Faculty Scholarship
Showing 281 - 290 of 733 Items
Eikonal methods applied to gravitational scattering amplitudes
Date: 2011-01-01
Creator: Stephen G. Naculicha, Howard J. Schnitzerb
Access: Open access
- We apply factorization and eikonal methods from gauge theories to scattering amplitudes in gravity. We hypothesize that these amplitudes factor into an IR-divergent soft function and an IR-finite hard function, with the former given by the expectation value of a product of gravitational Wilson line operators. Using this approach, we show that the IR-divergent part of the n-graviton scattering amplitude is given by the exponential of the one-loop IR divergence, as originally discovered byWeinberg, with no additional subleading IR-divergent contributions in dimensional regularization. © SISSA 2011.
Computing word length in alternate presentations of thompson's group F
Date: 2009-12-01
Creator: Matthew Horak, Melanie Stein, Jennifer Taback
Access: Open access
- We introduce a new method for computing the word length of an element of Thompson's group F with respect to a "consecutive" generating set of the form Xn = {x0,x1, ⋯, xn}, which is a subset of the standard infinite generating set for F. We use this method to show that (F, Xn) is not almost convex, and has pockets of increasing, though bounded, depth dependent on n. © 2009 World Scientific Publishing Company.
Identification of the determinants for the specific recognition of single-strand telomeric DNA by Cdc13
Date: 2006-01-24
Creator: Aimee M. Eldridge, Wayne A. Halsey, Deborah S. Wuttke
Access: Open access
- The single-strand overhang present at telomeres plays a critical role in mediating both the capping and telomerase regulation functions of telomeres. The telomere end-binding proteins, Cdc13 in Saccharomyces cerevisiae, Pot1 in higher eukaryotes, and TEBP in the ciliated protozoan Oxytricha nova, exhibit sequence-specific binding to their respective single-strand overhangs. S. cerevisiae telomeres are composed of a heterogeneous mixture of GT-rich telomeric sequence, unlike in higher eukaryotes which have a simple repeat that is maintained with high fidelity. In yeast, the telomeric overhang is recognized by the essential protein Cdc13, which coordinates end-capping and telomerase activities at the telomere. The Cdc13 DNA-binding domain (Cdc13-DBD) binds these telomere sequences with high affinity (3 pM) and sequence specificity. To better understand the basis for this remarkable recognition, we have investigated the binding of the Cdc13-DBD to a series of altered DNA substrates. Although an 11-mer of GT-rich sequence is required for full binding affinity, only three of these 11 bases are recognized with high specificity. This specificity differs from that observed in the other known telomere end-binding proteins, but is well suited to the specific role of Cdc13 at yeast telomeres. These studies expand our understanding of telomere recognition by the Cdc13-DBD and of the unique molecular recognition properties of ssDNA binding. © 2006 American Chemical Society.
Monteverde: Ecology and Conservation of a Tropical Cloud Forest
Date: 2000-01-01
Creator: Nalini M. Nadkarni, Nathaniel T. Wheelwright
Access: Open access
- The Monteverde Cloud Forest Reserve has captured the worldwide attention of biologists, conservationists, and ecologists and has been the setting for extensive investigation over the past 40 years. Roughly 40,000 ecotourists visit the Cloud Forest each year, and it is often considered the archetypal high-altitude rain forest. Featuring synthetic chapters and specific accounts written by more than 100 biologists and local residents, the 573-page book documents in a single volume everything known about the biological diversity of Monteverde, Costa Rica, and how to protect it. New short chapters which update and expand the research presented in the 2000 Oxford publication were written in 2014 and are now available.
Bilateral consequences of chronic unilateral deafferentation in the auditory system of the cricket gryllus bimaculatus
Date: 2011-04-01
Creator: Hadley Wilson Horch, Elizabeth Sheldon, Claire C. Cutting, Claire R. Williams, Dana M., Riker, Hannah R. Peckler, Rohit B. Sangal
Access: Open access
- The auditory system of the cricket has the unusual ability to respond to deafferentation by compensatory growth and synapse formation. Auditory interneurons such as ascending neuron 2 (AN-2) in the cricket Gryllus bimaculatus possess a dendritic arbor that normally grows up to, but not over, the midline of the prothoracic ganglion. After chronic deafferentation throughout larval development, however, the AN-2 dendritic arbor changes dramatically, and medial dendrites sprout across the midline where they form compensatory synapses with the auditory afferents from the contralateral ear. We quantified the extent of the effects of chronic, unilateral deafferentation by measuring several cellular parameters of 3 different neuronal components of the auditory system: the deafferented AN-2, the contralateral (or nondeafferented) AN-2 and the contralateral auditory afferents. Neuronal tracers and confocal microscopy were used to visualize neurons, and double-label experiments were performed to examine the cellular relationship between pairs of cells. Dendritic complexity was quantified using a modified Sholl analysis, and the length and volume of processes and presynaptic varicosities were assessed under control and deafferented conditions. Chronic deafferentation significantly influenced the morphology of all 3 neuronal components examined. The overall dendritic complexity of the deafferented AN-2 dendritic arbor was reduced, while both the contralateral AN-2 dendritic arbor and the remaining, intact, auditory afferents grew longer. We found no significant changes in the volume or density of varicosities after deafferentation. These complex cellular changes after deafferentation are interpreted in the light of the reported differential regulation of vesicle-associated membrane protein and semaphorin 2a. Copyright © 2011 S. Karger AG, Basel.
