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: 11 to 20 of 130

Publication Record


pHlash: a new genetically encoded and ratiometric luminescence sensor of intracellular pH.
Zhang Y, Xie Q, Robertson JB, Johnson CH
(2012) PLoS One 7: e43072
MeSH Terms: Cell Line, Cytoplasm, Cytosol, Energy Transfer, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, HeLa Cells, Humans, Hydrogen-Ion Concentration, Luminescence, Luminescent Proteins, Saccharomyces cerevisiae, Sodium Fluoride, Time Factors
Show Abstract · Added February 12, 2015
We report the development of a genetically encodable and ratiometic pH probe named "pHlash" that utilizes Bioluminescence Resonance Energy Transfer (BRET) rather than fluorescence excitation. The pHlash sensor-composed of a donor luciferase that is genetically fused to a Venus fluorophore-exhibits pH dependence of its spectral emission in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification in vivo. Its spectral ratio response is H(+) specific; neither Ca(++), Mg(++), Na(+), nor K(+) changes the spectral form of its luminescence emission. Moreover, it can be used to image pH in single cells. This is the first BRET-based sensor of H(+) ions, and it should allow the approximation of pH in cytosolic and organellar compartments in applications where current pH probes are inadequate.
0 Communities
1 Members
0 Resources
14 MeSH Terms
β1 integrin NPXY motifs regulate kidney collecting-duct development and maintenance by induced-fit interactions with cytosolic proteins.
Mathew S, Lu Z, Palamuttam RJ, Mernaugh G, Hadziselimovic A, Chen J, Bulus N, Gewin LS, Voehler M, Meves A, Ballestrem C, Fässler R, Pozzi A, Sanders CR, Zent R
(2012) Mol Cell Biol 32: 4080-91
MeSH Terms: Amino Acid Motifs, Amino Acid Sequence, Animals, Cell Line, Cytosol, Humans, Integrin beta1, Integrin beta3, Kidney Tubules, Collecting, Membrane Proteins, Mice, Molecular Sequence Data, Mutation, Neoplasm Proteins, Protein Binding, Protein Conformation, Talin, Tyrosine
Show Abstract · Added February 24, 2014
Loss of β1 integrin expression inhibits renal collecting-system development. Two highly conserved NPXY motifs in the distal β1 tail regulate integrin function by associating with phosphtyrosine binding (PTB) proteins, such as talin and kindlin. Here, we define the roles of these two tyrosines in collecting-system development and delineate the structural determinants of the distal β1 tail using nuclear magnetic resonance (NMR). Mice carrying alanine mutations have moderate renal collecting-system developmental abnormalities relative to β1-null mice. Phenylalanine mutations did not affect renal collecting-system development but increased susceptibility to renal injury. NMR spectra in bicelles showed the distal β1 tail is disordered and does not interact with the model membrane surface. Alanine or phenylalanine mutations did not alter β1 structure or interactions between α and β1 subunit transmembrane/cytoplasmic domains; however, they did decrease talin and kindlin binding. Thus, these studies highlight the fact that the functional roles of the NPXY motifs are organ dependent. Moreover, the β1 cytoplasmic tail, in the context of the adjacent transmembrane domain in bicelles, is significantly different from the more ordered, membrane-associated β3 integrin tail. Finally, tyrosine mutations of β1 NPXY motifs induce phenotypes by disrupting their interactions with critical integrin binding proteins like talins and kindlins.
1 Communities
4 Members
1 Resources
18 MeSH Terms
Modelling cell polarization driven by synthetic spatially graded Rac activation.
