Bcl-xL) across three major molecular breast cancer subtypes, Luminal (A and B), HER2-enriched, and Basal-like...
December 30, 2016: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28036027/the-phosphorylation-of-pdx-1-by-protein-kinase-ck2-is-crucial-for-its-stability
#11
Sabrina Klein, Rui Meng, Mathias Montenarh, Claudia Götz
The homeodomain protein PDX-1 is a critical regulator of pancreatic development and insulin production in pancreatic β-cells. We have recently shown that PDX-1 is a substrate of protein kinase CK2; a multifunctional protein kinase which is implicated in the regulation of various cellular aspects, such as differentiation, proliferation, and survival. The CK2 phosphorylation site of PDX-1 is located within the binding region of the E3 ubiquitin ligase adaptor protein PCIF1. To study the interaction between PDX-1 and PCIF1 we used immunofluorescence analysis, co-immunoprecipitation, GST-pull-down studies, and proximity ligation assay (PLA)...
December 28, 2016: Pharmaceuticals
https://www.readbyqxmd.com/read/28017718/maturation-and-processing-of-the-amyloid-precursor-protein-is-regulated-by-the-potassium-sodium-hyperpolarization-activated-cyclic-nucleotide-gated-ion-channel-2-hcn2
#12
Susanne Frykman, Mitsuhiro Inoue, Atsushi Ikeda, Yasuhiro Teranishi, Takahiro Kihara, Jolanta L Lundgren, Natsuko G Yamamoto, Nenad Bogdanovic, Bengt Winblad, Sophia Schedin-Weiss, Lars O Tjernberg
The toxic amyloid β-peptide (Aβ) is a key player in Alzheimer Disease (AD) pathogenesis and selective inhibition of the production of this peptide is sought for. Aβ is produced by the sequential cleavage of the Aβ precursor protein (APP) by β-secretase (to yield APP-C-terminal fragment β (APP-CTFβ) and soluble APPβ (sAPPβ)) and γ-secretase (to yield Aβ). We reasoned that proteins that associate with γ-secretase are likely to regulate Aβ production and to be targets of pharmaceutical interventions and therefore performed a pull-down assay to screen for such proteins in rat brain...
December 23, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27990343/homogeneous-and-digital-proximity-ligation-assays-for-the-detection-of-clostridium-difficile-toxins-a-and-b
#13
Harvinder S Dhillon, Gemma Johnson, Mark Shannon, Christina Greenwood, Doug Roberts, Stephen Bustin
BACKGROUND: The proximity ligation assay (PLA) detects proteins via their interaction with pairs of proximity probes, which are antibodies coupled to noncomplementary DNA oligonucleotides. The binding of both proximity probes to their epitopes on the target protein brings the oligonucleotides together, allowing them to be bridged by a third oligonucleotide with complementarity to the other two. This enables their ligation and the detection of the resulting amplicon by real-time quantitative PCR (qPCR), which acts as a surrogate marker for the protein of interest...
December 2016: Biomolecular Detection and Quantification
https://www.readbyqxmd.com/read/27975258/proximity-ligation-assay-a-tool-to-study-endogenous-interactions-between-tau-and-its-neuronal-partners
#14
Alexis Bretteville, Florie Demiautte, Julien Chapuis
Tau is a microtubule associated protein (MAP) that is expressed in neurons of the central nervous system. Tau proteins are deregulated in a group of pathologies, including Alzheimer's disease, commonly called tauopathies. Therefore intensive research has been conducted to understand both the regulation of Tau and its involvement in neuronal cellular pathways. Since its originally described interactor tubulin, Tau has been described to interact with several other proteins, including tyrosine kinases (Src, Fyn, Lck) and Phospholipase C-γ...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27960030/detection-of-receptor-heteromerization-using-in-situ-proximity-ligation-assay
#15
Ivone Gomes, Salvador Sierra, Lakshmi A Devi
Although G protein-coupled receptor (GPCR) heteromerization has been extensively demonstrated in vitro using heterologous cells that overexpress epitope-tagged receptors, their presence in endogenous systems is less well established. This is because a criterion to identify receptor heteromerization is the demonstration that the two interacting receptors are present not only in the same cell but also in the same subcellular compartment in close enough proximity to allow for direct receptor-receptor interaction...
