bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus Sequence Typing of Mycoplasma hyorhinis Strains Identified by a Real-Time TaqMan PCR Assay
Authors: Tocqueville Véronique , Ferré Séverine , Nguyen Ngoc Hong Phuc , Kempf Isabelle , Marois-Créhan Corinne 
Published: March 2014

ABSTRACTA real-time TaqMan PCR assay based on the gene encoding the protein p37 was developed to detectMycoplasma hyorhinis. Its specificity was validated with 29 epidemiologically unrelatedM. hyorhinisstrains (28 field strains and one reference strain) and other mycoplasma species or with other microorganisms commonly found in pigs. The estimated detection limit of this qPCR assay was 125 microorganism equivalents/μl. The same 29 epidemiologically unrelatedM. hyorhinisstrains and four previously fully sequenced strains were typed by two portable typing methods, the sequencing of the p37 gene and a multilocus sequence typing (MLST) scheme. The first method revealed 18 distinct nucleotide sequences and insufficient discriminatory power (0.934). The MLST scheme was developed with the sequenced genomes of theM. hyorhinisstrains HUB-1, GDL-1, MCLD, and SK76 and based on the genesdnaA,rpoB,gyrB,gltX,adk, andgmk. In total, 2,304 bp of sequence was analyzed for each strain. MLST was capable of subdividing the 33 strains into 29 distinct sequence types. The discriminatory power of the method was >0.95, which is the threshold value for interpreting typing results with confidence (D= 0.989). Population analysis showed that recombination inM. hyorhinisoccurs and that strains are diverse but with a certain clonality (one unique clonal complex was identified). The new qPCR assay and the robust MLST scheme are available for the acquisition of new knowledge onM. hyorhinisepidemiology. A web-accessible database has been set up for theM. hyorhinisMLST scheme athttp://pubmlst.org/mhyorhinis/.
Reinitiation after Translation of Two Upstream Open Reading Frames (ORF) Governs Expression of the ORF35-37 Kaposi's Sarcoma-Associated Herpesvirus Polycistronic mRNA
Authors: Kronstad Lisa M. , Brulois Kevin F. , Jung Jae U. , Glaunsinger Britt A. 
Published: March 2014

ABSTRACT
The Kaposi's sarcoma-associated herpesvirus (KSHV) ORF36 protein kinase is translated as a downstream gene from the ORF35-37 polycistronic mRNA via a unique mechanism involving short upstream open reading frames (uORFs) located in the 5′ untranslated region. Here, we confirm that ORF35-37 is functionally dicistronic during infection and demonstrate that mutation of the dominant uORF restricts KSHV replication. Leaky scanning past the uORFs facilitates ORF35 expression, while a reinitiation mechanism after translation of the uORFs enables ORF36 expression.
Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-Particle
Authors: Organtini Lindsey J. , Makhov Alexander M. , Conway James F. , Hafenstein Susan , Carson Steven D. 
Published: March 2014

ABSTRACT
The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and catalyzing conformational changes in the virus that result in formation of the altered, noninfectious A-particle. Kinetic analyses show that the apparent first-order rate constant for the inactivation of CVB3 by soluble CAR (sCAR) at physiological temperatures varies nonlinearly with sCAR concentration. Cryo-electron microscopy (cryo-EM) reconstruction of the CVB3-CAR complex resulted in a 9.0-Å resolution map that was interpreted with the four available crystal structures of CAR, providing a consensus footprint for the receptor binding site. The analysis of the cryo-EM structure identifies important virus-receptor interactions that are conserved across picornavirus species. These conserved interactions map to variable antigenic sites or structurally conserved regions, suggesting a combination of evolutionary mechanisms for receptor site preservation. The CAR-catalyzed A-particle structure was solved to a 6.6-Å resolution and shows significant rearrangement of internal features and symmetric interactions with the RNA genome.

