bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Detection of Extended-Spectrum-Beta-Lactam Resistance by DNA Microarray-Based Genotyping of TEM, SHV, and CTX-M Genes
Authors: Leinberger Dirk M. , Grimm Verena , Rubtsova Maya , Weile Jan , Schröppel Klaus , Wichelhaus Thomas A. , Knabbe Cornelius , Schmid Rolf D. , Bachmann Till T. 
Published: December 2009

ABSTRACTExtended-spectrum beta-lactamases (ESBL) of the TEM, SHV, or CTX-M type confer resistance to beta-lactam antibiotics in Gram-negative bacteria. The activity of these enzymes against beta-lactam antibiotics and their resistance against inhibitors can be influenced by genetic variation at the single-nucleotide level. Here, we describe the development and validation of an oligonucleotide microarray for the rapid identification of ESBLs in Gram-negative bacteria by simultaneously genotypingblaTEM,blaSHV, andblaCTX-M. The array consists of 618 probes that cover mutations responsible for 156 amino acid substitutions. As this comprises unprecedented genotyping coverage, the ESBL array has a high potential for epidemiological studies and infection control. With an assay time of 5 h, the ESBL microarray also could be an attractive option for the development of rapid antimicrobial resistance tests in the future. The validity of the DNA microarray was demonstrated with 60 blinded clinical isolates, which were collected during clinical routines. Fifty-eight of them were characterized phenotypically as ESBL producers. The chip was characterized with regard to its resolution, phenotype-genotype correlation, and ability to resolve mixed genotypes. ESBL phenotypes could be correctly ascribed to ESBL variants ofblaCTX-M(76%),blaSHV(22%), or both (2%), whereas no ESBL variant ofblaTEMwas found. The most prevalent ESBLs identified were CTX-M-15 (57%) and SHV-12 (18%).
Caspofungin Etest Endpoint for
Aspergillus
Isolates Shows Poor Agreement with the Reference Minimum Effective Concentration
Authors: Fuller Jeff , Schofield Adam , Jiwa Safeer , Sand Crystal , Jansen Brad , Rennie Robert 
Published: December 2009

ABSTRACT

The Clinical and Laboratory Standards Institute (CLSI) M38-A2 reference broth microdilution (BMD) method for the antifungal susceptibility testing of filamentous fungi now includes guidelines for testing echinocandin activity using the minimum effective concentration (MEC) as the endpoint measurement. In this study, we compared the caspofungin Etest MIC on RPMI agar and Mueller-Hinton agar (supplemented with glucose and methylene blue [MGM]) to the BMD MEC for 345 clinical
Aspergillus
isolates, including
A. flavus
,
A. fumigatus
,
A. nidulans
,
A. niger
, and
A. terreus
. The essential agreement (±1 log
2
dilution) of the Etest on MGM and RPMI agar with the reference BMD MEC was 18 and 26%, respectively. The geometric mean values for BMD MEC and MGM Etest were 0.137 and 0.024 μg/ml, respectively, and the geometric mean values for BMD and RPMI agar were 0.128 and 0.031 μg/ml, respectively. Comparatively, 91% of paired MGM and RPMI Etest results were within 2 log
2
dilutions of each other and consistently produced clearly defined endpoints. In conclusion, the caspofungin Etest MIC, like the BMD MEC, is a reproducible endpoint but is markedly lower than the reference BMD. In anticipation of susceptibility breakpoint assignments, optimization studies will be required to improve the concordance of these two assays so that the potential for underreporting echinocandin resistance in
Aspergillus
is mitigated.
Two-Step Scheme for Rapid Identification and Differentiation of
Legionella pneumophila
and Non-
Legionella pneumophila
Species
Authors: Zhan Xiao-Yong , Li Lian-Qing , Hu Chao-Hui , Zhu Qing-Yi 
Published: December 2009

