bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence of three genotypic clusters of Bemisia tabaci and the rapid spread of the B biotype in south India
Authors: Rekha A.R. , Maruthi M.N. , Muniyappa V. , Colvin J.
Published: November 2005

The whitefly, Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae), is generally considered to have originated from the Indian subcontinent, although little information has so far been collected on the molecular diversity of populations present in this region. The genetic diversity of B. tabaci populations from Karnataka State, south India was analysed using the random amplified polymorphic DNA‐polymerase chain reaction (RAPD‐PCR) technique and partial mitochondrial cytochrome oxidase I (mtCOI) gene sequences (689 bases) of 22 selected samples. A total of 108 whitefly samples analysed by RAPD‐PCR produced 89 polymorphic bands, and cluster analyses grouped them according to their geographic origin into ‘north’ and ‘south’ Karnataka. Phylogenetic analysis of mtCOI gene sequences with reference B. tabaci sequences from other Asian countries divided them into three genotypic clusters. Each cluster was supported with high bootstrap values (82–100%) and the individuals belonging to each cluster shared high nucleotide identities (up to 100%). This indicated at least three distinct genotypes, apparently indigenous to India, which are also present in China, Malaysia, Nepal, Pakistan, and Thailand. These coexist with the B biotype, which was first reported in India in 1999, and has since spread rapidly to other states in south India. The B biotype was more common than the indigenous B. tabaci, in locations where it had been present for more than 2 years. This is reminiscent of the situation in the Americas during the early 1990s, where the B biotype replaced existing biotypes and caused unprecedented losses to agriculture.
Induction of Innate Immune Response Genes by Sin Nombre Hantavirus Does Not Require Viral Replication
Authors: Prescott Joseph , Ye Chunyan , Sen Ganes , Hjelle Brian
Published: November 2005

Maladaptive immune responses are considered to be important factors in the pathogenesis of the two diseases caused by hantaviruses, hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome (HCPS). While the intensity of adaptive antiviral T-cell responses seems to correlate with the severity of HCPS, there is increasing evidence that innate antiviral responses by endothelial cells, the native targets for hantavirus infection in vivo, are induced within hours of exposure to infectious hantaviruses. To investigate early events in the innate response to Sin Nombre virus (SNV), the principal etiologic agent of HCPS in North America, we treated human endothelial cells with live virus, or virus subjected to inactivation by UV irradiation at minimal doses required to inhibit replication, and assayed host expression of interferon-stimulated genes (ISG) by microarray and reverse transcription-PCR. We show herein that a variety of ISG are induced between 4 and 24 h after exposure to both live and killed virus. The levels of such induction at early time points (before 24 h) were generally higher in cells treated with SNV particles that had been killed by exposure to UV irradiation. Additionally, SNV exposed to increasing doses of UV irradiation induced ISG better than live virus despite increased disruption of viral RNA integrity. However, SNV replication was required for continued ISG overexpression by 3 days posttreatment. These results suggest that hantavirus particles may themselves be capable of early induction of ISG and that ongoing production of viral particles during infection could contribute to the pathogenic process.
Luxury at a Cost? Recombinant Mouse Hepatitis Viruses Expressing the Accessory Hemagglutinin Esterase Protein Display Reduced Fitness In Vitro
Authors: Lissenberg A. , Vrolijk M. M. , van Vliet A. L. W. , Langereis M. A. , de Groot-Mijnes J. D. F. , Rottier P. J. M. , de Groot R. J.
Published: November 2005

Group 2 coronaviruses encode an accessory envelope glycoprotein species, the hemagglutinin esterase (HE), which possesses sialate-
O
-acetylesterase activity and which, presumably, promotes virus spread and entry in vivo by facilitating reversible virion attachment to O-acetylated sialic acids. While HE may provide a strong selective advantage during natural infection, many laboratory strains of mouse hepatitis virus (MHV) fail to produce the protein. Apparently, their HE genes were inactivated during cell culture adaptation. For this report, we have studied the molecular basis of this phenomenon. By using targeted RNA recombination, we generated isogenic recombinant MHVs which differ exclusively in their expression of HE and produce either the wild-type protein (HE
+
), an enzymatically inactive HE protein (HE
0
), or no HE at all. HE expression or the lack thereof did not lead to gross differences in in vitro growth properties. Yet the expression of HE was rapidly lost during serial cell culture passaging. Competition experiments with mixed infections revealed that this was not due to the enzymatic activity: MHVs expressing HE
+
or HE
0
propagated with equal efficiencies. During the propagation of recombinant MHV-HE
+
, two types of spontaneous mutants accumulated. One produced an anchorless HE, while the other had a Gly-to-Trp substitution at the predicted C-terminal residue of the HE signal peptide. Neither mutant incorporated HE into virion particles, suggesting that wild-type HE reduces the in vitro propagation efficiency, either at the assembly stage or at a postassembly level. Our findings demonstrate that the expression of “luxury” proteins may come at a fitness penalty. Apparently, under natural conditions the costs of maintaining HE are outweighed by the benefits.
Expression of Hemagglutinin Esterase Protein from Recombinant Mouse Hepatitis Virus Enhances Neurovirulence
Authors: Kazi Lubna , Lissenberg Arjen , Watson Richard , de Groot Raoul J. , Weiss Susan R.
Published: November 2005

