bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a Fiber-Modified Adenovirus Vector Vaccine against Foot-and-Mouth Disease in Cattle
Authors: Medina Gisselle N. , Montiel Nestor , Diaz-San Segundo Fayna , Sturza Diego , Ramirez-Medina Elizabeth , Grubman Marvin J. , de los Santos Teresa 
Published: November 2015

ABSTRACT

Novel vaccination approaches against foot-and-mouth disease (FMD) include the use of replication-defective human adenovirus type 5 (Ad5) vectors that contain the capsid-encoding regions of FMD virus (FMDV). Ad5 containing serotype A24 capsid sequences (Ad5.A24) has proved to be effective as a vaccine against FMD in livestock species. However, Ad5-vectored FMDV serotype O1 Campos vaccine (Ad5.O1C.2B) provides only partial protection of cattle against homologous challenge. It has been reported that a fiber-modified Ad5 vector expressing Arg-Gly-Asp (RGD) enhances transduction of antigen-presenting cells (APC) in mice. In the current study, we assessed the efficacy of a fiber-modified Ad5 (Adt.O1C.2B.RGD) in cattle. Expression of FMDV capsid proteins was superior in cultured cells infected with the RGD-modified vector. Furthermore, transgene expression of Adt.O1C.2B.RGD was enhanced in cell lines that constitutively express integrin α
v
β6, a known receptor for FMDV. In contrast, capsid expression in cattle-derived enriched APC populations was not enhanced by infection with this vector. Our data showed that vaccination with the two vectors yielded similar levels of protection against FMD in cattle. Although none of the vaccinated animals had detectable viremia, FMDV RNA was detected in serum samples from animals with clinical signs. Interestingly, CD4
+
and CD8
+
gamma interferon (IFN-γ)
+
cell responses were detected at significantly higher levels in animals vaccinated with Adt.O1C.2B.RGD than in animals vaccinated with Ad5.O1C.2B. Our results suggest that inclusion of an RGD motif in the fiber of Ad5-vectored FMD vaccine improves transgene delivery and cell-mediated immunity but does not significantly enhance vaccine performance in cattle.
Draft Genome Sequence of the Ant-Associated Fungus
Phialophora attae
(CBS 131958)
Authors: Moreno Leandro F. , Stielow J. Benjamin , de Vries Michel , Weiss Vinicius A. , Vicente Vania A. , de Hoog Sybren 
Published: November 2015

ABSTRACT

The black yeast
Phialophora attae
was isolated from the cuticle of tropical ant gynes. The ant-fungus association is sustained due to symbiotic evolutionary adaptations that allow fungal assimilation and tolerance of toxic compounds produced by the ant. The genome sequence of the first ant-associated fungus,
P. attae
, is presented here.
Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India
Authors: Saxena Rituja , Chaudhary Nikhil , Dhakan Darshan B. , Sharma Vineet K. 
Published: November 2015

ABSTRACT

This paper reports the draft genome sequence of the proteobacterium
Gulbenkiania mobilis
strain MB1, a sulfur-metabolizing thermophile isolated from a hot spring located in Pachmarhi, India. This study reports the first draft genome sequence of any species from the genus
Gulbenkiania
.
Genome Sequence of Streptococcus phocae subsp.
phocae
Strain ATCC 51973
T
Isolated from a Harbor Seal (
Phoca vitulina
)
Authors: Avendaño-Herrera Ruben , Poblete-Morales Matías 
Published: November 2015

ABSTRACT

Streptococcus phocae
subsp.
phocae
is a pathogen that affects different pinniped and mammalian species. This announcement reports the genome sequence of the type strain ATCC 51973 isolated in Norway from clinical specimens of harbor seal (
Phoca vitulina
), revealing interesting genes related to possible virulence factors.
Draft Genome Sequences of Two South African Bacillus anthracis Strains
Authors: Lekota Kgaugelo E. , Mafofo Joseph , Madoroba Evelyn , Rees Jasper , van Heerden Henriette , Muchadeyi Farai C. 
Published: November 2015

