bluuebunny/crossref_metadata_2025 huggingface dataset:
Fisher information as the basis for the Schrödinger wave equation
Authors: Frieden B. Roy
Published: March 2005

It is shown that the assumption that nature acts to make optimum estimates of position maximally in error leads to the Schrödinger (energy) wave equation (SWE). In this way, the SWE follows from a simple statement of uncertainty. The approach grows out of probability estimation theory, in particular the principle of minimum Fisher information (or maximum Cramer–Rao bound). The minimized Fisher information turns out to be proportional to the mean kinetic energy of the particle. This approach is an attractive supplement to conventional ways of introducing quantum mechanics to students, since it avoids the use of imperfect physical models (such as vibrating strings) or the immediate need for complex momentum operators, and follows from a plausible assumption as to how nature works.
Some results on the relativistic Doppler effect for accelerated motion
Authors: Cochran W.
Published: March 2005

It is shown how the Doppler-shifted frequencies that result from the uniform acceleration of a source of light, and/or of the receiver, can be derived, and that very simple formulas often apply. For completeness it is shown how a basic equation can be extended to apply in an accelerated frame of reference.
The Ellis geometry
Authors: Clément Gérard
Published: March 2005

The general relativistic wormhole metric studied by H. G. Ellis is discussed. (AIP)
Quasiperiodic structures: Another type of long-range order for condensed matter
Authors: Janot Christian , Dubois Jean-Marie , Boissieu Marc de
Published: March 2005

Quasicrystals are materials whose structure cannot be understood within classical crystallography rules. Quasiperiodic lattices, with long-range order but without periodic translations in three dimensions, are shown to describe correctly these new structures. They are also derivable from structures that are periodic in a higher dimensional space. Neutron diffraction patterns, with contrast variation effects, have recently provided reasonable insight into the description of one icosahedral quasicrystal so that it is now possible to say where the atoms should be in a perfect quasicrystal.
Extensions of the Feynman–Hellman theorem and applications
Authors: Singh S. Brajamani , Singh C. A.
Published: March 2005

Epstein’s [Am. J. Phys. 22, 613 (1954)] off-diagonal and higher-order extensions of the Feynman–Hellmann theorem, obtained by using the basic technique of parameter differentiation under the integral sign, are further pursued. Epstein’s rederivation of the Rayleigh–Schrödinger perturbation expansion is also extended to include the degenerate case. The same approach is also used to obtain the Lennard-Jones–Brillouin–Wigner perturbation theory. The quantum virial theorem and its off-diagonal generalization is deduced and its application is illustrated by taking the example of the linear harmonic oscillator. The semiclassical expression for the kinetic energy is obtained directly from the quantization condition.
Some general commutation rules and identities for three-dimensional quantum-mechanical operators
Authors: García Alvarez Edgardo T. , González Alejandro D.
Published: March 2005

A general proof of several formulas used in three-dimensional quantum problems is presented. By considering the two vector operators A and B having Cartesian components that satisfy the canonical commutation relations—as the position and momentum operators do—we obtain commutation rules and relations for the projection onto each another. All of these rules and relations have symmetry under A↔B exchange. This symmetry suggests, in the particular case of position and momentum operators, a new operator, the projection of r onto p, which seems to be useful in dissipative quantum problems.
A computer-assisted approach to learning physics concepts
Authors: Hicks R. B. , Laue H.
Published: March 2005

A study is described that tested the effectiveness of computer-assisted tutorial modules in dispelling common student misconceptions in first-year mechanics. Most of the subject matter for the tutorial modules was based on examples drawn from kinematics and dynamics, which one would find on many first-year physics tests. One of the examples, involving qualitative comparison of speeds of two differently moving objects, has been the subject of investigations of student misconceptions conducted by other workers. The present study involved a total of 96 student volunteers drawn from all of our first-year physics courses. The results of the study suggest that computer-assisted tutorials of the kind described here can be effective in teaching material that presents conceptual difficulties, and is often not learned directly from textbooks or from lectures delivered to large classes.
Coherent states and accidental degeneracy for a charged particle in a magnetic field
Authors: Loyola G. , Moshinsky M. , Szczepaniak A.
Published: March 2005

The coherent state solution for a charged particle in a constant magnetic field and its implication for the accidental degeneracy present in the problem are discussed. Furthermore, a simple derivation is given for the density of electrons per unit area in the plane perpendicular to the magnetic field, which is required for the understanding of the quantum Hall effect.
A computer-assisted free-fall experiment for the freshman laboratory
Authors: Quick Stuart M.
Published: March 2005

A robust apparatus, which includes a microcomputer to control the release of a body, perform the necessary timings, and measure its average speed, is used by freshman students to study free-fall motion. A procedure is suggested that enables students in one laboratory period to collect data to find ‘‘g’’ from least-squares fits of the functions s=v0t− 1/2 gt2, v=v0−gt, and v2=v20−2gs.
Kramers–Kronig in two lines
Authors: Hu Ben Yu-Kuang
Published: March 2005

A short derivation of the Kramers–Kronig relations is presented.
Cognizable worlds: The anthropic principle and the fundamental constants of nature
Authors: Greenstein George , Kropf Allen
Published: March 2005