Murine hepatitis virus (MHV) infection provides a model system for the study of hepatitis, acute encephalitis, and chronic demyelinating disease. The spike glycoprotein, S, which mediates receptor binding and membrane fusion, plays a critical role in MHV pathogenesis. However, viral proteins other than S also contribute to pathogenicity. The JHM strain of MHV is highly neurovirulent and expresses a second spike glycoprotein, the hemagglutinin esterase (HE), which is not produced by MHV-A59, a hepatotropic but only mildly neurovirulent strain. To investigate a possible role for HE in MHV-induced neurovirulence, isogenic recombinant MHV-A59 viruses were generated that produced either (i) the wild-type protein, (ii) an enzymatically inactive HE protein, or (iii) no HE at all (A. Lissenberg, M. M. Vrolijk, A. L. W. van Vliet, M. A. Langereis, J. D. F. de Groot-Mijnes, P. J. M. Rottier, and R. J. de Groot, J. Virol.
79:
15054-15063, 2005 [accompanying paper]). A second, mirror set of recombinant viruses was constructed in which, in addition, the MHV-A59 S gene had been replaced with that from MHV-JHM. The expression of HE in combination with A59 S did not affect the tropism, pathogenicity, or spread of the virus in vivo. However, in combination with JHM S, the expression of HE, regardless of whether it retained esterase activity or not, resulted in increased viral spread within the central nervous system and in increased neurovirulence. Our findings suggest that the properties of S receptor utilization and/or fusogenicity mainly determine organ and host cell tropism but that HE enhances the efficiency of infection and promotes viral dissemination, at least in some tissues, presumably by serving as a second receptor-binding protein.
Ubiquitination of the Prototype Foamy Virus Envelope Glycoprotein Leader Peptide Regulates Subviral Particle Release
Authors: Stanke Nicole , Stange Annett , Lüftenegger Daniel , Zentgraf Hanswalter , Lindemann Dirk
Published: November 2005

Foamy virus (FV) particle egress is unique among retroviruses because of its essential requirement for Gag and Env coexpression for budding and particle release. The FV glycoprotein undergoes a highly unusual biosynthesis resulting in the generation of three particle-associated, mature subunits, leader peptide (LP), surface (SU), and transmembrane (TM), derived from a precursor protein by posttranslational proteolysis mediated by furin or furinlike proteases. Previously at least three LP products of different molecular weights were detected in purified FV particles. Here we demonstrate that the higher-molecular-weight forms gp28
LP
and gp38
LP
are ubiquitinated variants of the major gp18
LP
cleavage product, which has a type II membrane topology. Furthermore, we show that all five lysine residues located within the N-terminal 60-amino-acid cytoplasmic domain of gp18
LP
can potentially be ubiquitinated, however, there seems to be a preference for using the first three. Inactivation of ubiquitination sites individually resulted in no obvious phenotype. However, simultaneous inactivation of the first three or all five ubiquitination sites in gp18
LP
led to a massive increase in subviral particles released by these mutant glycoproteins that were readily detectable by electron microscopy analysis upon expression of the ubiquitination-deficient glycoprotein by itself or in a proviral context. Surprisingly, only the quintuple ubiquitination mutant showed a two- to threefold increase in single-cycle infectivity assays, whereas all other mutants displayed infectivities similar to that of the wild type. Taken together, these data suggest that the balance between viral and subviral particle release of FVs is regulated by ubiquitination of the glycoprotein LP.
Transcriptional Analysis of Latent and Inducible Kaposi's Sarcoma-Associated Herpesvirus Transcripts in the K4 to K7 Region
Authors: Taylor Jennifer L. , Bennett Heather N. , Snyder Beth A. , Moore Patrick S. , Chang Yuan
Published: November 2005

Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-2 herpesvirus with a genome containing a long unique coding region (LUR) flanked by GC-rich terminal repeat sequences. The LUR encodes approximately 90 annotated open reading frames (ORFs) with complex patterns of gene expression during viral latency, reactivation, and de novo infection. To identify unannotated KSHV genes, we examined the region between 21,500 and 30,000 bp of the KSHV LUR, representing approximately 8.5 kb of sequence. This region encodes seven known single-exon ORFs (
K4
,
K4.1
,
K4.2
,
K5
,
K6
,
K7
, and
PAN
), but previous computer analyses have failed to identify additional likely genes in the remaining 5.2 kb. We identified four novel transcripts using Northern blotting, phage library screening, and 5′ rapid amplification of cDNA ends analysis in the region between ORFs
K4.2
and
K7
. In vitro analysis of KSHV-infected primary effusion lymphoma cell lines in the presence of 12-
O
-tetradecanoylphorbol-13-acetate and phosphonoformic acid suggests that one latent transcript is coterminal with the previously annotated
K3
gene encoding an ubiquitin-ligase known to downregulate major histocompatibility complex class I expression. This alternatively spliced transcript may contribute to KSHV adaptive immune evasion during latent infection. Other transcripts are inducible, including a 6.1-kb transcript that is the largest transcript found in the KSHV genome to date.
Effect of Bottlenecking on Evolution of the Nonstructural Protein 3 Gene of Hepatitis C Virus during Sexually Transmitted Acute Resolving Infection
Authors: Quer Josep , Esteban Juan Ignacio , Cos Joan , Sauleda Sílvia , Ocaña Laura , Martell María , Otero Teresa , Cubero Maria , Palou Eduard , Murillo Pedro , Esteban Rafael , Guàrdia Jaume
Published: November 2005

