bluuebunny/crossref_metadata_2025_split huggingface dataset:
Typing and Clustering of Yersinia pseudotuberculosis Isolates by Restriction Fragment Length Polymorphism Analysis Using Insertion Sequences
Authors: Voskresenskaya E. , Savin C. , Leclercq A. , Tseneva G. , Carniel E. 
Published: March 2014

ABSTRACT

Yersinia pseudotuberculosis
is an enteropathogen that has an animal reservoir and causes human infections, mostly in temperate and cold countries. Most of the methods previously used to subdivide
Y. pseudotuberculosis
were performed on small numbers of isolates from a specific geographical area. One aim of this study was to evaluate the typing efficiency of restriction fragment length polymorphism of insertion sequence hybridization patterns (IS-RFLP) compared to other typing methods, such as serotyping, ribotyping, and multilocus sequence typing (MLST), on the same set of 80 strains of
Y. pseudotuberculosis
of global origin. We found that IS
100
was not adequate for IS-RFLP but that both IS
285
and IS
1541
efficiently subtyped
Y. pseudotuberculosis
. The discriminatory index (DI) of IS
1541
-RFLP (0.980) was superior to those of IS
285
-RFLP (0.939), ribotyping (0.944), MLST (0.861), and serotyping (0.857). The combination of the two IS (2IS-RFLP) further increased the DI to 0.998. Thus, IS-RFLP is a powerful tool for the molecular typing of
Y. pseudotuberculosis
and has the advantage of exhibiting well-resolved banding patterns that allow for a reliable comparison of strains of worldwide origin. The other aim of this study was to assess the clustering power of IS-RFLP. We found that 2IS-RFLP had a remarkable capacity to group strains with similar genotypic and phenotypic markers, thus identifying robust populations within
Y. pseudotuberculosis
. Our study thus demonstrates that 2IS- and even IS
1541
-RFLP alone might be valuable tools for the molecular typing of global isolates of
Y. pseudotuberculosis
and for the analysis of the population structure of this species.
Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections
Authors: Gaulke Christopher A. , Porter Matthew , Han Yan-Hong , Sankaran-Walters Sumathi , Grishina Irina , George Michael D. , Dang Angeline T. , Ding Shou-Wei , Jiang Guochun , Korf Ian , Dandekar Satya 
Published: March 2014

ABSTRACT

Epithelial barrier dysfunction during human immunodeficiency virus (HIV) infection has largely been attributed to the rapid and severe depletion of CD4
+
T cells in the gastrointestinal (GI) tract. Although it is known that changes in mucosal gene expression contribute to intestinal enteropathy, the role of small noncoding RNAs, specifically microRNA (miRNA), has not been investigated. Using the simian immunodeficiency virus (SIV)-infected nonhuman primate model of HIV pathogenesis, we investigated the effect of viral infection on miRNA expression in intestinal mucosa. SIV infection led to a striking decrease in the expression of mucosal miRNA compared to that in uninfected controls. This decrease coincided with an increase in 5′-3′-exoribonuclease 2 protein and alterations in DICER1 and Argonaute 2 expression. Targets of depleted miRNA belonged to molecular pathways involved in epithelial proliferation, differentiation, and immune response. Decreased expression of several miRNA involved in maintaining epithelial homeostasis in the gut was localized to the proliferative crypt region of the intestinal epithelium. Our findings suggest that SIV-induced decreased expression of miRNA involved in epithelial homeostasis, disrupted expression of miRNA biogenesis machinery, and increased expression of XRN2 are involved in the development of epithelial barrier dysfunction and gastroenteropathy.

IMPORTANCE
MicroRNA (miRNA) regulate the development and function of intestinal epithelial cells, and many viruses disrupt normal host miRNA expression. In this study, we demonstrate that SIV and HIV disrupt expression of miRNA in the small intestine during infection. The depletion of several key miRNA is localized to the proliferative crypt region of the gut epithelium. These miRNA are known to control expression of genes involved in inflammation, cell death, and epithelial maturation. Our data indicate that this disruption might be caused by altered expression of miRNA biogenesis machinery during infection. These findings suggest that the disruption of miRNA in the small intestine likely plays a role in intestinal enteropathy during HIV infection.
Nuclear Magnetic Resonance Structure Revealed that the Human Polyomavirus JC Virus Agnoprotein Contains an α-Helix Encompassing the Leu/Ile/Phe-Rich Domain
Authors: Coric Pascale , Saribas A. Sami , Abou-Gharbia Magid , Childers Wayne , White Martyn K. , Bouaziz Serge , Safak Mahmut 
Published: March 2014

