bluuebunny/crossref_metadata_2025_split huggingface dataset:
Barcode Identifiers as a Practical Tool for Reliable Species Assignment of Medically Important Black Yeast Species
Authors: Heinrichs Guido , de Hoog G. Sybren , Haase Gerhard 
Published: July 2012

ABSTRACTHerpotrichiellaceous black yeasts and relatives comprise severe pathogens flanked by nonpathogenic environmental siblings. Reliable identification by conventional methods is notoriously difficult. Molecular identification is hampered by the sequence variability in the internal transcribed spacer (ITS) domain caused by difficult-to-sequence homopolymeric regions and by poor taxonomic attribution of sequences deposited in GenBank. Here, we present a potential solution using short barcode identifiers (27 to 50 bp) based on ITS2 ribosomal DNA (rDNA), which allows unambiguous definition of species-specific fragments. Starting from proven sequences of ex-type and authentic strains, we were able to describe 103 identifiers. Multiple BLAST searches of these proposed barcode identifiers in GenBank revealed uniqueness for 100 taxonomic entities, whereas the three remaining identifiers each matched with two entities, but the species of these identifiers could easily be discriminated by differences in the remaining ITS regions. Using the proposed barcode identifiers, a 4.1-fold increase of 100% matches in GenBank was achieved in comparison to the classical approach using the complete ITS sequences. The proposed barcode identifiers will be made accessible for the diagnostic laboratory in a permanently updated online database, thereby providing a highly practical, reliable, and cost-effective tool for identification of clinically important black yeasts and relatives.
Investigation of False-Positive Results Given by the QuantiFERON-TB Gold In-Tube Assay
Authors: Slater Madeline , Parsonnet Julie , Banaei Niaz 
Published: July 2012

ABSTRACT
We investigated a sudden increase in the rate of positive QuantiFERON-TB Gold In-Tube results from 10% to 31% at a U.S. academic institution. Direct comparison of the TB antigen tubes with tubes from a different lot number identified that a potential problem with the TB antigen vials in a certain tube lot was the likely cause of the elevated positive rate. The underlying defect remains unknown. This finding warrants refinement of quality control programs by the manufacturer and users.
A Multilocus Sequence Typing Scheme Implies Population Structure and Reveals Several Putative Novel Achromobacter Species
Authors: Spilker Theodore , Vandamme Peter , LiPuma John J. 
Published: July 2012

ABSTRACT

The genus
Achromobacter
currently is comprised of seven species, including
Achromobacter xylosoxidans
, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of “
Achromobacter
-like” strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed
in silico
analyses of whole-genome sequences of several phylogenetically related genera, including
Bordetella
,
Burkholderia
,
Cupriavidus
,
Herminiimonas
,
Janthinobacterium
,
Methylibium
, and
Ralstonia
, for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse
Achromobacter
isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced
Achromobacter
strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named
Achromobacter
species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found.
Diversity of the Cronobacter Genus as Revealed by Multilocus Sequence Typing
Authors: Joseph S. , Sonbol H. , Hariri S. , Desai P. , McClelland M. , Forsythe S. J. 
Published: July 2012

ABSTRACT

Cronobacter
(previously known as
Enterobacter sakazakii
) is a diverse bacterial genus consisting of seven species:
C. sakazakii
,
C. malonaticus
,
C. turicensis
,
C. universalis
,
C. muytjensii
,
C. dublinensis
, and
C. condimenti
. In this study, we have used a multilocus sequence typing (MLST) approach employing the alleles of 7 genes (
atpD
,
fusA
,
glnS
,
gltB
,
gyrB
,
infB
, and
ppsA
; total length, 3,036 bp) to investigate the phylogenetic relationship of 325
Cronobacter
species isolates. Strains were chosen on the basis of their species, geographic and temporal distribution, source, and clinical outcome. The earliest strain was isolated from milk powder in 1950, and the earliest clinical strain was isolated in 1953. The existence of seven species was supported by MLST. Intraspecific variation ranged from low diversity in
C. sakazakii
to extensive diversity within some species, such as
C. muytjensii
and
C. dublinensis
, including evidence of gene conversion between species. The predominant species from clinical sources was found to be
C. sakazakii. C. sakazakii
sequence type 4 (ST4) was the predominant sequence type of cerebral spinal fluid isolates from cases of meningitis.
Unrecognized Norovirus Infections in Health Care Institutions and Their Clinical Impact
Authors: Beersma Matthias F. C. , Sukhrie Faizel H. A. , Bogerman Jolanda , Verhoef Linda , Mde Melo Mariana , Vonk Alieke G. , Koopmans Marion 
Published: July 2012