Sexual partners of patients infected with the hepatitis C virus (HCV) often have detectable HCV-specific T-cell responses in the absence of seroconversion, suggesting unapparent, spontaneously resolving infection. To determine whether differences in the evolutionary potential of bottlenecked inoculum may explain the low rate of HCV persistence after sexual exposure, we have investigated changes in the entire HCV nonstructural 3 (NS3) gene over time in a chronic carrier and compared his viral quasispecies with that of the acute-phase isolate of his sexual partner, who developed acute resolving hepatitis C. The overall rate of accumulation of mutations, estimated by regression analysis of six consecutive consensus NS3 sequences over 8 years, was 1.5 × 10−3mutations per site per year, with small intersample fluctuations related to changes in environmental conditions. Comparison of quasispecies parameters in one isolate of the chronic carrier with those of the acute-phase isolate of the infected partner revealed a higher heterogeneity and lower proportion of nonsynonymous mutations in the former. All NS3 sequences from the acute-phase isolate clustered with a single sequence from the chronic isolate, despite complete HLA mismatch between the patients, suggesting bottlenecking during transmission. The low risk of viral persistence after sexual exposure to HCV may be related to the selection of a limited number of viral particles carrying a particular combination of mutations which may further limit the potential of a relatively homogeneous quasispecies to rapidly diversify and overcome the immune response of the exposed host.
The Papain-Like Protease of Severe Acute Respiratory Syndrome Coronavirus Has Deubiquitinating Activity
Authors: Barretto Naina , Jukneliene Dalia , Ratia Kiira , Chen Zhongbin , Mesecar Andrew D. , Baker Susan C.
Published: November 2005

Replication of the genomic RNA of severe acute respiratory syndrome coronavirus (SARS-CoV) is mediated by replicase polyproteins that are processed by two viral proteases, papain-like protease (PLpro) and 3C-like protease (3CLpro). Previously, we showed that SARS-CoV PLpro processes the replicase polyprotein at three conserved cleavage sites. Here, we report the identification and characterization of a 316-amino-acid catalytic core domain of PLpro that can efficiently cleave replicase substrates in
trans
-cleavage assays and peptide substrates in fluorescent resonance energy transfer-based protease assays. We performed bioinformatics analysis on 16 papain-like protease domains from nine different coronaviruses and identified a putative catalytic triad (Cys1651-His1812-Asp1826) and zinc-binding site. Mutagenesis studies revealed that Asp1826 and the four cysteine residues involved in zinc binding are essential for SARS-CoV PLpro activity. Molecular modeling of SARS-CoV PLpro suggested that this catalytic core may also have deubiquitinating activity. We tested this hypothesis by measuring the deubiquitinating activity of PLpro by two independent assays. SARS CoV-PLpro hydrolyzed both diubiquitin and ubiquitin-7-amino-4-methylcoumarin (AMC) substrates, and hydrolysis of ubiquitin-AMC is approximately 180-fold more efficient than hydrolysis of a peptide substrate that mimics the PLpro replicase recognition sequence. To investigate the critical determinants recognized by PLpro, we performed site-directed mutagenesis on the P6 to P2′ residues at each of the three PLpro cleavage sites. We found that PLpro recognizes the consensus cleavage sequence LXGG, which is also the consensus sequence recognized by cellular deubiquitinating enzymes. This similarity in the substrate recognition sites should be considered during the development of SARS-CoV PLpro inhibitors.
The Papain-Like Protease from the Severe Acute Respiratory Syndrome Coronavirus Is a Deubiquitinating Enzyme
Authors: Lindner Holger A. , Fotouhi-Ardakani Nasser , Lytvyn Viktoria , Lachance Paule , Sulea Traian , Ménard Robert
Published: November 2005

The severe acute respiratory syndrome coronavirus papain-like protease (SARS-CoV PLpro) is involved in the processing of the viral polyprotein and, thereby, contributes to the biogenesis of the virus replication complex. Structural bioinformatics has revealed a relationship for the SARS-CoV PLpro to herpesvirus-associated ubiquitin-specific protease (HAUSP), a ubiquitin-specific protease, indicating potential deubiquitinating activity in addition to its function in polyprotein processing (T. Sulea, H. A. Lindner, E. O. Purisima, and R. Menard, J. Virol.
79:
4550-4551, 2005). In order to confirm this prediction, we overexpressed and purified SARS-CoV PLpro (amino acids [aa]1507 to 1858) from
Escherichia coli
. The purified enzyme hydrolyzed ubiquitin-7-amino-4-methylcoumarin (Ub-AMC), a general deubiquitinating enzyme substrate, with a catalytic efficiency of 13,100 M
−1
s
−1
, 220-fold more efficiently than the small synthetic peptide substrate Z-LRGG-AMC, which incorporates the C-terminal four residues of ubiquitin. In addition, SARS-CoV PLpro was inhibited by the specific deubiquitinating enzyme inhibitor ubiquitin aldehyde, with an inhibition constant of 210 nM. The purified SARS-CoV PLpro disassembles branched polyubiquitin chains with lengths of two to seven (Ub2-7) or four (Ub4) units, which involves isopeptide bond cleavage. SARS-CoV PLpro processing activity was also detected against a protein fused to the C terminus of the ubiquitin-like modifier ISG15, both in vitro using the purified enzyme and in HeLa cells by coexpression with SARS-CoV PLpro (aa 1198 to 2009). These results clearly establish that SARS-CoV PLpro is a deubiquitinating enzyme, thereby confirming our earlier prediction. This unexpected activity for a coronavirus papain-like protease suggests a novel viral strategy to modulate the host cell ubiquitination machinery to its advantage.
Genetic Analysis of Influenza Virus NS1 Gene: a Temperature-Sensitive Mutant Shows Defective Formation of Virus Particles
Authors: Garaigorta Urtzi , Falcón Ana M. , Ortín Juan
Published: November 2005

