Other search tools

About this data

The publication data currently available has been vetted by Vanderbilt faculty, staff, administrators and trainees. The data itself is retrieved directly from NCBI's PubMed and is automatically updated on a weekly basis to ensure accuracy and completeness.

If you have any questions or comments, please contact us.

Results: 1 to 10 of 38

Publication Record

Connections

Use of Electron Paramagnetic Resonance in Biological Samples at Ambient Temperature and 77 K.
Elajaili HB, Hernandez-Lagunas L, Ranguelova K, Dikalov S, Nozik-Grayck E
(2019) J Vis Exp :
MeSH Terms: Animals, Antimycin A, Bleomycin, Bronchoalveolar Lavage Fluid, Cattle, Cell Compartmentation, Electron Spin Resonance Spectroscopy, Lung, Mice, Mitochondria, Oxidation-Reduction, RAW 264.7 Cells, Superoxides, Temperature
Show Abstract · Added March 26, 2019
The accurate and specific detection of reactive oxygen species (ROS) in different cellular and tissue compartments is essential to the study of redox-regulated signaling in biological settings. Electron paramagnetic resonance spectroscopy (EPR) is the only direct method to assess free radicals unambiguously. Its advantage is that it detects physiologic levels of specific species with a high specificity, but it does require specialized technology, careful sample preparation, and appropriate controls to ensure accurate interpretation of the data. Cyclic hydroxylamine spin probes react selectively with superoxide or other radicals to generate a nitroxide signal that can be quantified by EPR spectroscopy. Cell-permeable spin probes and spin probes designed to accumulate rapidly in the mitochondria allow for the determination of superoxide concentration in different cellular compartments. In cultured cells, the use of cell permeable 1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine (CMH) along with and without cell-impermeable superoxide dismutase (SOD) pretreatment, or use of cell-permeable PEG-SOD, allows for the differentiation of extracellular from cytosolic superoxide. The mitochondrial 1-hydroxy-4-[2-triphenylphosphonio)-acetamido]-2,2,6,6-tetramethyl-piperidine,1-hydroxy-2,2,6,6-tetramethyl-4-[2-(triphenylphosphonio)acetamido] piperidinium dichloride (mito-TEMPO-H) allows for measurement of mitochondrial ROS (predominantly superoxide). Spin probes and EPR spectroscopy can also be applied to in vivo models. Superoxide can be detected in extracellular fluids such as blood and alveolar fluid, as well as tissues such as lung tissue. Several methods are presented to process and store tissue for EPR measurements and deliver intravenous 1-hydroxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine (CPH) spin probe in vivo. While measurements can be performed at room temperature, samples obtained from in vitro and in vivo models can also be stored at -80 °C and analyzed by EPR at 77 K. The samples can be stored in specialized tubing stable at -80 °C and run at 77 K to enable a practical, efficient, and reproducible method that facilitates storing and transferring samples.
0 Communities
1 Members
0 Resources
14 MeSH Terms
Cyclin G1 and TASCC regulate kidney epithelial cell G-M arrest and fibrotic maladaptive repair.
Canaud G, Brooks CR, Kishi S, Taguchi K, Nishimura K, Magassa S, Scott A, Hsiao LL, Ichimura T, Terzi F, Yang L, Bonventre JV
(2019) Sci Transl Med 11:
MeSH Terms: Animals, Autophagy, Cell Compartmentation, Cell Cycle Checkpoints, Cell Dedifferentiation, Cyclin G1, Disease Models, Animal, Disease Progression, Epithelial Cells, Fibrosis, Humans, Kidney, Kidney Tubules, Proximal, LLC-PK1 Cells, Male, Mice, Renal Insufficiency, Chronic, Swine, TOR Serine-Threonine Kinases, Wound Healing
Show Abstract · Added March 14, 2019
Fibrosis contributes to the progression of chronic kidney disease (CKD). Severe acute kidney injury can lead to CKD through proximal tubular cell (PTC) cycle arrest in the G-M phase, with secretion of profibrotic factors. Here, we show that epithelial cells in the G-M phase form target of rapamycin (TOR)-autophagy spatial coupling compartments (TASCCs), which promote profibrotic secretion similar to the senescence-associated secretory phenotype. Cyclin G1 (CG1), an atypical cyclin, promoted G-M arrest in PTCs and up-regulated TASCC formation. PTC TASCC formation was also present in humans with CKD. Prevention of TASCC formation in cultured PTCs blocked secretion of profibrotic factors. PTC-specific knockout of a key TASCC component reduced the rate of kidney fibrosis progression in mice with CKD. CG1 induction and TASCC formation also occur in liver fibrosis. Deletion of CG1 reduced G-M phase cells and TASCC formation in vivo. This study provides mechanistic evidence supporting how profibrotic G-M arrest is induced in kidney injury and how G-M-arrested PTCs promote fibrosis, identifying new therapeutic targets to mitigate kidney fibrosis.
Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
0 Communities
1 Members
0 Resources
20 MeSH Terms
Visualization of lipid raft membrane compartmentalization in living RN46A neuronal cells using single quantum dot tracking.
Chang JC, Rosenthal SJ
(2012) ACS Chem Neurosci 3: 737-43
MeSH Terms: Animals, Cell Compartmentation, Cell Line, Transformed, G(M1) Ganglioside, Membrane Microdomains, Neurons, Quantum Dots, Rats
Show Abstract · Added May 27, 2014
Lipid rafts are cholesterol-enriched subdomains in the plasma membrane that have been reported to act as a platform to facilitate neuronal signaling; however, they are suspected to have a very short lifetime, up to only a few seconds, which calls into question their roles in biological signaling. To better understand their diffusion dynamics and membrane compartmentalization, we labeled lipid raft constituent ganglioside GM1 with single quantum dots through the connection of cholera toxin B subunit, a protein that binds specifically to GM1. Diffusion measurements revealed that single quantum dot-labeled GM1 ganglioside complexes undergo slow, confined lateral diffusion with a diffusion coefficient of ∼7.87 × 10(-2) μm(2)/s and a confinement domain about 200 nm in size. Further analysis of their trajectories showed lateral confinement persisting on the order of tens of seconds, comparable to the time scales of the majority of cellular signaling and biological reactions. Hence, our results provide further evidence in support of the putative function of lipid rafts as signaling platforms.
0 Communities
1 Members
0 Resources
8 MeSH Terms
LZAP inhibits p38 MAPK (p38) phosphorylation and activity by facilitating p38 association with the wild-type p53 induced phosphatase 1 (WIP1).
An H, Lu X, Liu D, Yarbrough WG
(2011) PLoS One 6: e16427
MeSH Terms: Cell Compartmentation, Cell Cycle Proteins, Humans, Intracellular Signaling Peptides and Proteins, Nerve Tissue Proteins, Phosphoprotein Phosphatases, Phosphorylation, Protein Binding, Protein Phosphatase 2C, Tumor Suppressor Protein p53, Tumor Suppressor Proteins, p38 Mitogen-Activated Protein Kinases
Show Abstract · Added June 27, 2013
LZAP (Cdk5rap3, C53) is a putative tumor suppressor that inhibits RelA, Chk1 and Chk2 and activates p53. LZAP is lost in a portion of human head and neck squamous cell carcinoma and experimental loss of LZAP expression is associated with enhanced invasion, xenograft tumor growth and angiogenesis. p38 MAPK can increase or decrease proliferation and cell death depending on cellular context. LZAP has no known enzymatic activity, implying that its biological functions are likely mediated by its protein-protein interactions. To gain further insight into LZAP activities, we searched for LZAP-associated proteins (LAPs). Here we show that the LZAP binds p38, alters p38 cellular localization, and inhibits basal and cytokine-stimulated p38 activity. Expression of LZAP inhibits p38 phosphorylation in a dose-dependent fashion while loss of LZAP enhances phosphorylation and activation with resultant phosphorylation of p38 downstream targets. Mechanistically, the ability of LZAP to alter p38 phosphorylation depended, at least partially, on the p38 phosphatase, Wip1. Expression of LZAP increased both LZAP and Wip1 binding to p38. Taken together, these data suggest that LZAP activity includes inhibition of p38 phosphorylation and activation.