Can the anthropic principle be used to understand the values of the fundamental constants of nature and, conversely, can the existence of life be said to arise from a remarkable feat of fine tuning on the part of the cosmos? The conditions required for the existence of life that depend upon stellar, atomic, and molecular structure are focused on and the degree to which these conditions would have been met had the fundamental constants been different from their known values is analyzed. The tentative answer to both questions is no.
Adiabatic invariance or scaling?
Authors: Gignoux C. , Brut F.
Published: March 2005

The usual pedagogical example of adiabatic invariance—a bouncing ball between two parallel walls moving at constant velocities—is inappropriately chosen. It is shown that the action integral is exactly conserved in this problem, whatever the wall velocities. The adiabatic invariance must be considered in the case of varying wall velocities. This result leads to the examination of the cavities of arbitrary shape that are transformed in a homothetical way, the ratio of the transformation varying linearly with time. This situation is shown to be equivalent to the problem of a particle in a fixed cavity, with new space and time scales. The action invariance for a rectangular parallelepipedal box or a spherical cavity is one of the consequences of this scaling. When a large number of structureless particles are moving inside such transformed cavities, the system could reach a thermal equilibrium whatever the deformation velocity may be. Finally, in the equivalent quantum situation, a simple operator transforms the time-dependent state vector in the varying cavity into that of the fixed cavity.
Interactive computer simulation and analysis of Newtonian dynamics
Authors: Eubank S. , Miner W. , Tajima T. , Wiley J.
Published: March 2005

A computer program is described for numerical simulation of one-dimensional oscillators and mappings suitable for use in classes ranging from introductory dynamics to more advanced nonlinear dynamics. Properties of the algorithms used for integrating the equations of motion are discussed as well as some of the interesting physics that can be studied, giving illustrations produced with the program.
Spin-flips in Dirac scattering by a one-dimensional barrier
Authors: Glass Solomon J. , Mendlowitz H.
Published: March 2005

A Dirac particle scattered by a potential barrier varying in one dimension is treated. The incident momentum is three-dimensional. It is shown that the scattered amplitudes have contributions due to spin-flip.
Measurement of refractive index by double-exposure speckle pattern recording
Authors: Buah-Bassuah P. K. , Francini F. , Molesini G.
Published: March 2005

An experimental approach is presented to the measurement of the refractive index of materials based on the optical properties of speckle patterns. The sample being characterized is shaped in the form of a plane parallel plate and so inserted in a speckle-forming beam. Speckles are recorded on a photographic plate with a double-exposure technique producing a twin speckle pattern. Decoding of such a recorded pattern leads to the desired information.
An approximate analytic solution of the spectral inverse problem
Authors: Engelke Ray
Published: March 2005

An important problem of nonrelativistic quantum theory is: Given a bound-state energy spectrum, determine the space dependence of a potential function that will produce that spectrum. This is sometimes called the ‘‘spectral inverse’’ problem. Here, by use of the first-order WKB energy quantization condition, an approximate analytic solution of this problem is given for the case of one-dimensional symmetric oscillators and for a class of radial oscillators. This is done by reformulating the WKB quantization condition as an Abel integral equation that relates the quantum number to the potential’s space dependence. The resultant integral equation can be solved exactly. The harmonic oscillator and the hydrogen atom problems are used to demonstrate the method. The solution for the case of one-dimensional asymmetric oscillators is also briefly discussed and the Morse oscillator is used as an example. Finally, the history of the spectral inverse problem is reviewed and the conditions necessary for its exact solution are discussed. In particular, the conditions required for the inversion process to be unique are considered.
The transmission of a b
o
u
n
d
e
d microwave beam through a dielectric slab
Authors: Navasquillo J. , Such V. , Pomer F.
Published: March 2005

A theoretical and experimental study of the transmission of a bounded microwave beam through a dielectric slab is presented. The theoretical treatment is based on representing the incident and transmitted beams in terms of an angular spectrum of plane waves. The transmitted beam suffers a direction shift, with respect to the incident beam direction, that is larger than that predicted by geometrical optics. The experimental results are in agreement with the theoretical values.
An extension of the Eisberg–Resnick treatment for electron energies in many-electron atoms
Authors: Whitaker M. A. B. , Bennett I.
Published: March 2005

Eisberg and Resnick present a simple argument for the energy of an electron in a multielectron atom using the concept of shielding from electrons in inner shells. The results of such a treatment are unfortunately confined so as to be out of range of experimental values. Here, the effect of electrons in outer shells is included, and, in the nonrelativistic region, energies are obtained for electrons in the first and second shells in reasonable agreement with experiment.
Transition-state theory for quantum and classical particle escape from a finite square well
Authors: Tsao J. Y.
Published: March 2005

A precise statement of transition-state theory is given. The theory is made intuitive and precise by the introduction of a ‘‘semipermeable’’ barrier between reactant and product. The theory is then illustrated by calculating, both quantum and classical mechanically, the rate of particle escape from a finite square well. The two calculations are fundamentally different and illuminate different aspects of the theory. Finally, the solution is recast into the Arrhenian form with which it is usually identified, and physically satisfying expressions for the rate prefactor, activation energy, and activation entropy are obtained.
Fresnel lenses
Authors: Aničin B. A. , Babović V. M. , Davidović D. M.
Published: March 2005

This article contains a description of the discovery of the stepped lenses that today bear Fresnel’s name, based on a monograph written by Fresnel himself in 1822. Although it stands in the shadow of the rest of his activity, in particular the theory of transverse light waves, including polarization, diffraction, and birefringence, this invention could be regarded as a very interesting and very early result of government-sponsored research activity in science and technology, to be used in lighthouses for at least a century, and to remain important in other fields of modern optics.
Demonstration of single-electron buildup of an interference pattern
Authors: Tonomura A. , Endo J. , Matsuda T. , Kawasaki T. , Ezawa H.
Published: March 2005

