Digital Commons Network^™

Mass Spectrometry Assisted Assignment Of Nmr Resonances In Reductively 13C-Methylated Proteins, Megan A. Macnaughtan, Austin M. Kane, James H. Prestegard

Faculty Publications

Reductive 13C-methylation of proteins has been used as an isotope labeling strategy to study protein structure, function, and dynamics by nuclear magnetic resonance (NMR) spectroscopy. However, assigning the resulting 13C-dimethylamine peaks in a 1H-13C NMR spectrum has proved to be difficult, but it is important to expand the scope of the method. The assignment strategy presented here utilizes mass spectrometry (MS) for sequence identification and varying 13C/12C isotope ratios to correlate with NMR data. The site-specific reactivity of the lysines and N-terminal amine of a protein is exploited to produce a sample with varying 13C/12C ratios at each dimethylamine. MS …

The Paley-Wiener Theorem For The Jacobi Transform And The Local Huygens' Principle For Root Systems With Even Multiplicities, Thomas Branson, Gestur Ólafsson, Angela Pasquale

Faculty Publications

This note is a continuation of the previous paper by same authors [this issue]. Its purpose is to extend the results to the context of root systems with even multiplicities. Under the even multiplicity assumption, we prove a local Paley-Wiener theorem for the Jacobi transform and the strong Huygens' principle for the wave equation associated with the modified compact Laplace operator. © 2005 Royal Netherlands Academy of Arts and Sciences.

The Paley-Wiener Theorem And The Local Huygens' Principle For Compact Symmetric Spaces: The Even Multiplicity Case, Thomas Branson, Gestur Ólafsson, Angela Pasquale

Faculty Publications

We prove a Paley-Wiener theorem for a class of symmetric spaces of the compact type, in which all root multiplicities are even. This theorem characterizes functions of small support in terms of holomorphic extendability and exponential type of their (discrete) Fourier transforms. We also provide three independent new proofs of the strong Huygens' principle for a suitable constant shift of the wave equation on odd-dimensional spaces from our class. © 2005 Royal Netherlands Academy of Arts and Sciences.

Search For Coherent Charged Pion Production In Neutrino-Carbon Interactions, M. Hasegawa, E. Aliu, S. Andringa, S. Aoki, J. Argyriades, K. Asakura, R. Ashie, H. Berns, H. Bhang, A. Blondel, S. Borghi, J. Bouchez, J. Burguet-Castell, D. Casper, C. Cavata, A. Cervera, S. M. Chen, K. O. Cho, J. H. Choi, U. Dore, X. Espinal, M. Fechner, E. Fernandez, Y. Fukuda, J. Gomez-Cadenas, R. Gran, T. Hara, T. Hasegawa

Faculty Publications

We report the result from a search for charged-current coherent pion production induced by muon neutrinos with a mean energy of 1.3 GeV. The data are collected with a fully active scintillator detector in the K2K long-baseline neutrino oscillation experiment. No evidence for coherent pion production is observed, and an upper limit of 0.60×10-2 is set on the cross section ratio of coherent pion production to the total charged-current interaction at 90% confidence level. This is the first experimental limit for coherent charged pion production in the energy region of a few GeV. © 2005 The American Physical Society.

Upper Limits From The Ligo And Tama Detectors On The Rate Of Gravitational-Wave Bursts, B. Abbott, R. Abbott, R. Adhikari, A. Ageev, J. Agresti, P. Ajith, B. Allen, J. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Araya, H. Armandula, M. Ashley, F. Asiri, P. Aufmuth, C. Aulbert, S. Babak, R. Balasubramanian, S. Ballmer, B. C. Barish, C. Barker, D. Barker, M. Barnes, B. Barr, M. A. Barton, K. Bayer, R. Beausoleil, K. Belczynski, R. Bennett, S. J. Berukoff, J. Betzwieser, B. Bhawal

Faculty Publications

We report on the first joint search for gravitational waves by the TAMA and LIGO collaborations. We looked for millisecond-duration unmodeled gravitational-wave bursts in 473 hr of coincident data collected during early 2003. No candidate signals were found. We set an upper limit of 0.12 events per day on the rate of detectable gravitational-wave bursts, at 90% confidence level. From software simulations, we estimate that our detector network was sensitive to bursts with root-sum-square strain amplitude above approximately 1-3×10-19Hz-1/2 in the frequency band 700-2000 Hz. We describe the details of this collaborative search, with particular emphasis on its advantages and …

