bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a compact suspension system for a neutrally buoyant underwater acoustic intensity probe
Authors: McConnell James A.
Published: September 2008

Practical use of neutrally buoyant underwater acoustic intensity probes requires a suspension system to position them in some preferred orientation with respect to an acoustic field of interest. However, since these probes typically contain a moving coil geophone to facilitate particle velocity measurements, the design of such suspension systems is not trivial. On one hand, theory mandates that the dynamics of the geophone will not be adversely affected by the suspension as long as the mass-spring system created by the probe and the elastic members has a low-resonance frequency and high quality factor relative to that of the geophone. However, by meeting these two design criteria, wave effects (e.g., flexural resonances) in the elastic members can become a limiting factor in the performance of the device, particularly at high frequencies. This paper presents theoretical and experimental results of an effort to design a compact suspension system that embodies the aforementioned design considerations, but has relatively low susceptibilty to flexural resonances. [Work supported by the Acoustics Technology Branch of the Naval Air Warfare Center—Aircraft Division, via the DoD Small Business Innovation Research Program.]
Automatic classification of the acoustical situation using amplitude-modulation spectrograms
Authors: Tchorz Jürgen , Kollmeier Birger
Published: September 2008

A fast and reliable classification of the acoustical situation is an important prerequisite for modern speech processing schemes. Noise suppression algorithms in digital hearing aids, for example, are strongly dependent on a proper noise level estimation. The classification algorithm which is presented is based on so-called amplitude-modulation spectrograms (AMS). It is motivated by neurophysiological findings in the auditory cortex in mammals. Its basic idea is that both spectral and temporal information of the signal is used to attain a separation between ‘‘acoustical objects’’ within the signal. Spectral information is gained by splitting the input signal into different frequency bands, temporal information is gained by analyzing amplitude modulations in each frequency band. Thus for each analysis frame of the input signal, a two-dimensional AMS pattern is created. Signals with similar spectral shape but different temporal properties are clearly distinct in the AMS representation. A neural network is trained on a large number of AMS patterns which were generated from speech and noise samples. After training, an automatic classification of speech and noise from ‘‘unknown’’ sources is performed with high accuracy. Furthermore, an estimate of the present signal-to-noise ratio is supplied for mixed input signals.
Irregular modes at the endshield of a heating system motor
Authors: Heise Ulrich
Published: September 2008

Nowadays, more and more modern heating systems are not installed in separated rooms, so the expectation of noise comfort has been increased for the last years. A noise and vibration optimization was made at an electric motors b-sided endshield. Sometimes, the old endshield emitted airborne noise. This was caused by the structure-borne noise of the bearings together with a mode of the endshield. A modal analysis was made to detect the disturbing mode. The amazing thing of this test was that the (0,1) mode frequency has a higher resonance frequency as the (1,1) mode. Normally the (1,1) mode frequency has a 1.594 higher frequency than the (0,1) mode resonance [N. H. Fletcher and T. D. Rossing, The Physics of Musical Instruments (1991), pp. 69–71]. The b-sided bearings can make a mass coupling from the rotor to the endshield in radial direction, but not in this way in the axial direction. The (1,1) mode of the endshield had nearly the same structure-borne amplitude as the (0,1) mode, but the (1,1) mode does not transmit airborne noise. This depends on the mechanical dimensions of the (1,1) mode, because this mode is working with its dimensions on an acoustical short circuit on air.
Shock wave–inertial microbubble interaction
Authors: Zhong Pei , Xi Xufeng , Zhu Songlin , Lin Haifan
Published: September 2008

To produce in situ shock wave–inertial microbubble interaction, an annular ellipsoidal reflector, confocal but 15 mm shorter in major axis than the ellipsoidal reflector of a XL-1 lithotripter, was fabricated and combined with the XL-1 reflector. With this modification, a small portion of the spark-generated spherical shock wave is reflected and diffracted by the annular reflector, producing a weak shock wave approximately 8.5 μs in front of the lithotripter pulse. This preceding shock wave (−0.96<P<−1.91 MPa at 25 kV) induces inertial microbubbles, which expand to a maximum size of 100 to 200 μm before being collapsed in situ by the ensuing lithotripter pulse. High-speed shadowgraph imaging and passive cavitation detection have revealed strong secondary shock wave emission immediately following the propagating lithotripter shock front and microjet formation along the wave propagation direction, features that are absent from the standard lithotripter pulses. With optimal pulse combination, membrane permeabilization of mouse lymphoid cells produced by the modified shock waves is substantially enhanced (up to 91%) at low dosage (<50 shocks), and cell injury is significantly increased (up to 50%) at high dosage (>100 shocks), compared to standard lithotripter pulses. [Work supported by NIH R21 HL60327.]
The University of Central Florida Rail Noise Model
Authors: Wayson Roger L. , MacDonald John M.
Published: September 2008

The Railway Noise Model (RNM) is a point source simulation model using a Windows-based program written in Visual Basic. Locomotives and rail cars are input by the laser using a graphical interface. The interface allows spreadsheet-type format or the user may use the mouse to drag and drop railroad tracks and barriers and to place receivers. The model has the ability to model heavy rail and light rail locomotives and rail cars. The user can observe defined trains moving along the railroad tracks to check input. Leq sound levels are calculated and reported during the simulation and then tabulated at the conclusion of simulation. The algorithms of the RNM follow the U.S. Federal Transit Authority Noise and Vibration Impact Assessment (DOT-T-95-16) guidelines. The Railway Noise Model uses Lmax passby levels from REMEL curves to compute sound levels. The RNM simulates a 24-h period of rail traffic and computes Ldn, Lmax, SEL, and Leq levels at the receivers. Testing has shown that the RNM results match those of the FTA promulgated spreadsheet. The RNM is capable of modeling complex geometries and conditions not available in the FTA spreadsheet and supports all noise sources available in the spreadsheet.
Ultrasonic absorption in concrete
Authors: Turner Joseph A.
Published: September 2008

