bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Strain Nodes and Electrode Configuration on Piezoelectric Energy Harvesting From Cantilevered Beams
Authors: Erturk A. , Tarazaga P. A. , Farmer J. R. , Inman D. J.
Published: January 2009

For the past five years, cantilevered beams with piezoceramic layer(s) have been frequently used as piezoelectric energy harvesters for vibration-to-electric energy conversion. Typically, the energy harvester beam is located on a vibrating host structure and the dynamic strain induced in the piezoceramic layer(s) results in an alternating voltage output across the electrodes. Vibration modes of a cantilevered piezoelectric energy harvester other than the fundamental mode have certain strain nodes where the dynamic strain distribution changes sign in the direction of beam length. It is theoretically explained and experimentally demonstrated in this paper that covering the strain nodes of vibration modes with continuous electrodes results in strong cancellations of the electrical outputs. A detailed dimensionless analysis is given for predicting the locations of the strain nodes of a cantilevered beam in the absence and presence of a tip mass. Since the cancellation issue is not peculiar to clamped-free boundary conditions, dimensionless data of modal strain nodes are tabulated for some other practical boundary condition pairs and these data can be useful in modal actuation problems as well. How to avoid the cancellation problem in energy harvesting by using segmented electrode pairs is described for single-mode and multimode vibrations of a cantilevered piezoelectric energy harvester. An electrode configuration-based side effect of using a large tip mass on the electrical response at higher vibration modes is discussed theoretically and demonstrated experimentally.
Crack Identification in a Rotating Shaft via the Reverse Directional Frequency Response Functions
Authors: Seo Yun-Ho , Lee Chong-Won , Park K. C.
Published: January 2009

A method is proposed for identifying the location of an open transverse crack in flexible rotor systems by modeling the crack as a localized element with rotating asymmetry. It exploits the strong correlations between the modal constants of the reverse directional frequency response functions (r-dFRFs) and the degree and location of asymmetry. A map of the modal constants of the r-dFRFs for all elements is constructed to identify the location of crack by comparing the identified modal constants to those of the reference map. This paper also addresses practical issues associated with measurement noises and limited number of sensors. The proposed crack identification method is finally applied to a flexible rotor system with an open transverse crack in order to demonstrate the identification procedure for detection of the crack location.
Stability of a Nonlinear Axially Moving String With the Kelvin–Voigt Damping
Authors: Shahruz S. M.
Published: January 2009

In this note, a nonlinear axially moving string with the Kelvin–Voigt damping is considered. It is proved that the string is stable, i.e., its transversal displacement converges to zero when the axial speed of the string is less than a certain critical value. The proof is established by showing that a Lyapunov functional corresponding to the string decays to zero exponentially. It is also shown that the string displacement is bounded when a bounded distributed force is applied to it transversally. Furthermore, a few open problems regarding the stability of strings with the Kelvin–Voigt damping are stated.
Darwin's Originality
Authors: Bowler Peter J.
Published: January 2009

Charles Darwin's theory of natural selection has been hailed as one of the most innovative contributions to modern science. When first proposed in 1859, however, it was widely rejected by his contemporaries, even by those who accepted the general idea of evolution. This article identifies those aspects of Darwin's work that led him to develop this revolutionary theory, including his studies of biogeography and animal breeding, and his recognition of the role played by the struggle for existence.
Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon
Authors: Turanov Anton A. , Lobanov Alexey V. , Fomenko Dmitri E. , Morrison Hilary G. , Sogin Mitchell L. , Klobutcher Lawrence A. , Hatfield Dolph L. , Gladyshev Vadim N.
Published: January 2009

Strict one-to-one correspondence between codons and amino acids is thought to be an essential feature of the genetic code. However, we report that one codon can code for two different amino acids with the choice of the inserted amino acid determined by a specific 3′ untranslated region structure and location of the dual-function codon within the messenger RNA (mRNA). We found that the codon UGA specifies insertion of selenocysteine and cysteine in the ciliate
Euplotes crassus
, that the dual use of this codon can occur even within the same gene, and that the structural arrangements of
Euplotes
mRNA preserve location-dependent dual function of UGA when expressed in mammalian cells. Thus, the genetic code supports the use of one codon to code for multiple amino acids.
Self-Organization of a Mesoscale Bristle into Ordered, Hierarchical Helical Assemblies
Authors: Pokroy Boaz , Kang Sung H. , Mahadevan L. , Aizenberg Joanna
Published: January 2009

Mesoscale hierarchical helical structures with diverse functions are abundant in nature. Here we show how spontaneous helicity can be induced in a synthetic polymeric nanobristle assembling in an evaporating liquid. We use a simple theoretical model to characterize the geometry, stiffness, and surface properties of the pillars that favor the adhesive self-organization of bundles with pillars wound around each other. The process can be controlled to yield highly ordered helical clusters with a unique structural hierarchy that arises from the sequential assembly of self-similar coiled building blocks over multiple length scales. We demonstrate their function in the context of self-assembly into previously unseen structures with uniform, periodic patterns and controlled handedness and as an efficient particle-trapping and adhesive system.
Suppression of Metallic Conductivity of Single-Walled Carbon Nanotubes by Cycloaddition Reactions
Authors: Kanungo Mandakini , Lu Helen , Malliaras George G. , Blanchet Graciela B.
Published: January 2009