IMPORTANCE
This report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ∼9-Å resolution for the interpretation of cryo-EM complex maps. The analysis of receptor binding elucidates two complementary mechanisms for preservation of the low-affinity (initial) interaction of the receptor and defines the kinetics of receptor-catalyzed conformational change to the A-particle.
The C-Terminal Repeat Domains of nsP3 from the Old World Alphaviruses Bind Directly to G3BP
Authors: Panas Marc D. , Ahola Tero , McInerney Gerald M. 
Published: March 2014

ABSTRACT
The Old World alphaviruses block stress granule assembly by sequestration of RasGAP SH3-domain binding protein (G3BP). Here, we show that the proline-rich sequences in the hypervariable domain of nonstructural protein 3 (nsP3) of both Semliki Forest virus and Chikungunya virus were dispensable for binding to G3BP. nsP3 variants with or without this domain colocalized with G3BP. Furthermore, we show that the C-terminal repeat motifs of nsP3 were sufficient for G3BP binding.
Pseudorabies Virus pUL46 Induces Activation of ERK1/2 and Regulates Herpesvirus-Induced Nuclear Envelope Breakdown
Authors: Schulz Katharina S. , Liu XueQiao , Klupp Barbara G. , Granzow Harald , Cohen Jeffrey I. , Mettenleiter Thomas C. 
Published: March 2014

ABSTRACT

Herpesvirus capsid morphogenesis occurs in the nucleus, while final maturation takes place in the cytosol, requiring translocation of capsids through the nuclear envelope. The nuclear egress complex, consisting of homologs of herpes simplex virus pUL31 and pUL34, is required for efficient nuclear egress via primary envelopment and de-envelopment. Recently, we described an alternative mode of nuclear escape by fragmentation of the nuclear envelope induced by replication-competent pUL31 and pUL34 deletion mutants of the alphaherpesvirus pseudorabies virus (PrV), which had been selected by serial passaging in cell culture. Both passaged viruses carry congruent mutations in seven genes, including
UL46
, which encodes one of the major tegument proteins. Herpesvirus pUL46 homologs have recently been shown to activate the PI3K-Akt and ERK1/2 signaling pathways, which are involved in regulation of mitosis and apoptosis. Since in uninfected cells fragmentation of the nuclear envelope occurs during mitosis and apoptosis, we analyzed whether pUL46 of PrV is involved in signaling events impairing the integrity of the nuclear envelope. We show here that PrV pUL46 is able to induce phosphorylation of ERK1/2 and, thus, expression of ERK1/2 target genes but fails to activate the PI3K-Akt pathway. Deletion of UL46 from PrV-ΔUL34Pass and PrV-ΔUL31Pass or replacement by wild-type UL46 resulted in enhanced nuclear envelope breakdown, indicating that the mutations in pUL46 may limit the extent of NEBD. Thus, although pUL46 induces ERK1/2 phosphorylation, controlling the integrity of the nuclear envelope is independent of the ERK1/2 signaling pathway.

IMPORTANCE
Herpesvirus nucleocapsids can leave the nucleus by regulated, vesicle-mediated transport through the nuclear envelope, designated nuclear egress, or by inducing nuclear envelope breakdown (NEBD). The viral proteins involved in NEBD are unknown. We show here that the pseudorabies virus tegument protein pUL46 induces the ERK1/2 signaling pathway and modulates NEBD. However, these two processes are independent and ERK1/2 signaling induced by pUL46 is not involved in herpesvirus-induced NEBD.
Mucosal Immunization with a Candidate Universal Influenza Vaccine Reduces Virus Transmission in a Mouse Model
Authors: Price Graeme E. , Lo Chia-Yun , Misplon Julia A. , Epstein Suzanne L. 
Published: March 2014

ABSTRACT
Pandemic influenza is a major public health concern, but conventional strain-matched vaccines are unavailable early in a pandemic. Candidate “universal” vaccines targeting the viral antigens nucleoprotein (NP) and matrix 2 (M2), which are conserved among all influenza A virus strains and subtypes, could be manufactured in advance for use at the onset of a pandemic. These vaccines do not prevent infection but can reduce disease severity, deaths, and virus titers in the respiratory tract. We hypothesized that such immunization may reduce virus transmission from vaccinated, infected animals. To investigate this hypothesis, we studied mouse models for direct-contact and airborne transmission of H1N1 and H3N2 influenza viruses. We established conditions under which virus transmission occurs and showed that transmission efficiency is determined in part at the level of host susceptibility to infection. Our findings indicate that virus transmission between mice has both airborne and direct-contact components. Finally, we demonstrated that immunization with recombinant adenovirus vectors expressing NP and M2 significantly reduced the transmission of virus to cohoused, unimmunized mice in comparison to controls. These findings have broad implications for the impact of conserved-antigen vaccines, not only in protecting the vaccinated individual but also in protecting others by limiting influenza virus transmission and potentially reducing the size of epidemics.