ABSTRACT

Noroviruses (NoVs) have emerged as the leading cause of acute viral gastroenteritis (GE) in humans. Although diagnostic facilities have greatly improved, significant underdiagnosis of NoV in hospitals may still occur, thereby increasing clinical burden and nosocomial spread. We evaluated the underdiagnosis of sporadic NoV infections in a tertiary care hospital and estimated its clinical impact. From December 2008 until July 2009, fecal samples specifically referred for bacterial but not viral examination were retrospectively tested for NoV by real-time PCR. The clinical and virological data from patients with undiagnosed NoV infection (missed patients) were evaluated and compared with those from patients with recognized NoV. During the study period, 45 patients with undiagnosed NoV were detected, whereas 50 patients were regularly diagnosed. The missed NoV cases were more frequently adults than children (80% versus 46%;
P
< 0.001). The viral load levels did not differ between the diagnosed and missed patients, but missed patients more frequently presented without diarrhea (20% versus 4%;
P
< 0.07). The newly admitted missed NoV cases with GE underwent more diagnostic imaging (24% versus 4%;
P
< 0.01) and tended to be hospitalized longer. When missed-NoV patients were included, the number of nosocomial clusters doubled and missed patients were index cases in 5 of the 6 clusters. These data indicate that NoV infections are frequently missed despite routine laboratory testing and demonstrate that underdiagnosis of NoV patients is associated with costly abdominal imaging and nosocomial clustering. Awareness of NoV infection in adult patients and education about the importance of viral GE should be increased.
Detection of Carbapenemases in Enterobacteriaceae by a Commercial Multiplex PCR
Authors: Kaase Martin , Szabados Florian , Wassill Lars , Gatermann Sören G. 
Published: July 2012

ABSTRACT

A commercial multiplex PCR (hyplex SuperBug ID) was tested with a collection of 132 clinical
Enterobacteriaceae
strains producing different carbapenemases. The sensitivity for the detection of KPC-, VIM-, NDM-, and OXA-48-encoding genes was 100%, whereas two IMP variants were missed.
Hepatitis B Virus DNA Splicing in Lebanese Blood Donors and Genotype A to E Strains: Implications for Hepatitis B Virus DNA Quantification and Infectivity
Authors: El Chaar Mira , El Jisr Tamima , Allain Jean-Pierre 
Published: July 2012

ABSTRACTHepatitis B virus (HBV) is one of the major viruses transmissible by blood that causes chronic infection in immunocompromised individuals. The study of 61 HBV carrier blood donors from Lebanon revealed multiple patterns of spliced HBV DNA. HBV DNA splicing was examined and quantified in samples of five genotypes and in seroconversion panels. The Lebanese sample median viral load was 1.5 ×102IU/ml. All strains were genotype D, serotype ayw; 35 clustered as subgenotype D1 and 7 clustered as subgenotype D2. Three splice variants (SP1, SP1A, and Pol/S) were observed in 12 high-viral-load samples. Twenty samples of each genotype, A to E, were tested for the presence of HBV spliced DNA and SP1-specific splice variant. An unspliced HBV genome was dominant, but 100% of strains with a viral load of ≥105copies/ml contained various proportions of spliced DNA. SP1 was detected in 56/100 (56%) samples in levels that correlated with the overall viral load. HBV DNA quantification with S (unspliced) and X (total DNA) regions provided different levels of viral load, with the difference corresponding to spliced DNA. During the highly infectious window period, the SP1 variant became detectable shortly after the hepatitis B surface antigen (HBsAg), suggesting a correlation between the initiation of splicing and the production of detectable levels of HBsAg. The quantification of HBV DNA with primers located outside and inside the spliced region might provide different estimations of viral load and differentiate between infectious and defective viral genomes. The role of splicing neoproteins in HBV replication and interaction with the host remains to be determined.
Genotyping of 353 Staphylococcus aureus Bloodstream Isolates Collected between 2004 and 2009 at a Norwegian University Hospital and Potential Associations with Clinical Parameters
Authors: Aamot Hege Vangstein , Blomfeldt Anita , Eskesen Arne N. 
Published: July 2012

ABSTRACT

We analyzed 353
Staphylococcus aureus
bloodstream isolates from 2004 to 2009 to identify dominant genotypes, changes over time, and associations between genotype, phenotype, and clinical parameters. The isolates were genotyped with regard to
spa
type and presence of Panton-Valentine leukocidin and toxic shock syndrome toxin 1-encoding genes. A high level of genetic diversity was detected. All but three isolates were methicillin sensitive. Interestingly,
spa
clonal complex 021 showed a weak association with higher all-cause hospital mortality.
Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity
Authors: Cousins Matthew M. , Ou San-San , Wawer Maria J. , Munshaw Supriya , Swan David , Magaret Craig A. , Mullis Caroline E. , Serwadda David , Porcella Stephen F. , Gray Ronald H. , Quinn Thomas C. , Donnell Deborah , Eshleman Susan H. , Redd Andrew D. 
Published: July 2012

