bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectrum of Clinically Relevant
Acremonium
Species in the United States
Authors: Perdomo H. , Sutton D. A. , García D. , Fothergill A. W. , Cano J. , Gené J. , Summerbell R. C. , Rinaldi M. G. , Guarro J. 
Published: November 2010

ABSTRACT

Some species in the polyphyletic fungal genus
Acremonium
are important opportunist pathogens. Determining the actual spectrum of species and their incidence in the clinical setting, however, has long been hampered because of the difficulties encountered in phenotypic species-level identification. The goal of this study was to re-identify a large number of clinical isolates morphologically and to confirm the identifications by comparing sequences of the internal transcribed spacer region of the rRNA gene of these isolates to those of type or reference strains of well-known
Acremonium
species. Of the 119 isolates referred to a United States reference laboratory under the name
Acremonium
, only 75 were identified morphologically as belonging to that genus. The remainder (44 isolates) were identified as belonging to other morphologically similar genera. The
Acremonium
clinical isolates were related to species of Hypocreales, Sordariales, and of an
incertae sedis
family of ascomycetes, Plectosphaerellaceae. A total of 50 of the 75
Acremonium
isolates (67%) could be identified by molecular means, the prevalent species being
Acremonium kiliense
(15 isolates),
A. sclerotigenum
-
A. egyptiacum
(11 isolates),
A. implicatum
(7 isolates),
A. persicinum
(7 isolates), and
A. atrogriseum
(4 isolates). One of the most interesting findings of our study was that we identified several species among this large collection of clinical isolates that had not previously been reported from human infections, and we failed to confirm other
Acremonium
species, such as
A. potronii
,
A. recifei
, and
A. strictum
, that had been considered significant. The most common anatomic sites for
Acremonium
isolates were the respiratory tract (41.3%), nails (10.7%), and the eye (9.3%). Antifungal susceptibility testing demonstrated high MICs for all agents tested, except for terbinafine. Since numerous isolates could not be identified, we concluded that the list of opportunistic
Acremonium
species is far from be complete and that a considerable number of additional species will be discovered.
Breakthrough
Hormographiella aspergillata
Infections Arising in Neutropenic Patients Treated Empirically with Caspofungin
Authors: Suarez Felipe , Olivier Gaelle , Garcia-Hermoso Dea , Randriamalala Edouard , Ghez David , Bruneau Julie , Kauffmann-Lacroix Catherine , Bougnoux Marie-Elisabeth , Lortholary Olivier 
Published: November 2010

ABSTRACT

Hormographiella aspergillata
, a filamentous basidiomycete, has rarely been involved in human infections. We describe 2 febrile neutropenic patients who developed a severe pulmonary infection due to
H. aspergillata
while receiving empirical caspofungin therapy for presumed fungal pneumonia. After introduction of liposomal amphotericin B, one patient, who had neutrophil recovery, presented a favorable outcome, while the other, who remained neutropenic throughout the course of infection, died. Resistant fungi, including basidiomycetes, may emerge during empirical treatment with caspofungin in febrile neutropenic patients. A rapid switch to any other potent antifungal should be rapidly considered in case of failure of caspofungin in this setting.
Prevalence and Characterization of Human
Shigella
Infections in Henan Province, China, in 2006
Authors: Xia Shengli , Xu Bianli , Huang Lili , Zhao Jia-Yong , Ran Lu , Zhang Jin , Chen Haomin , Pulsrikarn Chaiwat , Pornruangwong Srirat , Aarestrup Frank M. , Hendriksen Rene S. 
Published: November 2010

