bluuebunny/crossref_metadata_2025 huggingface dataset:
Transparent conducting amorphous Zn–Sn–O films deposited by simultaneous dc sputtering
Authors: Moriga Toshihiro , Hayashi Yukako , Kondo Kumiko , Nishimura Yusuke , Murai Kei-ichiro , Nakabayashi Ichiro , Fukumoto Hidenori , Tominaga Kikuo
Published: July 2004

The films of ZnO–SnO2 system were deposited on glass substrates by simultaneous dc magnetron sputtering apparatus, in which ZnO and SnO2:Sb (Sb2O5 3 wt % doped) targets faced each other. The substrate temperatures were maintained at 150, 250, and 350 °C, respectively. As an experimental parameter, current ratio δ=IZn/(IZn+ISn), which corresponds to ZnO target current (IZn) divided by the sum of ZnO and SnO2:Sb target currents (IZn+ISn), was adopted. Amorphous transparent films appeared for 0.50⩽δ⩽0.73, which could be correlated to compositions as [Zn]/([Sn]+[Zn])=0.33–0.67 by x-ray fluorescent analysis. At [Zn]/([Sn]+[Zn])=1/2 (δ=0.62), 2/3 (δ=0.73) and all other ratios in as-deposited films, neither crystalline ZnSnO3 nor Zn2SnO4 was obtained. Minimum resistivity of 4–6×10−2 Ω cm was found at δ=0.50, whose composition was approximately SnO2⋅ZnSnO3. Resistivity increased linearly with an increase of the current ratio, until the composition reached Zn2SnO4. The amorphous phase showed a constant Hall mobility of ∼10 cm2/V s and a linear decrease in carrier concentration with increasing Zn content.
Anisotropic growth of chromium films during sputter deposition on substrates in planetary motion
Authors: Janssen G. C. A. M. , Alkemade P. F. A. , Sivel V. G. M. , Grachev S. Yu. , Kamminga J.-D.
Published: July 2004

Chromium films were deposited in an industrial PVD machine, designed to coat three-dimensional (3D) objects. The machine is equipped with a substrate table that allows a planetary motion of the substrates in front of the target. Films with thickness ranging from 30 nm to 8.5 μm were deposited on Si wafers. All films are under tensile stress. The stress in the thinner films is radially symmetric. The stress in the thicker films is distinctly asymmetric. This asymmetric stress leads to an asymmetry in wafer curvature for the substrates covered with the thicker films. The thinner films exhibit a 110 fiber texture. The thicker films exhibit a “single crystal” type texture. A top view of the thicker films obtained by scanning electron microscopy shows anisotropy in grain shape. We discuss the coinciding occurrence of anisotropy in stress and microstructure.
Polymeric aperture masks for high performance organic integrated circuits
Authors: Muyres Dawn V. , Baude Paul F. , Theiss Steven , Haase Michael , Kelley Tommie W. , Fleming Patrick
Published: July 2004

The use of polymeric aperture masks to fabricate high performance pentacene-based integrated circuits is presented. The aperture masks are fabricated using a laser ablation process with capabilities of generating 10 μm features. A mask set consisting of 4–6 aligned layers has been fabricated and has been used to demonstrate functional rf-powered integrated circuits with 20 μm gate lengths. Devices consisted of shadow-mask patterned layers of gold, alumina, and pentacene. TFT mobilities greater than 2 cm2/V s were measured and propagation delays from 7-stage ring oscillators of less than 5 μs were observed. This all-additive, dry patterning method has been extended to the production of samples as large as 6 in.×6 in. Larger aperture masks are under investigation and continuing efforts are focused on automation of the alignment process.
Distinct Ensemble Codes in Hippocampal Areas CA3 and CA1
Authors: Leutgeb Stefan , Leutgeb Jill K. , Treves Alessandro , Moser May-Britt , Moser Edvard I.
Published: July 2004

The hippocampus has differentiated into an extensively connected recurrent stage (CA3) followed by a feed-forward stage (CA1). We examined the function of this structural differentiation by determining how cell ensembles in rat CA3 and CA1 generate representations of rooms with common spatial elements. In CA3, distinct subsets of pyramidal cells were activated in each room, regardless of the similarity of the testing enclosure. In CA1, the activated populations overlapped, and the overlap increased in similar enclosures. After exposure to a novel room, ensemble activity developed slower in CA3 than CA1, suggesting that the representations emerged independently.
Pairing Gap and In-Gap Excitations in Trapped Fermionic Superfluids
Authors: Kinnunen J. , Rodríguez M. , Törmä P.
Published: July 2004

We consider trapped atomic Fermi gases with Feshbach-resonance enhanced interactions in pseudogap and superfluid temperatures. We calculate the spectrum of radio-frequency (or laser) excitations for transitions that transfer atoms out of the superfluid state. The spectrum displays the pairing gap and also the contribution of unpaired atoms, that is, in-gap excitations. The results support the conclusion that a superfluid, in which pairing is a manybody effect, was observed in recent experiments on radio-frequency spectroscopy of the pairing gap.
Observation of the Pairing Gap in a Strongly Interacting Fermi Gas
Authors: Chin C. , Bartenstein M. , Altmeyer A. , Riedl S. , Jochim S. , Denschlag J. Hecker , Grimm R.
Published: July 2004

We studied fermionic pairing in an ultracold two-component gas of
6
Li atoms by observing an energy gap in the radio-frequency excitation spectra. With control of the two-body interactions through a Feshbach resonance, we demonstrated the dependence of the pairing gap on coupling strength, temperature, and Fermi energy. The appearance of an energy gap with moderate evaporative cooling suggests that our full evaporation brought the strongly interacting system deep into a superfluid state.
Basic Residues of the Retroviral Nucleocapsid Play Different Roles in Gag-Gag and Gag-Ψ RNA Interactions
Authors: Lee Eun-Gyung , Linial Maxine L.
Published: July 2004