ABSTRACT
Agnoprotein is a small multifunctional regulatory protein required for sustaining the productive replication of JC virus (JCV). It is a mostly cytoplasmic protein localizing in the perinuclear area and forms highly stable dimers/oligomers through a Leu/Ile/Phe-rich domain. There have been no three-dimensional structural data available for agnoprotein due to difficulties associated with the dynamic conversion from monomers to oligomers. Here, we report the first nuclear magnetic resonance (NMR) structure of a synthetic agnoprotein peptide spanning amino acids Thr17 to Glu55 where Lys23 to Phe39 encompassing the Leu/Ile/Phe-rich domain forms an amphipathic α-helix. On the basis of these structural data, a number of Ala substitution mutations were made to investigate the role of the α-helix in the structure and function of agnoprotein. Single L29A and L36A mutations exhibited a significant negative effect on both protein stability and viral replication, whereas the L32A mutation did not. In addition, the L29A mutant displayed a highly nuclear localization pattern, in contrast to the pattern for the wild type (WT). Interestingly, a triple mutant, the L29A+L32A+L36A mutant, yielded no detectable agnoprotein expression, and the replication of this JCV mutant was significantly reduced, suggesting that Leu29 and Leu36 are located at the dimer interface, contributing to the structure and stability of agnoprotein. Two other single mutations, L33A and E34A, did not perturb agnoprotein stability as drastically as that observed with the L29A and L36A mutations, but they negatively affected viral replication, suggesting that the role of these residues is functional rather than structural. Thus, the agnoprotein dimerization domain can be targeted for the development of novel drugs active against JCV infection.

IMPORTANCE
Agnoprotein is a small regulatory protein of JC virus (JCV) and is required for the successful completion of the viral replication cycle. It forms highly stable dimers and oligomers through its hydrophobic (Leu/Ile/Phe-rich) domain, which has been shown to play essential roles in the stability and function of the protein. In this work, the Leu/Ile/Phe-rich domain has been further characterized by NMR studies using an agnoprotein peptide spanning amino acids T17 to Q54. Those studies revealed that the dimerization domain of the protein forms an amphipathic α-helix. Subsequent NMR structure-based mutational analysis of the region highlighted the critical importance of certain amino acids within the α-helix for the stability and function of agnoprotein. In conclusion, this study provides a solid foundation for developing effective therapeutic approaches against the dimerization domain of the protein to inhibit its critical roles in JCV infection.
Cryo-Electron Microscopy Study of Insect Cell-Expressed Enterovirus 71 and Coxsackievirus A16 Virus-Like Particles Provides a Structural Basis for Vaccine Development
Authors: Gong Minqing , Zhu Hongtao , Zhou Jun , Yang Chunting , Feng Jing , Huang Xiaojun , Ji Gang , Xu Honglin , Zhu Ping 
Published: March 2014

ABSTRACT
Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are the two most common etiological agents responsible for the epidemics of hand, foot, and mouth disease (HFMD), a childhood illness with occasional severe neurological complications. A number of vaccine candidates against EV71 or CA16 have been reported; however, no vaccine is currently available for clinical use. Here, we generated a secreted version of EV71 and CA16 virus-like particles (VLPs) using a baculovirus-insect cell expression system and reconstructed the three-dimensional (3D) structures of both VLPs by cryo-electron microscopy (cryo-EM) single-particle analysis at 5.2-Å and 5.5-Å resolutions, respectively. The reconstruction results showed that the cryo-EM structures of EV71 and CA16 VLPs highly resemble the recently published crystal structures for EV71 natural empty particles and CA16 135S-like expanded particles, respectively. Our cryo-EM analysis also revealed that the majority of previously identified linear neutralizing epitopes are well preserved on the surface of EV71 and CA16 VLPs. In addition, both VLPs were able to induce efficiently neutralizing antibodies against various strains of EV71 and CA16 viruses in mouse immunization. These studies provide a structural basis for the development of insect cell-expressed VLP vaccines and for a potential bivalent VLP vaccine against both EV71- and CA16-associated HFMD.

