bluuebunny/crossref_metadata_2025 huggingface dataset:
Multicenter Comparison of the VITEK 2 Antifungal Susceptibility Test with the CLSI Broth Microdilution Reference Method for Testing Amphotericin B, Flucytosine, and Voriconazole against
Candida
spp
Authors: Pfaller M. A. , Diekema D. J. , Procop G. W. , Rinaldi M. G.
Published: October 2007

A fully automated commercial antifungal susceptibility test system (VITEK 2; bioMérieux, Inc., Hazelwood, MO) was compared in three different laboratories with the Clinical and Laboratory Standards Institute (formerly the NCCLS) reference broth microdilution method (BMD) by testing 2 quality control strains, 10 reproducibility strains, and 426 isolates of
Candida
spp. against amphotericin B, flucytosine, and voriconazole. Reference BMD MIC endpoints were established after 24 and 48 h of incubation. VITEK 2 system MIC endpoints were determined spectrophotometrically after 9.1 to 27.1 h of incubation (mean, 12 to 14 h). Excellent essential agreement (within 2 dilutions) between the VITEK 2 system and the 24- and 48-h BMD MICs was observed for all three antifungal agents: amphotericin B, 99.1% and 97%, respectively; flucytosine, 99.1% and 98.8%, respectively; and voriconazole, 96.7% and 96%, respectively. Both intra- and interlaboratory agreements were >98% for all three drugs. The overall categorical agreements between the VITEK 2 system and BMD for flucytosine and voriconazole were 98.1 to 98.6% at the 24-h BMD time point and 96.9 to 97.4% at the 48-h BMD time point. The VITEK 2 system reliably detected flucytosine and voriconazole resistance among
Candida
spp. and demonstrated excellent quantitative and qualitative agreement with the reference BMD method.
Multicenter Trials Need To Use the Same Assay for Hepatitis C Virus Viral Load Determination
Authors: Laperche Syria , Bouchardeau Françoise , Thibault Vincent , Pozzetto Bruno , Vallet Sophie , Rosenberg Arielle R. , Roque-Afonso Anne-Marie , Gassin Michèle , Stoll-Keller Françoise , Trimoulet Pascale , Gault Elyanne , Chanzy Bruno , Mercier Bernard , Branger Michel , Pawlotsky Jean-Michel , Henquell Cécile , Lunel Françoise , Gaudy-Graffin Catherine , Alain Sophie , Chaix Marie-Laure , Duverlie Gilles , Izopet Jacques , Lefrère Jean-Jacques
Published: October 2007

This study, involving 20 laboratories and using currently available assays for hepatitis C virus RNA quantification, demonstrated that differences in viral load values are due not to interlaboratory variations but rather to the nature of the assay itself. This underlines the importance of using the same assay in multicenter studies or when monitoring antiviral therapy.
Burkholderia pseudomallei
Endophthalmitis
Authors: Chen Kuan-Jen , Sun Ming-Hui , Hou Chiun-Ho , Sun Chi-Chin , Chen Tun-Lu
Published: October 2007

Melioidosis is an infectious disease caused by
Burkholderia pseudomallei
, a gram-negative bacillus. We report a case of endogenous endophthalmitis caused by
B. pseudomallei
that was treated with systemic and intravitreal ceftazidime. Finally, the patient achieved a final visual acuity of 20/60 without complication.
Differential Activation of Human Monocyte-Derived and Plasmacytoid Dendritic Cells by West Nile Virus Generated in Different Host Cells
Authors: Silva Maria Carlan , Guerrero-Plata Antonieta , Gilfoy Felicia D. , Garofalo Roberto P. , Mason Peter W.
Published: October 2007

Dendritic cells (DCs) play a central role in innate immunity and antiviral responses. In this study, we investigated the production of alpha interferon (IFN-α) and inducible chemokines by human monocyte-derived dendritic cells (mDCs) and plasmacytoid dendritic cells (pDCs) infected with West Nile virus (WNV), an emergent pathogen whose infection can lead to severe cases of encephalitis in the elderly, children, and immunocompromised individuals. Our experiments demonstrated that WNV grown in mammalian cells (WNVVero) was a potent inducer of IFN-α secretion in pDCs and, to a lesser degree, in mDCs. The ability of WNVVeroto induce IFN-α in pDCs did not require viral replication and was prevented by the treatment of cells with bafilomycin A1 and chloroquine, suggesting that it was dependent on endosomal Toll-like receptor recognition. On the other hand, IFN-α production in mDCs required viral replication and was associated with the nuclear translocation of IRF3 and viral antigen expression. Strikingly, pDCs failed to produce IFN-α when stimulated with WNV grown in mosquito cells (WNVC7/10), while mDCs responded similarly to WNVVeroor WNVC7/10. Moreover, the IFN-dependent chemokine IP-10 was produced in substantial amounts by pDCs in response to WNVVerobut not WNVC7/10, while interleukin-8 was produced in greater amounts by mDCs infected with WNVC7/10than in those infected with WNVVero. These findings suggest that cell-specific mechanisms of WNV recognition leading to the production of type I IFN and inflammatory chemokines by DCs may contribute to both the innate immune response and disease pathogenesis in human infections.
A Self-Excisable Infectious Bacterial Artificial Chromosome Clone of Varicella-Zoster Virus Allows Analysis of the Essential Tegument Protein Encoded by
ORF9
Authors: Tischer B. Karsten , Kaufer Benedikt B. , Sommer Marvin , Wussow Felix , Arvin Ann M. , Osterrieder Nikolaus
Published: October 2007

