bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comment on Boltzmann's H-Theorem and Time Reversal
Authors: Eggarter T. P.
Published: September 2005

The standard textbook discussion of Boltzmann's H-theorem is analyzed and found unsatisfactory. An improved presentation is suggested.
Inexpensive Mechanical Model of a Josephson Weak Link
Authors: Rochlin Gene I. , Hansma Paul K.
Published: September 2005

We have built and used a simple, inexpensive, mechanical model of a Josephson weak link consisting of a pendulum and an aluminum disk, both mounted on a common shaft. The pendulum is driven at constant torque by a weight hanging on a thread wrapped around the shaft and damped by the eddy currents induced in the aluminum disk by a permanent magnet. As this model has an equation of motion that is formally identical to the circuit equation proposed by Stewart and McCumber for a Josephson weak link, the differing I vs V characteristics of various weak links can be simulated and understood with the model. The time evolution of the analogs of both the difference in phase across the weak link, φ, and the instantaneous supercurrent, ic sinφ, can be directly observed. The low cost and reliability of the model makes it practical to construct in classroom quantities for undergraduate laboratories as a supplement to or substitute for conventional cryogenic Josephson effect experiments.
Conversations with Albert Einstein. II
Authors: Shankland R. S.
Published: September 2005

Professor Einstein's views on the experimental basis for relativity theory and his attitude toward quantum mechanics continue to be of general interest. This paper is based on notes on these subjects made by the writer after each of five visits with Einstein at Princeton during 1950–1954 and not fully reported or discussed previously.
A Discrete Grading System for Physics Examinations
Authors: McDaniels D. K.
Published: September 2005

Advantages of a discrete system of scoring for certain types of tests are discussed on the basis of data from Ph.D. qualifying examinations. A criterion is suggested for the partial-credit level above which an answer is scored as ‘correct’ under the discrete system. Results from the discrete and the continuous (conventional) grading procedures are compared. It is suggested that the discrete scoring method may provide additional meaningful data for the evaluation of student performance on certain types of examinations.
The Electron Density in the Thomas-Fermi Theory
Authors: Harrington David R.
Published: September 2005

A simple derivation of the expression for the local electron density in terms of the potential, required for the Thomas-Fermi theory, is described. This derivation, based upon earlier work using the WKB (Wentzel-Kramers-Brillouin) approximation, avoids the introduction of the local density of states in phase space by making use of the correspondence principle and the Bohr-Sommerfeld quantization condition.
Noise Measurements in a University: An Open-Ended Student Experiment
Authors: Silvidi Anthony A. , Kristopson Louis J.
Published: September 2005

The results from a student instigated study of the noise levels on a major university campus is reported. It is shown that these measurements can be the simpler beginnings of a more complicated open-ended experiment which takes the student out of the traditional laboratory into a more realistic environment and provides socially relevant and potentially useful information.
Light, Color, and Photography: A Course for Artists and Others
Authors: Lietz Gerard P.
Published: September 2005

An optics course, which emphasizes phenomena in lieu of mathematics, is described. Because the course has proven especially interesting to artists, it is suggested that similar courses be considered at other institutions. Applications of interest to artists are pointed out.
Environmental Physics—A Course
Authors: Hare M. G.
Published: September 2005

This paper describes a new course on “Environmental Physics” which the author teaches at his institution. The article gives the syllabus for this course and shows the great variety of topics to which physics can be applied outside of the realm of pure academic physics.
Analysis of the Free Fall Experiment
Authors: Humphrey Clyde L.
Published: September 2005

Five methods found in the literature for analysing the data obtained in the classical free fall experiment are compared to a method proposed by this author. Statistical analysis is used to show that the author's method, a correct application of the method of differences, yields a more precise mean value of acceleration. Experimental results verify the statistical predictions.
Velocity without Limits
Authors: Saletan Eugene
Published: September 2005

Velocity is defined in a way that does not use the idea of going to a limit and that is suitable for elementary physics courses. It is shown that this definition can be used to calculate velocities (i.e., to take derivatives) algebraically for many simple time dependencies. The expression a = −ω2R for centripetal acceleration is also derived without using the concept of limit.
Zero-Point Energy in a Bounded Continuum
Authors: Onley D. S.
Published: September 2005

The zero-point energy of a quantal continuum, despite the fact that it is infinite, is generally supposed to be tractable in the sense that it does not necessarily imply an infinite value for any measurable quantity. In the case of a bounded continuum, the zero-point energy may undergo a change upon adiabatic changes in the boundary conditions and thus manifest itself as a force on the boundary. It is an obvious requirement that this force should be finite, but conditions under which this is true are found to be stringent; more generally, the assumption of zero-point energy would lead to infinite results for boundary forces. It is suggested that, for the continuum, zero-point energy is a dispensable concept and arises only from over zealous application of the canonical quantization rules.
Analog Computer Simulation of Krönig-Penny Model
Authors: Razdan K. N. , Brennan W. D.
Published: September 2005

An analog computer program for the generation of Krönig-Penny model wave functions is described. The first nine wave functions for a well model of differing heights and widths are plotted as an example. The potentiometer settings for these nine wave functions are tabulated.
The Classical Problem of Charge and Pole
Authors: Carter E. F. , Cohen H. A.
Published: September 2005