The propagation of ultrasound in concrete is greatly affected by the heterogeneous composition. An ultrasonic plane wave will attenuate as it propagates. Part of this attenuation is due to scattering effects which result from the aggregate. Another component of the attenuation is due to true dissipation from viscoelastic effects. Total attenuation has been previously proposed as a materials characterization parameter, although the distinction between scattering attenuation and dissipation is often not made. Experimental results are presented which should help separate these effects. Absorption measurements were made on a number of specimens with differing aggregate composition and water–cement ratio. The absorption is shown to be independent of the nature of the aggregate, as expected. In addition, the absorption is shown to be dependent upon the water–cement ratio and thus is related to the strength. Frequency dependence of absorption is also discussed. It is anticipated that ultrasonic absorption may be a useful parameter for characterizing concrete material properties. [Work supported by the Nebraska Research Initiative and Layman Fund.]
Propagation of a short acoustic pulse in a medium with two relaxation processes. Exact solution
Authors: Maksimov German A. , Larichev Vladimir A.
Published: September 2008

Shape distortion of a short acoustic pulse during its propagation through relaxation media is an important source of information about relaxation time’s spectrum (RTS). The basic relations for pulse acoustic diagnostics were developed in the work [G. A. Maksimov, Acoust. Phys. 42, 541–550 (1996)] by using known exact solutions as well as asymptotic analysis. Only two exact solutions for short-pulse distortion due to relaxation are known at present. They are the solution for single relaxation process [J. A. Morriso, Q. Appl. Math. 14, 153–169 (1956); J. D. Achenbach and C. C. Chao, J. Mech. Phys. Solids. 10, 245–252 (1962)] and the solution for the distributed spectrum being proportional to inverted relaxation time [S. Z. Dunin and G. A. Maximov, Izv. ANSSSR Appl. Math. Mech. 54, 480–484 (1990) (in Russian)] . The new analytical representation of Green’s function for pulse propagating in media with two relaxation processes is obtained. This representation consists of three parts, which describe acoustic precursor as well as high- and low-frequency components of pulse body. The high-frequency component can be written in an invariant form that is fair for arbitrary RTS. The low-frequency component has more complicated dependence on parameters of RTS. The analysis of this dependence is made and analytical expressions are obtained. The usefulness of these expressions is confirmed by comparison with results of direct numerical calculations.
On the investigation of the stressed state of the elastic and piezoelectric bodies
Authors: Kalinchuk Valery V. , Belyankova Tatyana I. , Puzanoff Yury E. , Zaitseva Irina A.
Published: September 2008

The solutions of the set of dynamic problems on the oscillations of the electroelastic prestressed medium is the basis of the detailed analysis of the influence of the initial stressed state’s type and initial stress’s value to the structure of the surface wave field and to the resonance phenomena arising from the interaction between the medium and the external concentrated elements. The initial stressed state is considered to be homogeneous or changing with the depth. It has been defined by the parameters of the external concentrated elements under which the initial stress’s influence to the dynamics is maximal. The high efficiency of using the resonance phenomena for the nondestructive control of stressed state’s character and the initial (residual) stress’s value has been established. [Work supported by RFFI.]
Chlamydophila felisCF0218 Is a Novel TMH Family Protein with Potential as a Diagnostic Antigen for Diagnosis ofC. felisInfection
Authors: Ohya Kenji , Takahara Yu , Kuroda Etsuko , Koyasu Saori , Hagiwara Shigeyuki , Sakamoto Maki , Hisaka Mitsuaki , Morizane Kazuko , Ishiguro Shinryou , Yamaguchi Tsuyoshi , Fukushi Hideto
Published: September 2008

Chlamydophila felisis a causative agent of acute and chronic conjunctivitis and pneumonia in cats (feline chlamydiosis). Also,C. felisis a suspected zoonotic agent of such diseases as non-Chlamydia trachomatisconjunctivitis in humans, although this is controversial. At present, there is no serodiagnostic system that specifically detectsC. felisinfection conveniently. Current systems use antigens such as lipopolysaccharide that cross-react with all chlamydia species. In addition, it is difficult to distinguish between cats that are vaccinated with the commercial vaccine againstC. felisand cats that are infected withC. felis. Here, we describe a new candidate diagnostic antigen for diagnosis ofC. felisinfection, CF0218, that was obtained by screening a genomic expression library ofC. felisFe/C-56 withC. felis-immunized serum. CF0218 was a putative transmembrane head (TMH) family protein with bilobed hydrophobic motifs at its N terminus, and orthologues of CF0218 were not found in theChlamydophila pneumoniaeorChlamydia trachomatisgenomes. The recombinant CF0218 was not recognized by antiserum againstC. trachomatis, suggesting that CF0218 isC. felisspecific. CF0218 transcription during the course ofC. felisinfection was confirmed by reverse transcription-PCR. By indirect immunofluorescence analysis, CF0218 was colocalized with theC. felis-formed inclusion bodies in the infected cells. The antibody response against CF0218 was elevated followingC. felisinfection but not by vaccination in experimentally vaccinated and infected cats. These results suggest that CF0218, a novel TMH family protein ofC. felis, possesses potential as aC. felisinfection-specific diagnostic antigen.
Characterization of a Recombinant Newcastle Disease Virus Vaccine Strain
Authors: Cho Sun-Hee , Kwon Hyuk-Joon , Kim Tae-Eun , Kim Jae-Hong , Yoo Han-Sang , Park Man-Hoon , Park Young-Ho , Kim Sun-Joong
Published: September 2008