The
Orthoretrovirus
Gag interaction (I) domain maps to the nucleocapsid (NC) domain in the Gag polyprotein. We used the yeast two-hybrid system to analyze the role of
Alpharetrovirus
NC in Gag-Gag interactions and also examined the efficiency of viral assembly and release in vivo. We could delete either or both of the two Cys-His (CH) boxes without abrogating Gag-Gag interactions. We found that as few as eight clustered basic residues, attached to the C terminus of the spacer peptide separating the capsid (CA) and NC domains in the absence of NC, was sufficient for Gag-Gag interactions. Our results support the idea that a sufficient number of basic residues, rather than the CH boxes, play the important role in Gag multimerization. We also examined the requirement for basic residues in Gag for packaging of specific packaging signal (Ψ)-containing RNA. Using a yeast three-hybrid RNA-protein interaction assay, second-site suppressors of a packaging-defective Gag mutant were isolated, which restored Ψ RNA binding. These suppressors mapped to the p10 or CA domains in Gag and resulted in either introduction of a positively charged residue or elimination of a negatively charged one. These results imply that the structural interactions of NC with other domains of Gag are necessary for Ψ RNA binding. Taken together, our results show that while Gag assembly only requires a certain number of positively charged amino acids, Gag binding to genomic RNA for packaging requires more complex interactions inherent in the protein tertiary structure.
Diverse Hepatitis C Virus Glycoproteins Mediate Viral Infection in a CD81-Dependent Manner
Authors: McKeating J. A. , Zhang L. Q. , Logvinoff C. , Flint M. , Zhang J. , Yu J. , Butera D. , Ho D. D. , Dustin L. B. , Rice C. M. , Balfe P.
Published: July 2004

We recently reported that retroviral pseudotypes bearing the hepatitis C virus (HCV) strain H and Con1 glycoproteins, genotype 1a and 1b, respectively, require CD81 as a coreceptor for virus-cell entry and infection. Soluble truncated E2 cloned from a number of diverse HCV genotypes fail to interact with CD81, suggesting that viruses of diverse origin may utilize different receptors and display altered cell tropism. We have used the pseudotyping system to study the tropism of viruses bearing diverse HCV glycoproteins. Viruses bearing these glycoproteins showed a 150-fold range in infectivity for hepatoma cells and failed to infect lymphoid cells. The level of glycoprotein incorporation into particles varied considerably between strains, generally reflecting the E2 expression level within transfected cells. However, differences in glycoprotein incorporation were not associated with virus infectivity, suggesting that infectivity is not limited by the absolute level of glycoprotein. All HCV pseudotypes failed to infect HepG2 cells and yet infected the same cells after transduction to express human CD81, confirming the critical role of CD81 in HCV infection. Interestingly, these HCV pseudotypes differed in their ability to infect HepG2 cells expressing a panel of CD81 variants, suggesting subtle differences in the interaction of CD81 residues with diverse viral glycoproteins. Our current model of HCV infection suggests that CD81, together with additional unknown liver specific receptor(s), mediate the virus-cell entry process.
Analysis of Integration Sites of Jaagsiekte Sheep Retrovirus in Ovine Pulmonary Adenocarcinoma
Authors: Cousens Christina , Bishop Jeanette V. , Philbey Adrian W. , Gill Clare A. , Palmarini Massimo , Carlson Jonathan O. , DeMartini James C. , Sharp J. Michael
Published: July 2004

Ovine pulmonary adenocarcinoma (OPA) is an infectious lung tumor of sheep caused by Jaagsiekte sheep retrovirus (JSRV). To test the hypothesis that JSRV insertional mutagenesis is involved in the oncogenesis of OPA, we cloned and characterized 70 independent integration sites from 23 cases of OPA. Multiple integration sites were identified in most tumors. BLAST analysis of the sequences did not disclose any potential oncogenic motifs or any identical integration sites in different tumors. Thirty-seven of the integration sites were mapped to individual chromosomes by PCR with a panel of sheep-hamster hybrid cell lines. Integration sites were found on 20 of the 28 sheep chromosomes, suggesting a random distribution. However, four integration sites from four different tumors mapped to chromosome 16. By Southern blot hybridization, probes derived from two of these sites mapped to within 5 kb of each other on normal sheep DNA. These sites were found within a single sheep bacterial artificial chromosome clone and were further mapped to only 2.5 kb apart, within an uncharacterized predicted gene and less than 200 kb from a mitogen-activated protein kinase-encoding gene. These findings suggest that there is at least one common integration site for JSRV in OPA and add weight to the hypothesis that insertional mutagenesis is involved in the development of this tumor.
Effect of Membrane Curvature-Modifying Lipids on Membrane Fusion by Tick-Borne Encephalitis Virus
Authors: Stiasny Karin , Heinz Franz X.
Published: July 2004

