Genome packaging in multi-segmented dsRNA viruses: distinct mechanisms with similar outcomes

Segmented double-stranded (ds)RNA viruses share remarkable similarities in their replication strategy and capsid structure. During virus replication, positive-sense single-stranded (+)RNAs are packaged into procapsids, where they serve as templates for dsRNA synthesis, forming progeny particles containing a complete equimolar set of genome segments. How the +RNAs are recognized and stoichiometrically packaged remains uncertain. Whereas bacteriophages of the Cystoviridae family rely on specific RNA–protein interactions to select appropriate +RNAs for packaging, viruses of the Reoviridae instead rely on specific inter-molecular interactions between +RNAs that guide multi-segmented genome assembly. While these families use distinct mechanisms to direct +RNA packaging, both yield progeny particles with a complete set of genomic dsRNAs

Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties

MRSA model of learning and adaptation: a qualitative study among the general public

<p>Abstract</p> <p>Background</p> <p>More people in the US now die from Methicillin Resistant <it>Staphylococcus aureus </it>(MRSA) infections than from HIV/AIDS. Often acquired in healthcare facilities or during healthcare procedures, the extremely high incidence of MRSA infections and the dangerously low levels of literacy regarding antibiotic resistance in the general public are on a collision course. Traditional medical approaches to infection control and the conventional attitude healthcare practitioners adopt toward public education are no longer adequate to avoid this collision. This study helps us understand how people acquire and process new information and then adapt behaviours based on learning.</p> <p>Methods</p> <p>Using constructivist theory, semi-structured face-to-face and phone interviews were conducted to gather pertinent data. This allowed participants to tell their stories so their experiences could deepen our understanding of this crucial health issue. Interview transcripts were analysed using grounded theory and sensitizing concepts.</p> <p>Results</p> <p>Our findings were classified into two main categories, each of which in turn included three subthemes. First, in the category of <it>Learning</it>, we identified how individuals used their <it>Experiences with MRSA</it>, to answer the questions: <it>What was learned? </it>and, <it>How did learning occur? </it>The second category, <it>Adaptation </it>gave us insights into <it>Self-reliance, Reliance on others</it>, and <it>Reflections on the MRSA journey</it>.</p> <p>Conclusions</p> <p>This study underscores the critical importance of educational programs for patients, and improved continuing education for healthcare providers. Five specific results of this study can reduce the vacuum that currently exists between the knowledge and information available to healthcare professionals, and how that information is conveyed to the public. These points include: 1) a common model of MRSA learning and adaptation; 2) the self-directed nature of adult learning; 3) the focus on general MRSA information, care and prevention, and antibiotic resistance; 4) the interconnected nature of adaptation; and, 5) the need for a consistent step by step plan to deal with MRSA provided at the time of diagnosis.</p

Are parents identifying positive aspects to parenting their child with an intellectual disability or are they just coping? A qualitative exploration

Although acknowledging the stress of raising their child with intellectual disabilities, parents also report that their child has brought about many positive changes in themselves and family. This study reports what parents perceive to be a positive aspect of parenting their child, as currently what constitutes a ‘positive’ is unclear. Seven key themes were identified; an increased sense of personal strength and confidence, changed priorities, greater appreciation of life, pleasure in the child’s accomplishments, increased faith/spirituality, more meaningful relationships and the positive effect that the child has on the wider community. Interpretive examination of the themes reveals that the positive aspects identified consist mostly of meaning-focused coping strategies. These enable parents to adapt successfully to the stressful experiences of raising their child and therefore could be amenable to meaning-focused therapeutic interventions for parents with newly diagnosed children or for those unable to identify any positive aspects of parenting their child

Rotavirus Rearranged Genomic RNA Segments Are Preferentially Packaged into Viruses Despite Not Conferring Selective Growth Advantage to Viruses

The rotavirus (RV) genome consists of 11 double-stranded RNA segments. Sometimes, partial sequence duplication of an RNA segment leads to a rearranged RNA segment. To specify the impact of rearrangement, the replication efficiencies of human RV with rearranged segments 7, 11 or both were compared to these of the homologous human wild-type RV (wt-RV) and of the bovine wt-RV strain RF. As judged by viral growth curves, rotaviruses with a rearranged genome (r-RV) had no selective growth advantage over the homologous wt-RV. In contrast, r-RV were selected over wt-RV during competitive experiments (i.e mixed infections between r-RV and wt-RV followed by serial passages in cell culture). Moreover, when competitive experiments were performed between a human r-RV and the bovine wt-RV strain RF, which had a clear growth advantage, rearranged segments 7, 11 or both always segregated in viral progenies even when performing mixed infections at an MOI ratio of 1 r-RV to 100 wt-RV. Lastly, bovine reassortant viruses that had inherited a rearranged segment 7 from human r-RV were generated. Although substitution of wt by rearranged segment 7 did not result in any growth advantage, the rearranged segment was selected in the viral progenies resulting from mixed infections by bovine reassortant r-RV and wt-RV, even for an MOI ratio of 1 r-RV to 107 wt-RV. Lack of selective growth advantage of r-RV over wt-RV in cell culture suggests a mechanism of preferential packaging of the rearranged segments over their standard counterparts in the viral progeny