ABSTRACT

In 2006, 3,531 fecal samples were collected from patients with diarrhea in Henan Province, China. A total of 467 (13.2%)
Shigella
strains were isolated and serotyped. Seventy-one
Shigella flexneri
strains were characterized by MIC determination, pulsed-field gel electrophoresis (PFGE), and detection of genes encoding cephalosporin resistance. Most infections were caused by
S. flexneri
variant X [IV:(7),8] (27.6%),
S. sonnei
(24.2%), and
S. flexneri
2a (20.8%). However, large regional differences were observed. Significantly higher odds (2.0) of females compared to males were infected with
S. flexneri
2a. Untypeable
S. flexneri
(−:6) isolates were absent among males, as were untypeable
S. flexneri
[I:(7),8] isolates among females. Patient ages ranged from 2 months to 82 years, with 231 subjects (49.7%) <5 years of age. Most of the patients were male (62.1% [
n
= 290]). Infections peaked in July; week 27 with 38 cases (8.1%). All of the 71
S. flexneri
conferred resistance to nalidixic acid; in addition, 21% (
n
= 15) and 79% (
n
= 56) were high- and low-level resistant to ciprofloxacin, respectively. Six
S. flexneri
isolates {serotype 2b [II:7,(8)] and 2b [II:(3),4;7,(8)]} harbored the
bla
CTX-M-14
or
bla
CTX-M-15
gene. A total of 52 unique XbaI PFGE patterns were observed among the 71
S. flexneri
isolates with 11 distinct PFGE clusters. This study revealed a high prevalence of shigellosis with geographical differences in the distribution of serotypes in the distribution of serotypes and also differences in comparisons by gender. A high frequency of resistance, including 100% resistance to ciprofloxacin and resistance to extended-spectrum cephalosporins, was observed. We detected several isolates exhibiting the same PFGE type and MIC profile, indicating multiple undetected outbreaks.
A Twist on Lyme: the Challenge of Diagnosing European Lyme Neuroborreliosis
Authors: Makhani Naila , Morris Shaun K. , Page Andrea V. , Brophy Jason , Lindsay L. Robbin , Banwell Brenda L. , Richardson Susan E. 
Published: November 2010

ABSTRACT

Lyme neuroborreliosis is a tick-borne illness with central and peripheral nervous system manifestations. Clinical features and methods for accurate diagnosis differ across world regions owing to different causative
Borrelia
species. The importance of these distinctions is highlighted by a 12-year-old Canadian girl who acquired Lyme neuroborreliosis in Europe.
HIV-1 Load Comparison Using Four Commercial Real-Time Assays
Authors: Bourlet Thomas , Signori-Schmuck Anne , Roche Laurent , Icard Vinca , Saoudin Henia , Trabaud Mary-Anne , Tardy Jean-Claude , Morand Patrice , Pozzetto Bruno , Ecochard René , André Patrice 
Published: November 2010

ABSTRACT

The HIV-1 RNA viral load is commonly used for the monitoring of disease progression and antiretroviral treatment of HIV-1-infected patients. Since the misestimating of values could lead to inappropriate therapeutical management, the comparative performances, especially the ability to span the genetic diversity of HIV-1, of available automated real-time assays need to be evaluated. We conducted a prospective study with 74 consenting patients enrolled between March 2007 and November 2008. A blood sample was obtained at the time of diagnosis of HIV seropositivity and blindly tested for HIV-1 RNA by at least 4 commercial tests: the Abbott
m
2000 RealTi
m
e HIV-1, bioMérieux NucliSens EasyQ HIV-1, version 1.2 (v1.2), and Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) v1.0 and v2.0 assays. The means of difference were null between CAP/CTM v2.0 and Abbott for CRF02_AG subtypes but positive in favor of CAP/CTM v2.0 for genotype B and negative in favor of NucliSens for all genotypes. The standard deviation (SD) of difference ranged from 0.3 to 0.59, depending on the considered couples of assays. Reliabilities of these four tests, appreciated by the standard deviation of difference between the measurement and the estimated “true” viral load and by the coefficient of reliability, were significantly different (
P
< 10
−4
) among each other. Significant differences were also observed within each group of HIV-1 genotype. The global disparity was higher for CRF02_AG than for B subtypes. This study indicates a risk of viral load misestimating or discrepancies between techniques, depending on the HIV-1 subtype, and speaks in favor of using the same assay for the monitoring of HIV-1-infected patients.
Staphylococcal IgM Enzyme-Linked Immunosorbent Assay for Diagnosis of Periprosthetic Joint Infections
Authors: Artini Marco , Romanò Carlo , Manzoli Lamberto , Scoarughi Gian Luca , Papa Rosanna , Meani Enzo , Drago Lorenzo , Selan Laura 
Published: November 2010