Holmes WR, Lin B, Levchenko A, Edelstein-Keshet L
(2012) PLoS Comput Biol 8: e1002366
MeSH Terms: Cell Membrane, Cell Polarity, Cell Shape, Computational Biology, Computer Simulation, Cytosol, Enzyme Activation, Feedback, Physiological, HeLa Cells, Humans, Models, Biological, Phosphatidylinositols, Receptor Cross-Talk, cdc42 GTP-Binding Protein, rac GTP-Binding Proteins, rho GTP-Binding Proteins
Show Abstract · Added February 26, 2016
The small GTPase Rac is known to be an important regulator of cell polarization, cytoskeletal reorganization, and motility of mammalian cells. In recent microfluidic experiments, HeLa cells endowed with appropriate constructs were subjected to gradients of the small molecule rapamycin leading to synthetic membrane recruitment of a Rac activator and direct graded activation of membrane-associated Rac. Rac activation could thus be triggered independent of upstream signaling mechanisms otherwise responsible for transducing activating gradient signals. The response of the cells to such stimulation depended on exceeding a threshold of activated Rac. Here we develop a minimal reaction-diffusion model for the GTPase network alone and for GTPase-phosphoinositide crosstalk that is consistent with experimental observations for the polarization of the cells. The modeling suggests that mutual inhibition is a more likely mode of cell polarization than positive feedback of Rac onto its own activation. We use a new analytical tool, Local Perturbation Analysis, to approximate the partial differential equations by ordinary differential equations for local and global variables. This method helps to analyze the parameter space and behaviour of the proposed models. The models and experiments suggest that (1) spatially uniform stimulation serves to sensitize a cell to applied gradients. (2) Feedback between phosphoinositides and Rho GTPases sensitizes a cell. (3) Cell lengthening/flattening accompanying polarization can increase the sensitivity of a cell and stabilize an otherwise unstable polarization.
0 Communities
1 Members
0 Resources
16 MeSH Terms
SIX2 and CITED1, markers of nephronic progenitor self-renewal, remain active in primitive elements of Wilms' tumor.
Murphy AJ, Pierce J, de Caestecker C, Taylor C, Anderson JR, Perantoni AO, de Caestecker MP, Lovvorn HN
(2012) J Pediatr Surg 47: 1239-49
MeSH Terms: Biomarkers, Tumor, Blotting, Western, Cell Nucleus, Cytosol, Gene Expression Regulation, Neoplastic, Homeodomain Proteins, Humans, Immunoenzyme Techniques, Kidney, Kidney Neoplasms, Microscopy, Fluorescence, Neoplasm Proteins, Neoplastic Stem Cells, Nephrons, Nerve Tissue Proteins, Nuclear Proteins, Prognosis, RNA, Messenger, RNA, Neoplasm, Reverse Transcriptase Polymerase Chain Reaction, Single-Blind Method, Transcription Factors, Wilms Tumor
Show Abstract · Added January 28, 2014
PURPOSE - SIX2 and CITED1 are transcriptional regulators that specify self-renewing nephronic progenitor cells of the embryonic kidney. We hypothesized that SIX2, which promotes and maintains this stem cell population, and CITED1 remain active in Wilms' tumor (WT).
METHODS - To evaluate expression domains and the pathogenic significance of SIX2 and CITED1 across WT, the Children's Oncology Group provided 40 WT specimens of stages I to IV (n = 10 per stage), which were enriched for unfavorable histology (n = 20) and treatment failure (relapse or death, n = 20). SIX2 and CITED1 protein expression was evaluated qualitatively (immunohistochemistry) and quantitatively (Western blot, or WB). Gene transcription was estimated using quantitative real-time polymerase chain reaction (qRT-PCR).
RESULTS - SIX2 was visualized by immunohistochemistry in 36 (94.7%) of 38 specimens. Protein and messenger RNA expression of SIX2 were quantitatively similar across all stages of disease (P = .48 WB; P = 0.38 qPCR), in favorable or unfavorable histology (P = 0.51 WB; P = 0.58 qPCR), and in treatment failure or success (P = 0.86 WB; P = 0.49 qPCR). Although CITED1 expression paralleled SIX2 qualitatively, no quantitative correlation between SIX2 and CITED1 expression was observed (Spearman correlation coefficient, 0.28; P = 0.08). As in the fetal kidney, overlapping, but also distinct, WT cellular expression domains were observed between SIX2 and CITED1.