The wave–particle duality of electrons was demonstrated in a kind of two-slit interference experiment using an electron microscope equipped with an electron biprism and a position-sensitive electron-counting system. Such an experiment has been regarded as a pure thought experiment that can never be realized. This article reports an experiment that successfully recorded the actual buildup process of the interference pattern with a series of incoming single electrons in the form of a movie.
Centennial of Hertz’ radio waves
Authors: Adawi I.
Published: March 2005

A glimpse of the life and work of Heinrich Hertz is given on the occasion of the centennial of his discovery of radio waves (1888). The importance of his work in verifying Maxwell’s theory and establishing the electromagnetic wave nature of light is discussed.
On the buildup of laser oscillation from noise
Authors: Milonni P. W.
Published: March 2005

It is well known that laser oscillation is initiated by spontaneous radiation ‘‘noise.’’ Evidence for this is often based on the complete theory of laser oscillation, including the quantization of the electromagnetic field. In this article, the buildup of laser oscillation from quantum noise is demonstrated using the most elementary classical equation describing the amplification of laser intensity.
How big is a cyclotron?
Authors: Brown Lowell S.
Published: March 2005

The radius of the orbit of a particle of given energy in a laboratory cyclotron is computed in terms of the Bohr radius of the hydrogen atom a0 and the fine structure constant α.
On an alternative type of water barometer
Authors: Vandyck M. A.
Published: March 2005

A type of water/gas barometer is studied, which is accurate, easy to build, and the size of which is similar to the one of the usual mercury barometer.
Long-buried dismantling of a centuries-old myth: Newton’s P
r
i
n
c
i
p
i
a and inverse-square orbits
Authors: Weinstock Robert
Published: March 2005

The author’s 1982 report of the fallacy inherent in Newton’s treatment of inverse-square orbits in the Principia was anticipated by Ferdinand Rosenberger in his 1895 book-length study of Newton’s life and work [Isaac Newton und Seine Physikalischen Principien (Barth, Leipzig, 1895)]. A new alternative formulation of the case against the Principia treatment is offered as surpassing in effectiveness that of Rosenberger and the essentially equivalent 1982 formulation by the author. Also offered is exposure of a long-enduring misrepresentation of a portion of the Principia that deals with inverse-square orbits.
Stellar structure and the art of building boats
Authors: Celnikier Ludwik M.
Published: March 2005

Acton and Squire’s [Solving Equations with Physical Understanding (Hilger, Bristol, 1985)] ‘‘trial function’’ method of handling boundary value problems is used to find approximate solutions to the equations of stellar structure; the calculations involved are as simple to carry out as the usual order-of-magnitude estimates, but are correct to a few tens of a percent. The method is also used to investigate why an order-of-magnitude estimate of solar luminosity can be wrong by up to three orders of magnitude, while a similar estimate of the central temperature can be closer to acceptable values.
Electrical conductivity in granular media and Branly’s coherer: A simple experiment
Authors: Falcon Eric , Castaing Bernard
Published: March 2005

We show how a simple laboratory experiment can illustrate certain electrical transport properties of metallic granular media. At a low critical external voltage, a transition from an insulating to a conductive state is observed. This transition comes from an electro-thermal coupling in the vicinity of the microcontacts between grains where microwelding occurs. Our apparatus allows us to obtain an implicit determination of the microcontact temperature, which is analogous to the use of a resistive thermometer. The experiment also helps us explain an old problem, Branly’s coherer effect, which was used as a radio wave detector for the first wireless radio transmission, and is based on the sensitivity of the conductivity of metal filings to an electromagnetic wave.
The impact of epistemology on learning: A case study from introductory physics
Authors: Lising Laura , Elby Andrew
Published: March 2005

We discuss a case study of the influence of epistemology on learning for a student in an introductory college physics course. An analysis of videotaped class work, written work, and interviews indicates that many of the student’s difficulties were epistemological in nature. Our primary goals are to show instructors and curriculum developers that a student’s personal epistemological stance—her ideas about knowledge and learning—can have a direct, causal influence on her learning of physics, and to describe a mechanism for this interaction. This influence exists even when research-based curriculum materials provide implicit epistemological support. For this reason, curriculum materials and teaching techniques could become more effective by explicitly attending to students’ epistemologies.
In Vivo Selection of Respiratory Syncytial Viruses Resistant to Palivizumab
Authors: Zhao Xiaodong , Sullender Wayne M.
Published: March 2005

Palivizumab (PZ) is the only monoclonal antibody currently available for use in humans against an infectious disease. PZ is administered prophylactically for respiratory syncytial virus (RSV) infections. RSV selected in cell culture for growth in the presence of PZ develops F gene mutations and can be resistant to PZ prophylaxis in cotton rats. Here, we evaluated the potential for PZ-resistant RSV mutants to arise in vivo. Cotton rats were immunosuppressed with cyclophosphamide, administered PZ, and inoculated intranasally with RSV. Lungs were harvested 12 weeks after RSV infection, reverse transcription-PCR-amplified F gene fragments were cloned into plasmids, and the nucleotide sequences of the cloned cDNAs were determined. Three of the five animals had mixed populations of lung virus, and over 50% of the clones from the three animals revealed F gene mutations associated with resistance to PZ. A virus completely resistant to PZ neutralization was recovered from the lung homogenate of a rat that had received PZ. Thus, prolonged pulmonary replication of RSV in the presence of PZ was followed by the appearance of viruses resistant to PZ. The potential for the development of resistance is a consideration as the antibody is used prophylactically against RSV and as passively administered antibodies are under development for other infections, including emerging viruses and agents of biodefense.
Herpes Simplex Virus Infection Stabilizes Cellular IEX-1 mRNA
Authors: Hsu Wei-Li , Saffran Holly A. , Smiley James R.
Published: March 2005