The high carrier mobility of films of semiconducting single-walled carbon nanotubes (SWNTs) is attractive for electronics applications, but the presence of metallic SWNTs leads to high off-currents in transistor applications. The method presented here, cycloaddition of fluorinated olefins, represents an effective approach toward converting the “as grown” commercial SWNT mats into high-mobility semiconducting tubes with high yield and without further need for carbon nanotube separation. Thin-film transistors, fabricated from percolating arrays of functionalized carbon nanotubes, exhibit mobilities >100 square centimeters per volt-second and on-off ratios of 100,000. This method should allow for the use of semiconducting carbon nanotubes in commercial electronic devices and provide a low-cost route to the fabrication of electronic inks.
Comparison of Intracellular Cytokine Flow Cytometry and an Enzyme Immunoassay for Evaluation of Cellular Immune Response to Active Tuberculosis
Authors: Leung Wai Lin , Law Kai Leung , Leung Veronica Sui Shan , Yip Chi Wai , Leung Chi Chiu , Tam Cheuk Ming , Kam Kai Man
Published: January 2009

A prospective cross-sectional blinded study of 28 patients (21 male and 7 female patients; mean age, 44 years) with suspected active tuberculosis (TB) attending a TB and chest clinic is described. Blood was taken for immune cell enumeration, a whole-blood enzyme-linked immunosorbent assay (ELISA) for the detection of gamma interferon (IFN-γ) by the QuantiFERON-TB Gold (QFT-G) assay, and intracellular cytokine flow cytometry (ICC) analysis; and sputum was simultaneously taken for bacteriological culture for
Mycobacterium tuberculosis
. Twelve healthy subjects were included as controls. The performance characteristics of the QFT-G and ICC assays for the detection of active TB were compared. Among the patients with active TB, we found (i) normal to slightly elevated peripheral CD4
+
and CD8
+
T-cell counts but a significant reduction in the number of NK cells; (ii) CD4
+
T cells were the major cell type producing IFN-γ, a type 1 cytokine; (iii) small percentages of CD8
+
T cells were also primed for IFN-γ production; (iv) the production of interleukin-4 (IL-4), a type 2 cytokine, was not prominent; and (v) the sensitivity and the specificity of the QFT-G assay were 88.2% and 18%, respectively, and those of the ICC assay were 94.1% and 36.4%, respectively. The specificities of the blood tests were likely underestimated due to cross-reaction to a non-
M. tuberculosis
mycobacterial infection and the lack of a confirmatory test that could be used to diagnose latent
M. tuberculosis
infection. Flow cytometry accurately locates the pool of immunological effector cells responsible for cytokine production during active TB. The ICC assay is an additional useful tool for the diagnosis of active TB.
Serological Diagnosis of Human Herpes Simplex Virus Type 1 and 2 Infections by Luciferase Immunoprecipitation System Assay
Authors: Burbelo Peter D. , Hoshino Yo , Leahy Hannah , Krogmann Tammy , Hornung Ronald L. , Iadarola Michael J. , Cohen Jeffrey I.
Published: January 2009

Highly quantitative and high-throughput serological tests for evaluation of humoral responses to herpes simplex virus 1 (HSV-1) and HSV-2 are not available. The efficacy of luciferase immunoprecipitation system (LIPS) assays for antibody profiling and serologic diagnosis of HSV-1 and HSV-2 infection was investigated using a panel of five recombinant HSV antigens. Plasma samples from subjects seropositive for HSV-1 and/or HSV-2 or seronegative for HSV-1 and HSV-2 that had previously been analyzed by Western blotting and the Focus Plexus immunoassay were evaluated. The LIPS test measuring anti-gG1 antibody titers was 96% sensitive and 96% specific for detecting HSV-1 infection, compared with the Focus immunoassay, and was 92% sensitive and 96% specific, compared with Western blotting. The results for the anti-gG2 LIPS test for HSV-2 precisely matched those for Western blotting, with 100% sensitivity and 100% specificity, and showed robust antibody titers in all the HSV-2-infected samples that were over 1,000 times higher than those in HSV-2-negative or HSV-1-positive samples. Antibodies to three additional HSV-2 proteins, gB, gD, and ICP8, were detected in many of the HSV-1- and/or HSV-2-infected plasma samples and showed preferentially higher immunoreactivity in HSV-2-infected plasma. The titers of antibodies to these three HSV-2 antigens also significantly correlated with each other (
R
= 0.75 to 0.81;
P
< 0.0001). These studies indicate that the robust anti-gG1 and anti-gG2 antibody responses detected by LIPS assays are useful for HSV-1 and HSV-2 detection and suggest that profiling of antibody responses to a panel of HSV proteins may be useful for characterizing individual humoral responses to infection and for monitoring responses to vaccines.
Simultaneous Detection of
Haemophilus influenzae
Type b Polysaccharide-Specific Antibodies and
Neisseria meningitidis
Serogroup A, C, Y, and W-135 Polysaccharide-Specific Antibodies in a Fluorescent-Bead-Based Multiplex Immunoassay
Authors: de Voer Richarda M. , Schepp Rutger M. , Versteegh Florens G. A. , van der Klis Fiona R. M. , Berbers Guy A. M.
Published: January 2009

We expanded the meningococcal serogroup A, C, Y, and W-135 multiplex immunoassay (MIA) to simultaneously detect immunoglobulin type G antibodies directed toward
Haemophilus influenzae
type b polysaccharide (HibPS). The monoplex HibPS assay was compared to a HibPS-specific competitive enzyme-linked immunosorbent assay and showed a good correlation (
R
= 0.96). Furthermore, no cross-reactivity between HibPS and the four meningococcal serogroups was detected. This pentaplex meningococcal Hib MIA is a useful tool to investigate serological responses toward different childhood PS vaccines.
Multicenter Evaluation of the Cepheid Xpert Methicillin-Resistant
Staphylococcus aureus
(MRSA) Test as a Rapid Screening Method for Detection of MRSA in Nares
Authors: Wolk D. M. , Picton E. , Johnson D. , Davis T. , Pancholi P. , Ginocchio C. C. , Finegold S. , Welch D. F. , de Boer M. , Fuller D. , Solomon M. C. , Rogers B. , Mehta M. S. , Peterson L. R.
Published: January 2009

