1. Rapid loop-mediated isothermal amplification assays for grapevine yellows phytoplasmas on crude leaf-vein homogenate has the same performance as qPCRPolona Kogovšek, Nataša Mehle, Anja Pugelj, Tjaša Jakomin, Hans-Josef Schroers, Maja Ravnikar, Marina Dermastia, 2017, izvirni znanstveni članek Povzetek: A fluorescence-based real-time loop-mediated isothermal amplification (LAMP) assay for ‘Candidatus Phytoplasama solani’ (Bois noir phytoplasma; BNp) detection was developed and optimised for rapid laboratory and on-site BNp detection. This assay is highly specific, rapid and as sensitive as qPCR. It was validated according to European and Mediterranean Plant Protection Organisation recommendations. In addition, 286 grapevine leaf samples from the 2015 growing season were tested with this new real-time LAMP assay and an assay previously developed for detection of Flavescence dorée phytoplasma (FDp). These LAMP assays for detection of both BNp and FDp used without any DNA extraction step, which is a required step for qPCR analysis, were comparably effective to qPCR, and positive results were obtained in less than 35 min.
Ključne besede: real-time LAMP, grapevine yellows phytoplasma, validation
Objavljeno v DiRROS: 24.07.2024; Ogledov: 22; Prenosov: 9
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2. Validating the potential of double-stranded RNA targeting Colorado potato beetle mesh gene in laboratory and field trialsMarko Petek, Anna Coll Rius, Rok Ferenc, Jaka Razinger, Kristina Gruden, 2020, izvirni znanstveni članek Povzetek: Colorado potato beetle (CPB) is an agricultural pest of solanaceous crops, notorious for its rapid resistance development to chemical pesticides. Foliar spraying of dsRNA formulations is a promising innovative technology providing highly specific and environmentally acceptable option for CPB management. We designed dsRNA to silence CPB mesh gene (dsMESH) and performed laboratory feeding trials to assess impacts on beetle survival and development. We compared the effectiveness of in vivo and in vitro produced dsRNA in a series of laboratory experiments. We additionally performed a field trial in which the efficacy of dsRNA sprayed onto potato foliage was compared to a spinosad-based insecticide. We showed that dsMESH ingestion consistently and significantly impaired larval growth and decreased larval survival in laboratory feeding experiments. In vivo produced dsRNA performed similarly as in vitro synthesized dsRNA in laboratory settings. In the field trial, dsMESH was as effective in controlling CPB larvae as a commercial spinosad insecticide, its activity was however slower. We discuss limitations and benefits of a potential dsMESH-based CPB management strategy and list some important RNAi based CPB research topics, which will have to be addressed in future.
Ključne besede: RNA interference, RNA interference feeding, ds RNA, gene silencing, RNAi pest control, survival analysis, field trial
Objavljeno v DiRROS: 22.07.2024; Ogledov: 31; Prenosov: 8
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3. Looking beyond virus detection in RNA sequencing data : lessons learned from a community-based effort to detect cellular plant pathogens and pestsAnnelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Gaafar, Oscar Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovšek, Irena Mavrič Pleško, 2023, izvirni znanstveni članek Povzetek: High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.
