bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass Spectrometry Biotyper System Identifies Enteric Bacterial Pathogens Directly from Colonies Grown on Selective Stool Culture Media
Authors: He Ying , Li Haijing , Lu Xuedong , Stratton Charles W. , Tang Yi-Wei 
Published: September 2010

ABSTRACT

We evaluated the performance and cost-effectiveness of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry-based Biotyper system for the routine identification of common enteric bacterial pathogens seen in middle Tennessee from suspicious colonies grown on selective stool culture media. A total of 304 suspicious colonies were selected and further identified from 605 stool specimens. The suspicious colonies were analyzed by the Biotyper system, and the results were compared to those from routine phenotypic methods, which identified 22
Salmonella
species, 39
Shigella
species, 3 enterohemorrhagic
Escherichia coli
(EHEC) isolates, 2
Yersinia enterocolitica
isolates, 2
Campylobacter
species, and 236 gastrointestinal normal flora isolates. The Biotyper system correctly identified the
Salmonella
species,
Yersinia enterocolitica
, and
Campylobacter
species but failed to distinguish the
Shigella
species and EHEC isolates from
E. coli
. Among the 236 normal flora isolates, 233 (98.7%) and 228 (96.6%) agreed at the genus and species levels, respectively, between the phenotypic and Biotyper methods. Organism identification scores were insignificantly different between colonies directly from selective media and subsequently from pure subculture. The entire Biotyper identification procedure, from smear preparation to final result reporting, can be completed within 30 min. The Biotyper system provides a rapid and simple screening tool for identifying many, but not all, suspicious colonies grown on selective media within 24 h after inoculation, which shortens test turnaround time by 2 to 3 days.
Evaluation of Three Influenza A and B Real-Time Reverse Transcription-PCR Assays and a New 2009 H1N1 Assay for Detection of Influenza Viruses
Authors: Selvaraju Suresh B. , Selvarangan Rangaraj 
Published: September 2010

ABSTRACT

The performance characteristics of three real-time influenza A/B virus reverse transcription-PCR (RT-PCR) assays and two real-time 2009 H1N1 RT-PCR assays were evaluated using previously characterized clinical specimens. A total of 150 respiratory specimens from children (30 influenza A/H1 virus-, 30 influenza A/H3 virus-, 30 2009 H1N1-, and 30 influenza B virus-positive specimens and 30 influenza virus-negative specimens) were tested with the CDC influenza A/B PCR (CDC), ProFlu
+
multiplex real-time RT-PCR assay (ProFlu
+
), and MGB Alert Influenza A/B & RSV RUO (MGB) assays. A second set of 157 respiratory specimens (100 2009 H1N1-, 22 seasonal influenza A/H1-, and 15 seasonal influenza A/H3-positive specimens and 20 influenza-negative specimens) were tested with a new laboratory-developed 2009 H1N1 RT-PCR and the CDC 2009 H1N1 assay. The overall sensitivities of the CDC, ProFlu
+
, and MGB assays for detection of influenza A and B viruses were 100%, 98.3%, and 94%, respectively. The ProFlu
+
assay failed to detect one influenza A/H1 virus-positive specimen and yielded one unresolved result with another influenza A/H1 virus-positive specimen. The MGB assay detected 84/87 (96.5%) of influenza A and B viruses and 26/30 (86.6%) of 2009 H1N1 viruses. The new laboratory-developed 2009 H1N1 RT-PCR assay detected 100/100 (100%) 2009 H1N1 virus-positive specimens, while the CDC SW Inf A and SW H1 PCR assays failed to detect one and three low-positive 2009 H1N1-positive specimens, respectively. The CDC influenza A/B virus assay and the newly developed 2009 H1N1 RT-PCR assay with an internal control can be set up in two separate reactions in the same assay for routine clinical testing to detect influenza A and B viruses and to specifically identify the 2009 H1N1 influenza virus.
Stimulation of Human Dendritic Cells by Wild-Type and M Protein Mutant Vesicular Stomatitis Viruses Engineered To Express Bacterial Flagellin
Authors: Ahmed Maryam , Puckett Shelby , Arimilli Subhashini , Braxton Cassandra L. , Mizel Steven B. , Lyles Douglas S. 
Published: September 2010