December 13, 2016: Current Protocols in Pharmacology
https://www.readbyqxmd.com/read/27932549/proteolytic-degradation-of-heat-shock-protein-a2-occurs-in-response-to-oxidative-stress-in-male-germ-cells-of-the-mouse
#16
Elizabeth G Bromfield, R John Aitken, Eileen A McLaughlin, Brett Nixon
STUDY QUESTION: Does oxidative stress compromise the protein expression of heat shock protein A2 (HSPA2) in the developing germ cells of the mouse testis? SUMMARY ANSWER: Oxidative stress leads to the modification of HSPA2 by the lipid aldehyde 4-hydroxynonenal (4HNE) and initiates its degradation via the ubiquitin-proteasome system. WHAT IS KNOWN ALREADY: Previous work has revealed a deficiency in HSPA2 protein expression within the spermatozoa of infertile men that have failed fertilization in a clinical setting...
December 8, 2016: Molecular Human Reproduction
https://www.readbyqxmd.com/read/27930836/hepatitis-c-virus-infection-propagates-through-interactions-between-syndecan-1-and-cd81-and-impacts-the-hepatocyte-glycocalyx
#17
Boyan Grigorov, Emma Reungoat, Alice Gentil Dit Maurin, Mihayl Varbanov, Julie Blaising, Maud Michelet, Rachel Manuel, Romain Parent, Birke Bartosch, Fabien Zoulim, Florence Ruggiero, Eve-Isabelle Pécheur
The hepatitis C virus (HCV) infects hepatocytes after binding to heparan sulfate proteoglycans, in particular Syndecan-1, followed by recognition of the tetraspanin CD81 and other receptors. Heparan sulfate proteoglycans are found in a specific microenvironment coating the hepatocyte surface called the glycocalyx and are receptors for extracellular matrix proteins, cytokines, growth factors, lipoproteins, and infectious agents. We investigated the mutual influence of HCV infection on the glycocalyx and revealed new links between Syndecan-1 and CD81...
December 8, 2016: Cellular Microbiology
https://www.readbyqxmd.com/read/27924568/visualization-of-ras-mapk-signaling-in-situ-by-the-proximity-ligation-assay-pla
#18
Zijian Tang, Chengkai Dai
RAS/MAPK signaling responds to diverse extracellular cues and regulates a wide array of cellular processes. Given its biological importance, abnormalities in RAS/MAPK signaling cascade have been intimately implicated in numerous human diseases, including cancer. Herein, we describe a novel methodology to study activation of this pivotal signaling pathway. The Proximity Ligation Assay (PLA) is employed to monitor kinase-substrate interactions between MEK1 and HSF1, or MEK1 and ERK1 in situ.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924567/the-nuclear-translocation-of-erk
#19
Denise A Berti, Rony Seger
The ERK1 and ERK2 (ERK1/2) cascade is a central signaling pathway activated by a wide variety of extracellular agents that transmit the messages of G Protein Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Being such a central pathway, the activity of the cascade is well regulated, including by dynamic changes of the subcellular localization of components of the ERK1/2 cascade. In resting cells, ERK1/2 are localized in the cytosol due to their interactions with different anchoring proteins. After stimulation, ERK1/2 are phosphorylated by MEK1/2 on their regulatory TEY motif, which permits their detachment from the anchoring proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27923366/3c-digital-pcr-for-quantification-of-chromatin-interactions
#20
Meijun Du, Liang Wang
BACKGROUND: Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. In addition, qPCR is often limited to a certain cycle number, making it difficult to detect fragment ligations with low frequency...
December 6, 2016: BMC Molecular Biology
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