Herpes simplex virus (HSV) virion host shutoff protein (vhs) destabilizes cellular and viral mRNAs. Previous work from several laboratories has indicated that vhs accelerates the turnover of most host mRNAs and provided evidence that at least some of these are degraded via endonucleolytic cleavage near regions of translational initiation followed by 5′→3′ decay. In contrast, several recent reports have argued that vhs is selective, preferentially targeting a subset of mRNAs including some that bear AU-rich instability elements (such as the stress-inducible IEX-1 mRNA). These reports concluded that vhs triggers deadenylation, 3′ cleavage, and 3′→5′ decay of IEX-1 mRNA. However, we report here that HSV infection does not increase the rate of degradation of IEX-1 mRNA; rather, actinomycin D chase assays indicate that the transcript is stabilized relative to that in uninfected cells in both the presence and absence of functional vhs. Moreover, deadenylated but otherwise intact IEX-1 mRNA was readily detected in uninfected cells cultured under our experimental conditions, and its relative abundance did not increase following HSV type 1 (HSV-1) infection. We confirm that HSV infection increases the relative abundance of a discrete 0.75-kb 3′-truncated IEX-1 RNA species in a vhs-dependent manner. This truncated transcript was also detected (albeit at lower levels) in cells infected with vhs mutants and in uninfected cells, where it increased in abundance in response to tumor necrosis factor alpha, cycloheximide, and puromycin. We conclude that IEX-1 mRNA is not preferentially degraded during HSV-1 infection and that HSV-1 instead inhibits the normal turnover of this mRNA.
Requirements for the Selective Degradation of Endoplasmic Reticulum-Resident Major Histocompatibility Complex Class I Proteins by the Viral Immune Evasion Molecule mK3
Authors: Wang Xiaoli , Connors Rose , Harris Michael R. , Hansen Ted H. , Lybarger Lonnie
Published: March 2005

Recent studies suggest that certain viral proteins co-opt endoplasmic reticulum (ER) degradation pathways to prevent the surface display of major histocompatibility complex class I molecules to the immune system. A novel example of such a molecule is the mK3 protein of gammaherpesvirus 68. mK3 belongs to an extensive family of structurally similar viral and cellular proteins that function as ubiquitin ligases using a conserved RING-CH domain. In the specific case of mK3, it selectively targets the rapid degradation of nascent class I heavy chains in the ER while they are associated with the class I peptide-loading complex (PLC). We present here evidence that the PLC imposes a relative proximity and/or orientation on the RING-CH domain of mK3 that is required for it to specifically target class I molecules for degradation. Furthermore, we demonstrate that full assembly of class I molecules with peptide is not a prerequisite for mK3-mediated degradation. Surprisingly, although the cytosolic tail of class I is required for rapid mK3-mediated degradation, we observed that a class I mutant lacking lysine residues in its cytosolic tail was ubiquitinated and degraded in the presence of mK3 in a manner indistinguishable from wild-type class I molecules. These findings are consistent with a “partial dislocation” model for turnover of ER proteins and define some common features of ER degradation pathways initiated by structurally distinct herpesvirus proteins.
Impaired Monocyte Maturation in Response to CpG Oligodeoxynucleotide Is Related to Viral RNA Levels in Human Immunodeficiency Virus Disease and Is at Least Partially Mediated by Deficiencies in Alpha/Beta Interferon Responsiveness and Production
Authors: Jiang Wei , Lederman Michael M. , Salkowitz Janelle R. , Rodriguez Benigno , Harding Clifford V. , Sieg Scott F.
Published: March 2005

The biological activity of CpG oligodeoxynucleotide 2216 (ODN2216), a Toll-like receptor 9 agonist, was investigated with monocytes from human immunodeficiency virus (HIV)-negative and HIV-positive (HIV+) donors. Exposure of peripheral blood mononuclear cells to CpG ODN2216 led to decreased expression of the monocyte marker CD14 and increased expression of the dendritic cell marker CD83, as well as increased expression of HLA-DR, CD40, CD80, and CD86 among the monocytes. Several features of the CpG ODN-induced maturation were diminished in monocytes from HIV+ donors, and these deficiencies were related to increased viremia but not to CD4 cell counts. Alpha interferon (IFN-α) was implicated as at least a partial mediator of the CpG ODN-induced monocyte maturation. Reduced production of IFN-α in response to CpG ODN and reduced frequencies of plasmacytoid dendritic cells, the principal IFN-α-producing cell type in peripheral blood, were observed in peripheral blood mononuclear cells from HIV+ donors. These deficiencies also were related to levels of plasma HIV RNA. Responses of monocytes from HIV+ donors to direct stimulation with IFN-α also were partially impaired. Thus, reduced production of IFN-α and reduced IFN-α responsiveness may contribute to diminished functional responses to CpG ODN in HIV disease. Application of CpG ODNs in HIV disease for adjuvant or immunoregulatory purposes may be particularly useful for HIV+ donors without high-level viremia.
Control of VP16 Translation by the Herpes Simplex Virus Type 1 Immediate-Early Protein ICP27
Authors: Ellison Kimberly S. , Maranchuk Robert A. , Mottet Kelly L. , Smiley James R.
Published: March 2005

