1. Development and validation of a one-step reverse transcription real-time PCR assay for simultaneous detection and identification of tomato mottle mosaic virus and tomato brown rugose fruit virusAntonio Tiberini, Ariana Manglli, Anna Taglienti, Ana Vučurović, Jakob Brodarič, Luca Ferretti, Marta Luigi, Andrea Gentili, Nataša Mehle, 2022, original scientific article Abstract: settingsOrder Article Reprints
Open AccessArticle
Development and Validation of a One-Step Reverse Transcription Real-Time PCR Assay for Simultaneous Detection and Identification of Tomato Mottle Mosaic Virus and Tomato Brown Rugose Fruit Virus
by Antonio Tiberini 1,*,Ariana Manglli 1,Anna Taglienti 1ORCID,Ana Vučurović 2ORCID,Jakob Brodarič 2ORCID,Luca Ferretti 1,Marta Luigi 1ORCID,Andrea Gentili 1 andNataša Mehle 2,3ORCID
1
CREA—Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Roma, Italy
2
Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
3
School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri, Glavni trg 8, SI-5271 Vipava, Slovenia
*
Author to whom correspondence should be addressed.
Plants 2022, 11(4), 489; https://doi.org/10.3390/plants11040489
Submission received: 30 December 2021 / Revised: 31 January 2022 / Accepted: 9 February 2022 / Published: 11 February 2022
(This article belongs to the Special Issue Tobamoviruses and Interacting Viruses in Modern Agriculture)
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Abstract
Tobamovirus species represent a threat to solanaceous crops worldwide, due to their extreme stability and because they are seed borne. In particular, recent outbreaks of tomato brown rugose fruit virus in tomato and pepper crops led to the establishment of prompt control measures, and the need for reliable diagnosis was urged. Another member of the genus, tomato mottle mosaic virus, has recently gained attention due to reports in different continents and its common features with tomato brown rugose fruit virus. In this study, a new real-time RT-PCR detection system was developed for tomato brown rugose fruit virus and tomato mottle mosaic virus on tomato leaves and seeds using TaqMan chemistry. This test was designed to detect tomato mottle mosaic virus by amplifying the movement protein gene in a duplex assay with the tomato brown rugose fruit virus target on the CP-3’NTR region, which was previously validated as a single assay. The performance of this test was evaluated, displaying analytical sensitivity 10−5–10−6-fold dilution for seeds and leaves, respectively, and good analytical specificity, repeatability, and reproducibility. Using the newly developed and validated test, tomato brown rugose fruit virus detection was 100% concordant with previously performed analyses on 106 official samples collected in 2021 from different continents.
Keywords: real-time PCR, tomato mottle mosaic virus, tomato brown rugose fruit virus, leaves detection, seeds detections, performance criteria
Published in DiRROS: 16.07.2024; Views: 0; Downloads: 2
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3. Is it function or fashion? : an integrative analysis of morphology, performance, and metabolism in a colour polymorphic lizardVeronica Gomes, Anamarija Žagar, Guillem Pérez i de Lanuza, Tatjana Simčič, Miguel A. Carretero, 2022, original scientific article Abstract: Colour polymorphism may be accompanied by alternative expressions of phenotypic traits that are directly or indirectly related to fitness, and selection forces may act on the traits separately or concurrently. In polymorphic species, natural selection may act through frequency- or density-dependent mechanisms and maintain polymorphism through interactions among morphs. We used an integrative approach to examine functionally relevant and interrelated life history traits in the context of colour polymorphism in the European wall lizard (Podarcis muralis). Body, head and limb morphology, bite and locomotor performance, and physiology, particularly metabolic and antioxidant capacity, were analysed in the three pure colour morphs (yellow, orange, white) and the two mosaic morphs (yellow-orange and white-orange). Morphological differences between morphs were present but subtle and consisted mainly of variations in head length. Head size and bite force were strongly associated between and within morphs. Limb and boot morphology and locomotor performance (sprinting and climbing) were variably associated among morphs. Finally, variation in biochemical indicators of cellular metabolism and antioxidant capacity appeared to be largely independent of morphology and performance. The results provide evidence for existing and non-existing relationships between colour and morphology, performance, and physiology that could have short- and long-term effects on selection.