ABSTRACT
Delayed orthopedic joint prosthesis infections (DOJP-Is) due to staphylococci frequently result in prosthetic revision. Specific and noninvasive diagnostic tests are unavailable, and DOJP-Is are commonly diagnosed at advanced stages of disease. An enzyme-linked immunosorbent assay (ELISA) was developed to detect serum antibodies against staphylococcal slime polysaccharide antigens. Using a cutoff of 0.35 ELISA units, the test showed a specificity of 95.1% (95% confidence interval [CI], 85.4 to 98.7%) and a sensitivity of 89.7% (71.5 to 97.3%) on a sample of 90 individuals.
Human Parainfluenza Virus Type 2 L Protein Regions Required for Interaction with Other Viral Proteins and mRNA Capping
Authors: Nishio Machiko , Tsurudome Masato , Garcin Dominique , Komada Hiroshi , Ito Morihiro , Le Mercier Philippe , Nosaka Tetsuya , Kolakofsky Daniel 
Published: November 2010

ABSTRACT
The large RNA polymerase (L) protein of human parainfluenza virus type 2 (hPIV2) binds the nucleocapsid, phosphoprotein, and V protein, as well as itself, and these interactions are essential for transcription and replication of the viral RNA genome. Although all of these interactions were found to be mediated through the domains within the N terminus of L, the C terminus of the L protein was also required for minigenome reporter gene expression. We have identified a highly conserved rubulavirus domain near the C terminus of the L protein that is required for mRNA synthesis but not for genome replication. Remarkably, this region of L shares homology with a conserved region of cellular capping enzymes that binds GTP and forms a lysyl-GMP enzyme intermediate, the first step in the cellular capping reaction. We propose that this conserved region of L also binds GTP (or GDP) to carry out the second step of the unconventional nonsegmented negative-strand virus capping reaction.
The Receptor-Binding Domain of Influenza Virus Hemagglutinin Produced in
Escherichia coli
Folds into Its Native, Immunogenic Structure
Authors: DuBois Rebecca M. , Aguilar-Yañez José Manuel , Mendoza-Ochoa Gonzalo I. , Oropeza-Almazán Yuriana , Schultz-Cherry Stacey , Alvarez Mario Moisés , White Stephen W. , Russell Charles J. 
Published: November 2010

ABSTRACT

The hemagglutinin (HA) surface glycoprotein promotes influenza virus entry and is the key protective antigen in natural immunity and vaccines. The HA protein is a trimeric envelope glycoprotein consisting of a globular receptor-binding domain (HA-RBD) that is inserted into a membrane fusion-mediating stalk domain. Similar to other class I viral fusion proteins, the fusogenic stalk domain spontaneously refolds into its postfusion conformation when expressed in isolation, consistent with this domain being trapped in a metastable conformation. Using X-ray crystallography, we show that the influenza virus HA-RBD refolds spontaneously into its native, immunogenic structure even when expressed in an unglycosylated form in
Escherichia coli
. In the 2.10-Å structure of the HA-RBD, the receptor-binding pocket is intact and its conformational epitopes are preserved. Recombinant HA-RBD is immunogenic and protective in ferrets, and the protein also binds with specificity to sera from influenza virus-infected humans. Overall, the data provide a structural basis for the rapid production of influenza vaccines in
E. coli
. From an evolutionary standpoint, the ability of the HA-RBD to refold spontaneously into its native conformation suggests that influenza virus acquired this domain as an insertion into an ancestral membrane-fusion domain. The insertion of independently folding domains into fusogenic stalk domains may be a common feature of class I viral fusion proteins.
A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication
Authors: Oke Muse , Kerou Melina , Liu Huanting , Peng Xu , Garrett Roger A. , Prangishvili David , Naismith James H. , White Malcolm F. 
Published: November 2010

ABSTRACT

The
Rudiviridae
are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the
Poxviridae
and other large cytoplasmic eukaryotic viruses. Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between an active-site tyrosine and the 5′ end of the DNA, releasing a 3′ DNA end as a primer for DNA synthesis. The enzyme can also catalyze the joining reaction that is necessary to reseal the DNA hairpin and terminate replication. The dimeric structure points to a simple mechanism through which two closely positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral replication are discussed.
Coordinated Leading and Lagging Strand DNA Synthesis by Using the Herpes Simplex Virus 1 Replication Complex and Minicircle DNA Templates
Authors: Stengel Gudrun , Kuchta Robert D. 
Published: November 2010