0 Communities
1 Members
0 Resources
12 MeSH Terms
A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity.
Kouranti I, McLean JR, Feoktistova A, Liang P, Johnson AE, Roberts-Galbraith RH, Gould KL
(2010) PLoS Biol 8:
MeSH Terms: Cell Compartmentation, Cell Polarity, Chromatography, Liquid, Endocytosis, Enzymes, Microscopy, Confocal, Proteomics, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Tandem Mass Spectrometry, Ubiquitination
Show Abstract · Added March 5, 2014
Ubiquitination and deubiquitination are reciprocal processes that tune protein stability, function, and/or localization. The removal of ubiquitin and remodeling of ubiquitin chains is catalyzed by deubiquitinating enzymes (DUBs), which are cysteine proteases or metalloproteases. Although ubiquitination has been extensively studied for decades, the complexity of cellular roles for deubiquitinating enzymes has only recently been explored, and there are still several gaps in our understanding of when, where, and how these enzymes function to modulate the fate of polypeptides. To address these questions we performed a systematic analysis of the 20 Schizosaccharomyces pombe DUBs using confocal microscopy, proteomics, and enzymatic activity assays. Our results reveal that S. pombe DUBs are present in almost all cell compartments, and the majority are part of stable protein complexes essential for their function. Interestingly, DUB partners identified by our study include the homolog of a putative tumor suppressor gene not previously linked to the ubiquitin pathway, and two conserved tryptophan-aspartate (WD) repeat proteins that regulate Ubp9, a DUB that we show participates in endocytosis, actin dynamics, and cell polarity. In order to understand how DUB activity affects these processes we constructed multiple DUB mutants and find that a quintuple deletion of ubp4 ubp5 ubp9 ubp15 sst2/amsh displays severe growth, polarity, and endocytosis defects. This mutant allowed the identification of two common substrates for five cytoplasmic DUBs. Through these studies, a common regulatory theme emerged in which DUB localization and/or activity is modulated by interacting partners. Despite apparently distinct cytoplasmic localization patterns, several DUBs cooperate in regulating endocytosis and cell polarity. These studies provide a framework for dissecting DUB signaling pathways in S. pombe and may shed light on DUB functions in metazoans.
0 Communities
1 Members
0 Resources
11 MeSH Terms
The ClC-3 Cl-/H+ antiporter becomes uncoupled at low extracellular pH.
Matsuda JJ, Filali MS, Collins MM, Volk KA, Lamb FS
(2010) J Biol Chem 285: 2569-79
MeSH Terms: Acids, Animals, Aorta, Cell Compartmentation, Cell Line, Chloride Channels, Chlorides, Glutamic Acid, Green Fluorescent Proteins, Humans, Hydrogen, Hydrogen-Ion Concentration, Kidney, Membrane Potentials, Mesylates, Mice, Mice, Mutant Strains, Muscle, Smooth, Vascular, Mutagenesis, Patch-Clamp Techniques, RNA, Small Interfering, Sulfhydryl Reagents
Show Abstract · Added February 22, 2016
Adenovirus expressing ClC-3 (Ad-ClC-3) induces Cl(-)/H(+) antiport current (I(ClC-3)) in HEK293 cells. The outward rectification and time dependence of I(ClC-3) closely resemble an endogenous HEK293 cell acid-activated Cl(-) current (ICl(acid)) seen at extracellular pH
0 Communities
1 Members
0 Resources
22 MeSH Terms
Cone arrestin binding to JNK3 and Mdm2: conformational preference and localization of interaction sites.