Ključne besede: plant viruses, plant virus detection, plant virology, high-throughput sequencing, RNA sequencing, plant tissues, plant pathogen, diagnostics, high-throughput sequencing, metagenomics, metatranscriptomics
Objavljeno v DiRROS: 12.07.2024; Ogledov: 87; Prenosov: 29
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4. Reply to Horacek, M.; Cannavan, A. : Comment on “Sinkoviˇc et al. Isotope Fingerprints of Common and Tartary Buckwheat Grains and Milling Fractions: A Preliminary Study. Foods 2022, 11, 1414”Lovro Sinkovič, Nives Ogrinc, Doris Potočnik, Vladimir Meglič, 2022, drugi znanstveni članki Ključne besede: hulls, isotope fingerprints, grain milling, milling process, milling fractions preparing, soil conditions, environment
Objavljeno v DiRROS: 27.07.2023; Ogledov: 467; Prenosov: 139
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5. Potato (Solanum tuberosum) - a new host for the root-knot nematode Meloidogyne inornataBarbara Gerič Stare, Nik Susič, Maja Starovič, Saša Širca, 2022, drugi znanstveni članki Ključne besede: pathogenicity, plant-parasitic nematodes, nematodes, root-knot nematodes, potato
Objavljeno v DiRROS: 27.07.2023; Ogledov: 490; Prenosov: 203
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7. The effect of dietary fibre content on skatole and indole production in faeces of immunocatrsted male pigsMaja Prevolnik, Urška Tomažin, Marjeta Čandek-Potokar, Martin Škrlep, Nina Batorek Lukač, Etienne Labussiere, 2015, objavljeni znanstveni prispevek na konferenci Ključne besede: prašiči, prehrana prašičev, vlaknine, imunokastracija
Objavljeno v DiRROS: 06.09.2022; Ogledov: 755; Prenosov: 291
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9. Carcass and meat quality traits of pig fatteners from Slovenian Breeding programmeMaja Prevolnik, Martin Škrlep, Dejan Škorjanc, Marjeta Čandek-Potokar, 2008, objavljeni znanstveni prispevek na konferenci Povzetek: The aim of the present study was the comparison of carcass and meat quality traits of commercial pigs of various crossbreeds from two major Slovenian herds. The analysis is based on phenotypic data from field trials which have been collected in the last past five years within the Slovenian breeding programme. Important differences in carcass traits were observed between two herds and were associated to different crossbreeds used. In spite of that economically important result on the slaughter line (lean meat %) was similar for both herds. Meat quality traits were also significantly different between the two herds. Again, the difference could be ascribed to crossbreeds used. However, since the herd effect is connected with abattoir effect, different ante-mortem conditions and/or lower robustness of these animals to premortal stress could also be contributed to the observed differences. The presented results give important information on the state-of-the-art regarding meat quality of Slovenian pigs.
Ključne besede: pigs, carcass quality, meat, breeding programs, Slovenia
Objavljeno v DiRROS: 06.09.2022; Ogledov: 774; Prenosov: 266
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10. Influence of housing conditions on reliability of immunocastration and consequences for growth performance of male pigsKevin Kress, Ulrike Weiler, Sonja Schmucker, Marjeta Čandek-Potokar, Milka Vrecl, Gregor Fazarinc, Martin Škrlep, Nina Batorek Lukač, Volker Stefanski, 2020, izvirni znanstveni članek Povzetek: Immunocastration is a sustainable alternative to piglet castration but faces limited market acceptance. The phenomenon of non-responders has not to date been examined in detail, but adverse and stressful housing conditions (e.g., mixing of groups) might impair the success of vaccinations. Therefore, we evaluated the influence of housing conditions on the immune response after two Improvac® vaccinations at an age of 12 and 22 weeks, respectively. Boars, immunocastrates and barrows (n = 48 each) were assigned to three different housing conditions (n = 36 enriched, n = 36 standard n = 72 repeated social mixing). Immune response was quantified by measuring GnRH-binding and its consequences for testosterone concentrations, development of the genital tract and boar taint. Growth performance was evaluated via average daily gain (ADG). GnRH-binding and testosterone levels revealed that immunocastration reliably suppressed testicular functions after the 2nd vaccination. Housing conditions did not modify testicular function but influenced ADG as animals under mixing grew slower than those under enriched conditions. Gonadal status had only a slight impact on ADG except in immunocastrates, which showed a temporarily higher ADG after the 2nd vaccination. The results show that immunocastration is a reliable procedure under different housing conditions and competitive in terms of growth performance.
Ključne besede: immunocastration, vaccination, Improvac, non-responder, immune response, housing conditions, surgical castration, boar taint, growth performance, genital tract
Objavljeno v DiRROS: 06.09.2022; Ogledov: 827; Prenosov: 281
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