To perform a genetic analysis of the influenza A virus NS1 gene, a library of NS1 mutants was generated by PCR-mediated mutagenesis. A collection of mutant ribonucleic proteins containing the nonstructural genes was generated from the library that were rescued for an infectious virus mutant library by a novel RNP competition virus rescue procedure. Several temperature-sensitive (ts) mutant viruses were obtained by screening of the mutant library, and the sequences of their NS1 genes were determined. Most of the mutations identified led to amino acid exchanges and concentrated in the N-terminal region of the protein, but some of them occurred in the C-terminal region. Mutant 11C contained three mutations that led to amino acid exchanges, V18A, R44K, and S195P, all of which were required for the ts phenotype, and was characterized further. Several steps in the infection were slightly altered: (i) M1, M2, NS1, and neuraminidase (NA) accumulations were reduced and (ii) NS1 protein was retained in the nucleus in a temperature-independent manner, but these modifications could not justify the strong virus titer reduction at restrictive temperature. The most dramatic phenotype was the almost complete absence of virus particles in the culture medium, in spite of normal accumulation and nucleocytoplasmic export of virus RNPs. The function affected in the 11C mutant was required late in the infection, as documented by shift-up and shift-down experiments. The defect in virion production was not due to reduced NA expression, as virus yield could not be rescued by exogenous neuraminidase treatment. All together, the analysis of 11C mutant phenotype may indicate a role for NS1 protein in a late event in virus morphogenesis.
Th-Cytotoxic T-Lymphocyte Chimeric Epitopes Extended by
N
ε
-Palmitoyl Lysines Induce Herpes Simplex Virus Type 1-Specific Effector CD8
+
Tc
1
Responses and Protect against Ocular Infection
Authors: Zhang Xiuli , Issagholian Annie , Berg Eric A. , Fishman Jordan B. , Nesburn Anthony B. , BenMohamed Lbachir
Published: November 2005

Molecularly defined vaccine formulations capable of inducing antiviral CD8
+
T-cell-specific immunity in a manner compatible with human delivery are limited. Few molecules achieve this target without the support of an appropriate immunological adjuvant. In this study, we investigate the potential of totally synthetic palmitoyl-tailed helper-cytotoxic-T-lymphocyte chimeric epitopes (Th-CTL chimeric lipopeptides) to induce herpes simplex virus type 1 (HSV-1)-specific CD8
+
T-cell responses. As a model antigen, the HSV-1 glycoprotein B (498-505) (gB
498-505
) CD8
+
CTL epitope was synthesized in line with the Pan DR peptide (PADRE), a universal CD4
+
Th epitope. The peptide backbone, composed solely of both epitopes, was extended by N-terminal attachment of one (PAM-Th-CTL), two [(PAM)
2
-Th-CTL], or three [(PAM)
3
-Th-CTL] palmitoyl lysines and delivered to H2
b
mice in adjuvant-free saline. Potent HSV-1 gB
498-505
-specific antiviral CD8
+
T-cell effector type 1 responses were induced by each of the palmitoyl-tailed Th-CTL chimeric epitopes, irrespective of the number of lipid moieties. The palmitoyl-tailed Th-CTL chimeric epitopes provoked cell surface expression of major histocompatibility complex and costimulatory molecules and production of interleukin-12 and tumor necrosis factor alpha proinflammatory cytokines by immature dendritic cells. Following ocular HSV-1 challenge, palmitoyl-tailed Th-CTL-immunized mice exhibited a decrease of virus replication in the eye and in the local trigeminal ganglion and reduced herpetic blepharitis and corneal scarring. The rational of the molecularly defined vaccine approach presented in this study may be applied to ocular herpes and other viral infections in humans, providing steps are taken to include appropriate Th and CTL epitopes and lipid groups.
Respiratory Syncytial Virus-Inducible BCL-3 Expression Antagonizes the STAT/IRF and NF-κB Signaling Pathways by Inducing Histone Deacetylase 1 Recruitment to the Interleukin-8 Promoter
Authors: Jamaluddin Mohammad , Choudhary Sanjeev , Wang Shaofei , Casola Antonella , Huda Ruksana , Garofalo Roberto P. , Ray Sutapa , Brasier Allan R.
Published: November 2005

Respiratory syncytial virus (RSV) is a paramyxovirus that produces airway inflammation, in part by inducing interleukin-8 (IL-8) expression, a CXC-type chemokine, via the NF-κB/RelA and STAT/IRF signaling pathways. In RSV-infected A549 cells, IL-8 transcription attenuates after 24 h in spite of ongoing viral replication and persistence of nuclear RelA, suggesting a mechanism for transcriptional attenuation. RSV infection induces B-cell lymphoma protein -3 (Bcl-3) expression 6 to 12 h after viral infection, at times when IL-8 transcription is inhibited. By contrast, 293 cells, deficient in inducible Bcl-3 expression, show no attenuation of IL-8 transcription. We therefore examined Bcl-3's role in terminating virus-inducible IL-8 transcription. Transient expression of Bcl-3 potently inhibited virus-inducible IL-8 transcription by disrupting both the NF-κB and STAT/IRF pathways. Although previously Bcl-3 was thought to capture 50-kDa NF-κB1 isoforms in the cytoplasm, immunoprecipitation (IP) and electrophoretic mobility shift assays indicate that nuclear Bcl-3 associates with NF-κB1 without affecting DNA binding. Additionally, Bcl-3 potently inhibited the STAT/IRF pathway. Nondenaturing co-IP assays indicate that nuclear Bcl-3 associates with STAT-1 and histone deacetylase 1 (HDAC-1), increasing HDAC-1 recruitment to the IL-8 promoter. Treatment with the HDAC inhibitor trichostatin A blocks attenuation of IL-8 transcription. A nuclear targeting-deficient Bcl-3 is unable to enhance HDAC-1-mediated chemokine repression. Finally, small inhibitory RNA-mediated Bcl-3 “knockdown” resulted in enhanced RSV-induced chemokine expression in A549 cells. These data indicate that Bcl-3 is a virus-inducible inhibitor of chemokine transcription by interfering with the NF-κB and STAT/IRF signaling pathways by complexing with them and recruiting HDAC-1 to attenuate target promoter activity.
Genomic Sequence Analysis of Epstein-Barr Virus Strain GD1 from a Nasopharyngeal Carcinoma Patient
Authors: Zeng Mu-Sheng , Li Da-Jiang , Liu Qing-Lun , Song Li-Bing , Li Man-Zhi , Zhang Ru-Hua , Yu Xing-Juan , Wang Hui-Min , Ernberg Ingemar , Zeng Yi-Xin
Published: November 2005