In this paper the classical dynamics of interacting electrically charged particles where one or both possess magnetic charge is reviewed. The equations of motion are obtained, and the vector constants of motion are derived. A consistent canonical formalism is developed while related aspects such as scale invariance and the geometry of the motion are also discussed.
Black Holes and Pulsars in the Introductory Physics Course
Authors: Orear Jay , Salpeter E. E.
Published: September 2005

A semi-quantitative presentation of gravitational collapse into white dwarfs, neutron stars, and black holes is given at the level of the introductory college physics course. Final radii, star composition, and critical masses are estimated using basic principles from the introductory course.
Lagrangian Formalism for a Classical Particle Moving in Riemannian Space with Dissipative Forces
Authors: Denman Harry H. , Kupferman Peter N.
Published: September 2005

Equations of motion are generated for a classical particle in a Riemannian space with arbitrary metric, moving in a velocity-independent potential, and acted upon by a linear frictional force. Only the Lagrangian formalism is used, but the Lagrangian function is not of standard form. As an example, a satellite moving in a linearly-viscous atmosphere is considered. This approach yields immediately a constant of the motion which is a generalization of the usual angular momentum. A particle moving on the viscous surface of a sphere is also discussed. Finally, the equation of motion for a particle moving in one dimension subject to a frictional force quadratic in the velocity is generated geometrically by choosing an appropriate nonanalytic metric.
Introducing Scattering Theory with a Computer
Authors: Merrill John R.
Published: September 2005

This article presents a new way to introduce scattering theory. This new method is based on the use of a computer (even a small one) to calculate classical particle trajectories and then quantum mechanical phase shifts. The method is very visual and is easy to explain as well as to perform. The students gain a much better physical understanding of the scattering process than has previously been possible.
Undergraduate Coherent Optics Laboratory
Authors: Yu F. T. S. , Wang E. Y.
Published: September 2005

Teaching coherent optics from an engineering viewpoint in a laboratory for undergraduate electrical engineering students has been an exciting and motivating experience. The philosophy, objectives, and experimental contents of this undergraduate laboratory offer a possible exposure for our undergraduates to modern coherent optics. We report in this paper on an undergraduate engineering laboratory in this field. The basic philosophy and objectives of the chosen experiments are briefly described. A few examples of the experiments are illustrated. An overall laboratory evaluation and concluding remarks are also given. In short, it is found from the response of the students that the laboratory is exciting, motivating, and stimulating. Generally, the students favor having this coherent optics laboratory.
Modified Hamilton's Principle
Authors: Ray John R.
Published: September 2005

It is proven that the modified Hamilton's principle, in which both the coordinates and momenta are varied independently, can be derived from Hamilton's principle in which only the coordinates are varied independently.
Science for the Nonscience Major: A Course for Adults
Authors: Fryshman Bernard
Published: September 2005

With adults returning to college in ever-increasing numbers, it is important to meet the special needs of these people when designing a “Science for the Nonscience Major” course. A curriculum prepared for use at Brooklyn College is described, together with a discussion that might enable its adoption in other institutions.
Quantitative, Molecular Light-Scattering Experiment
Authors: Shaw D. E. , Hones M. J. , Wunderlich F. J.
Published: September 2005

A straightforward experiment to study the scattering of monochromatic light by molecules is described. The principal aim of the experiment is to quantitatively illustrate the polarization of the scattered light as a function of the scattering angle. With these data a direct confirmation of certain aspects of the far field theory of electromagnetic radiation from a dipole is made. A theoretical expression for the polarization of radiation scattered by molecules is presented.
The Frank C. Walz Lecture Halls: A New Concept in the Design of Lecture Auditoria
Authors: Bartlett Albert A.
Published: September 2005

A report is presented of the design criteria and the results of the first year's use of two new physics lecture halls (seating 222 and 346 students, respectively) whose design was governed by a desire to reduce or eliminate many of the problems that arise in the use of conventional lecture halls. The thoughtful application of a few simple scientific principles has produced a whole new concept in the functional design of lecture auditoria. These two lecture halls have proven to be a great success, not only for lecturing in physics but for general university use in many fields, and the success of these halls may well mark this design as an architectural breakthrough.
Concepts in Many-Body Systems Illustrated by Coupled Oscillators
Authors: Grimvall Göran , Gunnarsson Olle
Published: September 2005

The system of coupled oscillators forms a very simple many-body system that can be treated exactly within elementary quantum mechanics. This system is used to introduce important many-body concepts, such as spectral function, propagator or Green function, sum rule, and elementary excitation. These concepts are briefly discussed for the real system of conduction electrons interacting with lattice vibrations.
Relativity Twins in the Kerr Metric
Authors: Markley F. Landis
Published: September 2005

We discuss the clock paradox for the case of clocks in co-revolving and counter-revolving circular orbits in the Kerr metric. We derive an exact formula for the difference in the two clock rates, which is exceedingly small in physically realizable measurements.
Comparison of the Hartree-Fock and Maximum Overlap Orbitals for a Simple Model
Authors: Latham W. P. , Kobe D. H.
Published: September 2005

A simple model consisting of two particles in a common oscillator potential interacting with each other through a harmonic oscillator coupling is solved exactly for the singlet ground state in one dimension. The Hartree-Fock orbitals and the maximum overlap orbitals are then obtained. The expectation values of several operators are calculated from these independent particle models and compared with each other and with the true values to ascertain the validity of the two approximations.
Evolution of a Concentrated, Media-Activated Physics Course
Authors: Baez Albert V.
Published: September 2005

