bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of a Rat Hepatitis E Virus Strain Isolated in the United States
Authors: Debing Yannick , Emerson Suzanne U. , Purcell Robert H. , Neyts Johan , Dallmeier Kai 
Published: November 2014

ABSTRACT
Hepatitis E virus is a common cause of acute hepatitis in humans. Related viruses have been isolated from multiple animal species, including rats, but their impact on human health is unclear. We present the first full-length genome sequence of a rat hepatitis E virus strain isolated in the United States (LA-B350).
Draft Genome Sequence of Pseudomonas aeruginosa ATCC 33988, a Bacterium Highly Adapted to Fuel-Polluted Environments
Authors: Brown Lisa M. , Gunasekera Thusitha S. , Ruiz Oscar N. 
Published: November 2014

ABSTRACT

Pseudomonas aeruginosa
ATCC 33988 is highly adapted to grow in jet and diesel fuel, with a defined regulation of adaptive genes and metabolization of
n
-alkanes. The draft genome of strain ATCC 33988 is 6.4 Mb in size, with 5,975 coding sequences and 66.3% G+C content, and it is highly similar to that of the clinical strain
P. aeruginosa
PAO1.
Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp.
lactis
TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese
Authors: Velly H. , Renault P. , Abraham A.-L. , Loux V. , Delacroix-Buchet A. , Fonseca F. , Bouix M. 
Published: November 2014

ABSTRACT

Lactococcus lactis
is a lactic acid bacterium used in the production of many fermented foods, such as dairy products. Here, we report the genome sequence of
L. lactis
subsp.
lactis
TOMSC161, isolated from nonscalded curd pressed cheese. This genome sequence provides information in relation to dairy environment adaptation.
Draft Genome Sequence of
Rhizobium
sp. H41, a Rock-Weathering Bacterium from a Weathered Rock Surface
Authors: Xi Jun , Sheng Xiafang , He Linyan 
Published: November 2014

ABSTRACT

Rhizobium
sp. H41 isolated from weathered tuff can weather tuff and release Fe, Si, and Al from the rock under nutrient-poor conditions. Here, we report the draft genome sequence of strain H41, which may facilitate a better understanding of the molecular mechanism involved in rock weathering by the bacterium.
Complete Genome Sequence of Cellulophaga lytica HI1 Using PacBio Single-Molecule Real-Time Sequencing
Authors: Asahina Audrey Y. , Hadfield Michael G. 
Published: November 2014

ABSTRACT

We report here the complete genome sequence of
Cellulophaga lytica
HI1 isolated from a seawater table located at the Kewalo Marine Laboratory (Honolulu, HI). This is the first complete
de novo
genome assembly of
C. lytica
HI1 using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a single scaffold of 3.8 Mb.
Detection of Intracellular Parasites by Use of the CellaVision DM96 Analyzer during Routine Screening of Peripheral Blood Smears
Authors: Racsa Lori D. , Gander Rita M. , Southern Paul M. , McElvania TeKippe Erin , Doern Christopher , Luu Hung S. 
Published: November 2014

