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Abstract: High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
Keywords: plant virus, high-throughput sequencing, bioinformatics, detection, discovery
Published in DiRROS: 05.08.2024; Views: 66; Downloads: 65
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Abstract: We describe different aspects of the reproductive biology, mating behavior, and vibratory communication of the pentatomid Edessa meditabunda (Fabr.). This species shows lower copulation frequency and reproductive potential with longer sexual maturation period compared to other species of pentatomids. Females with multiple mating show increased fecundity when compared with single-mated females and both increased fecundity and reduced longevity when compared with virgin females. Courtship and mating behavior and vibratory signals are typical and similar to what was observed in other species of pentatomids, except that males started the courtship. These results constitute the first paper on biology, behavior, and vibratory communication among species of the subfamily Edessinae.
Keywords: animal ecology, animal communication
Published in DiRROS: 05.08.2024; Views: 120; Downloads: 108
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Abstract: The “stem cells” discipline represents one of the most dynamic areas in biomedicine. While adult marine/aquatic invertebrate stem cell (MISC) biology is of prime research and medical interest, studies on stem cells from organisms outside the classical vertebrate (e.g., human, mouse, and zebrafish) and invertebrate (e.g., Drosophila, Caenorhabditis) models have not been pursued vigorously. Marine/aquatic invertebrates constitute the largest biodiversity and the widest phylogenetic radiation on Earth, from morphologically simple organisms (e.g., sponges, cnidarians), to the more complex mollusks, crustaceans, echinoderms, and protochordates. These organisms contain a kaleidoscope of MISC-types that allow the production of a large number of novel bioactive-molecules, many of which are of significant potential interest for human health. MISCs further participate in aging and regeneration phenomena, including whole-body regeneration. For years, the European MISC-community has been highly fragmented and has established scarce ties with biomedical industries in an attempt to harness MISCs for human welfare. Thus, it is important to (i) consolidate the European community of researchers working on MISCs; (ii) promote and coordinate European research on MISC biology; (iii) stimulate young researchers to embark on research in MISC-biology; (iv) develop, validate, and share novel MISC tools and methodologies; (v) establish the MISC discipline as a forefront interest of biomedical disciplines, including nanobiomedicine; and (vi) establish collaborations with industries to exploit MISCs as sources of bioactive molecules. In order to fill the recognized gaps, the EC-COST Action 16203 “MARISTEM” has recently been launched. At its initial stage, the consortium unites 26 scientists from EC countries, Cooperating countries, and Near Neighbor Countries.
Keywords: aging, bioactive molecules, blue biotechnology, cancer, cell culture, COST Action, Europe, marine/aquatic invertebrates, regeneration, stem cells
Published in DiRROS: 24.07.2024; Views: 309; Downloads: 88
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Abstract: Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution.
Published in DiRROS: 22.07.2024; Views: 110; Downloads: 122
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Abstract: Purpose Intumescent coatings are nowadays a dominant passive system used to protect structural materials in case of fire. Due to their reactive swelling behaviour, intumescent coatings are particularly complex materials to be modelled and predicted, which can be extremely useful especially for performance-based fire safety designs. In addition, many parameters influence their performance, and this challenges the definition and quantification of their material properties. Several approaches and models of various complexities are proposed in the literature, and they are reviewed and analysed in a critical literature review. Design/methodology/approach Analytical, finite-difference and finite-element methods for modelling intumescent coatings are compared, followed by the definition and quantification of the main physical, thermal, and optical properties of intumescent coatings: swelled thickness, thermal conductivity and resistance, density, specific heat capacity, and emissivity/absorptivity. Findings The study highlights the scarce consideration of key influencing factors on the material properties, and the tendency to simplify the problem into effective thermo-physical properties, such as effective thermal conductivity. As a conclusion, the literature review underlines the lack of homogenisation of modelling approaches and material properties, as well as the need for a universal modelling method that can generally simulate the performance of intumescent coatings, combine the large amount of published experimental data, and reliably produce fire-safe performance-based designs. Research limitations/implications Due to their limited applicability, high complexity and little comparability, the presented literature review does not focus on analysing and comparing different multi-component models, constituted of many model-specific input parameters. On the contrary, the presented literature review compares various approaches, models and thermo-physical properties which primarily focusses on solving the heat transfer problem through swelling intumescent systems. Originality/value The presented literature review analyses and discusses the various modelling approaches to describe and predict the behaviour of swelling intumescent coatings as fire protection for structural materials. Due to the vast variety of available commercial products and potential testing conditions, these data are rarely compared and combined to achieve an overall understanding on the response of intumescent coatings as fire protection measure. The study highlights the lack of information and homogenisation of various modelling approaches, and it underlines the research needs about several aspects related to the intumescent coating behaviour modelling, also providing some useful suggestions for future studies.
Keywords: intumescent coatings, fire protection, modelling, structural fire engineering, fire safety, performance-based design
Published in DiRROS: 17.04.2024; Views: 270; Downloads: 129
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