The first U.S. multicenter clinical trial to assess the performance of the Cepheid Xpert MRSA assay (Xpert MRSA) was conducted. The assay is a qualitative test designed for the rapid detection of methicillin-resistant
Staphylococcus aureus
(MRSA) directly from nares swabs. This novel test combines integrated nucleic acid extraction and automated real-time PCR for the detection of a MRSA-specific signature sequence. A total of 1,077 nares specimens were collected from seven geographically distinct health care sites across the United States with prevalence rates ranging from 5.2% to 44%. Nares specimens were tested by (i) the Xpert MRSA assay, (ii) direct culture on CHROMagar MRSA medium (direct CM culture), and (iii) broth-enriched culture (Trypticase soy broth with 6.5% sodium chloride) followed by plating onto CHROMagar MRSA medium (broth-enriched CM culture). When direct CM culture was designated the reference method, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert MRSA assay were 94.3%, 93.2%, 73.0%, and 98.8%, respectively. When broth-enriched CM culture was used as the reference method, the clinical sensitivity, specificity, PPV, and NPV of the Xpert MRSA assay were 86.3%, 94.9%, 80.5%, and 96.6%, respectively. The BD GeneOhm MRSA (BDGO) assay was performed as a comparative molecular method. No statistical performance differences were observed between the Xpert MRSA and BDGO assays when they were compared to culture methods. From this large-scale, multicenter clinical comparison, we conclude that the Xpert MRSA assay is a simple, rapid, and accurate method for performing active surveillance for MRSA in a variety of health care populations.
Evaluation of an Automated Nucleic Acid Extractor for Hepatitis C Virus Load Quantification
Authors: Martró Elisa , García-Sierra Nerea , González Victoria , Saludes Verónica , Matas Lurdes , Ausina Vicenç
Published: January 2009

The increasing use of molecular methods strongly motivates clinical laboratories to introduce automated nucleic acid extractors. We compared the easyMAG (bioMérieux) with a manual extraction method for hepatitis C virus (HCV) load quantification (RealTi
me
HCV; Abbott). Both methods were comparable, and, therefore, the easyMAG is suitable to be implemented in our laboratory for the management of HCV-infected patients.
Generation of Herpesvirus Entry Mediator (HVEM)-Restricted Herpes Simplex Virus Type 1 Mutant Viruses: Resistance of HVEM-Expressing Cells and Identification of Mutations That Rescue Nectin-1 Recognition
Authors: Uchida Hiroaki , Shah Waris A. , Ozuer Ali , Frampton Arthur R. , Goins William F. , Grandi Paola , Cohen Justus B. , Glorioso Joseph C.
Published: January 2009

Both initial infection and cell-to-cell spread by herpes simplex virus type 1 (HSV-1) require the interaction of the viral glycoprotein D (gD) with an entry receptor on the cell surface. The two major HSV entry receptors, herpesvirus entry mediator (HVEM) and nectin-1, mediate infection independently but are coexpressed on a variety of cells. To determine if both receptors are active in these instances, we have established mutant viruses that are selectively impaired for recognition of one or the other receptor. In plaque assays, these viruses showed approximately 1,000-fold selectivity for the matched receptor over the mismatched receptor. Separate assays showed that each virus is impaired for both infection and spread through the mismatched receptor. We tested several human tumor cell lines for susceptibility to these viruses and observed that HT29 colon carcinoma cells are susceptible to infection by nectin-1-restricted virus but are highly resistant to HVEM-restricted virus infection, despite readily detectable HVEM expression on the cell surface. HVEM cDNA isolated from HT29 cells rendered HSV-resistant cells permissive for infection by the HVEM-restricted virus, suggesting that HT29 cells lack a cofactor for HVEM-mediated infection or express an HVEM-specific inhibitory factor. Passaging of HVEM-restricted virus on nectin-1-expressing cells yielded a set of gD missense mutations that each restored functional recognition of nectin-1. These mutations identify residues that likely play a role in shaping the nectin-1 binding site of gD. Our findings illustrate the utility of these receptor-restricted viruses in studying the early events in HSV infection.
P64, a Novel Major Virion DNA-Binding Protein Potentially Involved in Condensing the
Spodoptera frugiperda Ascovirus 1a
Genome
Authors: Tan Yeping , Spears Tatsinda , Bideshi Dennis K. , Johnson Jeffrey J. , Hice Robert , Bigot Yves , Federici Brian A.
Published: January 2009

We recently identified 21 structural proteins in the virion of
Spodoptera frugiperda ascovirus 1a
(SfAV1a), a virus with a large, double-stranded DNA genome of 157 kbp, which attacks species of the lepidopteran family Noctuidae. The two most abundant virion proteins were the major capsid protein and a novel protein (P64) of 64 kDa that contained two distinct domains not known previously to occur together. The amino-terminal half of P64 (residues 1 to 263) contained four repeats (a recently recognized motif with an unknown function) of a virus-specific two-cysteine adaptor. Adjoined to this, the carboxy-terminal half of P64 (residues 279 to 455) contained 14 copies of a highly basic, tandemly repeated motif rich in arginine and serine, having an 11- to 13-amino-acid consensus sequence, SPSQRRSTS(V/K)(A/S)RR, yielding a predicted isoelectric point of 12.2 for this protein. In the present study, we demonstrate by Southwestern analysis that SfAV1a P64 was the only virion structural protein that bound DNA. Additional electrophoretic mobility shift assays showed that P64 bound SfAV1a as well as non-SfAV1a DNA. Furthermore, we show through immunogold labeling of ultrathin sections that P64 is a component of virogenic stroma and appears to be progressively incorporated into the SfAV1a DNA core during virion assembly. As no other virion structural protein bound DNA and no basic DNA-binding proteins of lower mass are encoded by the SfAV1a genome or were identified by proteomic analysis, our results suggest that P64's function is to condense the large genome of this virus and assist in packaging this genome into its virion.
Internal Initiation Stimulates Production of p8 Minicore, a Member of a Newly Discovered Family of Hepatitis C Virus Core Protein Isoforms
Authors: Eng Francis J. , Walewski Jose L. , Klepper Arielle L. , Fishman Sarah L. , Desai Suresh M. , McMullan Laura K. , Evans Matthew J. , Rice Charles M. , Branch Andrea D.
Published: January 2009

