bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement of the Sensitivity of the Whole-Blood Gamma Interferon Assay for Diagnosis ofMycobacterium bovisInfections in Cattle
Authors: Denis Michel , Wedlock D. Neil , McCarthy Allison R. , Parlane Natalie A. , Cockle Paul J. , Vordermeier H. Martin , Hewinson R. Glyn , Buddle Bryce M.
Published: September 2007

In this study, we determined if the sensitivity of the currently available in vitro test to detect bovine tuberculosis could be enhanced by adding the following immunomodulators: interleukin-2 (IL-2); granulocyte-macrophage colony-stimulating factor (GM-CSF); antibodies neutralizing IL-10 and transforming growth factor β (TGF-β); mono-methyl-l-arginine, which blocks nitric oxide production; andl-methyl-tryptophan, which interferes with the indoleamine dioxygenase pathway. Blood was obtained from uninfected control cattle, experimentally infected cattle, cattle responding positively to the skin test in tuberculosis-free areas (false positives), and cattle naturally infected withMycobacterium bovisfrom New Zealand and Great Britain. Gamma interferon (IFN-γ) responses to bovine purified protein derivative (PPD-b), avian purified protein derivative, and a fusion protein of ESAT-6 and CFP-10 were measured. Mono-methyl-l-arginine,l-methyl-tryptophan, or an antibody neutralizing TGF-β had minimal impact on IFN-γ production. IL-2 and GM-CSF promoted IFN-γ release whether antigen was present or not. In contrast, adding an antibody against IL-10 enhanced only antigen-specific responses. In particular, addition of anti-IL-10 to ESAT-6/CFP-10-stimulated blood cultures enhanced the test sensitivity. Furthermore, whole blood cells from field reactors produced substantial amounts of IL-10 upon stimulation with PPD-b or ESAT-6/CFP-10. Testing “false-positive” cattle from tuberculosis-free areas of New Zealand revealed that addition of anti-IL-10 did not compromise the test specificity. Therefore, the use of ESAT-6/CFP-10 with anti-IL-10 could be useful to detect cattle potentially infected with tuberculosis, which are not detected using current procedures.
Antiplatelet Drug Therapy Moderates Immune-Mediated Liver Disease and Inhibits Viral Clearance in Mice Infected with a Replication-Deficient Adenovirus
Authors: Iannacone Matteo , Sitia Giovanni , Narvaiza Iñigo , Ruggeri Zaverio M. , Guidotti Luca G.
Published: September 2007

Treatment with a low dose of combined aspirin and clopidogrel, two antiplatelet drugs widely used in humans, markedly reduced the homing of virus-specific cytotoxic T lymphocytes and virus-nonspecific inflammatory leukocytes to the liver of mice acutely infected with a hepatotropic, replication-deficient,
lacZ
-expressing adenovirus (RAd35). Consequently, aspirin/clopidogrel-induced platelet dysfunction greatly diminished liver disease severity and inhibited viral clearance. Along with the finding that aspirin/clopidogrel caused neither bleeding nor anemia, our results suggest that antiplatelet drugs may be considered to limit excessive liver immunopathology and/or to facilitate the persistence of hepatotropic viral vectors utilized in gene therapy.
Preliminary Evaluation of a Multiplex Reverse Transcription-PCR Assay Combined with a New DNA Chip Hybridization Assay for Detecting Respiratory Syncytial Virus
Authors: Causse Manuel , García-Mayorgas Ángel D. , Gutiérrez Juan B. , Casal Manuel
Published: September 2007

DNA chips represent a major advance in microbiology laboratories, enabling the detection of a wide range of possible pathogens using a single test. This study compared a multiplex reverse transcription-PCR combined with DNA chip hybridization (ProDect BCS RV chip; bcs Biotech) with the indirect immunofluorescence test commonly used to detect respiratory viruses. A total of 39 respiratory viruses (38 respiratory syncytial viruses [RSVs] and 1 influenza A virus) were detected in samples from 96 patients using the immunofluorescence test, while 36 viruses (34 RSV, 1 influenza A virus, and 1 influenza B virus) were detected by the DNA chip technique. Results showed a good level of agreement between the two tests for RSV detection; the incidence of other viruses was low, since samples were taken from patients with suspected bronchiolitis. DNA chips displayed high sensitivity (94.6%) and specificity (100%).
Multilocus Sequence Typing Compared to Pulsed-Field Gel Electrophoresis for Molecular Typing of
Pseudomonas aeruginosa
Authors: Johnson Jennifer K. , Arduino Sonia M. , Stine O. Colin , Johnson Judith A. , Harris Anthony D.
Published: September 2007

For hospital epidemiologists, determining a system of typing that is discriminatory is essential for measuring the effectiveness of infection control measures. In situations in which the incidence of resistant
Pseudomonas aeruginosa
is increasing, the ability to discern whether it is due to patient-to-patient transmission versus an increase in patient endogenous strains is often made on the basis of molecular typing. The present study compared the discriminatory abilities of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for 90
P. aeruginosa
isolates obtained from cultures of perirectal surveillance swabs from patients in an intensive care unit. PFGE identified 85 distinct types and 76 distinct groups when similarity cutoffs of 100% and 87%, respectively, were used. By comparison, MLST identified 60 sequence types that could be clustered into 11 clonal complexes and 32 singletons. By using the Simpson index of diversity (
D
), PFGE had a greater discriminatory ability than MLST for
P. aeruginosa
isolates (
D
values, 0.999 versus 0.975, respectively). Thus, while MLST was better for detecting genetic relatedness, we determined that PFGE was more discriminatory than MLST for determining genetic differences in
P. aeruginosa
.
MP1
Homologue-Based Multilocus Sequence System for Typing the Pathogenic Fungus
Penicillium marneffei
: a Novel Approach Using Lineage-Specific Genes
Authors: Woo Patrick C. Y. , Lau Candy C. Y. , Chong Ken T. K. , Tse Herman , Tsang Dominic N. C. , Lee Rodney A. , Tse Cindy W. S. , Que Tak-lun , Chung Liliane M. W. , Ngan Antonio H. Y. , Hui Wai-ting , Wong Samson S. Y. , Lau Susanna K. P. , Yuen Kwok-yung
Published: September 2007