Enveloped viruses enter cells by fusion of their own membrane with a cellular membrane. Incorporation of inverted-cone-shaped lipids such as lysophosphatidylcholine (LPC) into the outer leaflet of target membranes has been shown previously to impair fusion mediated by class I viral fusion proteins, e.g., the influenza virus hemagglutinin. It has been suggested that these results provide evidence for the stalk-pore model of fusion, which involves a hemifusion intermediate (stalk) with highly bent outer membrane leaflets. Here, we investigated the effect of inverted-cone-shaped LPCs and the cone-shaped oleic acid (OA) on the membrane fusion activity of a virus with a class II fusion protein, the flavivirus tick-borne encephalitis virus (TBEV). This study included an analysis of lipid mixing, as well as of the steps preceding or accompanying fusion, i.e., binding to the target membrane and lipid-induced conformational changes in the fusion protein E. We show that the presence of LPC in the outer leaflet of target liposomes strongly inhibited TBEV-mediated fusion, whereas OA caused a very slight enhancement, consistent with a fusion mechanism involving a lipid stalk. However, LPC also impaired the low-pH-induced binding of a soluble form of the E protein to liposomes and its conversion into a trimeric postfusion structure that requires membrane binding at low pH. Because inhibition is already observed before the lipid-mixing step, it cannot be determined whether impairment of stalk formation is a contributing factor in the inhibition of fusion by LPC. These data emphasize, however, the importance of the composition of the target membrane in its interactions with the fusion peptide that are crucial for the initiation of fusion.
Caspases Mediate Processing of the Capsid Precursor and Cell Release of Human Astroviruses
Authors: Méndez Ernesto , Salas-Ocampo Elizabeth , Arias Carlos F.
Published: July 2004

In this work we have shown that astrovirus infection induces apoptosis of Caco-2 cells, since fragmentation of cellular DNA, cleavage of cellular proteins which are substrate of activated caspases, and a change in the mitochondrial transmembrane potential occur upon virus infection. The human astrovirus Yuc8 polyprotein capsid precursor VP90 is initially processed to yield VP70, and we have shown that this processing is trypsin independent and occurs intracellularly through four cleavages at its carboxy-terminal region. We further showed that VP90-VP70 processing is mediated by caspases, since it was blocked by the pancaspase inhibitor benzyloxycarbonyl-Val-Ala-Asp fluoromethylketone (z-VAD-fmk), and it was promoted by the apoptosis inducer TNF-related apoptosis-inducing ligand (TRAIL). Although the cell-associated virus produced in the presence of these compounds was not affected, the release of infectious virus to the cell supernatant was drastically reduced in the presence of z-VAD-fmk and increased by TRAIL, indicating that VP90-VP70 cleavage is important for the virus particles to be released from the cell. This is the first report that describes the induction and utilization of caspase activity by a virus to promote processing of the capsid precursor and dissemination of the viral particles.
Baculovirus Vectors Elicit Antigen-Specific Immune Responses in Mice
Authors: Facciabene Andrea , Aurisicchio Luigi , La Monica Nicola
Published: July 2004

To characterize the induction of antigen-specific immune response mediated by baculovirus, vectors expressing the E2 glycoprotein of hepatitis C virus or the carcinoembryonic antigen (CEA) under the control of the cytomegalovirus immediate-early promoter-enhancer were constructed. Additionally, a baculovirus vector encoding the E2 glycoprotein (Bac-G-E2) and expressing vesicular stomatitis virus glycoprotein (VSV-G) in the viral envelope was generated by inserting the VSV-G coding sequence downstream of the polyhedrin promoter. Mice were subjected to intramuscular, intranasal, or subcutaneous inoculations with Bac-E2 and the cellular immune response was monitored by ELISPOT and intracellular staining. Additionally, humoral response was monitored by titrating anti-E2 antibodies. Induction of a measurable anti-E2 T-cell response was observed only after intramuscular injection and was predominantly CD8
+
specific. The immunogenic properties of baculovirus as vaccine vector were not restricted to E2 because a CEA-specific CD4
+
T-cell response was observed upon intramuscular injection of Bac-CEA. Interestingly, the Bac-G-E2 vector was shown to be a more efficient immunogen than Bac-E2, in view of the 10-fold difference in the minimal dose required to elicit a measurable T-cell response upon intramuscular injection. Induction of inflammatory cytokines such as gamma interferon, tumor necrosis factor alpha, and interleukin-6 was detected as early as 6 h postinjection of Bac-G-E2. Most importantly, both vectors elicited CD8
+
T cells with effector function capable of lysing target cells loaded with a hepatitis C virus-specific epitope. Additionally, enhanced NK cytolytic activity was detected in immunized mice. Thus, these results further demonstrate that baculovirus may be considered a useful vector for gene therapy.
Model for the Interaction of Gammaherpesvirus 68 RING-CH Finger Protein mK3 with Major Histocompatibility Complex Class I and the Peptide-Loading Complex
Authors: Wang Xiaoli , Lybarger Lonnie , Connors Rose , Harris Michael R. , Hansen Ted H.
Published: July 2004

The mK3 protein of gammaherpesvirus 68 and the kK5 protein of Kaposi's sarcoma-associated herpesvirus are members of a family of structurally related viral immune evasion molecules that all possess a RING-CH domain with ubiquitin ligase activity. These proteins modulate the expression of major histocompatibility complex class I molecules (mK3 and kK5) as well as other molecules like ICAM-1 and B7.2 (kK5). Previously, mK3 was shown to ubiquitinate nascent class I molecules, resulting in their rapid degradation, and this process was found to be dependent on TAP and tapasin, endoplasmic reticulum molecules involved in class I assembly. Here, we demonstrate that in murine cells, kK5 does not affect class I expression but does downregulate human B7.2 molecules in a TAP/tapasin-independent manner. These differences in substrate specificity and TAP/tapasin dependence between mK3 and kK5 permitted us, using chimeric molecules, to map the sites of mK3 interaction with TAP/tapasin and to determine the requirements for substrate recognition by mK3. Our findings indicate that mK3 interacts with TAP1 and -2 via their C-terminal domains and with class I molecules via their N-terminal domains. Furthermore, by orienting the RING-CH domain of mK3 appropriately with respect to class I, mK3 binding to TAP/tapasin, rather than the presence of unique sequences in class I, appears to be the primary determinant of substrate specificity.
Human Cytomegalovirus-Encoded Interleukin-10 Homolog Inhibits Maturation of Dendritic Cells and Alters Their Functionality
Authors: Chang W. L. William , Baumgarth Nicole , Yu Dong , Barry Peter A.
Published: July 2004