Herpes simplex virus (HSV) ICP27 is an essential and multifunctional regulator of gene expression that modulates the synthesis and maturation of viral and cellular mRNAs. Processes that are affected by ICP27 include transcription, pre-mRNA splicing, polyadenylation, and nuclear RNA export. We have examined how ICP27 influences the expression of the essential HSV tegument protein and transactivator of immediate-early gene expression VP16. We monitored the effects of ICP27 on the levels, nuclear export, and polyribosomal association of VP16 mRNA and on the amount and stability of VP16 protein. Deletion of ICP27 reduced the levels of VP16 mRNA without altering its nuclear export or the stability of the encoded protein. However, the translational yield of the VP16 mRNA produced in the absence of ICP27 was reduced 9- to 80-fold relative to that for wild-type infection, suggesting a defect in translation. In the absence of ICP27, the majority of cytoplasmic VP16 mRNA was not associated with actively translating polyribosomes but instead cosedimented with 40S ribosomal subunits, indicating that the translational defect is likely at the level of initiation. These effects were mRNA specific, as polyribosomal analysis of two cellular transcripts (glyceraldehyde-3-phosphate dehydrogenase and β-actin) and two early HSV transcripts (thymidine kinase and ICP8) indicated that ICP27 is not required for efficient translation of these mRNAs. Thus, we have uncovered a novel mRNA-specific translational regulatory function of ICP27.
Cooperative Effect of Gag Proteins p12 and Capsid during Early Events of Murine Leukemia Virus Replication
Authors: Lee Sook-Kyung , Nagashima Kunio , Hu Wei-Shau
Published: March 2005

The Gag polyprotein of murine leukemia virus (MLV) is processed into matrix (MA), p12, capsid (CA), and nucleocapsid (NC) proteins. p12 affects early events of virus replication and contains a PPPY motif important for virus release. To probe the functions of p12 in the early steps of MLV replication, we tested whether p12 can be replaced by spleen necrosis virus (SNV) p18, human immunodeficiency virus type 1 p6, or Rous sarcoma virus p2b. Analyses revealed that all chimeras generated virions at levels similar to that of MLV
gag-pol
; however, none of them could support MLV vector replication, and all of them exhibited severely reduced DNA synthesis upon virus infection. Because a previously reported SNV
gag
-MLV
pol
chimera, but not the MLV hybrid with SNV p18, can support replication of an MLV vector, we hypothesized that other Gag proteins act cooperatively with p12 during the early phase of virus replication. To test this hypothesis, we generated three more MLV-based chimeras containing SNV CA, p18-CA, or p18-CA-NC. We found that the MLV chimera containing SNV p18-CA or p18-CA-NC could support MLV vector replication, but the chimera containing SNV CA could not. Furthermore, viruses derived from the MLV chimera with SNV CA could synthesize viral DNA upon infection but were blocked at a post-reverse-transcription step and generated very little two long terminal repeat circle DNA, thereby producing a phenotype similar to that of the provirus formation-defective p12 mutants. Taken together, our data indicate that when p12/p18 or CA was from different viruses, despite abundant virus production and proper Gag processing, the resulting viruses were not infectious. However, when p12/p18 and CA were from the same virus, even though they were from SNV and not MLV, the resulting viruses were infectious. Therefore, these results suggest a cooperative effect of p12 and CA during the early events of MLV replication.
Hepatitis B Virus X Protein Stimulates Viral Genome Replication via a DDB1-Dependent Pathway Distinct from That Leading to Cell Death
Authors: Leupin Olivier , Bontron Séverine , Schaeffer Céline , Strubin Michel
Published: March 2005

The hepatitis B virus (HBV) X protein (HBx) is essential for virus infection and has been implicated in the development of liver cancer associated with chronic infection. HBx can interact with a number of cellular proteins, and in cell culture, it exhibits pleiotropic activities, among which is its ability to interfere with cell viability and stimulate HBV replication. Previous work has demonstrated that HBx affects cell viability by a mechanism that requires its binding to DDB1, a highly conserved protein implicated in DNA repair and cell cycle regulation. We now show that an interaction with DDB1 is also needed for HBx to stimulate HBV genome replication. Thus, HBx point mutants defective for DDB1 binding fail to complement the low level of replication of an HBx-deficient HBV genome when provided in
trans
, and one such mutant regains activity when directly fused to DDB1. Furthermore, DDB1 depletion by RNA interference specifically compromises replication of wild-type HBV, indicating that HBx produced from the viral genome also functions in a DDB1-dependent fashion. We also show that HBx in association with DDB1 acts in the nucleus and stimulates HBV replication mainly by enhancing viral mRNA levels, regardless of whether the protein is expressed from the HBV genome itself or supplied in
trans
. Interestingly, whereas HBx induces cell death in both HepG2 and Huh-7 hepatoma cell lines, it enhances HBV replication only in HepG2 cells, suggesting that the two activities involve distinct DDB1-dependent pathways.
A 57-Nucleotide Upstream Early Polyadenylation Element in Human Papillomavirus Type 16 Interacts with hFip1, CstF-64, hnRNP C1/C2, and Polypyrimidine Tract Binding Protein
Authors: Zhao Xiaomin , Öberg Daniel , Rush Margaret , Fay Joanna , Lambkin Helen , Schwartz Stefan
Published: March 2005