ABSTRACT

Vesicular stomatitis viruses (VSVs) containing wild-type (wt) or mutant matrix (M) proteins are being developed as candidate vaccine vectors due to their ability to induce innate and adaptive immunity. Viruses with wt M protein, such as recombinant wild-type (rwt) virus, stimulate maturation of dendritic cells (DC) through Toll-like receptor 7 (TLR7) and its adaptor molecule MyD88. However, M protein mutant viruses, such as rM51R-M virus, stimulate both TLR7-positive and TLR7-negative DC subsets. The goal of this study was to determine whether the ability of rwt and rM51R-M viruses to induce maturation of human DC can be enhanced by engineering these vectors to express bacterial flagellin. Flagellin expressed from the rwt virus genome partially protected human DC from VSV-induced shutoff of host protein synthesis and promoted the production of interleukin 6 (IL-6) and IL-1β. In addition, DC infected with rwt virus expressing flagellin were more effective at stimulating gamma interferon (IFN-γ) production from CD8
+
allogeneic T cells than DC infected with rwt virus. Although rM51R-M virus effectively stimulated human DC, flagellin expressed from the rM51R-M virus genome enhanced the production of cytokines. Furthermore, mice immunized with both rwt and rM51R-M viruses expressing flagellin had enhanced anti-VSV antibody responses
in vivo
. Therefore, rwt and rM51R-M viruses expressing flagellin may be promising vectors for the delivery of foreign antigen due to their potential to stimulate DC function.
Bovine Foamy Virus Transactivator BTas Interacts with Cellular RelB To Enhance Viral Transcription
Authors: Wang Jian , Tan Juan , Guo Hongyan , Zhang Qicheng , Jia Rui , Xu Xuan , Geng Yunqi , Qiao Wentao 
Published: September 2010

ABSTRACT

Viruses are obligate intracellular parasites that depend on cellular machinery for their efficient transcription and replication. In a previous study we reported that bovine foamy virus (BFV) is able to activate the nuclear factor κB (NF-κB) pathway through the action of its transactivator BTas to enhance viral transcription. However, the mechanism used by NF-κB to enhance BFV transcription remains elusive. To address this question, we employed a yeast two-hybrid assay to screen for BTas-interacting proteins. We found that RelB, a member of NF-κB protein family, interacts with BTas. We confirmed the putative RelB-BTas interaction
in vitro
and
in vivo
and identified the protein regions responsible for the RelB-BTas interaction. Using a luciferase reporter assay, we next showed that RelB enhances BFV transcription (BTas-induced long terminal repeat [LTR] transactivation) and that this process requires both the localization of the RelB-BTas interaction in the nucleus and the Rel homology domain of RelB. The knockdown of the cellular endogenous RelB protein using small interfering RNA (siRNA) significantly attenuated BTas-induced LTR transcription. The results of chromatin immunoprecipitation (ChIP) analysis showed that endogenous RelB binds to the viral LTR in BFV-infected cells. Together, these results suggest that BFV engages the RelB protein as a cotransactivator of BTas to enhance viral transcription. In addition, our findings indicate that BFV infection upregulates cellular RelB expression through BTas-induced NF-κB activation. Thus, this study demonstrates the existence of a positive-feedback circuit in which BFV utilizes the host's NF-κB pathway through the RelB protein for efficient viral transcription.
Distinct Stability States of Disease-Associated Human Prion Protein Identified by Conformation-Dependent Immunoassay
Authors: Choi Young Pyo , Peden Alexander H. , Gröner Albrecht , Ironside James W. , Head Mark W. 
Published: September 2010

ABSTRACTThe phenotypic and strain-related properties of human prion diseases are, according to the prion hypothesis, proposed to reside in the physicochemical properties of the conformationally altered, disease-associated isoform of the prion protein (PrPSc), which accumulates in the brains of patients suffering from Creutzfeldt-Jakob disease and related conditions, such as Gerstmann-Straussler-Scheinker disease. Molecular strain typing of human prion diseases has focused extensively on differences in the fragment size and glycosylation site occupancy of the protease-resistant prion protein (PrPres) in conjunction with the presence of mutations and polymorphisms in the prion protein gene (PRNP). Here we report the results of employing an alternative strategy that specifically addresses the conformational stability of PrPScand that has been used previously to characterize animal prion strains transmitted to rodents. The results show that there are at least two distinct conformation stability states in human prion diseases, neither of which appears to correlate fully with the PrPrestype, as judged by fragment size or glycosylation, thePRNPcodon 129 status, or the presence or absence of mutations inPRNP. These results suggest that conformational stability represents a further dimension to a complete description of potentially phenotype-related properties of PrPScin human prion diseases.
Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections
Authors: Brown Joseph N. , Palermo Robert E. , Baskin Carole R. , Gritsenko Marina , Sabourin Patrick J. , Long James P. , Sabourin Carol L. , Bielefeldt-Ohmann Helle , García-Sastre Adolfo , Albrecht Randy , Tumpey Terrence M. , Jacobs Jon M. , Smith Richard D. , Katze Michael G. 
Published: September 2010