A recombinant La Sota strain (KBNP-C4152R2L) in which fusion (F) and hemagglutinin-neuraminidase (HN) genes were replaced with those of a contemporary genotype VIId virus, KBNP-4152, has been developed. To attenuate the virulence of the recombinant strain, the F cleavage motif was mutated from112RRQKR116to112GRQAR116, and to reduce pathogenic instability, a codon which does not allow changes to basic amino acids by single point mutation was inserted at codon 115. In addition a six-nucleotide sequence was inserted into the intergenic region between matrix protein and F genes for attenuation without breaking the “rule-of-six.” The HN protein length was increased from 571 to 577 as a marker. Serological tests revealed that the antigenicity of KBNP-C4152R2L was similar to that of KBNP-4152 but distinct from that of the La Sota strain. KBNP-C4152R2L was avirulent (intracerebral pathogenicity index, 0.0; mean death time, >168 h) and stable in pathogenicity through in vivo passages. The killed oil emulsion of and live KBNP-C4152R2L were completely protective against mortality and egg drop caused by virulent strains, and KBNP-C4152R2L was applicable to in ovo vaccination. Therefore, KBNP-C4152R2L is a promising vaccine strain and viral vector in terms of antigenicity, productivity, safety, and pathogenic stability.
Cross-Reactivity between Immunoglobulin G Antibodies of Whales and Dolphins Correlates with Evolutionary Distance
Authors: Nollens Hendrik H. , Ruiz Carolina , Walsh Michael T. , Gulland Frances M. D. , Bossart Gregory , Jensen Eric D. , McBain James F. , Wellehan James F. X.
Published: September 2008

Growing morphological and molecular evidence indicates that the porpoises, dolphins, and whales evolved within the even-toed ungulates, formerly known as Artiodactyla. These animals are now grouped in the Cetartiodactyla. We evaluated the antigenic similarity of the immunoglobulin G (IgG) molecules of 15 cetacean species and the domestic cow. The similarity was scored using three distinct antibodies raised against bottlenose dolphin (Tursiops truncatus) IgG in a Western blot, an indirect enzyme-linked immunosorbent assay (ELISA), and a competitive ELISA format. A score was generated for the genetic distance between each species andT. truncatususing the cytochromebsequence. Each antibody displayed a distinct pattern of reactivity with the IgG antibodies of the various species. The monoclonal antibody (MAb) specific for the γ heavy chain ofT. truncatuswas reactive with all monodontids, delphinids, and phocoenids. The light-chain-specific MAb reacted with IgG of delphinoid and phocoenid species and one of the two mysticete species tested. The polyclonal antibody was broadly cross-reactive across all cetaceans and the domestic cow. Using the MAb specific for the γ heavy chain, the degree of IgG cross-reactivity ranged from less than 17% for the mysticetes to 106% for killer whaleOrcinus orca. The IgG in beaked whale and baleen whale sera was significantly less cross-reactive with bottlenose dolphin IgG than sera from other toothed whales. A strong negative correlation was demonstrated between antigenic cross-reactivity of IgG molecules and the genetic distance of their hosts. The data generated will be useful for the development of clinical serodiagnostics in diverse cetacean species.
Analysis of Mixed Sequencing Chromatograms and Its Application in Direct 16S rRNA Gene Sequencing of Polymicrobial Samples
Authors: Kommedal Øyvind , Karlsen Bjarte , Sæbø Øystein
Published: September 2008

Investigation of clinical samples by direct 16S rRNA gene sequencing provides the possibility to detect nonviable bacteria and bacteria with special growth requirements. This approach has been particularly valuable for the diagnosis of patients who have received antibiotics prior to sample collection. In specimens containing more than one bacterium, direct sequencing gives mixed chromatograms that complicate further interpretation. We designed an algorithm able to analyze these ambiguous chromatograms and implemented it as a Web-based service. The algorithm contains both a new base-calling procedure and a new database search procedure. 16S rRNA gene sequencing was performed on polybacterial suspensions prepared in the laboratory. The computer program identified all bacteria correctly to the species level in 23 out of 23 samples containing two different bacteria. For samples containing three different bacteria, correct identification to the species level was achieved for three out of five and to the genus level for five out of five.
Sequencing of
hsp65
Gene for Identification of
Mycobacterium
Species Isolated from Environmental and Clinical Sources in Rio de Janeiro, Brazil
Authors: Senna Simone G. , Battilana Jaqueline , Costa Juliana C. , Silva Marlei G. , Duarte Rafael S. , Fonseca Leila S. , Suffys Philip N. , Bogo Mauricio R.
Published: September 2008

