bluuebunny/crossref_metadata_2025 huggingface dataset:
A System Identification Technique Using Bias Current Perturbation for Determining the Effective Rotor Origin of Active Magnetic Bearings
Authors: Prins Robert J. , Kasarda Mary E. F. , Bates Prins Samantha C.
Published: May 2007

Locating the effective rotor origin of an active magnetic bearing (AMB) is an important step toward accurate characterization of the bearing air gaps for field tuning, performance analyses, and some shaft force measurement techniques. Specifically, application of current-based force measurement techniques to AMBs requires accurate modeling of air gaps in order to predict dynamic forces with accuracy. This paper discusses the application of a system identification technique that employs perturbation of the bias current and allows the user to establish the location of the effective rotor origin, an important step in characterizing the actual bearing gap. The technique analyzes the AMB system’s response to the perturbation of bias currents in conjunction with a magnetic circuit model to infer the center position. The effective rotor origin identification technique developed here does not require additional hardware and is suitable for use in the general class of AMBs in field applications. For our purposes, the effective rotor origin of an electro-magnet biased magnetic bearing is defined as the unique rotor location for which a magnetic circuit based force model of the bearing is satisfied for zero position offset of the rotor along each control axis. Note that the effective rotor origin referred to here is the radial origin.
Simulation of Squeeze-Film Damping of Microplates Actuated by Large Electrostatic Load
Authors: Younis Mohammad I. , Nayfeh Ali H.
Published: May 2007

We present a new method for simulating squeeze-film damping of microplates actuated by large electrostatic loads. The method enables the prediction of the quality factors of microplates under a limited range of gas pressures and applied electrostatic loads up to the pull-in instability. The method utilizes the nonlinear Euler-Bernoulli beam equation, the von Kármán plate equations, and the compressible Reynolds equation. The static deflection of the microplate is calculated using the beam model. Analytical expressions are derived for the pressure distribution in terms of the plate mode shapes around the deflected position using perturbation techniques. The static deflection and the analytical expressions are substituted into the plate equations, which are solved using a finite-element method. Several results are presented showing the effect of the pressure and the electrostatic force on the structural mode shapes, the pressure distributions, the natural frequencies, and the quality factors.
A Stochastic Model for the Random Impact Series Method in Modal Testing
Authors: Zhu W. D. , Zheng N. A. , Wong C. N.
Published: May 2007

A novel stochastic model is developed to describe a random series of impacts in modal testing that can be performed manually or by using a specially designed random impact device. The number of the force pulses, representing the impacts, is modeled as a Poisson process with stationary increments. The force pulses are assumed to have an arbitrary, deterministic shape function, and random amplitudes and arrival times. The force signal in a finite time interval is shown to consist of a wide-sense stationary part and two nonstationary parts. The expectation of the force spectrum is obtained from two approaches. The expectations of the average power densities associated with the entire force signal and the stationary part of it are determined and compared. The analytical expressions are validated by numerical solutions for two different types of shape functions. A numerical example is given to illustrate the advantages of the random impact series over a single impact and an impact series with deterministic arrival times of the pulses in estimating the frequency response function. The model developed can be used to describe a random series of pulses in other applications.
The Role of Damping and Definition of the Robust Damping Factor for a Self-Exciting Mechanism With Constant Friction
Authors: Sinou J-J. , Fritz G. , Jézéquel L.
Published: May 2007

This paper presents a linear two-degree-of-freedom model in order to analyze friction-induced instabilities that are governed by modal interaction. The role of structural damping on flutter instability is undertaken, and the effects of the structural damping ratio between the stable and unstable modes are investigated in order to clarify and to explain the mechanical process of flutter instability. In certain conditions, it is demonstrated that the merging scenario and the unstable mode may change due to this structural damping ratio. Discussions not only demontrate the role of strutural damping and the associated mechanical process but also define the robust damping factor in order to avoid design errors and to reduce flutter instability.
Dynamics of a Rotating Shaft Subject to a Three-Directional Moving Load
Authors: Ouyang Huajiang , Wang Minjie
Published: May 2007

This paper presents a dynamic model for the vibration of a rotating Rayleigh beam subjected to a three-directional load acting on the surface of the beam and moving in the axial direction. The model takes into account the axial movement of the axial force component. More significantly, the bending moment produced by this force component is included in the model. Lagrange’s equations of motion for the modal coordinates are derived based on the assumed mode method and then solved by a fourth-order Runge-Kutta algorithm. It is found that the bending moment induced by the axial force component has a significant influence on the dynamic response of the shaft, even when the axial force and speed are low and, hence, must be considered in such problems as turning operations.
Structural-Acoustic Optimization of Sandwich Panels
Authors: Franco Francesco , Cunefare Kenneth A. , Ruzzene Massimo
Published: May 2007

Sandwich panels comprising face sheets enclosing a core are increasingly common structural elements in a variety of applications, including aircraft fuselages, flight surfaces, vehicle panels, lightweight enclosures, and bulkheads. This paper presents the optimization of various innovative sandwich configurations for minimization of their structural-acoustic response. Laminated face sheets and core geometries comprising honeycomb and trusslike structures are considered. The design flexibility associated with the class of considered composite structures and with truss-core configurations provides the opportunity of tailoring the structure to the load and dynamic response requirements of a particular application. The results demonstrate how the proper selection of selected key parameters can achieve effective reduction of the radiated sound power and how the identified optimal configurations can achieve noise reduction over different frequency ranges and for various source configurations.
Vibratory Characteristics of Axially-Loaded Timoshenko Beams With Arbitrary Number of Cracks
Authors: Aydin Kamil
Published: May 2007