To date, the only entire Epstein-Barr virus (EBV) genomic sequence available in the database is the prototype B95.8, which was derived from an individual with infectious mononucleosis. A causative link between EBV and nasopharyngeal carcinoma (NPC), a disease with a distinctly high incidence in southern China, has been widely investigated. However, no full-length analysis of any substrain of EBV from this area has been reported. In this study, we analyzed the entire genomic sequence of an EBV strain from a patient with NPC in Guangdong, China. This EBV strain was termed GD1 (Guangdong strain 1), and the full-length sequence of GD1 was submitted to the GenBank database. The assigned accession number is
AY961628
. The entire GD1 sequence is 171,656 bp in length, with 59.5% G+C content and 40.5% A+T content. We detected many sequence variations in GD1 compared to prototypical strain B95.8, including 43 deletion sites, 44 insertion sites, and 1,413 point mutations. Furthermore, we evaluated the frequency of some of these GD1 mutations in Cantonese NPC patients and found them to be highly prevalent. These findings suggest that GD1 is highly representative of the EBV strains isolated from NPC patients in Guangdong, China, an area with the highest incidence of NPC in the world. Furthermore, these findings provide the second full-length sequence analysis of any EBV strain as well as the first full-length sequence analysis of an NPC-derived EBV strain.
A Homozygous Nonsense Mutation (428G→A) in the Human Secretor (
FUT2
) Gene Provides Resistance to Symptomatic Norovirus (GGII) Infections
Authors: Thorven Maria , Grahn Ammi , Hedlund Kjell-Olof , Johansson Hugo , Wahlfrid Christer , Larson Göran , Svensson Lennart
Published: November 2005

Noroviruses (formerly Norwalk-like viruses) are a major cause of acute gastroenteritis worldwide and are associated with a significant number of nosocomial and food-borne outbreaks. In this study we show that the human secretor
FUT2
gene, which codes for an α(1,2)-fucosyltransferase synthesizing the H-type 1 antigen in saliva and mucosa, is associated with susceptibility to norovirus infections. Allelic polymorphism characterization at nucleotide 428 for symptomatic (
n
= 53) and asymptomatic (
n
= 62) individuals associated with nosocomial and sporadic norovirus outbreaks revealed that homozygous nonsense mutation (428G→A) in
FUT2
segregated with complete resistance for the disease. Of all symptomatic individuals, 49% were homozygous (SeSe) and 51% heterozygous (Sese
428
) secretors, and none were secretor negative (se
428
se
428
), in contrast to 20% nonsecretors (se
428
se
428
) among Swedish blood donors (
n
= 104) (
P
< 0.0002) and 29% for asymptomatic individuals associated with nosocomial outbreaks (
P
< 0.00001). Furthermore, saliva from secretor-positive and symptomatic patients but not from secretor-negative and asymptomatic individuals bound the norovirus strain responsible for that particular outbreak. This is the first report showing that the
FUT2
nonsecretor (se
428
se
428
) genotype is associated with resistance to nosocomial and sporadic outbreaks with norovirus.
A Combination DNA and Attenuated Simian Immunodeficiency Virus Vaccine Strategy Provides Enhanced Protection from Simian/Human Immunodeficiency Virus-Induced Disease
Authors: Amara Rama Rao , Patel Kalpana , Niedziela Genevieve , Nigam Pragati , Sharma Sunita , Staprans Silvija I. , Montefiori David C. , Chenareddi Lakshmi , Herndon James G. , Robinson Harriet L. , McClure Harold M. , Novembre Francis J.
Published: November 2005

Among the most effective vaccine candidates tested in the simian immunodeficiency virus (SIV)/macaque system, live attenuated viruses have been shown to provide the best protection from challenge. To investigate if preimmunization would increase the level of protection afforded by live attenuated SIVmac239Δnef (Δnef), macaques were given two priming immunizations of DNA encoding SIV Gag and Pol proteins, with control macaques receiving vector DNA immunizations. In macaques receiving the SIV DNA inoculation, SIV-specific cellular but not humoral responses were readily detectable 2 weeks after the second DNA inoculation. Following boosting with live attenuated virus, control of Δnef replication was superior in SIV-DNA-primed macaques versus vector-DNA-primed macaques and was correlated with higher levels of CD8
+
/gamma-interferon-positive and/or interleukin-2-positive cells. Challenge with an intravenous inoculation of simian/human immunodeficiency virus (SHIV) strain SHIV89.6p resulted in infection of all animals. However, macaques receiving SIV DNA as the priming immunizations had statistically lower viral loads than control animals and did not develop signs of disease, whereas three of seven macaques receiving vector DNA showed severe CD4
+
T-cell decline, with development of AIDS in one of these animals. No correlation of immune responses to protection from disease could be derived from our analyses. These results demonstrate that addition of a DNA prime to a live attenuated virus provided better protection from disease following challenge than live attenuated virus alone.
SOCS1 and SOCS3 Are Targeted by Hepatitis C Virus Core/gC1qR Ligation To Inhibit T-Cell Function
Authors: Yao Zhi Qiang , Waggoner Stephen N. , Cruise Michael W. , Hall Caroline , Xie Xuefang , Oldach David W. , Hahn Young S.
Published: November 2005

