bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequences of Three Turkey Orthoreovirus Strains Isolated in Hungary
Authors: Dandár Eszter , Fehér Enikő , Bálint Ádám , Kisfali Péter , Melegh Béla , Mató Tamás , Kecskeméti Sándor , Palya Vilmos , Bányai Krisztián , Farkas Szilvia L. 
Published: November 2015

ABSTRACT
We have investigated the genomic properties of three turkey reovirus strains—19831M09, D1246, and D1104—isolated in Hungary in 2009. Sequence identity values and phylogenetic calculations indicated genetic conservativeness among the studied Hungarian strains and a close relationship with strains isolated in the United States.
Draft Genome Sequence of
Pseudoalteromonas
sp. Strain R3, a Red-Pigmented
l
-Amino Acid Oxidase-Producing Bacterium
Authors: Yu Zhiliang , Zhao Minyan , Qiu Juanping 
Published: November 2015

ABSTRACT

Here, we report a draft 5.58-Mb genome sequence of
Pseudoalteromonas
sp. strain R3, isolated from an intertidal-zone sludge sample, which has
l
-amino acid oxidase activity. The genomics information of this strain will facilitate the study of
l
-amino acid oxidase, quorum sensing, and the relationship of the two.
Complete Genome Sequence of Mayaro Virus Imported from the Amazon Basin to São Paulo State, Brazil
Authors: Mota Mânlio Tasso Oliveira , Vedovello Danila , Estofolete Cassia , Malossi Camila Dantas , Araújo João Pessoa , Nogueira Maurício Lacerda 
Published: November 2015

ABSTRACT
Mayaro (MAYV) is a neglected arbovirus from the tropical Americas. Here, we report the complete genome of an MAYV isolate from a patient returning from the Amazon basin and complaining of arthralgia, high fever, and headache, who was attended at an emergency service of São José do Rio Preto, São Paulo state, Brazil.
Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the
Chloroflexi
Class
Ardenticatenia
Authors: Hemp James , Ward Lewis M. , Pace Laura A. , Fischer Woodward W. 
Published: November 2015

ABSTRACT

We report here the draft genome sequence of
Ardenticatena maritima
110S, the first sequenced member of class
Ardenticatenia
of the phylum
Chloroflexi
. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase.
Draft Genome of
Thermanaerothrix daxensis
GNS-1, a Thermophilic Facultative Anaerobe from the
Chloroflexi
Class
Anaerolineae
Authors: Pace Laura A. , Hemp James , Ward Lewis M. , Fischer Woodward W. 
Published: November 2015

ABSTRACT

We present the draft genome of
Thermanaerothrix daxensis
GNS-1, a thermophilic member of the
Chloroflexi
phylum. This organism was initially characterized as a nonmotile, strictly anaerobic fermenter; however, genome analysis demonstrates that it encodes genes for a flagellum and multiple pathways for aerobic and anaerobic respiration.
Draft Genome Sequence of Prosthecomicrobium hirschii ATCC 27832
T
Authors: Daniel Jeremy J. , Givan Scott A. , Brun Yves V. , Brown Pamela J. B. 
Published: November 2015

ABSTRACT

We report the draft genome sequence of
Prosthecomicrobium hirschii
ATCC 27832
T
, an alphaproteobacterium with remarkable cellular morphologies. The chromosome comprises 6,484,983 bp in six scaffolds with a G+C content of 69%, and 6,066 potential coding sequences.
Complete Genome Sequence of Campylobacter jejuni RM1285, a Rod-Shaped Morphological Variant
Authors: Gunther Nereus W. , Bono James L. , Needleman David S. 
Published: November 2015

ABSTRACT

Campylobacter jejuni
is a spiral shaped Gram-negative food-borne bacterial pathogen of humans found on poultry products. Strain RM1285 is a rod-shaped variant of this species. The genome of RM1285 was determined to be 1,635,803 bp, with a G+C content of 30.5%.
Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp.
enterica
Serovar Thompson Associated with Cilantro
Authors: Parker Craig T. , Huynh Steven , Gorski Lisa , Cooper Kerry K. , Miller William G. 
Published: November 2015