CONCLUSION - SIX2 and CITED1 remain active across all disease characteristics of WT. Activity of these genes in WT potentially identifies a population of self-renewing cancer cells that exhibit an embryonic, stemlike phenotype. Taken together, these transcriptional regulators may be fundamental to WT cellular self-renewal and may represent targets for novel therapies that promote terminal differentiation.
Copyright © 2012 Elsevier Inc. All rights reserved.
2 Communities
3 Members
0 Resources
23 MeSH Terms
Myofilament Ca sensitization increases cytosolic Ca binding affinity, alters intracellular Ca homeostasis, and causes pause-dependent Ca-triggered arrhythmia.
Schober T, Huke S, Venkataraman R, Gryshchenko O, Kryshtal D, Hwang HS, Baudenbacher FJ, Knollmann BC
(2012) Circ Res 111: 170-9
MeSH Terms: Action Potentials, Animals, Arrhythmias, Cardiac, Calcium, Calcium Signaling, Cytosol, Homeostasis, Humans, Intracellular Fluid, Mice, Mice, Transgenic, Mutation, Myofibrils, Protein Binding, Up-Regulation
Show Abstract · Added May 27, 2014
RATIONALE - Ca binding to the troponin complex represents a major portion of cytosolic Ca buffering. Troponin mutations that increase myofilament Ca sensitivity are associated with familial hypertrophic cardiomyopathy and confer a high risk for sudden death. In mice, Ca sensitization causes ventricular arrhythmias, but the underlying mechanisms remain unclear.
OBJECTIVE - To test the hypothesis that myofilament Ca sensitization increases cytosolic Ca buffering and to determine the resulting arrhythmogenic changes in Ca homeostasis in the intact mouse heart.
METHODS AND RESULTS - Using cardiomyocytes isolated from mice expressing troponin T (TnT) mutants (TnT-I79N, TnT-F110I, TnT-R278C), we found that increasing myofilament Ca sensitivity produced a proportional increase in cytosolic Ca binding. The underlying cause was an increase in the cytosolic Ca binding affinity, whereas maximal Ca binding capacity was unchanged. The effect was sufficiently large to alter Ca handling in intact mouse hearts at physiological heart rates, resulting in increased end-diastolic [Ca] at fast pacing rates, and enhanced sarcoplasmic reticulum Ca content and release after pauses. Accordingly, action potential (AP) regulation was altered, with postpause action potential prolongation, afterdepolarizations, and triggered activity. Acute Ca sensitization with EMD 57033 mimicked the effects of Ca-sensitizing TnT mutants and produced pause-dependent ventricular ectopy and sustained ventricular tachycardia after acute myocardial infarction.
CONCLUSIONS - Myofilament Ca sensitization increases cytosolic Ca binding affinity. A major proarrhythmic consequence is a pause-dependent potentiation of Ca release, action potential prolongation, and triggered activity. Increased cytosolic Ca binding represents a novel mechanism of pause-dependent arrhythmia that may be relevant for inherited and acquired cardiomyopathies.
0 Communities
1 Members
0 Resources
15 MeSH Terms
Ontogeny of angiotensin type 2 and type 1 receptor expression in mice.