We have investigated the role of the human papillomavirus type 16 (HPV-16) early untranslated region (3′ UTR) in HPV-16 gene expression. We found that deletion of the early 3′ UTR reduced the utilization of the early polyadenylation signal and, as a consequence, resulted in read-through into the late region and production of late L1 and L2 mRNAs. Deletion of the U-rich 3′ half of the early 3′ UTR had a similar effect, demonstrating that the 57-nucleotide U-rich region acted as an enhancing upstream element on the early polyadenylation signal. In accordance with this, the newly identified hFip1 protein, which has been shown to enhance polyadenylation through U-rich upstream elements, interacted specifically with the HPV-16 upstream element. This upstream element also interacted specifically with CstF-64, hnRNP C1/C2, and polypyrimidine tract binding protein, suggesting that these factors were either enhancing or regulating polyadenylation at the HPV-16 early polyadenylation signal. Mutational inactivation of the early polyadenylation signal also resulted in increased late mRNA production. However, the effect was reduced by the activation of upstream cryptic polyadenylation signals, demonstrating the presence of additional strong RNA elements downstream of the early polyadenylation signal that direct cleavage and polyadenylation to this region of the HPV-16 genome. In addition, we identified a 3′ splice site at genomic position 742 in the early region with the potential to produce E1 and E4 mRNAs on which the E1 and E4 open reading frames are preceded only by the suboptimal E6 AUG. These mRNAs would therefore be more efficiently translated into E1 and E4 than previously described HPV-16 E1 and E4 mRNAs on which E1 and E4 are preceded by both E6 and E7 AUGs.
Wide Range of Quasispecies Diversity during Primary Hepatitis C Virus Infection
Authors: Herring Belinda L. , Tsui Rose , Peddada Lorraine , Busch Michael , Delwart Eric L.
Published: March 2005

Hepatitis C virus (HCV) infections may be initiated by multiple infectious particles, resulting in a genetically heterogeneous viral population, or by a single particle, leading to a clonal population in the initial stage of infection. To determine which of these scenarios is most common, we evaluated the genetic diversity of HCV quasispecies in 12 seronegative subjects with primary infection following community exposures, six acutely infected recipients of HCV-seropositive blood transfusions and six seropositive individuals with infections of undetermined durations. RNA isolated from plasma and a region of the HCV envelope gene including the first hypervariable region (HVR-1) was reverse transcription-PCR amplified and subcloned, and multiple plasmid clones were sequenced. Phylogenetic analysis indicated that all HCV variants clustered by individuals. Genetic distances among HCV variants within recently infected subjects ranged from 1 to 7.8%. On the basis of the estimated mutation rate of HCV in vivo and the
Taq
polymerase error rate, primary infection viral quasispecies were classified as genetically heterogeneous when the maximum sequence divergence between genetic variants in the same person was >3%. Heterogeneous quasispecies were detected in 4 of 12 preseroconversion subjects, 1 of 6 transfusion recipients, and 4 of 6 seropositive subjects. The high level of viral quasispecies genetic diversity found in at least a third of recently infected individuals is consistent with the transmission of multiple infectious particles. Community-acquired HCV infection, predominantly the result of needle sharing by injection drug users, therefore appears to be frequently initiated by the successful transmission of multiple viral variants.
Kinetic Factors Control Efficiencies of Cell Entry, Efficacies of Entry Inhibitors, and Mechanisms of Adaptation of Human Immunodeficiency Virus
Authors: Platt Emily J. , Durnin James P. , Kabat David
Published: March 2005

Replication of human immunodeficiency virus type 1 (HIV-1) in diverse conditions limiting for viral entry into cells frequently leads to adaptive mutations in the V3 loop of the gp120 envelope glycoprotein. This has suggested that the V3 loop limits the efficiencies of HIV-1 infections, possibly by directly affecting gp120-coreceptor affinities. In contrast, V3 loop mutations that enable HIV-1
JR-CSF
to use the low-affinity mutant coreceptor CCR5(Y14N) are shown here to have negligible effects on the virus-coreceptor affinity but to dramatically accelerate the irreversible conformational conversion of the envelope gp41 subunits from a three-stranded coil into a six-helix bundle. This slow step is blocked irreversibly by the inhibitor T-20. To further evaluate the role of entry rates in controlling infection efficiencies and viral adaptations, we developed methods to quantitatively measure viral entry kinetics. The virions were adsorbed by spinoculation at 4°C onto HeLa-CD4/CCR5 cell clones that either had limiting or saturating concentrations of CCR5. After warming to 37°C, the completion of entry was monitored over time by the resistance of infections to the competitive CCR5 inhibitor TAK-779. Our results suggest that the efficiency of entry of cell-attached infectious HIV-1 is principally controlled by three kinetic processes. The first is a lag phase that is caused in part by the concentration-dependent reversible association of virus with CD4 and CCR5 to form an equilibrium assemblage of complexes. Second, this assembly step lowers but does not eliminate a large activation energy barrier for a rate-limiting, CCR5-dependent conformational change in gp41 that is sensitive to blockage by T-20. The rate of infection therefore depends on the fraction of infectious virions that are sufficiently saturated with CCR5 to undergo this conformational change and on the magnitude of the activation energy barrier. Although only a small fraction of fully assembled viral complexes overcome this barrier per hour, the ensuing steps of entry are rapidly completed within 5 to 10 min. Thus, this barrier limits the overall flow rate at which the attached virions enter cells, but it has no effect on the lag time that precedes this entry flow. Third, a relatively rapid and kinetically dominant process of viral inactivation, which may partly involve endocytosis, competes with infectious viral entry. Our results suggest that the V3 loop of gp120 has a major effect on the rate-limiting coreceptor-dependent conformational change in gp41 and that adaptive viral mutations, including V3 loop mutations, function kinetically by accelerating this inherently slow step in the entry pathway.
Viral Induction of Central Nervous System Innate Immune Responses
Authors: Rempel J. D. , Quina L. A. , Blakely-Gonzales P. K. , Buchmeier M. J. , Gruol D. L.
Published: March 2005