ABSTRACT

A rapid two-step scheme based on PCR amplification and enzymatic digestion analysis of a 226-bp fragment of the 16S rRNA gene was developed to identify the
Legionella
genus by PCR amplification and to differentiate the
Legionella pneumophila
and non-
Legionella pneumophila
species by enzymatic digestion analysis. Among 42 ATCC strains (16 strains of
L. pneumophila
and 26 strains of non-
L. pneumophila
) and 200
Legionella
isolates from environmental water samples, including pools, rivers, lakes, and cooling towers in Guangdong province, 99.59% of
L. pneumophila
and non-
L. pneumophila
strains were correctly identified and differentiated by this scheme. The procedure of this two-step identification and differentiation scheme is simple and takes only about 4 h. These results suggest that this two-step scheme provides a simple and convenient method for the rapid identification and differentiation of
L. pneumophila
and non-
L. pneumophila
species.
Evaluation of Risk Factors for Coinfection or Cocolonization with Vancomycin-Resistant Enterococcus and Methicillin-Resistant
Staphylococcus aureus
Authors: Reyes Katherine , Malik Rushdah , Moore Carol , Donabedian Susan , Perri Mary , Johnson Laura , Zervos Marcus 
Published: December 2009

ABSTRACT

We retrospectively evaluated 410 patients with coinfection or cocolonization due to vancomycin-resistant (VR) enterococcus (VRE) and methicillin-resistant
Staphylococcus aureus
(MRSA). The prevalence rate was 19.8%. Risk factors included isolation of VR
Enterococcus faecalis
and use of linezolid or clindamycin. Inc18-like
vanA
plasmids were found in 7% of VR
E. faecalis
isolates and none of the VR
E. faecium
isolates.
Nucleolin Associates with the Human Cytomegalovirus DNA Polymerase Accessory Subunit UL44 and Is Necessary for Efficient Viral Replication
Authors: Strang Blair L. , Boulant Steeve , Coen Donald M. 
Published: December 2009

ABSTRACT

In the eukaryotic cell, DNA replication entails the interaction of multiple proteins with the DNA polymerase processivity factor PCNA. As the structure of the presumptive human cytomegalovirus (HCMV) DNA polymerase processivity factor UL44 is highly homologous to that of PCNA, we hypothesized that UL44 also interacts with numerous proteins. To investigate this possibility, recombinant HCMV expressing FLAG-tagged UL44 was generated and used to immunoprecipitate UL44 and associated proteins from infected cell lysates. Unexpectedly, nucleolin, a major protein component of the nucleolus, was identified among these proteins by mass spectrometry and Western blotting. The association of nucleolin and UL44 in infected cell lysate was confirmed by reciprocal coimmunoprecipitation in the presence and absence of nuclease. Western blotting and immunofluorescence assays demonstrated that the level of nucleolin increases during infection and that nucleolin becomes distributed throughout the nucleus. Furthermore, the colocalization of nucleolin and UL44 in infected cell nuclei was observed by immunofluorescence assays. Assays of HCMV-infected cells treated with small interfering RNA (siRNA) targeting
nucleolin
mRNA indicated that nucleolin was required for efficient virus production, viral DNA synthesis, and the expression of a late viral protein, with a correlation between the efficacy of knockdown and the effect on virus replication. In contrast, the level of neither global protein synthesis nor the replication of an unrelated virus (reovirus) was reduced in siRNA-treated cells. Taken together, our results indicate an association of nucleolin and UL44 in HCMV-infected cells and a role for nucleolin in viral DNA synthesis.
A Rotavirus Spike Protein Conformational Intermediate Binds Lipid Bilayers
Authors: Trask Shane D. , Kim Irene S. , Harrison Stephen C. , Dormitzer Philip R. 
Published: December 2009

ABSTRACT
During rotavirus entry, a virion penetrates a host cell membrane, sheds its outer capsid proteins, and releases a transcriptionally active subviral particle into the cytoplasm. VP5*, the rotavirus protein believed to interact with the membrane bilayer, is a tryptic cleavage product of the outer capsid spike protein, VP4. When a rotavirus particle uncoats, VP5* folds back, in a rearrangement that resembles the fusogenic conformational changes in enveloped-virus fusion proteins. We present direct experimental evidence that this rearrangement leads to membrane binding. VP5* does not associate with liposomes when mounted as part of the trypsin-primed spikes on intact virions, nor does it do so after it has folded back into a stably trimeric, low-energy state. But it does bind liposomes when they are added to virions before uncoating, and VP5* rearrangement is then triggered by addition of EDTA. The presence of liposomes during the rearrangement enhances the otherwise inefficient VP5* conformational change. A VP5* fragment, VP5CT, produced from monomeric recombinant VP4 by successive treatments with chymotrypsin and trypsin, also binds liposomes only when the proteolysis proceeds in their presence. A monoclonal antibody that neutralizes infectivity by blocking a postattachment entry event also blocks VP5* liposome association. We propose that VP5* binds lipid bilayers in an intermediate conformational state, analogous to the extended intermediate conformation of enveloped-virus fusion proteins.
Dynamics of Coronavirus Replication-Transcription Complexes
Authors: Hagemeijer Marne C. , Verheije Monique H. , Ulasli Mustafa , Shaltiël Indra A. , de Vries Lisa A. , Reggiori Fulvio , Rottier Peter J. M. , de Haan Cornelis A. M. 
Published: December 2009

