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Current seasonal influenza virus vaccines induce responses primarily against immunodominant but highly plastic epitopes in the globular head of the hemagglutinin (HA) glycoprotein. Because of viral antigenic drift at these sites, vaccines need to be updated and readministered annually. To increase the breadth of influenza vaccine–mediated protection, we developed an antigenically complex mixture of recombinant HAs designed to redirect immune responses to more conserved domains of the protein. Vaccine-induced antibodies were disproportionally redistributed to the more conserved stalk of the HA without hindering, and in some cases improving, antibody responses against the head domain. These improved responses led to increased protection against homologous and heterologous viral challenges in both mice and ferrets compared with conventional vaccine approaches. Thus, antigenically complex protein mixtures can at least partially overcome HA head domain antigenic immunodominance and may represent a step toward a more universal influenza vaccine. Editor's summary: A major goal for next-generation influenza vaccines is to elicit antibody responses to more conserved regions, such as the hemagglutinin (HA) stalk. To accomplish this, Luo et al. used a mutagenesis approach to generate a mixture of recombinant HAs that could be used as a vaccine. The mutations were limited to the immunodominant Sb site of the HA head, which the authors hypothesized would push the antibody response to favor immunosubdominant domains. The authors found that vaccination with the HA mixture could boost immune responses against the stalk without negatively affecting head-specific responses. This translated into superior protection against homologous and heterologous influenza challenges in mice and ferrets, supporting further development of this remixed influenza vaccine. —Courtney Malo [ABSTRACT FROM AUTHOR]

Climatic refugia have often been associated with hotspots of richness and endemism, and identified on the basis of molecular or paleobotanical information. Here, we apply a phylogenetic analysis to 18,000 plant communities distributed across the Pyrenees, a south European mountain range, to identify climatic refugia from imprints of relictuality inferred from species' evolutionary distinctiveness (ED). We produced a genus-level phylogenetic tree to calculate the standardized mean ED value of plant communities (cED). Then, we explored which habitats concentrate the plant communities with the highest cED and the interrelated effect of past (long-term climatic stability) and present (topographic and spatial position) factors. Results show strong differences of cED among habitats: forests ranked first, followed by some open habitats like high altitude wetlands. Climate stability and roughness positively influenced cED. A weak negative association resulted between the two diversity measurements (richness and endemism rate) and also with cED. We propose that forests acted as "mobile refugia" during the glacial-interglacial periods, supported by paleoenvironmental reconstructions revealing continuous presence at regional scale of key broadleaved trees at that time. Azonal habitats like the endemic-poor humid communities at high elevation would have also played an important role as more permanent microrefugia. Our approach identifies a variety of habitats and plant assemblages that have successfully withstood past climate change in different ways, and therefore would hold an important evolutionary potential to cope with current climate change. Given their potential role in preserving biodiversity, they should be integrated in future conservation agendas. [ABSTRACT FROM AUTHOR]

Influenza A viruses encode their genomes across eight, negative sense RNA segments. The six largest segments produce mRNA transcripts that do not generally splice; however, the two smallest segments are actively spliced to produce the essential viral proteins NEP and M2. Thus, viral utilization of RNA splicing effectively expands the viral coding capacity without increasing the number of genomic segments. As a first step towards understanding why splicing is not more broadly utilized across genomic segments, we designed and inserted an artificial intron into the normally nonsplicing NA segment. This insertion was tolerated and, although viral mRNAs were incompletely spliced, we observed only minor effects on viral fitness. To take advantage of the unspliced viral RNAs, we encoded a reporter luciferase gene in frame with the viral ORF such that when the intron was not removed the reporter protein would be produced. This approach, which we also show can be applied to the NP encoding segment and in different viral genetic backgrounds, led to high levels of reporter protein expression with minimal effects on the kinetics of viral replication or the ability to cause disease in experimentally infected animals. These data together show that the influenza viral genome is more tolerant of splicing than previously appreciated and this knowledge can be leveraged to develop viral genetic platforms with utility for biotechnology applications. Author summary: Unlike most host mRNAs, many viral mRNAs encode multiple discrete, functional proteins. One method influenza A viruses use to increase the protein products from two of their eight RNA genome segments is splicing. Splicing requires host machinery to remove part of the viral mRNA, the intron, to generate a different mRNA product. Although only certain influenza viral segments naturally splice, we were interested in whether additional segments could splice to produce multiple proteins. We inserted artificial introns harboring reporter genes into otherwise nonsplicing genomic segments of an H1N1 influenza A virus and found that this modification was well tolerated by the virus. We further demonstrated that an unrelated H3N2 influenza A virus could similarly support splicing and express a reporter protein from an artificial intron. These findings have implications for our understanding of how viruses expand their coding capacity with a limited genome. Additionally, encoding reporter proteins in spliced intronic sequences also represents a new method of generating reporter viruses requiring limited manipulation of the viral RNA. [ABSTRACT FROM AUTHOR]

