bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of the suppression effect of polyethylene glycol on copper electroplating by electrochemical impedance spectroscopy
Authors: Hung Chi-Cheng , Lee Wen-Hsi , Wang Ying-Lang , Chan Din-Yuen , Hwang Gwo-Jen
Published: September 2008

Polyethylene glycol (PEG) is an additive that is commonly used as a suppressor in the semiconductor copper (Cu)-electroplating process. In this study, electrochemical impedance spectroscopy (EIS) was used to analyze the electrochemical behavior of PEG in the Cu-electroplating process. Polarization analysis, cyclic-voltammetry stripping, and cell voltage versus plating time were examined to clarify the suppression behavior of PEG. The equivalent circuit simulated from the EIS data shows that PEG inhibited the Cu-electroplating rate by increasing the charge-transfer resistance as well as the resistance of the adsorption layer. The presence of a large inductance demonstrated the strong adsorption of cuprous-PEG-chloride complexes on the Cu surface during the Cu-electroplating process. Increasing the PEG concentration appears to increase the resistances of charge transfer, the adsorption layer, and the inductance of the electroplating system.
Low energy secondary ion mass spectrometry with sub-keV O2+ beams at glancing incidence
Authors: Jiang Z. X. , Kim K. , Guenther T. , Robichaud B. , Benavides J. , Contreras L. , Sieloff D. D.
Published: September 2008

The ever increasing interest in surface analysis techniques with excellent depth resolution, great detection sensitivity, and good throughput has been a driving force for development of dynamic secondary ion mass spectrometry using low energy primary beams. This work investigated sputtering erosion of Si and emission of secondary ions from Si bombarded by sub-keV O2+ beams at glancing incidence. It was demonstrated that surface roughening remained minimal for 250 and 500eV O2+ beams at an angle of incidence above 80° but developed rapidly at angles between 60° and 80°. The depth resolution for B and Ge appeared very different at the glancing incidence and changed dramatically in opposite ways as the angle of incidence decreased. The difference in the depth resolution was explained by the different diffusion/segregation behavior between B and Ge during O2+ bombardment. In general, the use of sub-keV O2+ beams at the glancing incidence (above 80°) favored a thinner altered layer, a short surface transient, a minimal apparent shift in depth profiles, a better depth resolution (not for B in Si), a good sputter rate, but a poor yield of the positive secondary ions. To address the issues with the low ion yield, we identified optimal cluster ions for common dopant such as boron and nitrogen. Good sensitivity was achieved for analyses of boron in Si by detecting BO2− as the characteristic secondary ion. A parallel study published elsewhere suggested SiN− as an ideal candidate for detection of nitrogen in ultrathin oxynitride [Z. X. Jiang et al., Surf. Interface Anal. (in press)]. For analyses of thin SiGe films in Si at glancing incidence, detection of Ge+ provided fairly good sensitivity. Applications of an O2+ beam at 250eV 83° for analyses of shallow boron implant demonstrated superior accuracy in the measured near-surface boron distribution. Also the characterization of thin SiGe films exhibited excellent depth resolving power for Ge in Si although the ion yield of Ge+ was low.
Measurement of reactive and condensable gas permeation using a mass spectrometer
Authors: Zhang Xiao Dong , Lewis Jay S. , Parker Charles B. , Glass Jeffrey T. , Wolter Scott D.
Published: September 2008

Permeation of water vapor, oxygen, nitrogen, and carbon dioxide through polymer films is measured by the programed valving mass spectrometry (PVMS) method. The results are calibrated with a standard permeation rate for each gas to determine the detection sensitivity. The calibrated lower detection limits are 1.90×10−7g∕m2day for water vapor, 2.81×10−2cm3∕m2day for oxygen, 2.15×10−2cm3∕m2day for nitrogen, and 3.29×10−2cm3∕m2day for carbon dioxide. The lower detection limits presented here for water vapor, nitrogen, and carbon dioxide are more than two orders of magnitude lower than the corresponding values offered by the NIST-traceable standard techniques. In addition, the PVMS water vapor lower detection limit meets the sensitivity requirement for detecting “ultrabarrier” water vapor permeation rates, while the oxygen lower detection limit is higher than that offered by the standard technique. However, the results suggest a modified measurement protocol and/or system modifications to overcome this limitation. Effusivity through a flow orifice was also examined using the PVMS method for the above gases. The effusion results from the flow orifice, combined with the permeation results from polymer samples, provide insight into the factors that may influence gas detection sensitivities.
Bayard-Alpert ionization gauge sensitivity for C7F14
Authors: Kim S.-H. , Heinrich J. R. , Miller M. J. , Merlino R. L.
Published: September 2008

Various empirical methods are applied to estimate the Bayard-Alpert ionization gauge relative sensitivity for C7F14. These values are compared to a measured value obtained by calibrating the ion gauge tube pressure sensor against a capacitance manometer.
Identification and quantification of iron silicide phases in thin films
Authors: Miquita D. R. , González J. C. , da Silva M. I. N. , Rodrigues W. N. , Moreira M. V. B. , Paniago R. , Ribeiro-Andrade R. , Magalhães-Paniago R. , Pfannes H.-D. , de Oliveira A. G.
Published: September 2008

Iron silicide samples were grown on Si (111) substrates by solid phase epitaxy and reactive deposition epitaxy. The different iron silicide phases and their correlations with the growth parameters were analyzed by x-ray photoelectron spectroscopy, conversion electron Mössbauer spectroscopy, x-ray diffraction, atomic force microscopy, and magnetic force microscopy. The authors investigated the potential of each technique for identifying and quantifying of the phases. In particular, the authors used a semiquantitative analysis of magnetic force microscopy images to spatially resolve the semiconductor β-FeSi2 phase.
Trench profile angle beveling
Authors: Chen Hui , Wang Q.
Published: September 2008