ABSTRACT
Coronaviruses induce in infected cells the formation of double-membrane vesicles (DMVs) in which the replication-transcription complexes (RTCs) are anchored. To study the dynamics of these coronavirus replicative structures, we generated recombinant murine hepatitis coronaviruses that express tagged versions of the nonstructural protein nsp2. We demonstrated by using immunofluorescence assays and electron microscopy that this protein is recruited to the DMV-anchored RTCs, for which its C terminus is essential. Live-cell imaging of infected cells demonstrated that small nsp2-positive structures move through the cytoplasm in a microtubule-dependent manner. In contrast, large fluorescent structures are rather immobile. Microtubule-mediated transport of DMVs, however, is not required for efficient replication. Biochemical analyses indicated that the nsp2 protein is associated with the cytoplasmic side of the DMVs. Yet, no recovery of fluorescence was observed when (part of) the nsp2-positive foci were bleached. This result was confirmed by the observation that preexisting RTCs did not exchange fluorescence after fusion of cells expressing either a green or a red fluorescent nsp2. Apparently, nsp2, once recruited to the RTCs, is not exchanged with nsp2 present in the cytoplasm or at other DMVs. Our data show a remarkable resemblance to results obtained recently by others with hepatitis C virus. The observations point to intriguing and as yet unrecognized similarities between the RTC dynamics of different plus-strand RNA viruses.
The Prostate Cancer-Associated Human Retrovirus XMRV Lacks Direct Transforming Activity but Can Induce Low Rates of Transformation in Cultured Cells
Authors: Metzger Michael J. , Holguin Christiana J. , Mendoza Ramon , Miller A. Dusty 
Published: December 2009

ABSTRACT

The human retrovirus XMRV (xenotropic murine leukemia virus-related virus) is associated with prostate cancer, but a causal relationship has not been established. Here, we have used cultured fibroblast and epithelial cell lines to test the hypothesis that XMRV might have direct transforming activity but found only rare transformation events, suggestive of indirect transformation, even when the target cells expressed the human Xpr1 cell entry receptor for XMRV. Characterization of cells from three transformed foci showed that all were infected with and produced XMRV, and one produced a highly active transforming virus, presumably generated by recombination between XMRV and host cell nucleic acids. Given the sequence similarity of XMRV to mink cell focus-forming (MCF) viruses and the enhanced leukemogenic activity of the latter, we tested XMRV for related MCF-like cytopathic activities in cultured mink cells but found none. These results indicate that XMRV has no direct transforming activity but can activate endogenous oncogenes, resulting in cell transformation. As part of these experiments, we show that XMRV can infect and be produced at a high titer from human HT-1080 fibrosarcoma cells that express TRIM5α (
Ref1
), showing that XMRV is resistant to TRIM5α restriction. In addition, XMRV poorly infects NIH 3T3 cells expressing human Xpr1 but relatively efficiently infects BALB 3T3 cells expressing human Xpr1, showing that XMRV is a B-tropic virus and that its infectivity is regulated by the
Fv1
mouse locus.
Effect of Dimerizing Domains and Basic Residues on
In Vitro
and
In Vivo
Assembly of Mason-Pfizer Monkey Virus and Human Immunodeficiency Virus
Authors: Bohmová Karolína , Hadravová Romana , Štokrová Jitka , Tůma Roman , Ruml Tomáš , Pichová Iva , Rumlová Michaela 
Published: December 2009

