The Transcriptional Landscape of Marek’s Disease Virus in Primary Chicken B Cells Reveals Novel Splice Variants and Genes

Marek’s disease virus (MDV) is an oncogenic alphaherpesvirus that infects chickens and poses a serious threat to poultry health. In infected animals, MDV efficiently replicates in B cells in various lymphoid organs. Despite many years of research, the viral transcriptome in primary target cells of MDV remained unknown. In this study, we uncovered the transcriptional landscape of the very virulent RB1B strain and the attenuated CVI988/Rispens vaccine strain in primary chicken B cells using high-throughput RNA-sequencing. Our data confirmed the expression of known genes, but also identified a novel spliced MDV gene in the unique short region of the genome. Furthermore, de novo transcriptome assembly revealed extensive splicing of viral genes resulting in coding and non-coding RNA transcripts. A novel splicing isoform of MDV UL15 could also be confirmed by mass spectrometry and RT-PCR. In addition, we could demonstrate that the associated transcriptional motifs are highly conserved and closely resembled those of the host transcriptional machinery. Taken together, our data allow a comprehensive re-annotation of the MDV genome with novel genes and splice variants that could be targeted in further research on MDV replication and tumorigenesis

Biogenic Nitrogen Gas Production at the Oxic–Anoxic Interface in the Cariaco Basin, Venezuela

Excess nitrogen gas (N2xs) was measured in samples collected at six locations in the eastern and western sub-basins of the Cariaco Basin, Venezuela, in September 2008 (non-upwelling conditions) and March 2009 (upwelling conditions). During both sampling periods, N2xs concentrations were below detection in surface waters, increasing to ~ 22 μmol N kg−1 at the oxic–anoxic interface ([O2] \u3c ~ 4 μmol kg−1, ~ 250 m). Below the oxic–anoxic interface (300–400 m), the average concentration of N2xs was 24.7 ± 1.9 μmol N kg−1 in September 2008 and 27.5 ± 2.0 μmol N kg−1 in March 2009, i.e., N2xs concentrations within this depth interval were ~ 3 μmol N kg−1 higher (p \u3c 0.001) during the upwelling season compared to the non-upwelling period. These results suggest that N-loss in the Cariaco Basin may vary seasonally in response to changes in the flux of sinking particulate organic matter. We attribute the increase in N2xs concentrations, or N-loss, observed during upwelling to: (1) higher availability of fixed nitrogen derived from suspended and sinking particles at the oxic–anoxic interface and/or (2) enhanced ventilation at the oxic–anoxic interface during upwelling

A 2k2k-Vertex Kernel for Maximum Internal Spanning Tree

We consider the parameterized version of the maximum internal spanning tree problem, which, given an $n$-vertex graph and a parameter $k$, asks for a spanning tree with at least $k$ internal vertices. Fomin et al. [J. Comput. System Sci., 79:1-6] crafted a very ingenious reduction rule, and showed that a simple application of this rule is sufficient to yield a $3k$-vertex kernel. Here we propose a novel way to use the same reduction rule, resulting in an improved $2k$-vertex kernel. Our algorithm applies first a greedy procedure consisting of a sequence of local exchange operations, which ends with a local-optimal spanning tree, and then uses this special tree to find a reducible structure. As a corollary of our kernel, we obtain a deterministic algorithm for the problem running in time $4^k \cdot n^{O(1)}$

Outcome of the ‘Drip-and-Ship’ Paradigm among Patients with Acute Ischemic Stroke: Results of a Statewide Study

www.karger.com/cee This is an Open Access article licensed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License (www.karger.com/OA-license), applicable to the online version of the article only. Distribution for non-commercial purposes only.

No Consensus on Definition Criteria for Stroke Registry Common Data Elements

www.karger.com/cee This is an Open Access article licensed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License (www.karger.com/OA-license), applicable to the online version of the article only. Distribution for non-commercial purposes only

Global observational needs and resources for marine biodiversity

Otros autores: Best, B., Brandt, A., Goodwin, K., Iken, A., Marques, A., Miloslavich, P., Ostrowski, M., Turner, W., Achterberg, E., Barry, T., Bigatti, G., Henry, L.A., Ramiro-Sánchez, B., Durán, P., Morato, T., Murray Roberts, J., García-Alegre, A., Cuadrado, M., Murton, B.The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the spatial scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation extending back several millions of years. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation

Disturbance indicator values for European plants

Motivation Indicator values are numerical values used to characterize the ecological niches of species and to estimate their occurrence along gradients. Indicator values on climatic and edaphic niches of plant species have received considerable attention in ecological research, whereas data on the optimal positioning of species along disturbance gradients are less developed. Here, we present a new data set of disturbance indicator values identifying optima along gradients of natural and anthropogenic disturbance for 6382 vascular plant species based on the analysis of 736,366 European vegetation plots and using expert-based characterization of disturbance regimes in 236 habitat types. The indicator values presented here are crucial for integrating disturbance niche optima into large-scale vegetation analyses and macroecological studies. Main types of variables contained We set up five main continuous indicator values for European vascular plants: disturbance severity, disturbance frequency, mowing frequency, grazing pressure and soil disturbance. The first two indicators are provided separately for the whole community and for the herb layer. We calculated the values as the average of expert-based estimates of disturbance values in all habitat types where a species occurs, weighted by the number of plots in which the species occurs within a given habitat type. Spatial location and grain Europe. Vegetation plots ranging in size from 1 to 1000 m(2). Time period and grain Vegetation plots mostly sampled between 1956 and 2013 (= 5th and 95th quantiles of the sampling year, respectively). Major taxa and level of measurement Species-level indicator values for vascular plants. Software format csv file