This study evaluated the biodiversity of 28 clinical and 24 environmental
Mycobacterium
isolates from Rio de Janeiro, Brazil, by using
hsp65
sequences, with the aim of contributing to a better understanding of the genetic diversity and usefulness of this marker. An extensive phylogenetic analysis was performed. The nucleotide diversity was similar between clinical (0.06508) and environmental (0.06221) isolates.
Detection of Perinatal Cytomegalovirus Infection and Sensorineural Hearing Loss in Belgian Infants by Measurement of Automated Auditory Brainstem Response
Authors: Verbeeck Jannick , Van Kerschaver Erwin , Wollants Elke , Beuselinck Kurt , Stappaerts Luc , Van Ranst Marc
Published: September 2008

Since auditory disability causes serious problems in the development of speech and in the total development of a child, it is crucial to diagnose possible hearing impairment as soon as possible after birth. This study evaluates the neonatal hearing screening program in Flanders, Belgium. The auditory ability of 118,438 babies was tested using the automated auditory brainstem response. We selected 194 babies with indicative hearing impairment and 332 matched controls to investigate the association between the presence of human cytomegalovirus (HCMV) in urine samples and sensorineural hearing loss and to analyze the sensibility and specificity of a cell culture assay and a quantitative PCR detection method. Our results indicate that significantly more babies with confirmed hearing impairment were HCMV positive after birth. Further, based on the results of our study, babies with HCMV viral loads above 4.5 log copies/ml urine seem to be 1.4 times more likely to have confirmed hearing impairment. Our follow-up study suggests that the hearing impairment of children infected with HCMV after birth is less likely to improve than that of HCMV-negative infants. Our results confirm that the presence of HCMV before or shortly after birth influences the outcome of hearing impairment.
Rapid Identification of Mycobacteria from Smear-Positive Sputum Samples by Nested PCR-Restriction Fragment Length Polymorphism Analysis
Authors: Wu Tsu-Lan , Chia Ju-Hsin , Kuo An-Jing , Su Lin-Hui , Wu Ting-Shu , Lai Hsin-Chih
Published: September 2008

The rapid identification of mycobacteria from smear-positive sputum samples is an important clinical issue. Furthermore, the availability of a cheap, technically simple, and accurate method also would benefit mycobacterial laboratories in developing countries. In the present study, we aimed to develop an assay allowing the identification of theMycobacterium tuberculosiscomplex (MTBC) and other frequently isolated nontuberculous mycobacteria (NTM) directly from smear-positive sputum samples. A nested PCR-restriction fragment length polymorphism analysis (nested-PRA) assay that focuses on the analysis of thehsp65gene was developed and evaluated for its efficiency compared to that of traditional culture methods and 16S rRNA gene sequencing identification. A total of 204 smear-positive and culture-positive sputum specimens were prospectively collected for analysis between November 2005 and May 2006. The samples were classified according to an acid-fast bacillus (AFB) staining scale as rare/1+, 2+, or 3+. The results of the nested-PRA showed that the identification rate for AFB 3+, AFB 2+, and AFB rare/1+ samples was 100, 95, and 53%, respectively, and that the overall identification rate was 89%. All positive results by the nested-PRA method agreed with the results by culture and 16S rRNA gene sequence analysis. The nested-PRA appears to have clinical applicability when used for the direct identification of mycobacterial organisms (both MTBC and NTM) that are present in smear-positive sputum samples, especially for countries in which MTBC is endemic.
Real-Time PCR Measurement of Persistence of
Bordetella pertussis
DNA in Nasopharyngeal Secretions during Antibiotic Treatment of Young Children with Pertussis
Authors: Bidet Philippe , Liguori Sandrine , De Lauzanne Agathe , Caro Valérie , Lorrot Mathie , Carol Agnès , Faye Albert , Guiso Nicole , Bingen Edouard , Bonacorsi Stéphane
Published: September 2008

We used real-time PCR to examine the persistence of
Bordetella pertussis
DNA in serial nasopharyngeal aspirates from 22 children treated for pertussis. After 5 days of treatment, PCR was positive for all 21 assessable patients. After 14 and 21 days, PCR was still positive for 83% (10/12) and 66% (4/6) of assessable patients, respectively. One patient was tested 1 month after treatment initiation, and
B. pertussis
DNA was still detectable. Quantitative analysis showed that the DNA concentration diminished during treatment in all except one case. The PCR cycle threshold at which
B. pertussis
DNA became detectable increased by a mean of 1.7 cycles per day (range, 0.86 to 3.68 cycles per day). Real-time PCR can thus be used to diagnose pertussis in young children for up to 3 weeks after treatment initiation. Its potential value for assessing the treatment outcome remains to be determined.
The Cellular Antiviral Protein Viperin Is Attenuated by Proteasome-Mediated Protein Degradation in Japanese Encephalitis Virus-Infected Cells
Authors: Chan Yi-Lin , Chang Tsung-Hsien , Liao Ching-Len , Lin Yi-Ling
Published: September 2008

Viperin is identified as an antiviral protein induced by interferon (IFN), viral infections, and pathogen-associated molecules. In this study, we found that viperin is highly induced at the RNA level by Japanese encephalitis virus (JEV) and Sindbis virus (SIN) and that viperin protein is degraded in JEV-infected cells through a proteasome-dependent mechanism. Promoter analysis revealed that SIN induces viperin expression in an IFN-dependent manner but that JEV by itself activates the viperin promoter through IFN regulatory factor-3 and AP-1. The overexpression of viperin significantly decreased the production of SIN, but not of JEV, whereas the proteasome inhibitor MG132 sustained the protein level and antiviral effect of viperin in JEV-infected cells. Knockdown of viperin expression by RNA interference also enhanced the replication of SIN, but not that of JEV. Our results suggest that even though viperin gene expression is highly induced by JEV, it is negatively regulated at the protein level to counteract its antiviral effect. In contrast, SIN induces viperin through the action of IFN, and viperin exhibits potent antiviral activity against SIN.
Active-Site Mutations in the South African Human Immunodeficiency Virus Type 1 Subtype C Protease Have a Significant Impact on Clinical Inhibitor Binding: Kinetic and Thermodynamic Study
Authors: Mosebi Salerwe , Morris Lynn , Dirr Heini W. , Sayed Yasien
Published: September 2008