Thermodynamic Consistency Of The Dynamical Mean-Field Theory Of The Double-Exchange Model, Randy S. Fishman, Juana Moreno, Thomas Maier, Mark Jarrell

Faculty Publications

We find that standard diagrammatic perturbation theory does not exist for the dynamical mean-field theory of the double-exchange model because the vertex function cannot be expanded in terms of the bare vertex function and the full Green's function G (i νl) αα. Nevertheless, a functional Φ satisfying the condition δΦ δG (i νn) αα =Σ (i νn) αα can be constructed because the curl of the self-energy with respect to the Green's function vanishes: δΣ (i νn) αα δG (i νl) ββ -δΣ (i νl) ββ δG (i νn) αα =0. The connection between the functional Φ and the free …

Fluctuations And Noise: A General Model With Applications, R. F. O'Connell

Faculty Publications

A wide variety of dissipative and fluctuation problems involving a quantum system in a heat bath can be described by the independent-oscillator (10) model Hamiltonian. Using Heisenberg equations of motion, this leads to a generalized quantum Langevin equation (QLE) for the quantum system involving two quantities which encapsulate the properties of the heat bath. Applications include: atomic energy shifts in a blackbody radiation heat bath; solution of the problem of runaway solutions in QED; electrical circuits (resistively shunted Josephson barrier, microscopic tunnel junction, etc.); conductivity calculations (since the QLE gives a natural separation between dissipative and fluctuation forces); dissipative quantum …

The Identity Of Catfishes Identified As Mystus Cavasius (Hamilton, 1822) (Teleostei: Bagridae), With A Description Of A New Species From Myanmar, Prosanta Chakrabarty, Heok Hee Ng

Faculty Publications

The identity of South Asian riverine bagrid catfishes usually referred to as Mystus cavasius (Hamilton, 1822) is reviewed. Three species comprise what is currently understood as M. cavasius: M. cavasius s. str. from northern India, M. seengtee from southern India and a new species, M. falcarius, from the Salween and Irrawaddy river drainages in Myanmar and the shorter river drainages in southern Myanmar. Mystus seengtee is resurrected from synonymy with M. cavasius and both species are redescribed. The three species differ from other congeners with a long-based adipose fin in having a combination of a black spot in front of …

Conformational Studies Of The Tetramerization Site Of Human Erythroid Spectrin By Cysteine-Scanning Spin-Labeling Epr Methods, Shahila Mehboob, Bing Hao Luo, Wentao Fu, Michael E. Johnson, L. W.M. Fung

Faculty Publications

We used cysteine-scanning and spin-labeling methods to prepare singly spin labeled recombinant peptides for electron paramagnetic resonance studies of the partial domain regions at the tetramerization site (N-terminal end of α and C-terminal end of β) of erythroid spectrin. The values of the inverse line width parameter (ΔH0-1) from a family of SpoI-1-368Δ peptides scanning residues 21-30 exhibited a periodicity of ∼3.5-4. We used molecular dynamics calculations to show that the asymmetric mobility of this helix is not necessarily due to tertiary contacts, but is likely due to intrinsic properties of helix C′, a helix with a heptad pattern sequence. …

On Pancyclic Representable Matroids, Brian Beavers, James Oxley

Faculty Publications

Bondy proved that an n-vertex simple Hamiltonian graph with at least n2/4 edges has cycles of every length unless it is isomorphic to Kn/2,n/2. This paper considers finding circuits of every size in GF(q)-representable matroids with large numbers of elements. A consequence of the main result is that a rank-r simple binary matroid with at least 2r-1 elements either has circuits of all sizes or is isomorphic to AG(r-1,2). © 2005 Elsevier B.V. All rights reserved.