ABSTRACT

The host proteome response and molecular mechanisms that drive disease
in vivo
during infection by a human isolate of the highly pathogenic avian influenza virus (HPAI) and 1918 pandemic influenza virus remain poorly understood. This study presents a comprehensive characterization of the proteome response in cynomolgus macaque (
Macaca fascicularis
) lung tissue over 7 days of infection with HPAI (the most virulent), a reassortant virus containing 1918 hemagglutinin and neuraminidase surface proteins (intermediate virulence), or a human seasonal strain (least virulent). A high-sensitivity two-dimensional liquid chromatography-tandem mass spectroscopy strategy and functional network analysis were implemented to gain insight into response pathways activated in macaques during influenza virus infection. A macaque protein database was assembled and used in the identification of 35,239 unique peptide sequences corresponding to approximately 4,259 proteins. Quantitative analysis identified an increase in expression of 400 proteins during viral infection. The abundance levels of a subset of these 400 proteins produced strong correlations with disease progression observed in the macaques, distinguishing a “core” response to viral infection from a “high” response specific to severe disease. Proteome expression profiles revealed distinct temporal response kinetics between viral strains, with HPAI inducing the most rapid response. While proteins involved in the immune response, metabolism, and transport were increased rapidly in the lung by HPAI, the other viruses produced a delayed response, characterized by an increase in proteins involved in oxidative phosphorylation, RNA processing, and translation. Proteomic results were integrated with previous genomic and pathological analysis to characterize the dynamic nature of the influenza virus infection process.
Herpesviruses and Chromosomal Integration
Authors: Morissette Guillaume , Flamand Louis 
Published: September 2010

ABSTRACT
Herpesviruses are members of a diverse family of viruses that colonize all vertebrates from fish to mammals. Although more than one hundred herpesviruses exist, all are nearly identical architecturally, with a genome consisting of a linear double-stranded DNA molecule (100 to 225 kbp) protected by an icosahedral capsid made up of 162 hollow-centered capsomeres, a tegument surrounding the nucleocapsid, and a viral envelope derived from host membranes. Upon infection, the linear viral DNA is delivered to the nucleus, where it circularizes to form the viral episome. Depending on several factors, the viral cycle can proceed either to a productive infection or to a state of latency. In either case, the viral genetic information is maintained as extrachromosomal circular DNA. Interestingly, however, certain oncogenic herpesviruses such as Marek's disease virus and Epstein-Barr virus can be found integrated at low frequencies in the host's chromosomes. These findings have mostly been viewed as anecdotal and considered exceptions rather than properties of herpesviruses. In recent years, the consistent and rather frequent detection (in approximately 1% of the human population) of human herpesvirus 6 (HHV-6) viral DNA integrated into human chromosomes has spurred renewed interest in our understanding of how these viruses infect, replicate, and propagate themselves. In this review, we provide a historical perspective on chromosomal integration by herpesviruses and present the current state of knowledge on integration by HHV-6 with the possible clinical implications associated with viral integration.
Dendritic Cell-Specific Antigen Delivery by Coronavirus Vaccine Vectors Induces Long-Lasting Protective Antiviral and Antitumor Immunity
Authors: Cervantes-Barragan Luisa , Züst Roland , Maier Reinhard , Sierro Sophie , Janda Jozef , Levy Frederic , Speiser Daniel , Romero Pedro , Rohrlich Pierre-Simon , Ludewig Burkhard , Thiel Volker 
Published: September 2010