Human immunodeficiency virus (HIV) infections in sub-Saharan Africa represent about 56% of global infections. Study of active-site mutations (the V82A single mutation and the V82F I84V double mutation) in the less-studied South African HIV type 1 subtype C (C-SA) protease indicated that neither mutation had a significant impact on the proteolytic functioning of the protease. However, the binding affinities of, and inhibition by, saquinavir, ritonavir, indinavir, and nelfinavir were weaker for each variant than for the wild-type protease, with the double mutant exhibiting the most dramatic change. Therefore, our results show that the C-SA V82F I84V double mutation decreased the binding affinities of protease inhibitors to levels significantly lower than that required for effective inhibition.
Growth Determinants for H5N1 Influenza Vaccine Seed Viruses in MDCK Cells
Authors: Murakami Shin , Horimoto Taisuke , Mai Le Quynh , Nidom Chairul A. , Chen Hualan , Muramoto Yukiko , Yamada Shinya , Iwasa Ayaka , Iwatsuki-Horimoto Kiyoko , Shimojima Masayuki , Iwata Akira , Kawaoka Yoshihiro
Published: September 2008

H5N1 influenza A viruses are exacting a growing human toll, with more than 240 fatal cases to date. In the event of an influenza pandemic caused by these viruses, embryonated chicken eggs, which are the approved substrate for human inactivated-vaccine production, will likely be in short supply because chickens will be killed by these viruses or culled to limit the worldwide spread of the infection. The Madin-Darby canine kidney (MDCK) cell line is a promising alternative candidate substrate because it supports efficient growth of influenza viruses compared to other cell lines. Here, we addressed the molecular determinants for growth of an H5N1 vaccine seed virus in MDCK cells, revealing the critical responsibility of the Tyr residue at position 360 of PB2, the considerable requirement for functional balance between hemagglutinin (HA) and neuraminidase (NA), and the partial responsibility of the Glu residue at position 55 of NS1. Based on these findings, we produced a PR8/H5N1 reassortant, optimized for this cell line, that derives all of its genes for its internal proteins from the PR8(UW) strain except for the NS gene, which derives from the PR8(Cambridge) strain; its N1 NA gene, which has a long stalk and derives from an early H5N1 strain; and its HA gene, which has an avirulent-type cleavage site sequence and is derived from a circulating H5N1 virus. Our findings demonstrate the importance and feasibility of a cell culture-based approach to producing seed viruses for inactivated H5N1 vaccines that grow robustly and in a timely, cost-efficient manner as an alternative to egg-based vaccine production.
Within-Host Genetic Diversity of Endemic and Emerging Parvoviruses of Dogs and Cats
Authors: Hoelzer Karin , Shackelton Laura A. , Holmes Edward C. , Parrish Colin R.
Published: September 2008

Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence diversity. To determine the extent and structure of intrahost genetic diversity in a recently emerged single-stranded DNA virus, we analyzed viral population structures during natural infections of animals with canine parvovirus (CPV) or its ancestor, feline panleukopenia virus (FPV). We compared infections that occurred shortly after CPV emerged with more recent infections and examined the population structure of CPV after experimental cross-species transmission to cats. Infections with CPV and FPV showed limited genetic diversity regardless of the analyzed host tissue or year of isolation. Coinfections with genetically distinct viral strains were detected in some cases, and rearranged genomes were seen in both FPV and CPV. The sporadic presence of some sequences with multiple mutations suggested the occurrence of either particularly error-prone viral replication or coinfection by more distantly related strains. Finally, some potentially organ-specific host effects were seen during experimental cross-species transmission, with many of the mutations located in the nonstructural protein NS2. These included residues with evidence of positive selection at the population level, which is compatible with a role of this protein in host adaptation.
Charge Cluster-to-Alanine Scanning of UL128 for Fine Tuning of the Endothelial Cell Tropism of Human Cytomegalovirus
Authors: Schuessler Andrea , Sampaio Kerstin Laib , Sinzger Christian
Published: September 2008

The viral genes UL128, UL130, and UL131A have been identified as major determinants of endothelial cell (EC) tropism of human cytomegalovirus (HCMV), with deletion of either gene causing a null phenotype. We hypothesized that a functional scanning of these genes by minor genetic modifications would allow for the generation of mutants with an intermediate phenotype. By combining charge cluster-to-alanine (CCTA) mutagenesis with markerless mutagenesis of a bacterial artificial chromosome-cloned endotheliotropic HCMV strain, we analyzed UL128 in order to identify functional sites and hence enable targeted modulation of the EC tropism of HCMV. A total of nine mutations in eight charge clusters were tested. Three of the CCTA mutations severely reduced EC tropism, three were irrelevant, two had a weak effect on cell tropism, and one mutation in the most C-terminal cluster caused an intermediate phenotype. All of the highly effective mutations were located in a core region (amino acids 72 to 106) which appears to be particularly crucial for EC tropism. The intermediate effect of mutations in the C-terminal cluster could be modulated by varying the number of amino acids replaced with alanine. This study provides a rational approach for targeted modulation of HCMV cell tropism, which may aid in the development of HCMV strains with a desired degree of attenuation.
Role of Hypercytokinemia in NF-κB p50-Deficient Mice after H5N1 Influenza A Virus Infection
Authors: Droebner Karoline , Reiling Sarah Julia , Planz Oliver
Published: September 2008