Gao J, Chao J, Parbhu KJ, Yu L, Xiao L, Gao F, Gao L
(2012) J Renin Angiotensin Aldosterone Syst 13: 341-52
MeSH Terms: Animals, Animals, Newborn, Antibodies, Brain, Cell Membrane, Cytosol, Fetus, Gene Expression Regulation, Developmental, Male, Mice, Mice, Inbred C57BL, Models, Biological, RNA, Messenger, Rats, Real-Time Polymerase Chain Reaction, Receptor, Angiotensin, Type 1, Receptor, Angiotensin, Type 2, Spinal Cord
Show Abstract · Added August 5, 2014
In the current experiment, we determined angiotensin type 2 receptor (AT2R) and angiotensin type 1 receptor (AT1R) protein expression by western blot analysis in developing normal mice. The results indicate that: (1) in all detected brain regions and in the spinal cord, adult mice exhibited significantly higher AT2R expression and lower AT1R expression in total protein extracts compared to fetuses and neonates; (2) other major organs, including heart, lung, liver and kidney, exhibited the same expression pattern as the brain and spinal cord; (3) reciprocal changes in AT2R and AT1R expression were found in the total protein extracts from the brainstems of mice from one-day prenatal to six weeks of age, and there was a negative correlation between AT2R and AT1R protein expression; (4) in both membrane and cytosolic fractions from the brainstem, adult mice exhibited higher AT2R and lower AT1R expression than did fetuses and neonates; and (5) in the brainstem, there were no significant differences in AT2R and AT1R messenger RNA (mRNA) levels among fetal, neonatal and adult mice. The above results reconfirmed our previous finding in rats that adult animals have higher AT2R and lower AT1R expression compared to fetuses and neonates. These data imply an involvement of AT1R in fetal development and of AT2R in adult function.
0 Communities
1 Members
0 Resources
18 MeSH Terms
Studies of the mechanistic details of the pH-dependent association of botulinum neurotoxin with membranes.
Mushrush DJ, Koteiche HA, Sammons MA, Link AJ, McHaourab HS, Lacy DB
(2011) J Biol Chem 286: 27011-8
MeSH Terms: Botulinum Toxins, Type A, Cytosol, Hydrogen-Ion Concentration, Membranes, Artificial, Models, Chemical, Protein Multimerization, Protein Structure, Tertiary, Protein Transport
Show Abstract · Added May 7, 2013
Botulinum neurotoxin (BoNT) belongs to a large class of toxic proteins that act by enzymatically modifying cytosolic substrates within eukaryotic cells. The process by which a catalytic moiety is transferred across a membrane to enter the cytosol is not understood for any such toxin. BoNT is known to form pH-dependent pores important for the translocation of the catalytic domain into the cytosol. As a first step toward understanding this process, we investigated the mechanism by which the translocation domain of BoNT associates with a model liposome membrane. We report conditions that allow pH-dependent proteoliposome formation and identify a sequence at the translocation domain C terminus that is protected from proteolytic degradation in the context of the proteoliposome. Fluorescence quenching experiments suggest that residues within this sequence move to a hydrophobic environment upon association with liposomes. EPR analyses of spin-labeled mutants reveal major conformational changes in a distinct region of the structure upon association and indicate the formation of an oligomeric membrane-associated intermediate. Together, these data support a model of how BoNT orients with membranes in response to low pH.
0 Communities
2 Members
0 Resources
8 MeSH Terms
E2 conjugating enzyme selectivity and requirements for function of the E3 ubiquitin ligase CHIP.
Soss SE, Yue Y, Dhe-Paganon S, Chazin WJ
(2011) J Biol Chem 286: 21277-86
MeSH Terms: Cytosol, DNA, Escherichia coli, Magnetic Resonance Spectroscopy, Molecular Conformation, Mutagenesis, Site-Directed, Protein Conformation, Protein Denaturation, Protein Folding, Protein Interaction Mapping, Recombinant Proteins, Triticum, Ubiquitin, Ubiquitin-Conjugating Enzymes, Ubiquitin-Protein Ligases
Show Abstract · Added March 7, 2014
The transfer of ubiquitin (Ub) to a substrate protein requires a cascade of E1 activating, E2 conjugating, and E3 ligating enzymes. E3 Ub ligases containing U-box and RING domains bind both E2∼Ub conjugates and substrates to facilitate transfer of the Ub molecule. Although the overall mode of action of E3 ligases is well established, many of the mechanistic details that determine the outcome of ubiquitination are poorly understood. CHIP (carboxyl terminus of Hsc70-interacting protein) is a U-box E3 ligase that serves as a co-chaperone to heat shock proteins and is critical for the regulation of unfolded proteins in the cytosol. We have performed a systematic analysis of the interactions of CHIP with E2 conjugating enzymes and found that only a subset bind and function. Moreover, some E2 enzymes function in pairs to create products that neither create individually. Characterization of the products of these reactions showed that different E2 enzymes produce different ubiquitination products, i.e. that E2 determines the outcome of Ub transfer. Site-directed mutagenesis on the E2 enzymes Ube2D1 and Ube2L3 (UbcH5a and UbcH7) established that an SPA motif in loop 7 of E2 is required for binding to CHIP but is not sufficient for activation of the E2∼Ub conjugate and consequent ubiquitination activity. These data support the proposal that the E2 SPA motif provides specificity for binding to CHIP, whereas activation of the E2∼Ub conjugate is derived from other molecular determinants.