A trench bevel etch process is developed as a method to produce trench profiles with a prerequired angle. This process depends on both surface reaction and gas conductance along the trench. To study the surface reaction probability, activation energies were measured for SF6 and CF4 chemistries and were found to be 6 and 140meV, respectively. It has been demonstrated that CF4 etch chemistry is in surface-reaction-rate-limited regime and contributes little to the trench beveling. SF6 chemistry with its low activation energy is in reactant-transport-rate-limited regime and contributes significantly to the bevel process. The dependences of bevel etch on trench aspect ratio was also investigated in detail. It has been found that high aspect ratio trench produces larger bevel angle than that does for small aspect ratio. A phenomenological model was constructed by introducing reactant conduction loss L and sidewall reaction loss S to quantitatively describe the effects of both reactant transport and surface reaction. Through comparison of theoretical modeling and experiment, an S value between 0.8 and 1 is reached to explain the experimental results from SF6 chemistry. This result demonstrates the SF6 is a spontaneous surface reaction and is consistent with our activation energy measurement.
Plasma-assisted molecular beam epitaxy and characterization of SnO2 (101) on r-plane sapphire
Authors: White M. E. , Tsai M. Y. , Wu F. , Speck J. S.
Published: September 2008

Plasma-assisted molecular beam epitaxy has been shown to be a viable and practical method for producing high quality tin oxide, SnO2. Phase-pure epitaxial single crystalline SnO2 (101) thin films of 1μm in thickness were reproducibly grown on r-plane sapphire Al2O3 (101¯2) substrates. The SnO2 epitaxy progressed in the Volmer–Weber growth mode. A minimum on-axis ω-scan full width at half maximum of 0.22° for the SnO2 (101) peak was measured indicating relatively low film mosaic. An epitaxial relationship of [010]SnO2∥[1¯21¯0]sapphire and [1¯01]SnO2∥[1¯011]sapphire was determined between the film and substrate. A SnO2 film tilt of 1.3° around the [010]SnO2 toward [0001]sapphire was measured. A dislocation density of 8×109cm−2 was measured. Hall effect measurements quantified an unintentionally doped electron concentration for different samples in a range (0.3–3.0)×1017cm−3 with a corresponding electron mobility range of 20–100cm2∕Vs. The SnO2 growth behavior was determined to be in one of the two distinct growth regimes. An oxygen-rich regime was characterized by a linear increase in the film growth rate with increasing Sn flux; whereas, the films grown entirely in the Sn-rich regime showed a decrease in the growth rate with increased Sn flux.
The effectiveness of HCl and HF cleaning of Si0.85Ge0.15 surface
Authors: Sun Yun , Liu Zhi , Sun Shiyu , Pianetta Piero
Published: September 2008

The cleaning of Si0.85Ge0.15 surfaces using HCl and HF solutions is studied using synchrotron radiation photoelectron spectroscopy. The HF solution is found to be effective in removing both the Si oxide and the Ge oxide while the HCl solution can only remove part of the Ge oxide. For samples treated with HF, four spectral components are needed to fit the Ge 3d photoemission spectra. One is the bulk component and the other three are attributed to the surface Ge atoms with monohydride, dihydride, and trihydride terminations, respectively.
Growth and ellipsometric characterizations of highly (111)-oriented Bi2Ti2O7 films on platinized silicon by metal organic decomposition method
Authors: Hu Z. G. , Li Y. W. , Zhu M. , Yue F. Y. , Zhu Z. Q. , Chu J. H.
Published: September 2008

Optical properties and electronic structure of Bi2Ti2O7 (BTO) films on platinized silicon substrates have been investigated using near-infrared-ultraviolet spectroscopic ellipsometry. The optical dispersion in the photon energy range of 0.73–5.8eV has been extracted by fitting the experimental data with a four-phase layered model. The Tauc–Lorentz dispersion function has been fundamentally applied and describes the optical response of the BTO films well. The refractive index in the transparent region can be reasonably fitted by a single oscillator function and the maximum electronic transition occurs near 4.2eV for the BTO material. The long wavelength refractive index n(0) can be estimated to about 1.7 at zero point. The fundamental band gap energy was determined to be about 3.2eV, which was supported by different theoretical evaluation methods. The present results can be important for future applications of BTO-based electro-optics and optoelectronic devices.
Deterioration of seal reliability due to noncoaxial arrangement of ConFlat type flanges and gasket
Authors: Kurokouchi Satoshi
Published: September 2008

Certain combinations of commercially available ConFlat type flanges with a gasket can yield an excessively wide gap between the gasket’s outer rim and the flange’s gasket-retaining counter. (The present ISO Technical Specification for the ConFlat type sealing system allows a maximum gap of some 0.8mm width.) Tightening this type of flange-and-gasket combination almost never results in a perfect coaxial arrangement; rather, it produces eccentric arrangements of the matching flanges and sandwiched gaskets. In a tightening test with coaxially arranged flanges and eccentrically arranged gaskets, seal performance was independent of the gap width, whether or not baking was included in the test conditions. The results indicate that the existing “capture model” lacks validity as a rationale for the seal mechanism of the ConFlat system. By contrast, the eccentric arrangement of matching flanges did prove to have a strong influence on seal reliability, particularly where the tightening test includes a baking process. The negative impact on seal reliability observed in eccentric arrangements can be ascribed to local bending that occurs on the tightened gasket and the consequent diminution of seal area and seal pressure. Annealing of the gasket material during the baking process lowers seal pressure further, thus increasing the probability of leaks.
Response to Comment on "A Global Map of Human Impact on Marine Ecosystems"
Authors: Selkoe Kimberly A. , Kappel Carrie V. , Halpern Benjamin S. , Micheli Fiorenza , D'Agrosa Caterina , Bruno John , Casey Kenneth S. , Ebert Colin , Fox Helen E. , Fujita Rod , Heinemann Dennis , Lenihan Hunter S. , Madin Elizabeth M. P. , Perry Matt , Selig Elizabeth R. , Spalding Mark , Steneck Robert , Walbridge Shaun , Watson Reg
Published: September 2008