IMPORTANCE
The recent outbreaks of hand, foot, and mouth disease (HFMD) in the Asia Pacific region spurred the search for effective vaccines against EV71 and CA16 viruses, the two most common etiological agents responsible for HFMD. In this paper, we show that secreted versions of EV71 and CA16 VLPs generated in the baculovirus-insect cell expression system highly resemble the crystal structures of their viral conterparts and that the majority of previously identified linear neutralizing epitopes are well preserved on the VLP surfaces. In addition, the generated VLPs can efficiently induce neutralizing antibodies against various strains of EV71 and CA16 viruses in mouse immunization. These studies provide a structural basis for the development of insect cell-expressed VLP vaccines and for a potential bivalent VLP vaccine against both EV71- and CA16-associated HFMD.
The Tripartite Virions of the Brome Mosaic Virus Have Distinct Physical Properties That Affect the Timing of the Infection Process
Authors: Vaughan Robert , Tragesser Brady , Ni Peng , Ma Xiang , Dragnea Bogdan , Kao C. Cheng 
Published: March 2014

ABSTRACT
The three subsets of virions that comprise the Brome mosaic virus (BMV) were previously thought to be indistinguishable. This work tested the hypothesis that distinct capsid-RNA interactions in the BMV virions allow different rates of viral RNA release. Several results support distinct interactions between the capsid and the BMV genomic RNAs. First, the deletion of the first eight residues of the BMV coat protein (CP) resulted in the RNA1-containing particles having altered morphologies, while those containing RNA2 were unaffected. Second, subsets of the BMV particles separated by density gradients into a pool enriched for RNA1 (B1) and for RNA2 and RNA3/4 (B2.3/4) were found to have different physiochemical properties. Compared to the B2.3/4 particles, the B1 particles were more sensitive to protease digestion and had greater resistivity to nanoindentation by atomic force microscopy and increased susceptibility to nuclease digestion. Mapping studies showed that portions of the arginine-rich N-terminal tail of the CP could interact with RNA1. Mutational analysis in the putative RNA1-contacting residues severely reduced encapsidation of BMV RNA1 without affecting the encapsidation of RNA2. Finally, during infection of plants, the more easily released RNA1 accumulated to higher levels early in the infection.

IMPORTANCE
Viruses with genomes packaged in distinct virions could theoretically release the genomes at different times to regulate the timing of gene expression. Using an RNA virus composed of three particles, we demonstrated that the RNA in one of the virions is released more easily than the other two
in vitro
. The differential RNA release is due to distinct interactions between the viral capsid protein and the RNAs. The ease of RNA release is also correlated with the more rapid accumulation of that RNA in infected plants. Our study identified a novel role for capsid-RNA interactions in the regulation of a viral infection.
Individualisation of drug treatments for patients with long-term conditions: a review of concepts
Authors: Denford S , Frost J , Dieppe P , Cooper Chris , Britten N 
Published: March 2014

ObjectivesPatients and policy makers advocate that drug treatments should be individualised. However, the term is used in a variety of ways. We set out to identify the range of related terminology and concepts in the general field of individualisation, map out the relationships between these concepts and explore how patients’ perspectives are considered.DesignWe consulted members of an established patient and public involvement group about their experience of medicine taking for long-term conditions and their ideas about individualisation. We then conducted a scoping review of the literature to explore how terms surrounding individualisation of drug treatment are used and defined in the literature, and to explore the extent to which patients’ perspectives are represented, with a view to informing future recommendations as to how individualisation can be operationalised.MethodsWe identified relevant literature using a range of search strategies. Two researchers independently extracted definitions of terms using a template. Inductive and deductive methods were used to explore the data.ResultsDefinitions were categorised according to the following themes: medical management; pharmacogenetics, the patient's perspective; interactions between the healthcare provider and patient and management of long-term conditions.ConclusionsWithin the literature reviewed, the involvement of patients in the ongoing management of drug treatment was largely absent. We propose the use of a new term ‘mutually agreed tailoring’ (MAT). This describes the ongoing pharmacological management of conditions that incorporates patients’ specific needs, experiences and existing strategies for using their medications, and the professionals’ clinical judgement. This usually includes patients monitoring their symptoms and, with the support of the professional, making appropriate product, dose or timing adjustments as necessary. Our previous work suggests that many patients and doctors are successfully practising MAT, so we suggest that a formal description may facilitate wider utilisation of strategies that will improve patient outcomes.
Nedd8-Activating Enzyme Inhibitor MLN4924 Provides Synergy with Mitomycin C through Interactions with ATR, BRCA1/BRCA2, and Chromatin Dynamics Pathways
Authors: Garcia Khristofer , Blank Jonathan L. , Bouck David C. , Liu Xiaozhen J. , Sappal Darshan S. , Hather Greg , Cosmopoulos Katherine , Thomas Michael P. , Kuranda Mike , Pickard Michael D. , Liu Ray , Bandi Syamala , Smith Peter G. , Lightcap Eric S. 
Published: March 2014