T cells play an important role in the control of hepatitis C virus (HCV) infection. We have previously demonstrated that the HCV core inhibits T-cell responses through interaction with gC1qR. We show here that core proteins from chronic and resolved HCV patients differ in sequence, gC1qR-binding ability, and T-cell inhibition. Specifically, chronic core isolates bind to gC1qR more efficiently and inhibit T-cell proliferation as well as gamma interferon (IFN-γ) production more profoundly than resolved core isolates. This inhibition is mediated by the disruption of STAT phosphorylation through the induction of SOCS molecules. Silencing either SOCS1 or SOCS3 by small interfering RNA dramatically augments the production of IFN-γ in T cells, thereby abrogating the inhibitory effect of core. Additionally, the ability of core proteins from patients with chronic infections to induce SOCS proteins and suppress STAT activation greatly exceeds that of core proteins from patients with resolved infections. These results suggest that the HCV core/gC1qR-induced T-cell dysfunction involves the induction of SOCS, a powerful inhibitor of cytokine signaling, which represents a novel mechanism by which a virus usurps the host machinery for persistence.
Phylogenetic Incongruence among Oncogenic Genital Alpha Human Papillomaviruses
Authors: Narechania Apurva , Chen Zigui , DeSalle Rob , Burk Robert D.
Published: November 2005

The human papillomaviruses (HPVs) have long been thought to follow a monophyletic pattern of evolution with little if any evidence for recombination between genomes. On the basis of this model, both oncogenicity and tissue tropism appear to have evolved once. Still, no systematic statistical analyses have shown whether monophyly is the rule across all HPV open reading frames (ORFs). We conducted a taxonomic analysis of 59 mucosal/genital HPVs using whole-genome and sliding-window similarity measures; maximum-parsimony, neighbor-joining, and Bayesian phylogenetic analyses; and localized incongruence length difference (LILD) analyses. The algorithm for the LILD analyses localized incongruence by calculating the tree length differences between constrained and unconstrained nodes in a total-evidence tree across all HPV ORFs. The process allows statistical evaluation of every ORF/node pair in the total-evidence tree. The most significant incongruence was observed at the putative high-risk (i.e., cancer-associated) node, the common oncogenic ancestor for alpha HPV species 9 (e.g., HPV type 16 [HPV16]), 11, 7 (e.g., HPV18), 5, and 6. Although these groups share early-gene homology, including high degrees of similarity among E6 and E7, groups 9 and 11 diverge from groups 7, 5, and 6 with respect to L2 and L1. The HPV species groups primarily associated with cervical and anogenital cancers appear to follow two distinct evolutionary paths, one conferred by the early genes and another by the late genes. The incongruence in the genital HPV phylogeny could have occurred from an early recombination event, an ecological niche change, and/or asymmetric genome convergence driven by intense selection. These data indicate that the phylogeny of the oncogenic HPVs is complex and that their evolution may not be monophyletic across all genes.
Severe Acute Respiratory Syndrome Coronavirus Infection of Human Ciliated Airway Epithelia: Role of Ciliated Cells in Viral Spread in the Conducting Airways of the Lungs
Authors: Sims Amy C. , Baric Ralph S. , Yount Boyd , Burkett Susan E. , Collins Peter L. , Pickles Raymond J.
Published: November 2005

Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 as an important cause of severe lower respiratory tract infection in humans, and in vitro models of the lung are needed to elucidate cellular targets and the consequences of viral infection. The SARS-CoV receptor, human angiotensin 1-converting enzyme 2 (hACE2), was detected in ciliated airway epithelial cells of human airway tissues derived from nasal or tracheobronchial regions, suggesting that SARS-CoV may infect the proximal airways. To assess infectivity in an in vitro model of human ciliated airway epithelia (HAE) derived from nasal and tracheobronchial airway regions, we generated recombinant SARS-CoV by deletion of open reading frame 7a/7b (ORF7a/7b) and insertion of the green fluorescent protein (GFP), resulting in SARS-CoV GFP. SARS-CoV GFP replicated to titers similar to those of wild-type viruses in cell lines. SARS-CoV specifically infected HAE via the apical surface and replicated to titers of 10
7
PFU/ml by 48 h postinfection. Polyclonal antisera directed against hACE2 blocked virus infection and replication, suggesting that hACE2 is the primary receptor for SARS-CoV infection of HAE. SARS-CoV structural proteins and virions localized to ciliated epithelial cells. Infection was highly cytolytic, as infected ciliated cells were necrotic and shed over time onto the luminal surface of the epithelium. SARS-CoV GFP also replicated to a lesser extent in ciliated cell cultures derived from hamster or rhesus monkey airways. Efficient SARS-CoV infection of ciliated cells in HAE provides a useful in vitro model of human lung origin to study characteristics of SARS-CoV replication and pathogenesis.
Cytotoxic T-Lymphocyte Escape Does Not Always Explain the Transient Control of Simian Immunodeficiency Virus SIVmac239 Viremia in Adenovirus-Boosted and DNA-Primed Mamu-A*01-Positive Rhesus Macaques
Authors: McDermott Adrian B. , O'Connor David H. , Fuenger Sarah , Piaskowski Shari , Martin Sarah , Loffredo John , Reynolds Matthew , Reed Jason , Furlott Jessica , Jacoby Timothy , Riek Cara , Dodds Elizabeth , Krebs Kendall , Davies Mary-Ellen , Schleif William A. , Casimiro Danilo R. , Shiver John W. , Watkins D. I.
Published: November 2005