Song X, Gurevich EV, Gurevich VV
(2007) J Neurochem 103: 1053-62
MeSH Terms: Active Transport, Cell Nucleus, Ambystoma, Animals, Arrestin, Binding Sites, Cell Compartmentation, Cell Line, Cell Nucleus, Cytoplasm, Green Fluorescent Proteins, Humans, Indoles, Mitogen-Activated Protein Kinase 10, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Protein Transport, Proto-Oncogene Proteins c-mdm2, Retina, Retinal Cone Photoreceptor Cells, Signal Transduction
Show Abstract · Added December 10, 2013
Arrestins are multi-functional regulators of G protein-coupled receptors. Receptor-bound arrestins interact with >30 remarkably diverse proteins and redirect the signaling to G protein-independent pathways. The functions of free arrestins are poorly understood, and the interaction sites of the non-receptor arrestin partners are largely unknown. In this study, we show that cone arrestin, the least studied member of the family, binds c-Jun N-terminal kinase (JNK3) and Mdm2 and regulates their subcellular distribution. Using arrestin mutants with increased or reduced structural flexibility, we demonstrate that arrestin in all conformations binds JNK3 comparably, whereas Mdm2 preferentially binds cone arrestin 'frozen' in the basal state. To localize the interaction sites, we expressed separate N- and C-domains of cone and rod arrestins and found that individual domains bind JNK3 and remove it from the nucleus as efficiently as full-length proteins. Thus, the arrestin binding site for JNK3 includes elements in both domains with the affinity of partial sites on individual domains sufficient for JNK3 relocalization. N-domain of rod arrestin binds Mdm2, which localizes its main interaction site to this region. Comparable binding of JNK3 and Mdm2 to four arrestin subtypes allowed us to identify conserved residues likely involved in these interactions.
0 Communities
1 Members
0 Resources
21 MeSH Terms
Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta.
Citovsky V, Lee LY, Vyas S, Glick E, Chen MH, Vainstein A, Gafni Y, Gelvin SB, Tzfira T
(2006) J Mol Biol 362: 1120-31
MeSH Terms: Biological Assay, Biomarkers, Cell Compartmentation, Dimerization, Electroporation, Fluorescent Dyes, Genetic Vectors, Green Fluorescent Proteins, Luminescent Proteins, Microscopy, Confocal, Models, Biological, Molecular Sequence Data, Plant Cells, Plant Proteins, Plants, Plasmids, Protein Binding, Protein Multimerization, Recombinant Fusion Proteins
Show Abstract · Added March 5, 2014
Bimolecular fluorescence complementation (BiFC) represents one of the most advanced and powerful tools for studying and visualizing protein-protein interactions in living cells. In this method, putative interacting protein partners are fused to complementary non-fluorescent fragments of an autofluorescent protein, such as the yellow spectral variant of the green fluorescent protein. Interaction of the test proteins may result in reconstruction of fluorescence if the two portions of yellow spectral variant of the green fluorescent protein are brought together in such a way that they can fold properly. BiFC provides an assay for detection of protein-protein interactions, and for the subcellular localization of the interacting protein partners. To facilitate the application of BiFC to plant research, we designed a series of vectors for easy construction of N-terminal and C-terminal fusions of the target protein to the yellow spectral variant of the green fluorescent protein fragments. These vectors carry constitutive expression cassettes with an expanded multi-cloning site. In addition, these vectors facilitate the assembly of BiFC expression cassettes into Agrobacterium multi-gene expression binary plasmids for co-expression of interacting partners and additional autofluorescent proteins that may serve as internal transformation controls and markers of subcellular compartments. We demonstrate the utility of these vectors for the analysis of specific protein-protein interactions in various cellular compartments, including the nucleus, plasmodesmata, and chloroplasts of different plant species and cell types.
0 Communities
1 Members
0 Resources
19 MeSH Terms
Serotonin-, protein kinase C-, and Hic-5-associated redistribution of the platelet serotonin transporter.