Our results provide an important first step toward a full assessment of how human activities act cumulatively to affect the condition of the oceans. Fisheries (and climate change) impacts are some of the hardest to map and measure accurately. Consequently, species-specific considerations and fine-scale analyses should be left to more nuanced regional-scale replicates of our mapping framework.
Activation of Aldehyde Dehydrogenase-2 Reduces Ischemic Damage to the Heart
Authors: Chen Che-Hong , Budas Grant R. , Churchill Eric N. , Disatnik Marie-Hélène , Hurley Thomas D. , Mochly-Rosen Daria
Published: September 2008

There is substantial interest in the development of drugs that limit the extent of ischemia-induced cardiac damage caused by myocardial infarction or by certain surgical procedures. Here, using an unbiased proteomic search, we identified mitochondrial aldehyde dehydrogenase 2 (ALDH2) as an enzyme whose activation correlates with reduced ischemic heart damage in rodent models. A high-throughput screen yielded a small-molecule activator of ALDH2 (Alda-1) that, when administered to rats before an ischemic event, reduced infarct size by 60%, most likely through its inhibitory effect on the formation of cytotoxic aldehydes. In vitro, Alda-1 was a particularly effective activator of ALDH2*2, an inactive mutant form of the enzyme that is found in 40% of East Asian populations. Thus, pharmacologic enhancement of ALDH2 activity may be useful for patients with wild-type or mutant ALDH2 who are subjected to cardiac ischemia, such as during coronary bypass surgery.
Cooling, Heating, Generating Power, and Recovering Waste Heat with Thermoelectric Systems
Authors: Bell Lon E.
Published: September 2008

Thermoelectric materials are solid-state energy converters whose combination of thermal, electrical, and semiconducting properties allows them to be used to convert waste heat into electricity or electrical power directly into cooling and heating. These materials can be competitive with fluid-based systems, such as two-phase air-conditioning compressors or heat pumps, or used in smaller-scale applications such as in automobile seats, night-vision systems, and electrical-enclosure cooling. More widespread use of thermoelectrics requires not only improving the intrinsic energy-conversion efficiency of the materials but also implementing recent advancements in system architecture. These principles are illustrated with several proven and potential applications of thermoelectrics.
Postseismic Relaxation Along the San Andreas Fault at Parkfield from Continuous Seismological Observations
Authors: Brenguier F. , Campillo M. , Hadziioannou C. , Shapiro N. M. , Nadeau R. M. , Larose E.
Published: September 2008

Seismic velocity changes and nonvolcanic tremor activity in the Parkfield area in California reveal that large earthquakes induce long-term perturbations of crustal properties in the San Andreas fault zone. The 2003 San Simeon and 2004 Parkfield earthquakes both reduced seismic velocities that were measured from correlations of the ambient seismic noise and induced an increased nonvolcanic tremor activity along the San Andreas fault. After the Parkfield earthquake, velocity reduction and nonvolcanic tremor activity remained elevated for more than 3 years and decayed over time, similarly to afterslip derived from GPS (Global Positioning System) measurements. These observations suggest that the seismic velocity changes are related to co-seismic damage in the shallow layers and to deep co-seismic stress change and postseismic stress relaxation within the San Andreas fault zone.
Imaging of Transient Structures Using Nanosecond in Situ TEM
Authors: Kim Judy S. , LaGrange Thomas , Reed Bryan W. , Taheri Mitra L. , Armstrong Michael R. , King Wayne E. , Browning Nigel D. , Campbell Geoffrey H.
Published: September 2008

The microstructure and properties of a material depend on dynamic processes such as defect motion, nucleation and growth, and phase transitions. Transmission electron microscopy (TEM) can spatially resolve these nanoscale phenomena but lacks the time resolution for direct observation. We used a photoemitted electron pulse to probe dynamic events with “snapshot” diffraction and imaging at 15-nanosecond resolution inside of a dynamic TEM. With the use of this capability, the moving reaction front of reactive nanolaminates is observed in situ. Time-resolved images and diffraction show a transient cellular morphology in a dynamically mixing, self-propagating reaction front, revealing brief phase separation during cooling, and thus provide insights into the mechanisms driving the self-propagating high-temperature synthesis.
Degradation of microRNAs by a Family of Exoribonucleases in
Arabidopsis
Authors: Ramachandran Vanitharani , Chen Xuemei
Published: September 2008

microRNAs (miRNAs) play crucial roles in numerous developmental and metabolic processes in plants and animals. The steady-state levels of miRNAs need to be properly controlled to ensure normal development. Whereas the framework of miRNA biogenesis is established, factors involved in miRNA degradation remain unknown. Here, we show that a family of exoribonucleases encoded by the
SMALL RNA DEGRADING NUCLEASE
(
SDN
) genes degrades mature miRNAs in
Arabidopsis
. SDN1 acts specifically on single-stranded miRNAs in vitro and is sensitive to the 2′-
O
-methyl modification on the 3′ terminal ribose of miRNAs. Simultaneous knockdown of three
SDN
genes in vivo results in elevated miRNA levels and pleiotropic developmental defects. Therefore, we have uncovered the enzymes that degrade miRNAs and demonstrated that miRNA turnover is crucial for plant development.
Expression of Nonstructural Rotavirus Protein NSP4 Mimics Ca
2+
Homeostasis Changes Induced by Rotavirus Infection in Cultured Cells
Authors: Díaz Yuleima , Chemello Maria Elena , Peña Franshelle , Aristimuño Olga Carolina , Zambrano Jose Luis , Rojas Hector , Bartoli Fulvia , Salazar Leiria , Chwetzoff Serge , Sapin Catherine , Trugnan Germain , Michelangeli Fabian , Ruiz Marie Christine
Published: September 2008