Adenovirus 5 (Ad5) vectors show promise as human immunodeficiency virus vaccine candidates. Indian rhesus macaques vaccinated with Ad5-gagcontrolled simian-human immunodeficiency virus SHIV89.6P viral replication in the absence of Env immunogens that might elicit humoral immunity. Here we immunized 15 macaques using either a homologous Ad5-gag/Ad5-gag(Ad5/Ad5) or a heterologous DNA-gag/Ad5-gag(DNA/Ad5) prime-boost regimen and challenged them with a high dose of simian immunodeficiency virus SIVmac239. Macaques vaccinated with the DNA/Ad5 regimen experienced a brief viral load nadir of less than 10,000 viral copies per ml blood plasma that was not seen in Mamu-A*01-negative DNA/Ad5 vaccinees, Mamu-A*01-positive Ad5/Ad5 vaccinees, or vaccine-naive controls. Interestingly, most of these animals were not durably protected from disease progression when challenged with SIVmac239. To investigate the reasons underlying this short-lived vaccine effect, we investigated breadth of the T-cell response, immunogenetic background, and viral escape from CD8+lymphocytes that recognize immunodominant T-cell epitopes. We show that these animals do not mount unusually broad cellular immune response, nor do they express unusual major histocompatibility complex class I alleles. Viral recrudescence occurred in four of the five Mamu-A*01-positive vaccinated macaques. However, only a single animal in this group demonstrated viral escape in the immunodominant Gag181-189CM9 response. These results suggest that viral “breakthrough” in vaccinated animals and viral escape are not inextricably linked and underscore the need for additional research into the mechanisms of vaccine failure.
Restriction of Human Immunodeficiency Virus Type 1 by TRIM-CypA Occurs with Rapid Kinetics and Independently of Cytoplasmic Bodies, Ubiquitin, and Proteasome Activity
Authors: Perez-Caballero David , Hatziioannou Theodora , Zhang Fengwen , Cowan Simone , Bieniasz Paul D.
Published: November 2005

TRIM-CypA is an owl monkey-specific variant of the retrovirus restriction factor TRIM5α. Here, we exploit its modular domain organization and cyclosporine sensitivity to probe the kinetics and mechanism of TRIM5-mediated restriction. Time of addition/withdrawal experiments reveal that inhibition of incoming human immunodeficiency virus type 1 capsids by TRIM-CypA occurs within minutes of their delivery to the target cell cytoplasm. However, while TRIM-CypA restriction is partly dependent on a RING domain, restriction occurs independently of the ubiquitin/proteasome system. Moreover, tagged TRIM-CypA proteins can be fully active as restriction factors without forming cytoplasmic bodies.
Hepatitis C Virus (HCV) and Hepatitis B Virus (HBV) Can Coinfect the Same Hepatocyte in the Liver of Patients with Chronic HCV and Occult HBV Infection
Authors: Rodríguez-Íñigo E. , Bartolomé J. , Ortiz-Movilla N. , Platero C. , López-Alcorocho J. M. , Pardo M. , Castillo I. , Carreño V.
Published: November 2005

In this work, we have shown that hepatitis C virus (HCV) and hepatitis B virus (HBV) can coexist in the same hepatocyte using double fluorescent in situ hybridization in liver biopsy samples from patients with chronic HCV infection with occult HBV infection. Digital image analysis of hybridization signals showed that the HBV DNA levels in coinfected hepatocytes were lower than those in cells infected only with HBV. This finding supports the hypothesis of inhibition of HBV replication by HCV. Furthermore, HCV RNA levels were lower in coinfected cells than in cells infected only with HCV, suggesting that HBV may also inhibit HCV replication.
Lateral plantar nerve injury following steroid injection for plantar fasciitis
Authors: Snow D M , Reading J , Dalal R
Published: November 2005

A 41 year old man presented with pain and numbness affecting the lateral aspect of his foot after a steroid injection for plantar fasciitis. Examination confirmed numbness and motor impairment of the lateral plantar nerve. The findings were confirmed by electromyographic studies. The anatomy of the lateral plantar nerve and correct technique for injection to treat plantar fasciitis are discussed.
Neuromuscular and biomechanical characteristic changes in high school athletes: a plyometric versus basic resistance program
Authors: Lephart S M , Abt J P , Ferris C M , Sell T C , Nagai T , Myers J B , Irrgang J J
Published: November 2005

Background:In order to improve neuromuscular and biomechanical characteristic deficits in female athletes, numerous injury prevention programs have been developed and have successfully reduced the number of knee ligament injuries. However, few have investigated the neuromuscular and biomechanical changes following these training programs. It is also largely unknown what type of program is better for improving the landing mechanics of female athletes.

Objectives:To investigate the effects of an 8 week plyometric and basic resistance training program on neuromuscular and biomechanical characteristics in female athletes.

Methods:Twenty seven high school female athletes participated either in a plyometric or a basic resistance training program. Knee and hip strength, landing mechanics, and muscle activity were recorded before and after the intervention programs. In the jump-landing task, subjects jumped as high as they could and landed on both feet. Electromyography (EMG) peak activation time and integrated EMG of thigh and hip muscles were recorded prior to (preactive) and subsequent to (reactive) foot contact.

Results:Both groups improved knee extensor isokinetic strength and increased initial and peak knee and hip flexion, and time to peak knee flexion during the task. The peak preactive EMG of the gluteus medius and integrated EMG for the gluteus medius during the preactive and reactive time periods were significantly greater for both groups.