Caster - A Concept For A Black Hole Finder Probe Based On The Use Of New Scintillator Technologies, Mark L. Mcconnell, Peter F. Bloser, Gary Case, Michael Cherry, James Cravens, T. Gregory Guzik, Kevin Hurley, R. Marc Kippen, John Macri, Richard S. Miller, William Paciesas, James M. Ryan, Bradley Schaefer, J. Gregory Stacy, W. Thomas Vestrand, John P. Wefel

Faculty Publications

The primary scientific mission of the Black Hole Finder Probe (BHFP), part of the NASA Beyond Einstein program, is to survey the local Universe for black holes over a wide range of mass and accretion rate. One approach to such a survey is a hard X-ray coded-aperture imaging mission operating in the 10-600 keV energy band, a spectral range that is considered to be especially useful in the detection of black hole sources. The development of new inorganic scintillator materials provides improved performance (for example, with regards to energy resolution and timing) that is well suited to the BHFP science …

Spectra Of High-Redshift Type Ia Supernovae And A Comparison With Their Low-Redshift Counterparts, I. M. Hook, D. A. Howell, G. Aldering, R. Amanullah, M. S. Burns, A. Conley, S. E. Deustua, R. Ellis, S. Fabbro, V. Fadeyev, G. Folatelli, G. Garavini, R. Gibbons, G. Goldhaber, A. Goobar, D. E. Groom, A. G. Kim, R. A. Knop, M. Kowalski, C. Lidman, S. Nobili, P. E. Nugent, R. Pain, C. R. Pennypacker, S. Perlmutter, P. Ruiz-Lapuente, G. Sainton, B. E. Schaefer, E. Smith, A. L. Spadafora, V. Stanishev, R. C. Thomas, N. A. Walton

Faculty Publications

We present spectra for 14 high-redshift (0.17 < z < 0.83) supernovae, which were discovered by the Supernova Cosmology Project as part of a campaign to measure cosmological parameters. The spectra are used to determine the redshift and classify the supernova type, essential information if the supernova are to be used for cosmological studies. Redshifts were derived either from the spectrum of the host galaxy or from the spectrum of the supernova itself. We present evidence that these supernovae are of Type Ia (SNe Ia) by matching to spectra of nearby supernovae. We find that the dates of the spectra relative to maximum light determined from this fitting process are consistent with the dates determined from the photometric light curves, and, moreover, the spectral time sequences for SNe Ia at low and high redshift are indistinguishable. We also show that the expansion velocities measured from blueshifted Ca H and K are consistent with those measured for low-redshift SNe Ia. From these first-level quantitative comparisons we find no evidence for evolution in SN Ia properties between these low- and high-redshift samples. Thus, even though our samples may not be complete, we conclude that there is a population of SNe Ia at high redshift whose spectral properties match those at low redshift. © 2005. The American Astronomical Society. All rights reserved.

Towards Scalable Linear-Optical Quantum Computers, J. P. Dowling, J. D. Franson, H. Lee, G. J. Milburn

Faculty Publications

Scalable quantum computation with linear optics was considered to be impossible due to the lack of efficient two-qubit logic gates, despite the ease of implementation of one-qubit gates. Two-qubit gates necessarily need a non-linear interaction between the two photons, and the efficiency of this non-linear interaction is typically very small in bulk materials. However, it has recently been shown that this barrier can be circumvented with effective non-linearities produced by projective measurements, and with this work linear-optical quantum computing becomes a new avenue towards scalable quantum computation. We review several issues concerning the principles and requirements of this scheme. © …

Classical And Quantum General Relativity: A New Paradigm, Rodolfo Gambini, Jorge Pullin

Faculty Publications

We argue that recent developments in discretizations of classical and quantum gravity imply a new paradigm for doing research in these areas. The paradigm consists in discretizing the theory in such a way that the resulting discrete theory has no constraints. This solves many of the hard conceptual problems of quantum gravity. It also appears as a useful tool in some numerical simulations of interest in classical relativity. We outline some of the salient aspects and results of this new framework. © World Scientific Publishing Company.