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986 (CADPH-99A2345) are associated with a 1999 outbreak in contaminated cilantro. We report here the complete genome sequences and annotation of these two
S
. Thompson strains. These genomes are distinct and provide additional data for our understanding of
S. enterica
.
Complete Genome Sequence of Caulobacter crescentus Podophage Percy
Authors: Lerma Roxann A. , Tidwell T. J. , Cahill Jesse L. , Rasche Eric S. , Kuty Everett Gabriel F. 
Published: November 2015

ABSTRACT

Podophage Percy infects
Caulobacter crescentus
, a Gram-negative bacterium that divides asymmetrically and is a commonly used model organism to study the cell cycle, asymmetric cell division, and cell differentiation. Here, we announce the sequence and annotated complete genome of the phiKMV-like podophage Percy and note its prominent features.
Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme
Authors: Mussa Huda J. , VanWagoner Timothy M. , Morton Daniel J. , Seale Thomas W. , Whitby Paul W. , Stull Terrence L. 
Published: November 2015

ABSTRACT

Nontypeable
Haemophilus influenzae
is an important cause of human disease. Strains were selected for genome sequencing to represent the breadth of nontypeable strains within the species, as previously defined by the electrophoretic mobility of 16 metabolic enzymes.
Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum
Firmicutes
)
Authors: Lee Ruth D. , Jospin Guillaume , Lang Jenna M. , Eisen Jonathan A. , Coil David A. 
Published: November 2015

ABSTRACT

Here, we present the draft genome sequence of
Bacillus vietnamensis
UCD-SED5 (phylum
Firmicutes
). This strain was isolated from sediment surrounding
Zostera marina
roots near the UC Davis Bodega Marine Laboratory (Bodega, Bay, California) and represents the second genome of this species. The assembly consists of 4,325,707 bp, in 108 contigs.
Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland
Authors: Wels Michiel , Serrano L. Mariela , Eibrink Beerd-Jan , Backus Lennart , Bongers Roger S. , Vriesendorp Bastienne , Siezen Roland J. , van Hijum Sacha A. F. T. , Meijer Wilco C. 
Published: November 2015

ABSTRACT

The lactic acid bacterium
Streptococcus thermophilus
is widely used for the fermentation of dairy products. Here, we present the draft genome sequence of
S. thermophilus
C106 isolated from an artisanal cheese produced in the countryside of Ireland.
Complete Genome Sequences of Three Clinical Isolates of Dengue Virus Serotype 1 from South Korean Travelers
Authors: Go Yun Young , Jung Eunhye , Jeong Young Eui , Balasuriya Udeni B. R. 
Published: November 2015

ABSTRACT
In this study, we report the complete genome sequences of three clinical isolates of dengue virus serotype 1 isolated from South Korean travelers returning from different countries in Southeast Asia. The nucleotide sequence identities ranged from 91.5 to 92.2%, while the amino acid sequence identities ranged from 97.5 to 97.9% among the three clinical isolates.
Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic
ptxP3
Lineage
Authors: Bart Marieke J. , van der Heide Han G. J. , Zeddeman Anne , Heuvelman Kees , van Gent Marjolein , Mooi Frits R. 
Published: November 2015

ABSTRACT

Pathogen adaptation has contributed to the resurgence of pertussis. To facilitate our understanding of this adaptation we report here 11 completely closed and annotated
Bordetella pertussis
genomes representing the pandemic
ptxP3
lineage. Our analyses included six strains which do not produce the vaccine components pertactin and/or filamentous hemagglutinin.
Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (
Echinacea purpurea
) Witches’ Broom Disease in Taiwan
Authors: Chang Shu-Heng , Cho Shu-Ting , Chen Chung-Li , Yang Jun-Yi , Kuo Chih-Horng 
Published: November 2015