The edge betweenness centrality of an edge is loosely defined as the fraction of shortest paths between all pairs of vertices passing through that edge. In this paper, we investigate graphs where the edge betweenness centrality of edges is uniform. It is clear that if a graph G is edge-transitive (its automorphism group acts transitively on its edges) then G has uniform edge betweenness centrality. However this sufficient condition is not necessary. Graphs that are not edge-transitive but have uniform edge betweenness centrality appear to be very rare. Of the over 11.9 million connected graphs on up to ten vertices, there are only four graphs that are not edge-transitive but have uniform edge betweenness centrality. Despite this rarity among small graphs, we present methods for creating infinite classes of graphs with this unusual combination of properties. [ABSTRACT FROM AUTHOR]

Objective Magnetic resonance (MR) diffusion-weighted imaging (DWI) is sensitive to small acute ischemic lesions and might help diagnose transient ischemic attack (TIA). Reclassification of patients with TIA and a DWI lesion as 'stroke' is under consideration. We assessed DWI positivity in TIA and implications for reclassification as stroke. Methods We searched multiple sources, without language restriction, from January 1995 to July 2012. We used PRISMA guidelines, and included studies that provided data on patients presenting with suspected TIA who underwent MR DWI and reported the proportion with an acute DWI lesion. We performed univariate random effects meta-analysis to determine DWI positive rates and influencing factors. Results We included 47 papers and 9,078 patients (range = 18-1,693). Diagnosis was by a stroke specialist in 26 of 47 studies (55%); all studies excluded TIA mimics. The pooled proportion of TIA patients with an acute DWI lesion was 34.3% (95% confidence interval [CI] = 30.5-38.4, range = 9-67%; I2 = 89.3%). Larger studies (n > 200) had lower DWI-positive rates (29%; 95% CI = 23.2-34.6) than smaller (n < 50) studies (40.1%; 95% CI = 33.5-46.6%; p = 0.035), but no other testable factors, including clinician speciality and time to scanning, reduced or explained the 7-fold DWI-positive variation. Interpretation The commonest DWI finding in patients with definite TIA is a negative scan. Available data do not explain why ⅔ of patients with definite specialist-confirmed TIA have negative DWI findings. Until these factors are better understood, reclassifying DWI-positive TIAs as strokes is likely to increase variance in estimates of global stroke and TIA burden of disease. ANN NEUROL 2014;75:67-76 [ABSTRACT FROM AUTHOR]

Background: Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. Results: We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. Conclusion: Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the Palawan peacock-pheasantPolyplectron napoleonisis 16,710 bp and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control-region. All protein-coding genes use the standard ATG start codon, except forcox1which has GTG start codon. Seven out of 13 PCGs have TAA stop codons, two have AGG (cox1andnd6), and three PCGs (nd2, cox2andnd4) have incomplete stop codon of just T– – nucleotide. [ABSTRACT FROM AUTHOR]

The Germain's Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae) is classified as Near Threatened on the IUCN Red List. The complete mitochondrial genome of P. germaini is 16,699 bp, consisting of 13 protein-coding genes, 2 rRNA, 22 tRNA genes and 1 control region. All of the 13 protein-coding genes have ATG as start codon. Eight of the 13 protein-coding genes have TAA as stop codon. [ABSTRACT FROM AUTHOR]