A simple and efficient analytical approach is presented to determine the vibrational frequencies and mode shape functions of axially-loaded Timoshenko beams with an arbitrary number of cracks. The local compliance induced by a crack is described by a massless rotational spring model. A set of boundary conditions are used as initial parameters to define the mode shape of the segment of the beam before the first crack. Using this, the remaining set of boundary conditions and recurrence formula developed in the study, the mode shape function of vibration of the beam containing multiple cracks can be easily determined. Four different classical boundary conditions (pinned-pinned, clamped-pinned, clamped-free, and clamped-clamped) are considered. Elastically-restrained support condition with concentrated masses is also considered. Three crack depths and five axial force levels representing the conditions under service loads are used. A parametric study is carried out for each case of support conditions to investigate the effect of crack and axial load on the vibrational properties of cracked Timoshenko beams. The influence of crack on the buckling load of the beam is also studied statically. Part of the results obtained is checked against the published values. The study concludes that the crack location, crack severity, and axial force level strongly affect the eigenfrequencies.
Lateral Vibration of Two Axially Translating Beams Interconnected by a Winkler Foundation
Authors: Gaith Mohamed , Müftü Sinan
Published: May 2007

Transverse vibration of two axially moving beams connected by a Winkler elastic foundation is analyzed analytically. The two beams are tensioned, translating axially with a common constant velocity, simply supported at their ends, and of different materials and geometry. The natural frequencies and associated mode shapes are obtained. The natural frequencies of the system are composed of two infinite sets describing in-phase and out-of-phase vibrations. In case the beams are identical, these modes become synchronous and asynchronous, respectively. Divergence instability occurs at a critical velocity and a critical tension; and, divergence and flutter instabilities coexist at postcritical speeds, and divergence instability takes place precritical tensions. The effects of the mass, flexural rigidity, and axial tension ratios of the two beams are presented.
Childhood Origins of Adult Resistance to Science
Authors: Bloom Paul , Weisberg Deena Skolnick
Published: May 2007

Resistance to certain scientific ideas derives in large part from assumptions and biases that can be demonstrated experimentally in young children and that may persist into adulthood. In particular, both adults and children resist acquiring scientific information that clashes with common-sense intuitions about the physical and psychological domains. Additionally, when learning information from other people, both adults and children are sensitive to the trustworthiness of the source of that information. Resistance to science, then, is particularly exaggerated in societies where nonscientific ideologies have the advantages of being both grounded in common sense and transmitted by trustworthy sources.
Mesoscale Eddies Drive Increased Silica Export in the Subtropical Pacific Ocean
Authors: Benitez-Nelson Claudia R. , Bidigare Robert R. , Dickey Tommy D. , Landry Michael R. , Leonard Carrie L. , Brown Susan L. , Nencioli Francesco , Rii Yoshimi M. , Maiti Kanchan , Becker Jamie W. , Bibby Thomas S. , Black Wil , Cai Wei-Jun , Carlson Craig A. , Chen Feizhou , Kuwahara Victor S. , Mahaffey Claire , McAndrew Patricia M. , Quay Paul D. , Rappé Michael S. , Selph Karen E. , Simmons Melinda P. , Yang Eun Jin
Published: May 2007

Mesoscale eddies may play a critical role in ocean biogeochemistry by increasing nutrient supply, primary production, and efficiency of the biological pump, that is, the ratio of carbon export to primary production in otherwise nutrient-deficient waters. We examined a diatom bloom within a cold-core cyclonic eddy off Hawai`i. Eddy primary production, community biomass, and size composition were markedly enhanced but had little effect on the carbon export ratio. Instead, the system functioned as a selective silica pump. Strong trophic coupling and inefficient organic export may be general characteristics of community perturbation responses in the warm waters of the Pacific Ocean.
The New Synthesis in Moral Psychology
Authors: Haidt Jonathan
Published: May 2007

People are selfish, yet morally motivated. Morality is universal, yet culturally variable. Such apparent contradictions are dissolving as research from many disciplines converges on a few shared principles, including the importance of moral intuitions, the socially functional (rather than truth-seeking) nature of moral thinking, and the coevolution of moral minds with cultural practices and institutions that create diverse moral communities. I propose a fourth principle to guide future research: Morality is about more than harm and fairness. More research is needed on the collective and religious parts of the moral domain, such as loyalty, authority, and spiritual purity.
Wilms Tumor Suppressor WTX Negatively Regulates WNT/ß-Catenin Signaling
Authors: Major Michael B. , Camp Nathan D. , Berndt Jason D. , Yi XianHua , Goldenberg Seth J. , Hubbert Charlotte , Biechele Travis L. , Gingras Anne-Claude , Zheng Ning , MacCoss Michael J. , Angers Stephane , Moon Randall T.
Published: May 2007

