bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epstein-Barr Virus Nuclear Protein EBNA3A Is Critical for Maintaining Lymphoblastoid Cell Line Growth
Authors: Maruo Seiji , Johannsen Eric , Illanes Diego , Cooper Andrew , Kieff Elliott 
Published: September 2003

ABSTRACT

To evaluate the role of Epstein-Barr Virus (EBV) nuclear antigen 3A (EBNA3A) in the continuous proliferation of EBV-infected primary B lymphocytes as lymphoblastoid cell lines (LCLs), we derived LCLs that are infected with a recombinant EBV genome that expresses EBNA3A fused to a 4-hydroxy-tamoxifen (4HT)-dependent mutant estrogen receptor hormone binding domain (EBNA3AHT). The LCLs grew similarly to wild-type LCLs in medium with 4HT despite a reduced level of EBNA3AHT fusion protein expression. In the absence of 4HT, EBNA3AHT moved from the nucleus to the cytoplasm and was degraded. EBNA3AHT-infected LCLs were unable to grow in medium without 4HT. The precise time to growth arrest varied inversely with cell density. Continued maintenance in medium without 4HT resulted in cell death, whereas readdition of 4HT restored cell growth. Expression of other EBNAs and LMP1, of CD23, and of c-
myc
was unaffected by EBNA3A inactivation. Wild-type EBNA3A expression from an oriP plasmid transfected into the LCLs protected the EBNA3AHT-infected LCLs from growth arrest and death in medium without 4HT, whereas EBNA3B or EBNA3C expression was unable to protect the LCLs from growth arrest and death. These experiments indicate that EBNA3A has a unique and critical role for the maintenance of LCL growth and ultimately survival. The EBNA3AHT-infected LCLs are also useful for genetic and biochemical analyses of the role of EBNA3A domains in LCL growth.
Purification, Identification, and Biochemical Characterization of a Host-Encoded Cysteine Protease That Cleaves a
Leishmaniavirus
Gag-Pol Polyprotein
Authors: Carrion Ricardo , Ro Young-Tae , Patterson Jean L. 
Published: September 2003

ABSTRACT

Leishmania RNA virus (LRV) is a double-stranded RNA virus that infects some strains of the protozoan parasite
Leishmania
. As with other totiviruses, LRV presumably expresses its polymerase by a ribosomal frameshift, resulting in a capsid-polymerase fusion protein. We have demonstrated previously that an LRV capsid-polymerase polyprotein is specifically cleaved by a
Leishmania
-encoded cysteine protease. This study reports the purification of this protease through a strategy involving anion-exchange chromatography and affinity chromatography. By using a Sepharose-immobilized lectin, concanavalin A, we isolated a fraction enriched with LRV polyprotein-specific protease activity. Analysis of the active fraction by sodium dodecyl sulfate-polyacrylamide gel electrophoreses and silver staining revealed a 50-kDa protein that, upon characterization by high-pressure liquid chromatography electrospray tandem mass spectrometry (electrospray ionization/MS/MS), was identified as a cysteine protease of trypanosomes. A partial amino acid sequence derived from the MS/MS data was compared with a protein database using BLAST software, revealing homology with several cysteine proteases of
Leishmania
and other trypanosomes. The protease exhibited remarkable temperature stability, while inhibitor studies characterized the protease as a trypsin-like cysteine protease—a novel finding for
Leishmania
. To elucidate substrate preferences, a panel of deletion mutations and single-amino-acid mutations were engineered into a Gag-Pol fusion construct that was subsequently transcribed and translated in vitro and then used in cleavage assays. The data suggest that there are a number of cleavage sites located within a 153-amino-acid region spanning both the carboxy-terminal capsid region and the amino-terminal polymerase domain, with LRV capsid exhibiting the greatest susceptibility to proteolysis.
Characterization of the Expression, Intracellular Localization, and Replication Complex Association of the Putative Mouse Hepatitis Virus RNA-Dependent RNA Polymerase
Authors: Brockway Sarah M. , Clay Corrie T. , Lu Xiao Tao , Denison Mark R. 
Published: September 2003