The hepatitis C virus (HCV)
core
gene is more conserved at the nucleic acid level than is necessary to preserve the sequence of the core protein, suggesting that it contains information for additional functions. We used a battery of anticore antibodies to test the hypothesis that the
core
gene directs the synthesis of core protein isoforms. Infectious viruses, replicons, and RNA transcripts expressed a p8 minicore containing the C-terminal portion of the p21 core protein and lacking the N-terminal portion. An interferon resistance mutation, U271A, which creates an AUG at codon 91, upregulated p8 expression in Con1 replicons, suggesting that p8 is produced by an internal initiation event and that 91-AUG is the preferred, but not the required, initiation codon. Synthesis of p8 was independent of p21, as shown by the abundant production of p8 from transcripts containing an UAG stop codon that blocked p21 production. Three infectious viruses, JFH-1 (2a
core
), J6/JFH (2a
core
), and H77/JFH (1a
core
), and a bicistronic construct, Bi-H77/JFH, all expressed both p8 and larger isoforms. The family of minicores ranges in size from 8 to 14 kDa. All lack the N-terminal portion of the p21 core. In conclusion, the
core
gene contains an internal signal that stimulates the initiation of protein synthesis at or near codon 91, leading to the production of p8. Infectious viruses of both genotype 1 and 2 HCV express a family of larger isoforms, in addition to p8. Minicores lack significant portions of the RNA binding domain of p21 core. Studies are under way to determine their functions.
An HLA-A2-Restricted T-Cell Epitope Mapped to the BNLF2a Immune Evasion Protein of Epstein-Barr Virus That Inhibits TAP
Authors: Bell Melissa J. , Abbott Rachel J. M. , Croft Nathan P. , Hislop Andrew D. , Burrows Scott R.
Published: January 2009

The early lytic cycle protein of Epstein-Barr virus (EBV), BNLF2a, has recently been shown to play a critical role in immune evasion by inhibiting the peptide transporter associated with antigen processing (TAP), thereby blocking antigen-specific CD8+T-cell recognition of many lytic cycle antigens. Surprisingly, we now show that a peptide (50VLFGLLCLL58) from the hydrophobic C-terminal region of this small (60-amino-acid) EBV protein is efficiently presented by the common class I allele HLA-A2 for recognition by cytotoxic T lymphocytes. The mechanism for this unexpected finding was revealed by experiments showing that this epitope is processed and presented independently of TAP.
Reovirus FAST Protein Transmembrane Domains Function in a Modular, Primary Sequence-Independent Manner To Mediate Cell-Cell Membrane Fusion
Authors: Clancy Eileen K. , Duncan Roy
Published: January 2009

The FAST proteins are a unique family of virus-encoded cell-cell membrane fusion proteins. In the absence of a cleavable N-terminal signal peptide, a single-pass transmembrane domain (TMD) functions as a reverse signal-anchor to direct the FAST proteins into the plasma membrane in an Nexo/Ccyttopology. There is little information available on the role of the FAST protein TMD in the cell-cell membrane fusion reaction. We show that in the absence of conservation in the length or primary amino acid sequence, the p14 TMD can be functionally exchanged with the TMDs of the p10 and p15 FAST proteins. This is not the case for chimeric p14 proteins containing the TMDs of two different enveloped viral fusion proteins or a cellular membrane protein; such chimeric proteins were defective for both pore formation and syncytiogenesis. TMD structural features that are conserved within members of the FAST protein family presumably play direct roles in the fusion reaction. Molecular modeling suggests that the funnel-shaped architecture of the FAST protein TMDs may represent such a conserved structural and functional motif. Interestingly, although heterologous TMDs exert diverse influences on the trafficking of the p14 FAST protein, these TMDs are capable of functioning as reverse signal-anchor sequences to direct p14 into lipid rafts in the correct membrane topology. The FAST protein TMDs are therefore not primary determinants of type III protein topology, but they do play a direct, sequence-independent role in the membrane fusion reaction.
Modified Vaccinia Virus Ankara Triggers Chemotaxis of Monocytes and Early Respiratory Immigration of Leukocytes by Induction of CCL2 Expression
Authors: Lehmann Michael H. , Kastenmuller Wolfgang , Kandemir Judith D. , Brandt Florian , Suezer Yasemin , Sutter Gerd
Published: January 2009