In order to facilitate the generation of mutant viruses of varicella-zoster virus (VZV), the agent causing varicella (chicken pox) and herpes zoster (shingles), we generated a full-length infectious bacterial artificial chromosome (BAC) clone of the P-Oka strain. First, mini-F sequences were inserted into a preexisting VZV cosmid, and the SuperCos replicon was removed. Subsequently, mini-F-containing recombinant virus was generated from overlapping cosmid clones, and full-length VZV DNA recovered from the recombinant virus was established in
Escherichia coli
as an infectious BAC. An inverted duplication of VZV genomic sequences within the mini-F replicon resulted in markerless excision of vector sequences upon virus reconstitution in eukaryotic cells. Using the novel tool, the role in VZV replication of the major tegument protein encoded by
ORF9
was investigated. A markerless point mutation introduced in the start codon by two-step en passant Red mutagenesis abrogated
ORF9
expression and resulted in a dramatic growth defect that was not observed in a revertant virus. The essential nature of
ORF9
for VZV replication was ultimately confirmed by restoration of the growth of the
ORF9
-deficient mutant virus using
trans
-complementation via baculovirus-mediated gene transfer.
Type I Interferon Production during Herpes Simplex Virus Infection Is Controlled by Cell-Type-Specific Viral Recognition through Toll-Like Receptor 9, the Mitochondrial Antiviral Signaling Protein Pathway, and Novel Recognition Systems
Authors: Rasmussen Simon B. , Sørensen Louise N. , Malmgaard Lene , Ank Nina , Baines Joel D. , Chen Zhijian J. , Paludan Søren R.
Published: October 2007

Recognition of viruses by germ line-encoded pattern recognition receptors of the innate immune system is essential for rapid production of type I interferon (IFN) and early antiviral defense. We investigated the mechanisms of viral recognition governing production of type I IFN during herpes simplex virus (HSV) infection. We show that early production of IFN in vivo is mediated through Toll-like receptor 9 (TLR9) and plasmacytoid dendritic cells, whereas the subsequent alpha/beta IFN (IFN-α/β) response is derived from several cell types and induced independently of TLR9. In conventional DCs, the IFN response occurred independently of viral replication but was dependent on viral entry. Moreover, using a HSV-1 UL15 mutant, which fails to package viral DNA into the virion, we found that entry-dependent IFN induction also required the presence of viral genomic DNA. In macrophages and fibroblasts, where the virus was able to replicate, HSV-induced IFN-α/β production was dependent on both viral entry and replication, and ablated in cells unable to signal through the mitochondrial antiviral signaling protein pathway. Thus, during an HSV infection in vivo, multiple mechanisms of pathogen recognition are active, which operate in cell-type- and time-dependent manners to trigger expression of type I IFN and coordinate the antiviral response.
Two-Way Antigenic Cross-Reactivity between Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Group 1 Animal CoVs Is Mediated through an Antigenic Site in the N-Terminal Region of the SARS-CoV Nucleoprotein
Authors: Vlasova Anastasia N. , Zhang Xinsheng , Hasoksuz Mustafa , Nagesha Hadya S. , Haynes Lia M. , Fang Ying , Lu Shan , Saif Linda J.
Published: October 2007

In 2002, severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged in humans, causing a global epidemic. By phylogenetic analysis, SARS-CoV is distinct from known CoVs and most closely related to group 2 CoVs. However, no antigenic cross-reactivity between SARS-CoV and known CoVs was conclusively and consistently demonstrated except for group 1 animal CoVs. We analyzed this cross-reactivity by an enzyme-linked immunosorbent assay (ELISA) and Western blot analysis using specific antisera to animal CoVs and SARS-CoV and SARS patient convalescent-phase or negative sera. Moderate two-way cross-reactivity between SARS-CoV and porcine CoVs (transmissible gastroenteritis CoV [TGEV] and porcine respiratory CoV [PRCV]) was mediated through the N but not the spike protein, whereas weaker cross-reactivity occurred with feline (feline infectious peritonitis virus) and canine CoVs. UsingEscherichia coli-expressed recombinant SARS-CoV N protein and fragments, the cross-reactive region was localized between amino acids (aa) 120 to 208. The N-protein fragments comprising aa 360 to 412 and aa 1 to 213 reacted specifically with SARS convalescent-phase sera but not with negative human sera in ELISA; the fragment comprising aa 1 to 213 cross-reacted with antisera to animal CoVs, whereas the fragment comprising aa 360 to 412 did not cross-react and could be a potential candidate for SARS diagnosis. Particularly noteworthy, a single substitution at aa 120 of PRCV N protein diminished the cross-reactivity. We also demonstrated that the cross-reactivity is not universal for all group 1 CoVs, because HCoV-NL63 did not cross-react with SARS-CoV. One-way cross-reactivity of HCoV-NL63 with group 1 CoVs was localized to aa 1 to 39 and at least one other antigenic site in the N-protein C terminus, differing from the cross-reactive region identified in SARS-CoV N protein. The observed cross-reactivity is not a consequence of a higher level of amino acid identity between SARS-CoV and porcine CoV nucleoproteins, because sequence comparisons indicated that SARS-CoV N protein has amino acid identity similar to that of infectious bronchitis virus N protein and shares a higher level of identity with bovine CoV N protein within the cross-reactive region. The TGEV and SARS-CoV N proteins are RNA chaperons with long disordered regions. We speculate that during natural infection, antibodies target similar short antigenic sites within the N proteins of SARS-CoV and porcine group 1 CoVs that are exposed to an immune response. Identification of the cross-reactive and non-cross-reactive N-protein regions allows development of SARS-CoV-specific antibody assays for screening animal and human sera.
Chaperones Activate Hepadnavirus Reverse Transcriptase by Transiently Exposing a C-Proximal Region in the Terminal Protein Domain That Contributes to ε RNA Binding
Authors: Stahl Michael , Beck Jürgen , Nassal Michael
Published: October 2007