A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of
Penicillium marneffei
, the most important thermal dimorphic fungus causing respiratory, skin, and systemic mycosis in Southeast Asia. The sequences of 11 housekeeping genes were identical among 10 strains of
P. marneffei
, but those of
MP1
and its 13 homologues, a novel superfamily of mannoproteins in the subdivision Pezizomycotina of Ascomycetes, mostly species of
Penicillium
and
Aspergillus
, showed significant variations. Therefore, a multilocus sequence typing (MLST) system for
P. marneffei
was constructed using
MP1
(549 bp) and the four of its homologues (
MPLP4
[337 bp],
MPLP7
[347 bp],
MPLP10
[546 bp], and
MPLP13
[422 bp]) that showed the greatest variations. Among the 2,201 bp of the five loci, 183 polymorphic sites were observed in 44 strains of
P. marneffei
. The median number of alleles at each locus was five (range, 5 [
MPLP4
,
MPLP7
, and
MPLP13
] to 15 [
MPLP10
]). Four of the five genes had nonsynonymous substitution/synonymous substitution (

d
n

/

d
s

) ratios of >1. A total of 35 different sequence types (STs) were assigned to the 44
P. marneffei
isolates, with 28 of the 35 STs identified only once. The discriminatory power was 0.9884.
MP1
and its homologues were better than housekeeping genes for MLST in
P. marneffei
. Due to their more rapid evolutionary rates, lineage-specific genes may be better candidates than housekeeping genes for sequence-based typing, especially in microbes that evolve slowly or have evolved recently.
Quantitative Detection of
Staphylococcus aureus
and
Enterococcus faecalis
DNA in Blood To Diagnose Bacteremia in Patients in the Intensive Care Unit
Authors: Peters Remco P. H. , van Agtmael Michiel A. , Gierveld Sonja , Danner Sven A. , Groeneveld A. B. Johan , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M.
Published: September 2007

Direct detection of bacterial DNA in blood offers a fast alternative to blood culture and is presumably unaffected by the prior use of antibiotics. We evaluated the performance of two real-time PCR assays for the quantitative detection of
Staphylococcus aureus
bacteremia and for
Enterococcus faecalis
bacteremia directly in blood samples, without prior cultivation. Whole-blood samples for PCR were obtained simultaneously with blood cultures from patients admitted to the intensive care unit of our hospital. After the extraction of DNA from 200 μl of blood, real-time PCR was performed for the specific detection and quantification of
S. aureus
and
E. faecalis
DNA. The sensitivity for bacteremia of the
S. aureus
PCR was 75% and that of the
E. faecalis
PCR was 73%, and both tests had high specificity values (93 and 96%, respectively). PCR amplification reactions were positive for
S. aureus
for 10 (7%) blood samples with negative blood cultures, and 7 (4%) PCR reactions were positive for
E. faecalis
. The majority of these PCR results were likely (50%) or possibly (42%) related to infection with the specific microorganism, based on clinical data and radiological and microbiological investigations. PCR results were concordant for 95% of paired whole-blood samples, and blood culture results were concordant for 97% of the paired samples. We conclude that the detection of
S. aureus
and
E. faecalis
DNA in blood by real-time PCR enables a rapid diagnosis of bacteremia and that a positive DNAemia is related to proven or possible infection with the specific microorganism in the majority of patients with negative blood cultures.
Revised Culture-Based System for Identification of
Malassezia
Species
Authors: Kaneko Takamasa , Makimura Koichi , Abe Michiko , Shiota Ryoko , Nakamura Yuka , Kano Rui , Hasegawa Atsuhiko , Sugita Takashi , Shibuya Shuichi , Watanabe Shinichi , Yamaguchi Hideyo , Abe Shigeru , Okamura Noboru
Published: September 2007

Forty-six strains of
Malassezia
spp. with atypical biochemical features were isolated from 366 fresh clinical isolates from human subjects and dogs. Isolates obtained in this study included 2 (4.7%) lipid-dependent
M. pachydermatis
isolates; 1 (2.4%) precipitate-producing and 6 (14.6%) non-polyethoxylated castor oil (Cremophor EL)-assimilating
M. furfur
isolates; and 37 (34.3%)
M. slooffiae
isolates that were esculin hydrolyzing, 17 (15.7%) that were non-tolerant of growth at 40°C, and 2 (1.9%) that assimilated polyethoxylated castor oil. Although their colony morphologies and sizes were characteristic on CHROMagar
Malassezia
medium (CHROM), all strains of
M. furfur
developed large pale pink and wrinkled colonies, and all strains of
M. slooffiae
developed small (<1 mm) pale pink colonies on CHROM. These atypical strains were distinguishable by the appearance of their colonies grown on CHROM. Three clinically important
Malassezia
species,
M. globosa, M. restricta
, and
M. furfur
, were correctly identified by their biochemical characteristics and colony morphologies. The results presented here indicate that our proposed identification system will be useful as a routine tool for the identification of clinically important
Malassezia
species in clinical laboratories.
Validation of a PCR-Oligochromatography Test for Detection of
Trypanozoon
Parasites in a Multicenter Collaborative Trial
Authors: Claes F. , Deborggraeve S. , Verloo D. , Mertens P. , Crowther J. R. , Leclipteux T. , Büscher P.
Published: September 2007