Orthopoxviruses commonly enter into humans and animals via the respiratory tract. Herein, we show that immigration of leukocytes into the lung is triggered via intranasal infection of mice with modified vaccinia virus Ankara (MVA) and not with the vaccinia virus (VACV) Elstree, Wyeth, or Western Reserve (WR) strain. Immigrating cells were identified as monocytes, neutrophils, and CD4+lymphocytes by flow cytometry and could be detected 24 h and 48 h postinfection. Using an in vitro chemotaxis assay, we confirmed that infection with MVA induces the expression of a soluble chemotactic factor for monocytes, identified as CCL2 (monocyte chemotactic protein-1 [MCP-1]). In contrast to infection with several other VACV strains, MVA induced the expression of CCL2, CCL3, CCL4, and CXCL10 in the human monocytic cell line THP-1 as well as in primary human monocytes. Thus, MVA, and not the VACV Elstree, Wyeth, or WR strain, consistently triggered the expression of a panel of chemokines, including CCL2, in the murine lung, correlating considerably with the immigration of leukocytes. Using CCL2-deficient mice, we demonstrate that CCL2 plays a key role in MVA-triggered respiratory immigration of leukocytes. Moreover, UV irradiation of MVA prevented CCL2 expression in vitro and in vivo as well as respiratory immigration of leukocytes, demonstrating the requirement for an activated molecular viral life cycle. We propose that MVA-triggered chemokine expression causes early immigration of leukocytes to the site of infection, a feature that is important for rapid immunization and its safety and efficiency as a viral vector.
E4orf1
Limits the Oncolytic Potential of the
E1B
-
55K
Deletion Mutant Adenovirus
Authors: Thomas Michael A. , Broughton Robin S. , Goodrum Felicia D. , Ornelles David A.
Published: January 2009

Clinical trials have shown oncolytic adenoviruses to be tumor selective with minimal toxicity toward normal tissue. The virus ONYX-015, in which the gene encoding the early region 1B 55-kDa (
E1B
-
55K
) protein is deleted, has been most effective when used in combination with either chemotherapy or radiation therapy. Therefore, improving the oncolytic nature of tumor-selective adenoviruses remains an important objective for improving this form of cancer therapy. Cells infected during the G
1
phase of the cell cycle with the
E1B
-
55K
deletion mutant virus exhibit a reduced rate of viral late protein synthesis, produce fewer viral progeny, and are less efficiently killed than cells infected during the S phase. Here we demonstrate that the G
1
restriction imposed on the
E1B
-
55K
deletion mutant virus is due to the viral oncogene encoded by open reading frame 1 of early region 4 (
E4orf1
).
E4orf1
has been reported to signal through the phosphatidylinositol 3′-kinase pathway leading to the activation of Akt, mTOR, and p70 S6K. Evidence presented here shows that
E4orf1
may also induce the phosphorylation of Akt and p70 S6K in a manner that depends on Rac1 and its guanine nucleotide exchange factor Tiam1. Accordingly, agents that have been reported to disrupt the Tiam1-Rac1 interaction or to prevent phosphorylation of the ribosomal S6 kinase partially alleviated the
E4orf1
restriction to late viral protein synthesis and enhanced tumor cell killing by the
E1B
-
55K
mutant virus. These results demonstrate that
E4orf1
limits the oncolytic nature of a conditionally replicating adenovirus such as ONYX-015. The therapeutic value of similar oncolytic adenoviruses may be improved by abrogating
E4orf1
function.
Identifying Sites Bound by Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) in the Human Genome: Defining a Position-Weighted Matrix To Predict Sites Bound by EBNA1 in Viral Genomes
Authors: Dresang Lindsay R. , Vereide David T. , Sugden Bill
Published: January 2009

We identified binding sites for Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) in the human genome using chromatin immunoprecipitation and microarrays. The sequences for these newly identified sites were used to generate a position-weighted matrix (PWM) for EBNA1's DNA-binding sites. This PWM helped identify additional DNA-binding sites for EBNA1 in the genomes of EBV, Kaposi's sarcoma-associated herpesvirus, and cercopithecine herpesvirus 15 (CeHV-15) (also called herpesvirus papio 15). In particular, a homologue of the Rep* locus in EBV was predicted in the genome of CeHV-15, which is notable because Rep* of EBV was not predicted by the previously developed consensus sequence for EBNA1's binding DNA. The Rep* of CeHV-15 functions as an origin of DNA synthesis in the EBV-positive cell line Raji; this finding thus builds on a set of DNA-binding sites for EBNA1 predicted in silico.
Inhibition of the Ubiquitin-Proteasome System Prevents Vaccinia Virus DNA Replication and Expression of Intermediate and Late Genes
Authors: Satheshkumar P. S. , Anton Luis C. , Sanz Patrick , Moss Bernard
Published: January 2009

The ubiquitin-proteasome system has a central role in the degradation of intracellular proteins and regulates a variety of functions. Viruses belonging to several different families utilize or modulate the system for their advantage. Here we showed that the proteasome inhibitors MG132 and epoxomicin blocked a postentry step in vaccinia virus (VACV) replication. When proteasome inhibitors were added after virus attachment, early gene expression was prolonged and the expression of intermediate and late genes was almost undetectable. By varying the time of the removal and addition of MG132, the adverse effect of the proteasome inhibitors was narrowly focused on events occurring 2 to 4 h after infection, the time of the onset of viral DNA synthesis. Further analyses confirmed that genome replication was inhibited by both MG132 and epoxomicin, which would account for the effect on intermediate and late gene expression. The virus-induced replication of a transfected plasmid was also inhibited, indicating that the block was not at the step of viral DNA uncoating. UBEI-41, an inhibitor of the ubiquitin-activating enzyme E1, also prevented late gene expression, supporting the role of the ubiquitin-proteasome system in VACV replication. Neither the overexpression of ubiquitin nor the addition of an autophagy inhibitor was able to counter the inhibitory effects of MG132. Further studies of the role of the ubiquitin-proteasome system for VACV replication may provide new insights into virus-host interactions and suggest potential antipoxviral drugs.
Herpes Simplex Virus UL12.5 Targets Mitochondria through a Mitochondrial Localization Sequence Proximal to the N Terminus
Authors: Corcoran Jennifer A. , Saffran Holly A. , Duguay Brett A. , Smiley James R.
Published: January 2009