All hepatitis B viruses replicate by protein-primed reverse transcription, employing a specialized reverse transcriptase, P protein, that carries a unique terminal protein (TP) domain. To initiate reverse transcription, P protein must bind to a stem-loop, ε, on the pregenomic RNA template. TP then provides a Y residue for covalent attachment of the first nucleotide of an ε-templated DNA oligonucleotide (priming reaction) that serves to initiate full-length minus-strand DNA synthesis. ε binding requires the chaperone-dependent conversion of inactive P protein into an activated, metastable form designated P*. However, how P* differs structurally from P protein is not known. Here we used an in vitro reconstitution system for active duck hepatitis B virus P combined with limited proteolysis, site-specific antibodies, and defined P mutants to structurally compare nonactivated versus chaperone-activated versus primed P protein. The data show that Hsp70 action, under conditions identical to those required for functional activation, transiently exposes the C proximal TP region which is, probably directly, involved in ε RNA binding. Notably, after priming and ε RNA removal, a very similar new conformation appears stable without further chaperone activity; hence, the activation of P protein is triggered by energy-consuming chaperone action but may be completed by template RNA binding.
Interaction of Vesicular Stomatitis Virus P and N Proteins: Identification of Two Overlapping Domains at the N Terminus of P That Are Involved in N
0
-P Complex Formation and Encapsidation of Viral Genome RNA
Authors: Chen Mingzhou , Ogino Tomoaki , Banerjee Amiya K.
Published: October 2007

The nucleocapsid (N) protein of nonsegmented negative-strand (NNS) RNA viruses, when expressed in eukaryotic cells, aggregates and forms nucleocapsid-like complexes with cellular RNAs. The phosphoprotein (P) has been shown to prevent such aggregation by forming a soluble complex with the N protein free from cellular RNAs (designated N
0
). The N
0
-P complex presumably mediates specific encapsidation of the viral genome RNA. The precise mechanism by which the P protein carries out this function remains unclear. Here, by using a series of deleted and truncated mutant forms of the P protein of vesicular stomatitis virus (VSV), Indiana serotype, we present evidence that the N-terminal 11 to 30 amino acids (aa) of the P protein are essential in keeping the N protein soluble. Furthermore, glutathione
S
-transferase fused to the N-terminal 40 aa by itself is able to form the N
0
-P complex. Interestingly, the N-terminal 40-aa stretch failed to interact with the viral genome N-RNA template whereas the C-terminal 72 aa of the P protein interacted specifically with the latter. With an in vivo VSV minigenome transcription system, we further show that a deletion mutant form of P (PΔ1-10) lacking the N-terminal 10 aa which is capable of forming the N
0
-P complex was unable to support VSV minigenome transcription, although it efficiently supported transcription in vitro in a transcription-reconstitution reaction when used as purified protein. However, the same mutant protein complemented minigenome transcription when expressed together with a transcription-defective P deletion mutant protein containing N-terminal aa 1 to 210 (PΔII+III). Since the minigenome RNA needs to be encapsidated before transcription ensues, it seems that the entire N-terminal 210 aa are required for efficient genome RNA encapsidation. Taking these results together, we conclude that the N-terminal 11 to 30 aa are required for N
0
-P complex formation but the N-terminal 210 aa are required for genome RNA encapsidation.
Human Herpesvirus 6A (HHV-6A) and HHV-6B Alter E2F1/Rb Pathways and E2F1 Localization and Cause Cell Cycle Arrest in Infected T Cells
Authors: Mlechkovich Guy , Frenkel Niza
Published: October 2007

E2F transcription factors play pivotal roles in controlling the expression of genes involved in cell viability as well as genes involved in cell death. E2F1 is an important constituent of this protein family, which thus far contains eight members. The interaction of E2F1 with its major regulator, retinoblastoma protein (Rb), has been studied extensively in the past two decades, concentrating on the role of E2F1 in transcriptional regulation and the role of Rb in cell replication and cancer formation. Additionally, the effect of viral infections on E2F1/Rb interactions has been analyzed for different viruses, concentrating on cell division, which is essential for viral replication. In the present study, we monitored E2F1-Rb interactions during human herpesvirus 6A (HHV-6A) and HHV-6B infections of SupT1 T cells. The results have shown the following dramatic alterations in E2F1-Rb pathways compared to the pathways of parallel mock-infected control cultures. (i) The E2F1 levels were elevated during viral infections. (ii) The cellular localization of E2F1 was dramatically altered, and it was found to accumulate both in the cytoplasmic and nuclear fractions, as opposed to the strict nuclear localization seen in the mock-infected cells. (iii) Although E2F1 expression was elevated, two exemplary target genes, cyclin E and MCM5, were not upregulated. (iv) The Rb protein was dephosphorylated early postinfection, a trait that also occurred with UV-inactivated virus. (v) Infection was associated with significant reduction of E2F1/Rb complexing. (vi) HHV-6 infections were accompanied by cell cycle arrest. The altered E2F1-Rb interactions and functions might contribute to the observed cell cycle arrest.
Mapping Protease Inhibitor Resistance to Human Immunodeficiency Virus Type 1 Sequence Polymorphisms within Patients
Authors: Poon Art F. Y. , Kosakovsky Pond Sergei L. , Richman Douglas D. , Frost Simon D. W.
Published: October 2007