A PCR-oligochromatography test for diagnosis of human and animal trypanosomiasis was evaluated through a multicenter ring trial with six laboratories testing a set of 21 blinded samples, resulting in qualitative data (positive or negative). Results showed an intralaboratory repeatability (accordance) of 88.7% (credible interval [CI], 84.4 to 92.5%) and an interlaboratory repeatability (concordance) of 88.1% (CI, 84.3 to 92.3%).
First Report of Macrolide-Resistant Strains and Description of a Novel Nucleotide Sequence Variation in the P1 Adhesin Gene in
Mycoplasma pneumoniae
Clinical Strains Isolated in France over 12 Years
Authors: Pereyre S. , Charron A. , Renaudin H. , Bébéar C. , Bébéar C. M.
Published: September 2007

Mycoplasma pneumoniae
isolates are divided in two types based on the sequence variations in the P1 adhesin gene. The type of P1 adhesin gene of 155 clinical isolates of
M. pneumoniae
collected in France between 1994 and 2006 was determined by a PCR-restriction fragment length polymorphism method. Until 1995, all strains belonged to type 1. In 1996 and 1997, type 1 was still predominant, but type 2 increased. Finally, since 1998, both types were present in about the same proportion. In our study, a novel sequence of the P1 adhesin gene was described in one strain. This strain could not be classified into type 1 or 2 because of variability in both P1 gene repeat elements, RepMP4 and RepMP2/3. This new sequence was certainly issued from recombination with repetitive sequences localized outside of the P1 gene in the
M. pneumoniae
chromosome. Moreover, MICs of erythromycin, tetracycline, and ciprofloxacin were determined for the 155 isolates. All isolates remained susceptible to tetracycline and ciprofloxacin, but two macrolide-resistant strains, isolated from two children in 1999, were identified. They harbored an A-to-G substitution at position 2058 or 2059 (
Escherichia coli
numbering) in domain V of 23S rRNA, associated with resistance to macrolides, lincosamides, and ketolides. To our knowledge, this is the first description of macrolide-resistant isolates of
M. pneumoniae
in France, but at this time, there is no sign of recent diffusion of resistant strains.
Direct Visualization ofPropionibacterium acnesin Prostate Tissue by Multicolor Fluorescent In Situ Hybridization Assay
Authors: Alexeyev Oleg A. , Marklund Ingrid , Shannon Beverley , Golovleva Irina , Olsson Jan , Andersson Charlotte , Eriksson Irene , Cohen Ronald , Elgh Fredrik
Published: September 2007

Prostate tissues from patients with prostate cancer and benign prostatic hyperplasia (BPH) frequently contain histological inflammation, and a proportion of these patients show evidence ofPropionibacterium acnesinfection in the prostate gland. We developed a multicolor fluorescent in situ hybridization (FISH) assay targetingP. acnes23S rRNA along with a 14-kb region of theP. acnesgenome. This assay was used to analyze prostate tissues from patients with prostate cancer and BPH.P. acnesinfection of the prostate gland was demonstrated in prostatic tissue in 5 of 10 randomly selected prostate cancer patients. FISH analysis and confocal laser microscopy imaging revealed intracellular localization and stromal biofilm-like aggregates as common forms ofP. acnesinfection in prostate tissues from both prostate cancer and BPH patients. A sequential analysis of prostate tissue from individual patients suggested thatP. acnescan persist for up to 6 years in the prostate gland. These results indicate thatP. acnescan establish a persistent infection in the prostate gland. Further study is needed to clarify the link between this bacterium and prostatic inflammation which may contribute to the development of BPH and prostate cancer.
Detection of Bloodstream Infections in Adults: How Many Blood Cultures Are Needed?
Authors: Lee Andrew , Mirrett Stanley , Reller L. Barth , Weinstein Melvin P.
Published: September 2007

Although several reports have shown that two to three 20-ml blood cultures are adequate for the detection of bacteremia and fungemia in adults, a recent study (F. R. Cockerill et al., Clin. Infect. Dis. 38:1724-1730, 2004) found that two blood cultures detected only 80% of bloodstream infections and that three blood cultures detected 96% of episodes. We reviewed data at two university hospitals to determine whether the recent observations by Cockerill et al. are applicable more widely. We assessed all blood cultures obtained from adult inpatients from 1 January 2004 through 31 December 2005 at Robert Wood Johnson University Hospital and Duke University Medical Center. All instances in which ≥3 blood cultures per patient were obtained during a 24-h period were included. The medical records of patients who met the inclusion criteria were reviewed retrospectively to determine the clinical significance of the positive blood culture (true infection versus contamination). Data were analyzed to determine the cumulative sensitivity of blood cultures obtained sequentially during the 24-h time period. Of 629 unimicrobial episodes with ≥3 blood cultures obtained during the 24-h period, 460 (73.1%) were detected with the first blood culture, 564 (89.7%) were detected with the first two blood cultures, 618 (98.2%) were detected with the first three blood cultures, and 628 (99.8%) were detected with the first four blood cultures. Of 351 unimicrobial episodes with ≥4 blood cultures obtained during the 24-h period, 257 (73.2%) were detected with the first blood culture, 308 (93.9%) were detected with the first two blood cultures, 340 (96.9%) were detected with the first three blood cultures, and 350 (99.7%) were detected with the first four blood cultures. Among unimicrobial episodes,
Staphylococcus aureus
was more likely to be detected with the first blood culture (approximately 90% detected with the first blood culture). There were 58 polymicrobial episodes in which ≥3 blood cultures were obtained. Forty-seven (81.0%) were detected with the first blood culture, 54 (93.1%) were detected with the first two blood cultures, and 58 (100%) were detected with the first three blood cultures. The results of this study indicate that two blood cultures in a 24-h period will detect approximately 90% of bloodstream infections in adults. To achieve a detection rate of >99%, as many as four blood cultures may be needed. The previously held axiom that virtually all bloodstream infections can be detected with two to three blood cultures may no longer be valid but may also depend on the definition of the “first” blood culture obtained (see Materials and Methods and Discussion in the text).
Type- and Subcomplex-Specific Neutralizing Antibodies against Domain III of Dengue Virus Type 2 Envelope Protein Recognize Adjacent Epitopes
Authors: Sukupolvi-Petty Soila , Austin S. Kyle , Purtha Whitney E. , Oliphant Theodore , Nybakken Grant E. , Schlesinger Jacob J. , Roehrig John T. , Gromowski Gregory D. , Barrett Alan D. , Fremont Daved H. , Diamond Michael S.
Published: September 2007

