bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of
Staphylococcus
Species Directly from Positive Blood Culture Broth by Use of Molecular and Conventional Methods
Authors: Mehta Maitry S. , Paule Suzanne M. , Thomson Richard B. , Kaul Karen L. , Peterson Lance R. 
Published: February 2009

ABSTRACT

We compared two real-time PCR assays (both by the use of melting curve analysis) for their ability to identify
Staphylococcus
species directly from 200 positive blood culture bottles. The PCR assays correctly identified 83% to 94% of the
Staphylococcus
isolates to species clusters. Molecular testing significantly outperformed commercially available latex tests (sensitivity for both latex tests, <15%) when it was used directly with broth from signal-positive blood cultures.
Attenuated Foot-and-Mouth Disease Virus RNA Carrying a Deletion in the 3′ Noncoding Region Can Elicit Immunity in Swine
Authors: Rodríguez Pulido Miguel , Sobrino Francisco , Borrego Belén , Sáiz Margarita 
Published: February 2009

ABSTRACT
We constructed foot-and-mouth disease virus (FMDV) mutants bearing independent deletions of the two stem-loop structures predicted in the 3′ noncoding region of viral RNA, SL1 and SL2, respectively. Deletion of SL2 was lethal for viral infectivity in cultured cells, while deletion of SL1 resulted in viruses with slower growth kinetics and downregulated replication associated with impaired negative-strand RNA synthesis. With the aim of exploring the potential of an RNA-based vaccine against foot-and-mouth disease using attenuated viral genomes, full-length chimeric O1K/C-S8 RNAs were first inoculated into pigs. Our results show that FMDV viral transcripts could generate infectious virus and induce disease in swine. In contrast, RNAs carrying the ΔSL1 mutation on an FMDV O1K genome were innocuous for pigs but elicited a specific immune response including both humoral and cellular responses. A single inoculation with 500 μg of RNA was able to induce a neutralizing antibody response. This response could be further boosted by a second RNA injection. The presence of the ΔSL1 mutation was confirmed in viruses isolated from serum samples of RNA-inoculated pigs or after transfection and five passages in cell culture. These findings suggest that deletion of SL1 might contribute to FMDV attenuation in swine and support the potential of RNA technology for the design of new FMDV vaccines.
Human Immunodeficiency Virus Integrates Directly into Naïve Resting CD4+T Cells but Enters Naïve Cells Less Efficiently than Memory Cells
Authors: Dai Jihong , Agosto Luis M. , Baytop Clifford , Yu Jianqing J. , Pace Matthew J. , Liszewski Megan K. , O'Doherty Una 
Published: February 2009

ABSTRACTResting CD4+T cells restrict human immunodeficiency virus (HIV) infection at or before reverse transcription, resulting in slower kinetics of reverse transcription. In a previous study, we showed that, despite this restriction at reverse transcription, HIV integration occurs in resting CD4+T cells, albeit with slower kinetics. In that study, the resting T cells were a mixture of memory and naïve cells. Here we asked whether the more quiescent naïve cell subset could be directly infected by HIV and, if so, whether the level of integration in naïve cells was comparable to that in memory cells. We found that HIV integrates in the naïve subset of resting CD4+T cells without prior activation of the cells. The level of integration (proviruses/cell) in naïve cells was lower than that in memory cells. This difference between naïve and memory cells was observed whether we inoculated the cells with R5 or X4 HIV and could not be explained solely by differences in coreceptor expression. The presence of endogenous dendritic cells did not change the number of proviruses/cell in memory or naïve cells, and deoxynucleoside pools were equally limiting. Our results instead indicate the existence of a novel restriction point in naïve T cells at viral fusion that results in reduced levels of fusion to naïve CD4+T cells. We conclude that HIV can integrate into both naïve and memory cells directly. Our data further support our hypothesis that integrated proviral infection of resting T cells can be established without T-cell activation.
Gamma Interferon-Induced Interferon Regulatory Factor 1-Dependent Antiviral Response Inhibits Vaccinia Virus Replication in Mouse but Not Human Fibroblasts
Authors: Trilling Mirko , Le Vu Thuy Khanh , Zimmermann Albert , Ludwig Holger , Pfeffer Klaus , Sutter Gerd , Smith Geoffrey L. , Hengel Hartmut 
Published: February 2009