IMPORTANCE
Using a mouse model of influenza A virus transmission, we demonstrate that a candidate “universal” influenza vaccine both protects vaccinated animals from lethal infection and reduces the transmission of virus from vaccinated to nonvaccinated mice. This vaccine induces immunity against proteins conserved among all known influenza A virus strains and subtypes, so it could be used early in a pandemic before conventional strain-matched vaccines are available and could potentially reduce the spread of infection in the community.
An Important Role for Mitochondrial Antiviral Signaling Protein in the Kaposi's Sarcoma-Associated Herpesvirus Life Cycle
Authors: West John A. , Wicks Megan , Gregory Sean M. , Chugh Pauline , Jacobs Sarah R. , Zhang Zhigang , Host Kurtis M. , Dittmer Dirk P. , Damania Blossom 
Published: March 2014

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) has been shown to be recognized by two families of pattern recognition receptors (PRRs), Toll-like receptors (TLRs) and NOD-like receptors (NLRs). Here we show that MAVS and RIG-I (retinoic acid-inducible gene 1), an RLR family member, also have a role in suppressing KSHV replication and production. In the context of primary infection, we show that in cells with depleted levels of MAVS or RIG-I, KSHV transcription is increased, while beta interferon (IFN-β) induction is attenuated. We also observed that MAVS and RIG-I are critical during the process of reactivation. Depletion of MAVS and RIG-I prior to reactivation led to increased viral load and production of infectious virus. Finally, MAVS depletion in latent KSHV-infected B cells leads to increased viral gene transcription. Overall, this study suggests a role for MAVS and RIG-I signaling during different stages of the KSHV life cycle.

IMPORTANCE
We show that RIG-I and its adaptor protein, MAVS, can sense KSHV infection and that these proteins can suppress KSHV replication following primary infection and/or viral reactivation.
An Immature Retroviral RNA Genome Resembles a Kinetically Trapped Intermediate State
Authors: Grohman Jacob K. , Gorelick Robert J. , Kottegoda Sumith , Allbritton Nancy L. , Rein Alan , Weeks Kevin M. 
Published: March 2014

ABSTRACT
Retroviral virions initially assemble in an immature form that differs from that of the mature infectious particle. The RNA genomes in both immature and infectious particles are dimers, and interactions between the RNA dimer and the viral Gag protein ensure selective packaging into nascent immature virions. We used high-sensitivity selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) to obtain nucleotide-resolution structural information from scarce, femtomole quantities of Moloney murine leukemia virus (MuLV) RNA inside authentic virions and from viral RNA extracted from immature (protease-minus) virions. Our secondary structure model of the dimerization and packaging domain indicated that a stable intermolecular duplex known as PAL2, previously shown to be present in mature infectious MuLV particles, was sequestered in an alternate stem-loop structure inside immature virions. The intermediate state corresponded closely to a late-folding intermediate that we detected in time-resolved studies of the free MuLV RNA, suggesting that the immature RNA structure reflects trapping of the intermediate folding state by interactions in the immature virion. We propose models for the RNA-protein interactions that trap the RNA in the immature state and for the conformational rearrangement that occurs during maturation of virion particles.

IMPORTANCE
The structure of the RNA genome in mature retroviruses has been studied extensively, whereas very little was known about the RNA structure in immature virions. The immature RNA structure is important because it is the form initially selected for packaging in new virions and may have other roles. This lack of information was due to the difficulty of isolating sufficient viral RNA for study. In this work, we apply a high-sensitivity and nucleotide-resolution approach to examine the structure of the dimerization and packaging domain of Moloney murine leukemia virus. We find that the genomic RNA is packaged in a high-energy state, suggesting that interactions within the virion hold or capture the RNA before it reaches its most stable state. This new structural information makes it possible to propose models for the conformational changes in the RNA genome that accompany retroviral maturation.
Cell Surface Vimentin Is an Attachment Receptor for Enterovirus 71
Authors: Du Ning , Cong Haolong , Tian Hongchao , Zhang Hua , Zhang Wenliang , Song Lei , Tien Po 
Published: March 2014