ABSTRACT

Mouse hepatitis virus (MHV) RNA synthesis is mediated by a viral RNA-dependent RNA polymerase (RdRp) on membrane-bound replication complexes in the host cell cytoplasm. However, it is not known how the putative MHV RdRp (Pol) is targeted to and retained on cellular membranes. In this report, we show that a 100-kDa protein was stably detected by an anti-Pol antiserum as a mature product throughout the virus life cycle. Gradient fractionation and biochemical extraction experiments demonstrated that Pol was not an integral membrane protein but was tightly associated with membranes and coimmunoprecipitated with the replicase proteins 3CLpro, p22, and p12. By immunofluorescence confocal microscopy, Pol colocalized with viral proteins at replication complexes, distinct from sites of virion assembly, over the entire course of infection. To determine if Pol associated with cellular membranes in the absence of other viral factors, the
pol
domain of gene 1 was cloned and expressed in cells as a fusion with green fluorescent protein, termed Gpol. In Gpol-expressing cells that were infected with MHV, but not in mock-infected cells, Gpol relocalized from a diffuse distribution in the cytoplasm to punctate foci that colocalized with markers for replication complexes. Expression of Gpol deletion mutants established that the conserved enzymatic domains of Pol were dispensable for replication complex association, but a 38-amino-acid domain in the RdRp unique region of Pol was required. This study demonstrates that viral or virus-induced factors are necessary for Pol to associate with membranes of replication complexes, and it identifies a defined region of Pol that may mediate its interactions with those factors.
Human Cytomegalovirus UL99-Encoded pp28 Is Required for the Cytoplasmic Envelopment of Tegument-Associated Capsids
Authors: Silva Maria C. , Yu Qian-Chun , Enquist Lynn , Shenk Thomas 
Published: September 2003

ABSTRACT

The human cytomegalovirus UL99-encoded pp28 is a myristylated phosphoprotein that is a constituent of the virion. The pp28 protein is positioned within the tegument of the virus particle, a protein structure that resides between the capsid and envelope. In the infected cell, pp28 is found in a cytoplasmic compartment derived from the Golgi apparatus, where the virus buds into vesicles to acquire its final membrane. We have constructed two mutants of human cytomegalovirus that fail to produce the pp28 protein, a substitution mutant (BAD
sub
UL99) and a point mutant (BAD
pm
UL99), and we have propagated them by complementation in pp28-expressing fibroblasts. Both mutant viruses are profoundly defective for growth in normal fibroblasts; no infectious virus could be detected after infection. Whereas normal levels of viral DNA and late proteins were observed in mutant virus-infected cells, large numbers of tegument-associated capsids accumulated in the cytoplasm that failed to acquire an envelope. We conclude that pp28 is required for the final envelopment of the human cytomegalovirus virion in the cytoplasm.
Nef Does Not Affect the Efficiency of Human Immunodeficiency Virus Type 1 Fusion with Target Cells
Authors: Tobiume Minoru , Lineberger Janet E. , Lundquist Christopher A. , Miller Michael D. , Aiken Christopher 
Published: September 2003

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) accessory protein Nef stimulates viral infectivity by an unknown mechanism. Recent studies have suggested that Nef may act by regulating the efficiency of virus entry into cells. Here we provide evidence to the contrary. Using a quantitative assay of HIV-1 virus-cell fusion, we observed equivalent rates and extents of fusion of wild-type and Nef-defective HIV-1 particles with MT-4 cells and CD4-expressing HeLa cells. In studies using soluble CD4 (sCD4) to inhibit infection, wild-type and Nef-defective HIV-1 escaped the sCD4 block with similar kinetics. We conclude that Nef acts at a postentry step in infection, probably by facilitating intracellular transport of the HIV-1 ribonucleoprotein complex.
Edge Detection Using Block Truncation Coding
Authors: Hu Yu-Chen , Chang Chin-Chen 
Published: August 2003

In this paper, a new edge detection scheme based on block truncation coding (BTC) is proposed. As we know, the BTC is a simple and fast scheme for digital image compression. To detect an edge boundary using the BTC scheme, the bit plane information of each BTC-compressed block is exploited, and a simple block type classifier is introduced. The experimental results show that the proposed scheme clearly detects the edge boundaries of digital images while requiring very little computational complexity. Meanwhile, the edge detection process can be incorporated into all BTC variant schemes. In other words, the newly proposed scheme provides a good approach for the detection of edge boundaries using block truncation coding.
RHEED Study of the Si(100) Surface Structure with Temperature
Authors: Quentel G. , Müller P. , Gauch M. , Hammadi Z. 
Published: August 2003

