Faculty Scholarship
Showing 461 - 470 of 733 Items
Specific sequences within arginine-glycine-rich domains affect mRNA-binding protein function
Date: 2009-08-05
Creator: Anne E. McBride, Ana K. Conboy, Shanique P. Brown, Chaiyaboot Ariyachet, Kate L., Rutledge
Access: Open access
- The discovery of roles for arginine methylation in intracellular transport and mRNA splicing has focused attention on the methylated arginine-glycine (RG)-rich domains found in many eukaryotic RNA-binding proteins. Sequence similarity among these highly repetitive RG domains, combined with interactions between RG-rich proteins, raises the question of whether these regions are general interaction motifs or whether there is specificity within these domains. Using the essential Saccharomyces cerevisiae mRNA-binding protein Npl3 (ScNpl3) as a model system, we first tested the importance of the RG domain for protein function. While Npl3 lacking the RG domain could not support growth of cells lacking Npl3, surprisingly, expression of the RG domain alone supported partial growth of these cells. To address the specificity of this domain, we created chimeric forms of ScNpl3 with RG-rich domains of S. cerevisiae nucleolar proteins, Gar1 and Nop1 (ScGar1, ScNop1), or of the Candida albicans Npl3 ortholog (CaNpl3). Whereas the CaNpl3 RG chimeric protein retained nearly wild-type function in S. cerevisiae, the ScGar1 and ScNop1 RG domains significantly reduced Npl3 function and self-association, indicating RG domain specificity. Nuclear localization of Npl3 also requires specific RG sequences, yet heterologous RG domains allow similar modulation of Npl3 transport by arginine methylation.
MnNiO3 revisited with modern theoretical and experimental methods
Date: 2017-11-07
Creator: Allison L. Dzubak, Chandrima Mitra, Michael Chance, Stephen Kuhn, Gerald E., Jellison, Athena S. Sefat, Jaron T. Krogel, Fernando A. Reboredo
Access: Open access
- MnNiO3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å3, which compares well to the experimental value of 94.4 Å3. A bulk modulus of 217 GPa is predicted for MnNiO3. We rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO3.
The power of context in networks: Ideal point models with social interactions
Date: 2019-01-01
Creator: Mohammad T. Irfan, Tucker Gordon
Access: Open access
- Game theory has been widely used for modeling strategic behaviors in networked multiagent systems. However, the context within which these strategic behaviors take place has received limited attention. We present a model of strategic behavior in networks that incorporates the behavioral context, focusing on the contextual aspects of congressional voting. One salient predictive model in political science is the ideal point model, which assigns each senator and each bill a number on the real line of political spectrum. We extend the classical ideal point model with network-structured interactions among senators. In contrast to the ideal point model's prediction of individual voting behavior, we predict joint voting behaviors in a game-theoretic fashion. The consideration of context allows our model to outperform previous models that solely focus on the networked interactions with no contextual parameters. We focus on two fundamental problems: learning the model using real-world data and computing stable outcomes of the model with a view to predicting joint voting behaviors and identifying most influential senators. We demonstrate the effectiveness of our model through experiments using data from the 114th U.S. Congress.
Long-term maintenance of channel distribution in a central pattern generator neuron by neuromodulatory inputs revealed by decentralization in organ culture
Date: 2001-09-15
Creator: Adi Mizrahi, Patsy S. Dickinson, Peter Kloppenburg, Valerie Fénelon, Deborah J., Baro, Ronald M. Harris-Warrick, Pierre Meyrand, John Simmers
Access: Open access
- Organotypic cultures of the lobster (Homarus gammarus) stomatogastric nervous system (STNS) were used to assess changes in membrane properties of neurons of the pyloric motor pattern-generating network in the long-term absence of neuromodulatory inputs to the stomatogastric ganglion (STG). Specifically, we investigated decentralization-induced changes in the distribution and density of the transient outward current, IA, which is encoded within the STG by the shal gene and plays an important role in shaping rhythmic bursting of pyloric neurons. Using an antibody against lobster shal K+ channels, we found shal immunoreactivity in the membranes of neuritic processes, but not somata, of STG neurons in 5 d cultured STNS with intact modulatory inputs. However, in 5 d decentralized STG, shal immunoreactivity was still seen in primary neurites but was likewise present in a subset of STG somata. Among the neurons displaying this altered shal localization was the pyloric dilator (PD) neuron, which remained rhythmically active in 5 d decentralized STG. Two-electrode voltage clamp was used to compare IA in synaptically isolated PD neurons in long-term decentralized STG and nondecentralized controls. Although the voltage dependence and kinetics of IA changed little with decentralization, the maximal conductance of IA in PD neurons increased by 43.4%. This increase was consistent with the decentralization-induced increase in shal protein expression, indicating an alteration in the density and distribution of functional A-channels. Our results suggest that, in addition to the short-term regulation of network function, modulatory inputs may also play a role, either directly or indirectly, in controlling channel number and distribution, thereby maintaining the biophysical character of neuronal targets on a long-term basis.