Neutralization of flaviviruses in vivo correlates with the development of an antibody response against the viral envelope (E) protein. Previous studies demonstrated that monoclonal antibodies (MAbs) against an epitope on the lateral ridge of domain III (DIII) of the West Nile virus (WNV) E protein strongly protect against infection in animals. Based on X-ray crystallography and sequence analysis, an analogous type-specific neutralizing epitope for individual serotypes of the related flavivirus dengue virus (DENV) was hypothesized. Using yeast surface display of DIII variants, we defined contact residues of a panel of type-specific, subcomplex-specific, and cross-reactive MAbs that recognize DIII of DENV type 2 (DENV-2) and have different neutralizing potentials. Type-specific MAbs with neutralizing activity against DENV-2 localized to a sequence-unique epitope on the lateral ridge of DIII, centered at the FG loop near residues E383 and P384, analogous in position to that observed with WNV-specific strongly neutralizing MAbs. Subcomplex-specific MAbs that bound some but not all DENV serotypes and neutralized DENV-2 infection recognized an adjacent epitope centered on the connecting A strand of DIII at residues K305, K307, and K310. In contrast, several MAbs that had poor neutralizing activity against DENV-2 and cross-reacted with all DENV serotypes and other flaviviruses recognized an epitope with residues in the AB loop of DIII, a conserved region that is predicted to have limited accessibility on the mature virion. Overall, our experiments define adjacent and structurally distinct epitopes on DIII of DENV-2 which elicit type-specific, subcomplex-specific, and cross-reactive antibodies with different neutralizing potentials.
7SL RNA Mediates Virion Packaging of the Antiviral Cytidine Deaminase APOBEC3G
Authors: Wang Tao , Tian Chunjuan , Zhang Wenyan , Luo Kun , Sarkis Phuong Thi Nguyen , Yu Lillian , Liu Bindong , Yu Yunkai , Yu Xiao-Fang
Published: September 2007

Cytidine deaminase APOBEC3G (A3G) has broad antiviral activity against diverse retroviruses and/or retrotransposons, and its antiviral functions are believed to rely on its encapsidation into virions in an RNA-dependent fashion. However, the cofactors of A3G virion packaging have not yet been identified. We demonstrate here that A3G selectively interacts with certain polymerase III (Pol III)-derived RNAs, including Y3 and 7SL RNAs. Among A3G-binding Pol III-derived RNAs, 7SL RNA was preferentially packaged into human immunodeficiency virus type 1 (HIV-1) particles. Efficient packaging of 7SL RNA, as well as A3G, was mediated by the RNA-binding nucleocapsid domain of HIV-1 Gag. A3G mutants that had reduced 7SL RNA binding but maintained wild-type levels of mRNA and tRNA binding were packaged poorly and had impaired antiviral activity. Reducing 7SL RNA packaging by overexpression of SRP19 proteins inhibited 7SL RNA and A3G virion packaging and impaired its antiviral function. Thus, 7SL RNA that is encapsidated into diverse retroviruses is a key cofactor of the antiviral A3G. This selective interaction of A3G with certain Pol III-derived RNAs raises the question of whether A3G and its cofactors may have as-yet-unidentified cellular functions.
Myristoylation Is Required for Human Immunodeficiency Virus Type 1 Gag-Gag Multimerization in Mammalian Cells
Authors: Li Hua , Dou Jun , Ding Lingmei , Spearman Paul
Published: September 2007

The Gag protein of human immunodeficiency virus type 1 directs the virion assembly process. Gag proteins must extensively multimerize during the formation of the spherical immature virion shell. In vitro, virus-like particles can be generated from Gag proteins that lack the N-terminal myristic acid modification or the nucleocapsid (NC) protein. The precise requirements for Gag-Gag multimerization under conditions present in mammalian cells, however, have not been fully elucidated. In this study, a Gag-Gag multimerization assay measuring fluorescence resonance energy transfer was employed to define the Gag domains that are essential for homomultimerization. Three essential components were identified: protein-protein interactions contributed by residues within both the N- and C-terminal domains of capsid (CA), basic residues in NC, and the presence of myristic acid. The requirement of myristic acid for multimerization was reproduced using the heterologous myristoylation sequence from v-
src
. Only when a leucine zipper dimerization motif was placed in the position of NC was a nonmyristoylated Gag protein able to multimerize. These results support a three-component model for Gag-Gag multimerization that includes membrane interactions mediated by the myristoylated N terminus of Gag, protein-protein interactions between CA domains, and NC-RNA interactions.
Divergence and Recombination of Clinical Herpes Simplex Virus Type 2 Isolates
Authors: Norberg Peter , Kasubi Mabula J. , Haarr Lars , Bergström Tomas , Liljeqvist Jan-Åke
Published: September 2007