ABSTRACTVaccinia virus (VACV) replicates in mouse and human fibroblasts with comparable kinetics and efficiency, yielding similar titers of infectious progeny. Here we demonstrate that gamma interferon (IFN-γ) but not IFN-α or IFN-β pretreatment of mouse fibroblasts prior to VACV infection induces a long-lasting antiviral state blocking VACV replication. In contrast, high doses of IFN-γ failed to establish an antiviral state in human fibroblasts. In mouse fibroblasts, IFN-γ impeded the viral replication cycle at the level of late gene transcription and blocked the multiplication of VACV genomes. The IFN-γ-induced antiviral state invariably prevented the growth of different VACV strains but was not effective against the replication of ectromelia virus. The IFN-γ effect required intact IFN-γ receptor signaling prior to VACV infection through Janus kinase 2 (Jak2) and signal transducer and activator of transcription 1 (STAT1). The permissive state of IFN-γ-treated human cells was unrelated to the VACV-encoded IFN decoy receptors B8 and B18 and associated with a complete disruption of STAT1 homodimer formation and DNA binding. Unlike human fibroblasts, mouse cells responded with long-lasting STAT1 activation which was preserved after VACV infection. The deletion of the IFN regulatory factor 1 (IRF-1) gene from mouse cells rescued efficient VACV replication, demonstrating that IRF-1 target genes have a critical role in VACV control. These data have implications for the understanding of VACV pathogenesis and identify an incongruent IFN-γ response between the human host and the mouse model.
Identification of a Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Variant Resistant to Cold Inactivation
Authors: Kassa Aemro , Finzi Andrés , Pancera Marie , Courter Joel R. , Smith Amos B. , Sodroski Joseph 
Published: February 2009

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein trimer consists of gp120 and gp41 subunits and undergoes a series of conformational changes upon binding to the receptors, CD4 and CCR5/CXCR4, that promote virus entry. Surprisingly, we found that the envelope glycoproteins of some HIV-1 strains are functionally inactivated by prolonged incubation on ice. Serial exposure of HIV-1 to extremes of temperature, followed by expansion of replication-competent viruses, allowed selection of a temperature-resistant virus. The envelope glycoproteins of this virus resisted cold inactivation due to a single passage-associated change, H66N, in the gp120 exterior envelope glycoprotein. Histidine 66 is located within the gp41-interactive inner domain of gp120 and, in other studies, has been shown to decrease the sampling of the CD4-bound conformation by unliganded gp120. Substituting asparagine or other amino acid residues for histidine 66 in cold-sensitive HIV-1 envelope glycoproteins resulted in cold-stable phenotypes. Cold inactivation of the HIV-1 envelope glycoproteins occurred even at high pH, indicating that protonation of histidine 66 is not necessary for this process. Increased exposure of epitopes in the ectodomain of the gp41 transmembrane envelope glycoprotein accompanied cold inactivation, but shedding of gp120 did not. An amino acid change in gp120 (S375W) that promotes the CD4-bound state or treatment with soluble CD4 or a small-molecule CD4 mimic resulted in increased cold sensitivity. These results indicate that the CD4-bound intermediate of the HIV-1 envelope glycoproteins is cold labile; avoiding the CD4-bound state increases temperature stability.
Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis
Authors: Victoria Joseph G. , Kapoor Amit , Li Linlin , Blinkova Olga , Slikas Beth , Wang Chunlin , Naeem Asif , Zaidi Sohail , Delwart Eric 
Published: February 2009

ABSTRACT

We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the
Picornaviridae
family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel
Picornaviridae
genus and four new viral species (members of the
Dicistroviridae
,
Nodaviridae
, and
Circoviridae
families and the
Bocavirus
genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel
Enterovirus
genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.
Four Major Envelope Proteins of White Spot Syndrome Virus Bind To Form a Complex
Authors: Zhou Qing , Xu Limei , Li Hui , Qi Yi-Peng , Yang Feng 
Published: February 2009