Interleukin-10 (IL-10) suppresses the maturation and cytokine production of dendritic cells (DCs), key regulators of adaptive immunity, and prevents the activation and polarization of naïve T cells towards protective gamma interferon-producing effectors. We hypothesized that human cytomegalovirus (HCMV) utilizes its viral IL-10 homolog (cmvIL-10) to attenuate DC functionality, thereby subverting the efficient induction of antiviral immune responses. RNA and protein analyses demonstrated that the cmvIL-10 gene was expressed with late gene kinetics. Treatment of immature DCs (iDCs) with supernatant from HCMV-infected cultures inhibited both the lipopolysaccharide-induced DC maturation and proinflammatory cytokine production. These inhibitory effects were specifically mediated through the IL-10 receptor and were not observed when DCs were treated with supernatant of cells infected with a cmvIL-10-knockout mutant. Incubation of iDCs with recombinant cmvIL-10 recapitulated the inhibition of maturation. Furthermore, cmvIL-10 had pronounced long-term effects on those DCs that could overcome this inhibition of maturation. It enhanced the migration of mature DCs (mDCs) towards the lymph node homing chemokine but greatly reduced their cytokine production. The inability of mDCs to secrete IL-12 was maintained, even when they were restimulated by the activated T-cell signal CD40 ligand in the absence of cmvIL-10. Importantly, cmvIL-10 potentiates these anti-inflammatory effects, at least partially, by inducing endogenous cellular IL-10 expression in DCs. Collectively, we show that cmvIL-10 causes long-term functional alterations at all stages of DC activation.
Chimeras of Duck and Heron Hepatitis B Viruses Provide Evidence for Functional Interactions between Viral Components of Pregenomic RNA Encapsidation
Authors: Ostrow Kristin M. , Loeb Daniel D.
Published: July 2004

Packaging of hepadnavirus pregenomic RNA (pgRNA) into capsids, or encapsidation, requires several viral components. The viral polymerase (P) and the capsid subunit (C) are necessary for pgRNA encapsidation. Previous studies of duck hepatitis B virus (DHBV) indicated that two
cis-
acting sequences on pgRNA are required for encapsidation: ε, which is near the 5′ end of pgRNA, and region II, located near the middle of pgRNA. Later studies suggested that the intervening sequence between these two elements may also make a contribution. It has been demonstrated for DHBV that ε interacts with P to facilitate encapsidation, but it is not known how other
cis-
acting sequences contribute to encapsidation. We analyzed chimeras of DHBV and a related virus, heron hepatitis B virus (HHBV), to gain insight into the interactions between the various viral components during pgRNA encapsidation. We learned that having ε and P derived from the same virus was not sufficient for high levels of encapsidation, implying that other viral interactions contribute to encapsidation. Chimeric analysis showed that a large sequence containing region II may interact with P and/or C for efficient encapsidation. Further analysis demonstrated that possibly an RNA-RNA interaction between the intervening sequence and region II facilitates pgRNA encapsidation. Together, these results identify functional interactions among various viral components that contribute to pgRNA encapsidation.
A Short Peptide at the Amino Terminus of the Sendai Virus C Protein Acts as an Independent Element That Induces STAT1 Instability
Authors: Garcin Dominique , Marq Jean-Baptiste , Iseni Fréderic , Martin Stephen , Kolakofsky Daniel
Published: July 2004

The Sendai virus C protein acts to dismantle the interferon-induced cellular antiviral state in an MG132-sensitive manner, in part by inducing STAT1 instability. This activity of C maps to the first 23 amino acids (C
1-23
) of the 204-amino-acid (aa)-long protein (C
1-204
). C
1-23
was found to act as an independent viral element that induces STAT1 instability, since this peptide fused to green fluorescent protein (C
1-23
/GFP) is at least as active as C
1-204
in this respect. This peptide also induces the degradation of C
1-23
/GFP and other proteins to which it is fused. Most of C
1-204
, and particularly its amino-terminal half, is predicted to be structurally disordered. C
1-23
as a peptide was found to be disordered by circular dichroism, and the first 11 aa have a strong potential to form an amphipathic α-helix in low concentrations of trifluoroethanol, which is thought to mimic protein-protein interaction. The critical degradation-determining sequence of C
1-23
was mapped by mutation to eight residues near its N terminus:
4
FLKKILKL
11
. All the large hydrophobic residues of
4
FLKKILKL
11
, plus its ability to form an amphipathic α-helix, were found to be critical for STAT1 degradation. In contrast, C
1-23
/GFP self-degradation did not require
8
ILKL
11
, nor the ability to form an α-helix throughout this region. Remarkably, C
1-23
/GFP also stimulated C
1-204
degradation, and this degradation in
trans
required the same peptide determinants as for STAT1. Our results suggest that C
1-204
coordinates its dual activities of regulating viral RNA synthesis and counteracting the host innate antiviral response by sensing both its own intracellular concentration and that of STAT1.
Human Respiratory Coronavirus OC43: Genetic Stability and Neuroinvasion
Authors: St-Jean Julien R. , Jacomy Hélène , Desforges Marc , Vabret Astrid , Freymuth François , Talbot Pierre J.
Published: July 2004