Herpes simplex virus type 2 (HSV-2) infects the genital mucosa and is one of the most common sexually transmitted viruses. Here we sequenced a segment comprising 3.5% of the HSV-2 genome, including genes coding for glycoproteins G, I, and E, from 27 clinical isolates from Tanzania, 10 isolates from Norway, and 10 isolates from Sweden. The sequence variation was low compared to that described for clinical HSV-1 isolates, with an overall similarity of 99.6% between the two most distant HSV-2 isolates. Phylogenetic analysis revealed a divergence into at least two genogroups arbitrarily designated A and B, supported by high bootstrap values and evolutionarily separated at the root. Genogroup A contained isolates collected in Tanzania, and genogroup B contained isolates collected in Tanzania and Scandinavia, implying that the genetic variability of HSV-2 is higher in Tanzania than in Scandinavia. Recombination network analysis and bootscan analysis revealed a complex pattern of phylogenetically conflicting informative sites in the sequence alignments. These signals were present in synonymous and nonsynonymous sites in all three genes and were not accumulated in specific regions, observations arguing against positive selection. Since the PHI test applied solely to synonymous sites revealed a high statistical probability of recombination, we suggest as a novel finding that homologous recombination is, as reported earlier for HSV-1 and varicella-zoster virus, a prominent feature in the evolution of HSV-2.
SH3 Binding Motif 1 in Influenza A Virus NS1 Protein Is Essential for PI3K/Akt Signaling Pathway Activation
Authors: Shin Yeun-Kyung , Li Yang , Liu Qiang , Anderson Deborah H. , Babiuk Lorne A. , Zhou Yan
Published: September 2007

Recent studies have demonstrated that influenza A virus infection activates the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway by binding of influenza NS1 protein to the p85 regulatory subunit of PI3K. Our previous study proposed that two polyproline motifs in NS1 (amino acids 164 to 167 [PXXP], SH3 binding motif 1, and amino acids 213 to 216 [PPXXP], SH3 binding motif 2) may mediate binding to the p85 subunit of PI3K. Here we performed individual mutational analyses on these two motifs and demonstrated that SH3 binding motif 1 contributes to the interactions of NS1 with p85β, whereas SH3 binding motif 2 is not required for this process. Mutant viruses carrying NS1 with mutations in SH3 binding motif 1 failed to interact with p85β and induce the subsequent activation of PI3K/Akt pathway. Mutant virus bearing mutations in SH3 binding motif 2 exhibited similar phenotype as the wild-type (WT) virus. Furthermore, viruses with mutations in SH3 binding motif 1 induced more severe apoptosis than did the WT virus. Our data suggest that SH3 binding motif 1 in NS1 protein is required for NS1-p85β interaction and PI3K/Akt activation. Activation of PI3K/Akt pathway is beneficial for virus replication by inhibiting virus induced apoptosis through phosphorylation of caspase-9.
Degradation of Nuclear Factor Kappa B during Foot-and-Mouth Disease Virus Infection
Authors: de los Santos Teresa , Diaz-San Segundo Fayna , Grubman Marvin J.
Published: September 2007

We have previously shown that the leader proteinase (Lpro) of foot-and-mouth disease virus (FMDV) interferes with the innate immune response by blocking the translation of interferon (IFN) protein and by reducing the immediate-early induction of beta IFN mRNA and IFN-stimulated genes. Here, we report that Lproregulates the activity of nuclear factor κB (NF-κB). Analysis of NF-κB-dependent reporter gene expression in BHK-21 cells demonstrated that infection with wild-type (WT) virus has an inhibitory effect compared to infection with a genetically engineered mutant lacking the leader coding region. The expression of endogenous NF-κB-dependent genes tumor necrosis factor alpha and RANTES is also reduced in WT virus-infected primary porcine cells. This inhibitory effect is neither the result of a decrease in the level of the mRNA of p65/RelA, a subunit of NF-κB, nor a block on the nuclear translocation of p65/RelA, but instead appears to be a consequence of the degradation of accumulated p65/RelA. Viral Lprois localized to the nucleus of infected cells, and there is a correlation between the translocation of Lproand the decrease in the amount of nuclear p65/RelA. By using a recombinant cardiovirus expressing Lpro, we demonstrate that the disappearance of p65/RelA takes place in the absence of any other FMDV product. The observation that Lprodisrupts the integrity of NF-κB suggests a global mechanism by which FMDV antagonizes the cellular innate immune and inflammatory responses to viral infection.
Molecular and Structural Bases for the Antigenicity of VP2 of Infectious Bursal Disease Virus
Authors: Letzel Tobias , Coulibaly Fasseli , Rey Felix A. , Delmas Bernard , Jagt Erik , van Loon Adriaan A. M. W. , Mundt Egbert
Published: September 2007