ABSTRACT

Assembly of immature retroviral particles is a complex process involving interactions of several specific domains of the Gag polyprotein localized mainly within capsid protein (CA), spacer peptide (SP), and nucleocapsid protein (NC). In the present work we focus on the contribution of NC to the oligomerization of CA leading to assembly of Mason-Pfizer monkey virus (M-PMV) and HIV-1. Analyzing
in vitro
assembly of substitution and deletion mutants of ΔProCANC, we identified a “spacer-like” sequence (NC
15
) at the M-PMV NC N terminus. This NC
15
domain is indispensable for the assembly and cannot be replaced with oligomerization domains of GCN4 or CREB proteins. Although the M-PMV NC
15
occupies a position analogous to that of the HIV-1 spacer peptide, it could not be replaced by the latter one. To induce the assembly, both M-PMV NC
15
and HIV-1 SP1 must be followed by a short peptide that is rich in basic residues. This region either can be specific, i.e., derived from the downstream NC sequence, or can be a nonspecific positively charged peptide. However, it cannot be replaced by heterologous interaction domains either from GCN4 or from CREB. In summary, we report here a novel M-PMV spacer-like domain that is functionally similar to other retroviral spacer peptides and contributes to the assembly of immature-virus-like particles.
Multiple Diverse Circoviruses Infect Farm Animals and Are Commonly Found in Human and Chimpanzee Feces
Authors: Li Linlin , Kapoor Amit , Slikas Beth , Bamidele Oderinde Soji , Wang Chunlin , Shaukat Shahzad , Masroor Muhammad Alam , Wilson Michael L. , Ndjango Jean-Bosco N. , Peeters Martine , Gross-Camp Nicole D. , Muller Martin N. , Hahn Beatrice H. , Wolfe Nathan D. , Triki Hinda , Bartkus Joanne , Zaidi Sohail Zahoor , Delwart Eric 
Published: December 2009

ABSTRACT

Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the
Circoviridae
family we tentatively named “
Cyclovirus
” whose genetic diversity is comparable to that of all the known species in the
Circovirus
genus.
Circoviridae
detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25
Cyclovirus
species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.
Heterotypic Humoral and Cellular Immune Responses following Norwalk Virus Infection
Authors: Lindesmith Lisa C. , Donaldson Eric , Leon Juan , Moe Christine L. , Frelinger Jeffrey A. , Johnston Robert E. , Weber David J. , Baric Ralph S. 
Published: December 2009

ABSTRACT

Norovirus immunity is poorly understood as the limited data available on protection after infection are often contradictory. In contrast to the more prominent GII noroviruses, GI norovirus infections are less frequent in outbreaks. The GI noroviruses display very complex patterns of heterotypic immune responses following infection, and many individuals are highly susceptible to reinfection. To study the immune responses and mechanisms of GI.1 persistence, we built structural models and recombinant virus-like particles (VLPs) of five GI strains: GI.1-1968, GI.1-2001, GI.2-1999, GI.3-1999, and GI.4-2000. Structural models of four GI genotype capsid P domain dimers suggested that intragenotype structural variation is limited, that the GI binding pocket is mostly preserved between genotypes, and that a conserved, surface-exposed epitope may allow for highly cross-reactive immune responses. GI VLPs bound to histo-blood group antigens (HBGAs) including fucose, Lewis, and A antigens. Volunteers infected with GI.1-1968 (
n
= 10) had significant increases between prechallenge and convalescent reactive IgG for all five GI VLPs measured by enzyme immunoassay. Potential cross-neutralization of GI VLPs was demonstrated by convalescent-phase serum cross-blockade of GI VLP-HBGA interaction. Although group responses were significant for all GI VLPs, each individual volunteer demonstrated a unique VLP blockade pattern. Further, peripheral blood mononuclear cells (PBMCs) were stimulated with each of the VLPs, and secretion of gamma interferon (IFN-γ) was measured. As seen with blockade responses, IFN-γ secretion responses differed by individual. Sixty percent responded to at least one GI VLP, with only two volunteers responding to GI.1 VLP. Importantly, four of five individuals with sufficient PBMCs for cross-reactivity studies responded more robustly to other GI VLPs. These data suggest that preexposure history and deceptive imprinting may complicate PBMC and B-cell immune responses in some GI.1-1968-challenged individuals and highlight a potential complication in the design of efficacious norovirus vaccines.
A Single Tyrosine in the Severe Acute Respiratory Syndrome Coronavirus Membrane Protein Cytoplasmic Tail Is Important for Efficient Interaction with Spike Protein
Authors: McBride Corrin E. , Machamer Carolyn E. 
Published: December 2009