ABSTRACT

Conventional microscopy is the gold standard for malaria diagnosis. The CellaVision DM96 is a digital hematology analyzer that utilizes neural networks to locate, digitize, and preclassify leukocytes and characterize red blood cell morphology. This study compared the detection rates of
Plasmodium
and
Babesia
species on peripheral blood smears utilizing the CellaVision DM96 with the rates for a routine red blood cell morphology scan. A total of 281 slides were analyzed, consisting of 130 slides positive for
Plasmodium
or
Babesia
species and 151 negative controls. Slides were blinded, randomized, and analyzed by CellaVision and microscopy for red cell morphology scans. The technologists were blinded to prior identification results. The parasite detection rate was 73% (95/130) for CellaVision and 81% (105/130) for microscopy for positive samples. The interobserver agreement between CellaVision and microscopy was fair, as Cohen's kappa coefficient equaled 0.36. Pathologist review of CellaVision images identified an additional 15 slides with parasites, bringing the total number of detectable positive slides to 110 of 130 (85%).
Plasmodium ovale
had the lowest rate of detection at 56% (5 of 9);
Plasmodium malariae
and
Babesia
spp. had the highest rate of detection at 100% (3/3 and 6/6, respectively). The detection rate by CellaVision was 100% (23/23) when the parasitemia was ≥2.5%. The detection rate for <0.1% parasitemia was 63% (15/24). Technologists appropriately classified all negative specimens. The percentage of positive specimens detectable by CellaVision (73%) approaches results for microscopy on routine scan of peripheral blood smears for red blood cell morphology.
High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods
Authors: Quer Josep , Gregori Josep , Rodríguez-Frias Francisco , Buti Maria , Madejon Antonio , Perez-del-Pulgar Sofia , Garcia-Cehic Damir , Casillas Rosario , Blasi Maria , Homs Maria , Tabernero David , Alvarez-Tejado Miguel , Muñoz Jose Manuel , Cubero Maria , Caballero Andrea , delCampo Jose Antonio , Domingo Esteban , Belmonte Irene , Nieto Leonardo , Lens Sabela , Muñoz-de-Rueda Paloma , Sanz-Cameno Paloma , Sauleda Silvia , Bes Marta , Gomez Jordi , Briones Carlos , Perales Celia , Sheldon Julie , Castells Lluis , Viladomiu Lluis , Salmeron Javier , Ruiz-Extremera Angela , Quiles-Pérez Rosa , Moreno-Otero Ricardo , López-Rodríguez Rosario , Allende Helena , Romero-Gómez Manuel , Guardia Jaume , Esteban Rafael , Garcia-Samaniego Javier , Forns Xavier , Esteban Juan Ignacio 
Published: November 2014

ABSTRACT
Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.
Utility of Measuring (1,3)-β-
d
-Glucan in Cerebrospinal Fluid for Diagnosis of Fungal Central Nervous System Infection
Authors: Lyons Jennifer L. , Thakur Kiran T. , Lee Rick , Watkins Tonya , Pardo Carlos A. , Carson Kathryn A. , Markley Barbara , Finkelman Malcolm A. , Marr Kieren A. , Roos Karen L. , Zhang Sean X. 
Published: November 2014

ABSTRACT

(1-3)-β-
d
-Glucan (BDG) from cerebrospinal fluid (CSF) is a promising marker for diagnostic and prognostic aid of central nervous system (CNS) fungal infection, but its relationship to serum values has not been studied. Herein, we detected BDG from CSF at levels 2-fold lower than those in serum in patients without evidence of fungal disease but 25-fold higher than those in in serum in noncryptococcal CNS fungal infections. CSF BDG may be a useful biomarker in the evaluation of fungal CNS disease.
Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis
Authors: Deng Xiangyu , Shariat Nikki , Driebe Elizabeth M. , Roe Chandler C. , Tolar Beth , Trees Eija , Keim Paul , Zhang Wei , Dudley Edward G. , Fields Patricia I. , Engelthaler David M. 
Published: November 2014

ABSTRACT

A retrospective investigation was performed to evaluate whole-genome sequencing as a benchmark for comparing molecular subtyping methods for
Salmonella enterica
serotype Enteritidis and survey the population structure of commonly encountered
S. enterica
serotype Enteritidis outbreak isolates in the United States. A total of 52
S. enterica
serotype Enteritidis isolates representing 16 major outbreaks and three sporadic cases collected between 2001 and 2012 were sequenced and subjected to subtyping by four different methods: (i) whole-genome single-nucleotide-polymorphism typing (WGST), (ii) multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA), (iii) clustered regularly interspaced short palindromic repeats combined with multi-virulence-locus sequence typing (CRISPR-MVLST), and (iv) pulsed-field gel electrophoresis (PFGE). WGST resolved all outbreak clusters and provided useful robust phylogenetic inference results with high epidemiological correlation. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed the other methods in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of
S. enterica
serotype Enteritidis. Our results suggested that whole-genome sequencing makes a viable platform for the evaluation and benchmarking of molecular subtyping methods.
Kinetics of Poliovirus Shedding following Oral Vaccination as Measured by Quantitative Reverse Transcription-PCR versus Culture
Authors: Taniuchi Mami , Begum Sharmin , Uddin Md Jashim , Platts-Mills James A. , Liu Jie , Kirkpatrick Beth D. , Chowdhury Anwarul H. , Jamil Khondoker M. , Haque Rashidul , Petri William A. , Houpt Eric R. 
Published: November 2014