Resistance genotyping provides an important resource for the clinical management of patients infected with human immunodeficiency virus type 1 (HIV-1). However, resistance to protease (PR) inhibitors (PIs) is a complex phenotype shaped by interactions among nearly half of the residues in HIV-1 PR. Previous studies of the genetic basis of PI resistance focused on fixed substitutions among populations of HIV-1, i.e., host-specific adaptations. Consequently, they are susceptible to a high false discovery rate due to founder effects. Here, we employ sequencing “mixtures” (i.e., ambiguous base calls) as a site-specific marker of genetic variation within patients that is independent of the phylogeny. We demonstrate that the transient response to selection by PIs is manifested as an excess of nonsynonymous mixtures. Using a sample of 5,651 PR sequences isolated from both PI-naive and -treated patients, we analyze the joint distribution of mixtures and eight PIs as a Bayesian network, which distinguishes residue-residue interactions from direct associations with PIs. We find that selection for resistance is associated with the emergence of nonsynonymous mixtures in two distinct groups of codon sites clustered along the substrate cleft and distal regions of PR, respectively. Within-patient evolution at several positions is independent of PIs, including those formerly postulated to be involved in resistance. These positions are under strong positive selection in the PI-naive patient population, implying that other factors can produce spurious associations with resistance, e.g., mutational escape from the immune response.
Analysis of Venezuelan Equine Encephalitis Virus Capsid Protein Function in the Inhibition of Cellular Transcription
Authors: Garmashova Natalia , Atasheva Svetlana , Kang Wenli , Weaver Scott C. , Frolova Elena , Frolov Ilya
Published: October 2007

The encephalitogenic New World alphaviruses, including Venezuelan (VEEV), eastern (EEEV), and western equine encephalitis viruses, constitute a continuing public health threat in the United States. They circulate in Central, South, and North America and have the ability to cause fatal disease in humans and in horses and other domestic animals. We recently demonstrated that these viruses have developed the ability to interfere with cellular transcription and use it as a means of downregulating a cellular antiviral response. The results of the present study suggest that the N-terminal, ∼35-amino-acid-long peptide of VEEV and EEEV capsid proteins plays the most critical role in the downregulation of cellular transcription and development of a cytopathic effect. The identified VEEV-specific peptide C
VEE
33-68 includes two domains with distinct functions: the α-helix domain, helix I, which is critically involved in supporting the balance between the presence of the protein in the cytoplasm and nucleus, and the downstream peptide, which might contain a functional nuclear localization signal(s). The integrity of both domains not only determines the intracellular distribution of the VEEV capsid but is also essential for direct capsid protein functioning in the inhibition of transcription. Our results suggest that the VEEV capsid protein interacts with the nuclear pore complex, and this interaction correlates with the protein's ability to cause transcriptional shutoff and, ultimately, cell death. The replacement of the N-terminal fragment of the VEEV capsid by its Sindbis virus-specific counterpart in the VEEV TC-83 genome does not affect virus replication in vitro but reduces cytopathogenicity and results in attenuation in vivo. These findings can be used in designing a new generation of live, attenuated, recombinant vaccines against the New World alphaviruses.
Dynamics of T-Cell Responses and Memory T Cells during Primary Simian Immunodeficiency Virus Infection in Cynomolgus Macaques
Authors: Karlsson Ingrid , Malleret Benoît , Brochard Patricia , Delache Benoît , Calvo Julien , Le Grand Roger , Vaslin Bruno
Published: October 2007

Cellular immune responses make an important contribution to both the control of human immunodeficiency virus (HIV) replication and disease progression. We used a pathogenic model of SIVmac251 infection of cynomolgus macaques to longitudinally evaluate cellular immune responses in association with various rates of disease progression. We found an inverse relationship between plasma viral load and the simian immunodeficiency virus (SIV)-specific T cells responses in peripheral blood and lymph nodes. SIV-specific T-cell responses in peripheral blood were transient during primary infection, with the highest responses detected around 3 months after infection. There was also a transient increase of central memory CD8
+
T cells in peripheral blood during primary infection, and effector memory T-cell counts in peripheral lymph nodes were increased. This study emphasizes the importance of the early virus-specific immune responses in the outcome of HIV/SIV disease and provides details about the changes of virus-specific immune responses over time.
Inhibition of Alpharetrovirus Replication by a Range of Human APOBEC3 Proteins
Authors: Wiegand Heather L. , Cullen Bryan R.
Published: October 2007

The mammalian APOBEC3 family of cytidine deaminases includes members that can act as potent inhibitors of retroviral infectivity and retrotransposon mobility. Here, we have examined whether the alpharetrovirus Rous sarcoma virus (RSV) is susceptible to inhibition by a range of human APOBEC3 proteins. We report that RSV is highly susceptible to inhibition by human APOBEC3G, APOBEC3F, and APOBEC3B and moderately susceptible to inhibition by human APOBEC3C and APOBEC3A. For all five proteins, inhibition of RSV infectivity was associated with selective virion incorporation and with C-to-T editing of the proviral DNA minus strand. In the case of APOBEC3G, editing appeared to be critical for effective inhibition. These data represent the first report of inhibition of retroviral infectivity and induction of proviral DNA editing by human APOBEC3A and reveal that alpharetroviruses, which do not normally encounter APOBEC3 proteins in their avian hosts, are susceptible to inhibition by all human APOBEC3 proteins tested. These data further suggest that the resistance of mammalian retroviruses to inhibition by the APOBEC3 proteins expressed in their normal host species is likely to have evolved subsequent to the appearance of this family of mammalian antiretroviral proteins some 35 million years ago; i.e., the base state of a naïve retrovirus is susceptibility to inhibition.
ERK- and JNK-Dependent Signaling Pathways Contribute toBombyx moriNucleopolyhedrovirus Infection
Authors: Katsuma Susumu , Mita Kazuei , Shimada Toru
Published: October 2007