This paper describes the evolution of a highly concentrated introductory physics course based on the spiral approach taught at Harvard University during the summers of 1967–1971, inclusive. It describes a teaching-learning strategy based on the use of the overhead projector, the tape recorder, films, film loops, and closed circuit TV in autolectures, seminars, micronotes, laboratory sessions with multiple options, and demonstration lectures. Student feedback from questionnaires was used to improve the course over a period of years. An unexpected spin-off was the discovery that the autolecture could be used to convert inexperienced graduate students into competent teaching assistants over a period of a few summers and that students could produce short autolectures as a means of reporting on special laboratory projects and learning valuable communication skills.
Observer in the Classroom
Authors: Carroll Kathleen A.
Published: September 2005

An observer in the classroom describes some of the problems and experiences that were encountered in observing and interacting with instructors in physics classes. The methods and areas of observation leading to the most effective improvement of teaching are explained in detail.
Conducting-Paper—Liquid-Crystal Fields Displays
Authors: Jones Thomas B. , Vacanti David C.
Published: September 2005

A novel technique for the color visual display of two-dimensional electrostatic fields is described. Temperature-sensitive encapsulated liquid crystals in sheet form are bonded to carbon-impregnated conducting paper on which a prescribed electrode configuration has been painted. The joule heating of the conducting paper creates a non-uniform two-dimensional temperature field to which the liquid crystals respond with color changes. Bands of uniform color identify isotherms which under certain conditions correspond to lines of constant electric field magnitude. The technique is applied to the study of various problems in electrostatics and potential fluid flow.
An Introductory Mechanics Laboratory at UICC
Authors: Goldberg H. S.
Published: September 2005

A modified version of the MIT air table is used as the foundation for a new, noncalculus mechanics laboratory. The motivation is to streamline and simplify the required equipment and to de-emphasize experimental techniques so as to give students a better opportunity to articulate and test their understanding of the classroom concepts. By using faculty members as instructors in the laboratory we have enhanced the educational environment and have brought the laboratory and classroom closer to a single entity. Details of the modified MIT air table are included in Appendix A.
Experimentally Determined Functional Relationships for Small-Amplitude Oscillations
Authors: Grauer Albert D. , Pittman Charles E.
Published: September 2005

An experimental procedure is presented which enables the beginning or intermediate student of mechanics to use linear air track apparatus to determine the functional relationship between the period, mass, and spring constant for small amplitude oscillatory motion. The results of a typical set of experiments as well as two different methods for obtaining the desired mathematical expression are included. The resulting expression agrees well with that which can be derived analytically from Hooke's law.
Optical Rotatory Power in a Classical One-Electron Model
Authors: Desobry G. E. , Kabir P. K.
Published: September 2005

According to Kuhn, in a classical treatment of Drude's one-particle model, an electron constrained to move along a helix exhibits no optical activity. On the other hand, Condon, Altar, and Eyring showed that a quantum-mechanical one-particle model, an electron confined in a twisted anisotropic harmonic-oscillator well, possesses optical activity even in the classical limit. We therefore re-examined Kuhn's analysis and found that while the Drude model does not have the usual kind of optical activity, it does exhibit rotatory power which is proportional to the intensity of the incident light for low intensities. This effect has a simple physical interpretation.
Random-Walk Model of Thermal Noise for Students in Elementary Physics
Authors: Henry Richard W.
Published: September 2005

A random-walk model of electronic motion in a resistor connected to an integrating ammeter is used to obtain an expression for the rms thermal noise current as a function of integration time. The thermal noise current is compared with the shot noise current in a temperature-limited diode (also found by an elementary derivation), and a simple demonstration experiment is suggested for testing the theory. The derivations and demonstration should prove useful to students who are mathematically unsophisticated but who might someday be users of sensitive electronic instrumentation.
Comparing Antigenicity and Immunogenicity of Engineered gp120
Authors: Selvarajah Suganya , Puffer Bridget , Pantophlet Ralph , Law Mansun , Doms Robert W. , Burton Dennis R.
Published: September 2005

We have engineered monomeric gp120 in such a way as to favorably present the conserved epitope for the broadly neutralizing antibody b12 while lowering the exposure of epitopes recognized by some weakly neutralizing and nonneutralizing antibodies. The work presented here describes the immune response in rabbits immunized with two prototype, engineered gp120s to explore the relationship between antigenicity and immunogenicity for these mutants. The GDMR gp120 mutant (residues 473 to 476 on gp120 altered from GDMR to AAAA) has a series of substitutions on the edge of the CD4 binding site (CD4bs), and the mCHO gp120 mutant has seven extra glycans relative to the wild-type protein. Importantly, serum mapping showed that both mutants did not elicit antibodies against a number of epitopes that had been targeted for dampening. The sera from rabbits immunized with the GDMR gp120 mutant neutralized some primary viruses at levels somewhat better than the wild-type gp120 immune sera as a result of an increased elicitation of anti-V3 antibodies. Unlike wild-type gp120 immune sera, GDMR gp120 immune sera failed to neutralize HXBc2, a T-cell line adapted (TCLA) virus. This was associated with loss of CD4bs/CD4-induced antibodies that neutralize TCLA but not primary viruses. The mCHO gp120 immune sera did not neutralize primary viruses to any significant degree, reflecting the masking of epitopes of even weakly neutralizing antibodies without eliciting b12-like antibodies. These results show that antibody responses to multiple epitopes on gp120 can be dampened. More precise focusing to a neutralizing epitope will likely require several iterations comparing antigenicity and immunogenicity of engineered proteins.
Temporal and Anatomic Relationship between Virus Replication and Cytokine Gene Expression after Vaginal Simian Immunodeficiency Virus Infection
Authors: Abel Kristina , Rocke David M. , Chohan Barinderpal , Fritts Linda , Miller Christopher J.
Published: September 2005