ABSTRACTEnterovirus 71 (EV71) is a highly transmissible pathogenic agent that causes severe central nervous system diseases in infected infants and young children. Here, we reported that EV71 VP1 protein could bind to vimentin intermediate filaments expressed on the host cell surface. Soluble vimentin or an antibody against vimentin could inhibit the binding of EV71 to host cells. Accompanied with the reduction of vimentin expression on the cell surface, the binding of EV71 to cells was remarkably decreased. Further evidence showed that the N terminus of vimentin is responsible for the interaction between EV71 and vimentin. These results indicated that vimentin on the host cell surface may serve as an attachment site that mediated the initial binding and subsequently increased the infectivity of EV71.IMPORTANCEThis study delivers important findings on the roles of vimentin filaments in relation to EV71 infection and provides information that not only improves our understanding of EV71 pathogenesis but also presents us with potentially new strategies for the treatment of diseases caused by EV71 infections.
An exploratory trial implementing a community-based child oral health promotion intervention for Australian families from refugee and migrant backgrounds: a protocol paper for Teeth Tales
Authors: Gibbs Lisa , Waters Elizabeth , de Silva Andrea , Riggs Elisha , Moore Laurence , Armit Christine , Johnson Britt , Morris Michal , Calache Hanny , Gussy Mark , Young Dana , Tadic Maryanne , Christian Bradley , Gondal Iqbal , Watt Richard , Pradel Veronika , Truong Mandy , Gold Lisa 
Published: March 2014

IntroductionInequalities are evident in early childhood caries rates with the socially disadvantaged experiencing greater burden of disease. This study builds on formative qualitative research, conducted in the Moreland/Hume local government areas of Melbourne, Victoria 2006–2009, in response to community concerns for oral health of children from refugee and migrant backgrounds. Development of the community-based intervention described here extends the partnership approach to cogeneration of contemporary evidence with continued and meaningful involvement of investigators, community, cultural and government partners. This trial aims to establish a model for child oral health promotion for culturally diverse communities in Australia.Methods and analysisThis is an exploratory trial implementing a community-based child oral health promotion intervention for Australian families from refugee and migrant backgrounds. Families from an Iraqi, Lebanese or Pakistani background with children aged 1–4 years, residing in metropolitan Melbourne, were invited to participate in the trial by peer educators from their respective communities using snowball and purposive sampling techniques. Target sample size was 600. Moreland, a culturally diverse, inner-urban metropolitan area of Melbourne, was chosen as the intervention site. The intervention comprised peer educator led community oral health education sessions and reorienting of dental health and family services through cultural Competency Organisational Review (CORe).Ethics and disseminationEthics approval for this trial was granted by the University of Melbourne Human Research Ethics Committee and the Department of Education and Early Childhood Development Research Committee. Study progress and output will be disseminated via periodic newsletters, peer-reviewed research papers, reports, community seminars and at National and International conferences.Trial registration numberAustralian New Zealand Clinical Trials Registry (ACTRN12611000532909).
Using physician-linked mailed invitations in an organised colorectal cancer screening programme: effectiveness and factors associated with response
Authors: Tinmouth Jill , Baxter Nancy N , Paszat Lawrence F , Rabeneck Linda , Sutradhar Rinku , Yun Lingsong 
Published: March 2014

ObjectivesA central tenet of organised cancer screening is that all persons in a target population are invited. The aims of this study were to identify participant and physician factors associated with response to mailed physician-linked invitations (study 1) and to evaluate their effectiveness in an organised colorectal cancer (CRC) screening programme (study 2).Design and setting2 studies (study 1—cohort design and study 2—matched cohort design, comprising study 1 participants and a matched control group) were conducted in the context of Ontario's organised province-wide CRC screening programme.Participants102 family physicians and 11 302 associated eligible patients from a technical evaluation (‘the Pilot’) of large-scale mailed invitations for CRC screening were included. Matched controls were randomly selected using propensity scores from among eligible patients associated with family physicians in similar practice types as the Pilot physicians.InterventionPhysician-linked mailed invitation to have CRC screening.OutcomesUptake of faecal occult blood test (FOBT) within 6 months of mailed invitation (primary) and uptake of FOBT or colonoscopy within 6 months of mailed invitation (secondary).ResultsFactors significantly associated with uptake of FOBT included prior FOBT use, older participant age, greater participant comorbidity and having a female physician. In the matched analysis, Pilot participants were more likely to complete an FOBT (22% vs 8%, p<0.0001) or an FOBT or colonoscopy (25% vs 11%, p<0.0001) within 6 months of mailed invitation than matched controls. The number needed to invite to screen one additional person was 7.ConclusionsCentralised large-scale mailing of physician-linked invitations is feasible and effective in the context of organised CRC screening.
Evaluation of corneal anaesthesia after the application of topical 2 per cent lidocaine, 0.5 per cent bupivacaine and 1 per cent ropivacaine in dogs
Authors: Costa D. , Peña M. T. , Ríos J. , Leiva M. 
Published: March 2014