Mitogen-activated protein kinases (MAPKs) often play important roles in virus infection. To explore intracellular signaling pathways induced by baculovirus infection, we examined the involvement of MAPKs inBombyx morinucleopolyhedrovirus (BmNPV) infection of BmN cells. We found that specific inhibitors of extracellular signal-regulated kinase (ERK) kinase and c-Jun NH2-terminal kinase (JNK) significantly reduced occlusion body (OB) formation and budded virus (BV) production. Next, we quantified OB and BV production after applying the inhibitors at different times postinfection (p.i.). The inhibitors significantly reduced OB and BV production to various extents when applied at 12 h p.i., indicating that the reduction of BmNPV infectivity by these inhibitors occurs at the late stage of infection. Also, we observed that these inhibitors markedly repressed or deregulated the expression of delayed early, late, and very late gene products. Western blot analysis using phospho-MAPK-specific antibodies showed that ERK and JNK were activated at the late stage of BmNPV infection. In addition, the magnitude and pattern of MAPK activation were dependent on the multiplicity of infection. To verify the effects of the inhibitors on BmNPV infection, we also attempted to knock down theB. morigenesBmErkandBmJnk, which encode ERK and JNK, respectively. Knockdown ofBmErkandBmJnkresulted in the reduced production of OBs and BVs, confirming that BmERK and BmJNK are involved in the BmNPV infection process. Taken together, these results indicate that the activation of MAPK signaling pathways is required for efficient infection by BmNPV.
Increased Immunogenicity of a DNA-Launched Venezuelan Equine Encephalitis Virus-Based Replicon DNA Vaccine
Authors: Ljungberg Karl , Whitmore Alan C. , Fluet Meagan E. , Moran Timothy P. , Shabman Reed S. , Collier Martha L. , Kraus Annette A. , Thompson Joseph M. , Montefiori David C. , Beard Clayton , Johnston Robert E.
Published: October 2007

A novel genetic vaccine that is based on a Venezuelan equine encephalitis virus (VEE) replicon launched from plasmid DNA is described. The plasmid encodes a VEE replicon under the transcriptional control of the cytomegalovirus immediate-early promoter (VEE DNA). The VEE DNA consistently expressed 3- to 15-fold more green fluorescent protein in vitro than did a conventional DNA vaccine. Furthermore, transfection with the DNA-launched VEE replicon induced apoptosis and type I interferon production. Inoculation of mice with VEE DNA encoding human immunodeficiency virus type 1 gp160 significantly increased humoral responses by several orders of magnitude compared to an equal dose of a conventional DNA vaccine. These increases were also observed at 10- and 100-fold-lower doses of the VEE DNA. Cellular immune responses measured by gamma interferon and interleukin 2 enzyme-linked immunospot assay were significantly higher in mice immunized with the VEE DNA at decreased doses. The immune responses induced by the VEE DNA-encoded antigen, however, were independent of an intact type I interferon signaling pathway. Moreover, the DNA-launched VEE replicon induced an efficient prime to a VEE replicon particle (VRP) boost, increasing humoral and cellular immunity by at least 1 order of magnitude compared to VEE DNA only. Importantly, immunization with VEE DNA, as opposed to VRP, did not induce any anti-VRP neutralizing antibodies. Increased potency of DNA vaccines and reduced vector immunity may ultimately have an impact on the design of vaccination strategies in humans.
MAGNETIC AND MAGNETOIMPEDANCE PROPERTIES OF NiFe AND CoNiFe FILMS PRODUCED BY ELECTRODEPOSITION TECHNIQUE
Authors: ATALAY F. E. , KAYA H. , ATALAY SELCUK
Published: October 2007

Recently, many studies have been carried out to develop ternary CoNiFe (cobalt/nickel/iron) and NiFe alloys due to their capacity of providing an extremely high saturation flux density and a low coercive field strength. In this study, the magnetic properties of NiFe and CoNiFe microtubes were investigated. NiFe and CoNiFe magnetic films were prepared by electrodeposition onto copper wires with a diameter of 50 μm. Coercivity of 61 A/m and a maximum MI response of 186% at a frequency of 900 kHz were obtained for NiFe , which was produced in the pH 1.8 solution.
THERMALLY INDUCED RE-TRAPPING OF IMPURITY PAIRS IN SILICON
Authors: TESSEMA GENENE
Published: October 2007

Trapping and de-trapping of the acceptor-donor impurity pairs in semiconductors have been studied in crystalline silicon. The existence of such pairs in semiconductors are reported to have influence on the optical and electrical properties of materials. The perturbed γ - γ angular correlation (PAC) method is employed here to study such thermally induced dynamics of impurity complexes in the host lattice. The various types of pairs which are identified via the measured quadrupole interaction frequencies (QIF) showed distinct population of the complexes at different annealing temperatures. Efforts made to re-trap formed complexes after their dissociation by high sample temperatures produce positive results for some impurities.
ANISOTROPIC DEPENDENCE OF GIANT MAGNETO-IMPEDANCE OF AN AMORPHOUS FERROMAGNETIC RIBBON ON BIASING FIELD
Authors: KAVIRAJ B. , GHATAK S. K.
Published: October 2007

