1. Genome-informed design of a LAMP assay for the specific detection of the strain of ‘Candidatus Phytoplasma asteris’ phytoplasma occurring in grapevines in South AfricaŠpela Alič, Marina Dermastia, Johan Burger, Matthew Dickinson, Gerhard Pietersen, Gert Pietersen, Tanja Dreo, 2022, original scientific article Abstract: Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine ‘Candidatus Phytoplasma asteris’ that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.
Keywords: aster yellows, fruit, LAMP, molecular detection, pathogendetection, phytoplasma, Prokaryotes
Published in DiRROS: 17.07.2024; Views: 2; Downloads: 2
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2. 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: 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: 5; Downloads: 5
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3. Tomato brown rugose fruit virus in aqueous environments : survival and significance of water-mediated transmissionNataša Mehle, Katarina Bačnik, Irena Bajde, Jakob Brodarič, Adrian Fox, Ion Gutiérrez-Aguirre, Miha Kitek, Denis Kutnjak, Yue Lin Loh, Olivera Maksimović, Maja Ravnikar, Elise Vogel, Christine Vos, Ana Vučurović, 2023, original scientific article Abstract: Tomato brown rugose fruit virus (ToBRFV) has recently emerged as a major disease of tomatoes and peppers. ToBRFV is a seed- and contact-transmitted virus. In Slovenia, ToBRFV RNA was detected in samples of wastewater, river, and water used to irrigate plants. Even though the source of detected RNA could not be clearly established, this raised the question of the significance of the detection of ToBRFV in water samples and experimental studies were performed to address this question. The data presented here confirm that the release of virus particles from the roots of infected plants is a source of infectious ToBRFV particles in water and that the virus can remain infective up to four weeks in water stored at room temperature, while its RNA can be detected for much longer. These data also indicate that irrigation with ToBRFV-contaminated water can lead to plant infection. In addition, it has been shown that ToBRFV circulated in drain water in commercial tomato greenhouses from other European countries and that an outbreak of ToBRFV can be detected by regular monitoring of drain water. A simple method for concentrating ToBRFV from water samples and a comparison of the sensitivity of different methods, including the determination of the highest ToBRFV dilution still capable of infecting test plants, were also investigated. The results of our studies fill the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the role of water-mediated transmission, and provide a reliable risk assessment to identify critical points for monitoring and control.
Keywords: tomato brown rugose fruit virus, tomato, hydroponics, water-linked epidemiology, survival
Published in DiRROS: 12.07.2024; Views: 33; Downloads: 19
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4. A five-step framework for creating forests for the futureMarko Kovač, Gregor Božič, Andreja Ferreira, Gal Kušar, Boštjan Mali, 2024, original scientific article Abstract: Changing environmental conditions, disturbances, and escalating demands for forest ecosystem services require foresters to restore present forestlands with new forest generations that will exhibit ecological integrity, diversity, high adaptive capacity, and the ability to provide essential ecosystem services. Establishing such forests requires careful consideration of the forest landscape and site dynamics. In pursuit of these requirements, we developed a novel framework that enables the restoration of forest sites and promotes the desired features of the forest complex at the same time. This framework was designed with the methods of system engineering and was organized in the same way as the forest planning process. It was tested in the habitat type of Illyrian Fagus sylvatica forests belonging to the Natura 2000 network. The environmental, vegetation, and site conditions were investigated via field inspections, available forest management plans, and simple GIS analyses. Additionally, we established a seminatural stand composed of European beech, sessile oak, sycamore maple, silver fir, and some wild fruit tree species. The survival of planted species was assessed using census and simple random sampling, the performance of provenances by the Student’s test, while microhabitat factors were explored by a one-way ANOVA. The survival rate of key species was estimated to be 55.6%, while that of fruit species was estimated to be 94.5%. Our framework demonstrated satisfactory performance and contained sufficient benchmarks to facilitate consistent decision-making. In the discussion, we elucidate the framework’s primary features and attributes of the mixed stand, where we also expose some open issues to be addressed in the future.
Keywords: restoration, forest habitat type, indigenous species, planting, mixed stand, key species, fruit species
Published in DiRROS: 13.06.2024; Views: 117; Downloads: 83
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5. Morphologic variability of the Acer campestre L. populations in Bosnia and HerzegovinaStjepan Kvesić, Mirzeta Memišević Hodžić, Matjaž Čater, Dalibor Ballian, 2021, original scientific article Abstract: Morphologic variability from 25 populations of Acer campestre L. in Bosnia and Herzegovina was analyzed. Morphometric structure of variability and between-population variability was performed based on 10 fruit-parameter characteristics and 19 leaf-parameter characteristics using multivariate statistical analysis. Results confirmed the separation of three submediterranean populations as a group in relation to other tested populations, from which the Banja Luka population is different. Measured leaf parameters were confirmed as a predominant carrier of the morphologic separation between populations. In other Acer species populations within A. monspessulanum and A. intermedium species are separated mainly by fruit and much less by leaf parameters. The southernmost submediterranean populations from Trebinje, Ljubuški, and Mostar regions have smaller leaf areas, which consequently places them within the same morphologic group; their variability is in tight connection with eco-geo-graphical factors, where the ecological distance is a much better predictor of morphological variability compared to geographical distance. The air temperature had the biggest influence on morphological variability regarding the highest in-between correlation. Achieved results may serve for the continuation of the research in other areas of Acer campestre to determine the interactive effect of ecological, geographical, climatic, and migrational factors on their morphologic population plasticity.