ABSTRACT

Bacillus anthracis
is a Gram-positive bacterium that causes anthrax, mainly in herbivores through exotoxins and capsule produced on plasmids, pXO1 and pXO2. This paper compares the whole-genome sequences of two
B. anthracis
strains from an endemic region and a sporadic outbreak in South Africa. Sequencing was done using next-generation sequencing technologies.
Draft Genome Sequence of the Serratia rubidaea CIP 103234
T
Reference Strain, a Human-Opportunistic Pathogen
Authors: Bonnin Rémy A. , Girlich Delphine , Imanci Dilek , Dortet Laurent , Naas Thierry 
Published: November 2015

ABSTRACT

We provide here the first genome sequence of a
Serratia rubidaea
isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the
Serratia
genus.
Draft Genome Sequences of Two Isolates of the Plant-Pathogenic Fungus
Neonectria ditissima
That Differ in Virulence
Authors: Deng Cecilia H. , Scheper Reiny W. A. , Thrimawithana Amali H. , Bowen Joanna K. 
Published: November 2015

ABSTRACT

Neonectria ditissima
is the causal agent of apple canker. Here, we present the draft genome sequences of two isolates of
N. ditissima
that differ in virulence. Comparative genomics will enable pathogenicity determinants to be identified in this plant-pathogenic fungus.
Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the
Chloroflexi
Class
Anaerolineae
Authors: Hemp James , Ward Lewis M. , Pace Laura A. , Fischer Woodward W. 
Published: November 2015

ABSTRACT

We report the draft genome sequence of
Ornatilinea apprima
P3M-1, a strictly anaerobic member of the
Chloroflexi
class
Anaerolineae
. This genome provides insight into the diversity of metabolism within the
Anaerolineae
, and the evolution of respiration within the
Chloroflexi
.
Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the
Chloroflexi
Class
Anaerolineae
Authors: Ward Lewis M. , Hemp James , Pace Laura A. , Fischer Woodward W. 
Published: November 2015

ABSTRACT

We present the draft genome sequence of
Leptolinea tardivitalis
YMTK-2, a member of the
Chloroflexi
phylum. This organism was initially characterized as a strictly anaerobic nonmotile fermenter; however, genome analysis demonstrates that it encodes for a flagella and might be capable of aerobic respiration.
Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the
Chloroflexi
Class
Anaerolineae
Authors: Hemp James , Ward Lewis M. , Pace Laura A. , Fischer Woodward W. 
Published: November 2015

ABSTRACT

We report the draft genome sequence of
Levilinea saccharolytica
KIBI-1
,
a facultative anaerobic member of the
Chloroflexi
class
Anaerolineae
. While
L. saccharolytica
was characterized as an obligate anaerobe, genome analysis provides evidence for the presence of both aerobic respiration and partial denitrification pathways.
Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft
Authors: Coil David A. , Benardini James N. , Eisen Jonathan A. 
Published: November 2015

ABSTRACT

Here, we present the draft genome of
Bacillus safensis
JPL-MERTA-8-2, a strain found in a spacecraft assembly cleanroom before launch of the Mars Exploration Rovers. The assembly contains 3,671,133 bp in 14 contigs.
Draft Genome Sequence of Amikacin- and Kanamycin-Resistant Mycobacterium tuberculosis MT433 without
rrs
and
eis
Mutations
Authors: Sowajassatakul Angkanang , Coker Olabisi O. , Prammananan Therdsak , Chaiprasert Angkana , Phunpruch Saranya 
Published: November 2015

ABSTRACT

We announce the draft genome sequence of amikacin- and kanamycin-resistant
Mycobacterium tuberculosis
MT433, which has been previously described as the strain carrying an unknown resistance mechanism.
First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327)
Authors: Ehsani Elham , Jauregui Ruy , Geffers Robert , Jarek Michael , Boon Nico , Pieper Dietmar H. , Vilchez-Vargas Ramiro 
Published: November 2015