ABSTRACT

Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV
gag
and
env
from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (
n
= 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both
gag
and
env
(
P
< 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (
P
< 0.001 for all measures except for percent complexity in
gag
), and similar amounts of diversification were observed with both methods (
P
< 0.001 for all measures except for percent complexity in
gag
). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution.
A Member of a New Picornaviridae Genus Is Shed in Pig Feces
Authors: Sauvage Virginie , Ar Gouilh Meriadeg , Cheval Justine , Muth Erika , Pariente Kevin , Burguiere Ana , Caro Valérie , Manuguerra Jean-Claude , Eloit Marc 
Published: July 2012

ABSTRACT

During a study of the fecal microbiomes from two healthy piglets using high-throughput sequencing (HTS), we identified a viral genome containing an open reading frame encoding a predicted polyprotein of 2,133 amino acids. This novel viral genome displayed the typical organization of picornaviruses, containing three structural proteins (VP0, VP3, and VP1), followed by seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C
pro
, and 3D
pol
). Given its particular relationship with
Parechovirus
, we propose to name it “Pasivirus” for
Pa
recho
si
ster clade virus, with “Swine pasivirus 1” (SPaV1) as the type species. Fecal samples collected at an industrial farm from healthy sows and piglets from the same herd (25 and 75, respectively) with ages ranging from 4 to 28 weeks were analyzed for the presence of SPaV1 by one-step reverse transcription (RT)-PCR targeting a 3D region of 151 bp. SPaV1 was detected in fecal samples from 51/75 healthy piglets (68% of the animals) and in none of the 25 fecal samples from healthy sows, indicating that SPaV1 circulates through enteric infection of healthy piglets. We propose that SPaV1 represents the first member of a novel
Picornaviridae
genus related to parechoviruses.
The NS1 Protein of Influenza A Virus Blocks RIG-I-Mediated Activation of the Noncanonical NF-κB Pathway and p52/RelB-Dependent Gene Expression in Lung Epithelial Cells
Authors: Rückle Andrea , Haasbach Emanuel , Julkunen Ilkka , Planz Oliver , Ehrhardt Christina , Ludwig Stephan 
Published: July 2012

ABSTRACT
Influenza A virus (IAV) infection of epithelial cells activates NF-κB transcription factors via the canonical NF-κB signaling pathway, which modulates both the antiviral immune response and viral replication. Since almost nothing is known so far about a function of noncanonical NF-κB signaling after IAV infection, we tested infected cells for activation of p52 and RelB. We show that the viral NS1 protein strongly inhibits RIG-I-mediated noncanonical NF-κB activation and expression of the noncanonical target gene CCL19.
CCR5 Mutations Distinguish N-Terminal Modifications of RANTES (CCL5) with Agonist versus Antagonist Activity
Authors: Choi Won-Tak , Nedellec Rebecca , Coetzer Mia , Colin Philippe , Lagane Bernard , Offord Robin E. , Hartley Oliver , Mosier Donald E. 
Published: July 2012

ABSTRACT
CCR5 is the major HIV-1 entry coreceptor. RANTES/CCL5 analogs are more potent inhibitors of infection than native chemokines; one class activates and internalizes CCR5, one neither activates nor internalizes, and a third partially internalizes without activation. Here we show that mutations in CCR5 transmembrane domains differentially impact the activity of these three inhibitor classes, suggesting that the transmembrane region of CCR5, a key interaction site for inhibitors, is a sensitive molecular switch, modulating receptor activity.
Blocking Double-Stranded RNA-Activated Protein Kinase PKR by Japanese Encephalitis Virus Nonstructural Protein 2A
Authors: Tu Yu-Chun , Yu Chia-Yi , Liang Jian-Jong , Lin Elong , Liao Ching-Len , Lin Yi-Ling 
Published: July 2012