ABSTRACT
The origin-specific replication of the herpes simplex virus 1 genome requires seven proteins: the helicase-primase (UL5-UL8-UL52), the DNA polymerase (UL30-UL42), the single-strand DNA binding protein (ICP8), and the origin-binding protein (UL9). We reconstituted these proteins, excluding UL9, on synthetic minicircular DNA templates and monitored leading and lagging strand DNA synthesis using the strand-specific incorporation of dTMP and dAMP. Critical features of the assays that led to efficient leading and lagging stand synthesis included high helicase-primase concentrations and a lagging strand template whose sequence resembled that of the viral DNA. Depending on the nature of the minicircle template, the replication complex synthesized leading and lagging strand products at molar ratios varying between 1:1 and 3:1. Lagging strand products (∼0.2 to 0.6 kb) were significantly shorter than leading strand products (∼2 to 10 kb), and conditions that stimulated primer synthesis led to shorter lagging strand products. ICP8 was not essential; however, its presence stimulated DNA synthesis and increased the length of both leading and lagging strand products. Curiously, human DNA polymerase α (p70-p180 or p49-p58-p70-p180), which improves the utilization of RNA primers synthesized by herpesvirus primase on linear DNA templates, had no effect on the replication of the minicircles. The lack of stimulation by polymerase α suggests the existence of a macromolecular assembly that enhances the utilization of RNA primers and may functionally couple leading and lagging strand synthesis. Evidence for functional coupling is further provided by our observations that (i) leading and lagging strand synthesis produce equal amounts of DNA, (ii) leading strand synthesis proceeds faster under conditions that disable primer synthesis on the lagging strand, and (iii) conditions that accelerate helicase-catalyzed DNA unwinding stimulate decoupled leading strand synthesis but not coordinated leading and lagging strand synthesis.
Herpes Simplex Virus Type 1 Helicase-Primase: DNA Binding and Consequent Protein Oligomerization and Primase Activation
Authors: Chen Yan , Bai Ping , Mackay Shannon , Korza George , Carson John H. , Kuchta Robert D. , Weller Sandra K. 
Published: November 2010

ABSTRACT
The heterotrimeric helicase-primase complex of herpes simplex virus type I (HSV-1), consisting of UL5, UL8, and UL52, possesses 5′ to 3′ helicase, single-stranded DNA (ssDNA)-dependent ATPase, primase, and DNA binding activities. In this study we confirm that the UL5-UL8-UL52 complex has higher affinity for forked DNA than for ssDNA and fails to bind to fully annealed double-stranded DNA substrates. In addition, we show that a single-stranded overhang of greater than 6 nucleotides is required for efficient enzyme loading and unwinding. Electrophoretic mobility shift assays and surface plasmon resonance analysis provide additional quantitative information about how the UL5-UL8-UL52 complex associates with the replication fork. Although it has previously been reported that in the absence of DNA and nucleoside triphosphates the UL5-UL8-UL52 complex exists as a monomer in solution, we now present evidence that in the presence of forked DNA and AMP-PNP, higher-order complexes can form. Electrophoretic mobility shift assays reveal two discrete complexes with different mobilities only when helicase-primase is bound to DNA containing a single-stranded region, and surface plasmon resonance analysis confirms larger amounts of the complex bound to forked substrates than to single-overhang substrates. Furthermore, we show that primase activity exhibits a cooperative dependence on protein concentration while ATPase and helicase activities do not. Taken together, these data suggest that the primase activity of the helicase-primase requires formation of a dimer or higher-order structure while ATPase activity does not. Importantly, this provides a simple mechanism for generating a two-polymerase replisome at the replication fork.
Characterization of Bafinivirus Main Protease Autoprocessing Activities
Authors: Ulferts Rachel , Mettenleiter Thomas C. , Ziebuhr John 
Published: November 2010