Aberrant WNT signal transduction is involved in many diseases. In colorectal cancer and melanoma, mutational disruption of proteins involved in the degradation of β-catenin, the key effector of the WNT signaling pathway, results in stabilization of β-catenin and, in turn, activation of transcription. We have used tandem-affinity protein purification and mass spectrometry to define the protein interaction network of the β-catenin destruction complex. This assay revealed that WTX, a protein encoded by a gene mutated in Wilms tumors, forms a complex with β-catenin, AXIN1, β-TrCP2 (β-transducin repeat–containing protein 2), and APC (adenomatous polyposis coli). Functional analyses in cultured cells,
Xenopus
, and zebrafish demonstrate that WTX promotes β-catenin ubiquitination and degradation, which antagonize WNT/β-catenin signaling. These data provide a possible mechanistic explanation for the tumor suppressor activity of WTX.
Opsonophagocytic Activity and Other Serological Indications ofBordetella pertussisInfection in Military Recruits in Norway
Authors: Aase Audun , Herstad Tove Karin , Merino Samuel , Brandsdal Kari Torkildsen , Berdal Bjørn Peter , Aleksandersen Erja M. , Aaberge Ingeborg S.
Published: May 2007

Bordetella pertussisis the causative agent of pertussis (whooping cough). Despite high vaccination coverage, pertussis remains a significant disease in many countries. Besides vaccination, transient carriage ofBordetellaspp. or other cross-reacting organisms adds to the immunity against pertussis. However, the various immunological mechanisms conferring protection remain largely unknown. In this study, paired serum samples from 464 healthy Norwegian military recruits were collected, the first at enrolment and the second about 8 months later. The prevalence of pertussis during military service was examined by comparing the paired serum samples for immunoglobulin G (IgG) antibodies against pertussis toxin (PT) by enzyme-linked immunosorbent assay (ELISA). Seventy-eight percent of the recruits had low levels of IgG antibodies against PT in both samples. Conversely, 8.4% of the recruits demonstrated high anti-PT IgG levels in the first sample, indicative of recent pertussis prior to enrolment. One recruit experienced seroconversion, indicating pertussis during service. A subset of 248 serum samples with low, medium, and high anti-PT IgG titers were analyzed by a different ELISA kit for IgG and IgA antibodies against PT and filamentous hemagglutinin (FHA) and for opsonophagocytic activity (OPA), for induction of C3b deposition products, and for IgG binding with liveB. pertussisas the antigen. We observed high correlations between OPA and IgG against live bacteria (r= 0.83), between OPA and IgG anti-FHA (r= 0.79), between OPA and anti-PT IgG (r= 0.68), and between OPA and C3b binding (r= 0.70) (P< 0.0001 for all). Anti-PT IgA did not correlate closely with the other assays.
Discrepancy between
Mycobacterium tuberculosis
-Specific Gamma Interferon Release Assays Using Short and Prolonged In Vitro Incubation
Authors: Leyten Eliane M. S. , Arend Sandra M. , Prins Corine , Cobelens Frank G. J. , Ottenhoff Tom H. M. , van Dissel Jaap T.
Published: May 2007

The sensitivities of various gamma interferon release assays (IGRAs) for the detection of past latent
Mycobacterium tuberculosis
infection are not known. In this study, we aimed to assess the effects of various IGRA formats and in vitro incubation periods on test outcome. The results of the tuberculin skin test (TST) were compared with those of the QuantiFERON-TB Gold in-tube (QFT-GIT) test, an overnight enzyme-linked immunospot assay (ELISPOT), and a 6-day lymphocyte stimulation test (LST) by using the same
M. tuberculosis
-specific peptides and samples from 27 TST-positive persons with a history of exposure to
M. tuberculosis
, 4 patients cured of tuberculosis (TB), and 9 TST-negative controls. Among the TST-positive persons, the LST was more frequently positive (92%;
P
< 0.01) than either the QFT-GIT test (33%) or ELISPOT (46%). While good agreement was observed between the QFT-GIT test and ELISPOT (κ = 0.71) and between TST and LST (κ = 0.78), the agreement between TST or LST, on the one hand, and the QFT-GIT test or ELISPOT, on the other, was poor. These data indicate that the QFT-GIT test and overnight ELISPOT are less sensitive for the detection of past latent TB than the 6-day LST. The observed discrepancies between these IGRAs are most likely related to differences in incubation periods. Whether TST-positive persons with positive LST results but negative QFT-GIT and ELISPOT results are at risk for the development of TB needs to be elucidated before short-incubation IGRAs can be used for the screening of individuals for latent TB before immunosuppressive treatment.
PCR-Restriction Fragment Length Polymorphism Analysis of
Campylobacter jejuni
Genes Involved in Lipooligosaccharide Biosynthesis Identifies Putative Molecular Markers for Guillain-Barré Syndrome
Authors: Godschalk Peggy C. R. , van Belkum Alex , van den Braak Nicole , van Netten Diana , Ang C. Wim , Jacobs Bart C. , Gilbert Michel , Endtz Hubert P.
Published: May 2007

Molecular mimicry of
Campylobacter jejuni
lipooligosaccharides (LOS) by gangliosides in peripheral nerve tissue probably triggers the Guillain-Barré syndrome due to the induction of cross-reactive antibodies. PCR-restriction fragment length polymorphism analysis of
C. jejuni
genes involved in the biosynthesis of LOS demonstrated that specific genes were associated with the expression of ganglioside mimics and the development of neuropathy.
Identification of Medically Important
Candida
and Non-
Candida
Yeast Species by an Oligonucleotide Array
Authors: Leaw Shiang Ning , Chang Hsien Chang , Barton Richard , Bouchara Jean-Philippe , Chang Tsung Chain
Published: May 2007