ABSTRACT

Japanese encephalitis virus (JEV) is an enveloped flavivirus with a single-stranded, positive-sense RNA genome encoding three structural and seven nonstructural proteins. To date, the role of JEV nonstructural protein 2A (NS2A) in the viral life cycle is largely unknown. The interferon (IFN)-induced double-stranded RNA (dsRNA)-activated protein kinase (PKR) phosphorylates the eukaryotic translation initiation factor 2α subunit (eIF2α) after sensing viral RNA and results in global translation arrest as an important host antiviral defense response. In this study, we found that JEV NS2A could antagonize PKR-mediated growth inhibition in a galactose-inducible PKR-expressing yeast system. In human cells, PKR activation, eIF2α phosphorylation, and the subsequent translational inhibition and cell death triggered by dsRNA and IFN-α were also repressed by JEV NS2A. Moreover, among the four eIF2α kinases, NS2A specifically blocked the eIF2α phosphorylation mediated by PKR and attenuated the PKR-promoted cell death induced by the chemotherapeutic drug doxorubicin. A single point mutation of NS2A residue 33 from Thr to Ile (T33I) abolished the anti-PKR potential of JEV NS2A. The recombinant JEV mutant carrying the NS2A-T33I mutation showed reduced
in vitro
growth and
in vivo
virulence phenotypes. Thus, JEV NS2A has a novel function in blocking the host antiviral response of PKR during JEV infection.
Mutations That Hamper Dimerization of Foot-and-Mouth Disease Virus 3A Protein Are Detrimental for Infectivity
Authors: González-Magaldi Mónica , Postigo Raúl , de la Torre Beatriz G. , Vieira Yuri A. , Rodríguez-Pulido Miguel , López-Viñas Eduardo , Gómez-Puertas Paulino , Andreu David , Kremer Leonor , Rosas María F. , Sobrino Francisco 
Published: July 2012

ABSTRACT

Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. In other picornaviruses, homodimerization of 3A has been shown to be relevant for its biological activity. In this work, FMDV 3A homodimerization was evidenced by an
in situ
protein fluorescent ligation assay. A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. Nevertheless, while Q44R led to recovery of viruses that maintained the mutation, Q44D resulted in selection of infective viruses with substitution D44E with acidic charge but with structural features similar to those of the parental virus, suggesting that Q44 is involved in functions other than 3A dimerization.
An
ac34
Deletion Mutant of Autographa californica Nucleopolyhedrovirus Exhibits Delayed Late Gene Expression and a Lack of Virulence
In Vivo
Authors: Cai Yi , Long Zhao , Qiu Jianxiang , Yuan Meijin , Li Guanghong , Yang Kai 
Published: July 2012

ABSTRACT

Ac34 and its homologs are highly conserved in all sequenced alphabaculoviruses. In this paper, we show that
ac34
transcripts were detected from 6 to 48 h postinfection (p.i.) in
Autographa californica nucleopolyhedrovirus
(AcMNPV)-infected Sf9 cells. Ac34 localized to both the cytoplasm and the nuclei of infected cells but was not a viral structural protein. To determine the function of
ac34
in the viral life cycle, an
ac34
knockout AcMNPV (vAc34KO) was constructed. Compared with wild-type and repair viruses, vAc34KO exhibited an approximately 100-fold reduction in infectious virus production. Further investigations showed that the
ac34
deletion did not affect the replication of viral DNA, polyhedron formation, or nucleocapsid assembly but delayed the expression of late genes, such as
vp39
,
38k
, and
p6.9
. Bioassays revealed that vAc34KO was unable to establish a fatal infection in
Trichoplusia ni
larvae via
per os
inoculation. Few infectious progeny viruses were detected in the hemolymph of the infected larvae, indicating that the replication of vAc34KO was attenuated. These results suggest that Ac34 is an activator protein that promotes late gene expression and is essential for the pathogenicity of AcMNPV.
Identification of Human Astrovirus Genome-Linked Protein (VPg) Essential for Virus Infectivity
Authors: Fuentes Cristina , Bosch Albert , Pintó Rosa M. , Guix Susana 
Published: July 2012

ABSTRACT

Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The presence of such protein in the family
Astroviridae
has not been fully elucidated, although a putative VPg coding region in open reading frame 1a (ORF1a) of astrovirus with high amino acid sequence similarity to the VPg coding region of
Caliciviridae
has been previously identified. In this work we present several experimental findings that show that human astrovirus (HAstV) RNA encodes a VPg essential for viral infectivity: (i) RNase treatment of RNA purified from astrovirus-infected cells results in a single protein of 13 to 15 kDa, compatible with the predicted astrovirus VPg size; (ii) the antibody used to detect this 13- to 15-kDa protein is specifically directed against a region that includes the putative VPg coding region; (iii) the 13- to 15-kDa protein detected has been partially sequenced and the sequence obtained is contained in the computationally predicted VPg; (iv) the protein resulting from this putative VPg coding region is a highly disordered protein, resembling the VPg of sobemo-, calici- and potyviruses; (v) proteolytic treatment of the genomic RNA leads to loss of infectivity; and (vi) mutagenesis of Tyr-693 included in the putative VPg protein is lethal for HAstV replication, which strongly supports its functional role in the covalent link with the viral RNA.