Conclusions:Basic training alone induced favourable neuromuscular and biomechanical changes in high school female athletes. The plyometric program may further be utilised to improve muscular activation patterns.
Effects of dietary carbohydrate on delayed onset muscle soreness and reactive oxygen species after contraction induced muscle damage
Authors: Close G L , Ashton T , Cable T , Doran D , Noyes C , McArdle F , MacLaren D P M
Published: November 2005

Background:Delayed onset muscle soreness (DOMS) occurs after unaccustomed exercise and has been suggested to be attributable to reactive oxygen species (ROS). Previous studies have shown increased ROS after lengthening contractions, attributable to invading phagocytes. Plasma glucose is a vital fuel for phagocytes, therefore carbohydrate (CHO) status before exercise may influence ROS production and DOMS

Objective:To examine the effect of pre-exercise CHO status on DOMS, ROS production, and muscle function after contraction induced muscle damage.

Method:Twelve subjects performed two downhill runs, one after a high CHO diet and one after a low CHO diet. Blood samples were drawn for analysis of malondialdehyde, total glutathione, creatine kinase, non-esterified fatty acids, lactate, glucose, and leucocytes. DOMS and muscle function were assessed daily.

Results:The high CHO diet resulted in higher respiratory exchange ratio and lactate concentrations than the low CHO diet before exercise. The low CHO diet resulted in higher non-esterified fatty acid concentrations before exercise. DOMS developed after exercise and remained for up to 96 hours, after both diets. A biphasic response in creatine kinase occurred after both diets at 24 and 96 hours after exercise. Malondialdehyde had increased 72 hours after exercise after both diets, and muscle function was attenuated up to this time.

Conclusions:Downhill running resulted in increased ROS production and ratings of DOMS and secondary increases in muscle damage. CHO status before exercise had no effect.
MUONIC PROCESSES DYNAMIC IN SOLID HETEROGENEOUS H/D/T MIXTURE
Authors: ESKANDARI M. R. , MAHDAVI M. , REZAIE L.
Published: November 2005

The Ramsauer–Townsend effect in hydrogen is used in a heterogeneous solid hydrogen-deuterium-tritium (H/D/T) multi-layer system to provide forced resonance muonic deuterium-tritium molecule formation. The effects of hyperfine splitting in the μd atom on the final state of nuclear spins are studied in the μpd molecule at low temperature. As deuterium concentration increases, so does the spin-flip rate, thus reducing the initial population of the quartet (s=3/2) nuclear spin of the μpd molecule and enhancing the doublet (s=1/2) state. The doublet rate is dominant, and total fusion yield increases with deuterium concentration until the lack of protium atoms significantly reduces the rate of μpd molecule formation and μdd fusion dominates completely. The Wolfenstein–Gerstein effect and the no-quartet theorem in the solid H/D layer are considered by solving the muon dynamical equations for various deuterium concentrations. It is shown that the no-quartet theorem is not valid at low temperature and deuterium concentration, but is valid only if one neglects the mixed-symmetry components. The written coupled linear point dynamical equations for the suggested system are solved using the "Lsode" computer code. The results obtained for the optimum layer thicknesses and deuterium concentration are compared with the results of a solid homogeneous deuterium-tritium system in the same physical condition (temperature, density and deuterium concentration). It is shown that for the same physical conditions, the muon cycling coefficient of two isotopes of deuterium-tritium (D/T) has only 2.7% of the muon cycling coefficient of the suggested forced solid heterogeneous H/D/T fusion system. It is shown that with very little deuterium concentration (cd=0.005), the obtained muon cycling rate and coefficient are ~147 μ s -1 and 178, respectively.
CORRECTIONS TO THE NUCLEAR AXIAL VECTOR COUPLING IN A NUCLEAR MEDIUM
Authors: CARTER G. W. , HENLEY E. M.
Published: November 2005

There is experimental evidence of an increase in the temporal component of the weak axial vector current in nuclei. Most of this increase is accounted for by meson exchange currents. We consider further corrections from pions and the sigma mean-field. These corrections, however, are found to reduce the coupling, which is already insufficiently large.
THEORETICAL QUANTUM-INFORMATION PROPERTIES OF NUCLEI AND TRAPPED BOSE GASES
Authors: MOUSTAKIDIS CH. C. , CH. CHATZISAVVAS K. , PANOS C. P.
Published: November 2005

We will study fermionic systems like atomic nuclei and bosonic systems like the correlated atoms in a trap from an information-theoretical point of view. The Shannon and Onicescu information measures are calculated for the above systems by comparing the correlated and uncorrelated cases as functions of the strength of the short range correlations. One-body and two-body density and momentum distributions are employed. Thus, the effect of short-range correlations on the information content is evaluated. The magnitude of distinguishability between the correlated and uncorrelated densities is also discussed employing suitable measures for the distance of states i.e. the well known Kullback–Leibler relative entropy and the recently proposed Jensen–Shannon divergence entropy. We will see that the same information-theoretical properties hold for quantum many-body systems obeying Bose–Einstein and Fermi–Dirac (statistics).
INTRUDER LEVEL AND DEFORMATION IN THE SD-PAIR SHELL MODEL
Authors: LUO YAN AN , BAHRI CHAIRUL , PAN FENG , GUEORGUIEV V. G. , DRAAYER JERRY P.
Published: November 2005

The influence of the intruder level on nuclear deformation is studied within the framework of the nucleon-pair shell model, truncated to an SD-pair subspace. The results suggest that the intruder level has a tendency to reduce the deformation for nuclei in lower and middle shells, and plays an important role in determining the onset of rotational behavior.