Rotavirus infection modifies Ca
2+
homeostasis, provoking an increase in Ca
2+
permeation, the cytoplasmic Ca
2+
concentration ([Ca
2+
]
cyto
), and total Ca
2+
pools and a decrease in Ca
2+
response to agonists. A glycosylated viral protein(s), NSP4 and/or VP7, may be responsible for these effects. HT29 or Cos-7 cells were infected by the SA11 clone 28 strain, in which VP7 is not glycosylated, or transiently transfected with plasmids coding for NSP4-enhanced green fluorescent protein (EGFP) or NSP4. The permeability of the plasma membrane to Ca
2+
and the amount of Ca
2+
sequestered in the endoplasmic reticulum released by carbachol or ATP were measured in fura-2-loaded cells at the single-cell level under a fluorescence microscope or in cell suspensions in a fluorimeter. Total cell Ca
2+
pools were evaluated as
45
Ca
2+
uptake. Infection with SA11 clone 28 induced an increase in Ca
2+
permeability and
45
Ca
2+
uptake similar to that found with the normally glycosylated SA11 strain. These effects were inhibited by tunicamycin, indicating that inhibition of glycosylation of a viral protein other than VP7 affects the changes of Ca
2+
homeostasis induced by infection. Expression of NSP4-EGFP or NSP4 in transfected cells induced the same changes observed with rotavirus infection, whereas the expression of EGFP or EGFP-VP4 showed the behavior of uninfected and untransfected cells. Increased
45
Ca
2+
uptake was also observed in cells expressing NSP4-EGFP or NSP4, as evidenced in rotavirus infection. These results indicate that glycosylated NSP4 is primarily responsible for altering the Ca
2+
homeostasis of infected cells through an initial increase of cell membrane permeability to Ca
2+
.
Recovery of Infectious Virus by Transfection of In Vitro-Generated RNA from Tulane Calicivirus cDNA
Authors: Wei Chao , Farkas Tibor , Sestak Karol , Jiang Xi
Published: September 2008

Tulane virus (TV) is a newly reported calicivirus that was isolated from stool samples of captive rhesus macaques from the Tulane National Primate Research Center (TNPRC). The virus has been cultivated successfully in LLC-MK2 rhesus monkey kidney cells. Its complete genomic sequence suggests that TV represents a new genus and is evolutionarily more closely related to
Norovirus
than to any other genus of
Caliciviridae
. In this study, we demonstrated that RNA transcripts made in vitro from the full-length genomic cDNA of TV were infectious upon transfection into permissive LLC-MK2 cells. The recombinant virus exhibited plaque morphologies and growth kinetics similar to those of the wild-type virus in this cell line. Capping was required for TV RNA infectivity. Although a subgenomic RNA has been detected in TV-transfected cells, a separate subgenomic RNA transcript was not required for the initial transfection to establish the replication. Transfection of truncated RNA lacking open reading frame 2 (ORF2) and ORF3 or TV-norovirus chimeric RNA resulted in abortive replication without the production of infectious progeny viruses, indicating that both ORFs are essential for the replication of TV. A heterologous insertion at the 5′ end of the genome also hampered viral replication, suggesting that an authentic 5′ end of the genome is critical for replication. The availability of the complete genomic sequence and the reverse genetics system described herein make TV a valuable model for studying calicivirus pathogenesis and replication.
H5N1 Avian Influenza Virus Induces Apoptotic Cell Death in Mammalian Airway Epithelial Cells
Authors: Daidoji Tomo , Koma Takaaki , Du Anariwa , Yang Cheng-Song , Ueda Mayo , Ikuta Kazuyoshi , Nakaya Takaaki
Published: September 2008

In recent years, the highly pathogenic avian influenza virus H5N1 has raised serious worldwide concern about an influenza pandemic; however, the biology of H5N1 pathogenesis is largely unknown. To elucidate the mechanism of H5N1 pathogenesis, we prepared primary airway epithelial cells from alveolar tissues from 1-year-old pigs and measured the growth kinetics of three avian H5 influenza viruses (A/Crow/Kyoto/53/2004 [H5N1], A/Duck/Hong Kong/342/78 [H5N2], and A/Duck/Hong Kong/820/80 [H5N3]), the resultant cytopathicity, and possible associated mechanisms. H5N1, but not the other H5 viruses, strongly induced cell death in porcine alveolar epithelial cells (pAEpC), although all three viruses induced similar degrees of cytopathicity in chicken embryonic fibroblasts. Intracellular viral growth and the production of progeny viruses were comparable in pAEpC infected with each H5 virus. In contrast, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling-positive cells were detected only in H5N1-infected pAEpC, and the activities of caspases 3, 8, and 9 were significantly elevated in pAEpC infected with H5N1, but not with H5N2 and H5N3. These results suggest that only H5N1 induces apoptosis in pAEpC. H5N1 cytopathicity was inhibited by adding the caspase inhibitor z-VAD-FMK; however, there were no significant differences in viral growth or release of progeny viruses. Further investigations using reverse genetics demonstrated that H5N1 hemagglutinin protein plays a critical role in inducing caspase-dependent apoptosis in infected pAEpC. H5N1-specific cytopathicity was also observed in human primary airway epithelial cells. Taken together, these data suggest that avian H5N1 influenza virus leads to substantial cell death in mammalian airway epithelial cells due to the induction of apoptosis.
Temporal Dynamics of Cytomegalovirus Chromatin Assembly in Productively Infected Human Cells
Authors: Nitzsche Alexandra , Paulus Christina , Nevels Michael
Published: September 2008