Infectious bursal disease virus (IBDV), a member of the family
Birnaviridae
, is responsible for a highly contagious and economically important disease causing immunosuppression in chickens. IBDV variants isolated in the United States exhibit antigenic drift affecting neutralizing epitopes in the capsid protein VP2. To understand antigenic determinants of the virus, we have used a reverse-genetics approach to introduce selected amino acid changes—individually or in combination—into the VP2 gene of the classical IBDV strain D78. We thus generated a total of 42 mutants with changes in 8 amino acids selected by sequence comparison and their locations on loops P
BC
and P
HI
at the tip of the VP2 spikes, as shown by the crystal structure of the virion. The antibody reactivities of the mutants generated were assessed using a panel of five monoclonal antibodies (MAbs). Our results show that a few amino acids of the projecting domain of VP2 control the reactivity pattern. Indeed, the binding of four out of the five MAbs analyzed here is affected by mutations in these loops. Furthermore, their importance is highlighted by the fact that some of the engineered mutants display identical reactivity patterns but have different growth phenotypes. Finally, this analysis shows that a new field strain isolated from a chicken flock in Belgium (Bel-IBDV) represents an IBDV variant with a hitherto unobserved antigenic profile, involving one change (P222S) in the P
BC
loop. Overall, our data provide important new insights for devising efficient vaccines that protect against circulating IBDV strains.
The Impact of a Boosting Immunogen on the Differentiation of Secondary Memory CD8
+
T Cells
Authors: Hovav Avi-Hai , Panas Michael W. , Osuna Christa E. , Cayabyab Mark J. , Autissier Patrick , Letvin Norman L.
Published: September 2007

While recent studies have demonstrated that secondary CD8
+
T cells develop into effector-memory cells, the impact of particular vaccine regimens on the elicitation of these cells remains poorly defined. In the present study we evaluated the effect of three different immunogens—recombinant vaccinia, recombinant adenovirus, and plasmid DNA—on the generation of memory cellular immune responses. We found that vectors that induce the rapid movement of CD8
+
T cells into the memory compartment during a primary immune response also drive a rapid differentiation of these cells into effector-memory CD8
+
T cells following a secondary immunization. In contrast, the functional profiles of both CD8
+
and CD4
+
T cells, assessed by measuring antigen-stimulated gamma interferon and interleukin-2 production, were not predominantly shaped by the boosting immunogen. We also demonstrated that the in vivo expression of antigen by recombinant vectors was brief following boosting immunization, suggesting that antigen persistence has a minimal impact on the differentiation of secondary CD8
+
T cells. When used in heterologous or in homologous prime-boost combinations, these three vectors generated antigen-specific CD8
+
T cells with different phenotypic profiles. Expression of the memory-associated molecule CD27 on effector CD8
+
T cells decreased following heterologous but not homologous boosting, resulting in a phenotypic profile similar to that seen on primary CD8
+
T cells. These data therefore suggest that the phenotype of secondary CD8
+
T cells is determined predominantly by the boosting immunogen whereas the cytokine profile of these cells is shaped by both the priming and boosting immunogens.
Orally Administered Amyloidophilic Compound Is Effective in Prolonging the Incubation Periods of Animals Cerebrally Infected with Prion Diseases in a Prion Strain-Dependent Manner
Authors: Kawasaki Yuri , Kawagoe Keiichi , Chen Chun-jen , Teruya Kenta , Sakasegawa Yuji , Doh-ura Katsumi
Published: September 2007

The establishment of effective therapeutic interventions for prion diseases is necessary. We report on a newly developed amyloidophilic compound that displays therapeutic efficacy when administered orally. This compound inhibited abnormal prion protein formation in prion-infected neuroblastoma cells in a prion strain-dependent manner: effectively for RML prion and marginally for 22L prion and Fukuoka-1 prion. When the highest dose (0.2% [wt/wt] in feed) was given orally to cerebrally RML prion-inoculated mice from inoculation until the terminal stage of disease, it extended the incubation periods by 2.3 times compared to the control. The compound exerted therapeutic efficacy in a prion strain-dependent manner such as that observed in the cell culture study: most effective for RML prion, less effective for 22L prion or Fukuoka-1 prion, and marginally effective for 263K prion. Its effectiveness depended on an earlier start of administration. The glycoform pattern of the abnormal prion protein in the treated mice was modified and showed predominance of the diglycosylated form, which resembled that of 263K prion, suggesting that diglycosylated forms of abnormal prion protein might be least sensitive or resistant to the compound. The mechanism of the prion strain-dependent effectiveness needs to be elucidated and managed. Nevertheless, the identification of an orally available amyloidophilic chemical encourages the pursuit of chemotherapy for prion diseases.
In Vivo Changes in the Patterns of Chromatin Structure Associated with the Latent Herpes Simplex Virus Type 1 Genome in Mouse Trigeminal Ganglia Can Be Detected at Early Times after Butyrate Treatment
Authors: Neumann Donna M. , Bhattacharjee Partha S. , Giordani Nicole V. , Bloom David C. , Hill James M.
Published: September 2007

During herpes simplex virus type 1 (HSV-1) latency in mouse dorsal root ganglia (DRG), chromatin associated with the latency-associated transcript (LAT) region of the viral genome is hyperacetylated at lysines 9 and 14 of histone 3 [H3(K9, K14)], while lytic genes are hypoacetylated. Explanted DRG exhibit a pattern of deacetylation of the LAT enhancer followed by acetylation of the ICP0 promoter at early times postexplant. Recently, we reported that sodium butyrate induced in vivo reactivation of HSV-1 in latent mice. In this study, we assessed the effect of sodium butyrate on the chromatin patterns of latent and butyrate-treated mouse trigeminal ganglia (TG) via chromatin immunoprecipitation (ChIP). We detected deacetylation of acetyl H3(K9, K14) of the LAT promoter and LAT enhancer regions as early as 0.5 h post-butyrate treatment, and this deacetylation corresponded to an increase in the acetylation of the lytic promoters ICP0 and ICP4 at 0.5 h and 1 h post-butyrate treatment, respectively. This is the first study to combine in vivo reactivation with the examination of the HSV-1 genome through ChIP assays at early times after the introduction of in vivo reactivation stimuli.
Induction of Epidermal Growth Factor Receptor Expression by Epstein-Barr Virus Latent Membrane Protein 1 C-Terminal-Activating Region 1 Is Mediated by NF-κB p50 Homodimer/Bcl-3 Complexes
Authors: Thornburg Natalie J. , Raab-Traub Nancy
Published: September 2007