ABSTRACT

Amid polio eradication efforts, detection of oral polio vaccine (OPV) virus in stool samples can provide information about rates of mucosal immunity and allow estimation of the poliovirus reservoir. We developed a multiplex one-step quantitative reverse transcription-PCR (qRT-PCR) assay for detection of OPV Sabin strains 1, 2, and 3 directly in stool samples with an external control to normalize samples for viral quantity and compared its performance with that of viral culture. We applied the assay to samples from infants in Dhaka, Bangladesh, after the administration of trivalent OPV (tOPV) at weeks 14 and 52 of life (on days 0 [pre-OPV], +4, +11, +18, and +25 relative to vaccination). When 1,350 stool samples were tested, the sensitivity and specificity of the quantitative PCR (qPCR) assay were 89 and 91% compared with culture. A quantitative relationship between culture
+
/qPCR
+
and culture
−
/qPCR
+
stool samples was observed. The kinetics of shedding revealed by qPCR and culture were similar. qPCR quantitative cutoffs based on the day +11 or +18 stool samples could be used to identify the culture-positive shedders, as well as the long-duration or high-frequency shedders. Interestingly, qPCR revealed that a small minority (7%) of infants contributed the vast majority (93 to 100%) of the total estimated viral excretion across all subtypes at each time point. This qPCR assay for OPV can simply and quantitatively detect all three Sabin strains directly in stool samples to approximate shedding both qualitatively and quantitatively.
Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013
Authors: Demczuk Walter , Lynch Tarah , Martin Irene , Van Domselaar Gary , Graham Morag , Bharat Amrita , Allen Vanessa , Hoang Linda , Lefebvre Brigitte , Tyrrell Greg , Horsman Greg , Haldane David , Garceau Richard , Wylie John , Wong Tom , Mulvey Michael R. 
Published: November 2014

ABSTRACT

A large-scale, whole-genome comparison of Canadian
Neisseria gonorrhoeae
isolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While some
N. gonorrhoeae
multiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaic
penA
alleles, followed in 2000/2001 with the
penA
mosaic X allele and then in 2007 with ST1407 strains with the
penA
mosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated with
penA
mosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.
Clinical Outcomes of Enterobacteriaceae Infections Stratified by Carbapenem MICs
Authors: Patel Twisha S. , Nagel Jerod L. 
Published: November 2014

ABSTRACT

The Clinical and Laboratory Standards Institute (CLSI) lowered the MIC breakpoints for meropenem and imipenem from 4 mg/liter to 1 mg/liter for
Enterobacteriaceae
in 2010. The breakpoint change improves the probability of pharmacodynamic target attainment and eliminates the need for microbiology labs to perform confirmatory testing for
Klebsiella pneumoniae
carbapenemase (KPC) production or other beta-lactamases that hydrolyze carbapenems. However, there are limited data evaluating clinical outcomes of the affected breakpoints, and it is unknown if patients infected with
Enterobacteriaceae
with reduced susceptibility are more likely to have poor outcomes when treated with a carbapenem. We conducted a single-center retrospective matched-cohort analysis in adult patients with
Enterobacteriaceae
infections treated with meropenem, imipenem, or doripenem. Patients with
Enterobacteriaceae
infection with a carbapenem MIC of 2 to 8 mg/liter were matched based on pathogen, source of infection, comorbidities, and disease severity (1:1 ratio) to those with a carbapenem MIC of ≤1 mg/liter. A total of 36 patients were included in the study. The group with carbapenem MICs of 2 to 8 mg/liter had a significantly higher 30-day mortality than the group with carbapenem MICs of ≤1 mg/liter (38.9% compared to 5.6%,
P
= 0.04). Total hospital length of stay (LOS) and intensive care unit (ICU) LOS were longer in the group with MICs of 2 to 8 mg/liter than in the group with MICs of ≤1 mg/liter (57.6 days compared to 34.4 days [
P
= 0.06] and 56.6 days compared to 21.7 days [
P
< 0.01], respectively). Patients infected with
Enterobacteriaceae
with a carbapenem MIC of 2, 4, or 8 mg/liter had higher mortality rates and longer ICU LOS than matched cohorts with carbapenem MICs of ≤1 mg/liter, which supports CLSI's recommendation to lower susceptibility breakpoints for carbapenems.
Rotavirus Entry: a Deep Journey into the Cell with Several Exits
Authors: Arias Carlos F. , Silva-Ayala Daniela , López Susana 
Published: November 2014