ABSTRACT

The bacterial genus “
Candidatus
Phytoplasma” contains a group of insect-transmitted plant pathogens in the class
Mollicutes
. Here, we report a draft genome assembly and annotation of strain NCHU2014, which belongs to the 16SrII-A subgroup within this genus and is associated with purple coneflower witches’ broom disease in Taiwan.
Comparative Evaluation of Inoculation of Urine Samples with the Copan WASP and BD Kiestra InoqulA Instruments
Authors: Iversen Jesper , Stendal Gitta , Gerdes Cecilie M. , Meyer Christian H. , Andersen Christian Østergaard , Frimodt-Møller Niels 
Published: November 2015

ABSTRACTThis study evaluated the quantitative results from and quality of the inoculation patterns of urine specimens produced by two automated instruments, the Copan WASP and the BD InoqulA. Five hundred twenty-six urine samples submitted in 10-ml canisters containing boric acid were processed within 30 min on an InoqulA instrument plating 10 μl of specimen, and on two WASP instruments, one plating 1 μl of specimen (WASP-1), and the second plating 10 μl of WASP (WASP-10). All samples were incubated, analyzed, and digitally imaged using the BD Kiestra total lab automation system. The results were evaluated using a quantitative protocol and assessed for the presence or absence of ≥5 distinct colonies. Separate studies were conducted using quality control (QC) organisms to determine the relative accuracy of WASP-1, WASP-10, and InoqulA instruments compared to the results obtained with a calibrated pipette. The results with QC organisms were calculated as the ratios of the counts of the automated instruments divided by the counts for the calibrated pipette (the gold standard method). The ratios for the InoqulA instrument were closest to 1.0, with the smallest standard deviations indicating that compared to a calibrated pipette, the InoqulA results were more accurate than those with the WASP instrument. For clinical samples, the WASP instruments produced higher colony counts and more commensals than the InoqulA instrument, with differences most notable for WASP-1. The InoqulA instrument was significantly better at dispersing organisms with counts of ≥105bacteria/ml of urine than were the WASP-1 and WASP-10 instruments (P< 0.05). Our results suggest that the InoqulA quantitative results are more accurate than the WASP results, and, moreover, the number of isolated colonies produced by the InoqulA instrument was significantly greater than that produced by the WASP instrument.
Detection of Carbapenemase Production in a Collection of Enterobacteriaceae with Characterized Resistance Mechanisms from Clinical and Environmental Origins by Use of Both Carba NP and Blue-Carba Tests
Authors: García-Fernández Sergio , Morosini María-Isabel , Gijón Desirèe , Beatobe Lorena , Ruiz-Garbajosa Patricia , Domínguez Lucas , Cantón Rafael , Valverde Aránzazu 
Published: November 2015

ABSTRACT

Rapid-screening methods to confirm the presence of resistance mechanisms in multidrug-resistant bacteria are currently recommended. Carba NP and Blue-Carba tests were evaluated in carbapenemase-producing
Enterobacteriaceae
from hospital (
n
= 102) and environmental (
n
= 57) origins for detecting the different molecular classes among them. Both methods showed to be fast and cost-effective, with high sensitivity (98% to 100%) and specificity (100%), and may be easily introduced in the routine laboratory.
Evaluation of Oxacillin and Cefoxitin Disk and MIC Breakpoints for Prediction of Methicillin Resistance in Human and Veterinary Isolates of Staphylococcus intermedius Group
Authors: Wu M. T. , Burnham C.-A. D. , Westblade L. F. , Dien Bard J. , Lawhon S. D. , Wallace M. A. , Stanley T. , Burd E. , Hindler J. , Humphries R. M. 
Published: November 2015