During H5N1 influenza virus infection, proinflammatory cytokines are markedly elevated in the lungs of infected hosts. The significance of this dysregulated cytokine response in H5N1-mediated pathogenesis remains to be determined. To investigate the influence of hypercytokinemia, or “cytokine storm,” a transgenic mouse technology was used. The classical NF-κB pathway regulates the induction of most proinflammatory cytokines. Deletion of the p50 subunit leads to a markedly reduced expression of the NF-κB-regulated cytokines and chemokines. Here we show that H5N1 influenza virus infection of this transgenic mouse model resulted in a lack of hypercytokinemia but not in altered pathogenesis.
pH-Induced Activation of Arenavirus Membrane Fusion Is Antagonized by Small-Molecule Inhibitors
Authors: York Joanne , Dai Dongcheng , Amberg Sean M. , Nunberg Jack H.
Published: September 2008

The arenavirus envelope glycoprotein (GPC) mediates viral entry through pH-induced membrane fusion in the endosome. This crucial process in the viral life cycle can be specifically inhibited in the New World arenaviruses by the small-molecule compound ST-294. Here, we show that ST-294 interferes with GPC-mediated membrane fusion by targeting the interaction of the G2 fusion subunit with the stable signal peptide (SSP). We demonstrate that amino acid substitutions at lysine-33 of the Junín virus SSP confer resistance to ST-294 and engender de novo sensitivity to ST-161, a chemically distinct inhibitor of the Old World Lassa fever virus. These compounds, as well as a broadly active inhibitor, ST-193, likely share a molecular target at the SSP-G2 interface. We also show that both ST-294 and ST-193 inhibit pH-induced dissociation of the G1 receptor-binding subunit from GPC, a process concomitant with fusion activation. Interestingly, the inhibitory activity of these molecules can in some cases be overcome by further lowering the pH used for activation. Our results suggest that these small molecules act to stabilize the prefusion GPC complex against acidic pH. The pH-sensitive interaction between SSP and G2 in GPC represents a robust molecular target for the development of antiviral compounds for the treatment of arenavirus hemorrhagic fevers.
Antiretroviral Therapy prior to Acute Viral Replication Preserves CD4 T Cells in the Periphery but Not in Rectal Mucosa during Acute Simian Immunodeficiency Virus Infection
Authors: Kader Muhamuda , Hassan Wail M. , Eberly Matthew , Piatak Michael , Lifson Jeffrey D. , Roederer Mario , Mattapallil Joseph J.
Published: September 2008

The rectal mucosa is a major site for human immunodeficiency virus entry and CD4 T-cell depletion. The early and near-total loss of these cells from the rectal mucosa severely compromises the ability of the mucosal immune system to control various opportunistic infections. Protecting these cells from infection and destruction can delay disease progression, leading to a better long-term outcome. Here we show that effective suppression of viral infection in memory CD4 T cells from the rectal mucosa and peripheral blood to a very low level with antiretroviral therapy (ART) initiated prior to the peak of infection is associated with opposite outcomes in these tissues. A near-total loss of CD4 T cells in the rectal mucosa contrasted with preservation of most memory CD4 T cells in peripheral blood during the course of treatment. Interestingly, ART significantly reduced viral infection in memory CD4 T cells from both rectal mucosa and peripheral blood. Although early ART was of limited value in protecting the CD4 T cells in the rectal mucosa, the significant preservation of peripheral CD4 T cells could contribute to maintaining immune competence, leading to a better long-term outcome.
Influenza B Virus NS1-Truncated Mutants: Live-Attenuated Vaccine Approach
Authors: Hai Rong , Martínez-Sobrido Luis , Fraser Kathryn A. , Ayllon Juan , García-Sastre Adolfo , Palese Peter
Published: September 2008

Type B influenza viruses can cause substantial morbidity and mortality in the population, and vaccination remains by far the best means of protection against infections with these viruses. Here, we report the construction of mutant influenza B viruses for potential use as improved live-virus vaccine candidates. Employing reverse genetics, we altered the NS1 gene, which encodes a type I interferon (IFN) antagonist. The resulting NS1 mutant viruses induced IFN and, as a consequence, were found to be attenuated in vitro and in vivo. The absence of pathogenicity of the NS1 mutants in both BALB/c and C57BL/6 PKR
−/−
mice was confirmed. We also provide evidence that influenza B virus NS1 mutants induce a self-adjuvanted immune response and confer effective protection against challenge with both homologous and heterologous B virus strains in mice.
Hepatitis C Virus Core Protein Augments Androgen Receptor-Mediated Signaling
Authors: Kanda Tatsuo , Steele Robert , Ray Ranjit , Ray Ratna B.
Published: September 2008