ABSTRACT

Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes 3 major envelope proteins: spike (S), membrane (M), and envelope (E). Previous work identified a dibasic endoplasmic reticulum retrieval signal in the cytoplasmic tail of SARS-CoV S that promotes efficient interaction with SARS-CoV M. The dibasic signal was shown to be important for concentrating S near the virus assembly site rather than for direct interaction with M. Here, we investigated the sequence requirements of the SARS-CoV M protein that are necessary for interaction with SARS-CoV S. The SARS-CoV M tail was shown to be necessary for S localization in the Golgi region when the proteins were exogenously coexpressed in cells. This was specific, since SARS-CoV M did not retain an unrelated glycoprotein in the Golgi. Importantly, we found that an essential tyrosine residue in the SARS-CoV M cytoplasmic tail, Y
195
, was important for S-M interaction. When Y
195
was mutated to alanine, M
Y195A
no longer retained S intracellularly at the Golgi. Unlike wild-type M, M
Y195A
did not reduce the amount of SARS-CoV S carbohydrate processing or surface levels when the two proteins were coexpressed. Mutating Y
195
also disrupted SARS-CoV S-M interaction
in vitro
. These results suggest that Y
195
is necessary for efficient SARS-CoV S-M interaction and, thus, has a significant involvement in assembly of infectious virus.
Some Weak Convergence Theorems for a Family of Asymptotically Nonexpansive Nonself Mappings
Authors: Hao Yan , Cho SunYoung , Qin Xiaolong 
Published: December 2009

AbstractA one-step iteration with errors is considered for a family of asymptotically nonexpansive nonself mappings. Weak convergence of the purposed iteration is obtained in a Banach space.
Baptism, Conversion, and Grace: Reflections on the "Underlying Realities" Between Pentecostals, Methodists, and Catholics
Authors: Coulter Dale 
Published: December 2009

AbstractThe past four decades of dialogue between Methodists and Catholics as well as Pentecostals and Catholics reveal a shared soteriological substructure between each communion that is grounded in pneumatology. This article explores the shared substructure in order to point out the inherent tensions it raises with respect to baptism and conversion and then offer a possible solution as a way to advance the dialogues. The initial claim being made is that a tension exists in each communion between their commitment to the prevenient activity of the Spirit and their commitment to the sanctifying activity of the Spirit. This tension points toward a need for greater clarity on the modalities of the Spirit's presence in conversion. By reflecting on these modalities, a second claim is made that Pentecostals, Catholics, and Methodists may find agreement on the bestowal of the Spirit in infant baptism or infant dedication as part of the conversion process for those whose physical birth places them within the family of believers. The specific point of agreement would center on the Spirit's bestowal of the "will for faith" as a particular manifestation of sanctifying grace that serves to separate infants within the church from those outside the church who, nevertheless, still benefit from the Spirit's prevenient activity.
The Making of a Trinitarian Theologian: The Holy Spirit in Charles Wesley's Sermons
Authors: Vickers Jason 
Published: December 2009

AbstractThis article contends that, from 1738 to 1742, Charles Wesley developed a robust account of the work of the Holy Spirit. Moreover, by integrating his reflections on pneumatology into his wider theology, he evolved from a largely binitarian to a decidedly trinitarian understanding of salvation. While the article focuses primarily on the emergence of a strong pneumatology in Charles Wesley's undisputed sermons, it also provides occasional sideways glances at similar themes in his hymns and poetry.
One, One, One… One Way to God? A review essay of "In Jesus Name": The History and Beliefs of Oneness Pentecostals
Authors: Millner Marlon 
Published: December 2009

Abstract"In Jesus' Name" is a groundbreaking work on Oneness Pentecostalism. It seeks to be an exhaustive study, which historically situates OP culturally and theologically within a long tradition of Pietism dating back hundreds of years in Europe, and Christocentrism found in American Evangelicalism of the 19th century. However, in lifting up an African-American as the exemplar of Oneness Pentecostalism, the book introduces the person's "black heritage" as an interpretive key, but then fails to follow through on this insight, despite several works around Oneness Pentecostalism, in particular, and race. This leaves open the possibility that there is a significant hole in an otherwise comprehensive monograph. Indeed, closer attention to social location and the theological problem of race, would have paid off with material that indeed moves the tradition from so-called heterodoxy to a more robust, if contested, conversation with the dogmatic tradition, which the author seeks.