The objective of this study was to describe and compare the efficacy and duration of topical anaesthesia induced by 2 per cent lidocaine (L), 0.5 per cent bupivacaine (B) and 1 per cent ropivacaine (R) in the dog using 24 clinically healthy beagles with normal ocular examination. Dogs were randomly divided into three groups: 2 per cent lidocaine (n=8), 0.5 per cent bupivacaine (n=8) and 1 per cent ropivacaine (n=8). The baseline corneal touch threshold (CTT) was measured using a Cochet‐Bonnet aesthesiometer. Following baseline CTT measurement, a single drop of the assigned anaesthetic was applied to each eye and the CTT was measured bilaterally within one minute after administration and every five minutes until the basal CTT value was restored. Data were analysed with non‐parametric analysis of variance models and Dunnet's test for post hoc analysis. One per cent ropivacaine was the most effective drug (LCTTmax =3 cm, BCTTmax =2 cm, RCTTmax =0 cm; P<0.001), and had the shortest latency (LLatency =5 minutes, BLatency =5 minutes, RLatency =1 minute; P<0.001) and the smallest AUC (LAUC =80 cm×minute, BAUC =68.25 cm×minute, RAUC =36.88 cm×minute; P<0.001). There was no statistical difference in the duration of corneal anaesthesia between the groups (P=0.09) and all topical anaesthetics tested reduced corneal sensitivity, although 1 per cent ropivacaine had the maximal and quickest anaesthetic effect. This drug could be used for specific diagnostic procedures where quick and short, but effective, corneal anaesthesia is needed.
Coasts of Foxe Basin, Arctic Canada
Authors: Martini I. Peter , Morrison R. I. Guy 
Published: March 2014

Abstract

Foxe Basin is a down-faulted arctic basin floored by Palaeozoic carbonates, surrounded by metamorphic Precambrian terrains. Quaternary deposits consist of Pleistocene–Holocene glacial drift, and frost-shattered bedrock-clasts mostly reworked by sea waves during post-glacial emergence during the last 5000–6000 yr. The shallow, primarily micro- to meso-tidal sea is covered by ice for
c.
9–10 months each year. This ensures that the overall energy of the coasts is low, although strong storm waves develop during ice-free periods.
Puccinellia phryganodes
dominated salt marshes occur on muddy and sandy shores and grade into inland sedge-forb wetlands and
Dryas
-dominated tundra. Cold climate processes active on the emerged land have generated typical features such as frost heaving of bedrock blocks, solifluction lobes on slopes, frost boils in flatter areas, frost shattering and solution of surficial carbonate pebbles, thermokarst lakes, and shallow Cryosols.
Evolution of paraglacial coasts in response to changes in fluvial sediment supply
Authors: Hein Christopher J. , FitzGerald D. M. , Buynevich I. V. , Van Heteren S. , Kelley J. T. 
Published: March 2014

Abstract

Paraglacial coastal systems are formed on or proximal to formerly ice-covered terrain from sediments with direct or indirect glacial origin. This review addresses the roles of tectonic controls, glacial advances and retreats, sea-level changes, and coastal processes in sediment production, delivery and redistribution along the paraglacial Gulf of Maine coast (USA and Canada). Coastal accumulation forms are compositionally heterogeneous and found primarily at the seaward edge of the Gulf's largest estuaries; their existence is directly attributable to the availability of glacial sediments derived from erosion of weathered plutons within coastal river basins. Multiple post-glacial sea-level fluctuations drove the redistribution of these sediments across the modern lowland and inner shelf. Central to the formation of barrier systems was the paraglacial sand maximum, a time-transgressive phase of relative sea-level fall and enhanced fluvial sand export
c.
2000–4000 years following deglaciation. Vast quantities of sand and gravel were reworked landward during the subsequent transgression and combined with additional riverine sediments to form the modern barrier systems. Today, reduced fluvial sediment loads, anthropogenic modifications of barrier and river systems, and sea-level rise have combined to exacerbate long-term coastal erosion and may eventually force these barriers toward a state of rapid landward migration.