Keywords: colour morphs, sprint speed, climbing, bite force, physiology
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4. Can young-of-the-year invasive fish keep up with young-of-the-year native fish? A comparison of feeding rates between invasive sticklebacks and whitefish : a comparison of feeding rates between invasive sticklebacks and whitefishŽiga Ogorelec, Lars G. Rudstam, Dietmar Straile, 2022, original scientific article Abstract: Invasion of non-native species might alter food web structure and the strength of top-down control within lake ecosystems. As top-down control exerted by fish populations is often dominated by young of the year fish, the impact of new fish species might depend on the feeding rates of the juvenile fish. Here we provide comparative analyses of feeding rates of juvenile whitefish (Coregonus wartmanni) – a native and specialised planktivore and an invasive generalist (sticklebacks, Gasterosteus aculeatus). We studied feedings rates of whitefish and sticklebacks in aquaria experiments using 2 cm to 8 cm fish feeding on seven zooplankton species common to Lake Constance. As whitefish hatch several months earlier than sticklebacks, 0+ whitefish are larger than 0+ sticklebacks throughout the year and hence are predicted to have higher feeding rates on especially large zooplankton species. We show that sticklebacks as small as 2 cm were able to feed on the largest zooplankton species of Lake Constance. Further, stickleback feeding rates were similar to both the same size 0+ whitefish and the larger 0+ whitefish co-occurring with smaller 0+ sticklebacks. Hence, 0+ sticklebacks will compete with 0+ whitefish for the same zooplankton species, therefore the invasion of sticklebacks is unlikely to change the relative feeding pressure by individual 0+ fish on zooplankton species.
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5. Nanoscale transformations of amphiboles within human alveolar epithelial cellsRuggero Vigliaturo, Maja Jamnik, Goran Dražić, Marjetka Podobnik, Magda Tušek-Žnidarič, Giancarlo Della Ventura, Günther Redhammer, Nada Žnidaršič, Simon Caserman, Reto Gieré, 2022, original scientific article Abstract: Amphibole asbestos is related to lung fibrosis and several types of lung tumors. The disease-triggering mechanisms still challenge our diagnostic capabilities and are still far from being fully understood. The literature focuses primarily on the role and formation of asbestos bodies in lung tissues, but there is a distinct lack of studies on amphibole particles that have been internalized by alveolar epithelial cells (AECs). These internalized particles may directly interact with the cell nucleus and the organelles, exerting a synergistic action with asbestos bodies (AB) from a different location. Here we document the near-atomic- to nano-scale transformations induced by, and taking place within, AECs of three distinct amphiboles (anthophyllite, grunerite, “amosite”) with different Fe-content and morphologic features. We show that: (i) an Fe-rich layer is formed on the internalized particles, (ii) particle grain boundaries are transformed abiotically by the internal chemical environment of AECs and/or by a biologically induced mineralization mechanism, (iii) the Fe-rich material produced on the particle surface does not contain large amounts of P, in stark contrast to extracellular ABs, and (iv) the iron in the Fe-rich layer is derived from the particle itself. Internalized particles and ABs follow two distinct formation mechanisms reaching different physicochemical end-states.