Multi-wave coherent control of a solid-state single emitter

The authors acknowledge support by the European Research Council Starting Grant 'PICSEN' contract no. 306387.Coherent control of individual two-level systems (TLSs) is at the basis of any implementation of quantum information. An impressive level of control is now achieved using nuclear, vacancies and charge spins. Manipulation of bright exciton transitions in semiconductor quantum dots (QDs) is less advanced, principally due to the sub-nanosecond dephasing. Conversely, owing to their robust coupling to light, one can apply tools of nonlinear spectroscopy to achieve all-optical command. Here, we report on the coherent manipulation of an exciton via multi-wave mixing. Specifically, we employ three resonant pulses driving a single InAs QD. The first two induce a four-wave mixing (FWM) transient, which is projected onto a six-wave mixing (SWM) depending on the delay and area of the third pulse, in agreement with analytical predictions. Such a switch enables to demonstrate the generation of SWM on a single emitter and to engineer the spectro-temporal shape of the coherent response originating from a TLS. These results pave the way toward multi-pulse manipulations of solid state qubits via implementing the NMR-like control schemes in the optical domain.PostprintPeer reviewe

Three-Dimensional Structure of the Enveloped Bacteriophage Φ12: An Incomplete T = 13 Lattice Is Superposed on an Enclosed T = 1 Shell

BACKGROUND:Bacteriophage phi12 is a member of the Cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola. The genomes of the virus species contain three double-stranded (dsRNA) segments, and the virus capsid itself is organized in multiple protein shells. The segmented dsRNA genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the Cystoviridae similar to the Reoviridae. METHODOLOGY/PRINCIPAL FINDINGS:We present structural studies of cystovirus phi12 obtained using cryo-electron microscopy and image processing techniques. We have collected images of isolated phi12 virions and generated reconstructions of both the entire particles and the polymerase complex (PC). We find that in the nucleocapsid (NC), the phi12 P8 protein is organized on an incomplete T = 13 icosahedral lattice where the symmetry axes of the T = 13 layer and the enclosed T = 1 layer of the PC superpose. This is the same general protein-component organization found in phi6 NC's but the detailed structure of the entire phi12 P8 layer is distinct from that found in the best classified cystovirus species phi6. In the reconstruction of the NC, the P8 layer includes protein density surrounding the hexamers of P4 that sit at the 5-fold vertices of the icosahedral lattice. We believe these novel features correspond to dimers of protein P7. CONCLUSIONS/SIGNIFICANCE:In conclusion, we have determined that the phi12 NC surface is composed of an incomplete T = 13 P8 layer forming a net-like configuration. The significance of this finding in regard to cystovirus assembly is that vacancies in the lattice could have the potential to accommodate additional viral proteins that are required for RNA packaging and synthesis

Degradation of Cdc25A by \u3b2-TrCP during S phase and in response to DNA damage

The Cdc25A phosphatase is essential for cell-cycle progression because of its function in dephosphorylating cyclin-dependent kinases. In response to DNA damage or stalled replication, the ATM and ATR protein kinases activate the checkpoint kinases Chk1 and Chk2, which leads to hyperphosphorylation of Cdc25A1\u20133. These events stimulate the ubiquitin-mediated pro- teolysis of Cdc25A1,4,5 and contribute to delaying cell-cycle progression, thereby preventing genomic instability1\u20137. Here we report that b-TrCP is the F-box protein that targets phosphory- lated Cdc25A for degradation by the Skp1/Cul1/F-box protein complex. Downregulation of b-TrCP1 and b-TrCP2 expression by short interfering RNAs causes an accumulation of Cdc25A in cells progressing through S phase and prevents the degradation of Cdc25A induced by ionizing radiation, indicating that b-TrCP may function in the intra-S-phase checkpoint. Consistent with this hypothesis, suppression of b-TrCP expression results in radioresistant DNA synthesis in response to DNA damage\u2014a phenotype indicative of a defect in the intra-S-phase checkpoint that is associated with an inability to regulate Cdc25A properly. Our results show that b-TrCP has a crucial role in mediating the response to DNA damage through Cdc25A degradation

Field observations of canopy flows over complex terrain

The investigation of airflow over and within forests in complex terrain has been, until recently, limited to a handful of modelling and laboratory studies. Here, we present an observational dataset of airflow measurements inside and above a forest situated on a ridge on the Isle of Arran, Scotland. The spatial coverage of the observations all the way across the ridge makes this a unique dataset. Two case studies of across-ridge flow under near-neutral conditions are presented and compared with recent idealized two-dimensional modelling studies. Changes in the canopy profiles of both mean wind and turbulent quantities across the ridge are broadly consistent with these idealized studies. Flow separation over the lee slope is seen as a ubiquitous feature of the flow. The three-dimensional nature of the terrain and the heterogeneous forest canopy does however lead to significant variations in the flow separation across the ridge, particularly over the less steep western slope. Furthermore, strong directional shear with height in regions of flow separation has a significant impact on the Reynolds stress terms and other turbulent statistics. Also observed is a decrease in the variability of the wind speed over the summit and lee slope, which has not been seen in previous studies. This dataset should provide a valuable resource for validating models of canopy flow over real, complex terrain

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente