521. Phytoplasmas associated with declining of hazelnut (Corylus avellana) in SloveniaNataša Mehle, Nejc Jakoš, Miro Mešl, Jože Miklavc, Boštjan Matko, Mojca Rot, Alenka Ferlež Rus, Robert Brus, Marina Dermastia, 2019, izvirni znanstveni članek Povzetek: Hazelnut (Corylus avellana) is cultivated on 118 ha and ranks eighth in Slovenian fruit growing production, representing 2.8% of the total area of fruit plantations in the country. However, decline of some of the trees appeared in 2012 in two plantations located in eastern Slovenia. Together these orchards cover 5 ha, with around 1600 trees planted 12 to 15 years ago. By October 2018, ~12% of these trees had died, and an additional 12% showed decay symptoms. The dead and dying trees were scattered throughout both orchards, with no apparent pattern. The most affected cultivar was ‘Istrska dolgoplodna leska’. Using molecular diagnostic methods, we showed infection of symptomatic trees with three unrelated phytoplasmas: ‘Candidatus Phytoplasma fragariae’, of the 16SrXII-E phytoplasma subgroup, and phytoplasma of the 16SrV and 16SrIX groups. In 2018, the presence of ‘Ca. P. fragariae’ and/or phytoplasma of 16SrV group were confirmed in decayed hazelnut trees in eastern, north-eastern, central, south-eastern and western Slovenia. ‘Ca. P. fragariae’ has also been detected in a forest in south-western Slovenia, for Acer campestre, Carpinus betulus, Crataegus laevigata, Fraxinus ornus and Quercus petraea. All infected forest trees showed unusual dense proliferation of sprouts from roots and/or trunks. Molecular characterisations of partial 16S rRNA, secY, map and ribosomal protein genetic locus of hazelnut 16SrV phytoplasma isolates show that they are identical to isolates that can cause grapevine flavescence dorée disease. Here, the results of our recent study and the open questions on this burning issue for hazelnut production are presented. Ključne besede: Corylus avellana, ʼCandidatus Phytoplasma fragariaeʼ, 16SrV phytoplasma group, 16SrIX phytoplasma group, decline Objavljeno v DiRROS: 24.07.2024; Ogledov: 120; Prenosov: 90
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523. Comparative morphology refines the conventional model of spider reproductionYongjia Zhan, He Jiang, Qingqing Wu, Huitao Zhang, Zishang Bai, Matjaž Kuntner, Lihong Tu, 2019, izvirni znanstveni članek Povzetek: Our understanding of spider reproductive biology is hampered by the vast anatomical diversity and difficulties associated with its study. Although authors agree on the two general types of female spider genitalia, haplogyne (plesiomorphic) and entelegyne (apomorphic), our understanding of variation within each group mostly concerns the external genital part, while the internal connections with the reproductive duct are largely unknown. Conventionally and simplistically, the spermathecae of haplogynes have simple two-way ducts, and those of entelegynes have separate copulatory and fertilization ducts for sperm to be transferred in and out of spermathecae, respectively. Sperm is discharged from the spermathecae directly into the uterus externus (a distal extension of the oviduct), which, commonly thought as homologous in both groups, is the purported location of internal fertilization in spiders. However, the structural evolution from haplo- to entelegyny remains unresolved, and thus the precise fertilization site in entelegynes is ambiguous. We aim to clarify this anatomical problem through a widely comparative morphological study of internal female genital system in entelegynes. Our survey of 147 epigyna (121 examined species in 97 genera, 34 families) surprisingly finds no direct connection between the fertilization ducts and the uterus externus, which, based on the homology with basal-most spider lineages, is a dead-end caecum in entelegynes. Instead, fertilization ducts usually connect with a secondary uterus externus, a novel feature taking over the functional role of the plesiomorphic uterus externus. We hypothesize that the transition from haplo- to entelegyny entailed not only the emergence of the two separate duct systems (copulatory, fertilization), but also involved substantial morphological changes in the distal part of the oviduct. Thus, the common oviduct may have shifted its distal connection from the uterus externus to the secondary uterus externus, perhaps facilitating discharge of larger eggs. Our findings suggest that the conventional model of entelegyne reproduction needs redefinition. Ključne besede: spiders, comparative anatomy, genital anatomy Objavljeno v DiRROS: 23.07.2024; Ogledov: 280; Prenosov: 150
