Showing 1711 - 1720 of 3060 Items
Subleading-color contributions to gluon-gluon scattering in N = 4 SYM theory and relations to N = 8 supergravity
Date: 2008-11-01
Creator: Stephen G. Naculich
Horatiu Nastase
Howard J. Schnitzer
Access: Open access
- We study the subleading-color (nonplanar) contributions to the four-gluon scattering amplitudes in = 4 supersymmetric SU(N) Yang-Mills theory. Using the formalisms of Catani and of Sterman and Tejeda-Yeomans, we develop explicit expressions for the infrared-divergent contributions of all the subleading-color L-loop amplitudes up to three loops, and make some conjectures for the IR behavior for arbitrary L. We also derive several intriguing relations between the subleading-color one- and two-loop four-gluon amplitudes and the four-graviton amplitudes of = 8 supergravity. The exact one- and two-loop = 8 supergravity amplitudes can be expressed in terms of the one- and two-loop N-independent = 4 SYM amplitudes respectively, but the natural generalization to higher loops fails, despite having a simple interpretation in terms of the 't Hooft picture. We also find that, at least through two loops, the subleading-color amplitudes of = 4 SYM theory have uniform transcendentality (as do the leading-color amplitudes). Moreover, the = 4 SYM Catani operators, which express the IR-divergent contributions of loop amplitudes in terms of lower-loop amplitudes, are also shown to have uniform transcendentality, and to be the maximum transcendentality piece of the QCD Catani operators. © SISSA 2008.
An information theoretical approach to task-switching: Evidence from cognitive brain potentials in humans
Date: 2008-03-28
Creator: Francisco Barceló
José A. Periáñez
Erika Nyhus
Access: Open access
- This study aimed to clarify the neural substrates of behavioral switch and restart costs in intermittently instructed task-switching paradigms. Event-related potentials (ERPs) were recorded while participants were intermittently cued to switch or repeat their categorization rule (Switch task), or else they performed two perceptually identical control conditions (NoGo and Oddball). The three tasks involved different task-sets with distinct stimulus-response associations in each, but identical visual stimulation, consisting of frequent colored shapes (p = 0.9) and randomly interspersed infrequent black shapes (p = 0.1; '+' and 'x' symbols). Behavioral restart costs were observed in the first target responses following all black shapes in the Switch and NoGo tasks - but not in the Oddball task - and corresponded with enhanced fronto-centrally distributed early cue-locked P3 activity (peak latency 325-375 ms post-cue onset at the vertex). In turn, behavioral switch costs were associated with larger late cue-locked P3 amplitudes in the Switch task only (peak latency 400-450 ms post-cue onset at mid-parietal sites). Together with our information theoretical estimations, ERP results suggested that restart and switch costs indexed two neural mechanisms related to the preparatory resolution of uncertainty: (1) the intermittent re-activation of task-set information, and (2) the updating of stimulus-response mappings within an active task set, as indexed by early and late cue-locked P3 activations, respectively. In contrast, target-locked P3 activations reflected a functionally distinct mechanism related to the implementation of task-set information. We conclude that task-switching costs consist of both switch-specific and switch-unspecific processes during the preparation and execution stages of task performance. © 2008 Barceló, Periáñez and Nyhus.
Transvection-based gene regulation in Drosophila is a complex and plastic trait
Date: 2014-01-01
Creator: Xinyang Bing
Teresa Z. Rzezniczak
Jack R. Bateman
Thomas J.S. Merritt
Access: Open access
- Transvection, a chromosome pairing-dependent form of trans-based gene regulation, is potentially widespread in the Drosophila melanogaster genome and varies across cell types and within tissues in D. melanogaster, characteristics of a complex trait. Here, we demonstrate that the trans-interactions at the Malic enzyme (Men) locus are, in fact, transvection as classically defined and are plastic with respect to both genetic background and environment. Using chromosomal inversions, we show that trans-interactions at the Men locus are eliminated by changes in chromosomal architecture that presumably disrupt somatic pairing. We further show that the magnitude of transvection at the Men locus is modified by both genetic background and environment (temperature), demonstrating that transvection is a plastic phenotype. Our results suggest that transvection effects in D. melanogaster are shaped by a dynamic interplay between environment and genetic background. Interestingly, we find that cis-based regulation of the Men gene is more robust to genetic background and environment than trans-based. Finally, we begin to uncover the nonlocal factors that may contribute to variation in transvection overall, implicating Abd-B in the regulation of Men in cis and in trans in an allele-specific and tissue-specific manner, driven by differences in expression of the two genes across genetic backgrounds and environmental conditions.