The structural properties of clean silicon (100) surface have been investigated by RHEED. The clean surface is reconstructed and the RHEED pattern shows superstructures associated to (2×1) and (1×2) domains. We recorded the intensity of the integer, as well as half order rods of the RHEED pattern, as a function of the crystal temperature from room temperature to 1500 K. The (1×2) domain grows at the expense of the others until it predominates. Between 1170 K and 1350 K the RHEED intensity of half order spots varies quickly and passes through a maximum. Such a behavior could be interpreted as originating from step bunching due to the heating mode (Joule effect by using DC current). At around 1350 K the half order spot decreases abruptly. The analysis of the intensity profile change versus temperature shows that the half width increases as the intensity decreases until the spot disappears. Analysis suggests that at arround 1400 K there is a lack of order at the crystal surface, which could originate in an incomplete melting.
LEEM Determination of Critical Terrace Widths for Si/Si(111) Step Flow Growth
Authors: Altman M. S. , Chung W. F. , Franz T. 
Published: August 2003

The condition for step flow growth of Si on the Si(111)-(7 × 7) surface has been investigated using low energy electron microscopy (LEEM). The critical terrace width for step flow growth was found to be independent of the azimuthal direction. This is consistent with isotropic diffusion and step flow kinetics. The dependence of the critical terrace width upon temperature for fixed incident flux (0.1 monolayer/minute) has also been measured. The square of the critical terrace width exhibits an Arrhenius behavior between 750 and 80 K with prefactor A = 7.0 × 1019 nm 2 and activation energy E = 2.05 eV. These values are significantly larger than those determined by Iwanari et al. [J. Cryst. Growth119, 241 (1992)] at lower temperatures and similar flux. Possible origins of this discrepancy, including the validity of the Arrhenius description, are discussed.
Structured Roughness of Si Surface Obtained by Molecular Beam Epitaxy on Highly Misoriented Si(111) Substrate
Authors: Gay J.-M. , Lapéna L. , Ladevèze M. , Tolan M. 
Published: August 2003

We present the results of an X-ray analysis of the surface morphology of a sample obtained by Si MBE onto a higly misoriented Si(111) substrate. X-ray reflectivity and diffuse scattering provide a description of the surface. The amplitude of the surface profile is about 6.6 nm, with a sawtooth shape. Satellites in the diffuse scattering indicate a 215±5 nm periodicity int he miscut direction. The analysis of satellite intensities shows an asymmetry of the surface shape. The results are in agreement with AFM images of the surface.
Formation of Nanoscale Structures on the Ge(111) Surface Under Mechanical Loading
Authors: Korsukov V. , Lukyanenko A. , Obidov B. 
Published: August 2003

Surface layers of Ge(111) under external mechanical loading have been investigated by EELS on plasmons and RHEED techniques. The positions of plasmon peaks and the diffraction patters were found to be strongly influenced by the external stress. Lattice dilatation in the layers 1 and 10 nm thick was estimated from the energy shifts of plasmon peaks under the applied load. It has been concluded that under high stress values of the order of 1 GPa the surface layers of Ge(111) undergo a transformation from the single-crystal to nanocrystallin state.
Si(111)-(7 × 7) Under Silane UHV-LPCVD: A STM Study
Authors: Masson L. , Albertini D. , Thibaudau F. , Salvan F. 
Published: August 2003

In this work, we present a scanning tunneling microscopy (STM) study of the LPCVD (low pressure chemical vapor deposition) growth of Si on Si(111)-(7 × 7) using silane ( SiH 4) decomposition. Surface reactivities have been studied at room and high temperature (700 < T < 800 K ), and the major chemical mechanisms have been identified at an atomic scale on the basis of room temperature STM images of the reacted surfaces. The study provides a better understanding of nucleation and initial stages of growth. More particularly, we show that the growth kinetics and the final structure of the film are different from what is observed by molecular beam epitaxial (MBE) growth.
The Behavior of Cs on S-Covered Si(100)-(2 × 1) and Si(100)-(1 × 1) Surfaces
Authors: Papageorgopoulos Aris , Mosby Dwight , Papageorgopoulos C. A. 
Published: August 2003

In this work we study the adsoption of Cs on (a) clean Si(100)-(2 × 1), (b) 0.5 ML of S-covered Si(100)-(2 × 1) and (c) 1 ML of S-covered Si(100)-(1 × 1) in ultrahigh vacuum (UHV). LEED and AES measurements suggest that the array of a Cs monolayer on clean and S-covered Si(100)-(2 × 1) surfaces was that of the double layer model, according to which, half of the Cs atoms reside on the raised sites of the dimers and the other half in the troughs. However, Cs on 1 ML of S-covered Si(100)-covered Si(100)-(1 × 1) forms initially a coplanar monolayer with the Cs atoms residing only on the same kind of sites. The presence of S on the Si surfaces increases the subsequently deposited (at RT) coverage of Cs to more than 1 ML. Structural models of Cs on clean and S-covered Si(100) surfaces are proposed.
Halogen Interaction with the Ge(111) and Ge(100) Surfaces
Authors: Göthelid M. , Le Lay G. , Wigren C. , Björkqvist M. , Karlsson U. O. 
Published: August 2003