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524. Interactive exploration of heterogeneous biological networks with Biomine ExplorerVid Podpečan, Živa Ramšak, Kristina Gruden, Hannu Toivonen, Nada Lavrač, 2019, izvirni znanstveni članek Povzetek: Biomine Explorer is a web application that enables interactive exploration of large heterogeneous biological networks constructed from selected publicly available biological knowledge sources. It is built on top of Biomine, a system which integrates cross-references from several biological databases into a large heterogeneous probabilistic network. Biomine Explorer offers user-friendly interfaces for search, visualization, exploration and manipulation as well as public and private storage of discovered subnetworks with permanent links suitable for inclusion into scientific publications. A JSON-based web API for network search queries is also available for advanced users. Ključne besede: biological networks, bioinformatic Objavljeno v DiRROS: 23.07.2024; Ogledov: 185; Prenosov: 98
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525. Structural basis for the multitasking nature of the potato virus Y coat proteinAndreja Kežar, Luka Kavčič, Martin Pólak, Jiři Nováček, Ion Gutiérrez-Aguirre, Magda Tušek-Žnidarič, Anna Coll Rius, Katja Stare, Kristina Gruden, Maja Ravnikar, David Pahovnik, Ema Žagar, Franci Merzel, Gregor Anderluh, Marjetka Podobnik, 2019, izvirni znanstveni članek Povzetek: Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY’s flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA–coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein’s amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications. Ključne besede: plant pathogens, potato virus Y, viral RNA Objavljeno v DiRROS: 23.07.2024; Ogledov: 172; Prenosov: 148
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526. The transcriptome of Darwinʼs bark spider silk glands predicts proteins contributing to dragline silk toughnessJessica E. Garb, Robert A. Haney, Evelyn E. Schwager, Matjaž Gregorič, Matjaž Kuntner, Ingi Agnarsson, Todd A. Blackledge, 2019, izvirni znanstveni članek Povzetek: Darwin’s bark spider (Caerostris darwini) produces giant orb webs from dragline silk that can be twice as tough as other silks, making it the toughest biological material. This extreme toughness comes from increased extensibility relative to other draglines. We show C. darwini dragline-producing major ampullate (MA) glands highly express a novel silk gene transcript (MaSp4) encoding a protein that diverges markedly from closely related proteins and contains abundant proline, known to confer silk extensibility, in a unique GPGPQ amino acid motif. This suggests C. darwini evolved distinct proteins that may have increased its dragline’s toughness, enabling giant webs. Caerostris darwini’s MA spinning ducts also appear unusually long, potentially facilitating alignment of silk proteins into extremely tough fibers. Thus, a suite of novel traits from the level of genes to spinning physiology to silk biomechanics are associated with the unique ecology of Darwin’s bark spider, presenting innovative designs for engineering biomaterials. Ključne besede: spiders Objavljeno v DiRROS: 23.07.2024; Ogledov: 156; Prenosov: 99
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527. Accurate quantification and characterization of adeno-associated viral vectorsDavid Dobnik, Polona Kogovšek, Tjaša Jakomin, Nejc Košir, Magda Tušek-Žnidarič, Maja Leskovec, Stephen M. Kaminsky, Janet Mostrom, Hyunmi Lee, Maja Ravnikar, 2019, izvirni znanstveni članek Povzetek: One of the main challenges in the gene therapy viral vector development is to establish an optimized process for its large scale production. This requires optimization for upstream and downstream processes as well as methods that enable the step-by step analytical characterization of the virus, the results of which inform the iterative refinement of production for yield, purity and potency. The biggest problem here is a plethora of viral vector formulations, many of which