The ability of the central nervous system (CNS) to generate innate immune responses was investigated in an in vitro model of CNS infection. Cultures containing CNS cells were infected with mouse hepatitis virus-JHM, which causes fatal encephalitis in mice. Immunostaining indicated that viral infection had a limited effect on culture characteristics, overall cell survival, or cell morphology at the early postinfection times studied. Results from Affymetrix gene array analysis, assessed on RNA isolated from virally and sham-infected cultures, were compared with parallel protein assays for cytokine, chemokine, and cell surface markers. Of the 126 transcripts found to be differentially expressed between viral and sham infections, the majority were related to immunological responses. Virally induced increases in interleukin-6 and tumor necrosis factor alpha mRNA and protein expression correlated with the genomic induction of acute-phase proteins. Genomic and protein analysis indicated that viral infection resulted in prominent expression of neutrophil and macrophage chemotactic proteins. In addition, mRNA expression of nonclassical class I molecules H2-T10, -T17, -M2, and -Q10, were enhanced three- to fivefold in virus-infected cells compared to sham-infected cells. Thus, upon infection, resident brain cells induced a breadth of innate immune responses that could be vital in directing the outcome of the infection and, in vivo, would provide signals which would summon the peripheral immune system to respond to the infection. Further understanding of how these innate responses participate in immune protection or immunopathology in the CNS will be critical in efforts to intervene in severe encephalitis.
Human Immunodeficiency Virus Type 1-Induced Macrophage Gene Expression Includes the p21 Gene, a Target for Viral Regulation
Authors: Vázquez Nancy , Greenwell-Wild Teresa , Marinos Nancy J. , Swaim William D. , Nares Salvador , Ott David E. , Schubert Ulrich , Henklein Peter , Orenstein Jan M. , Sporn Michael B. , Wahl Sharon M.
Published: March 2005

In contrast to CD4+T cells, human immunodeficiency virus type 1 (HIV-1)-infected macrophages typically resist cell death, support viral replication, and consequently, may facilitate HIV-1 transmission. To elucidate how the virus commandeers the macrophage's intracellular machinery for its benefit, we analyzed HIV-1-infected human macrophages for virus-induced gene transcription by using multiple parameters, including cDNA expression arrays. HIV-1 infection induced the transcriptional regulation of genes associated with host defense, signal transduction, apoptosis, and the cell cycle, among which the cyclin-dependent kinase inhibitor 1A (CDKN1A/p21) gene was the most prominent. p21 mRNA and protein expression followed a bimodal pattern which was initially evident during the early stages of infection, and maximum levels occurred concomitant with active HIV-1 replication. Mechanistically, viral protein R (Vpr) independently regulates p21 expression, consistent with the reduced viral replication and lack of p21 upregulation by a Vpr-negative virus. Moreover, the treatment of macrophages with p21 antisense oligonucleotides or small interfering RNAs reduced HIV-1 infection. In addition, the synthetic triterpenoid and peroxisome proliferator-activated receptor γ ligand, 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO), which is known to influence p21 expression, suppressed viral replication. These data implicate p21 as a pivotal macrophage facilitator of the viral life cycle. Moreover, regulators of p21, such as CDDO, may provide an interventional approach to modulate HIV-1 replication.
The pp38 Gene of Marek's Disease Virus (MDV) Is Necessary for Cytolytic Infection of B Cells and Maintenance of the Transformed State but Not for Cytolytic Infection of the Feather Follicle Epithelium and Horizontal Spread of MDV
Authors: Gimeno I. M. , Witter R. L. , Hunt H. D. , Reddy S. M. , Lee L. F. , Silva R. F.
Published: March 2005

Marek's disease virus has a unique phosphoprotein, pp38, which is suspected to play an important role in Marek's disease pathogenesis. The objective of the present study was to utilize a mutant virus lacking the pp38 gene (rMd5Δpp38) to better characterize the biological function of pp38. This work shows that the pp38 gene is necessary to establish cytolytic infection in B cells but not in feather follicle epithelium, to produce an adequate level of latently infected T cells, and to maintain the transformed status in vivo.
Cultural identity, acculturation, and mental health among adolescents in east London’s multiethnic community
Authors: Bhui Kamaldeep , Stansfeld Stephen , Head Jenny , Haines Mary , Hillier Sheila , Taylor Stephanie , Viner Russell , Booy Robert
Published: March 2005

Study objective:To investigate cultural identity as a risk factor for mental health problems among adolescents.