The herpes simplex virus type 1 (HSV-1) gene
UL12
encodes a conserved alkaline DNase with orthologues in all herpesviruses. The HSV-1 UL12 gene gives rise to two separately promoted 3′ coterminal mRNAs which encode distinct but related proteins: full-length UL12 and UL12.5, an amino-terminally truncated form that initiates at UL12 codon 127. Full-length UL12 localizes to the nucleus where it promotes the generation of mature viral genomes from larger precursors. In contrast, UL12.5 is predominantly mitochondrial and acts to trigger degradation of the mitochondrial genome early during infection. We examined the basis for these very different subcellular localization patterns. We confirmed an earlier report that the amino-terminal region of full-length UL12 is required for nuclear localization and provide evidence that multiple nuclear localization determinants are present in this region. In addition, we demonstrate that mitochondrial localization of UL12.5 relies largely on sequences located between UL12 residues 185 and 245 (UL12.5 residues 59 to 119). This region contains a sequence that resembles a typical mitochondrial matrix localization signal, and mutations that reduce the positive charge of this element severely impaired mitochondrial localization. Consistent with matrix localization, UL12.5 displayed a detergent extraction profile indistinguishable from that of the matrix protein cyclophilin D. Mitochondrial DNA depletion required the exonuclease activity of UL12.5, consistent with the idea that UL12.5 located within the matrix acts directly to destroy the mitochondrial genome. These results clarify how two highly related viral proteins are targeted to different subcellular locations with distinct functional consequences.
Evolution of the Sabin Vaccine into Pathogenic Derivatives without Appreciable Changes in Antigenic Properties: Need for Improvement of Current Poliovirus Surveillance
Authors: Yakovenko Maria L. , Korotkova Ekaterina A. , Ivanova Olga E. , Eremeeva Tatyana P. , Samoilovich Elena , Uhova Iryna , Gavrilin Gene V. , Agol Vadim I.
Published: January 2009

The Sabin oral polio vaccine (OPV) may evolve into pathogenic viruses, causing sporadic cases and outbreaks of poliomyelitis. Such vaccine-derived polioviruses (VDPV) generally exhibit altered antigenicity. The current paradigm to distinguish VDPV from OPV and wild polioviruses is to characterize primarily those poliovirus isolates that demonstrate deviations from OPV in antigenic and genetic intratypic differentiation (ITD) tests. Here we report on two independent cases of poliomyelitis caused by VDPVs with “Sabin-like” properties in several ITD assays. The results suggest the existence of diverse pathways of OPV evolution and necessitate improvement of poliovirus surveillance, which currently potentially misses this class of VDPV.
Comparisons of CD8+T Cells Specific for Human Immunodeficiency Virus, Hepatitis C Virus, and Cytomegalovirus Reveal Differences in Frequency, Immunodominance, Phenotype, and Interleukin-2 Responsiveness
Authors: Jagannathan Prasanna , Osborne Christine M. , Royce Cassandra , Manion Maura M. , Tilton John C. , Li Li , Fischer Steven , Hallahan Claire W. , Metcalf Julia A. , McLaughlin Mary , Pipeling Matthew , McDyer John F. , Manley Thomas J. , Meier Jeffery L. , Altman John D. , Hertel Laura , Davey Richard T. , Connors Mark , Migueles Stephen A.
Published: January 2009

To better understand the components of an effective immune response to human immunodeficiency virus (HIV), the CD8+T-cell responses to HIV, hepatitis C virus (HCV), and cytomegalovirus (CMV) were compared with regard to frequency, immunodominance, phenotype, and interleukin-2 (IL-2) responsiveness. Responses were examined in rare patients exhibiting durable immune-mediated control over HIV, termed long-term nonprogressors (LTNP) or elite controllers, and patients with progressive HIV infection (progressors). The magnitude of the virus-specific CD8+T-cell response targeting HIV, CMV, and HCV was not significantly different between LTNP and progressors, even though their capacity to proliferate to HIV antigens was preserved only in LTNP. In contrast to HIV-specific CD8+T-cell responses of LTNP, HLA B5701-restricted responses within CMV pp65 were rare and did not dominate the total CMV-specific response. Virus-specific CD8+T cells were predominantly CD27+45RO+for HIV and CD27−45RA+for CMV; however, these phenotypes were highly variable and heavily influenced by the degree of viremia. Although IL-2 induced significant expansions of CMV-specific CD8+T cells in LTNP and progressors by increasing both the numbers of cells entering the proliferating pool and the number of divisions, the proliferative capacity of a significant proportion of HIV-specific CD8+T cells was not restored with exogenous IL-2. These results suggest that immunodominance by HLA B5701-restricted cells is specific to HIV infection in LTNP and is not a feature of responses to other chronic viral infections. They also suggest that poor responsiveness to IL-2 is a property of HIV-specific CD8+T cells of progressors that is not shared with responses to other viruses over which immunologic control is maintained.
Determinants Flanking the CD4 Binding Loop Modulate Macrophage Tropism of Human Immunodeficiency Virus Type 1 R5 Envelopes
Authors: Duenas-Decamp Maria José , Peters Paul J. , Burton Dennis , Clapham Paul R.
Published: January 2009