Abstract
MLN4924 is an investigational small-molecule inhibitor of the Nedd8-activating enzyme currently in phase I clinical trials. MLN4924 induces DNA damage via rereplication in most cell lines. This distinct mechanism of DNA damage may affect its ability to combine with standard-of-care agents and may affect the clinical development of MLN4924. As such, we studied its interaction with other DNA-damaging agents. Mitomycin C, cisplatin, cytarabine, UV radiation, SN-38, and gemcitabine demonstrated synergy in combination with MLN4924 in vitro. The combination of mitomycin C and MLN4924 was shown to be synergistic in a mouse xenograft model. Importantly, depletion of genes within the ataxia telangiectasia and Rad3 related (ATR) and BRCA1/BRCA2 pathways, chromatin modification, and transcription-coupled repair reduced the synergy between mitomycin C and MLN4924. In addition, comet assay demonstrated increased DNA strand breaks with the combination of MLN4924 and mitomycin C. Our data suggest that mitomycin C causes stalled replication forks, which when combined with rereplication induced by MLN4924 results in frequent replication fork collisions, leading to cell death. This study provides a straightforward approach to understand the mechanism of synergy, which may provide useful information for the clinical development of these combinations. Mol Cancer Ther; 13(6); 1625–35. ©2014 AACR.
Characterisation of the conformational changes in platelet factor 4 induced by polyanions: towards in vitro prediction of antigenicity
Authors: Brandt Sven , Krauel Krystin , Gottschalk Kay E. , Renné Thomas , Helm Christiane A. , Greinacher Andreas , Block Stephan 
Published: March 2014

SummaryHeparin-induced thrombocytopenia (HIT) is the most frequent drug-induced immune reaction affecting blood cells. Its antigen is formed when the chemokine platelet factor 4 (PF4) complexes with polyanions. By assessing polyanions of varying length and degree of sulfation using immunoassay and circular dichroism (CD)-spectroscopy, we show that PF4 structural changes resulting in antiparallel β-sheet content >30% make PF4/polyanion complexes antigenic. Further, we found that polyphosphates (polyP-55) induce antigenic changes on PF4, whereas fondaparinux does not. We provide a model suggesting that conformational changes exposing antigens on PF4/polyanion complexes occur in the hairpin involving AA 32–38, which form together with C-terminal AA (66–70) of the adjacent PF4 monomer a continuous patch on the PF4 tetramer surface, explaining why only tetrameric PF4 molecules express “HIT antigens”. The correlation of antibody binding in immunoassays with PF4 structural changes provides the intriguing possibility that CD-spectroscopy could become the first antibody-independent, in vitro method to predict potential immunogenicity of drugs. CD-spectroscopy could identify compounds during preclinical drug development that induce PF4 structural changes correlated with antigenicity. The clinical relevance can then be specifically addressed during clinical trials. Whether these findings can be transferred to other endogenous proteins requires further studies.
In vivo prostacyclin biosynthesis and effects of different aspirin regimens in patients with essential thrombocythaemia
Authors: Rocca Bianca , Squellerio Isabella , Dragani Alfredo , Veglia Fabrizio , Pagliaccia Francesca , Porro Benedetta , Barbieri Silvia Stella , Tremoli Elena , Patrono Carlo , Cavalca Viviana 
Published: March 2014