Keywords: differentiation, field maple, fruit, leaf, morphologic variability
Published in DiRROS: 03.01.2022; Views: 779; Downloads: 610
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6. The effect of olive fruit fly Bactrocera oleae (Rossi) infestation on certain chemical parameters of produced olive oilsVasilij Valenčič, Bojan Butinar, Maja Podgornik, Milena Bučar-Miklavčič, 2021, original scientific article Abstract: Olives affected by active and damaging infestation (olive fruit fly Bactrocera oleae (Rossi)) were assayed for their chemical composition. Biophenols were determined by HPLC, sterols, triterpenic dialcohols, and fatty acids by gas chromatography analysis. The acquired data were statistically analyzed. Oils produced from "Istrska belica" fruit affected by active infestation compared to the oils made from fruit affected by damaging infestation showed higher amounts of total oleuropein biofenols (377.3 versus (vs.) 106.6 mg/kg), total biophenols (755 vs. 377 mg/kg), lignans (85.3 vs. 32.9mg/kg), the dialdehydic formof decarboxymethyl oleuropein aglycone (DMO-AgldA) (148.3 vs. 49.0 mg/kg), its oxidized form (DMO-Agl-dA)ox (35.2 vs. 8.5 mg/kg), the dialdehydic form of oleuropein aglycone (O-Agl-dA) (61.1 vs. 8.0 mg/kg), the dialdehydic form of ligstroside aglycone (L-Agl-dA) (63.5 vs. 28.0 mg/kg), the aldehydic form of oleuropein aglycone (O-Agl-A) (40.6 vs. 8.4 mg/kg), and lower amounts of tyrosol (Tyr) (6.0 vs. 13. 9 mg/kg) and the aldehydic form of ligstroside aglycone (L-Agl-A) (13.8 vs. 40.3 mg/kg). Higher values of stigmasterol (2.99%) and lower values of campesterol (2.25%) were determined in oils affected by damaging infestation; an increase in triterpenic dialcohols was also observed (3.04% for damaging and 1.62% for active infestation). Oils affected by damaging infestation, compared to active infestation, showed lower amounts of oleic acid (73.89 vs. 75.15%) and higher amounts of myristic (0.013 vs. 0.011%), linoleic (7.27 vs. 6.48%), and linolenic (0.74 vs. 0.61%) acids.
Keywords: olives, Istrska belica, olive fruit fly, biophenols, sterols, triterpenic dialcohols, fatty acids
Published in DiRROS: 13.01.2021; Views: 1294; Downloads: 1158
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7. Morfološka analiza puhastega hrasta (Quercus pubescens Willd.) v SlovenijiMateja Jerše, Franc Batič, 2007, original scientific article Abstract: Z raziskavo smo poskusili ovrednotiti morfološke raznolikosti puhastega hrasta(Quercus pubescens Willd.) v Sloveniji. Raznolikost je posledica pestrosti rastišč in možnosti križanja z drugimi vrstami hrastov. Rezultati analize so bili dobljeni na osnovi meritev in opazovanja listov, plodov in kratkih poganjkov puhastegarasta, vzorčenih v osmih populacijah po Sloveniji. Na posamezni lokaciji je bilo izbranih do pet dreves in na posameznem drevesu nabranih do sto listov s kratkih poganjkov v osvetljenem delu krošnje. Na osebkih s plodovi so bili nabrani tudi plodovi. V laboratoriju je bilo na listih izmerjenih, ocenjenih in izračunanih 13 parametrov, na plodovih in kratkih poganjkih pa po en parameter. Uporabljene so bile deskriptivne, univariatne in multivariatne statistične metode za izvrednotenje rezultatov. Analize morfoloških parametrov so pokazale značilne razlike tako med posameznimi osebki v populacijah kot med populacijami. Ugotovljeno je bilo tudi, da vrsto Q. virgiliana (Ten.) Ten. lahko obravnavamo znotraj vrste Q. pubescens.
Keywords: puhasti hrast, Quercus pubescens Willd., Quercus virgiliana (Ten.), morfologija, listi, plodovi, Slovenija, oak, morphology, leaf, fruit, Slovenia
Published in DiRROS: 12.07.2017; Views: 5167; Downloads: 2059
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