Human immunodeficiency virus type 1 R5 viruses vary extensively in phenotype. Thus, R5 envelopes (env) in the brain tissue of individuals with neurological complications are frequently highly macrophage-tropic. Macrophage tropism correlates with the capacity of the envelope to exploit low CD4 levels for infection. In addition, the presence of an asparagine at residue 283 within the CD4 binding site has been associated with brain-derived envelopes, increased env-CD4 affinity, and enhanced macrophage tropism. Here, we identify additional envelope determinants of R5 macrophage tropism. We compared highly macrophage-tropic (B33) and non-macrophage-tropic (LN40) envelopes from brain and lymph node specimens of one individual. We first examined the role of residue 283 in macrophage tropism. Introduction of N283 into LN40 (T283N) conferred efficient macrophage infectivity. In contrast, substitution of N283 for the more conserved threonine in B33 had little effect on macrophage infection. Thus, B33 carried determinants for macrophage tropism that were independent of N283. We prepared chimeric B33/LN40 envelopes and used site-directed mutagenesis to identify additional determinants. The determinants of macrophage tropism that were identified included residues on the CD4 binding loop flanks that were proximal to CD4 contact residues and residues in the V3 loop. The same residues affected sensitivity to CD4-immunoglobulin G inhibition, consistent with an altered env-CD4 affinity. We predict that these determinants alter exposure of CD4 contact residues. Moreover, the CD4 binding loop flanks are variable and may contribute to a general mechanism for protecting proximal CD4 contact residues from neutralizing antibodies. Our results have relevance for env-based vaccines that will need to expose critical CD4 contact residues to the immune system.
Abrogation of the Postmitotic Checkpoint Contributes to Polyploidization in Human Papillomavirus E7-Expressing Cells
Authors: Heilman Susan A. , Nordberg Joshua J. , Liu Yingwang , Sluder Greenfield , Chen Jason J.
Published: January 2009

High-risk types of human papillomavirus (HPV) are considered the major causative agents of cervical carcinoma. The transforming ability of HPV resides in the E6 and E7 oncogenes, yet the pathway to transformation is not well understood. Cells expressing the oncogene E7 from high-risk HPVs have a high incidence of polyploidy, which has been shown to occur as an early event in cervical carcinogenesis and predisposes the cells to aneuploidy. The mechanism through which E7 contributes to polyploidy is not known. It has been hypothesized that E7 induces polyploidy in response to mitotic stress by abrogating the mitotic spindle assembly checkpoint. It was also proposed that E7 may stimulate rereplication to induce polyploidy. We have tested these hypotheses by using human epithelial cells in which E7 expression induces a significant amount of polyploidy. We find that E7-expressing cells undergo normal mitoses with an intact spindle assembly checkpoint and that they are able to complete cytokinesis. Our results also exclude DNA rereplication as a major mechanism of polyploidization in E7-expressing cells upon microtubule disruption. Instead, we have shown that while normal cells arrest at the postmitotic checkpoint after adaptation to the spindle assembly checkpoint, E7-expressing cells replicate their DNA and propagate as polyploid cells. Thus, abrogation of the postmitotic checkpoint leads to polyploidy formation in E7-expressing human epithelial cells. Our results suggest that downregulation of pRb is important for E7 to induce polyploidy and abrogation of the postmitotic checkpoint.
Differentially Stimulated CD4+T Cells Display Altered Human Immunodeficiency Virus Infection Kinetics: Implications for the Efficacy of Antiviral Agents
Authors: Vatakis Dimitrios N. , Nixon Christopher C. , Bristol Gregory , Zack Jerome A.
Published: January 2009

The activation state of CD4+T cells plays a crucial role in the establishment of a productive human immunodeficiency virus infection. Here, we show that T cells stimulated for 1 day demonstrated delayed kinetics of viral reverse transcription and integration compared to cells stimulated for 2 days prior to infection. As a result, the efficiency of reverse transcription and integration inhibitors differs in these differentially stimulated cells. These studies increase our understanding of how T cells support viral replication and provide insight regarding the efficiency of antiretroviral therapy in lymphoid compartments.
NON-CARTESIAN, TOPOGRAPHY-BASED AVALANCHE EQUATIONS AND APPROXIMATIONS OF GRAVITY DRIVEN FLOWS OF IDEAL AND VISCOUS FLUIDS
Authors: LUCA I. , TAI Y. C. , KUO C. Y.
Published: January 2009

When dealing with geophysical flows across three-dimensional topography or other thin layer flows, for the physical modelling and for computational reasons, it is more convenient to use curvilinear coordinates adapted to the basal solid surface, instead of the Cartesian coordinates. Using such curvilinear coordinates, e.g. introduced by Bouchut and Westdickenberg,3 and the corresponding contravariant components of vector and tensor fields, we derive in full generality the governing equations for the avalanche mass. These are next used to deduce (i) the thin layer equations for arbitrary topography, when the flowing mass is an ideal fluid, and (ii) the thin layer equations corresponding to arbitrary topography and to a viscous fluid that experiences bottom friction, modelled by a viscous sliding law.
GIANT MAGNETO-IMPEDANCE EFFECT OF MAGNETRON SPUTTERED Ni80Fe20/Cu COMPOSITE WIRES
Authors: ZHANG Q. , MAO Q. M. , RUAN J. Z. , WANG Q. J. , YANG X. L. , ZHAO Z. J. , SEET H. L. , LI X. P.
Published: January 2009