Cryopreservation Of Human Hematopoietic Stem And Progenitor Cells Loaded With Trehalose: Transient Permeabilization Via The Adenosine Triphosphate-Dependent P2z Receptor Channel, Sandhya S. Buchanan, Michael A. Menze, Steven C. Hand, David W. Pyatt, John F. Carpenter

Faculty Publications

Hematopoietic stem and progenitor cells (HPCs) are a heterogenic population of cells used to treat a number of human diseases. Multilineage differentiation is a required function in successful hematopoietic reconstitution after transplantation of cryopreserved grafts. Conventional use of the cryoprotectant dimethyl sulfoxide (DMSO) has resulted in some reports of infusion related toxicity attributed to DMSO and/or damage to cells during freeze-thawing procedures. The purpose of this study was to explore the use of trehalose, a nontoxic disaccharide of glucose, as an alternative cryoprotectant. Trehalose was introduced into HPCs using the P2Z receptor, known to form nonselective pores in the presence …

Diversity And Structure Of Bacterial Chemolithotrophic Communities In Pine Forest And Agroecosystem Soils, J. Tolli, G. M. King

Faculty Publications

Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) …

Glycosylphosphatidylinositol-Anchored Proteins Are Required For Cell Wall Synthesis And Morphogenesis In Arabidopsis, C. Stewart Gillmor, Wolfgang Lukowitz, Ginger Brininstool, John C. Sedbrook, Thorsten Hamann, Patricia Poindexter, Chris Somerville

Faculty Publications

Mutations at five loci named PEANUT1-5 (PNT) were identified in a genetic screen for radially swollen embryo mutants, pnt1 cell walls showed decreased crystalline cellulose, increased pectins, and irregular and ectopic deposition of pectins, xyloglucans, and callose. Furthermore, pnt1 pollen is less viable than the wild type, and pnt1 embryos were delayed in morphogenesis and showed defects in shoot and root meristems. The PNT1 gene encodes the Arabidopsis thaliana homolog of mammalian PIG-M, an endoplasmic reticulum-localized mannosyltransferase that is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor. All five pnt mutants showed strongly reduced accumulation of GPI-anchored proteins, suggesting that …

Mutation Of Sac1, An Arabidopsis Sac Domain Phosphoinositide Phosphatase, Causes Alterations In Cell Morphogenesis, Cell Wall Synthesis, And Actin Organization, Ruiqin Zhong, David H. Burk, C. Joseph Nairn, Alicia Wood-Jones, W. Herbert Morrison, Zheng Hua Ye

Faculty Publications

SAC (for suppressor of actin) domain proteins in yeast and animals have been shown to modulate the levels of phosphoinositides, thereby regulating several cellular activities such as signal transduction, actin cytoskeleton organization, and vesicle trafficking. Nine genes encoding SAC domain-containing proteins are present in the Arabidopsis thaliana genome, but their roles in plant cellular functions and plant growth and development have not been characterized. In this report, we demonstrate the essential roles of one of the Arabidopsis SAC domain proteins, AtSAC1, in plant cellular functions. Mutation of the AtSAC1 gene in the fragile fiber7 (fra7) mutant caused a dramatic decrease …

A Mobile Element Based Phylogeny Of Old World Monkeys, Jinchuan Xing, Hui Wang, Kyudong Han, David A. Ray, Cheney H. Huang, Leona G. Chemnick, Caro Beth Stewart, Todd R. Disotell, Oliver A. Ryder, Mark A. Batzer

Faculty Publications

SINEs (Short INterspersed Elements) are a class of non-autonomous mobile elements that are states, making them useful genetic systems for phylogenetic studies. Alu elements are the most successful SINE in primate genomes and have been utilized for resolving primate phylogenetic relationships and human population genetics. However, no Alu based phylogenetic analysis has yet been performed to resolve relationships among Old World monkeys. Using both a computational approach and polymerase chain reaction display methodology, we identified 285 new Alu insertions from sixteen Old World monkey taxa that were informative at various levels of catarrhine phylogeny. We have utilized these elements along …

Mega: A Medium-Energy Gamma-Ray Astronomy Mission Concept, P. F. Bloser, J. M. Ryan, M. L. Mcconnell, J. R. Macri, U. Bravar, G. Kanbach, R. Andritschke, M. Ajello, A. Zoglauer, S. D. Hunter, B. F. Phlips, E. A. Wulf, D. H. Hartmann, R. S. Miller, W. S. Paciesas, A. D. Zych, R. M. Kippen, T. Vestrand, M. L. Cherry, T. G. Guzik, J. G. Stacy, J. P. Wefel, V. Reglero, G. Di Cocco, J. P. Cravens