The incidence of yeast infections has increased in the recent decades, with
Candida albicans
still being the most common cause of infections. However, infections caused by less common yeasts have been widely reported in recent years. Based on the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 77 species of clinically relevant yeasts belonging to 16 genera. The ITS regions were amplified by PCR with a pair of fungus-specific primers, followed by hybridization of the digoxigenin-labeled PCR product to a panel of oligonucleotide probes immobilized on a nylon membrane for species identification. A collection of 452 yeast strains (419 target and 33 nontarget strains) was tested, and a sensitivity of 100% and a specificity of 97% were obtained by the array. The detection limit of the array was 10 pg of yeast genomic DNA per assay. In conclusion, yeast identification by the present method is highly reliable and can be used as an alternative to the conventional identification methods. The whole procedure can be finished within 24 h, starting from isolated colonies.
Increased Detection of Respiratory Syncytial Virus, Influenza Viruses, Parainfluenza Viruses, and Adenoviruses with Real-Time PCR in Samples from Patients with Respiratory Symptoms
Authors: van de Pol Alma C. , van Loon Anton M. , Wolfs Tom F. W. , Jansen Nicolaas J. G. , Nijhuis Monique , Breteler Els Klein , Schuurman Rob , Rossen John W. A.
Published: May 2007

Respiratory samples (
n
= 267) from hospitalized patients with respiratory symptoms were tested by real-time PCR, viral culture, and direct immunofluorescence for respiratory syncytial virus, influenza virus, parainfluenza viruses, and adenoviruses. Compared with conventional diagnostic tests, real-time PCR increased the diagnostic yields for these viruses from 24% to 43% and from 3.5% to 36% for children and adults, respectively.
Rapid Identification of Staphylococci Isolated in Clinical Microbiology Laboratories by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Carbonnelle Etienne , Beretti Jean-Luc , Cottyn Stéphanie , Quesne Gilles , Berche Patrick , Nassif Xavier , Ferroni Agnès
Published: May 2007

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) of intact bacteria yields a reproducible spectrum depending upon growth conditions, strain, or species. Using whole viable bacteria we describe here the application of MALDI-TOF-MS to the identification of coagulase-negative staphylococci (CoNS). Our aim was, once a bacterium has been recognized as
Micrococcaceae
, to identify peaks in the spectrum that can be used to identify the species or subspecies. MALDI-TOF-MS was performed using bacteria obtained from one isolated colony. One reference strain for each of the 23 clinically relevant species or subspecies of
Micrococcaceae
was selected. For each reference strain, the MALDI-TOF-MS profile of 10 colonies obtained from 10 different passages was analyzed. For each strain, only peaks that were conserved in the spectra of all 10 isolated colonies and with a relative intensity above 0.1 were retained, thus leading to a set of 3 to 14 selected peaks per strain. The MALDI-TOF-MS profile of 196 tested strains was then compared with that of the set of selected peaks of each of the 23 reference strains. In all cases the best hit was with the set of peaks of the reference strain belonging to the same species as that of the tested strain, thus demonstrating that the 23 sets of selected peaks can be used as a database for the rapid species identification of CoNS. Similar results were obtained using four different growth conditions. Extending this strategy to other groups of relevant pathogenic bacteria will allow rapid bacterial identification.
Fatal Relapse of a Purulent Pleurisy Caused by
Campylobacter fetus
subsp.
fetus
Authors: Decousser Jean-Winoc , Prouzet-Mauléon Valérie , Bartizel Christine , Gin Thomas , Colin Jean-Pierre , Fadel Nicolas , Holler C. , Pollet J. , Megraud Francis
Published: May 2007

Campylobacter fetus
is associated with invasive disease, while other
Campylobacter
species, such as
C. coli
and
C. jejuni
, are a common cause of bacterial diarrhea. Bacteremia has been well described, but pleurisy remains very uncommon. We report the recurrent isolation of a
C. fetus
subsp.
fetus
strain during two episodes of pleural effusion with a fatal outcome.
Hepatitis C Virus Induces Proteolytic Cleavage of Sterol Regulatory Element Binding Proteins and Stimulates Their Phosphorylation via Oxidative Stress
Authors: Waris Gulam , Felmlee Daniel Jeffery , Negro Francesco , Siddiqui Aleem
Published: May 2007

Hepatic steatosis is a common histological feature of chronic hepatitis C. Hepatitis C virus (HCV) gene expression has been shown to alter host cell cholesterol/lipid metabolism and thus induce hepatic steatosis. Since sterol regulatory element binding proteins (SREBPs) are major regulators of lipid metabolism, we sought to determine whether genotype 2a-based HCV infection induces the expression and posttranslational activation of SREBPs. HCV infection stimulates the expression of genes related to lipogenesis. HCV induces the proteolytic cleavage of SREBPs. HCV core and NS4b derived from genotype 3a are also individually capable of inducing the proteolytic processing of SREBPs. Further, we demonstrate that HCV stimulates the phosphorylation of SREBPs. Our studies show that HCV-induced oxidative stress and subsequent activation of the phosphatidylinositol 3-kinase (PI3-K)-Akt pathway and inactivation (phosphorylation) of PTEN (phosphatase and tensin homologue) mediate the transactivation of SREBPs. HCV-induced SREBP-1 and -2 activities were sensitive to antioxidant (pyrrolidine dithiocarbamate), Ca
2+
chelator 1,2-bis(aminophenoxy)ethane-
N
,
N
,
N
′,
N
′-tetraacetic acid-tetra(acetoxymethyl) ester (BAPTA-AM), and PI3-K inhibitor (LY294002). Collectively, these studies provide insight into the mechanisms of hepatic steatosis associated with HCV infection.
Coreceptor Tropism in Human Immunodeficiency Virus Type 1 Subtype D: High Prevalence of CXCR4 Tropism and Heterogeneous Composition of Viral Populations
Authors: Huang Wei , Eshleman Susan H. , Toma Jonathan , Fransen Signe , Stawiski Eric , Paxinos Ellen E. , Whitcomb Jeannette M. , Young Alicia M. , Donnell Deborah , Mmiro Francis , Musoke Philippa , Guay Laura A. , Jackson J. Brooks , Parkin Neil T. , Petropoulos Christos J.
Published: May 2007