ABSTRACT
Early events in white spot syndrome virus (WSSV) morphogenesis, particularly the formation of viral membranes, are poorly understood. The major envelope proteins of WSSV are VP28, VP26, VP24, and VP19. Our previous results indicated that VP28 interacts with VP26 and VP24. In the present study, we used coimmunoprecipitation assays and pull-down assays to confirm that the four major proteins in the WSSV envelope can form a multiprotein complex. Yeast two-hybrid assays were also used to test for interactions among the four proteins. In summary, three pairwise protein interactions (VP19-VP28, VP19-VP24, and VP24-VP26) and one self-association (VP24-VP24) were identified for the first time.
Genomic Epidemiology of a Dengue Virus Epidemic in Urban Singapore
Authors: Schreiber Mark J. , Holmes Edward C. , Ong Swee Hoe , Soh Harold S. H. , Liu Wei , Tanner Lukas , Aw Pauline P. K. , Tan Hwee Cheng , Ng Lee Ching , Leo Yee Sin , Low Jenny G. H. , Ong Adrian , Ooi Eng Eong , Vasudevan Subhash G. , Hibberd Martin L. 
Published: February 2009

ABSTRACTDengue is one of the most important emerging diseases of humans, with no preventative vaccines or antiviral cures available at present. Although one-third of the world's population live at risk of infection, little is known about the pattern and dynamics of dengue virus (DENV) within outbreak situations. By exploiting genomic data from an intensively studied major outbreak, we are able to describe the molecular epidemiology of DENV at a uniquely fine-scaled temporal and spatial resolution. Two DENV serotypes (DENV-1 and DENV-3), and multiple component genotypes, spread concurrently and with similar epidemiological and evolutionary profiles during the initial outbreak phase of a major dengue epidemic that took place in Singapore during 2005. Although DENV-1 and DENV-3 differed in viremia and clinical outcome, there was no evidence for adaptive evolution before, during, or after the outbreak, indicating that ecological or immunological rather than virological factors were the key determinants of epidemic dynamics.
Fewer Latent Herpes Simplex Virus Type 1 and Cytotoxic T Cells Occur in the Ophthalmic Division than in the Maxillary and Mandibular Divisions of the Human Trigeminal Ganglion and Nerve
Authors: Hüfner Katharina , Horn Anja , Derfuss Tobias , Glon Christine , Sinicina Inga , Arbusow Viktor , Strupp Michael , Brandt Thomas , Theil Diethilde 
Published: February 2009

ABSTRACT

Following primary infection of the mouth, herpes simplex virus type 1 (HSV-1) travels retrogradely along the maxillary (V2) or mandibular (V3) nerve to the trigeminal ganglion (TG), where it establishes lifelong latency. Symptomatic HSV-1 reactivations frequently manifest as herpes labialis, while ocular HSV-1 disease is rare. We investigated whether these clinical observations are mirrored by the distribution of latent HSV-1 as well as cytotoxic T-cell infiltration around the nerve cell bodies and in the nerve fibers. The three divisions of the TG were separated by using neurofilament staining and carbocyanine dye Di-I tracing and then screened by in situ hybridization for the presence of HSV-1 latency-associated transcript (LAT). The T-cell distribution and the pattern of cytolytic molecule expression were evaluated by immunohistochemistry. The Di-I-labeled neurons were largely confined to the nerve entry zone of the traced nerve branches. Very few Di-I-labeled neurons were found in adjacent divisions due to traversing fiber bundles. LAT was abundant in the V2 and V3 divisions of all TG but was scarce or totally absent in the ophthalmic (V1) division. CD8
+
T cells were found in all three divisions of the TG and in the respective nerves, clearly clustering in V2 and V3, which is indicative of a chronic inflammation. Only T cells surrounding neurons in the V2 and V3 ganglionic divisions expressed granzyme B. In conclusion, the large accumulation of LAT and cytotoxic T cells in the V2 and V3 but not in the V1 division of the TG reflects the sites supplied by the sensory fibers and the clinical reactivation patterns.
Reducing the Risk of Adeno-Associated Virus (AAV) Vector Mobilization with AAV Type 5 Vectors
Authors: Hewitt F. Curtis , Li Chengwen , Gray Steven J. , Cockrell Shelley , Washburn Michael , Samulski R. Jude 
Published: February 2009