The Epstein-Barr virus (EBV) is associated with the development of numerous malignancies, including the epithelial malignancy nasopharyngeal carcinoma (NPC). The viral oncoprotein latent membrane protein 1 (LMP1) is expressed in almost all EBV-associated malignancies and has profound effects on gene expression. LMP1 acts as a constitutively active tumor necrosis factor receptor and activates multiple forms of the NF-κB family of transcription factors. LMP1 has two domains that both activate NF-κB. In epithelial cells, LMP1 C-terminal activating region 1 (CTAR1) uniquely activates p50/p50-, p50/p52-, and p65-containing complexes while CTAR2 activates canonical p50/p65 complexes. CTAR1 also uniquely upregulates the epidermal growth factor receptor (EGFR). In NPC, NF-κB p50/p50 homodimers and the transactivator Bcl-3 were detected on the EGFR promoter. In this study, the role of NF-κB p50 and Bcl-3 in LMP1-mediated upregulation of EGFR was analyzed. In LMP1-CTAR1-expressing cells, chromatin immunoprecipitation detected p50 and Bcl-3 on the NF-κB consensus sites within the
egfr
promoter. Transient overexpression of p50 and Bcl-3 increased EGFR expression, confirming the regulation of EGFR by these factors. Treatment with p105/p50 siRNA effectively reduced p105/p50 levels but unexpectedly increased Bcl-3 expression and levels of p50/Bcl-3 complexes, resulting in increased EGFR expression. These data suggest that induction of p50/p50/Bcl-3 complexes by LMP1 CTAR1 mediates LMP1-induced EGFR upregulation and that formation of the p50/p50/Bcl-3 complex is negatively regulated by the p105 precursor. The distinct forms of NF-κB that are induced by LMP1 CTAR1 likely activate distinct cellular genes.
Characterization of a Second Vaccinia Virus mRNA-Decapping Enzyme Conserved in Poxviruses
Authors: Parrish Susan , Moss Bernard
Published: September 2007

Vaccinia virus (VACV) encodes enzymes that cap the 5′ end of viral mRNAs, which enhances their stability and translation. Nevertheless, recent studies demonstrated that the VACV D10 protein (VACV-WR_115) decaps mRNA, an enzymatic activity not previously shown to be encoded by a virus. The decapping activity of D10 is dependent on a Nudix hydrolase motif that is also present in the VACV D9 protein (VACV-WR_114), which shares 25% sequence identity with D10. Here, we showed that a purified recombinant VACV D9 fusion protein also decaps mRNA and that this activity was abolished by point mutations in the Nudix hydrolase motif. Decapping was specific for a methylated cap attached to RNA and resulted in the liberation of m
7
GDP. D9 differed from D10 in requiring a longer capped RNA substrate for optimal activity, having greater sensitivity to inhibition by uncapped RNA, and having lower sensitivity to inhibition by nucleotide cap analogs unattached to RNA. Since D9 is expressed early in infection and D10 late, we suggest that the two proteins enhance mRNA turnover and manipulate gene expression in a complementary and overlapping manner.
Kaposi's Sarcoma-Associated Herpesvirus Encodes an Ortholog of miR-155
Authors: Skalsky Rebecca L. , Samols Mark A. , Plaisance Karlie B. , Boss Isaac W. , Riva Alberto , Lopez M. Cecilia , Baker Henry V. , Renne Rolf
Published: September 2007

MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate gene expression by binding to 3′-untranslated regions (3′UTRs) of target mRNAs. Kaposi's sarcoma-associated herpesvirus (KSHV), a virus linked to malignancies including primary effusion lymphoma (PEL), encodes 12 miRNA genes, but only a few regulatory targets are known. We found that KSHV-miR-K12-11 shares 100% seed sequence homology with hsa-miR-155, an miRNA frequently found to be up-regulated in lymphomas and critically important for B-cell development. Based on this seed sequence homology, we hypothesized that both miRNAs regulate a common set of target genes and, as a result, could have similar biological activities. Examination of five PEL lines showed that PELs do not express miR-155 but do express high levels of miR-K12-11. Bioinformatic tools predicted the transcriptional repressor BACH-1 to be targeted by both miRNAs, and ectopic expression of either miR-155 or miR-K12-11 inhibited a BACH-1 3′UTR-containing reporter. Furthermore, BACH-1 protein levels are low in cells expressing either miRNA. Gene expression profiling of miRNA-expressing stable cell lines revealed 66 genes that were commonly down-regulated. For select genes, miRNA targeting was confirmed by reporter assays. Thus, based on our in silico predictions, reporter assays, and expression profiling data, miR-K12-11 and miR-155 regulate a common set of cellular targets. Given the role of miR-155 during B-cell maturation, we speculate that miR-K12-11 may contribute to the distinct developmental phenotype of PEL cells, which are blocked in a late stage of B-cell development. Together, these findings indicate that KSHV miR-K12-11 is an ortholog of miR-155.
Factors associated with long-term sick leave in sick-listed employees: a systematic review
Authors: Dekkers-Sánchez P M , Hoving J L , Sluiter J K , Frings-Dresen M H W
Published: September 2007

Objective:

The objective of this systematic review was to investigate which factors are associated with continued sick leave among workers on sick leave for at least 6 weeks.