The complete genome sequences of the human coronavirus OC43 (HCoV-OC43) laboratory strain from the American Type Culture Collection (ATCC), and a HCoV-OC43 clinical isolate, designated Paris, were obtained. Both genomes are 30,713 nucleotides long, excluding the poly(A) tail, and only differ by 6 nucleotides. These six mutations are scattered throughout the genome and give rise to only two amino acid substitutions: one in the spike protein gene (I958F) and the other in the nucleocapsid protein gene (V81A). Furthermore, the two variants were shown to reach the central nervous system (CNS) after intranasal inoculation in BALB/c mice, demonstrating neuroinvasive properties. Even though the ATCC strain could penetrate the CNS more effectively than the Paris 2001 isolate, these results suggest that intrinsic neuroinvasive properties already existed for the HCoV-OC43 ATCC human respiratory isolate from the 1960s before it was propagated in newborn mouse brains. It also demonstrates that the molecular structure of HCoV-OC43 is very stable in the environment (the two variants were isolated ca. 40 years apart) despite virus shedding and chances of persistence in the host. The genomes of the two HCoV-OC43 variants display 71, 53.1, and 51.2% identity with those of mouse hepatitis virus A59, severe acute respiratory syndrome human coronavirus Tor2 strain (SARS-HCoV Tor2), and human coronavirus 229E (HCoV-229E), respectively. HCoV-OC43 also possesses well-conserved motifs with regard to the genome sequence of the SARS-HCoV Tor2, especially in open reading frame 1b. These results suggest that HCoV-OC43 and SARS-HCoV may share several important functional properties and that HCoV-OC43 may be used as a model to study the biology of SARS-HCoV without the need for level three biological facilities.
Hepatitis C Virus Infection Activates the Immunologic (Type II) Isoform of Nitric Oxide Synthase and Thereby Enhances DNA Damage and Mutations of Cellular Genes
Authors: Machida Keigo , Cheng Kevin T.-H. , Sung Vicky M.-H. , Lee Ki Jeong , Levine Alexandra M. , Lai Michael M. C.
Published: July 2004

Hepatitis C virus (HCV) infection causes hepatitis, hepatocellular carcinoma, and B-cell lymphomas in a significant number of patients. Previously we have shown that HCV infection causes double-stranded DNA breaks and enhances the mutation frequency of cellular genes, including proto-oncogenes and immunoglobulin genes. To determine the mechanisms, we studied in vitro HCV infection of cell culture. Here we report that HCV infection activated the immunologic (type II) isoform of nitric oxide (NO) synthase (NOS), i.e., inducible NOS (iNOS), thereby inducing NO, which in turn induced DNA breaks and enhanced the mutation frequencies of cellular genes. Treatment of HCV-infected cells with NOS inhibitors or small interfering RNA specific for iNOS abolished most of these effects. Expression of the core protein or nonstructural protein 3 (NS3), but not the other viral proteins, in B cells or hepatocytes induced iNOS and DNA breaks, which could be blocked by NOS inhibitors. The core protein also enhanced the mutation frequency of cellular genes in hepatocytes derived from HCV core transgenic mice compared with that in control mice. The iNOS promoter was activated more than fivefold in HCV-infected cells, as revealed by a luciferase reporter assay driven by the iNOS promoter. Similarly, the core and NS3 proteins also induced the same effects. Therefore, we conclude that HCV infection can stimulate the production of NO through activation of the gene for iNOS by the viral core and NS3 proteins. NO causes DNA breaks and enhances DNA mutation. This sequence of events provides a mechanism for HCV pathogenesis and oncogenesis.
Beyond Help: Direct Effector Functions of Human Immunodeficiency Virus Type 1-Specific CD4+T Cells
Authors: Norris Philip J. , Moffett Howell F. , Yang Otto O. , Kaufmann Daniel E. , Clark Margaret J. , Addo Marylyn M. , Rosenberg Eric S.
Published: July 2004

The immune correlates of protection in human immunodeficiency virus type 1 (HIV-1) infection remain poorly defined, particularly the contribution of CD4+T cells. Here we explore the effector functions of HIV-1-specific CD4+T cells. We demonstrate HIV-1 p24-specific CD4+-T-cell cytolytic activity in peripheral blood mononuclear cells directly ex vivo and after enrichment by antigen-specific stimulation. We further show that in a rare long-term nonprogressor, both an HIV-1-specific CD4+-T-cell clone and CD4+T cells directly ex vivo exert potent suppression of HIV-1 replication. Suppression of viral replication was dependent on cell-cell contact between the effector CD4+T cells and the target cells. While the antiviral effector activity of CD8+T cells has been well documented, these results strongly suggest that HIV-1-specific CD4+T cells are capable of directly contributing to antiviral immunity.
Porcine Endogenous Retroviruses Infect Cells Lacking Cognate Receptors by an Alternative Pathway: Implications for Retrovirus Evolution and Xenotransplantation
Authors: Lavillette Dimitri , Kabat David
Published: July 2004

A PHQ motif near the amino termini of gammaretroviral envelope glycoprotein surface (SU) subunits is important for infectivity but not for incorporation into virions or binding to cognate receptors. The H residue of this motif is most critical, with all substitutions we tested being inactive. Interestingly, porcine endogenous retroviruses (PERVs) of all three host-range groups, A, B, and C, lack full PHQ motifs, but most members have an H residue at position 10. H10A PERV mutants are noninfectious but were efficiently transactivated by adding to the assays a PHQ-containing SU or receptor-binding subdomain (RBD) derived from a gibbon ape leukemia virus (GALV). A requirement of this transactivation was a functional GALV receptor on the cells. In contrast to this heterologous transactivation, PERV RBDs and SUs were inactive in all tested cells, including porcine ST-IOWA cells. Surprisingly, transactivation by GALV RBD enabled wild-type or H10A mutant PERVs of all three host-range groups to efficiently infect cells from humans and rodents that lack functional PERV receptors and it substantially enhanced infectivities of wild-type PERVs, even for cells with PERV receptors. Thus, PERVs can suboptimally infect cells that contain cognate receptors or they can employ a transactivation pathway to more efficiently infect all cells. This ability to infect cells lacking cognate receptors was previously demonstrated only for nontransmissible variant gammaretroviruses with recombinant and mutant envelope glycoproteins. We conclude that some endogenously inherited mammalian retroviruses also have a receptor-independent means for overcoming host-range and interference barriers, implying a need for caution in xenotransplantation, especially of porcine tissues.
Vaccinia Virus Morphogenesis: A13 Phosphoprotein Is Required for Assembly of Mature Virions
Authors: Unger Bethany , Traktman Paula
Published: July 2004