The magneto-impedance (MI) in an amorphous ribbon of nominal composition Fe 73.5 Nb 3 Cu 1 Si 13.5 B 9 has been measured at 1 MHz at room temperature for different configurations of exciting AC and biasing DC fields. A large drop in both resistance and reactance is observed as a function of the magnetic field. When the DC and AC fields are parallel but normal to the axis of the ribbon, a smaller magnetic field is needed to reduce the impedance to its small saturated value compared to the situation when the fields are along the axis of the ribbon. A larger DC field is required to lower the impedance when the DC field acts perpendicularly to the plane of the ribbon. Such anisotropy in magneto-impedance is related to the anisotropic response of the magnetization of the ribbon. The large change of impedance is attributed to a large variation of AC permeability on the direction and magnitude of the DC biasing field.
EFFECT OF α-PARTICLE ENERGIES ON CR-39 LINE-SHAPED PARAMETERS USING POSITRON ANNIHILATION TECHNIQUE (PAT)
Authors: ABDEL-RAHMAN M. A. , ABDEL-RAHMAN M. , LOTFY YAHIA A. , BADAWI EMAD A. , ABO-ELSOUD M. , EISSA M.
Published: October 2007

Polyallyl diglycol carbonate "CR-39" is widely used in etched track-type particle detectors. Doppler-broadening positron annihilation (DBPAT) provides direct information about core and valence electrons in CR-39 due to radiation effects. It provides a non-destructive and non-interfering probe having a detecting efficiency. This paper reports the effect of irradiation α-particle intensity emitted from an 241 Am (5.486 MeV) source on the line-shaped S- and W-parameters for the CR-39 samples. The behavior of the line-shaped S- and W-parameters can be related to the different phases. Modification of the CR-39 samples due to irradiation were studied using X-ray diffraction (XRD) and scanning electron microscopy (SEM) techniques. The XRD chart reveals a new peak that starts to appear at 2.86 MeV α-particle energy. The appearance of this peak might be related to the phase transition. The phase transition in the CR-39 polycarbonate remains complex.
ELECTRON–PHONON INTERACTION IN WURTZITEAlxGa1-xNTERNARY CRYSTAL
Authors: WEI SHU YI , ZHANG FANG , LI WEI , ZHAO ZU , HUANG WEN DENG
Published: October 2007

Optical vibrations of the lattice and the electron-optical-phonon interaction in wurtzite ternary nitride-based crystals was studied using the pseudo-unit-cell approach. The Fröhlich coupling constants, polaron energy shifts and the effective masses of the polaron in the system were investigated using the perturbation method. It was found that the LO and TO phonons in wurtzite AlxGa1-xN exhibit the one-mode behavior. The effects of the unit-cell volume varying with the composition x of ternary nitride-based crystals were also investigated.
PHOTOACOUSTIC STUDIES ON TiAlN NANOSTRUCTURED THIN FILMS
Authors: SRINIVASAN R. , IRUDAYARAJ A. ALBERT , KUPPUSAMI P. , MOHANDAS E. , KALAINATHAN S. , RAMACHANDRAN K.
Published: October 2007

Nanostructured titanium aluminium nitride ( TiAlN ) thin films were prepared on Si (111) substrate by reactive DC magnetron sputtering technique for various N 2 flow rates. X-ray diffraction showed that the films are nanocrystalline and the grain size decreases from 14 nm to 5 nm as the N 2 flow rate is increased. The thermal properties are then studied by photoacoustic (PA) spectroscopy. The study revealed an increase in thermal diffusivity and conductivity with increasing N 2 flow rates, and the measured values of the thermal properties are significantly lower than those obtained with bulk materials which constitute TiAlN .
NANOSILICON FOR PHOTONIC APPLICATIONS
Authors: GHOSHAL S. K. , MOHAN DEVENDRA , KASSA TADESSE TENAW , SHARMA SUNITA
Published: October 2007

This presentation is a short review of some scientific insights on the possibilities of photonic applications of nanostructured silicon ( NS – Si ), porous Si ( p - Si ) and Si nanocrystals ( NC – Si ), one of the most interesting problems in nano-crystallite physics. The emission mechanism of a very bright photo-luminescence (PL) band and relatively weak electro-luminescence (EL) are presently the main issue. The basic question lies in whether the emission is an extrinsic or intrinsic property of nanocrystals. It is important from a fundamental physics viewpoint because of the potential application of Si wires and quantum dots in optoelectronic devices and information technology. Nanostructuring silicon is an effective way to turn silicon into a photonic material. It is observed that low-dimensional (one and two dimensions) silicon shows light amplification, photon confinement, photon trapping as well as non-linear optical effects. There is strong evidence of light localization and gas sensing properties of such nanostructures. Future nano-technology would replace electrical with optical interconnects, which has appealing potential for higher-speed performance and immunity to signal cross talk.
BALANCEDNESS OF THE CLASS OF INFINITE PERMUTATION GAMES AND RELATED CLASSES OF GAMES
Authors: FRAGNELLI VITO , LLORCA NATIVIDAD , TIJS STEF
Published: October 2007

Recently it is proved that all infinite assignment games have a non-empty core. Using this fact, and a technique suggested by L. S. Shapley for finite permutation games, we prove similar results for infinite permutation games. Infinite transportation games can be interpreted as a generalization of infinite assignment games. We show that infinite transportation games are balanced via a related assignment game. By using certain core elements of infinite transportation games it can be shown that infinite pooling games have a non-empty core.
TWO-OBJECT TWO-BIDDER SIMULTANEOUS AUCTIONS
Authors: SZENTES BALÁZS
Published: October 2007

Symmetric equilibria are constructed for a class of symmetric auction games. The games all have two identical bidders bidding in two simultaneous sealed-bid auctions for identical objects. Information is complete and the objects are either complements or substitutes. In both cases a continuum of mixed-strategy equilibria are identified. All these equilibria have a surprising structure: The supports of all the mixtures that generate equilibria are two one-dimensional curves, and they surround a two-dimensional set of pure best responses.
BENEFIT FUNCTION AND DUALITY IN FINITE NORMAL FORM GAMES
Authors: BRIEC WALTER
Published: October 2007