ABSTRACTEfficient vaccination against infectious agents and tumors depends on specific antigen targeting to dendritic cells (DCs). We report here that biosafe coronavirus-based vaccine vectors facilitate delivery of multiple antigens and immunostimulatory cytokines to professional antigen-presenting cellsin vitroandin vivo. Vaccine vectors based on heavily attenuated murine coronavirus genomes were generated to express epitopes from the lymphocytic choriomeningitis virus glycoprotein, or human Melan-A, in combination with the immunostimulatory cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF). These vectors selectively targeted DCsin vitroandin vivoresulting in vector-mediated antigen expression and efficient maturation of DCs. Single application of only low vector doses elicited strong and long-lasting cytotoxic T-cell responses, providing protective antiviral and antitumor immunity. Furthermore, human DCs transduced with Melan-A-recombinant human coronavirus 229E efficiently activated tumor-specific CD8+T cells. Taken together, this novel vaccine platform is well suited to deliver antigens and immunostimulatory cytokines to DCs and to initiate and maintain protective immunity.IMPORTANCEVaccination against infectious agents has protected many individuals from severe disease. In addition, prophylactic and, most likely, also therapeutic vaccination against tumors will save millions from metastatic disease. This study describes a novel vaccine approach that facilitates delivery of viral or tumor antigens to dendritic cellsin vivo. Concomitant immunostimulation via the cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) was achieved through delivery by the same viral vector. Single immunization with only low doses of coronavirus-based vaccine vectors was sufficient to elicit (i) vigorous expansion and optimal differentiation of CD8+T cells, (ii) protective and long-lasting antiviral immunity, and (iii) prophylactic and therapeutic tumor immunity. Moreover, highly efficient antigen delivery to human DCs with recombinant human coronavirus 229E and specific stimulation of human CD8+T cells revealed that this approach is exceptionally well suited for translation into human vaccine studies.
Influenza A Virus Expresses High Levels of an Unusual Class of Small Viral Leader RNAs in Infected Cells
Authors: Umbach Jennifer L. , Yen Hui-Ling , Poon Leo L. M. , Cullen Bryan R. 
Published: September 2010

ABSTRACT
Evidence has recently accumulated suggesting that small noncoding RNAs, and particularly microRNAs, have the potential to strongly affect the replication and pathogenic potential of a range of human virus species. Here, we report the use of deep sequencing to comprehensively analyze small viral RNAs (18 to 27 nucleotides [nt]) produced during infection by influenza A virus. Although influenza A virus differs from most other RNA viruses in that it replicates its genome in the nucleus and is therefore exposed to the nuclear microRNA processing factors Drosha and DGCR8, we did not observe any microRNAs encoded by influenza virus genes. However, influenza virus infection did induce the expression of very high levels—over 100,000 copies per cell by 8 h postinfection—of a population of 18- to 27-nt small viral leader RNAs (leRNAs) that originated from the precise 5′ ends of all eight influenza virus genomic RNA (vRNA) segments. Like the vRNAs themselves, our data indicate that the leRNAs also bear a 5′-terminal triphosphate and are therefore not capable of functioning as microRNAs. Instead, the high-level production of leRNAs may imply a role in another aspect of the viral life cycle, such as regulation of the switch from viral mRNA transcription to genomic RNA synthesis.

IMPORTANCE
Influenza A virus is an important human pathogen that has the potential to give rise to serious pandemics. Here, we demonstrate that influenza A virus induces the expression of very high levels of small viral leader RNAs (leRNAs) within hours of infection. These RNAs are unusual in that they bear a 5′ triphosphate and originate from the very 5′ ends of the eight viral genomic RNA (vRNA) segments. Their high expression may imply an important role in the viral life cycle that could potentially serve as a novel target for antiviral drugs.
In Vivo Wall Shear Stress Distribution in the Carotid Artery
Authors: Markl Michael , Wegent Felix , Zech Timo , Bauer Simon , Strecker Christoph , Schumacher Martin , Weiller Cornelius , Hennig Jürgen , Harloff Andreas 
Published: September 2010

Background—

The purpose of this study was to analyze the in vivo distribution of absolute wall shear stress (WSS
abs
) and oscillatory shear index (OSI) in the carotid bifurcation and to evaluate its dependence on bifurcation geometry, the presence of internal carotid artery (ICA) stenosis, and recanalization therapy.