Design:A cross sectional school based population survey. Mental health problems were measured using the strengths and difficulties questionnaire. Pupils were classified into one of four cultural identity types on the basis of friendship and clothing choices.

Setting:East London.

Participants:2623 adolescents (aged 11–14) from a representative sample of 28 schools in east London.

Results:In comparison with marginalised adolescents who chose friends from neither their own or other cultures, fewer mental health problems were found among adolescents making culturally integrated friendship choices (friends from own and other cultures: OR = 0.6, 0.4 to 0.9), boys making integrated friendship choices (OR = 0.45, 0.22 to 0.91), and specifically among Bangladeshi pupils with integrated friendship choices (OR = 0.15, 0.04 to 0.55).

Conclusion:As measures of cultural identity, integrated friendship choices overall, and specifically for boys and Bangladeshi pupils, are associated with lower levels of adolescent mental health problems.
SEARCH FOR A CHARMONIUM ASSIGNMENT FOR THE X(3872)
Authors:   REPRESENTING THE BELLE COLLABORATION, OLSEN STEPHEN L.
Published: March 2005

We report recent results on the properties of the X(3872) produced via the B+→K+ X(3872) decay process in the Belle detector. We compare these properties with expectations for possible charmonium-state assignments.
THE FINAL STATE INTERACTION IN THE REACTIONS pp→K+(Λp) AND pp→π+(np)
Authors: HINTERBERGER F. , NEDEV S. N. , SIUDAK R.
Published: March 2005

The reactions pp→K+(Λp) and pp→π+(np) are measured with high missing mass resolution using the spectrometer BIG KARL at COSY. The pp→K+(Λp) missing mass spectrum is analyzed with respect to the final state interaction near the Λp production threshold. The observed spectrum can be described by factorizing the reaction amplitude in terms of a production amplitude and a final state enhancement factor. Parametrizing the enhancement factor in terms of the inverse Jost function allows a direct extraction of the low-energy phase-equivalent potential parameters. Constraints on the singlet and triplet scattering lengths and effective ranges can be deduced by fitting simultaneously the Λp invariant mass spectrum and the total cross section data of the free Λp scattering. A similar analysis shows that the reaction pp→π+(np) is dominated by the triplet contribution to the (np) final state interaction. An upper limit of a possible singlet contribution is deduced. Finally, the reaction pp→π+(np) allows to test the Fäldt-Wilkin extrapolation theorem where the triplet (np) continuum wave function is extrapolated to the wave function of the deuteron.
HADRON SPECTROSCOPY AT CLAS
Authors:   FOR THE CLAS COLLABORATION., WEYGAND DENNIS P.
Published: March 2005

Meson photoproduction was studied at the CEBAF Large Acceptance Spectrometer (CLAS) utilizing a 5.5 GeV/c photon beam incident on a hydrogen target. Here we report on the partial wave analyzes (PWA) performed on the exclusive final states π+π+π-n and K+K-π+n. In addition, CLAS has data on the final state π+π0π-p which will be reported in the near future. The analysis of the π+π+π- system shows clearly the a2(1320), as well as evidence for the a1(1260) and the π2(1670). The π1(1600), previously observed in π-p interactions, is seen very weakly here. In the K+K-π+n channel there is is evidence for the Θ+(1540) S=+1 baryon pentaquark. The PWA of this system gives an excellent description of the background which rules out mesonic reflection as a source of the signal.
VECTOR MESON PRODUCTION IN COLLISIONS OF NUCLEONS
Authors:   COSY-TOF COLLABORATION., BRINKMANN K.-TH. , ABDEL-BARY M. , ABDEL-SAMAD S. , CLEMENT H. , DOROSHKEVICH E. , DSHEMUCHADSE S. , DUTZ H. , EHRHARDT K. , ERHARDT A. , EYRICH W. , FILIPPI A. , FREIESLEBEN H. , FRITSCH M. , GEORGI J. , GILLITZER A. , GONSER P. , JÄKEL R. , KARSCH L. , KILIAN K. , KOCH H. , KREß J. , KUHLMANN E. , MARCELLO S. , MEYER W. , MICHEL P. , MORSCH H. P. , MÖLLER K. , MÖRTEL H. , NAUMANN L. , PINNA L. , PIZZOLOTTO L. , RODERBURG E. , SCHAMLOTT A. , SCHÖNMEIER P. , SCHROEDER W. , SCHULTE-WISSERMANN M. , SEFZICK T. , STEINKE M. , STINZING F. , SUN G. Y. , UCAR A. , ULLRICH W. , WAGNER G. J. , WAGNER M. , WILMS A. , WINTZ P. , WIRTH S. , WÜSTNER P. , ZUPRANSKI P.
Published: March 2005

The production of vector mesons in collisions between nucleons is studied in order to address a variety of issues concerning nucleon-nucleon interaction, reaction mechanism and properties of baryons. These studies are summarized with emphasis on the most recent experiments at the Time-of-Flight spectrometer TOF and results obtained at the COoler SYnchrotron COSY in Jülich. While currently the open questions regarding the so-called OZI violation, its relation to the meson exchange picture and the relative importance of contributions to the production mechanism from various channels within this formalism are still unresolved, the present-day experiments hold the potential to clarify the situation greatly. Possible extensions of the experimental program on vector mesons using 4π detection techniques for charged as well as neutral particles, in particular π0, are discussed.