Luenberger (1992, 1994) introduced a function he terms the benefit function, that converts preferences into a numerical function and has some cardinal meaning. In this paper, we show that the benefit function enjoys many interesting properties in a game theory context. We point out that the benefit function can be adapted to compare the mixed profiles of a game. Along this line, inspired from the Luenberger's approach, we propose a dual framework and establish a characterization of Nash equilibriums in terms of the benefit function. Moreover, some criterions are provided to identify the efficient mixed strategies of a game (which differ from the Pareto efficient strategies). Finally, we go a bit further proposing some issue in comparing profiles and equilibriums of a game. This we do using the so-called Σ-subdifferential of the benefit function.
Dura mater-derived FGF-2 mediates mitogenic signaling in calvarial osteoblasts
Authors: Li Shuli , Quarto Natalina , Longaker Michael T.
Published: October 2007

Although dura mater tissue is believed to have an important role in calvarial reossification in many in vivo studies, few studies have shown the direct effect of dura mater cells on osteoblasts. In addition, no reports have yet identified the potential factor(s) responsible for various biological activities exerted by dura mater on calvarial reossification (e.g., cell proliferation). In this study, we tested the effect of dura mater on calvarial-derived osteoblasts by performing both heterotypic coculture and by culturing osteoblast cells with conditioned media harvested from dura mater cells of juvenile (3-day-old) and adult (30-day-old) mice. The results presented here demonstrate that cellular proliferation of juvenile osteoblast cells was significantly increased by juvenile dura mater either in the coculture system or when dura mater cell-conditioned medium was applied to the osteoblast cells. Moreover, high levels of FGF-2 protein were detected in juvenile dura mater cells and their conditioned medium. In contrast, low levels of FGF-2 protein were detected in adult dura mater cells, whereas FGF-2 protein was not detectable in their conditioned medium. Abrogation of the mitogenic effect induced by juvenile dura mater cell-conditioned medium was achieved by introducing a neutralizing anti-FGF-2 antibody, thus indicating that FGF-2 may be responsible for the mitogenic effect of the juvenile dura mater. Moreover, data obtained by exploring the three major FGF-2 signaling pathways further reinforced the idea that FGF-2 might be an important paracrine signaling factor in vivo supplied by the underlying dura mater to the overlying calvarial osteoblasts.
Activation of ADP-ribosylation factor regulates biogenesis of the ATP7A-containing trans-Golgi network compartment and its Cu-induced trafficking
Authors: Holloway Zoe G. , Grabski Robert , Szul Tomasz , Styers Melanie L. , Coventry Julie A. , Monaco Anthony P. , Sztul Elizabeth
Published: October 2007

ATP7A (MNK) regulates copper homeostasis by translocating from a compartment localized within the trans-Golgi network to the plasma membrane (PM) in response to increased copper load. The mechanisms that regulate the biogenesis of the MNK compartment and the trafficking of MNK are unclear. Here we show that the architecture of the MNK compartment is linked to the structure of the Golgi ribbon. Depletion of p115 tethering factor, which causes fragmentation of the Golgi ribbon, also disrupts the MNK compartment. In p115-depleted cells, MNK localizes to punctate structures that pattern on Golgi ministacks dispersed throughout the cell. Despite altered localization MNK trafficking still occurs, and MNK relocates from and returns to the fragmented compartment in response to copper. We further show that the biogenesis of the MNK compartment requires activation of ADP-ribosylation factor (Arf)1 GTPase, shown previously to facilitate the biogenesis of the Golgi ribbon. Activation of cellular Arf1 is prevented by 1) expressing an inactive “empty” form of Arf (Arf1/N126I), 2) expressing an inactive form of GBF1 (GBF1/E794K), guanine nucleotide exchange factor for Arf1, or 3) treating cells with brefeldin A, an inhibitor of GBF1 that disrupts MNK into a diffuse pattern. Importantly, preventing Arf activation inhibits copper-responsive trafficking of MNK to the PM. Our findings support a model in which active Arf is essential for the generation of the MNK compartment and for copper-responsive trafficking of MNK from there to the PM. Our findings provide an exciting foundation for identifying Arf1 effectors that facilitate the biogenesis of the MNK compartment and MNK traffic.
A dibenzoylmethane derivative protects dopaminergic neurons against both oxidative stress and endoplasmic reticulum stress
Authors: Takano Katsura , Kitao Yasuko , Tabata Yoshiyuki , Miura Hikari , Sato Kosuke , Takuma Kazuhiro , Yamada Kiyofumi , Hibino Satoshi , Choshi Tominari , Iinuma Munekazu , Suzuki Hiroto , Murakami Rika , Yamada Masashi , Ogawa Satoshi , Hori Osamu
Published: October 2007

The enhancement of intracellular stresses such as oxidative stress and endoplasmic reticulum (ER) stress has been implicated in several neurodegenerative disorders including Parkinson's disease (PD). During a search for compounds that regulate ER stress, a dibenzoylmethane (DBM) derivative 14-26 (2,2′-dimethoxydibenzoylmethane) was identified as a novel neuroprotective agent. Analysis in SH-SY5Y cells and in PC12 cells revealed that the regulation of ER stress by 14-26 was associated with its anti-oxidative property. 14-26 prevented the production of reactive oxygen species (ROS) when the cells were exposed to oxidants such as hydrogen peroxide and 6-hydroxydopamine (6-OHDA) or an ER stressor brefeldin A (BFA). 14-26 also prevented ROS-induced damage in both the ER and the mitochondria, including the protein carbonylation in the microsome and the reduction of the mitochondrial membrane potential. Further examination disclosed the presence of the iron-chelating activity in 14-26. In vivo, 14-26 suppressed both oxidative stress and ER stress and prevented neuronal death in the substantia nigra pars compacta (SNpc) after injection of 6-OHDA in mice. These results suggest that 14-26 is an antioxidant that protects dopaminergic neurons against both oxidative stress and ER stress and could be a therapeutic candidate for the treatment of PD.
Opposing roles of EGF in IFN-α-induced epithelial barrier destabilization and tissue repair
Authors: Lechner Judith , Malloth Nadia A. , Jennings Paul , Heckl Daniel , Pfaller Walter , Seppi Thomas
Published: October 2007