Carneiro AM, Blakely RD
(2006) J Biol Chem 281: 24769-80
MeSH Terms: Animals, Blood Platelets, Cell Compartmentation, Cytoskeletal Proteins, DNA-Binding Proteins, Intracellular Signaling Peptides and Proteins, LIM Domain Proteins, Mice, Protein Kinase C, Protein Transport, Serotonin, Serotonin Plasma Membrane Transport Proteins, Synapses
Show Abstract · Added July 10, 2013
Emerging data indicate the existence of multiple regulatory processes supporting serotonin (5HT) transporter (SERT) capacity including regulated trafficking and catalytic activation, influenced by post-translational modifications and transporter-associated proteins. In the present study, using differential extraction and sedimentation procedures optimized for the purification of cytoskeletal and membrane-skeletal associated proteins, we analyze SERT localization in platelets. We find that most of the plasma membrane SERT is associated with the membrane skeleton. This association can be enhanced by both transporter activation and 5HT2A receptor activation. Inactivation of transport activity by phorbol ester treatment of intact platelets relocates SERT to the cytoskeleton fraction, consequently leading to transporter internalization. The translocation of SERT between these compartments is correlated with changes in the interaction with the LIM domain adaptor protein Hic-5. Co-immunoprecipitation and uptake activity studies suggest that Hic-5 is a determinant of transporter inactivation and relocation to a compartment subserving endocytic regulation. Associations of SERT with Hic-5 are evident in brain synaptosomes, suggesting the existence of parallel mechanisms operating to regulate SERT at serotonergic synapses.
1 Communities
2 Members
0 Resources
13 MeSH Terms
Hypoxia-induced gene expression occurs solely through the action of hypoxia-inducible factor 1alpha (HIF-1alpha): role of cytoplasmic trapping of HIF-2alpha.
Park SK, Dadak AM, Haase VH, Fontana L, Giaccia AJ, Johnson RS
(2003) Mol Cell Biol 23: 4959-71
MeSH Terms: Animals, Basic Helix-Loop-Helix Transcription Factors, Cell Compartmentation, Cell Hypoxia, Cell Nucleus, Cells, Cultured, Cytoplasm, Embryo, Mammalian, Endothelial Growth Factors, Fibroblasts, Gene Expression Regulation, Glucose Transporter Type 1, Hypoglycemia, Hypoxia-Inducible Factor 1, alpha Subunit, Intercellular Signaling Peptides and Proteins, Ligases, Lymphokines, Mice, Mice, Mutant Strains, Mixed Function Oxygenases, Monosaccharide Transport Proteins, Oxygen, Peptide Hydrolases, Phosphoglycerate Kinase, Proteasome Endopeptidase Complex, Repressor Proteins, Signal Transduction, Trans-Activators, Transcription Factors, Transcription, Genetic, Tumor Suppressor Proteins, Ubiquitin-Protein Ligases, Vascular Endothelial Growth Factor A, Vascular Endothelial Growth Factors, Von Hippel-Lindau Tumor Suppressor Protein
Show Abstract · Added August 19, 2013
The hypoxia-inducible factors 1alpha (HIF-1alpha) and 2alpha (HIF-2alpha) have extensive structural homology and have been identified as key transcription factors responsible for gene expression in response to hypoxia. They play critical roles not only in normal development, but also in tumor progression. Here we report on the differential regulation of protein expression and transcriptional activity of HIF-1alpha and -2alpha by hypoxia in immortalized mouse embryo fibroblasts (MEFs). We show that oxygen-dependent protein degradation is restricted to HIF-1alpha, as HIF-2alpha protein is detected in MEFs regardless of oxygenation and is localized primarily to the cytoplasm. Endogenous HIF-2alpha remained transcriptionally inactive under hypoxic conditions; however, ectopically overexpressed HIF-2alpha translocated into the nucleus and could stimulate expression of hypoxia-inducible genes. We show that the factor inhibiting HIF-1 can selectively inhibit the transcriptional activity of HIF-1alpha but has no effect on HIF-2alpha-mediated transcription in MEFs. We propose that HIF-2alpha is not a redundant transcription factor of HIF-1alpha for hypoxia-induced gene expression and show evidence that there is a cell type-specific modulator(s) that enables selective activation of HIF-1alpha but not HIF-2alpha in response to low-oxygen stress.
0 Communities
1 Members
0 Resources
35 MeSH Terms