In human immunodeficiency virus type 1 (HIV-1) subtype B, CXCR4 coreceptor use ranges from ∼20% in early infection to ∼50% in advanced disease. Coreceptor use by non-subtype B HIV is less well characterized. We studied coreceptor tropism of subtype A and D HIV-1 collected from 68 pregnant, antiretroviral drug-naive Ugandan women (HIVNET 012 trial). None of 33 subtype A or 10 A/D-recombinant viruses used the CXCR4 coreceptor. In contrast, nine (36%) of 25 subtype D viruses used both CXCR4 and CCR5 coreceptors. Clonal analyses of the nine subtype D samples with dual or mixed tropism revealed heterogeneous viral populations comprised of X4-, R5-, and dual-tropic HIV-1 variants. In five of the six samples with dual-tropic strains, V3 loop sequences of dual-tropic clones were identical to those of cocirculating R5-tropic clones, indicating the presence of CXCR4 tropism determinants outside of the V3 loop. These dual-tropic variants with R5-tropic-like V3 loops, which we designated “dual-R,” use CCR5 much more efficiently than CXCR4, in contrast to dual-tropic clones with X4-tropic-like V3 loops (“dual-X”). These observations have implications for pathogenesis and treatment of subtype D-infected individuals, for the association between V3 sequence and coreceptor tropism phenotype, and for understanding potential mechanisms of evolution from exclusive CCR5 use to efficient CXCR4 use by subtype D HIV-1.
Identification of Novel Rodent Herpesviruses, Including the First Gammaherpesvirus of
Mus musculus
Authors: Ehlers Bernhard , Küchler Judit , Yasmum Nezlisah , Dural Güzin , Voigt Sebastian , Schmidt-Chanasit Jonas , Jäkel Thomas , Matuschka Franz-Rainer , Richter Dania , Essbauer Sandra , Hughes David J. , Summers Candice , Bennett Malcolm , Stewart James P. , Ulrich Rainer G.
Published: May 2007

Rodent herpesviruses such as murine cytomegalovirus (host,
Mus musculus
), rat cytomegalovirus (host,
Rattus norvegicus
), and murine gammaherpesvirus 68 (hosts,
Apodemus
species) are important tools for the experimental study of human herpesvirus diseases. However, alphaherpesviruses, roseoloviruses, and lymphocryptoviruses, as well as rhadinoviruses, that naturally infect
Mus musculus
(house mouse) and other Old World mice are unknown. To identify hitherto-unknown rodent-associated herpesviruses, we captured
M. musculus
,
R. norvegicus
, and 14 other rodent species in several locations in Germany, the United Kingdom, and Thailand. Samples of trigeminal ganglia, dorsal root ganglia, brains, spleens, and other organs, as well as blood, were analyzed with a degenerate panherpesvirus PCR targeting the DNA polymerase (DPOL) gene. Herpesvirus-positive samples were subjected to a second degenerate PCR targeting the glycoprotein B (gB) gene. The sequences located between the partial DPOL and gB sequences were amplified by long-distance PCR and sequenced, resulting in a contiguous sequence of approximately 3.5 kbp. By DPOL PCR, we detected 17 novel betaherpesviruses and 21 novel gammaherpesviruses but no alphaherpesvirus. Of these 38 novel herpesviruses, 14 were successfully analyzed by the complete bigenic approach. Most importantly, the first gammaherpesvirus of
Mus musculus
was discovered (
Mus musculus
rhadinovirus 1 [MmusRHV1]). This virus is a member of a novel group of rodent gammaherpesviruses, which is clearly distinct from murine herpesvirus 68-like rodent gammaherpesviruses. Multigenic phylogenetic analysis, using an 8-kbp locus, revealed that MmusRHV1 diverged from the other gammaherpesviruses soon after the evolutionary separation of Epstein-Barr virus-like lymphocryptoviruses from human herpesvirus 8-like rhadinoviruses and alcelaphine herpesvirus 1-like macaviruses.
Varicella-Zoster Virus IE63, a Major Viral Latency Protein, Is Required To Inhibit the Alpha Interferon-Induced Antiviral Response
Authors: Ambagala Aruna P. N. , Cohen Jeffrey I.
Published: May 2007