The current knowledge about early innate immune responses at mucosal sites of human immunodeficiency virus (HIV) entry is limited but likely to be important in the design of effective HIV vaccines against heterosexual transmission. This study examined the temporal and anatomic relationship between virus replication, lymphocyte depletion, and cytokine gene expression levels in mucosal and lymphoid tissues in a vaginal-transmission model of HIV in rhesus macaques. The results of the study show that the kinetics of cytokine gene expression levels in the acute phase of infection are positively correlated with virus replication in a tissue. Thus, cytokine responses after vaginal simian immunodeficiency virus (SIV) inoculation are earliest and strongest in mucosal tissues of the genital tract and lowest in systemic lymphoid tissues. Importantly, the early cytokine response was dominated by the induction of proinflammatory cytokines, while the induction of cytokines with antiviral activity, alpha/beta interferon, occurred too late to prevent virus replication and dissemination. Thus, the early cytokine response favors immune activation, resulting in the recruitment of potential target cells for SIV. Further, unique cytokine gene expression patterns were observed in distinct anatomic locations with a rapid and persistent inflammatory response in the gut that is consistent with the gut being the major site of early CD4 T-cell depletion in SIV infection.
Four-Dimensional Visualization of the Simultaneous Activity of Alternative Adeno-Associated Virus Replication Origins
Authors: Glauser Daniel L. , Saydam Okay , Balsiger N. Alexander , Heid Irma , Linden R. Michael , Ackermann Mathias , Fraefel Cornel
Published: September 2005

The adeno-associated virus (AAV) inverted terminal repeats (ITRs) contain the AAV Rep protein-binding site (RBS) and the terminal resolution site (TRS), which together act as a minimal origin of DNA replication. The AAV p5 promoter also contains an RBS, which is involved in Rep-mediated regulation of promoter activity, as well as a functional TRS, and origin activity of these signals has in fact been demonstrated previously in the presence of adenovirus helper functions. Here, we show that in the presence of herpes simplex virus type 1 (HSV-1) and AAV Rep protein, p5 promoter-bearing plasmids are efficiently amplified to form large head-to-tail concatemers, which are readily packaged in HSV-1 virions if an HSV-1 DNA-packaging/cleavage signal is provided in
cis
. We also demonstrate simultaneous and independent replication from the two alternative AAV replication origins, p5 and ITR, on the single-cell level using multicolor-fluorescence live imaging, a finding which raises the possibility that both origins may contribute to the AAV life cycle. Furthermore, we assess the differential affinities of Rep for the two different replication origins, p5 and ITR, both in vitro and in live cells and identify this as a potential mechanism to control the replicative and promoter activities of p5.
Structural Peptides of a Nonenveloped Virus Are Involved in Assembly and Membrane Translocation
Authors: Chevalier Christophe , Galloux Marie , Pous Joan , Henry Céline , Denis Jérôme , Da Costa Bruno , Navaza Jorge , Lepault Jean , Delmas Bernard
Published: September 2005

The capsid of infectious bursal disease virus (IBDV), a nonenveloped virus of the family
Birnaviridae
, has a T=13l icosahedral shell constituted by a single protein, VP2, and several disordered peptides, all derived from the precursor pVP2. In this study, we show that two of the peptides, pep11 and pep46, control virus assembly and cell entry. Deletion of pep11 or even simple substitution of most of its residues blocks the capsid morphogenesis. Removal of pep46 also prevents capsid assembly but leads to the formation of subviral particles formed by unprocessed VP2 species. Fitting with the VP2 atomic model into three-dimensional reconstructions of these particles demonstrates that the presence of uncleaved pep46 causes a steric hindrance at the vertices, blocking fivefold axis formation. Mutagenesis of the pVP2 maturation sites confirms that C terminus processing is necessary for VP2 to acquire the correct icosahedral architecture. All peptides present on virions are accessible to proteases or biochemical labeling. One of them, pep46, is shown to induce large structural rearrangements in liposomes and to destabilize target membranes, demonstrating its implication in cell entry.
CD8
+
Lymphocytes Do Not Mediate Protection against Acute Superinfection 20 Days after Vaccination with a Live Attenuated Simian Immunodeficiency Virus
Authors: Stebbings Richard , Berry Neil , Waldmann Herman , Bird Pru , Hale Geoff , Stott Jim , North David , Hull Robin , Hall Joanna , Lines Jenny , Brown Stuart , D'Arcy Nikki , Davis Leanne , Elsley William , Edwards Cherry , Ferguson Deborah , Allen Jane , Almond Neil
Published: September 2005