The genomes of herpesviruses, including human cytomegalovirus (CMV), are double-stranded DNA molecules maintained as episomes during infection. The viral DNA lacks histones when encapsidated in the virion. However, it has been found histone associated inside infected cells, implying unidentified chromatin assembly mechanisms. Our results indicate that components of the host cell nucleosome deposition machinery target intranuclear CMV DNA, resulting in stepwise viral-chromatin assembly. CMV genomes undergo limited histone association and nucleosome assembly as early as 30 min after infection via DNA replication-independent mechanisms. Low average viral-genome chromatinization is maintained throughout the early stages of infection. The late phase of infection is characterized by a striking increase in average histone occupancy coupled with the process of viral-DNA replication. While the initial chromatinization affected all analyzed parts of the CMV chromosome, a subset of viral genomic regions, including the major immediate-early promoter, proved to be largely resistant to replication-dependent histone deposition. Finally, our results predict the likely requirement for an unanticipated chromatin disassembly process that enables packaging of histone-free DNA into progeny capsids.
Internal Deletions of IE2 86 and Loss of the Late IE2 60 and IE2 40 Proteins Encoded by Human Cytomegalovirus Affect the Levels of UL84 Protein but Not the Amount of UL84 mRNA or the Loading and Distribution of the mRNA on Polysomes
Authors: Sanders Rebecca L. , Del Rosario Christia J. , White Elizabeth A. , Spector Deborah H.
Published: September 2008

The major immediate-early (IE) region of human cytomegalovirus encodes two IE proteins, IE1 72 and IE2 86, that are translated from alternatively spliced transcripts that differ in their 3′ ends. Two other proteins that correspond to the C-terminal region of IE2 86, IE2 60 and IE2 40, are expressed at late times. In this study, we used IE2 mutant viruses to examine the mechanism by which IE2 86, IE2 60, and IE2 40 affect the expression of a viral DNA replication factor, UL84. Deletion of amino acids (aa) 136 to 290 of IE2 86 results in a significant decrease in UL84 protein during the infection. This loss of UL84 is both proteasome and calpain independent, and the stability of the protein in the context of infection with the mutant remains unaffected. The RNA for UL84 is expressed to normal levels in the mutant virus-infected cells, as are the RNAs for two other proteins encoded by this region, UL85 and UL86. Moreover, nuclear-to-cytoplasmic transport and the distribution of the UL84 mRNA on polysomes are unaffected. A region between aa 290 and 369 of IE2 86 contributes to the UL84-IE2 86 interaction in vivo and in vitro. IE2 86, IE2 60, and IE2 40 are each able to interact with UL84 in the mutant-infected cells, suggesting that these interactions may be important for the roles of UL84 and the IE2 proteins. Thus, these data have defined the contribution of IE2 86, IE2 60, and IE2 40 to the efficient expression of UL84 throughout the infection.
Group A Human Rotavirus Genomics: Evidence that Gene Constellations Are Influenced by Viral Protein Interactions
Authors: Heiman Erica M. , McDonald Sarah M. , Barro Mario , Taraporewala Zenobia F. , Bar-Magen Tamara , Patton John T.
Published: September 2008

Group A human rotaviruses (HRVs) are the major cause of severe viral gastroenteritis in infants and young children. To gain insight into the level of genetic variation among HRVs, we determined the genome sequences for 10 strains belonging to different VP7 serotypes (G types). The HRVs chosen for this study, D, DS-1, P, ST3, IAL28, Se584, 69M, WI61, A64, and L26, were isolated from infected persons and adapted to cell culture to use as serotype references. Our sequencing results revealed that most of the individual proteins from each HRV belong to one of three genotypes (1, 2, or 3) based on their similarities to proteins of genogroup strains (Wa, DS-1, or AU-1, respectively). Strains D, P, ST3, IAL28, and WI61 encode genotype 1 (Wa-like) proteins, whereas strains DS-1 and 69M encode genotype 2 (DS-1-like) proteins. Of the 10 HRVs sequenced, 3 of them (Se584, A64, and L26) encode proteins belonging to more than one genotype, indicating that they are intergenogroup reassortants. We used amino acid sequence alignments to identify residues that distinguish proteins belonging to HRV genotype 1, 2, or 3. These genotype-specific changes cluster in definitive regions within each viral protein, many of which are sites of known protein-protein interactions. For the intermediate viral capsid protein (VP6), the changes map onto the atomic structure at the VP2-VP6, VP4-VP6, and VP7-VP6 interfaces. The results of this study provide evidence that group A HRV gene constellations exist and may be influenced by interactions among viral proteins during replication.
Early B-Cell Activation after West Nile Virus Infection Requires Alpha/Beta Interferon but Not Antigen Receptor Signaling
Authors: Purtha Whitney E. , Chachu Karen A. , Virgin Herbert W. , Diamond Michael S.
Published: September 2008