ABSTRACT

Current adeno-associated virus (AAV) gene therapy vectors package a transgene flanked by the terminal repeats (TRs) of AAV type 2 (AAV2). Although these vectors are replication deficient, wild-type (wt) AAV2 prevalent in the human population could lead to replication and packaging of a type 2 TR (TR2)-flanked transgene in
trans
during superinfection by a helper virus, leading to “mobilization” of the vector genome from treated cells. More importantly, it appears likely that the majority of currently characterized AAV serotypes as well as the majority of new novel isolates are capable of rescuing and replicating AAV2 vector templates. To investigate this possibility, we flanked a green fluorescent protein transgene with type 2 and, the most divergent AAV serotype, type 5 TRs (TR2 or TR5). Consistent with AAV clades, AAV5 specifically replicated TR5 vectors, while AAV2 and AAV6 replicated TR2-flanked vectors. To exploit this specificity, we created a TR5 vector production system for Cap1 to Cap5. Next, we showed that persisting recombinant AAV genomes flanked by TR2s or TR5s were mobilized in vitro after addition of the cognate AAV Rep (as well as Rep6 for TR2) and adenoviral helper. Finally, we showed that a cell line containing a stably integrated wt AAV2 genome resulted in mobilization of a TR2-flanked vector but not a TR5-flanked vector upon adenoviral superinfection. Based on these data and the relative prevalence of wt AAV serotypes in the population, we propose that TR5 vectors have a significantly lower risk of mobilization and should be considered for clinical use.
Impact of Epitope Escape on PD-1 Expression and CD8 T-Cell Exhaustion during Chronic Infection
Authors: Blattman Joseph N. , Wherry E. John , Ha Sang-Jun , van der Most Robbert G. , Ahmed Rafi 
Published: February 2009

ABSTRACT

During some persistent viral infections, virus-specific T-cell responses wane due to the antigen-specific deletion or functional inactivation (i.e., exhaustion) of responding CD8 T cells. T-cell exhaustion often correlates with high viral load and is associated with the expression of the inhibitory receptor PD-1. In other infections, functional T cells are observed despite high levels of pathogen persistence. The reasons for these different T-cell fates during chronic viral infections are not clear. Here, we tracked the fate of virus-specific CD8 T cells in lymphocytic choriomeningitis virus (LCMV)-infected mice during viral clearance, the persistence of wild-type virus, or the selection and persistence of a viral variant that abrogates the presentation of a single epitope. Viral clearance results in PD-1
lo
functional virus-specific CD8 T cells, while the persistence of wild-type LCMV results in high PD-1 levels and T-cell exhaustion. However, following the emergence of a GP35V→A variant virus that abrogates the presentation of the GP33 epitope, GP33-specific CD8 T cells remained functional, continued to show low levels of PD-1, and reexpressed CD127, a marker of memory T-cell differentiation. In the same animals and under identical environmental conditions, CD8 T cells recognizing nonmutated viral epitopes became physically deleted or were PD-1
hi
and nonfunctional. Thus, the upregulation of PD-1 and the functional inactivation of virus-specific T cells during chronic viral infection is dependent upon continued epitope recognition. These data suggest that optimal strategies for vaccination should induce high-magnitude broadly specific T-cell responses that prevent cytotoxic T-lymphocyte escape and highlight the need to evaluate the function of vaccine-induced T cells in the context of antigens presented during virus persistence.
JC Virus-Specific Immune Responses in Human Immunodeficiency Virus Type 1 Patients with Progressive Multifocal Leukoencephalopathy
Authors: Khanna Nina , Wolbers Marcel , Mueller Nicolas J. , Garzoni Christian , Du Pasquier Renaud A. , Fux Christoph A. , Vernazza Pietro , Bernasconi Enos , Viscidi Raphael , Battegay Manuel , Hirsch Hans H. 
Published: February 2009