Varicella-zoster virus (VZV) open reading frame 63 (ORF63) is the most abundant transcript expressed during latency in human sensory ganglia. VZV with ORF63 deleted is impaired for replication in melanoma cells and fibroblasts and for latency in rodents. We found that replication of the ORF63 deletion mutant is fully complemented in U2OS cells, which have been shown to complement the growth of herpes simplex virus type 1 (HSV-1) ICP0 mutants. Since HSV-1 ICP0 mutants are hypersensitive to alpha interferon (IFN-α), we examined the effect of IFN-α on VZV replication. Replication of the ORF63 mutant in melanoma cells was severely inhibited in the presence of IFN-α, in contrast to other VZV mutants that were similarly impaired for replication or to parental virus. The VZV ORF63 mutant was not hypersensitive to IFN-γ. IFN-α inhibited viral-gene expression in cells infected with the ORF63 mutant at a posttranscriptional level. Since IFN-α stimulates gene products that can phosphorylate the α subunit of eukaryotic initiation factor 2 (eIF-2α) and inhibit translation, we determined whether cells infected with the ORF63 mutant had increased phosphorylation of eIF-2α compared with cells infected with parental virus. While phosphorylated eIF-2α was undetectable in uninfected cells or cells infected with parental virus, it was present in cells infected with the ORF63 mutant. Conversely, expression of IE63 (encoded by ORF63) in the absence of other viral proteins inhibited phosphorylation of eIF-2α. Since IFN-α has been shown to limit VZV replication in human skin xenografts, the ability of VZV IE63 to block the effects of the cytokine may play a critical role in VZV pathogenesis.
A Conserved Region in the F
2
Subunit of Paramyxovirus Fusion Proteins Is Involved In Fusion Regulation
Authors: Gardner Amanda E. , Dutch Rebecca E.
Published: May 2007

Paramyxoviruses utilize both an attachment protein and a fusion (F) protein to drive virus-cell and cell-cell fusion. F exists functionally as a trimer of two disulfide-linked subunits: F
1
and F
2
. Alignment and analysis of a set of paramyxovirus F protein sequences identified three conserved blocks (CB): one in the fusion peptide/heptad repeat A domain, known to play important roles in fusion promotion, one in the region between the heptad repeats of F
1
(CBF
1
) (A. E. Gardner, K. L. Martin, and R. E. Dutch, Biochemistry
46
:5094-5105, 2007), and one in the F
2
subunit (CBF
2
). To analyze the functions of CBF
2
, alanine substitutions at conserved positions were created in both the simian virus 5 (SV5) and Hendra virus F proteins. A number of the CBF
2
mutations resulted in folding and expression defects. However, the CBF
2
mutants that were properly expressed and trafficked had altered fusion promotion activity. The Hendra virus CBF
2
Y79A and P89A mutants showed significantly decreased levels of fusion, whereas the SV5 CBF
2
I49A mutant exhibited greatly increased cell-cell fusion relative to that for wild-type F. Additional substitutions at SV5 F I49 suggest that both side chain volume and hydrophobicity at this position are important in the folding of the metastable, prefusion state and the subsequent triggering of membrane fusion. The recently published prefusogenic structure of parainfluenza virus 5/SV5 F (H. S. Yin et al., Nature
439:
38-44, 2006) places CBF
2
in direct contact with heptad repeat A. Our data therefore indicate that this conserved region plays a critical role in stabilizing the prefusion state, likely through interactions with heptad repeat A, and in triggering membrane fusion.
Simian Varicella Virus Expresses a Latency-Associated Transcript That Is Antisense to Open Reading Frame 61 (ICP0) mRNA in Neural Ganglia of Latently Infected Monkeys
Authors: Ou Yang , Davis Kara A. , Traina-Dorge Vicki , Gray Wayne L.
Published: May 2007

Simian varicella virus (SVV) and varicella-zoster virus (VZV) are closely related alphaherpesviruses that cause varicella (chickenpox) in nonhuman primates and humans, respectively. After resolution of the primary disease, SVV and VZV establish latent infection of neural ganglia and may later reactivate to cause a secondary disease (herpes zoster). This study investigated SVV gene expression in neural ganglia derived from latently infected vervet monkeys. SVV transcripts were detected in neural ganglia, but not in liver or lung tissues, of latently infected animals. A transcript mapping to open reading frame (ORF) 61 (herpes simplex virus type 1 [HSV-1] ICP0 homolog) was consistently detected in latently infected trigeminal, cervical, and lumbar ganglia by reverse transcriptase PCR. Further analysis confirmed that this SVV latency-associated transcript (LAT) was oriented antisense to the gene 61 mRNA. SVV ORF 21 transcripts were also detected in 42% of neural ganglia during latency. In contrast, SVV ORF 28, 29, 31, 62, and 63 transcripts were not detected in ganglia, liver, or lung tissues of latently infected animals. The results demonstrate that viral gene expression is limited during SVV latency and that a LAT antisense to an ICP0 homolog is expressed. In this regard, SVV gene expression during latency is similar to that of HSV-1 and other neurotropic animal alphaherpesviruses but differs from that reported for VZV.
Minimal Region Sufficient for Genome Dimerization in the Human Immunodeficiency Virus Type 1 Virion and Its Potential Roles in the Early Stages of Viral Replication
Authors: Sakuragi Jun-ichi , Sakuragi Sayuri , Shioda Tatsuo
Published: May 2007