Mass spectrometric identification of pEGFYSQRYamide: A crustacean peptide hormone possessing a vertebrate neuropeptide Y (NPY)-like carboxy-terminus
Date: 2007-05-15
Creator: Elizabeth A. Stemmler, Emily A. Bruns, Noah P. Gardner, Patsy S. Dickinson, Andrew E., Christie
Access: Open access
- In invertebrates, peptides possessing the carboxy (C)-terminal motif -RXRFamide have been proposed as the homologs of vertebrate neuropeptide Y (NPY). Using matrix assisted laser desorption/ionization mass spectrometry, in combination with sustained off-resonance irradiation collision-induced dissociation and chemical and enzymatic reactions, we have identified the peptide pEGFYSQRYamide from the neuroendocrine pericardial organ (PO) of the crab Pugettia producta. This peptide is likely the same as that previously reported, but misidentified, as PAFYSQRYamide in several earlier reports (e.g. [Li, L., Kelley, W.P., Billimoria, C.P., Christie, A.E., Pulver, S.R., Sweedler, J.V., Marder, E. 2003. Mass spectrometric investigation of the neuropeptide complement and release in the pericardial organs of the crab, Cancer borealis. J. Neurochem. 87, 642-656; Fu, Q., Kutz, K.K., Schmidt, J.J., Hsu, Y.W., Messinger, D.I., Cain, S.D., de la Iglesia, H.O., Christie, A.E., Li, L. 2005. Hormone complement of the Cancer productus sinus gland and pericardial organ: an anatomical and mass spectrometric investigation. J. Comp. Neurol. 493, 607-626.]). The -QRYamide motif contained in pEGFYSQRYamide is identical to that present in many vertebrate members of the NPY superfamily. Mass spectrometric analysis conducted on the POs of several other decapods showed that pEGFYSQRYamide is present in three other brachyurans (Cancer borealis, Cancer irroratus and Cancer productus) as well as in one species from another decapod infraorder (Lithodes maja, an anomuran). Thus, our findings show that at least some invertebrates possess NPY-like peptides in addition to those exhibiting an -RXRFamide C-terminus, and raise the question as to whether the invertebrate -QRYamides are functionally and/or evolutionarily related to the NPY superfamily. © 2007 Elsevier Inc. All rights reserved.
Acoustic measurements of the stripe and the bubble quantum Hall phase
Date: 2015-04-01
Creator: M. E. Msall, W. Dietsche
Access: Open access
- We launch surface acousticwaves (SAW) along both the and the directions of aHall bar and measure the anisotropic conductivity in a high purity GaAs two-dimensional electron system in the quantum Hall regime of the stripe and the bubble phases. In the anisotropic stripe phase,SAW propagating along the 'easy' direction sense a compressible behavior (finite resistance)which is seen in standard transportmeasurement only if current flows along the 'hard' direction. In the isotropic bubble phase, the SAW data show compressible behavior in both directions, in marked contrast to the incompressible quantum Hall behavior seen in transport measurements. These results challenge models that assume that both the stripe and the bubble phase consist of incompressible domains and raise important questions about the role of domain boundaries in SAW propagation.
Collapse of a magnetized star to a black hole
Date: 2003-01-01
Creator: T.W. Baumgarte, S.L. Shapiro
Access: Open access
Cell wall-associated kinases and pectin perception
Date: 2016-01-01
Creator: Bruce D. Kohorn
Access: Open access
- The pectin matrix of the angiosperm cell wall is regulated in both synthesis and modification and greatly influences the direction and extent of cell growth. Pathogens, herbivory and mechanical stresses all influence this pectin matrix and consequently plant form and function. The cell wall-associated kinases (WAKs) bind to pectin and regulate cell expansion or stress responses depending upon the state of the pectin. This review explores the WAKs in the context of cell wall biology and signal transduction pathways.
The cell wall-associated kinases, WAKs, as pectin receptors
Date: 2012-05-08
Creator: Bruce D. Kohorn, Susan L. Kohorn
Access: Open access
- The wall-associated kinases, WAKs, are encoded by five highly similar genes clustered in a 30-kb locus in Arabidopsis. These receptor-like proteins contain a cytoplasmic serine threonine kinase, a transmembrane domain, and a less conserved region that is bound to the cell wall and contains a series of epidermal growth factor repeats. Evidence is emerging that WAKs serve as pectin receptors, for both short oligogalacturonic acid fragments generated during pathogen exposure or wounding, and for longer pectins resident in native cell walls. This ability to bind and respond to several types of pectins correlates with a demonstrated role for WAKs in both the pathogen response and cell expansion during plant development. © 2012 Kohorn and Kohorn.