ABSTRACTStaphylococcuspseudintermediusis a coagulase-positive species that colonizes the nares and anal mucosa of healthy dogs and cats. Human infections withS. pseudintermediusrange in severity from bite wounds and rhinosinusitis to endocarditis; historically, these infections were thought to be uncommon, but new laboratory methods suggest that their true incidence is underreported. Oxacillin and cefoxitin disk and MIC tests were evaluated for the detection ofmecA- ormecC-mediated methicillin resistance in 115 human and animal isolates of theStaphylococcus intermediusgroup (SIG), including 111Staphylococcuspseudintermediusand 4Staphylococcusdelphiniisolates, 37 of which weremecApositive. The disk and MIC breakpoints evaluated included the Clinical and Laboratory Standards Institute (CLSI) M100-S25Staphylococcus aureus/Staphylococcuslugdunensisoxacillin MIC breakpoints and cefoxitin disk and MIC breakpoints, the CLSI M100-S25 coagulase-negativeStaphylococcus(CoNS) oxacillin MIC breakpoint and cefoxitin disk breakpoint, the CLSI VET01-S2S. pseudintermediusoxacillin MIC and disk breakpoints, and the European Committee on Antimicrobial Susceptibility Testing (EUCAST)S. pseudintermediuscefoxitin disk breakpoint. The oxacillin results interpreted by the VET01-S2 (disk and MIC) and M100-S25 CoNS (MIC) breakpoints agreed with the results ofmecA/mecCPCR for all isolates, with the exception of one false-resistant result (1.3% ofmecA/mecCPCR-negative isolates). In contrast, cefoxitin tests performed poorly, ranging from 3 to 89% false susceptibility (very major errors) and 0 to 48% false resistance (major errors). BD Phoenix, bioMérieux Vitek 2, and Beckman Coulter MicroScan commercial automated susceptibility test panel oxacillin MIC results were also evaluated and demonstrated >95% categorical agreement withmecA/mecCPCR results if interpreted by using the M100-S25 CoNS breakpoint. The Alere penicillin-binding protein 2a test accurately detected allmecA-positive isolates, although for four isolates, cefoxitin induction was required prior to testing. These data demonstrate that the cefoxitin surrogate test does not reliably detect the presence ofmecAinS. pseudintermediusisolates and that laboratories should perform oxacillin disk or MIC tests of these isolates when they are encountered.
Directed Molecular Evolution of an Engineered Gammaretroviral Envelope Protein with Dual Receptor Use Shows Stable Maintenance of Both Receptor Specificities
Authors: Friis Kristina Pagh , Iturrioz Xavier , Thomsen Jonas , Alvear-Perez Rodrigo , Bahrami Shervin , Llorens-Cortes Catherine , Pedersen Finn Skou 
Published: November 2015

ABSTRACT
We have previously reported the construction of a murine leukemia virus-based replication-competent gammaretrovirus (SL3-AP) capable of utilizing the human G protein-coupled receptor APJ (hAPJ) as its entry receptor and its natural receptor, the murine Xpr1 receptor, with equal affinities. The apelin receptor has previously been shown to function as a coreceptor for HIV-1, and thus, adaptation of the viral vector to this receptor is of significant interest. Here, we report the molecular evolution of the SL3-AP envelope protein when the virus is cultured in cells harboring either the Xpr1 or the hAPJ receptor. Interestingly, the dual receptor affinity is maintained even after 10 passages in these cells. At the same time, the chimeric viral envelope protein evolves in a distinct pattern in the apelin cassette when passaged on D17 cells expressing hAPJ in three separate molecular evolution studies. This pattern reflects selection for reduced ligand-receptor interaction and is compatible with a model in which SL3-AP has evolved not to activate hAPJ receptor internalization.

IMPORTANCE
Few successful examples of engineered retargeting of a retroviral vector exist. The engineered SL3-AP envelope is capable of utilizing either the murine Xpr1 or the human APJ receptor for entry. In addition, SL3-AP is the first example of an engineered retrovirus retaining its dual tropism after several rounds of passaging on cells expressing only one of its receptors. We demonstrate that the virus evolves toward reduced ligand-receptor affinity, which sheds new light on virus adaptation. We provide indirect evidence that such reduced affinity leads to reduced receptor internalization and propose a novel model in which too rapid receptor internalization may decrease virus entry.
PACT- and RIG-I-Dependent Activation of Type I Interferon Production by a Defective Interfering RNA Derived from Measles Virus Vaccine
Authors: Ho Ting-Hin , Kew Chun , Lui Pak-Yin , Chan Chi-Ping , Satoh Takashi , Akira Shizuo , Jin Dong-Yan , Kok Kin-Hang 
Published: November 2015