In order to test the hypothesis that CD8
+
cytotoxic T lymphocytes mediate protection against acute superinfection, we depleted >99% of CD8
+
lymphocytes in live attenuated simian immunodeficiency virus macC8 (SIVmacC8) vaccinees from the onset of vaccination, maintained that depletion for 20 days, and then challenged with pathogenic, wild-type SIVmacJ5. Vaccinees received 5 mg per kg of humanized anti-CD8 monoclonal antibody (MAb) 1 h before inoculation, followed by the same dose again on days 3, 7, 10, 13, and 17. On day 13, peripheral CD8
+
T lymphocytes were >99% depleted in three out of four anti-CD8 MAb-treated vaccinees. At this time attenuated SIVmacC8 viral RNA loads in anti-CD8 MAb-treated vaccinees were significantly higher than control vaccinees treated contemporaneously with nonspecific human immunoglobulin. Lymphoid tissue CD8
+
T lymphocyte depletion was >99% in three out of four anti-CD8 MAb-treated vaccinees on the day of wild-type SIVmacJ5 challenge. All four control vaccinees and three out of four anti-CD8 MAb-treated vaccinees were protected against detectable superinfection with wild-type SIVmacJ5. Although superinfection with wild-type SIVmacJ5 was detected at postmortem in a single anti-CD8 MAb-treated vaccinee, this did not correlate with the degree of preceding CD8
+
T lymphocyte depletion. Clearance of attenuated SIVmacC8 viremia coincided with recovery of normal CD8
+
T lymphocyte counts between days 48 and 76. These results support the view that cytotoxic T lymphocytes are important for host-mediated control of SIV primary viremia but do not indicate a central role in protection against acute superinfection conferred by inoculation with live attenuated SIV.
Epstein-Barr Virus-Encoded Poly(A)
−
RNA Confers Resistance to Apoptosis Mediated through Fas by Blocking the PKR Pathway in Human Epithelial Intestine 407 Cells
Authors: Nanbo Asuka , Yoshiyama Hironori , Takada Kenzo
Published: September 2005

Our recent findings demonstrated that the Epstein-Barr virus-encoding small nonpolyadenylated RNA (EBER) confers resistance to various apoptotic stimuli and contributes to the maintenance of malignant phenotypes in Burkitt's lymphoma. In this study we investigated the role of EBER in the human epithelial Intestine 407 cell line, which is known to be susceptible to Fas (Apo1/CD95)-mediated apoptosis. Fas, a member of the tumor necrosis factor receptor family, transduces extracellular signals to the apoptotic cellular machinery, leading to cell death. Transfection of the EBER gene into Intestine 407 cells significantly protected the cells from Fas-mediated apoptosis, whereas EBER-negative cell lines underwent apoptosis after Fas treatment. EBER bound double-stranded RNA-dependent protein kinase R (PKR), an interferon-inducible serine/threonine kinase, and abrogated its kinase activity. Moreover, expression of the catalytically inactive dominant-negative PKR provided resistance to Fas-induced apoptosis. Expression of EBER or dominant-negative PKR also inhibited the cleavage of poly(ADP-ribose) polymerase, a mediator of the cellular response to DNA damage, downstream of the Fas-mediated apoptotic pathway. These results in combination indicate that EBER confers resistance to Fas-mediated apoptosis by blocking PKR activity in Intestine 407 cells, consistent with the idea that EBER contributes to the maintenance of epithelioid malignancies.
V3 Loop-Determined Coreceptor Preference Dictates the Dynamics of CD4+-T-Cell Loss in Simian-Human Immunodeficiency Virus-Infected Macaques
Authors: Ho Siu-hong , Shek Lili , Gettie Agegnehu , Blanchard James , Cheng-Mayer Cecilia
Published: September 2005

We used experimental infection of rhesus macaques with envelope gp120 V3 loop isogenic simian-human immunodeficiency virus (SHIV) molecular clones to more clearly define the impact of human immunodeficiency virus type 1 coreceptor usage in target cell selectivity and the rates of CD4+-T-cell depletion. Functional assays demonstrate that substitution of the V3 loop of the pathogenic CXCR4-tropic (X4) SHIVSF33A2molecular clone with the corresponding sequences from the CCR5-tropic (R5) SHIVSF162P3isolate resulted in a switch of coreceptor usage from CXCR4 to CCR5. The resultant R5 clone, designated SHIVSF33A2(V3), is replication competent in vivo, infecting two of two macaques by intravenous inoculation with peak viremia that is comparable to that seen in monkeys infected with X4-SHIVSF33A2. But while primary infection with the X4 clone was accompanied by rapid and significant loss of peripheral and secondary lymphoid CD4+T lymphocytes, infection with R5-SHIVSF33A2(V3)led to only a modest and transient loss. However, substantial depletion of intestinal CD4+T cells was observed in R5-SHIVSF33A2(V3)-infected macaques. Moreover, naïve T cells that expressed high levels of CXCR4 were rapidly depleted in X4-SHIVSF33A2-infected macaques, whereas R5-SHIVSF33A2(V3)infection mainly affected memory T cells that expressed CCR5. These findings in a unique isogenic system illustrate that coreceptor usage is the principal determinant of tissue and target cell specificity of the virus in vivo and dictates the dynamics of CD4+-T-cell depletion during SHIV infection.
Impact of the Placental Cytokine-Chemokine Balance on Regulation of Cell-Cell Contact-Induced Human Immunodeficiency Virus Type 1 Translocation across a Trophoblastic Barrier In Vitro
Authors: Derrien Muriel , Faye Albert , Dolcini Guillermina , Chaouat Gérard , Barré-Sinoussi Françoise , Menu Elisabeth
Published: September 2005