A comparative study of the interaction of iodine and chlorine with Ge(1111) and Ge(100) has been performed using photoelectron spectroscopy. On the Ge(111) surface both adsorbates preferentially occupy the on-top T 1 site. In addition small amounts of GeX 2 species are found in bridge sites (X=I or Cl). On Ge(100)–I only Ge is formed at room temperature with one iodine atom on each dimer atom dangling bond. The halogen coverage at saturation has been estimated from survey spectra including both the Ge 3d and the I 4d or Cl 2p levels and from detailed Ge 3d spectra. These two approaches yield significantly different values; this discrepancy is interpreted as reflecting the presence of molecular species on top of the chemisorbed adlayer.
Growth of Aluminum on Silicon: Comparison of the Si(111)7 × 7 and Si(111)δ7 × 7–D Surfaces
Authors: Kharamtsova E. A. , Gołek F. , Bauer E. 
Published: August 2003

The initial stages of Al film formation on the clean Si(111)7 × 7 and deuterium-induced Si(111)δ7 × 7–D surfaces have been investigated using AES, LEED and TDS. Our experimental data show that epitaxial Al films form on both surfaces though the growth mode depends strongly on the substrate temperature and surface conditions. At about 90 K Al grows on the (7 × 7) surface in the quasi-Frank–van der Merwe mode forming crystallites of size 10–15 Å with Al(111)‖Si(111) and predominantly [Formula: see text]. The azimuthal disorder of about 10° is considerably reduced by annealing at room temperature. At and above 300 K the films grow in the Stranski–Krastanov mode with epitaxial Al(111) and Al(100) orientations. On the δ7 × 7–D surface Al grows at room temperature in the Volmer–Weber mode with epitaxial Al(111) and Al(100) islands. The film does not become continuous even at 30 ML Al, the largest Al coverage studied.
Elastic Strain Relaxation in Si1-xGex Layers Epitaxially Grown on Si Substrates
Authors: Berbezier I. , Gallas B. , Derrien J. 
Published: August 2003

We have investigated the elastic strain relaxation in Si 1-x Ge x layers grown by the molecular beam epitaxy (MBE) technique and in situ controlled with RHEED. Up to ≈0.8% critical lattice mismatch (about 20% Ge) uniform strained and flat layers were grown both on (111) and on (001) Si substrates. Calculations of the elastic constants evidenced a tetragonal distortion about 50% higher on (001) than on (111) in the same experimental conditions. At higher misfits (and/or thicknesses) a growth instability was evidenced only on (001) Si substrates. Si 1-x Ge x layers there displayed a surface layer undulation. On the contrary, Si 1-x Ge x layers grown on (111) Si substrates remained smooth throughout the growth up to the plastic relaxation of the layers. To determine stress fields in the Si 1-x Ge x layers, a high spatial resolution convergent beam electron diffraction (CBED) experiment was performed with a field effect analytical microscope. The CBED technique was applied to two typical cases: totally strained layer and undulated dislocation-free layer. In the latter case, CBED patterns recorded on nanometer scale areas of an undulation crest (cross-section sample) showed a gradual elastic relaxation mainly directed along the growth axis (z). Moreover a triclinic distortion of the unit cell was pointed out. These results were confirmed on a plane view sample. In conclusion, our results show that the driving force for the undulation is not the in-plane elastic relaxation since CBED experiments proved an important elastic relaxation of the (001) Si 1-x Ge x layers along the z axis. This was in agreement with the calculations of the elastic constants. We think that this could be at the origin of the undulation.
The Atomic Structure of the Si(111)-Pb Buried Interface Grown on the ${\rm Si}(111)\mbox{-}(\sqrt{3}\times\sqrt{3})\mbox{-}{\rm Pb}$ Reconstruction
Authors: Howes P. B. , Edwards K. A. , Macdonald J. E. , Hibma T. , Bootsman T. , James M. A. , Nicklin C. L. 
Published: August 2003