Faculty Publications

The Medium Energy Gamma-ray Astronomy (MEGA) telescope concept will soon be proposed as a MIDEX mission. This mission would enable a sensitive all-sky survey of the medium-energy gamma-ray sky (0.4 - 50 MeV) and bridge the huge sensitivity gap between the COMPTEL and OSSE experiments on the Compton Gamma Ray Observatory, the SPI and IBIS instruments on INTEGRAL, and the visionary Advanced Compton Telescope (ACT) mission. The scientific goals include, among other things, compiling a much larger catalog of sources in this energy range, performing far deeper searches for supernovae, better measuring the galactic continuum and line emissions, and identifying …

The Reddening Of Red Supergiants: When Smoke Gets In Your Eyes, Philip Massey, Bertrand Plez, Emily M. Levesque, K. A.G. Olsen, Geoffrey C. Clayton, Eric Josselin

Faculty Publications

Deriving the physical properties of red supergiants (RSGs) depends on accurate corrections for reddening by dust. We use our recent modeling of the optical spectra of RSGs to address this topic. First, we find that previous broadband studies have underestimated the correction for extinction in the visible, and hence the luminosities (if derived from V); the shift in the effective wavelengths of the standard B and V bandpasses necessitates using an effective value of the ratio R′v = 4.2 to correct broadband photometry of RSGs if Rv = 3.1 for early-type stars viewed through the same dust, where we have …

Remarks On Monotone Control Systems With Multi-Valued Input-State Characteristics, Patrick De Leenheer, Michael Malisoff

Faculty Publications

We announce a new global small-gain theorem for feedback interconnections of monotone input-output systems with multi-valued input-state characteristics. This extends a small-gain theorem of Angeli and Sontag for monotone systems with singleton-valued characteristics. The proof of our theorem is based on Thieme's convergence theory for asymptotically autonomous systems. We also provide an illustrative example. © 2005 IEEE.

Direct Constraints On Antarctic Peninsula Ice Sheet Grounding Events Between 5.12 And 7.94 Ma, Philip J. Bart, Dave Egan, Sophie A. Warny

Faculty Publications

[1] How has the Antarctic Ice Sheet responded to or influenced global climate change? This simple question has been difficult to address because the long-term records of the ice sheet's fluctuations are poorly constrained with geologic data from Antarctica. Thus studies to date have not convincingly established how specific Antarctic Ice Sheet events correlate with climatic, eustatic, or other phenomena known from low-latitude and deep-sea records. This study focused on documenting the direct record of ice sheet advance and retreat to the Antarctic Peninsula's shelf edge. On the peninsula's outer shelf, seismic reflectors interpreted to be subglacial unconformities were correlated …

Enhancing The Stability Of Microsomal Cytochrome B5: A Rational Approach Informed By Comparative Studies With The Outer Mitochondrial Membrane Isoform, Na Sun, An Wang, Aaron B. Cowley, Adriana Altuve, Mario Rivera, David R. Benson

Faculty Publications

The outer mitochondrial membrane isoform of mammalian cytochrome b 5 (OM b5) is much less prone to lose heme than the microsomal isoform (Mc b5), with a conserved difference at position 71 (leucine versus serine) playing a major role. We replaced Ser71 in Mc b 5 with Leu, with the prediction that it would retard heme loss by diminishing polypeptide expansion accompanying rupture of the histidine to iron bonds. The strategy was partially successful in that it slowed dissociation of heme from its less stable orientation in bMc b5 (B). Heme dissociation from orientation A was accelerated to a similar …

Vicksburg: The Campaign That Opened The Mississippi, Terrence J. Winschel

Civil War Book Review

Vital Vicksburg

A study of the complex campaign

Lincoln: Original News Coverage From The New York Times, Frank J. Williams

Civil War Book Review

Contemporary coverage

News from Lincoln's lifetime

The Ongoing Civil War: New Versions Of Old Stories, John Benson

Civil War Book Review

The war after the war

Capsizing conventional views of history

Social Revolution: William Wells Brown's Manifesto, Gregory J.W. Urwin

Civil War Book Review

Social revolution

William Wells Brown's manifesto

Grant Comes East: A Novel Of The Civil War, Thomas Hill

Civil War Book Review

Alternative account

Authors produce their second what-if story

Reconstruction Relationship: Collection Reveals Postwar Attitudes, Sally G. Mcmillen

Civil War Book Review

Reconstruction relationship

Collection reveals postwar attitudes