Cells constituting the placental barrier secrete soluble factors that may participate in controlling human immunodeficiency virus type 1 (HIV-1) transmission from the mother to the fetus. In this study, we asked whether placental soluble factors (PSF) could limit cell-cell contact inducing HIV-1 production that occurs after inoculation of HIV-1-infected peripheral blood mononuclear cells (HIV-1+PBMCs) onto trophoblast-derived BeWo cells grown as tight and polarized barriers in a two-chamber system. The activity of recombinant chemokines and cytokines expressed by placental tissue and of factors secreted by either early or term placentae of HIV-1-negative women, was analyzed. We identified chemokines (RANTES and MIP-1β) and cytokines (tumor necrosis factor alpha and interleukin-8) that decreased and increased, respectively, viral production in trophoblast barrier cells inoculated with HIV-1+PBMCs. Unexpectedly, factors secreted by either early or term placentae of HIV-1-negative women enhanced viral production. Nevertheless, the same PSF did not favor infection of trophoblastic barriers with cell-free HIV-1 and strongly reduced viral production in PBMCs infected with cell-free HIV-1. Moreover, PSF contained chemokines (RANTES and MIP-1β) and a cytokine, leukemia inhibitory factor, exhibiting a strong anti-HIV-1 activity in our model of cell-to-cell infection. Together these data suggested that at the maternal interface the global activity of PSF is related to the synergistic action of several soluble factors with a balance in favor of an enhancing activity on the passage of viruses across the trophoblast barrier. This could explain the presence of viral sequences in trophoblasts in all placentae of HIV-1-infected women.
Replication of Minute Virus of Mice DNA Is Critically Dependent on Accumulated Levels of NS2
Authors: Choi Eun-Young , Newman Ann E. , Burger Lisa , Pintel David
Published: September 2005

Following transfection of murine fibroblasts, the lymphotropic strain of minute virus of mice (MVMi) does not efficiently produce progeny single-strand DNA (ssDNA). However, changing a single nucleotide in the MVMi 3′ splice site to that found in the fibrotropic strain MVMp enabled full DNA replication and production of ssDNA. This change enhanced excision of the large intron and the production of NS2, likely by improving interaction, in fibroblasts with the branch point-binding U2 snRNA. One function of NS2 involves interaction with the nuclear export protein Crm1. The defect in production of MVMi ssDNA in fibroblasts can also be overcome by introducing a mutation in MVMi NS2 that enhances its interaction with Crm1. Although MVMi contains a 3′ splice site that performs poorly in fibroblasts, MVMi generated at least as much R2 and NS2 in murine lymphocytes as did MVMp in fibroblasts. Therefore, it appears that MVMp has acquired a mutation that improves the excision of the large intron, as it adapted to fibroblasts to accommodate the need for NS2 for replication in these cells, and that the ratio of NS1 to NS2 may play a larger role in the host range of MVM than previously appreciated.
Identification of Complement Regulatory Domains in Vaccinia Virus Complement Control Protein
Authors: Mullick Jayati , Bernet John , Panse Yogesh , Hallihosur Sharanabasava , Singh Akhilesh K. , Sahu Arvind
Published: September 2005

Vaccinia virus encodes a homolog of the human complement regulators named vaccinia virus complement control protein (VCP). It is composed of four contiguous complement control protein (CCP) domains. Previously, VCP has been shown to bind to C3b and C4b and to inactivate the classical and alternative pathway C3 convertases by accelerating the decay of the classical pathway C3 convertase and (to a limited extent) the alternative pathway C3 convertase, as well as by supporting the factor I-mediated inactivation of C3b and C4b (the subunits of C3 convertases). In this study, we have mapped the CCP domains of VCP important for its cofactor activities, decay-accelerating activities, and binding to the target proteins by utilizing a series of deletion mutants. Our data indicate the following. (i) CCPs 1 to 3 are essential for cofactor activity for C3b and C4b; however, CCP 4 also contributes to the optimal activity. (ii) CCPs 1 to 2 are enough to mediate the classical pathway decay-accelerating activity but show very minimal activity, and all the four CCPs are necessary for its efficient activity. (iii) CCPs 2 to 4 mediate the alternative pathway decay-accelerating activity. (iv) CCPs 1 to 3 are required for binding to C3b and C4b, but the presence of CCP 4 enhances the affinity for both the target proteins. These results together demonstrate that the entire length of the protein is required for VCP's various functional activities and suggests why the four-domain structure of viral CCP is conserved in poxviruses.
The Amino Terminus of Epstein-Barr Virus Glycoprotein gH Is Important for Fusion with Epithelial and B Cells
Authors: Omerović Jasmina , Lev Lori , Longnecker Richard
Published: September 2005