Keywords: amphiboles, human alveolar epithelial cells, asbestos, lung cancer, nanoscale investigation, acS/TEM-EDXS, dual-EELS, asbestos-related tumors
Published in DiRROS: 16.07.2024; Views: 1; Downloads: 4
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6. Upregulation of cathepsin X in glioblastoma : interplay with γ-enolase and the effects of selective cathepsin X inhibitorsBernarda Majc, Anamarija Habič, Metka Novak, Ana Rotter, Andrej Porčnik, Jernej Mlakar, Vera Župunski, Urša Pečar Fonović, Damijan Knez, Nace Zidar, Stanislav Gobec, Janko Kos, Tamara Lah Turnšek, Anja Pišlar, Barbara Breznik, 2022, original scientific article Keywords: glioblastoma, cathepsin X, γ-enolase, tumor microenvironment, glioblastoma stem cells, cathepsin X inhibitors
Published in DiRROS: 16.07.2024; Views: 4; Downloads: 2
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7. Improving taxonomic practices and enhancing its extensibility—an example from araneologyJason E. Bond, Rebecca L. Godwin, Jordan D. Colby, Lacie G. Newton, Xavier J. Zahnle, Ingi Agnarsson, Christopher A. Hamilton, Matjaž Kuntner, 2022, original scientific article Abstract: Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinizespider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newlydescribed species. We evaluated what type of data were used to delineate species, whether data weremade freely available, whether an explicit species hypothesis was stated, what types of media wereused, the sample sizes, and the degree to which species constructs were integrative. The findings wereport reveal that taxonomy remains largely descriptive, not integrative, and provides no explicitconceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-thirdof all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies madedata freely available, and only ~14% of all newly described species employed more than one line ofevidence, with molecular data used in ~6% of the studies. These same trends have been discovered inother animal groups, and therefore we find it logical that taxonomists face an uphill challenge whenjustifying the scientific rigor of their field and securing the needed resources. To move taxonomyforward, we make recommendations that, if implemented, will enhance its rigor, repeatability, andscientific standards.
Keywords: taxonomy, taxonomic crisis, species concepts, data management, monographic research
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8. Water quality characteristics and source analysis of pollutants in the Maotiao river basin (SW China)Yinjiu Li, Qiuhua Li, Shulin Jiao, Chen Liu, Liuying Yang, Guojia Huang, Si Zhou, Mengshu Han, Anton Brancelj, 2022, original scientific article Abstract: Rivers are an important mediator between human activities and the natural environment. They provide multiple functions, including irrigation, transportation, food supply, recreation, and water supply. Therefore, evaluations of water quality and pollution sources are of great significance for ecological restoration and management of rivers. In this study, the improved “vušekriterijumska optimizacija i kompromisno rješenje” (VIKOR in Serbian; in English: Multicriteria Optimization and Compromise Solution), and a geodetector were used to analyze the water quality characteristics and pollution sources of the Maotiao River Basin (Gizhou province, SW China). The results showed that the water quality of the Maotiao River Basin deteriorated significantly during the summer drought period, as was evident in the reservoirs and lakes. It improved in the wet season (i.e., during the summer period) due to runoff dilution. Water quality decreased along the river’s course, from upstream to downstream sections. The results of the geographic detector analysis showed that agricultural areas were the primary factor affecting the spatial distribution of water quality in the river basin. In July, August, and November 2020, the influence of agricultural land was 0.72, 0.60, or 0.80, respectively, and the interactions among urban, industrial, agricultural, and forested areas explained 99.2%, 83.2%, or 99.9% of the spatial differentiation of water quality, respectively. Due to the influence of spatial scale, settlements have a small influence on the spatial distribution of water quality. Their impact factors were 0.38, −0.24, and −0.05, respectively. Notably, the negative relationship of water quality and forested areas reflects that topography, types of landscapes, and soil thickness have considerable influences on the Maotiao River Basin’s water quality. Based on the findings, we infer that good farmland water conservancy projects and comprehensive management of different types of landscapes, such as forests, agriculture, and urban area and water bodies, are of great significance for improving water quality.
Keywords: water quality, statistical data, VIKOR model, CRITIC model
Published in DiRROS: 16.07.2024; Views: 0; Downloads: 4
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9. Experimental validation of Monte Carlo based treatment planning system in bone density equivalent mediaĐeni Smilović Radojčić, Božidar Casar, David Rajlić, Manda Švabić Kolacio, Ignasi Méndez Carot, Nevena Obajdin, Dea Dundara Debeljuh, Slaven Jurković, 2020, original scientific article Published in DiRROS: 16.07.2024; Views: 7; Downloads: 4
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