Hepatitis C virus (HCV) infection is frequently associated with the development of hepatocellular carcinoma (HCC), which is one of the male-dominant diseases. Androgen signaling in liver may be related to carcinogenesis. In this study, we investigated whether HCV proteins cross talk with the androgen receptor (AR) signaling pathway for promotion of carcinogenesis. We have demonstrated that HCV core protein alone or in context with other HCV proteins enhances AR-mediated transcriptional activity and further augments in the presence of androgen. Subsequent study suggested that HCV core protein activates STAT3, which in turn enhances AR-mediated transcription. This activity was blocked by a pharmacological inhibitor of the Jak/Stat signaling pathway, AG490. Vascular endothelial growth factor (VEGF) is a target gene of AR in liver and plays an important role in angiogenesis. Therefore, we examined whether HCV infection modulates VEGF expression in hepatocytes. Our results demonstrated that HCV enhances VEGF expression and facilitates tube formation in human coronary microvascular endothelial cells in the presence of AR. Together, our results suggest that HCV core protein acts as a positive regulator in AR signaling, providing further insight into oncogenic potential in the development of HCC in HCV-infected individuals.
Efficient Subgroup C Avian Sarcoma and Leukosis Virus Receptor Activity Requires the IgV Domain of the Tvc Receptor and Proper Display on the Cell Membrane
Authors: Munguia Audelia , Federspiel Mark J.
Published: September 2008

We recently identified and cloned the receptor for subgroup C avian sarcoma and leukosis viruses [ASLV(C)], i.e., Tvc, a protein most closely related to mammalian butyrophilins, which are members of the immunoglobulin protein family. The extracellular domain of Tvc contains two immunoglobulin-like domains, IgV and IgC, which presumably each contain a disulfide bond important for native function of the protein. In this study, we have begun to identify the functional determinants of Tvc responsible for ASLV(C) receptor activity. We found that the IgV domain of the Tvc receptor is responsible for interacting with the glycoprotein of ASLV(C). Additional experiments demonstrated that a domain was necessary as a spacer between the IgV domain and the membrane-spanning domain for efficient Tvc receptor activity, most likely to orient the IgV domain a proper distance from the cell membrane. The effects on ASLV(C) glycoprotein binding and infection efficiency were also studied by site-directed mutagenesis of the cysteine residues of Tvc as well as conserved amino acid residues of the IgV Tvc domain compared to other IgV domains. In this initial analysis of Tvc determinants important for interacting with ASLV(C) glycoproteins, at least two aromatic amino acid residues in the IgV domain of Tvc, Trp-48 and Tyr-105, were identified as critical for efficient ASLV(C) infection. Interestingly, one or more aromatic amino acid residues have been identified as critical determinants in the other ASLV(A-E) receptors for a proper interaction with ASLV glycoproteins. This suggests that the ASLV glycoproteins may share a common mechanism of receptor interaction with an aromatic residue(s) on the receptor critical for triggering conformational changes in SU that initiate the fusion process required for efficient virus infection.
Molecular and Transmission Characteristics of Primary-Passaged Ovine Scrapie Isolates in Conventional and Ovine PrP Transgenic Mice
Authors: Thackray Alana M. , Hopkins Lee , Spiropoulos John , Bujdoso Raymond
Published: September 2008

A more complete assessment of ovine prion strain diversity will be achieved by complementing biological strain typing in conventional and ovine PrP transgenic mice with a biochemical analysis of the resultant PrPSc. This will provide a correlation between ovine prion strain phenotype and the molecular nature of different PrP conformers associated with particular prion strains. Here, we have compared the molecular and transmission characteristics of ovine ARQ/ARQ and VRQ/VRQ scrapie isolates following primary passage in
tg338
(VRQ) and
tg59
(ARQ) ovine PrP transgenic mice and the conventional mouse lines C57BL/6 (
Prnp

a

), RIII (
Prnp

a

), and VM (
Prnp

b

). Our data show that these different genotypes of scrapie isolates display similar incubation periods of >350 days in conventional and
tg59
mice. Facilitated transmission of sheep scrapie isolates occurred in
tg338
mice, with incubation times reduced to 64 days for VRQ/VRQ inocula and to ≤210 days for ARQ/ARQ samples. Distinct genotype-specific lesion profiles were seen in the brains of conventional and
tg59
mice with prion disease, which was accompanied by the accumulation of more conformationally stable PrPSc, following inoculation with ARQ/ARQ compared to VRQ/VRQ scrapie isolates. In contrast, the lesion profiles, quantities, and stability of PrPSc induced by the same inocula in
tg338
mice were more similar than in the other mouse lines. Our data show that primary transmission of different genotypes of ovine prions is associated with the formation of different conformers of PrPSc with distinct molecular properties and provide the basis of a molecular approach to identify the true diversity of ovine prion strains.
Novel Characteristics of the Function and Induction of Murine p56 Family Proteins
Authors: Fensterl Volker , White Christine L. , Yamashita Michifumi , Sen Ganes C.
Published: September 2008