ABSTRACT

We report the draft genome sequence of the
Acidovorax caeni
type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to
Acidovorax caeni
strain R-24608 is
Acidovorax
sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.
Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain E19, Isolated from a Horse in Chile
Authors: Cavalcante Ana Lídia Q. , Dias Larissa M. , Alves Jorianne T. C. , Veras Adonney A. O. , Guimarães Luis C. , Rocha Flávia S. , Gala-García Alfonso , Retamal Patricio , Ramos Rommel T. J. , Azevedo Vasco , Silva Artur , Carneiro Adriana R. 
Published: November 2015

ABSTRACT

Corynebacterium pseudotuberculosis
is related to several diseases infecting horses and small ruminants, causing economic losses to agribusiness. Here, we present the genome sequence of
C. pseudotuberculosis
strain E19. The genome includes one circular chromosome 2,367,956 bp (52.1% G+C content), with 2,112 genes predicted, 12 rRNAs, and 48 tRNAs.
Genome Sequence of the Atypical Symbiotic
Frankia
R43 Strain, a Nitrogen-Fixing and Hydrogen-Producing Actinobacterium
Authors: Pujic Petar , Bolotin Alexander , Fournier Pascale , Sorokin Alexei , Lapidus Alla , Richau Kerstin H. , Briolay Jerome , Mebarki Farida , Normand Philippe , Sellstedt Anita 
Published: November 2015

ABSTRACT

Frankia
strain R43 is a nitrogen-fixing and hydrogen-producing symbiotic actinobacterium that was isolated from nodules of
Casuarina cunninghamiana
but infects only
Elaeagnaceae
. This communication reports the genome of the strain R43 and provides insights into the microbe genomics and physiological potentials.
Complete Genome Sequences of Three Laboratory Strains of Dengue Virus (Serotypes 2, 3, and 4) Available in South Korea
Authors: Go Yun Young , Jung Eunhye , Balasuriya Udeni B. R. 
Published: November 2015

ABSTRACT

Here, we report the complete genome sequences of three laboratory strains of dengue virus serotype-2 (DENV-2/KBPV-VR-29), -3 (DENV-3/KBPV-VR-30), and -4 (DENV-4/KBPV-VR-31) obtained from the Korea Bank for Pathogenic Viruses (
http://kbpv.knrrc.or.kr
). The complete genetic information presented in this study on commonly used DENV laboratory strains provides valuable information for future studies.
Performance of the Cryptococcal Antigen Lateral Flow Assay in Non-HIV-Related Cryptococcosis
Authors: Jitmuang Anupop , Panackal Anil A. , Williamson Peter R. , Bennett John E. , Dekker John P. , Zelazny Adrian M. 
Published: November 2015

ABSTRACT
The cryptococcal antigen lateral flow assay (CrAg LFA) was evaluated for the diagnosis of cryptococcosis in HIV-negative patients. The sensitivity was excellent, suggesting that this assay can replace conventional testing based on latex agglutination (LA). CrAg LFA and LA titers were correlated but were not directly comparable, with implications for conversion between assays.
Epidemiologic and Genotypic Review of Carbapenemase-Producing Organisms in British Columbia, Canada, between 2008 and 2014
Authors: Sekirov Inna , Croxen Matthew A. , Ng Corrinne , Azana Robert , Chang Yin , Mataseje Laura , Boyd David , Mangat Chand , Mack Benjamin , Tadros Manal , Brodkin Elizabeth , Kibsey Pamela , Stefanovic Aleksandra , Champagne Sylvie , Mulvey Michael R. , Hoang Linda M. N. 
Published: November 2015