The Si(111)-Pb interface is a prototypical metal-semiconductor interface and has been the subject of a number of experimental studies. The Schottky barrier height is known to depend on the initial reconstruction formed by the first monolayer of Pb atoms and we have previously shown that there are structural differences between the buried interfaces. We present surface X-ray diffraction measurements of the interface grown from the incommensurate [Formula: see text] reconstruction and show that, in contrast to the starting surface, the interface comprises the junction between unreconstructed, bulk-like Si(111) and disordered, bulk-like Pb(111). This interface is contrasted with the interface formed by growth on the Si(111)-(7 × 7)-Pb reconstruction at which the starting reconstruction is preserved.
Monolayer Nitrogen Atom Incorporation at Buried Si-SiO2 Interfaces: Preparation by Remote Plasma Oxidation/Nitridation and Characterization by On-Line Auger Electron Spectroscopy
Authors: Lucovsky G. , Niimi H , Koh K. , Green M. L. 
Published: August 2003

This paper presents experimental studies in which N-atoms have been incorporated at Si-SiO 2 interfaces by forming the interface and oxide film by a 300°C remote-plasma-assisted nitridation/oxidation process using N 2 O . Process dynamics have been studied by on-line Auger electron spectroscopy (AES) by interrupted plasma processing. Based on AES studies using N 2 O , O 2 and sequenced N 2 O and O 2 source gases, reaction pathways for (i) N-atom incorporation at and/or (ii) removal from buried Si-SiO 2 interfaces have been identified, and contrasted with reaction pathways for nitridation using conventional furnace processing.
Atomic Structure of Hexagonal 6H– and 3C–SiC Surfaces
Authors: Schardt J. , Bernhardt J. , Starke U. , Heinz K. 
Published: August 2003

The crystallography of hexagonal SiC surfaces prepared ex situ by chemical methods was investigated by low energy electron diffraction (LEED) structure analysis. The surface morphology was analyzed by considering mixtures of domains with different surface layer stacking geometries. On the 6H–SiC(0001) surface ABCACB stacking is the dominating termination, covering about 80% of the surface. On [Formula: see text] all three possible surface stacking sequences are present. The (111) surface of a 3C–SiC film sample shows linear stacking of layers with only one domain orientation present. In contrast to the carbon-terminated 6H sample, the silicon-terminated surfaces are covered by an oxygen layer with the adatoms bound on top of silicon.
An ISS Study of Ga-Dimer Arrangement in the GaP(001)-(4 × 2) Surface
Authors: Oishi N. , Shoji F. , Konishi A. , Naitoh M. , Nishigaki S. 
Published: August 2003

A GaP(001) Ga-rich surface produced by ion sputtering followed by annealing exhibited a 4 × 2 LEED pattern with half streaks in the [110] direction. We have studied the structure of this surface by low-energy ion-scattering spectroscopy (ISS) using alkali ions ( Na +) .We have found a unit cell of the 4 × 2 structure consisting of two Ga dimers plus two dimer vacancies from the measured incidence-angle dependence of the scattered-ion intensity in the [Formula: see text] surface azimuth and an atomic separation in the Ga dimer being about 0.27 nm from that in the [110] surface azimuth. Evidence is presented showing the unit structures being arranged irregularly in the [Formula: see text] direction around the twofold positions.
Cs and Oxygen Adsorption on Ge(001) and GaAs(001) Surfaces Studied by Metastable De-Excitation Spectroscopy
Authors: Yamada K. , Nishigaki S. , Naitoh M. 
Published: August 2003

Metastable de-excitation spectroscopy (MDS) has been employed to elucidate the local electronic structure of oxygen plus alkali metal (Cs) coadsorbed layers on Ge(001)-(2×1) and GaAs(001)-(4×2) surfaces. Upon admission of oxygen at about 0.05–0.6 L, the MDS emission intensity due to Cs 6s-induced states [Formula: see text] mostly decreased, indicating direct transfer of [Formula: see text] electrons to oxygen. This initial step is followed by a steady process of substrate oxidation irrelevant to alkali charge transfer. Alkali-promoted oxygen uptake processes are discussed in connection with substrate-dependent variations in the [Formula: see text] charge states measured by MDS.
Growth of Cobalt on GaAs(001) Studied by Photoemission and Photoelectron Diffraction
Authors: Ababou S. , Lépine B. , Pingel R. , Godefroy A. , Quémerais A. , Guivarch A. , Jézéquel G. 
Published: August 2003

Co ultrathin films of increasing thickness (1–40 ML) are deposited on MBE grown GaAs(001) (As 2×4) substrates at RT and 200°C and studied by integrated photoemission and photoelectron diffraction. Co appears to grow on a reocted layer whose thickness strongly depends on deposition temperature (up to 4 nm at 200°C). This interfacial reacted layer appears to exhibit a layered structure composed of two compounds.