In this work, Ni 80 Fe 20/ Cu composite wires of length 50 mm, consisting a Cu core of diameter 100 μm, coated with a layer of Ni 80 Fe 20, were produced by RF magnetron sputtering. To obtain a uniform coating, the wires were spun during sputtering by a homemade system. The results showed that the spinning speed might affect the maximum MI ratio and the magnetic properties. The MI ratio of the sputtered wires increases with the wire spinning speed in the magnetron sputtering. The film thickness had a significant effect on the magnitude and the optimum frequency of the giant magneto-impedance effect. The maximum MI ratio can reach about 247.4% for the specimen with a Ni 80 Fe 20 coating thickness of 2.81 μm at 400 kHz. This large MI effect, obtained at such low frequency range, was correlated with the electromagnetic interaction between the inner core and the magnetic coating.
CRITICAL THICKNESS OF EPITAXIAL GROWN SEMICONDUCTOR FILMS WITH STRAINED STRUCTURE
Authors: LI J. C. , LI M. , JIANG Q.
Published: January 2009

The critical thickness of structural transition from a tetragonal structure to a normal bulk structure for epitaxial ultrathin films deposited on the metallic and semiconductor substrates is thermodynamically considered. It is found that equilibrium between the elastic energy of the tetrahedral structure and the film–substrate interface energy is present when a critical thickness is reached. The predictions of the critical thickness are in agreement with the experimental results of films.
PHASE COMPOSITION, MICROSTRUCTURE, AND TRIBOLOGICAL PROPERTY OF PLASMA-SPRAYED TiC-BASED COATING
Authors: SUN SHIBIN , ZOU ZENGDA , LIU XUEMEI , SHI HANCHAO
Published: January 2009

TiC -based wear resistant coating was prepared by plasma spraying using reconstituted composite powders doped with ultra-fine carbide. Phase composition and microstructure of as-sprayed coating were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM) utilizing backscattered imaging mode (BSE), and electron probe micro-analysis. Wear test was performed by using a ring-on-block tester under dry sliding condition. Results show that the coating adheres well to the substrate and no delamination appears. TiC content underwent pronounced reduction because of oxidation, reaction, and physical loss. Reactions between TiC and Mo and probably between dissociated C and Mo lead to the formation of Mo 2 C . Wear resistance of NiCrMo – TiC coating is about 4–8 times higher than that of substrate under different applied force. This work shed light on the reconstitution of spraying powder doped with ultra-fine reinforce phase particles, and the present results are important for the preparation of nano-doped TiC -based coatings.
INHIBITORY EFFECT AND ADSORPTION CHARACTERISTICS OF 2,3-DIAMINONAPHTHALENE AT ALUMINUM/HYDROCHLORIC ACID INTERFACE: EXPERIMENTAL AND THEORETICAL STUDY
Authors: OBOT I. B. , OBI-EGBEDI N. O.
Published: January 2009

The inhibitive effect of 2,3-diaminonaphthalene (2,3-DAN) for corrosion of aluminum in 1 M HCl was investigated using hydrogen evolution technique at 30 and 40°C. Quantum chemical calculation results showed that 2,3-DAN molecule possessed planar structure with a number of active centers, which aided the adsorption process. The Mulliken charge density, the highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) were found mainly focused around nitrogen atoms and the cyclic of the benzene as well. The presence of 2,3-DAN molecules in the corrosive medium (1 M HCl solution) inhibits the corrosion process of aluminum and as the concentration of 2,3-DAN increases the inhibition efficiency also increases but decreases with rise in temperature. The corrosion inhibition of 2,3-DAN was discussed in terms of blocking of the Al surface by adsorption of the molecules of the inhibitor at the active centers. It was found that the adsorption of 2,3-DAN onto the Al surface followed the Langmuir adsorption isotherm and 2,3-DAN adsorbed on Al surface probably by physisorption. The proposed physisorption mechanism was supported by the calculated values of Ea, Q ads , and ΔG ads .
STUDY OF CHEMICAL BATH DEPOSITION OF ZnS THIN FILMS WITH SUBSTRATE VIBRATION
Authors: BIAN Z. Q. , XU X. B. , CHU J. B. , SUN Z. , CHEN Y. W. , HUANG S. M.
Published: January 2009

An improved chemical bath deposition (CBD) technique has been provided to prepare zinc sulfide ( ZnS ) thin films on glass substrates deposited at 80–82°C using a mixed aqueous solution of zinc sulfate, ammonium sulfate, thiourea, hydrazine hydrate, and ammonia at the alkaline conditions. Both the traditional magnetic agitation and the substrates vibration by hand frequently were done simultaneously during the deposition. The substrates vibration reduced the formation and residence of gas bubbles on the glass substrates during growth and resulted in growth of clean ZnS thin films with high quality. Ammonia and hydrazine hydrate were used as complexing agents. It is found that hydrazine hydrate played an important role in growth of ZnS films. The structure and microstructure of ZnS films were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD) and UV-vis spectroscopic methods. The XRD showed a hexagonal structure. The formed ZnS films exhibited good optical properties with high transmittance in the visible region and the band gap value was estimated to be 3.5–3.70 eV.
SURFACE AND QUALITY MODIFICATION OF DIAMOND-LIKE CARBON FILMS BY CO2 LASER HEATING ASSISTED HOT FILAMENT CHEMICAL VAPOR DEPOSITION
Authors: AMORNKITBAMRUNG VITTAYA , TOPON ONG-ON
Published: January 2009

An infrared CO 2 laser was used for regional heating to study the heating effect on hot filament chemical vapor deposition of diamond-like carbon formation on Si (100) face substrates. The substrate surface temperature was about 450–500°C. The power of the laser called low, medium, and high raised the temperature of the substrate locally by 25, 45, and 55°C, respectively. At medium laser power, at the central laser beam region, a narrow Raman peak centered at 1438 cm-1 was detected. It can be concluded that this region has good-quality DLC. This moderate high-frequency peak corresponds to a fourfold-rotation-symmetry atom in an amorphous carbon network from the tight-binding molecular dynamics simulation of Wang and Ho.