The 70-amino-acid A13L protein is a component of the vaccinia virus membrane. We demonstrate here that the protein is expressed at late times of infection, undergoes phosphorylation at a serine residue(s), and becomes encapsidated in a monomeric form. Phosphorylation is dependent on Ser40, which lies within the proline-rich motif SPPP. Because phosphorylation of the A13 protein is only minimally affected by disruption of the viral F10 kinase or H1 phosphatase, a cellular kinase is likely to be involved. We generated an inducible recombinant in which A13 protein expression is dependent upon the inclusion of tetracycline in the culture medium. Repression of the A13L protein spares the biochemical progression of the viral life cycle but arrests virion morphogenesis. Virion assembly progresses through the formation of immature virions (IVs); however, these virions do not acquire nucleoids, and DNA crystalloids accumulate in the cytoplasm. Further development into intracellular mature virions is blocked, causing a 1,000-fold decrease in the infectious virus yield relative to that obtained in the presence of the inducer. We also determined that the temperature-sensitive phenotype of the viral mutant C
ts
40 is due to a nucleotide transition within the A13L gene that causes a Thr
48
→Ile substitution. This substitution disrupts the function of the A13 protein but does not cause thermolability of the protein; at the nonpermissive temperature, virion morphogenesis arrests at the stage of IV formation. The A13L protein, therefore, is part of a newly recognized group of membrane proteins that are dispensable for the early biogenesis of the virion membrane but are essential for virion maturation.
Characterization of the Mouse Adeno-Associated Virus
AAVS1
Ortholog
Authors: Dutheil Nathalie , Yoon-Robarts Miran , Ward Peter , Henckaerts Els , Skrabanek Lucy , Berns Kenneth I. , Campagne Fabien , Linden R. Michael
Published: July 2004

The nonpathogenic human adeno-associated virus (AAV) has developed a mechanism to integrate its genome into human chromosome 19 at 19q13.4 (termed
AAVS1
), thereby establishing latency. Here, we provide evidence that the chromosomal signals required for site-specific integration are conserved in the mouse genome proximal to the recently identified
Mbs85
gene. These sequence motifs can be specifically nicked by the viral Rep protein required for the initiation of site-specific AAV DNA integration. Furthermore, these signals can serve as a minimal origin for Rep-dependent DNA replication. In addition, we isolated the mouse Mbs85 proximal promoter and show transcriptional activity in three mouse cell lines.
Ngari Virus Is a Bunyamwera Virus Reassortant That Can Be Associated with Large Outbreaks of Hemorrhagic Fever in Africa
Authors: Gerrard Sonja R. , Li Li , Barrett Alan D. , Nichol Stuart T.
Published: July 2004

Two isolates of a virus of the genus
Orthobunyavirus
(family
Bunyaviridae
) were obtained from hemorrhagic fever cases during a large disease outbreak in East Africa in 1997 and 1998. Sequence analysis of regions of the three genomic RNA segments of the virus (provisionally referred to as Garissa virus) suggested that it was a genetic reassortant virus with S and L segments derived from Bunyamwera virus but an M segment from an unidentified virus of the genus
Orthobunyavirus
. While high genetic diversity (52%) was revealed by analysis of virus M segment nucleotide sequences obtained from 21 members of the genus
Orthobunyavirus
, the Garissa and Ngari virus M segments were almost identical. Surprisingly, the Ngari virus L and S segments showed high sequence identity with those of Bunyamwera virus, showing that Garissa virus is an isolate of Ngari virus, which in turn is a Bunyamwera virus reassortant. Ngari virus should be considered when investigating hemorrhagic fever outbreaks throughout sub-Saharan Africa.
The relation between bone marrow angiogenesis and the proliferation index Ki-67 in multiple myeloma
Authors: Alexandrakis M G , Passam F H , Dambaki C , Pappa C A , Stathopoulos E N
Published: July 2004

Aim:Angiogenesis correlates with disease progression in various haematological malignancies. This study investigated the association between microvascular density (MVD) and the Ki-67 proliferation index (Ki-67 PI), bone marrow infiltration, and C reactive protein (CRP) in patients with multiple myeloma.

Methods:Bone marrow MVD was examined in 44 biopsies at diagnosis and 15 in plateau phase by immunostaining the endothelial cells with a monoclonal antibody to CD34. The Ki-67 PI was evaluated by a double immunostaining technique using the monoclonal antibodies MIB-1 and CD38.

Results:MVD, Ki-67 PI, bone marrow infiltration, and CRP were significantly higher in pretreatment patients than in controls and decreased in patients achieving plateau phase. MVD significantly correlated with Ki-67 PI and infiltration, and Ki-67 correlated with infiltration.

Conclusion:In multiple myeloma, apart from being a marker of proliferative activity, Ki-67 is also associated with bone marrow angiogenesis and tumour burden.
Intraepithelial lymphocytes in the villous tip: do they indicate potential coeliac disease?
Authors: Biagi F , Luinetti O , Campanella J , Klersy C , Zambelli C , Villanacci V , Lanzini A , Corazza G R
Published: July 2004

Background:The counting of intraepithelial lymphocytes (IELs) in the villous tips of architecturally normal small bowel biopsy specimens was proposed as a method to measure mucosal infiltration in gluten sensitive patients.