ABSTRACT
Rotaviruses are the leading etiological agents of acute gastroenteritis in infants and young children worldwide. These nonenveloped viruses enter cells using different types of endocytosis and, depending on the virus strain, travel to different endosomal compartments before exiting to the cytosolic space. In this Gem, we review the viral and cellular factors involved in the different stages of a productive virus cell entry and share with the readers the journey that we have taken into the cell to learn about virus entry.
A Conserved Regulatory Module at the C Terminus of the Papillomavirus E1 Helicase Domain Controls E1 Helicase Assembly
Authors: Schuck Stephen , Stenlund Arne 
Published: November 2014

ABSTRACT
Viruses frequently combine multiple activities into one polypeptide to conserve coding capacity. This strategy creates regulatory challenges to ascertain that the combined activities are compatible and do not interfere with each other. The papillomavirus E1 protein, as many other helicases, has the intrinsic ability to form hexamers and double hexamers (DH) that serve as the replicative DNA helicase. However, E1 also has the more unusual ability to generate local melting by forming a double trimer (DT) complex that can untwist the double-stranded origin of DNA replication (ori) DNA in preparation for DH formation. Here we describe a switching mechanism that allows the papillomavirus E1 protein to form these two different kinds of oligomers and to transition between them. We show that a conserved regulatory module attached to the E1 helicase domain blocks hexamer and DH formation and promotes DT formation. In the presence of the appropriate trigger, the inhibitory effect of the regulatory module is relieved and the transition to DH formation can occur.

IMPORTANCE
This study provides a mechanistic understanding into how a multifunctional viral polypeptide can provide different, seemingly incompatible activities. A conserved regulatory sequence module attached to the AAA
+
helicase domain in the papillomavirus E1 protein allows the formation of different oligomers with different biochemical activities.
Class Switch Recombination and Somatic Hypermutation of Virus-Neutralizing Antibodies Are Not Essential for Control of Friend Retrovirus Infection
Authors: Kato Maiko , Tsuji-Kawahara Sachiyo , Kawasaki Yuri , Kinoshita Saori , Chikaishi Tomomi , Takamura Shiki , Fujisawa Makoto , Kawada Akira , Miyazawa Masaaki 
Published: November 2014

ABSTRACTToll-like receptor 7 and Myd88 are required for antiretroviral antibody and germinal center responses, but whether somatic hypermutation and class-switch recombination are required for antiretroviral immunity has not been examined. Mice deficient in activation-induced cytidine deaminase (AID) resisted Friend virus infection, produced virus-neutralizing antibodies, and controlled viremia. Passive transfer demonstrated that immune IgM from AID-deficient mice contributes to Friend virus control in the presence of virus-specific CD4+T cells.
Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus
Authors: Kint Joeri , Fernandez-Gutierrez Marcela , Maier Helena J. , Britton Paul , Langereis Martijn A. , Koumans Joseph , Wiegertjes Geert F. , Forlenza Maria 
Published: November 2014

ABSTRACT

Coronaviruses from both the
Alphacoronavirus
and
Betacoronavirus
genera interfere with the type I interferon (IFN) response in various ways, ensuring the limited activation of the IFN response in most cell types. Of the gammacoronaviruses that mainly infect birds, little is known about the activation of the host immune response. We show that the prototypical
Gammacoronavirus
, infectious bronchitis virus (IBV), induces a delayed activation of the IFN response in primary renal cells, tracheal epithelial cells, and a chicken cell line. In fact,
Ifnβ
expression is delayed with respect to the peak of viral replication and the accompanying accumulation of double-stranded RNA (dsRNA). In addition, we demonstrate that MDA5 is the primary sensor for
Gammacoronavirus
infections in chicken cells. Furthermore, we provide evidence that accessory proteins 3a and 3b of IBV modulate the response at the transcriptional and translational levels. Finally, we show that, despite the lack of activation of the IFN response during the early phase of IBV infection, the signaling of nonself dsRNA through both MDA5 and TLR3 remains intact in IBV-infected cells. Taken together, this study provides the first comprehensive analysis of host-virus interactions of a
Gammacoronavirus
with avian innate immune responses.

IMPORTANCE
Our results demonstrate that IBV has evolved multiple strategies to avoid the activation of the type I interferon response. Taken together, the present study closes a gap in the understanding of host-IBV interaction and paves the way for further characterization of the mechanisms underlying immune evasion strategies as well as the pathogenesis of gammacoronaviruses.
Replication of Boid Inclusion Body Disease-Associated Arenaviruses Is Temperature Sensitive in both Boid and Mammalian Cells
Authors: Hepojoki Jussi , Kipar Anja , Korzyukov Yegor , Bell-Sakyi Lesley , Vapalahti Olli , Hetzel Udo 
Published: November 2014

ABSTRACT

Boid inclusion body disease (BIDB) is a fatal disease of boid snakes, the etiology of which has only recently been revealed following the identification of several novel arenaviruses in diseased snakes. BIBD-associated arenaviruses (BIBDAV) are genetically divergent from the classical Old and New World arenaviruses and also differ substantially from each other. Even though there is convincing evidence that BIBDAV are indeed the etiological agent of BIBD, the BIBDAV reservoir hosts—if any exist besides boid snakes themselves—are not yet known. In this report, we use University of Helsinki virus (UHV; a virus that we isolated from a
Boa constrictor
with BIBD) to show that BIBDAV can also replicate effectively in mammalian cells, including human cells, provided they are cultured at 30°C. The infection induces the formation of cytoplasmic inclusion bodies (IB), comprised mainly of viral nucleoprotein (NP), similar to those observed in BIBD and in boid cell cultures. Transferring infected cells from 30°C to 37°C ambient temperature resulted in progressive declines in IB formation and in the amounts of viral NP and RNA, suggesting that BIBDAV growth is limited at 37°C. These observations indirectly indicate that IB formation is linked to viral replication. In addition to mammalian and reptilian cells, UHV infected arthropod (tick) cells when grown at 30°C. Even though our findings suggest that BIBDAV have a high potential to cross the species barrier, their inefficient growth at mammalian body temperatures indicates that the reservoir hosts of BIBDAV are likely species with a lower body temperature, such as snakes.

IMPORTANCE
The newly discovered boid inclusion body disease-associated arenaviruses (BIBDAV) of reptiles have drastically altered the phylogeny of the family
Arenavirus
. Prior to their discovery, known arenaviruses were considered mainly rodent-borne viruses, with each arenavirus species having its own reservoir host. BIBDAV have so far been demonstrated in captive boid snakes, but their possible reservoir host(s) have not yet been identified. Here we show, using University of Helsinki virus as a model, that these viruses are able to infect mammalian (including human) and arthropod cells. Our results provide
in vitro
proof of the considerable ability of arenaviruses to cross species barriers. However, our data indicate that BIBDAV growth occurs at 30°C but is inhibited at 37°C, implying that crossing of the species barrier would be hindered by the body temperature of mammalian species.