ABSTRACT

Carbapenemase-producing organisms (CPOs) are a serious emerging problem for health care facilities worldwide. Owing to their resistance to most antimicrobial therapies, CPOs are difficult to treat and pose a challenge for infection prevention and control. Since 2010, lab-based surveillance for CPOs and PCR-based testing were implemented in British Columbia (BC), Canada. A review of CPOs in BC from 2008 to March 2014 was done to characterize the resistance mechanisms and possible clonal strain transmission and to compare pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and plasmid restriction fragment length polymorphism (RFLP) as molecular typing tools. During this study period, a total of 177 CPO cases were identified. Patient demographics and travel history were reviewed, and a descriptive analysis was carried out. PFGE profiles, MLST, and plasmid RFLP analysis for a subset of
Escherichia coli
,
Klebsiella pneumoniae
, and
Enterobacter
species isolates were obtained and analyzed. Our findings demonstrate that CPOs have been increasing in number in BC over time, from 1 isolate/year retrospectively identified in 2008 and 2009 to 82 isolates in 2013 and 30 isolates in the first quarter of 2014. Overall,
K. pneumoniae
isolates lack clonality, although some seemingly related clusters have been found. Plasmid analysis showed evidence of the spread of plasmids carrying carbapenemase-encoding genes between the examined isolates. Analysis of
Enterobacter cloacae
isolates revealed a more clonal nature of these CPOs in BC. The presence of related clusters provides evidence of interpatient organism transmission both within and between institutions. Although in our study, NDM-harboring
E. cloacae
isolates appeared to spread clonally, the spread of carbapenem resistance in
K. pneumoniae
seems to be plasmid mediated.
Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes
Authors: Kwong Jason C. , Mercoulia Karolina , Tomita Takehiro , Easton Marion , Li Hua Y. , Bulach Dieter M. , Stinear Timothy P. , Seemann Torsten , Howden Benjamin P. 
Published: November 2015

ABSTRACT

Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of
Listeria monocytogenes
has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423
L. monocytogenes
isolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred
in silico
from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97
L. monocytogenes
isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective
L. monocytogenes
surveillance and investigated for other pathogens relevant to public health.
Agreement of Direct Antifungal Susceptibility Testing from Positive Blood Culture Bottles with the Conventional Method for Candida Species
Authors: Jabeen Kauser , Kumar Haresh , Farooqi Joveria , Mehboob Raunaq , Brandt Mary E. , Zafar Afia 
Published: November 2015

ABSTRACT

Early availability of antifungal susceptibilities can ensure timely institution of targeted therapy in candidemia, which can improve patient outcomes. This study prospectively determines the agreement between the results of direct testing of antifungal susceptibilities from blood culture bottles by disk diffusion and Etest and the results of standardized susceptibility testing methods; direct testing would allow susceptibility results to be available 1 to 2 days earlier. A total of 104 blood cultures with different
Candida
species (28%
C. albicans
, 27%
C. parapsilosis
, 26%
C. tropicalis
, etc.) were evaluated between January 2012 and May 2013 for agreement of fluconazole, voriconazole, and amphotericin B susceptibility results by disk diffusion. Agreement in MICs obtained by Etest was determined for fluconazole (21 isolates), voriconazole (28 isolates), amphotericin (29 isolates), and caspofungin (29 isolates). The kappa scores for categorical agreement were highest for fluconazole by disk diffusion (0.902, standard error [SE] = 0.076) and Etest (1.00, SE = 0.218) and for amphotericin B by disk diffusion (1.00, SE = 0.098). The Pearson correlation (
r
) of zone diameters was strongest for fluconazole (0.69) and amphotericin (0.70) and moderate for voriconazole (0.60), and the Pearson correlation of MICs was strongest for fluconazole (0.94) and caspofungin (0.88). However, the moderate correlation of amphotericin MICs with zone diameters (−0.42) precludes the use of amphotericin B disk diffusion for susceptibility testing. There were no very major errors; however, there were 1 (1%) major and 5 (4.8%) minor errors with disk diffusion and 4 (13.3%) minor errors with Etest. Thus, antifungal disk diffusion directly from blood culture bottles is a rapid and easy method for fluconazole and voriconazole susceptibility testing for timely tailoring of candidemia therapy.
Evaluation of an Immunochromatographic Lateral Flow Assay (OXA-48
K
-SeT) for Rapid Detection of OXA-48-Like Carbapenemases in Enterobacteriaceae
Authors: Wareham David W. , Shah Rishita , Betts Jonathan W. , Phee Lynette M. , Momin Muhd Haziq F. Abdul 
Published: November 2015