interfere with analytical techniques. We took adeno-associated virus (AAV) as an example and showed benefits of combined use of molecular methods and transmission electron microscopy (TEM) for viral vectors’ characterization and quantification. Results of the analyses showed that droplet digital PCR (ddPCR) performs better than quantitative real-time PCR (qPCR), in terms of robustness and assay variance, and this was especially relevant for partially purified (in-process) samples. Moreover, we demonstrate the importance of sample preparation prior to PCR analysis. We evaluated viral structure, presence of aggregates and impurities with TEM analysis and found that these impacted the differences in viral titers observed by qPCR and ddPCR and could be altered by sample preparation. These results serve as a guide for the establishment of the analytical methods required to provide measures of identity and purity for AAV viral vectors. Ključne besede: absolute quantification, AAV, gene therapy, electron microscopy, digital PCR, real-time PCR Objavljeno v DiRROS: 23.07.2024; Ogledov: 180; Prenosov: 106
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528. Genomic evidence of recombination in the basidiomycete Wallemia mellicolaSun Xiaohuan, Cene Gostinčar, Fang Chao, Janja Zajc, Hou Yong, Song Zewei, Nina Gunde-Cimerman, 2019, izvirni znanstveni članek Povzetek: One of the most commonly encountered species in the small basidiomycetous sub-phylum Wallemiomycotina is Wallemia mellicola, a xerotolerant fungus with a widespread distribution. To investigate the population characteristics of the species, whole genomes of twenty-five strains were sequenced. Apart from identification of four strains of clonal origin, the distances between the genomes failed to reflect either the isolation habitat of the strains or their geographical origin. Strains from different parts of the world appeared to represent a relatively homogenous and widespread population. The lack of concordance between individual gene phylogenies and the decay of linkage disequilibrium indicated that W. mellicola is at least occasionally recombining. Two versions of a putative mating-type locus have been found in all sequenced genomes, each present in approximately half of the strains. W. mellicola thus appears to be capable of (sexual) recombination and shows no signs of allopatric speciation or specialization to specific habitats. Ključne besede: population genomics, halotolerance, xerotolerance, basidiomycete, allergenic fungus, recombination Objavljeno v DiRROS: 23.07.2024; Ogledov: 153; Prenosov: 90
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529. Digital PCR as an effective tool for GMO quantification in complex matricesAlexandra Bogožalec Košir, Tina Demšar, Dejan Štebih, Jana Žel, Mojca Milavec, 2019, izvirni znanstveni članek Povzetek: The increased use of genetically modified organisms (GMOs) is accompanied by increased complexity of the matrices that contain GMOs. The most common DNA-based approach for GMO detection and quantification is real-time quantitative polymerase chain reaction (qPCR). However, as qPCR is sensitive to inhibitors and relies on standard curves for quantification, it has limited application in GMO quantification for complex matrices. To overcome this hurdle in DNA quantification, we present droplet digital PCR (ddPCR) assays that were designed to target ‘Roundup Ready’ soybean and the soybean reference gene. Three ddPCR assays were transferred from qPCR to QX100/QX200 ddPCR platforms and characterised. Together, the fitness-for-purpose study on four real-life samples and the use of a chamber-based PCR system, showed that dPCR has great potential to improve such measurements in GMO testing and monitoring of food authenticity. Ključne besede: genetically modified organisms, digital PCR, GMO quantification, complex matrices Objavljeno v DiRROS: 23.07.2024; Ogledov: 167; Prenosov: 90
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530. Poročilo o preskusu št.: LVG 2024-074 : vzorec št. 2024/00385Nikica Ogris, Špela Hočevar, Patricija Podkrajšek, Barbara Piškur, 2024, izvedensko mnenje, arbitražna odločba Ključne besede: varstvo gozdov, morfološke analize, Fusarium circinatum, Pinus, borov smolasti rak, PCR Objavljeno v DiRROS: 23.07.2024; Ogledov: 160; Prenosov: 0 Gradivo ima več datotek! Več... |