It has been suggested that the dimer initiation site/dimer linkage sequence (DIS/DLS) region of the human immunodeficiency virus type 1 (HIV-1) RNA genome plays an important role at various stages of the viral life cycle. Recently we found that the duplication of the DIS/DLS region on viral RNA caused the production of partially monomeric RNAs in virions, indicating that this region indeed mediates RNA-RNA interaction. In this report, we followed up on this finding to identify the necessary and sufficient region for RNA dimerization in the virion of HIV-1. The region thus identified was 144 bases in length, extending from the junction of R/U5 and U5/L stem-loops to the end of SL4. The
trans
-acting responsive element, polyadenylation signal, primer binding site, upper stem-loop of U5/L, and SL2 were not needed for the function of this region. The insertion of this region into the ectopic location of the viral genome did not affect the level of virion production by transfection. However, the resultant virions contained monomerized genomes and showed drastic reductions in infectivity. A reduction was observed especially in the reverse transcription process. An attempt to generate a replication-competent virus with monomerized genome was performed by the long-term culture of mutant virus-infected cells. All recovered viruses were wild-type revertants, indicating a fatal defect of the mutation. These results suggest that genome dimerization or DIS/DLS itself also plays an important role in the early stages of virus infection.
Hepatitis C Virus Envelope Glycoprotein E2 Glycans Modulate Entry, CD81 Binding, and Neutralization
Authors: Falkowska Emilia , Kajumo Francis , Garcia Edie , Reinus John , Dragic Tatjana
Published: May 2007

Hepatitis C virus (HCV) is a major human pathogen that causes serious liver disease, including cirrhosis and hepatocellular carcinoma. The primary target cells of HCV are hepatocytes, and entry is restricted by interactions of the envelope glycoproteins, E1 and E2, with cellular receptors. E1 and E2 form noncovalently linked heterodimers and are heavily glycosylated. Glycans contribute to protein folding and transport as well as protein function. In addition, glycans associated with viral envelopes mask important functional domains from the immune system and attenuate viral immunogenicity. Here, we explored the role of N- and O-linked glycans on E2, which is the receptor binding subunit of the HCV envelope. We identified a number of glycans that are critical for viral entry. Importantly, we showed that the removal of several glycans significantly increased the inhibition of entry by sera from HCV-positive individuals. Only some of the glycans that affected entry and neutralization were also important for CD81 binding. Our results show that HCV envelope-associated glycans play a crucial role in masking functionally important regions of E2 and suggest a new strategy for eliciting highly neutralizing antibodies against this virus.
Synthetic Reconstruction of Zoonotic and Early Human Severe Acute Respiratory Syndrome Coronavirus Isolates That Produce Fatal Disease in Aged Mice
Authors: Rockx Barry , Sheahan Timothy , Donaldson Eric , Harkema Jack , Sims Amy , Heise Mark , Pickles Raymond , Cameron Mark , Kelvin David , Baric Ralph
Published: May 2007

The severe acute respiratory syndrome (SARS) epidemic was characterized by high mortality rates in the elderly. The molecular mechanisms that govern enhanced susceptibility of elderly populations are not known, and robust animal models are needed that recapitulate the increased pathogenic phenotype noted with increasing age. Using synthetic biology and reverse genetics, we describe the construction of a panel of isogenic SARS coronavirus (SARS-CoV) strains bearing variant spike glycoproteins that are representative of zoonotic strains found in palm civets and raccoon dogs, as well as isolates spanning the early, middle, and late phases of the SARS-CoV epidemic. The recombinant viruses replicated efficiently in cell culture and demonstrated variable sensitivities to neutralization with antibodies. The human but not the zoonotic variants replicated efficiently in human airway epithelial cultures, supporting earlier hypotheses that zoonotic isolates are less pathogenic in humans but can evolve into highly pathogenic strains. All viruses replicated efficiently, but none produced clinical disease or death in young animals. In contrast, severe clinical disease, diffuse alveolar damage, hyaline membrane formation, alveolitis, and death were noted in 12-month-old mice inoculated with the palm civet HC/SZ/61/03 strain or early-human-phase GZ02 variants but not with related middle- and late-phase epidemic or raccoon dog strains. This panel of SARS-CoV recombinants bearing zoonotic and human epidemic spike glycoproteins will provide heterologous challenge models for testing vaccine efficacy against zoonotic reintroductions as well as provide the appropriate model system for elucidating the complex virus-host interactions that contribute to more-severe and fatal SARS-CoV disease and acute respiratory distress in the elderly.
Evidence for Cooperative Transforming Activity of the Human Pituitary Tumor Transforming Gene and Human T-Cell Leukemia Virus Type 1 Tax
Authors: Sheleg Sergey V. , Peloponese Jean-Marie , Chi Ya-Hui , Li Yan , Eckhaus Michael , Jeang Kuan-Teh
Published: May 2007

Aneuploidy is frequent in cancers. Recently it was found that pituitary tumor transforming gene (PTTG; also called Pds1p or securin) is overexpressed in many different tumors. Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that primarily infects CD4+T lymphocytes and causes adult T-cell leukemia. Here, we report that overexpression of human PTTG cooperated with the HTLV-I Tax oncoprotein in cellular transformation. Coexpression of Tax and PTTG enhanced chromosomal instability and neoplastic changes to levels greater than overexpression of either factor singularly. Cells that overexpressed both PTTG and Tax induced tumors more robustly in nude mice than cells that expressed either PTTG alone or Tax alone.
Distance-Dependent Processing of Adeno-Associated Virus Type 5 RNA Is Controlled by 5′ Exon Definition
Authors: Qiu Jianming , Cheng Fang , Pintel David
Published: May 2007