ABSTRACT

The production of functional nidovirus replication-transcription complexes involves extensive proteolytic processing by virus-encoded proteases. In this study, we characterized the viral main protease (M
pro
) of the type species,
White bream virus
(WBV), of the newly established genus
Bafinivirus
(order
Nidovirales
, family
Coronaviridae
, subfamily
Torovirinae
). Comparative sequence analysis and mutagenesis data confirmed that the WBV M
pro
is a picornavirus 3C-like serine protease that uses a Ser-His-Asp catalytic triad embedded in a predicted two-β-barrel fold, which is extended by a third domain at its C terminus. Bacterially expressed WBV M
pro
autocatalytically released itself from flanking sequences and was able to mediate proteolytic processing in
trans
. Using N-terminal sequencing of autoproteolytic processing products we tentatively identified Gln↓(Ala, Thr) as a substrate consensus sequence. Mutagenesis data provided evidence to suggest that two conserved His and Thr residues are part of the S1 subsite of the enzyme's substrate-binding pocket. Interestingly, we observed two N-proximal and two C-proximal autoprocessing sites in the bacterial expression system. The detection of two major forms of M
pro
, resulting from processing at two different N-proximal and one C-proximal site, in WBV-infected epithelioma papulosum cyprini cells confirmed the biological relevance of the biochemical data obtained in heterologous expression systems. To our knowledge, the use of alternative M
pro
autoprocessing sites has not been described previously for other nidovirus M
pro
domains. The data presented in this study lend further support to our previous conclusion that bafiniviruses represent a distinct group of viruses that significantly diverged from other phylogenetic clusters of the order
Nidovirales
.
Phylogeography of the Spring and Fall Waves of the H1N1/09 Pandemic Influenza Virus in the United States
Authors: Nelson Martha I. , Tan Yi , Ghedin Elodie , Wentworth David E. , St. George Kirsten , Edelman Laurel , Beck Eric T. , Fan Jiang , Lam Tommy Tsan-Yuk , Kumar Swati , Spiro David J. , Simonsen Lone , Viboud Cecile , Holmes Edward C. , Henrickson Kelly J. , Musser James M. 
Published: November 2010

ABSTRACT
Spatial variation in the epidemiological patterns of successive waves of pandemic influenza virus in humans has been documented throughout the 20th century but never understood at a molecular level. However, the unprecedented intensity of sampling and whole-genome sequencing of the H1N1/09 pandemic virus now makes such an approach possible. To determine whether the spring and fall waves of the H1N1/09 influenza pandemic were associated with different epidemiological patterns, we undertook a large-scale phylogeographic analysis of viruses sampled from three localities in the United States. Analysis of genomic and epidemiological data reveals distinct spatial heterogeneities associated with the first pandemic wave, March to July 2009, in Houston, TX, Milwaukee, WI, and New York State. In Houston, no specific H1N1/09 viral lineage dominated during the spring of 2009, a period when little epidemiological activity was observed in Texas. In contrast, major pandemic outbreaks occurred at this time in Milwaukee and New York State, each dominated by a different viral lineage and resulting from strong founder effects. During the second pandemic wave, beginning in August 2009, all three U.S. localities were dominated by a single viral lineage, that which had been dominant in New York during wave 1. Hence, during this second phase of the pandemic, extensive viral migration and mixing diffused the spatially defined population structure that had characterized wave 1, amplifying the one viral lineage that had dominated early on in one of the world's largest international travel centers.
Hepatitis B Virus Regulatory HBx Protein Binds to Adaptor Protein IPS-1 and Inhibits the Activation of Beta Interferon
Authors: Kumar Manish , Jung Sung Yun , Hodgson Amanda J. , Madden Charles R. , Qin Jun , Slagle Betty L. 
Published: November 2010

ABSTRACT
Hepatitis B virus (HBV) encodes the regulatory HBx protein, which is required for virus replication, although its specific role(s) in the replication cycle remains under investigation. An immunoprecipitation/mass spectrometry approach was used to identify four novel HBx binding proteins from the cytoplasmic fraction of HBx transgenic mouse livers. One of these HBx binding partners is beta interferon promoter stimulator 1 (IPS-1), an adaptor protein that plays a critical role in mediating retinoic acid-inducible gene I (RIG-I) signaling, which leads to the activation of beta interferon (IFN-β). The HBx-IPS-1 protein interaction was confirmed in plasmid-transfected HepG2 cells by reciprocal coimmunoprecipitation and Western blotting. We hypothesized that HBx might alter IPS-1 function since proteins of hepatitis C virus and hepatitis A virus similarly bind IPS-1 and target it for inactivation. The effect of HBx on IPS-1-mediated IFN-β signaling was tested in transfected 293T and HepG2 cells, and we show that HBx inhibits double-stranded DNA (dsDNA)-mediated IFN-β activation in a dose-dependent manner when expressed either alone or within the context of HBV replication. However, HBx does not inhibit poly(I:C)-activated IFN-β signaling. These results demonstrate that HBx interferes with the RIG-I pathway of innate immunity. Hepatitis B virus now joins hepatitis C virus and hepatitis A virus in targeting the same innate immune response pathway, presumably as a shared strategy to benefit replication of these viruses in the liver.