Rapid oligo-galacturonide induced changes in protein phosphorylation in arabidopsis
Date: 2016-04-01
Creator: Bruce D. Kohorn
Divya Hoon
Benjamin B. Minkoff
Michael R. Sussman
Susan L., Kohorn
Access: Open access
- The wall-associated kinases (WAKs)1 are receptor protein kinases that bind to long polymers of cross-linked pectin in the cell wall. These plasma-membrane-associated protein kinases also bind soluble pectin fragments called oligo-galacturonides (OGs) released from the wall after pathogen attack and damage. WAKs are required for cell expansion during development but bind water soluble OGs generated from walls with a higher affinity than the wall-associated polysaccharides. OGs activate a WAKdependent, distinct stress-like response pathway to help plants resist pathogen attack. In this report, a quantitative mass-spectrometric-based phosphoproteomic analysis was used to identify Arabidopsis cellular events rapidly induced by OGs in planta. Using N14/ N15 isotopic in vivo metabolic labeling, we screened 1,000 phosphoproteins for rapid OG-induced changes and found 50 proteins with increased phosphorylation, while there were none that decreased significantly. Seven of the phosphosites within these proteins overlap with those altered by another signaling molecule plants use to indicate the presence of pathogens (the bacterial "elicitor" peptide Flg22), indicating distinct but overlapping pathways activated by these two types of chemicals. Genetic analysis of genes encoding 10 OG-specific and two Flg22/OG-induced phosphoproteins reveals that null mutations in eight proteins compromise the OG response. These phosphorylated proteins with genetic evidence supporting their role in the OG response include two cytoplasmic kinases, two membrane-associated scaffold proteins, a phospholipase C, a CDPK, an unknown cadmium response protein, and a motor protein. Null mutants in two proteins, the putative scaffold protein REM1.3, and a cytoplasmic receptor like kinase ROG2, enhance and suppress, respectively, a dominant WAK allele. Altogether, the results of these chemical and genetic experiments reveal the identity of several phosphorylated proteins involved in the kinase/ phosphatase-mediated signaling pathway initiated by cell wall changes.
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.
Wall-associated kinase 1 (WAK1) is crosslinked in endomembranes, and transport to the cell surface requires correct cell-wall synthesis
Date: 2006-06-01
Creator: Bruce D. Kohorn
Masaru Kobayashi
Sue Johansen
Henry Perry Friedman
Andy, Fischer
Nicole Byers
Access: Open access
- The Arabidopsis thaliana wall-associated kinases (WAKs) bind to pectin with an extracellular domain and also contain a cytoplasmic protein kinase domain. WAKs are required for cell elongation and modulate sugar metabolism. This work shows that in leaf protoplasts a WAK1-GFP fusion protein accumulates in a cytoplasmic compartment that contains pectin. The WAK compartment contains markers for the Golgi, the site of pectin synthesis. The migration of WAK1-GFP to the cell surface is far slower than that of a cell surface receptor not associated with the cell wall, is influenced by the presence of fucose side chains on one or more unidentified molecules that might include pectin, and is dependent upon cellulose synthesis on the plasma membrane. WAK is crosslinked into a detergent-insoluble complex within the cytoplasmic compartment before it appears on the cell surface, and this is independent of fucose modification or cellulose synthesis. Thus, the assembly and crosslinking of WAKs may begin at an early stage within a cytoplasmic compartment rather than in the cell wall itself, and is coordinated with synthesis of surface cellulose.
Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila
Date: 2021-06-01
Creator: Myron Child
Jack R. Bateman
Amir Jahangiri
Armando Reimer
Nicholas C., Lammers
Nica Sabouni
Diego Villamarin
Grace C. McKenzie-Smith
Justine E. Johnson
Daniel Jost
Hernan G. Garcia
Access: Open access
- 3D eukaryotic genome organization provides the structural basis for gene regulation. In Drosophila melanogaster, genome folding is characterized by somatic homolog pairing, where homologous chromosomes are intimately paired from end to end; however, how homologs identify one another and pair has remained mysterious. Recently, this process has been proposed to be driven by specifically interacting “buttons” encoded along chromosomes. Here, we turned this hypothesis into a quantitative biophysical model to demonstrate that a button-based mechanism can lead to chromosome-wide pairing. We tested our model using live-imaging measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA labeling systems. We show solid agreement between model predictions and experiments in the pairing dynamics of individual homologous loci. Our results strongly support a button-based mechanism of somatic homolog pairing in Drosophila and provide a theoretical framework for revealing the molecular identity and regulation of buttons.
Positive Effects of Nonnative Invasive Phragmites australis on Larval Bullfrogs
Date: 2012-08-30
Creator: Mary Rogalski
Access: Open access
Identification of methylated proteins in the yeast small ribosomal subunit: A role for SPOUT methyltransferases in protein arginine methylation
Date: 2012-06-26
Creator: Brian D. Young
David I. Weiss
Cecilia I. Zurita-Lopez
Kristofor J. Webb
Steven G., Clarke
Anne E. McBride
Access: Open access
- We have characterized the posttranslational methylation of Rps2, Rps3, and Rps27a, three small ribosomal subunit proteins in the yeast Saccharomyces cerevisiae, using mass spectrometry and amino acid analysis. We found that Rps2 is substoichiometrically modified at arginine-10 by the Rmt1 methyltransferase. We demonstrated that Rps3 is stoichiometrically modified by ω- monomethylation at arginine-146 by mass spectrometric and site-directed mutagenic analyses. Substitution of alanine for arginine at position 146 is associated with slow cell growth, suggesting that the amino acid identity at this site may influence ribosomal function and/or biogenesis. Analysis of the three-dimensional structure of Rps3 in S. cerevisiae shows that arginine-146 makes contacts with the small subunit rRNA. Screening of deletion mutants encoding potential yeast methyltransferases revealed that the loss of the YOR021C gene results in the absence of methylation of Rps3. We demonstrated that recombinant Yor021c catalyzes ω-monomethylarginine formation when incubated with S-adenosylmethionine and hypomethylated ribosomes prepared from a YOR021C deletion strain. Interestingly, Yor021c belongs to the family of SPOUT methyltransferases that, to date, have only been shown to modify RNA substrates. Our findings suggest a wider role for SPOUT methyltransferases in nature. Finally, we have demonstrated the presence of a stoichiometrically methylated cysteine residue at position 39 of Rps27a in a zinc-cysteine cluster. The discovery of these three novel sites of protein modification within the small ribosomal subunit will now allow for an analysis of their functional roles in translation and possibly other cellular processes. © 2012 American Chemical Society.