Epstein-Barr virus (EBV) infects B lymphocytes and epithelial cells. While the glycoproteins required for entry into these two cell types differ, the gH/gL glycoprotein complex is essential for entry into both epithelial and B cells. Analysis of gH protein sequences from three gammaherpesviruses (EBV, marmoset, and rhesus) revealed a potential coiled-coil domain in the N terminus. Four leucines located in this region in EBV gH were replaced by alanines by site-directed mutagenesis and analyzed for cell-cell membrane fusion with B cells and epithelial cells. Reduction in fusion activity was observed for mutants containing L65A and/or L69A mutations, while substitutions in L55 and L74 enhanced the fusion activity of the mutant gH/gL complexes with both cell types. All of the mutants displayed levels of cell surface expression similar to those of wild-type gH and interacted with gL and gp42. The observation that a conservative mutation of leucine to alanine in the N terminus of EBV gH results in fusion-defective mutant gH/gL complexes is striking and points to an important role for this region in EBV-mediated membrane fusion with B lymphocytes and epithelial cells.
Stem-Loop IV in the 5′ Untranslated Region Is a
cis
-Acting Element in Bovine Coronavirus Defective Interfering RNA Replication
Authors: Raman Sharmila , Brian David A.
Published: September 2005

The 210-nucleotide (nt) 5′ untranslated region (UTR) in the positive-strand bovine coronavirus (BCoV) genome is predicted to contain four higher-order structures identified as stem-loops I to IV, which may function as
cis
-acting elements in genomic RNA replication. Here, we describe evidence that stem-loop IV, a bulged stem-loop mapping at nt 186 through 215, (i) is phylogenetically conserved among group 2 coronaviruses and may have a homolog in groups 1 and 3, (ii) exists as a higher-order structure on the basis of enzyme probing, (iii) is required as a higher-order element for replication of a BCoV defective interfering (DI) RNA in the positive but not the negative strand, and (iv) as a higher-order structure in wild-type (wt) and mutant molecules that replicate, specifically binds six cellular proteins in the molecular mass range of 25 to 58 kDa as determined by electrophoretic mobility shift and UV cross-linking assays; binding to viral proteins was not detected. Interestingly, the predicted stem-loop IV homolog in the severe acute respiratory syndrome (SARS) coronavirus appears to be group 1-like in that it is in part duplicated with a group 1-like conserved loop sequence and is not group 2-like, as would be expected by the SARS coronavirus group 2-like 3′ UTR structure. These results together indicate that stem-loop IV in the BCoV 5′ UTR is a
cis
-acting element for DI RNA replication and that it might function through interactions with cellular proteins. It is postulated that stem-loop IV functions similarly in the virus genome.
Impact of Human Immunodeficiency Virus Type 1 gp41 Amino Acid Substitutions Selected during Enfuvirtide Treatment on gp41 Binding and Antiviral Potency of Enfuvirtide In Vitro
Authors: Mink M. , Mosier S. M. , Janumpalli S. , Davison D. , Jin L. , Melby T. , Sista P. , Erickson J. , Lambert D. , Stanfield-Oakley S. A. , Salgo M. , Cammack N. , Matthews T. , Greenberg M. L.
Published: September 2005

Enfuvirtide (ENF), a novel human immunodeficiency virus type 1 (HIV-1) fusion inhibitor, has potent antiviral activity against HIV-1 both in vitro and in vivo. Resistance to ENF observed after in vitro passaging was associated with changes in a three-amino-acid (aa) motif, GIV, at positions 36 to 38 of gp41. Patients with ongoing viral replication while receiving ENF during clinical trials acquired substitutions within gp41 aa 36 to 45 in the first heptad repeat (HR-1) of gp41 in both population-based plasma virus sequences and proviral DNA sequences from isolates showing reduced susceptibilities to ENF. To investigate their impact on ENF susceptibility, substitutions were introduced into a modified pNL4-3 strain by site-directed mutagenesis, and the susceptibilities of mutant viruses and patient-derived isolates to ENF were tested. In general, susceptibility decreases for single substitutions were lower than those for double substitutions, and the levels of ENF resistance seen for clinical isolates were higher than those observed for the site-directed mutant viruses. The mechanism of ENF resistance was explored for a subset of the substitutions by expressing them in the context of a maltose binding protein chimera containing a portion of the gp41 ectodomain and measuring their binding affinity to fluorescein-labeled ENF. Changes in binding affinity for the mutant gp41 fusion proteins correlated with the ENF susceptibilities of viruses containing the same substitutions. The combined results support the key role of gp41 aa 36 to 45 in the development of resistance to ENF and illustrate that additional envelope regions contribute to the ENF susceptibility of fusion inhibitor-naïve viruses and resistance to ENF.
N-Terminal Gag Domain Required for Foamy Virus Particle Assembly and Export
Authors: Cartellieri Marc , Herchenröder Ottmar , Rudolph Wolfram , Heinkelein Martin , Lindemann Dirk , Zentgraf Hanswalter , Rethwilm Axel
Published: September 2005

Among the
Retroviridae
, foamy viruses (FVs) exhibit an unusual way of particle assembly and a highly specific incorporation of envelope protein into progeny virions. We have analyzed deletions and point mutants of the prototypic FV
gag
gene for capsid assembly and egress, envelope protein incorporation, infectivity, and ultrastructure. Deletions introduced at the 3′ end of
gag
revealed the first 297 amino acids (aa) to be sufficient for specific Env incorporation and export of particulate material. Deletions introduced at the 5′ end showed the region between aa 6 and 200 to be dispensable for virus capsid assembly but required for the incorporation of Env and particle egress. Point mutations were introduced in the 5′ region of
gag
to target residues conserved among FVs from different species. Alanine substitutions of residues in a region between aa 40 and 60 resulted in severe alterations in particle morphology. Furthermore, at position 50, this region harbors the conserved arginine that is presumably at the center of a signal sequence directing FV Gag proteins to a cytoplasmic assembly site.
Comprehensive Bioinformatic Analysis of the Specificity of Human Immunodeficiency Virus Type 1 Protease
Authors: You Liwen , Garwicz Daniel , Rögnvaldsson Thorsteinn
Published: September 2005