0 Communities
1 Members
0 Resources
15 MeSH Terms
Cytosolic phospholipase A2 as a molecular target for the radiosensitization of ovarian cancer.
Schulte RR, Linkous AG, Hallahan DE, Yazlovitskaya EM
(2011) Cancer Lett 304: 137-43
MeSH Terms: Adenocarcinoma, Animals, Antineoplastic Agents, Arachidonic Acids, Blotting, Western, Combined Modality Therapy, Cytoplasm, Enzyme Activation, Enzyme Inhibitors, Female, Humans, Mice, Mice, Nude, Ovarian Neoplasms, Phospholipases A2, Cytosolic, Radiation-Sensitizing Agents, Signal Transduction, Xenograft Model Antitumor Assays
Show Abstract · Added August 21, 2013
In ovarian cancer, the molecular targeted chemotherapeutics could increase the efficiency of low-dose radiotherapy while decreasing injury to adjusted organs. In irradiated A2780 human ovarian carcinoma cells, cytosolic phospholipase A2 (cPLA(2)) inhibitor AACOCF(3) prevented activation of pro-survival Akt signaling and enhanced cell death. The potential molecular mechanisms of this effect could involve signaling through lysophosphatidic acid receptors. In the heterotopic A2780 tumor model using nude mice, cPLA(2) inhibition significantly delayed tumor growth compared to treatment with radiation or vehicle alone. These results identify cPLA(2) as a molecular target to enhance the therapeutic ratio of radiation in ovarian cancer.
Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
0 Communities
1 Members
0 Resources
18 MeSH Terms
Mathematical model of PAR1-mediated activation of human platelets.
Lenoci L, Duvernay M, Satchell S, DiBenedetto E, Hamm HE
(2011) Mol Biosyst 7: 1129-37
MeSH Terms: Blood Platelets, Calcium, Cytosol, Exocytosis, Humans, Integrins, Models, Theoretical, Platelet Activation, Receptor, PAR-1, Signal Transduction, Thrombin
Show Abstract · Added December 10, 2013
Thrombin, one of the major proteases in the coagulation cascade, activates protease activated receptors 1 and 4 (PAR 1 and PAR4) to generate a network of intracellular signals that lead to stable platelet aggregation. Abnormal platelet activation could lead to either thrombosis or bleeding disorders, thus a predictive model of platelet activation would be an invaluable tool for the study of platelet function. In this work, we developed a computational model of PAR1-stimulated human platelet activation fully based on experimental observations. The model is represented by a system of ordinary differential equations (ODEs) describing the kinetics of the interacting components. The model is able to reproduce experimental dose responses and time-courses of cytosolic calcium (Ca(2+)), phosphatidylinositol 4,5-bisphosphate (PIP2), diacylglycerol (DAG), GTP-bound Ras-proximate-1 (Rap1GTP), secretion of dense-granules, and activation of integrin α2bβ3 (GPIIbIIIa). Because of the inherent complexity of such a model, we also provide a simple way to identify and divide the system into interlinked functional modules to reduce the number of unknown parameters. Both the full and the reduced kinetic models are shown to predict platelet behavior in response to PAR1 activation.
0 Communities
1 Members
0 Resources
11 MeSH Terms