ABSTRACT
The live attenuated measles virus vaccine is highly immunostimulatory. Identification and characterization of its components that activate the innate immune response might provide new strategies and agents for the rational design and development of chemically defined adjuvants. In this study, we report on the activation of type I interferon (IFN) production by a defective interfering (DI) RNA isolated from the Hu-191 vaccine strain of measles virus. We found that the Hu-191 virus induced IFN-β much more potently than the Edmonston strain. In the search for IFN-inducing species in Hu-191, we identified a DI RNA specifically expressed by this strain. This DI RNA, which was of the copy-back type, was predicted to fold into a hairpin structure with a long double-stranded stem region of 206 bp, and it potently induced the expression of IFN-β. Its IFN-β-inducing activity was further enhanced when both cytoplasmic RNA sensor RIG-I and its partner, PACT, were overexpressed. On the contrary, this activity was abrogated in cells deficient in PACT or RIG-I. The DI RNA was found to be associated with PACT in infected cells. In addition, both the 5′-di/triphosphate end and the double-stranded stem region on the DI RNA were essential for its activation of PACT and RIG-I. Taken together, our findings support a model in which a viral DI RNA is sensed by PACT and RIG-I to initiate an innate antiviral response. Our work might also provide a foundation for identifying physiological PACT ligands and developing novel adjuvants or antivirals.

IMPORTANCE
The live attenuated measles virus vaccine is one of the most successful human vaccines and has largely contained the devastating impact of a highly contagious virus. Identifying the components in this vaccine that stimulate the host immune response and understanding their mechanism of action might help to design and develop better adjuvants, vaccines, antivirals, and immunotherapeutic agents. We identified and characterized a defective interfering RNA from the Hu-191 vaccine strain of measles virus which has safely been used in millions of people for many years. We further demonstrated that this RNA potently induces an antiviral immune response through cellular sensors of viral RNA known as PACT and RIG-I. Similar types of viral RNA that bind with and activate PACT and RIG-I might retain the immunostimulatory property of measles virus vaccines but would not induce adaptive immunity. They are potentially useful as chemically defined vaccine adjuvants, antivirals, and immunostimulatory agents.
Persistent Simian Immunodeficiency Virus Infection Drives Differentiation, Aberrant Accumulation, and Latent Infection of Germinal Center Follicular T Helper Cells
Authors: Xu Huanbin , Wang Xiaolei , Malam Naomi , Aye Pyone P. , Alvarez Xavier , Lackner Andrew A. , Veazey Ronald S. 
Published: November 2015

ABSTRACT

CD4
+
follicular T helper (Tfh) cells play a prominent role in humoral immune responses, but the mechanisms of their accumulation and infection in AIDS remain unclear. Here we found that germinal center (GC) Tfh cells, defined here as CXCR5
+
PD-1
HIGH
CD4
+
T cells, do not express the HIV coreceptor CCR5 yet serve as a latent reservoir in GCs. With disease progression, an expansion of GC Tfh cells is accompanied by increases in dysfunctional CD8
+
T cells. In contrast, Tfh precursor (CXCR5
−
CD4
+
T) cells in lymph nodes do express CCR5 and differentiate into GC Tfh cells following interleukin-6 (IL-6) and IL-21 stimulation, and viral DNA is detectable in fully differentiated GC Tfh cells
ex vivo
. This suggests that SIV-infected GC Tfh cells may be derived from Tfh precursor cell subsets that become infected in marginal zones and then migrate into GCs as fully mature GC Tfh cells that serve as persistent virus reservoirs. These findings suggest that viral persistence in lymph nodes drives compensatory differentiation, aberrant accumulation, and latent infection of GC Tfh cells, resulting in marked impairment of humoral immune responses.

IMPORTANCE
Generation of antibodies that can effectively eliminate viruses requires interactions of B cells with highly specialized T cells in GCs of lymphoid tissues called follicular T helper cells. Here we show that in simian immunodeficiency virus infection, these cells are initially infected in a precursor stage that leads to alterations in their homing, accumulation, and function that may be responsible for the inability of human immunodeficiency virus-infected patients to generate effective antibody responses.