Balance between damaging influences and repair mechanisms determines the degree of tissue deterioration by inflammatory and other injury processes. Destabilization of the proximal tubular barrier has been previously shown to be induced by IFN-α, a cytokine crucial for linking innate and adaptive immune responses. EGF was implicated in rescue mechanisms from renal injury. To study the interplay between the two processes, we determined if EGF can prevent IFN-α-induced barrier permeabilization. EGF did not counteract but even exacerbated the IFN-α-induced decrease of transepithelial electrical resistance in LLC-PK1 monolayers. For this effect Erk1/2 activation was necessary, linking barrier regulation to EGF-induced cell cycle progression. In contrast to its damage-intensifying effect, EGF also facilitated the regeneration of epithelial barrier function after the termination of IFN-α treatment. This effect was not mediated by Erk1/2 activation or cell proliferation since U0126, an Erk1/2 inhibitor, did not prevent but ameliorated recovery. However, EGF accelerated the downregulation of caspase-3 in recovering cells. Similarly, a pan-caspase inhibitor was able to block caspase activity and, concomitantly, promote restoration of barrier function. Thus, barrier repair might be linked to an EGF-mediated antiapoptotic mechanism. EGF appears to sensitize epithelial cells to the detrimental effects of IFN-α but also helps to restore barrier function in the healing phase. The observed dual effect of EGF might be explained by the different impact of proproliferative and antiapoptotic signaling pathways during and after cytokine treatment. The timing of epithelial exposure to damaging agents and repair factors was identified as a crucial parameter determining tissue fate.
Atherosclerosis-prone hemodynamics differentially regulates endothelial and smooth muscle cell phenotypes and promotes pro-inflammatory priming
Authors: Hastings Nicole E. , Simmers Michael B. , McDonald Oliver G. , Wamhoff Brian R. , Blackman Brett R.
Published: October 2007

Atherosclerosis is an inflammatory disease that preferentially forms at hemodynamically compromised regions of altered shear stress patterns. Endothelial cells (EC) and smooth muscle cells (SMC) undergo phenotypic modulation during atherosclerosis. An in vitro coculture model was developed to determine the role of hemodynamic regulation of EC and SMC phenotypes in coculture. Human ECs and SMCs were plated on a synthetic elastic lamina and human-derived atheroprone, and atheroprotective shear stresses were imposed on ECs. Atheroprone flow decreased genes associated with differentiated ECs (endothelial nitric oxide synthase, Tie2, and Kruppel-like factor 2) and SMCs (smooth muscle α-actin and myocardin) and induced a proinflammatory phenotype in ECs and SMCs (VCAM-1, IL-8, and monocyte chemoattractant protein-1). Atheroprone flow-induced changes in SMC differentiation markers were regulated at the chromatin level, as indicated by decreased serum response factor (SRF) binding to the smooth muscle α-actin-CC(a/T)6GG (CArG) promoter region and decreased histone H4 acetylation. Conversely, SRF and histone H4 acetylation were enriched at the c- fos promoter in SMCs. In the presence of atheroprotective shear stresses, ECs aligned with the direction of flow and SMCs aligned more perpendicular to flow, similar to in vivo vessel organization. These results provide a novel mechanism whereby modulation of the EC phenotype by hemodynamic shear stresses, atheroprone or atheroprotective, play a critical role in mechanical-transcriptional coupling and regulation of the SMC phenotype.
Epidermal growth factor and sphingosine-1-phosphate stimulate Na+/H+exchanger activity in the human placental syncytiotrophoblast
Authors: Johnstone E. D. , Speake P. F. , Sibley C. P.
Published: October 2007

The Na+/H+exchanger (NHE) has a key role in intracellular pH ([pH]i) regulation of the syncytiotrophoblast in the human placenta and may have a role in the life cycle of this cell. In other cells the NHE (actually a family of up to 9 isoforms) is regulated by a variety of factors, but its regulation in the syncytiotrophoblast has not been studied. Here, we tested the hypotheses that EGF and sphingosine-1-phosphate (S1P), both of which affect trophoblast apoptosis and, in other cell types, NHE activity, stimulate syncytiotrophoblast NHE activity. Villous fragments from term human placentas were loaded with the pH-sensitive dye, BCECF. NHE activity was measured by following the recovery of syncytiotrophoblast [pH]ifollowing an imposed acid load, in the presence and absence of EGF, S1P, and specific inhibitors of NHE activity. Both EGF and S1P caused a dose-dependent upregulation of NHE activity in the syncytiotrophoblast. These effects were blocked by amiloride 500 μM (a nonspecific NHE blocker) and HOE694 100 μM (NHE blocker with NHE1 and 2 isoform selectivity). Effects of EGF were also reduced by the NHE3 selective blocker S3226 (used at 1 μM). These data provide the first evidence that both EGF and S1P stimulate NHE activity in the syncytiotrophoblast; they appear to do so predominantly by activating the NHE1 isoform.