Aims:To apply this straightforward method in duodenal biopsy specimens from patients affected by potential coeliac disease (PCD) to verify whether it can discriminate these patients from controls.

Methods:Paraffin wax embedded duodenal sections from 11 patients affected by PCD were stained with an antihuman CD3 antibody. Sections from 19 patients affected by treated coeliac disease (TCD) and 17 patients in whom coeliac disease was excluded were stained with the same antibody to serve as controls. The slides were examined blindly. IELs/20 enterocytes in five randomly chosen villous tips were counted. Patients affected by PCD were all on a gluten containing diet. They had an architecturally normal duodenal mucosa and were positive for endomysial antibody. Both TCD and non-coeliac controls were negative for endomysial antibody.

Results:The mean villous tip IEL scores were 4.6 (SD, 1.5; range, 1.4–7.8) in non-coeliac controls, 7.9 (SD, 4.0; range, 2.0–18.6) in TCD, and 9.2 (SD, 4.7; range, 5.8–21.8) in patients with PCD. The difference between PCD and non-coeliac controls was significant.

Conclusions:This is a very simple and sufficiently reliable method to count IELs. In patients with an architecturally normal duodenal mucosa, the IEL count in villous tips helps to distinguish between patients with PCD and non-coeliac controls.
Proliferative activity in postmenopausal endometrium: the lurking potential for giving rise to an endometrial adenocarcinoma
Authors: Sivridis E , Giatromanolaki A
Published: July 2004

Aims:To investigate proliferation in disease free postmenopausal endometrium and that harbouring endometrial adenocarcinoma—is there a dynamic, yet lurking, potential for atrophic endometrium to give rise to endometrial adenocarcinoma?

Material/methods:The study comprised 84 disease free endometria from asymptomatic postmenopausal women who had undergone hysterectomy for prolapse, and 50 endometrioid cell type endometrial adenocarcinomas with adjacent uninvolved postmenopausal endometrium. The non-neoplastic tissues were separated histologically into active, inactive, and mixed forms, although only the first two categories were studied immunohistochemically for oestrogen and progesterone receptors (ERs, PRs), epidermal growth factor receptor (EGFR), Ki-67, and angiogenic activity.

Results:All postmenopausal endometria were atrophic, but only 42 were inactive; of the remaining samples, 22 were weakly proliferative and 20 were mixed active and inactive. In contrast, the non-neoplastic component of 43 of the 50 endometrial adenocarcinomas examined was of the active form; four specimens were of the pure and 39 of the mixed form. Interestingly, high ER and PR expression was seen in active and inactive endometria, but only the former were EGFR positive and had high proliferative (Ki-67) and angiogenic activity. A similar trend was also shown by the non-neoplastic atrophic endometrium adjacent to endometrial adenocarcinoma.

Conclusions:At least half of the disease free postmenopausal atrophic endometria show a weak proliferative pattern, either diffuse or focal, probably as a response to continuous low level oestrogenic stimulation. These tissues have a latent, although very small, carcinogenic potential, as demonstrated by the immunohistochemical profile and their frequent association with adjacent endometrial adenocarcinoma.
Synchronous ileal and colonic adenocarcinomas associated with Crohn’s disease: report of a case with a focus on genetic alterations and carcinogenesis
Authors: Baisse B , Fontolliet C , Bian Y S , Vuilleumier H , Benhattar J
Published: July 2004

Patients with Crohn’s disease have an increased risk of developing intestinal tumours. However, the carcinogenic mechanisms remain poorly understood. To address this question, this report describes an unusual case of Crohn’s disease complicated by synchronous small intestinal and colonic adenocarcinomas. Genetic events in both the tumours and their adjacent mucosae were evaluated and the tumorigenesis of these cancers is discussed.
A review of the heritability of idiopathic nephrolithiasis
Authors: Griffin D G
Published: July 2004

Familial aggregations of nephrolithiasis were already noted in the early 19th century and over the intervening years there has been gradual progression in classifying the familial forms of nephrolithiasis. To date, there are at least 10 different monogenic conditions where those affected have a predisposition to nephrolithiasis. However, all of these rare conditions probably account for less than 2% of renal stone formers. This review, rather than considering these clearly defined disorders, concentrates on research into the broad band of stone formers who have a propensity to nephrolithiasis without an obvious discrete genetic basis.
Expression of vascular endothelial growth factor D is associated with hypoxia inducible factor (HIF-1α) and the HIF-1α target gene DEC1, but not lymph node metastasis in primary human breast carcinomas
Authors: Currie M J , Hanrahan V , Gunningham S P , Morrin H R , Frampton C , Han C , Robinson B A , Fox S B
Published: July 2004

Background:Vascular endothelial growth factor D (VEGF-D) induces angiogenesis and lymphangiogenesis. Nodal metastasis is recognised as a powerful prognostic marker in breast carcinoma, but the molecular mechanisms underlying this process are unknown. Although it has been suggested that VEGF-D may regulate nodal metastasis, this is based largely on animal models, its role in human disease being unclear.

Aims:To measure the pattern and degree of VEGF-D protein expression in normal and neoplastic human breast tissues.

Methods:The pattern and degree of VEGF-D expression was measured in normal tissue and invasive carcinomas, and expression was correlated with clinicopathological parameters, hypoxia markers, and survival. Because other VEGF family members are affected by oestrogen, whether VEGF-D is regulated by oestrogen in breast cancer cell lines was also assessed.