The B-cell response against West Nile virus (WNV), an encephaliticFlavivirusof global concern, is critical to controlling central nervous system dissemination and neurological sequelae, including death. Here, using a well-characterized mouse model of WNV infection, we examine the factors that govern early B-cell activation. Subcutaneous inoculation with a low dose of replicating WNV results in extensive B-cell activation in the draining lymph node (LN) within days of infection as judged by upregulation of the surface markers CD69, class II major histocompatibility complex, and CD86 on CD19+cells. B-cell activation in the LN but not the spleen was dependent on signals through the type I alpha/beta interferon (IFN-α/β) receptor. Despite significant activation in the draining LN at day 3 after infection, WNV-specific B cells were not detected by immunoglobulin M enzyme-linked immunospot analysis until day 7. Liposome depletion experiments demonstrate that B-cell activation after WNV infection was not affected by the loss of F4/80+or CD169+subcapsular macrophages. Nonetheless, LN myeloid cells were essential for control of viral replication and survival from infection. Overall, our data suggest that the massive, early polyclonal B-cell activation occurring in the draining LN after WNV infection is immunoglobulin receptor and macrophage independent but requires sustained signals through the type I IFN-α/β receptor.
An Alphavirus Replicon-Based Human Metapneumovirus Vaccine Is Immunogenic and Protective in Mice and Cotton Rats
Authors: Mok Hoyin , Tollefson Sharon J. , Podsiad Amy B. , Shepherd Bryan E. , Polosukhin Vasiliy V. , Johnston Robert E. , Williams John V. , Crowe James E.
Published: September 2008

Human metapneumovirus (hMPV) is a recently discovered paramyxovirus that causes upper and lower respiratory tract infections in infants, the elderly, and immunocompromised individuals worldwide. Here, we developed Venezuelan equine encephalitis virus replicon particles (VRPs) encoding hMPV fusion (F) or attachment (G) glycoproteins and evaluated the immunogenicity and protective efficacy of these vaccine candidates in mice and cotton rats. VRPs encoding hMPV F protein, when administered intranasally, induced F-specific virus-neutralizing antibodies in serum and immunoglobulin A (IgA) antibodies in secretions at the respiratory mucosa. Challenge virus replication was reduced significantly in both the upper and lower respiratory tracts following intranasal hMPV challenge in these animals. However, vaccination with hMPV G protein VRPs did not induce neutralizing antibodies or protect animals from hMPV challenge. Close examination of the histopathology of the lungs of VRP-MPV F-vaccinated animals following hMPV challenge revealed no enhancement of inflammation or mucus production. Aberrant cytokine gene expression was not detected in these animals. Together, these results represent an important first step toward the use of VRPs encoding hMPV F proteins as a prophylactic vaccine for hMPV.
Structural Evolution of
Reoviridae
Revealed by
Oryzavirus
in Acquiring the Second Capsid Shell
Authors: Miyazaki Naoyuki , Uehara-Ichiki Tamaki , Xing Li , Bergman Leif , Higashiura Akifumi , Nakagawa Atsushi , Omura Toshihiro , Cheng R. Holland
Published: September 2008

The conservation of the core structure and diversification of the external features among the turreted reoviruses appear to be relevant to structural evolution in facilitating the infection of diverse host species. The structure of
Rice ragged stunt virus
(RRSV), in the genus
Oryzavirus
of the family
Reoviridae
, is determined to show a core composed of capsid shell, clamps, and long turrets. The RRSV core structure is equivalent to the core structure of
Orthoreovirus
and the virion structure of
Cytoplasmic polyhedrosis virus
(CPV). In RRSV, five peripheral trimers surround each long turret and sit at the Q trimer position in the T=13
l
icosahedral symmetry, a structural feature unique to turreted reoviruses. That is, the core of RRSV is partially covered by 60 copies of the peripheral trimer. In contrast, the core of
Orthoreovirus
is covered by 200 copies of the trimer that sit at the Q, R, S, and T trimer positions. Our results suggest that among the three viruses, RRSV has a structure intermediate between that of
Orthoreovirus
and the CPV virion. This conclusion coincides with the results of the phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerases.
Dome-building eruptions: insights from analogue experiments
Authors: Lane S. J. , Phillips J. C. , Ryan G. A.
Published: September 2008

Laboratory flows, self-capped by high-viscosity fluid, exhibit vertical pressure gradients similar to those postulated within conduits feeding dome-building eruptions. Overpressure and pressure cycles exhibited at laboratory scale provide insight into the mechanism of tilt cycles at volcanic scale. Experimental pressure cycles correlated with the rate of gas escape, with pressure rise being controlled by diffusion of volatile into bubbles during times when gas escape from the flow was negligible. The increase in pressure continued until margin decrepitation created preferential pathways for rapid gas escape from permeable foam, thereby reducing pressure within the flow. As pressure reduced, the gas escape pathways sealed and diffusion repressurized the system. This implies that tilt cycles, such as those exhibited by the Soufrière Hills Volcano, Montserrat, result from a diffusively pumped process that oscillates around the viscous-elastic transition within the outer regions of the flow. Phases of open- and closed-system degassing result, with gas escaping through fractures created and maintained by the flow process itself. Fluid-dynamically, this mechanism generates an oscillation between Poiseuille flow and plug flow, with a 1-D model of plug motion giving a reasonable representation of observation in both experimental and volcanic cases.
Modelling the rapid near-surface expansion of gas slugs in low-viscosity magmas
Authors: James M. R. , Lane S. J. , Corder S. B.
Published: September 2008

The ascent of large gas bubbles (slugs) in vertical cylindrical conduits and low-viscosity magmas is simulated using 1D mathematical and 3D computational fluid dynamic (CFD) models. Following laboratory evidence, the 1D model defines a constant rise velocity for the slug base and allows gas expansion to accelerate the slug nose through the overlying fluid during ascent. The evolution of rapidly expanding gas slugs observed in laboratory experiments is reproduced well and, at volcano scales, predicts at-surface overpressures of several atmospheres without requiring any initial overpressure at depth. The near-surface dynamics increase slug nose velocities through the overlying magma by a factor of
c
. 2.5 and the gas expansion results in pre-burst magma surface velocities of
c
. 35 m s
−1
. To examine pressure distributions and the forces exerted on a conduit, 3D CFD simulations were carried out. At volcano scales, the vertical single forces during final slug ascent to the surface are
c
. 10
6
N, two orders of magnitude smaller than those associated with very-long-period seismic events at Stromboli. This supports a previous interpretation of these events in which they are generated by gas slugs flowing through changes in conduit geometry, rather than being the direct result of slug eruption processes.
In vitro neovasculogenic potential of resident adipose tissue precursors
Authors: Madonna Rosalinda , De Caterina Raffaele
Published: September 2008