Sri Lanka in 2017: Sluggish on many fronts
Date: 2018-01-01
Creator: Sree Padma
Access: Open access
- Sri Lanka's 69-year-old parliamentary democracy continues with power concentrated at the center, and consequently, the country's non-Sinhala-Buddhist minorities on the periphery continue to press for equal rights, while ethnic strife hinders prospects for unified progress. Maithripala Sirisena, president since 2015, promises reconciliation but has received little cooperation from the majority Sinhala Buddhists.
Targeted identification of glycosylated proteins in the gastric pathogen helicobacter pylori (Hp)
Date: 2013-09-01
Creator: Kanokwan Champasa, Scott A. Longwell, Aimee M. Eldridge, Elizabeth A. Stemmler, Danielle H., Dube
Access: Open access
- Virulence of the gastric pathogen Helicobacter pylori (Hp) is directly linked to the pathogen's ability to glycosylate proteins; for example, Hp flagellin proteins are heavily glycosylated with the unusual nine-carbon sugar pseudaminic acid, and this modification is absolutely essential for Hp to synthesize functional flagella and colonize the host's stomach. Although Hp's glycans are linked to pathogenesis, Hp's glycome remains poorly understood; only the two flagellin glycoproteins have been firmly characterized in Hp. Evidence from our laboratory suggests that Hp synthesizes a large number of as-yet unidentified glycoproteins. Here we set out to discover Hp's glycoproteins by coupling glycan metabolic labeling with mass spectrometry analysis. An assessment of the subcellular distribution of azide-labeled proteins by Western blot analysis indicated that glycoproteins are present throughout Hp and may therefore serve diverse functions. To identify these species, Hp's azide-labeled glycoproteins were tagged via Staudinger ligation, enriched by tandem affinity chromatography, and analyzed by multidimensional protein identification technology. Direct comparison of enriched azide-labeled glycoproteins with a mock-enriched control by both SDS-PAGE and mass spectrometry-based analyses confirmed the selective enrichment of azide-labeled glycoproteins. We identified 125 candidate glycoproteins with diverse biological functions, including those linked with pathogenesis. Mass spectrometry analyses of enriched azide-labeled glycoproteins before and after cleavage of O-linked glycans revealed the presence of Staudinger ligation-glycan adducts in samples only after beta-elimination, confirming the synthesis of O-linked glycoproteins in Hp. Finally, the secreted colonization factors urease alpha and urease beta were biochemically validated as glycosylated proteins via Western blot analysis as well as by mass spectrometry analysis of cleaved glycan products. These data set the stage for the development of glycosylation-based therapeutic strategies, such as new vaccines based on natively glycosylated Hp proteins, to eradicate Hp infection. Broadly, this report validates metabolic labeling as an effective and efficient approach for the identification of bacterial glycoproteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.
A 60 yr record of atmospheric carbon monoxide reconstructed from Greenland firn air
Date: 2013-08-19
Creator: V. V. Petrenko, P. Martinerie, P. Novelli, D. M. Etheridge, I., Levin, Z. Wang, T. Blunier, J. Chappellaz, J. Kaiser, P. Lang, L. P. Steele, S. Hammer, J. Mak, R. L. Langenfelds, J. Schwander, J. P. Severinghaus, E. Witrant, G. Petron, M. O. Battle, G. Forster, W. T. Sturges, J. F. Lamarque, K. Steffen, J. W.C. White
Access: Open access
- We present the first reconstruction of the Northern Hemisphere (NH) high latitude atmospheric carbon monoxide (CO) mole fraction from Greenland firn air. Firn air samples were collected at three deep ice core sites in Greenland (NGRIP in 2001, Summit in 2006 and NEEM in 2008). CO records from the three sites agree well with each other as well as with recent atmospheric measurements, indicating that CO is well preserved in the firn at these sites. CO atmospheric history was reconstructed back to the year 1950 from the measurements using a combination of two forward models of gas transport in firn and an inverse model. The reconstructed history suggests that Arctic CO in 1950 was 140-150 nmol mol-1, which is higher than today's values. CO mole fractions rose by 10-15 nmol mol-1 from 1950 to the 1970s and peaked in the 1970s or early 1980s, followed by a ≈ 30 nmol mol-1 decline to today's levels. We compare the CO history with the atmospheric histories of methane, light hydrocarbons, molecular hydrogen, CO stable isotopes and hydroxyl radicals (OH), as well as with published CO emission inventories and results of a historical run from a chemistry-transport model. We find that the reconstructed Greenland CO history cannot be reconciled with available emission inventories unless unrealistically large changes in OH are assumed. We argue that the available CO emission inventories strongly underestimate historical NH emissions, and fail to capture the emission decline starting in the late 1970s, which was most likely due to reduced emissions from road transportation in North America and Europe. © Author(s) 2013.
The Art Gallery Theorem for Polyominoes
Date: 2012-10-01
Creator: Therese Biedl, Mohammad T. Irfan, Justin Iwerks, Joondong Kim, Joseph S.B., Mitchell
Access: Open access
- We explore the art gallery problem for the special case that the domain (gallery) P is an m-polyomino, a polyform whose cells are m unit squares. We study the combinatorics of guarding polyominoes in terms of the parameter m, in contrast with the traditional parameter n, the number of vertices of P. In particular, we show that ⌊m+1/3⌋ point guards are always sufficient and sometimes necessary to cover an m-polyomino, possibly with holes. When m < 3n/4-4, the sufficiency condition yields a strictly lower guard number than ⌊ n/4⌋, given by the art gallery theorem for orthogonal polygons. © 2012 Springer Science+Business Media, LLC.
ERPs_and_Neural_Oscillations_during_Volitional_Suppression_of_Memory_Retrieval
Date: 2013-10-01
Creator: Brendan Eliot Depue, Nick Ketz, Matthew V. Mollison, Erika Nyhus, Marie T. Banich, Tim Curran
Access: Open access