Results:VEGF-D was significantly positively associated with hypoxia inducible factor (HIF-1α) (p = 0.03) and the HIF-1α regulated gene DEC1 (p = 0.001), but not lymph node status, the number of involved lymph nodes, patient age, tumour size, tumour grade, lymphovascular invasion, oestrogen receptor, progesterone receptor, c-erb-B2, or tumour histology (all p>0.05). There was no significant relation between tumour VEGF-D expression and relapse free (p = 0.78) or overall (p = 0.94) survival. VEGF-D expression was enhanced by oestrogen in MCF-7 and T47D breast cancer cells, and was blocked by hydroxytamoxifen.

Conclusion:These findings support a role for hypoxia and oestrogen induced VEGF-D in human breast cancer and also suggest that tamoxifen and related oestrogen antagonists may exert some of their antitumour effects through the abrogation of VEGF-D induced function.
Microvessel density and clinicopathological characteristics in hepatitis C virus and hepatitis B virus related hepatocellular carcinoma
Authors: Messerini L , Novelli L , Comin C E
Published: July 2004

Aims:To compare intratumorous microvessel density (MVD) and clinicopathological features in two different groups of hepatocellular carcinoma (HCC), namely: hepatitis B virus (HBV) related HCC (B-HCC) and HCV related HCC (C-HCC).

Methods:Fifty consecutive cases each of B-HCC and of C-HCC were studied. Microvessel numbers were assessed by staining for the antigen CD34; in each case, three areas with the highest numbers of microvessels were counted in both the intratumorous and the surrounding non-tumorous tissue; the mean value represented the final MVD.

Results:Patients with B-HCC were significantly younger than those with C-HCC (mean age, 60.1 (SD, 4.1)v66.4 (4.3) years); no significant differences were seen for sex or Child’s class distribution. The tumour diameter was larger in B-HCCs than in C-HCCs (mean, 5.6 (SD, 1.8)v3.8 (1.8) cm). Tumour microsatellite formation was significantly higher in C-HCCs (12v4 cases). No differences were found for histological subtype, degree of differentiation, tumour encapsulation, and vascular invasion. The mean MVD value was significantly higher in tumorous (mean, 54 (SD, 13.8)v38 (8.9)) and in the surrounding non-tumorous liver tissue (mean, 15 (SD, 4.3)v7 (3.1)) of C-HCCs.

Conclusions:C-HCCs present as smaller tumours in older patients, with a higher incidence of tumour microsatellite formation and higher MVD values both in the tumorous and the non-tumorous areas, suggesting a link between HCV infection, angiogenesis, and hepatocarcinogenesis.
Pineal yolk sac tumour with a solid pattern: a case report in a Chinese adult man with Down’s syndrome
Authors: Tan H W , Ty A , Goh S G N , Wong M C , Hong A , Chuah K L
Published: July 2004

Intracranial germ cell tumours are rare. The incidence of primary intracranial yolk sac tumour is even more uncommon, with only two reported cases being associated with Down’s syndrome in the English literature. This report details the findings of yolk sac tumour in the pineal region affecting a 22 year old Chinese man with Down’s syndrome. Histology revealed yolk sac tumour with only a solid pattern, potentially mimicking the more common germinoma in the pineal region. No other germ cell components were identified. This is the third report of intracranial yolk sac tumour manifesting in a patient with trisomy 21. The pathology of this tumour and its differential diagnoses are discussed.
Extensive psammomatous calcification of the uterus and cervix associated with a uterine serous carcinoma
Authors: Cameron R I , McCluggage W G
Published: July 2004

This report describes a uterine serous carcinoma with bilateral ovarian metastasis, which was associated with widespread extensive psammomatous calcification of the uterine leiomyomata, the myometrium, and the cervical stroma. These psammoma bodies were not associated with tumour or epithelial elements. This psammomatous calcification is rare, with no previous reports of similar cases. The presence of psammoma bodies is probably related to the serous carcinoma, raising the possibility that psammoma body formation in serous carcinomas is the result of a factor secreted locally by the tumour, rather than the widely held theory that their formation is secondary to necrosis, with subsequent dystrophic calcification within a papillary neoplasm.
ANOMALOUS BIAS DEPENDENCE OF THE NOISE IN POROUS SI LED
Authors: SZENTPÁLI BÉLA , MOHÁCSY TIBOR , BÁRSONY ISTVÁN
Published: July 2004

The current-voltage characteristics and the low-frequency noise spectra of p-type Si–Porous Si–Al diode like structures were investigated. Over 1 V forward biases a reasonable fit was obtained in the Fowler-Nordheim plot. Any attempts of accurately fitting the I-V characteristic by other known transport mechanisms failed. At lower biases, however, an additional current-component appears which shows a saturating character. This current component is ascribed to trap-assisted tunneling. The measured noise spectra show 1/f character; however the magnitude of the noise shows saturation with increasing biases instead of the usual case, where the noise power scales with I2, or V2. This finding is interpreted by a model of two parallel current paths. The noise arising from the smaller and saturating current determines the noise performance of the whole device.
NOISE ANALYSIS IN A 0.8 V FORWARD BODY-BIAS CMOS OP-AMP DESIGN
Authors: ZHANG C. , SRIVASTAVA A. , AJMERA P. K.
Published: July 2004

Noise model of a MOSFET, which includes the effect of forward-body bias, is proposed. Thermal noise and shot noise are extracted and their variations with the forward body-bias are compared. It is found that the shot noise increases with the forward body-bias and becomes significant above 0.4 V forward bias. A CMOS op-amp is designed utilizing forward body-bias technique combined with a level shift current mirror. The designed amplifier dissipates power of 40 μW and operates at ± 0.4 V to achieve a gain of 77 dB. The noise in this ultra low-power op-amp is also investigated. The total simulated output noise density of 320×10-12 V 2/ Hz in the ultra-low power op-amp design is slightly lower than the calculated 413×10-12 V 2/ Hz value from the proposed model.