SummaryEssential thrombocythaemia (ET) is characterised by enhanced platelet generation and thrombosis. Once daily (od) aspirin incompletely inhibits platelet thromboxane (TX)A2 production in ET. A twice daily (bid) dosing is necessary to fully inhibit TXA2. Whether this dosing regimen affects in vivo prostacyclin (PGI2) biosynthesis is unknown. PGI2 biosynthesis was characterised in 50 ET patients on enteric-coated (EC) aspirin 100 mg od, by measuring its urinary metabolite, 2,3-dinor-6-keto-PGF1α (PGI-M). Moreover, in a crossover study 22 patients poorly responsive to standard aspirin based on serum TXB2 levels (>4 ng/ml) were randomised to different seven-day aspirin regimens: EC aspirin 100 mg od, 100 mg bid, 200 mg od, or plain as-pirin 100 mg od. PGI-M measured 24 hours after the last aspirin intake (EC, 100 mg od) was similar in patients and healthy subjects both on (n=10) and off (n=30) aspirin. PGI-M was unrelated to in vivo TXA2 biosynthesis, and not affected by EC aspirin 100 mg bid or 200 mg od as compared to EC 100 mg od. PGI2 biosynthesis in aspirin-treated ET patients appears unrelated to TXA2 biosynthesis, and not affected by an improved aspirin regimen, demonstrating its vascular safety for future trials.
The Dispersal of Dense Water Formed in an Idealized Coastal Polynya on a Shallow Sloping Shelf
Authors: Zhang Weifeng G. , Cenedese Claudia 
Published: March 2014

Abstract
This study examines the dispersal of dense water formed in an idealized coastal polynya on a sloping shelf in the absence of ambient circulation and stratification. Both numerical and laboratory experiments reveal two separate bottom pathways for the dense water: an offshore plume moving downslope into deeper ambient water and a coastal current flowing in the direction of Kelvin wave propagation. Scaling analysis shows that the velocity of the offshore plume is proportional not only to the reduced gravity, bottom slope, and inverse of the Coriolis parameter, but also to the ratio of the dense water depth to total water depth. The dense water coastal current is generated by the along-shelf baroclinic pressure gradient. Its dynamics can be separated into two stages: (i) near the source region, where viscous terms are negligible, its speed is proportional to the reduced gravity wave speed and (ii) in the far field, where bottom drag becomes important and balances the pressure gradient, the velocity is proportional to Hc[g′/(LCd)]1/2 in which Hc is the water depth at the coast, g′ the reduced gravity, Cd the quadratic bottom drag coefficient, and L the along-shelf span of the baroclinic pressure gradient. The velocity scalings are verified using numerical and laboratory sensitivity experiments. The numerical simulations suggest that only 3%–23% of the dense water enters the coastal pathway, and the percentage depends highly on the ratio of the velocities of the offshore and coastal plumes. This makes the velocity ratio potentially useful for observational studies to assess the amount of dense water formed in coastal polynyas.
Intensified Diurnal Tides along the Oregon Coast
Authors: Osborne J. J. , Kurapov A. L. , Egbert G. D. , Kosro P. M. 
Published: March 2014

Abstract
Intensified diurnal tides are found along portions of the Oregon shelf (U.S. West Coast) based on analyses of high-frequency (HF) radar surface current data and outputs of a 1-km resolution ocean circulation model. The K1 tidal currents with magnitudes near 0.07 m s−1 over a wider part of the shelf (Heceta Bank complex; 44°–44.5°N), previously predicted by Erofeeva et al., are confirmed here by newly available HF radar data. Intensified diurnal tides are also found along the narrow shelf south of Heceta Bank. In the close vicinity of Cape Blanco (42.8°N), diurnal tidal currents (K1 and O1 constituents combined) may reach 0.3 m s−1. Appreciable differences in diurnal tide intensity are found depending on whether the model is forced with tides and winds (TW) or only tides. Also, diurnal variability in wind forcing is found to affect diurnal surface velocities. For the case forced by tides alone, results strongly depend on whether the model ocean is stratified [tides only, stratified (TOS)] or not [tides only, no stratification (TONS)]. In case TONS, coastal-trapped waves at diurnal frequencies do not occur over the narrow shelf south of 43.5°N, consistent with the dispersion analysis of a linear shallow-water model. However, in case TOS, diurnal tides are intensified in that area, associated with the presence of coastal-trapped waves. Case TW produces the strongest modeled diurnal tidal motions over the entire Oregon shelf, partially due to cross-shore tidal displacement (advection) of alongshore subinertial currents. At Cape Blanco, diurnal tidal variability dominates the modeled relative vorticity spectrum, suggesting that tides may influence the separation of the alongshore coastal jet at that location.