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

On rr-Simple kk-Path

An $r$-simple $k$-path is a {path} in the graph of length $k$ that passes through each vertex at most $r$ times. The $r$-SIMPLE $k$-PATH problem, given a graph $G$ as input, asks whether there exists an $r$-simple $k$-path in $G$. We first show that this problem is NP-Complete. We then show that there is a graph $G$ that contains an $r$-simple $k$-path and no simple path of length greater than $4\log k/\log r$. So this, in a sense, motivates this problem especially when one's goal is to find a short path that visits many vertices in the graph while bounding the number of visits at each vertex. We then give a randomized algorithm that runs in time $$\mathrm{poly}(n)\cdot 2^{O( k\cdot \log r/r)}$$ that solves the $r$-SIMPLE $k$-PATH on a graph with $n$ vertices with one-sided error. We also show that a randomized algorithm with running time $\mathrm{poly}(n)\cdot 2^{(c/2)k/ r}$ with $c<1$ gives a randomized algorithm with running time \poly(n)\cdot 2^{cn} for the Hamiltonian path problem in a directed graph - an outstanding open problem. So in a sense our algorithm is optimal up to an $O(\log r)$ factor

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

Influence of hydrodynamic processes on the fate of sedimentary organic matter on continental margins

Understanding the effects of hydrodynamic forcing on organic matter (OM) composition is important for assessment of organic carbon (OC) burial in marginal seas on regional and global scales. Here we examine the relationships between regional oceanographic conditions (bottom shear stress), and the physical characteristics (mineral surface area and grain size) and geochemical properties (OC content [OC%] and carbon isotope compositions [13C, 14C]) of a large suite of surface sediments from the Chinese marginal seas to assess the influence of hydrodynamic processes on the fate of OM on shallow continental shelves. Our results suggest that 14C content is primarily controlled by organo‐mineral interactions and hydrodynamically driven resuspension processes, highlighted by (i) positive correlations between 14C content and OC% (and surface area) and (ii) negative correlations between 14C content and grain size (and bottom shear stress). Hydrodynamic processes influence 14C content due to both OC aging during lateral transport and accompanying selective degradation of OM associated with sediment (re) mobilization, these effects being superimposed on the original 14C characteristics of carbon source. Our observations support the hypotheses of Blair and Aller (2012, https://doi.org/10.1146/annurev‐marine‐120709‐142717) and Leithold et al. (2016, https://doi.org/10.1016/j.earscirev.2015.10.011) that hydrodynamically driven sediment translocation results in greater OC 14C depletion in broad, shallow marginal seas common to passive margin settings than on active margins. On a global scale, this may influence the extent to which continental margins act as net carbon sources and sinks. Our findings thus suggest that hydrodynamic processes are important in shaping the nature, dynamics, and magnitude of OC export and burial in passive marginal seas

Molecular characterization of Miraflores peach variety and relatives using SSRs

The definitive version is published in: http://www.sciencedirect.com/science/journal/03044238Some traditional peach varieties, originated from the region of Aragón (Spain), were analysed by SSRs (Simple Sequence Repeats). The aim of this research was to characterize 19 clones related to ‘Miraflores’ variety, with unknown pedigrees, to assess their genetic diversity and to elucidate their possible relationships with 10 traditional peach varieties. Twenty SSR primer pairs with high levels of polymorphism, which have been previously developed for peach, were used in this study. A total of 46 alleles were obtained for all the microsatellites studied, ranging from one to six alleles per locus, with a mean value of 2.3 alleles per locus. Fourteen SSRs were polymorphic in the set of varieties studied and permitted to distinguish 16 different genotypes out of the 30 initially studied, although fourteen ‘Miraflores’ clones showed identical gel profiles. The genetic distance matrix was used to construct Neighbor joining cluster and to perform principal coordinate analysis which allowed the arrangement of all the genotypes according to their genetic relationships. The genetic relationships among these traditional peach varieties, and in particular among ‘Miraflores’ clones are discussed. The obtained results confirm that microsatellite markers are very useful for these purposes.We are thankful to T.N. Zhebentyayeva and G.L. Reighard for helpful comments on the manuscript. This research was funded by CICYT (Comisión Interministerial de Ciencia y Tecnología, AGL2002-04219 and AGL 2005-05533), INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, RF03-014-C2), Bilateral Spain-France (HF03-273) and DGA (A28, A44) projects and co-funded by the European Regional Development Fund. M. Bouhadida was supported by a fellowship from the AECI (Agencia Española de Cooperación Internacional) of the Spanish Ministry of Foreign Affairs.Peer reviewe

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

Plasma-photonic spatiotemporal synchronization of relativistic electron and laser beams

Modern particle accelerators and their applications increasingly rely on precisely coordinated interactions of intense charged particle and laser beams. Femtosecond-scale synchronization alongside micrometre-scale spatial precision are essential e.g. for pump-probe experiments, seeding and diagnostics of advanced light sources and for plasma-based accelerators. State-of-the-art temporal or spatial diagnostics typically operate with low-intensity beams to avoid material damage at high intensity. As such, we present a plasma-based approach, which allows measurement of both temporal and spatial overlap of high-intensity beams directly at their interaction point. It exploits amplification of plasma afterglow arising from the passage of an electron beam through a laser-generated plasma filament. The corresponding photon yield carries the spatiotemporal signature of the femtosecond-scale dynamics, yet can be observed as a visible light signal on microsecond-millimetre scales