Methods and Results—

Time-resolved 3D blood flow was acquired with flow-sensitive 4D MRI in 64 normal carotid bifurcations and 17 carotid arteries with moderate ICA stenosis (48±6%) or after surgical recanalization. Among 64 normal arteries, atherogenic wall parameters were consistently concentrated in proximal bulb regions of the common (CCA) and internal (ICA) carotid arteries. The fraction of the carotid bulb exposed to atherosclerosis-prone wall parameters (low WSS
abs
below and high OSI above group-defined 20% and 10% thresholds) was correlated with the individual bifurcation geometry. Multiple regressions revealed significant (
P
<0.01) relationships (β, 0.44 to 0.48) between the areas with atherosclerosis-prone wall parameters and the d
ICA
/d
CCA
diameter ratio. The size of regions exposed to high OSI demonstrated highly significant (
P
≤0.01) relationships with all analyzed geometry parameters (d
ICA
/d
CCA
β, 0.48; tortuosity β, ≤−0.56; bifurcation angle β, ≥0.47). Moderate ICA stenosis altered the distribution of wall parameters (45%/61% reduction of individually low WSS
abs
/high OSI in the proximal ICA), which were relocated to segments distal to the arterial stenosis. WSS
abs
/OSI topology after recanalization was similar compared with the normal wall parameter distribution.

Conclusions—
Flow-sensitive 4D MRI identified alterations in the segmental in vivo WSS distribution associated with atherosclerotic disease, surgical therapy, and individual bifurcation geometry and could be a valuable technique to assess the individual risk of flow-mediated atherosclerosis and carotid plaque progression.
When a place is not a place: encoding of spatial information is dependent on reward type
Authors: Sulikowski Danielle , Burke Darren 
Published: September 2010

AbstractThe adaptationist perspective investigates how an animal's cognition has been shaped by the informational properties of the environment. The information that is useful may vary from one context to another. In the current study we examine how manipulating the foraging context (the type of resource being foraged) could affect the way spatial information is used by the forager. Noisy miner birds (omnivorous honeyeaters) were given spatial working memory tasks in which they searched baited and unbaited feeders for either nectar or invertebrates. We hypothesised that noisy miners would encode the locations of baited and unbaited feeders equally well when foraging for nectar (all flowers, whether containing nectar or not are places to remember and avoid while foraging on a plant). When foraging for invertebrates, however, we predicted that noisy miner birds would not encode the locations of unbaited feeders as effectively as baited feeders (in a natural patch of invertebrates there is no cue to differentiate a point location where a prey item has not been found from the rest of the potentially homogenous patch). As predicted, birds foraging for invertebrates made more revisits to unbaited than baited feeders, with no such difference evident when birds were foraging for nectar.
Close social associations in animals and humans: functions and mechanisms of friendship
Authors: Massen Jorg , Sterck Elisabeth , de Vos Henk 
Published: September 2010

AbstractBoth humans and group-living animals associate and behave affiliatively more with some individuals than others. Human friendship has long been acknowledged, and recently scientists studying animal behaviour have started using the term friendship for close social associates in animals. Yet, while biologists describe friends as social tools to enhance fitness, social scientists describe human friendship as unconditional. We investigate whether these different descriptions reflect true differences in human friendship and animal close social associations or are a by-product of different research approaches: namely social scientists focussing on proximate and biologists on ultimate explanations. We first stress the importance of similar measures to determine close social associations, thereafter examine their ultimate benefits and proximate motivations, and discuss the latest findings on the central-neural regulation of social bonds. We conclude that both human friendship and animal close social associations are ultimately beneficial. On the proximate level, motivations for friendship in humans and for close social associations in animals are not necessarily based on benefits and are often unconditional. Moreover, humans share with many animals a similar physiological basis of sociality. Therefore, biologists and social scientist describe the same phenomenon, and the use of the term friendship for animals seems justified.
Calvin and the Quest for Christian Unity: An Unexpected Legacy
Authors: Cornick David 
Published: September 2010

AbstractThe paper argues that Calvin's reputation hides his work for the unity of the church. His mature ecclesiology was a thoughtful analysis of the catholicity of the church, and as an ecclesiastical statesman he sought to establish bonds of unity where he was able. His legacy could be of contemporary value in his Christocentrism, his lack of dogmatism about church order and his faithful tenacity.