Adeno-associated virus type 5 (AAV5) is unique among human AAV serotypes in that it uses a polyadenylation site [(pA)p] within the single small intron in the center of the genome. We previously reported that inhibition of polyadenylation at (pA)p, necessary for read-through of P41-generated capsid gene pre-mRNAs which are subsequently spliced, requires binding of U1 snRNP to the upstream donor. Inhibition was reduced as the distance between the cap site and the donor was increased (increasing the size of the 5′ exon). Here, we have demonstrated that U1-70K is a key component of U1 snRNP that mediates inhibition of polyadenylation at (pA)p. Furthermore, introduction of a U-rich stretch, predicted to target TIA-1 and thus increase the affinity of U1 snRNP binding to the intervening donor site, significantly augmented inhibition of (pA)p, while depletion of TIA-1 by siRNA increased (pA)p read-through. Finally, artificially tethering the cap binding complex (CBC) components CBP80 and CBP20 upstream of the intron donor increased inhibition of polyadenylation at (pA)p. Our results suggest that interaction with the CBC strengthens U1 snRNP binding to the downstream intron donor in a manner inversely proportional to the size of the 5′ exon, thus governing the competition between intron splicing and polyadenylation at (pA)p. This competition must be optimized to program both the levels of polyadenylation of P7- and P19-generated RNA at (pA)p required to produce proper levels of the essential Rep proteins and the splicing of P41-generated RNAs to produce the proper ratio of capsid proteins during AAV5 infection.
Estimating the Infectivity of CCR5-Tropic Simian Immunodeficiency Virus SIV
mac251
in the Gut
Authors: Wilson David P. , Mattapallil Joseph J. , Lay Matthew D. H. , Zhang Lei , Roederer Mario , Davenport Miles P.
Published: May 2007

CD4
+
T-cell depletion during acute human immunodeficiency virus infection occurs predominantly in the gastrointestinal mucosa. Using experimental data on SIV
mac251
viral load in blood and CD4
+
T cells in the jejunum, we modeled the kinetics of CD4
+
T-cell infection and death and estimated the viral infectivity. The infectivity of SIV
mac251
is higher than previously estimated for SHIV89.6P infection, but this higher infectivity is offset by a lower average peak viral load in SIV
mac251
. Thus, the dynamics of target cell infection and death are remarkably similar between a CXCR4- and a CCR5-tropic infection in vivo.
Ku80 Participates in the Targeting of Retroviral Transgenes to the Chromatin of CHO Cells
Authors: Masson Christel , Bury-Moné Stéphanie , Guiot Elvire , Saez-Cirion Asier , Schoëvaërt-Brossault Damien , Brachet-Ducos Corinne , Delelis Olivier , Subra Frédéric , Jeanson-Leh Laurence , Mouscadet Jean-François
Published: May 2007

The heterodimer Ku70/80 Ku is the DNA-binding component of the DNA-PK complex required for the nonhomologous end-joining pathway. It participates in numerous nuclear processes, including telomere and chromatin structure maintenance, replication, and transcription. Ku interacts with retroviral preintegration complexes and is thought to interfere with the retroviral replication cycle, in particular the formation of 2-long terminal repeat (LTR) viral DNA circles, viral DNA integration, and transcription. We describe here the effect of Ku80 on both provirus integration and the resulting transgene expression in cells transduced with retroviral vectors. We found that transgene expression was systematically higher in Ku80-deficient xrs6 cells than in Ku80-expressing CHO cells. This higher expression was observed irrespective of the presence of the viral LTR and was also not related to the nature of the promoter. Real-time PCR monitoring of the early viral replicative steps demonstrated that the absence of Ku80 does not affect the efficiency of transduction. We analyzed the transgene distributions localization in nucleus by applying a three-dimensional reconstruction model to two-dimensional fluorescence in situ hybridization images. This indicated that the presence of Ku80 resulted in a bias toward the transgenes being located at the periphery of the nucleus associated with their being repressed; in the absence of this factor the transgenes tend to be randomly distributed and actively expressed. Therefore, although not strictly required for retroviral integration, Ku may be involved in targeting retroviral elements to chromatin domains prone to gene silencing.
Type III Interferon (IFN) Induces a Type I IFN-Like Response in a Restricted Subset of Cells through Signaling Pathways Involving both the Jak-STAT Pathway and the Mitogen-Activated Protein Kinases
Authors: Zhou Zhangle , Hamming Ole J. , Ank Nina , Paludan Søren R. , Nielsen Anders L. , Hartmann Rune
Published: May 2007

Type III interferon (IFN) is a novel member of the interferon family. Type III IFN utilizes a receptor complex different from that of type I IFN, but both types of IFN induce STAT1, STAT2, and STAT3 activation. Here we describe a detailed comparison of signal transduction initiated by type I and type III IFN. Gene expression array analysis showed that IFN types I and III induced a similar subset of genes. In particular, no genes were induced uniquely by type III IFN. Next, we used chromatin immunoprecipitation (ChIP) analysis to investigate the promoter activation by types I and III IFN. The ChIP assays demonstrated that stimulation of cells with both type I and type III IFN resulted in the recruitment of ISGF3 transcription factor components to the promoter region of responsive genes and in an increase of polymerase II loading and histone acetylation. Whereas IFN type I signaling was observed for a broad spectrum of cell lines, type III IFN signaling was more restricted. The lack of IFN type III signaling was correlated with a low expression of the IL28Ra component of the IFN type III receptor, and IL28Ra overexpression was sufficient to restore IFN type III signaling. We also tested the activation of mitogen-activated protein (MAP) kinases by type III IFN and found that type III IFN relies strongly upon both p38 and JNK MAP kinases for gene induction.