The interferon-stimulated gene 56 (ISG56) family is induced strongly in response to virus infection, interferons (IFNs) and double-stranded RNA (dsRNA). In the mouse, this family comprises three members, ISG56, ISG54, and ISG49, which are clustered on chromosome 19 and encode the corresponding proteins p56, p54, and p49. Here, we report differential properties of these proteins and their distinct induction patterns in different cell types. All three murine proteins bound to the c-subunit of the translation initiation factor eIF3, but unlike the other members, p49 did not inhibit protein synthesis. Using a newly raised antibody, we demonstrated that both in vitro and in vivo, p49 expression was strongly induced by IFN, dsRNA, and Sendai virus. However, in kidney mesangial cells, as opposed to podocytes, encephalomyocarditis virus, vesicular stomatitis virus, or extracellular dsRNA did not induce any of the p56 family proteins, although they were robustly expressed after Sendai virus infection or dsRNA transfection. Furthermore, protein-specific differences in the regulation of p56 family members became evident in various leukocyte types: all three proteins were induced by IFN in T cells, but in B cells p56 and ISG56 mRNA could not be detected. Similarly, p56 was selectively uninducible in plasmacytoid dendritic cells, whereas in myeloid dendritic cells, all three family members were expressed. These results revealed novel cell type-, inducer-, and gene-specific regulation of the ISG56 family of genes.
Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases
Authors: Parrish Colin R. , Holmes Edward C. , Morens David M. , Park Eun-Chung , Burke Donald S. , Calisher Charles H. , Laughlin Catherine A. , Saif Linda J. , Daszak Peter
Published: September 2008

Host range is a viral property reflecting natural hosts that are infected either as part of a principal transmission cycle or, less commonly, as “spillover” infections into alternative hosts. Rarely, viruses gain the ability to spread efficiently within a new host that was not previously exposed or susceptible. These transfers involve either increased exposure or the acquisition of variations that allow them to overcome barriers to infection of the new hosts. In these cases, devastating outbreaks can result. Steps involved in transfers of viruses to new hosts include contact between the virus and the host, infection of an initial individual leading to amplification and an outbreak, and the generation within the original or new host of viral variants that have the ability to spread efficiently between individuals in populations of the new host. Here we review what is known about host switching leading to viral emergence from known examples, considering the evolutionary mechanisms, virus-host interactions, host range barriers to infection, and processes that allow efficient host-to-host transmission in the new host population.
Whole-Lake Fertilization Experiments in Coastal British Columbia Lakes: Empirical Relationships between Nutrient Inputs and Phytoplankton Biomass and Production
Authors: Stockner J. G. , Shortreed K. S.
Published: September 2008

Seventeen warm monomictic coastal lakes in British Columbia were studied from 1980 to 1983. Inorganic nitrogen and phosphorus were applied to 13 of the lakes in some or all years of the study. In the untreated condition, lakes were ultraoligotrophic with low concentrations of nutrients (1.0–4.1 μg total P-L−1at spring overturn), of average summer chlorophyll (0.49–2.57 μg∙L−1), and of average daily primary production (3.0–10.5 mg C∙m−3∙d−1). The lakes' oligotrophic condition is sustained by their low residence time (0.2–7.3 yr) and by low nutrient inputs from the generally steep granitic drainage basins. The lakes respond predictably to nitrogen and phosphorus additions and are generally phosphorus limited, as shown by the significant positive relationships between average summer chlorophyll and total phosphorus at spring overturn (r = 0.81) in unfertilized lakes, between average summer chlorophyll and phosphorus load from fertilizer (r2 = 0.62) in fertilized lakes, by the high average particulate C:N:P ratios (152:20:1), and by the high average TN:TP ratio (89).
Acidification Effects on Stream Biota and Organic Matter Processing
Authors: Burton Thomas M. , Stanford Richard M. , Allan Jon W.
Published: September 2008

Experimental acidification effects on stream biota and organic matter decomposition rates in natural, low-alkalinity (7–15 mg CaCO3/L) Michigan streams were studied using paired, artificial, recirculating streams. Acidification to pH 4 with sulfuric acid from pH 7.0 to 7.4 resulted in significant decreased decomposition rates for 5-g leaf packs of white birch (Betula papyrifera) and sugar maple (Acer saccharum). Populations of total macroinvertebrates on leaf packs in the acid stream were substantially reduced over a 264-d exposure period, whereas populations remained unchanged in the control stream. Detailed studies were conducted on a caddisfly, Lepidostoma liba, and an isopod, Asellus intermedius. The Lepidostoma population was resistant to short-term exposure to acidification, but significant mortality occurred after 80 d at pH 4 at 2–4 °C. Late instars were not affected by acidification and emerged after more than 60 d at 15–20 °C. Asellus was very sensitive to acidification with up to 93% mortality after only 24 d and with inhibition of reproduction. Acidification also resulted in increased mortality for a snail, Physa heterosiropha, and another caddisfly, Pycnopsyche sp.
Depth Distribution and Biomass of Submersed Aquatic Macrophyte Communities in Relation to Secchi Depth
Authors: Chambers Patricia A. , Kaiff Jacob
Published: September 2008

Using original data from eight lakes in southern Quebec and literature values from other fakes throughout the world, regression models were developed that allow prediction of the maximum depth of macrophyte colonization (zc) for angiosperms ((zc)0.5 = 1.33 log (D) + 1.40), bryophytes (zc)−0.5 = −0.48 log (D) + 0.81), and charophytes (log (zc) = 0.87 log (D) + 0.31) and the depth of maximum angiosperm biomass (zb)(zb0.5 = 0.54 log (D) + 1.15) from mean summer Secchi depth (D). Irradiance over the growing season at the maximum depth of colonization was about 1800 J/cm2(1 cal/cm2 = 0.239 J/cm2) for angiosperms and bryophytes and 1200 J/cm2for charophytes. These values represent, on average, 21 and 11% of the photo-synthetically available radiation incident on the water surface. Changes in maximum angiosperm biomass were, however, not correlated with Secchi depth. This suggests that while the depth distribution of aquatic macrophyte communities is primarily controlled by irradiance, environmental parameters other than irradiance and nutrients are also important in determining maximum angiosperm biomass in individual lakes.