ABSTRACT

Progressive multifocal leukoencephalopathy (PML) is a frequently fatal disease caused by uncontrolled polyomavirus JC (JCV) in severely immunodeficient patients. We investigated the JCV-specific cellular and humoral immunity in the Swiss HIV Cohort Study. We identified PML cases (
n
= 29), as well as three matched controls per case (
n
= 87), with prospectively cryopreserved peripheral blood mononuclear cells and plasma at diagnosis. Nested controls were matched according to age, gender, CD4
+
T-cell count, and decline. Survivors (
n
= 18) were defined as being alive for >1 year after diagnosis. Using gamma interferon enzyme-linked immunospot assays, we found that JCV-specific T-cell responses were lower in nonsurvivors than in their matched controls (
P
= 0.08), which was highly significant for laboratory- and histologically confirmed PML cases (
P
= 0.004). No difference was found between PML survivors and controls or for cytomegalovirus-specific T-cell responses. PML survivors showed significant increases in JCV-specific T cells (
P
= 0.04) and immunoglobulin G (IgG) responses (
P
= 0.005). IgG responses in survivors were positively correlated with CD4
+
T-cell counts (
P
= 0.049) and negatively with human immunodeficiency virus RNA loads (
P
= 0.03). We conclude that PML nonsurvivors had selectively impaired JCV-specific T-cell responses compared to CD4
+
T-cell-matched controls and failed to mount JCV-specific antibody responses. JCV-specific T-cell and IgG responses may serve as prognostic markers for patients at risk.
Exercising with reserve: exercise regulation by perceived exertion in relation to duration of exercise and knowledge of endpoint
Authors: Swart J , Lamberts R P , Lambert M I , Lambert E V , Woolrich R W , Johnston S , Noakes T D 
Published: February 2009

Objective:The purpose of this study was to examine ratings of perceived exertion (RPE) and performance during repetitive maximal effort 40 km time trials as well as after an intervention that aimed to decrease certainty about the remaining distance of the exercise bout. In addition, we examined the RPE during exercise bouts of markedly different duration.Methods:Part 1: 12 well-trained, competitive-level cyclists completed five 40 km time trials. During the final time trial all feedback was withheld until the final kilometre. In addition, to cause confusion about the remaining distance, they were asked to report their RPE at random intervals from 18 km to 38 km. Part 2: 6 well-trained, recreation-level cyclists randomly completed a 5 km, 10 km, 40 km and 100 km time trial.Results:Part 1: Mean RPE increased during the first four trials and decreased during the final trial. The rate of RPE progression increased in linearity during the first four trials and became more conservative in the final trial. These changes were directly related to performance. Part 2: Mean RPE for longer duration trials (40 km, 100 km) were lower during the first half of trial duration but matched those of shorter trials in the final 20%.Conclusions:Increased familiarity of the exercise bout and certainty about its endpoint are associated with a more aggressive RPE strategy that produces a superior exercise performance. Certainty about the endpoint and the duration of exercise affect both the RPE strategy and performance.
Would you dope? A general population test of the Goldman dilemma
Authors: Connor J M , Mazanov J 
Published: February 2009

Objective:To test Goldman's dilemma on a general population sample by asking whether they would take the Faustian bargain of a drug that guaranteed sporting success but would result in their death in 5 years' time. Between 1982 and 1995 a bi-annual survey using this dilemma suggested half of all elite athletes would take the drug.Design:A random telephone survey of 250 members of the Australian general public, with counterbalanced presentation of success and death.Main outcome measures:Respondents gave age, gender, sports engagement and response to the dilemma (yes/no).Results:Only two of a sample of 250 reported they would take the bargain offered by the dilemma.Conclusions:Athletes differ markedly from the general population in response to the dilemma. This raises significant practical and ethical dilemmas for athlete support personnel. The psychometry of the dilemma needs to be established more comprehensively for general and athlete populations.