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Povzetek: Background: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. Results: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. Conclusions: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies.
Ključne besede: tomato, weed, virus, viroid, virome, virus discovery, virus diversity, phylogenetics, metagenomics, viromics
Objavljeno v DiRROS: 13.04.2023; Ogledov: 579; Prenosov: 126
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Povzetek: Neuroendocrine neoplasms (NENs) of the lung encompass neuroendocrine tumors (NETs) composed of typical (TC) and atypical (AC) carcinoids and full-fledged carcinomas (NECs) inclusive of large cell neuroendocrine carcinoma (LCNEC) and small cell carcinoma (SCLC). NETs and NECs are thought to represent distinct and separate lesions with neither molecular overlap nor common developmental continuum. Two perspectives were addressed regarding the morphologic and molecular classification of lung NENs: (i) a supervised approach by browsing the traditional classification, the relevant gene alterations, and their clinical implications; and (ii) an unsupervised approach, by reappraising neoplasms according to risk factors and natural history of disease to construct an interpretation model relied on biological data. We herein emphasize lights and shadows of the current classification of lung NENs and provide an alternative outlook on these tumors focused on what we currently know about the biological determinants and the natural history of disease.
Ključne besede: neuroendocrine tumors, lung neoplasms, carcinoma, lung tumors, morphologic classification, molecular classification
Objavljeno v DiRROS: 02.02.2021; Ogledov: 1154; Prenosov: 764
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Povzetek: In a tokamak, the accurate estimation of the plasma boundary is essential to maximise the fusion performance and is also the first line of defence for the physical integrity of the device. In particular, the first wall components might get severely damaged if over-exposed to a high plasma thermal load. The most common approach to calculate the plasma geometry and related parameters is based in a large set of different types of magnetic sensors. Using this information, real-time plasma equilibrium codes infer a flux map and calculate the shape and geometry of the plasma boundary and its distance to a known reference (e.g. first wall). These are inputs to one or more controllers capable of acting on the shape and trajectory based in pre-defined requests. Depending on the device, the error of the estimated boundary distance must usually be less than 1 centimetre, which translates into very small errors on the magnetic measurement itself. Moreover, asymmetries in the plasma generated and surrounding magnetic fields can produce local shape deformations potentially leading to an unstable control of the plasma geometry. The JET tokamak was recently upgraded to a new and less thermally robust all-metal wall, also known as the ITER-like wall. Currently the shape controller system uses the output of a single reconstruction algorithm to drive the plasma geometry and the protection systems have no input from the plasma boundary reconstruction. These choices are historical and were due to architectural, hardware and processing power limitations. Taking advantage of new multi-core systems and of the already proved robustness of the JET real-time network, this paper proposes a distributed architecture for the real-time identification of faults in the magnetic measurements of the JET tokamak. Besides detecting simple faults, such as short-circuits and open-loops, the system compares the expected measurement at the coil location and the real measurement, producing a confidence valu- . Several magnetic reconstructions, using sensors from multiple toroidally distributed locations, can run in parallel, allowing for a voting or averaging scheme selection. Finally, any fault warnings can be directly fed to the real-time protection sequencer system, whose main function is to coordinate the protection of the JET's first wall.
Objavljeno v DiRROS: 24.11.2014; Ogledov: 3343; Prenosov: 0