Adipose tissue development is associated with neovascularization, which might be exploited therapeutically. We investigated the neovasculogenesis antigenic profile and kinetics in adipose tissue-derived stromal cells (ADSCs) to understand the potential of ADSCs to generate new vessels. Murine and human visceral adipose tissues were processed with collagenase to obtain ADSCs from the stromal vascular fraction. Freshly isolated murine and human ADSCs featured the expression of early markers of endothelial differentiation [uptake of DiI-labeled acetylated LDL, CD133, CD34, kinase insert domain receptor (KDR)], but not markers for more mature endothelial cells (CD31 and von Willebrand factor). In methylcellulose medium, multilocular cells positive for Oil Red O staining appeared after 6 days. After 10 days, clusters of ADSCs spontaneously formed branched tubelike structures, which were strongly positive for CD34 and CD31, while losing their ability to undergo adipocyte differentiation. In Matrigel, in the presence of endothelial growth factors ADSCs formed branched tubelike structures. By clonal assays in methylcellulose we also determined the frequency of granulocyte-macrophage (CFU-GM) and erythroid (BFU-E) colony-forming units from ADSCs, compared with bone marrow-derived stromal cells (BMSCs) used as a positive control. After 4–14 days, BMSCs formed 8 ± 3 BFU-E and 40 ± 10 CFU-GM, while ADSCs never produced colonies of myeloid progenitors. The developing adipose tissue has neovasculogenic potential, based on the recruitment of local rather than circulating progenitors. Adipose tissue might therefore be a viable autonomous source of cells for postnatal neovascularization.
Vasoconstrictive effect of hydrogen sulfide involves downregulation of cAMP in vascular smooth muscle cells
Authors: Lim Jia Jia , Liu Yi-Hong , Khin Ester Sandar Win , Bian Jin-Song
Published: September 2008

Hydrogen sulfide (H2S), a new endogenous mediator, produces both vasorelaxation and vasoconstriction. This study was designed to examine whether cAMP mediates the vasoconstrictive effect of H2S. We found that NaHS at a concentration range of 10–100 μM (yields ∼3–30 μM H2S) concentration-dependently reversed the vasodilation caused by isoprenaline and salbutamol, two β-adrenoceptor agonists, and forskolin, a selective adenylyl cyclase activator, in phenylephrine-precontracted rat aortic rings. Pretreatment with NaHS (10–100 μM) for 5 min also significantly attenuated the vasorelaxant effect of salbutamol and forskolin. More importantly, NaHS (5–100 μM) significantly reversed forskolin-induced cAMP accumulation in vascular smooth muscle cells. However, NaHS produced significant, but weaker, vasoconstriction in the presence of NG-nitro-l-arginine methyl ester (100 μM), a nitric oxide synthase inhibitor, or in endothelium-denuded aortic rings. Blockade of ATP-sensitive potassium channels with glibenclamide (10 μM) failed to attenuate the vasoconstriction induced by H2S. Taken together, we demonstrated for the first time that the vasoconstrictive effect of H2S involves the adenyly cyclase/cAMP pathway.
Glucagon receptor recycling: role of carboxyl terminus, β-arrestins, and cytoskeleton
Authors: Krilov Lada , Nguyen Amy , Miyazaki Teruo , Unson Cecilia G. , Bouscarel Bernard
Published: September 2008

Glucagon receptor (GR) activity and expression are altered in several diseases, including Type 2 diabetes. Previously, we investigated the mechanism of GR desensitization and internalization. The present study focused on the fate of internalized GR. Using both hamster hepatocytes and human embryonic kidney (HEK)-293 cells, we showed that internalized GR recycled to the plasma membrane within 30–60 min following stimulation of the cells with 100 nM glucagon. In HEK-293 cells and during recycling, GR colocalized with Rab4, Rab11, β-arrestin1, β-arrestin2, and actin filaments, in the cytosolic and/or perinuclear domains. Glucagon treatment triggered redistribution of actin filaments from the plasma membrane to the cytosol. GR coimmunoprecipitated with β-actin in both hepatocytes and HEK-293 cells. Downregulation of β-arrestin1 and β-arrestin2 or disruption of the cytoskeleton inhibited recycling, but not internalization of GR. Deletion of the GR carboxyl-terminal 70 amino acids abolished internalization of GR in response to glucagon while deletion of the last 40 amino acids only did not affect GR internalization and recycling. After exposure of the cells to either high concentrations or prolonged duration of glucagon, GR colocalized with lysosomes. GR degradation was inhibited by lysosomal, but not proteosomal, inhibitors. In conclusion, GR recycles through Rab4- and Rab11- positive vesicles. The actin cytoskeleton, β-arrestin1, β-arrestin2, and the receptor's carboxyl terminus are involved in recycling. Prolonged stimulation with glucagon targets GR for degradation in lysosomes. Therefore, the present study provides a better understanding of the GR recycling mechanism, which could become useful in the treatment of certain diseases, including diabetes.
Secreted bioactive factors fromBifidobacterium infantisenhance epithelial cell barrier function
Authors: Ewaschuk Julia B. , Diaz Hugo , Meddings Liisa , Diederichs Brendan , Dmytrash Andrea , Backer Jody , Looijer-van Langen Mirjam , Madsen Karen L.
Published: September 2008