Rapidly developing viral resistance to licensed human immunodeficiency virus type 1 (HIV-1) protease inhibitors is an increasing problem in the treatment of HIV-infected individuals and AIDS patients. A rational design of more effective protease inhibitors and discovery of potential biological substrates for the HIV-1 protease require accurate models for protease cleavage specificity. In this study, several popular bioinformatic machine learning methods, including support vector machines and artificial neural networks, were used to analyze the specificity of the HIV-1 protease. A new, extensive data set (746 peptides that have been experimentally tested for cleavage by the HIV-1 protease) was compiled, and the data were used to construct different classifiers that predicted whether the protease would cleave a given peptide substrate or not. The best predictor was a nonlinear predictor using two physicochemical parameters (hydrophobicity, or alternatively polarity, and size) for the amino acids, indicating that these properties are the key features recognized by the HIV-1 protease. The present in silico study provides new and important insights into the workings of the HIV-1 protease at the molecular level, supporting the recent hypothesis that the protease primarily recognizes a conformation rather than a specific amino acid sequence. Furthermore, we demonstrate that the presence of 1 to 2 lysine residues near the cleavage site of octameric peptide substrates seems to prevent cleavage efficiently, suggesting that this positively charged amino acid plays an important role in hindering the activity of the HIV-1 protease.
Envelope Protein Requirements for the Assembly of Infectious Virions of Porcine Reproductive and Respiratory Syndrome Virus
Authors: Wissink E. H. J. , Kroese M. V. , van Wijk H. A. R. , Rijsewijk F. A. M. , Meulenberg J. J. M. , Rottier P. J. M.
Published: September 2005

Virions of porcine reproductive and respiratory syndrome virus (PRRSV) contain six membrane proteins: the major proteins GP
5
and M and the minor proteins GP
2a
, E, GP
3
, and GP
4
. Here, we studied the envelope protein requirements for PRRSV particle formation and infectivity using full-length cDNA clones in which the genes encoding the membrane proteins were disrupted by site-directed mutagenesis. By transfection of RNAs transcribed from these cDNAs into BHK-21 cells and analysis of the culture medium using ultracentrifugation, radioimmunoprecipitation, and real-time reverse transcription-PCR, we observed that the production of viral particles is dependent on both major envelope proteins; no particles were released when either the GP
5
or the M protein was absent. In contrast, particle production was not dependent on the minor envelope proteins. Remarkably, in the absence of any one of the latter proteins, the incorporation of all other minor envelope proteins was affected, indicating that these proteins interact with each other and are assembled into virions as a multimeric complex. Independent evidence for such complexes was obtained by coexpression of the minor envelope proteins in BHK-21 cells using a Semliki Forest virus expression system. By analyzing the maturation of their N-linked oligosaccharides, we found that the glycoproteins were each retained in the endoplasmic reticulum unless expressed together, in which case they were collectively transported through the Golgi complex to the plasma membrane and were even detected in the extracellular medium. As the PRRSV particles lacking the minor envelope proteins are not infectious, we hypothesize that the virion surface structures formed by these proteins function in viral entry by mediating receptor binding and/or virus-cell fusion.
Formation of Vesicular Stomatitis Virus Pseudotypes Bearing Surface Proteins of Hepatitis B Virus
Authors: Saha Manujendra N. , Tanaka Atsushi , Jinno-Oue Atsushi , Shimizu Nobuaki , Tamura Kazushi , Shinagawa Masahiko , Chiba Joe , Hoshino Hiroo
Published: September 2005

It has been difficult to propagate and titrate hepatitis B virus (HBV) in tissue culture. We examined whether vesicular stomatitis virus (VSV) pseudotypes bearing HBV surface (HBs) proteins infectious for human cell lines could be prepared. For this, expression plasmids for three surface proteins, L, M, and S, of HBV were made. 293T cells were then transfected with these plasmids either individually or in different combinations. 293T cells expressing HBs proteins were infected with VSVΔG*-G, a recombinant VSV expressing green fluorescent protein (GFP), to make VSV pseudotypes. Culture supernatants together with cells were harvested and sonicated for a short time. The infectivities of freshly harvested supernatants were determined by quantifying the number of cells expressing GFP after neutralization with anti-VSV serum and mouse monoclonal antibodies (MAbs) against HBs protein. Among 14 cell lines tested for susceptibility to HBV pseudotype samples, HepG2, JHH-7, and 293T cells were judged to be the most susceptible. Namely, the infectious units (IU) of the culture supernatant samples neutralized with anti-VSV in the absence and presence of anti-HBs S MAbs and titrated on HepG2 cells ranged from 1,000 to 4,000 IU/ml and 200 to 400 IU/ml, respectively, suggesting the presence of VSVΔG*(HBV) pseudotypes. This infectivity was inhibited by treatment with lactoferrin or dextran sulfate. Pretreatment of the cells with trypsin or tunicamycin inhibited plating of the pseudotype samples. The HBV pseudotypes can be used to analyze early steps of HBV infection, including the entry mechanism of HBV.