Methods:

A systematic literature search was performed in Medline, EMBASE and PsycINFO, based on combinations of MeSH terms and free text words. Only cohort studies of workers on sick leave for more than 6 weeks at baseline were included. Outcome was measured in terms of factors related to long-term sick leave. The factors were classified first as predisposing, precipitating or perpetuating factors, and then as individual or work-related factors. Methodological quality was assessed for all studies and the strength of the evidence for each factor was assessed using the levels of evidence rating system.

Results:

Five cohort studies fulfilled all inclusion criteria and 77 factors were investigated. Of these, 16 different significant factors associated with long-term sick leave were identified and were all classified as predisposing factors. Evidence was found for 14 individual factors and two work-related factors. The level of evidence was found to be insufficient for all factors except older age and history of sick leave, which were found to have weak evidence.

Conclusions:

Based on this review, there is weak evidence that older age and history of sickness absence are factors associated with long-term sick leave in sick-listed employees. There is insufficient evidence for an effect of other individual or work-related factors on long-term sick leave. There are no published studies on perpetuating factors related to long-term sick leave.
Pharmacogenetics of Anti-HIV Drugs
Authors: Telenti A. , Zanger U. M.
Published: September 2007

Pharmacogenetics holds promise in HIV treatment because of the complexity and potential toxicity of multidrug therapies that are prescribed for long periods. Thus far, few candidate genes have been examined for a limited number of allelic variants, but a number of confirmed associations have already emerged. A change in paradigm emerges from the availability of the HapMap, the wealth of data on less-common genetic polymorphisms, and new genotyping technology. This review presents a comprehensive analysis of the existing literature on pharmacogenetic determinants of antiretroviral drug exposure, drug toxicity, as well as genetic markers associated with the rate of disease progression. It is expected that larger-scale comprehensive genome approaches will profoundly change the landscape of knowledge in the future.
Chemokines and Their Receptors: Drug Targets in Immunity and Inflammation
Authors: Viola Antonella , Luster Andrew D.
Published: September 2007

The chemokine system coordinates leukocyte migration in immunity and inflammation and is implicated in the pathogenesis of many human diseases. Although several successful strategies have been identified to develop drugs targeting chemokines and their receptors, this has not yet resulted in many new therapeutics. This is likely due to a complexity of the chemokine system, which was not initially appreciated, that is characterized by redundancy, pleiotropy, and differences among species. Nevertheless, our understanding of chemokine biology is continuing to grow and several promising drugs are currently being tested in late-stage clinical trials. In this review, we examine the role of chemokines in health and diseases and discuss strategies to target the chemokine system.
Advances in Comparative Physiology from High-Speed Imaging of Animal and Fluid Motion
Authors: Lauder George V. , Madden Peter G.A.
Published: September 2007

Since the time of Muybridge and Marey in the last half of the nineteenth century, studies of animal movement have relied on some form of high-speed or stop-action imaging to permit analysis of appendage and body motion. In the past ten years, the advent of megapixel-resolution high-speed digital imaging with maximal framing rates of 250 to 100,000 images per second has allowed new views of musculoskeletal function in comparative physiology that now extend to imaging flow around moving animals and the calculation of fluid forces produced by animals moving in fluids. In particular, the technique of digital particle image velocimetry (DPIV) has revolutionized our ability to understand how moving animals generate fluid forces and propel themselves through air and water. DPIV algorithms generate a matrix of velocity vectors through the use of image cross-correlation, which can then be used to calculate the force exerted on the fluid as well as locomotor work and power. DPIV algorithms can also be applied to images of moving animals to calculate the velocity of different regions of the moving animal, providing a much more detailed picture of animal motion than can traditional digitizing methods. Although three-dimensional measurement of animal motion is now routine, in the near future model-based kinematic reconstructions and volumetric analyses of animal-generated fluid flow patterns will provide the next step in imaging animal biomechanics and physiology.
Neuroeconomics
Authors: Loewenstein George , Rick Scott , Cohen Jonathan D.
Published: September 2007

Neuroeconomics has further bridged the once disparate fields of economics and psychology. Such convergence is almost exclusively attributable to changes within economics. Neuroeconomics has inspired more change within economics than within psychology because the most important findings in neuroeconomics have posed more of a challenge to the standard economic perspective. Neuro- economics has primarily challenged the standard economic assumption that decision making is a unitary process—a simple matter of integrated and coherent utility maximization—suggesting instead that it is driven by the interaction between automatic and controlled processes. This article reviews neuroeconomic research in three domains of interest to both economists and psychologists: decision making under risk and uncertainty, intertemporal choice, and social decision making. In addition to reviewing new economic models inspired by this research, we also discuss how neuroeconomics may influence future work in psychology.
Motives of theHumanAnimal: Comprehending, Managing, and Sharing Inner States
Authors: Higgins E. Tory , Pittman Thane S.
Published: September 2007

We propose that four fundamental developments of the human animal together produce distinct human motives: (a) social consciousness or awareness that the outcomes or significance of a person's action (self or other) depend upon how another person (self or other) reacts to it; (b) recognizing that people's inner states can mediate their outward behaviors; (c) relating the present to both the past and the future (mental time travel); and (d) sharing reality with other people. We review a typology of four categories of concern for these motivational developments: thoughts, feelings/attitudes, competencies, and reference values (goals and standards). We then review the recent research on three specific areas related to these motivational concerns: imagining future-self inner states, managing how others comprehend us, and sharing knowledge about the world.