ABSTRACT

We evaluated an immunochromatographic lateral flow assay to detect OXA-48-like carbapenemases (OXA-48
K
-SeT) in
Enterobacteriaceae
(
n
= 82). One hundred percent sensitivity and specificity were observed using bacteria recovered from both solid medium and spiked blood culture bottles, and the results were obtained in <10 min.
Mumps Virus Nucleoprotein Enhances Phosphorylation of the Phosphoprotein by Polo-Like Kinase 1
Authors: Pickar Adrian , Zengel James , Xu Pei , Li Zhuo , He Biao 
Published: November 2015

ABSTRACT
The viral RNA-dependent RNA polymerases (vRdRps) of nonsegmented, negative-sense viruses (NNSVs) consist of the enzymatic large protein (L) and the phosphoprotein (P). P is heavily phosphorylated, and its phosphorylation plays a critical role in viral RNA synthesis. Since NNSVs do not encode kinases, P is phosphorylated by host kinases. In this study, we investigate the roles that viral proteins play in the phosphorylation of mumps virus (MuV) P. We found that nucleoprotein (NP) enhances the phosphorylation of P. We have identified the serine/threonine kinase Polo-like kinase 1 (PLK1) as a host kinase that phosphorylates P and have found that phosphorylation of P by PLK1 is enhanced by NP. The PLK1 binding site in MuV P was mapped to residues 146 to 148 within the S(pS/T)P motif, and the phosphorylation site was identified as residues S292 and S294.

IMPORTANCE
It has previously been shown that P acts as a chaperone for NP, which encapsidates viral genomic RNA to form the NP-RNA complex, the functional template for viral RNA synthesis. Thus, it is assumed that phosphorylation of P may regulate NP's ability to form the NP-RNA complex, thereby regulating viral RNA synthesis. Our work demonstrates that MuV NP affects phosphorylation of P, suggesting that NP can regulate viral RNA synthesis by regulating phosphorylation of P.
High-Throughput Single-Cell Kinetics of Virus Infections in the Presence of Defective Interfering Particles
Authors: Akpinar Fulya , Timm Andrea , Yin John 
Published: November 2015

ABSTRACTDefective interfering particles (DIPs) are virus mutants that lack essential genes for growth. In coinfections with helper virus, the diversion of viral proteins to the replication and packaging of DIP genomes can interfere with virus production. Mounting cases of DIPs and DIP-like genomes in clinical and natural isolates, as well as growing interest in DIP-based therapies, underscore a need to better elucidate how DIPs work. DIP activity is primarily measured by its inhibition of virus infection yield, an endpoint that masks the dynamic and potentially diverse individual cell behaviors. Using vesicular stomatitis virus (VSV) as a model, we coinfected BHK cells with VSV DIPs and recombinant helper virus carrying a gene encoding a red fluorescent protein (RFP) whose expression correlates with the timing and level of virus release. For single cells within a monolayer, 10 DIPs per cell suppressed the reporter expression in only 1.2% of the cells. In most cells, it slowed and reduced viral gene expression, manifested as a shift in mean latent time from 4 to 6 h and reduced virus yields by 10-fold. For single cells isolated in microwells, DIP effects were more pronounced, reducing virus yields by 100-fold and extending latent times to 12 h, including individual instances above 20 h. Together, these results suggest that direct or indirect cell-cell interactions prevent most coinfected cells from being completely suppressed by DIPs. Finally, a gamma distribution model captures well how the infection kinetics quantitatively depends on the DIP dose. Such models will be useful for advancing a predictive biology of DIP-associated virus growth and infection spread.IMPORTANCEDuring the last century, basic studies in virology have focused on developing a molecular mechanistic understanding of how infectious viruses reproduce in their living host cells. However, over the last 10 years, the advent of deep sequencing and other powerful technologies has revealed in natural and patient infections that viruses do not act alone. Instead, viruses are often accompanied by defective virus-like particles that carry large deletions in their genomes and fail to replicate on their own. Coinfections of viable and defective viruses behave in unpredictable ways, but they often interfere with normal virus growth, potentially enabling infections to evade host immune surveillance. In the current study, controlled levels of defective viruses are coinfected with viable viruses that have been engineered to express a fluorescent reporter protein during infection. Unique profiles of reporter expression acquired from thousands of coinfected cells reveal how interference acts at multiple stages of infection.