Live probiotic bacteria are effective in reducing gut permeability and inflammation. We have previously shown that probiotics release peptide bioactive factors that modulate epithelial resistance in vitro. The objectives of this study were to determine the impact of factors released from Bifidobacteria infantis on intestinal epithelial cell permeability and tight junction proteins and to assess whether these factors retain their bioactivity when administered to IL-10-deficient mice. B. infantis conditioned medium (BiCM) was applied to T84 human epithelial cells in the presence and absence of TNF-α and IFN-γ. Transepithelial resistance (TER), tight junction proteins [claudins 1, 2, 3, and 4, zonula occludens (ZO)-1, and occludin] and MAP kinase activity (p38 and ERK) were examined. Acute effects of BiCM on intestinal permeability were assessed in colons from IL-10-deficient mice in Ussing chambers. A separate group of IL-1-deficient mice was treated with BiCM for 4 wk and then assessed for intestinal histological injury, cytokine levels, epithelial permeability, and immune response to bacterial antigens. In T84 cells, BiCM increased TER, decreased claudin-2, and increased ZO-1 and occludin expression. This was associated with enhanced levels of phospho-ERK and decreased levels of phospho-p38. BiCM prevented TNF-α- and IFN-γ-induced drops in TER and rearrangement of tight junction proteins. Inhibition of ERK prevented the BiCM-induced increase in TER and attenuated the protection from TNF-α and IFN-γ. Oral BiCM administration acutely reduced colonic permeability in mice whereas long-term BiCM treatment in IL-10-deficient mice attenuated inflammation, normalized colonic permeability, and decreased colonic and splenic IFN-γ secretion. In conclusion, peptide bioactive factors from B. infantis retain their biological activity in vivo and are effective in normalizing gut permeability and improving disease in an animal model of colitis. The effects of BiCM are mediated in part by changes in MAP kinases and tight junction proteins.
Significance of ERK nitration in portal hypertensive gastropathy and its therapeutic implications
Authors: Kinjo Nao , Kawanaka Hirofumi , Akahoshi Tomohiko , Yamaguchi Shohei , Yoshida Daisuke , Anegawa Go , Konishi Kozo , Tomikawa Morimasa , Tanoue Kazuo , Tarnawski Andrzej , Hashizume Makoto , Maehara Yoshihiko
Published: September 2008

Portal hypertensive (PHT) gastric mucosa increases susceptibility to injury and delayed mucosal healing. It is possible that nitration of ERK by peroxynitrite might alter MAPK (ERK) signaling in PHT gastric mucosa, leading to delayed mucosal healing, since excessive nitric oxide production is implicated in PHT gastric mucosa and MAPK (ERK) signaling induces cell proliferation and leads to gastric mucosal healing in response to injury. Portal hypertension was produced by staged portal vein ligation, and sham-operation (SO) rats served as controls. Lipid peroxide (LPO) and nitrotyrosine increased significantly in PHT gastric mucosa compared with SO rats. ERK activation was impaired in PHT gastric mucosa in response to ethanol injury, whereas no significant difference in the phosphorylation of MEK, an upstream molecule of ERK, was seen between the two groups. The nitration of ERK by peroxynitrite, as detected by the coimmunoprecipitation of ERK and nitrotyrosine, was significantly enhanced in PHT gastric mucosa. Administration of rebamipide, a gastroprotective drug that acts as an oxygen-derived free radical scavenger, significantly decreased LPO and nitrotyrosine as well as the nitration of ERK by peroxynitrite in PHT gastric mucosa, therefore normalizing ERK activation and restoring the gastric mucosal healing response to ethanol injury. Enhanced nitration of ERK by peroxynitrite is involved in the impaired MAPK (ERK) signaling in PHT gastric mucosa. These findings demonstrate a new molecular mechanism in which PHT gastric mucosa is predisposed to injury and impaired healing.
Bnip3 functions as a mitochondrial sensor of oxidative stress during myocardial ischemia and reperfusion
Authors: Kubli Dieter A. , Quinsay Melissa N. , Huang Chengqun , Lee Youngil , Gustafsson Åsa B.
Published: September 2008

Bcl-2/adenovirus E1B 19-kDa protein-interacting protein 3 (Bnip3) is a member of the Bcl-2 homology domain 3-only subfamily of proapoptotic Bcl-2 proteins and is associated with cell death in the myocardium. In this study, we investigated the potential mechanism(s) by which Bnip3 activity is regulated. We found that Bnip3 forms a DTT-sensitive homodimer that increased after myocardial ischemia-reperfusion (I/R). The presence of the antioxidant N-acetylcysteine reduced I/R-induced homodimerization of Bnip3. Overexpression of Bnip3 in cells revealed that most of exogenous Bnip3 exists as a DTT-sensitive homodimer that correlated with increased cell death. In contrast, endogenous Bnip3 existed mainly as a monomer under normal conditions in the heart. Screening of the Bnip3 protein sequence revealed a single conserved cysteine residue at position 64. Mutation of this cysteine to alanine (Bnip3C64A) or deletion of the NH2-terminus (amino acids 1-64) resulted in reduced cell death activity of Bnip3. Moreover, mutation of a histidine residue in the COOH-terminal transmembrane domain to alanine (Bnip3H173A) almost completely inhibited the cell death activity of Bnip3. Bnip3C64A had a reduced ability to interact with Bnip3, whereas Bnip3H173A was completely unable to interact with Bnip3, suggesting that homodimerization is important for Bnip3 function. A consequence of I/R is the production of reactive oxygen species and oxidation of proteins, which promotes the formation of disulfide bonds between proteins. Thus, these experiments suggest that Bnip3 functions as a redox sensor where increased oxidative stress induces homodimerization and activation of Bnip3 via cooperation of the NH2-terminal cysteine residue and the COOH-terminal transmembrane domain.