521. Increased diversity of citrus tristeza virus in EuropeJelena Zindović, Miroslav Čizmović, Ana Vučurović, Paolo Margaria, Dijana Škorić, 2023, original scientific article Abstract: This study investigated the genetic diversity of citrus tristeza virus (CTV) isolates from Montenegro and Croatia, European countries with the northernmost citrus growing regions situated on the Eastern Adriatic coast. Fifteen complete or nearly complete CTV genomes were reconstructed from high-throughput sequencing of samples collected in distinct municipalities in Montenegro and Opuzen municipality in Croatia. Phylogenetic analyses assigned some of the sequences to VT and T30 strains, previously recorded in Europe, while remarkably other isolates were placed in S1 and RB groups, which have not been reported in Europe so far. In addition, a new phylogenetic lineage including only isolates from Montenegro was delineated and tentatively proposed as the MNE cluster. Recombination analysis revealed evidence of 11 recombination events in the sequences obtained in this study, between isolates of related strains, within isolates of the same strain, and between distant strains. These findings show that CTV diversity in Europe is higher than reported before and calls for the re-evaluation of management strategies.
Keywords: complete genomes, genotyping, citrus tristeza virus, CTV, non-EU strain
Published in DiRROS: 29.03.2024; Views: 214; Downloads: 113
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522. Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbelliiNeža Orel, Eduard Fadeev, Gerhard J. Herndl, Valentina Turk, Tinkara Tinta, 2024, original scientific article Abstract: Background: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. Results: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. Conclusions: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
Keywords: whole-genome assembly, non-axenic culture, plasmid, marine bacteria, marine biology
Published in DiRROS: 28.03.2024; Views: 252; Downloads: 126
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528. Diketopyrrolopyrrole pigment core@multi-layer ▫$SiO_2$▫ shell with improved photochemical stabilityErika Švara Fabjan, Zineb Saghi, Paul A. Midgley, Mojca Otoničar, Goran Dražić, Miran Gaberšček, Andrijana Sever Škapin, 2018, original scientific article Abstract: A model organic pigment (diketopyrrolopyrrole) is encapsulated by a silica coating in order to improve its photochemical stability. Unlike in previous works where single-layer silica coatings were used for similar purposes, we here propose creation of a multi-layer silica shell synthesized via in-situ sol-gel method, which should significantly improve the homogeneity and thus the protection ability of the coating. This is done by repeating the basic two-step process (pigment surface modification and silica encapsulation) several times, creating the final protective shell in a layer-by-layer fashion. The compositional and structural properties of the prepared coatings is studied using Fourier-transform infrared spectroscopy, differential thermal and thermogravimetric analysis, nitrogen adsorption measurements and transmission electron microscopy. Photochemical stability of non-encapsulated and encapsulated pigment particles is evaluated via the so-called fast-irradiation method. Various correlations between the essential coating properties, such as thickness, porosity, SiO2 content, and the corresponding photochemical stability of the samples are established and discussed in detail. As a whole, our results confirm the basic hypothesis, that multiple-layered silica shells show improved pigment protection ability in comparison to the single-layer coatings.
Keywords: organic pigments, silica coating, encapsulation, morphology, photocemical stability
Published in DiRROS: 27.03.2024; Views: 250; Downloads: 86
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529. Lessons learned from the monitoring of retaining structures, built in demanding geotechnical conditions in SloveniaPavel Žvanut, Janko Logar, 2019, published scientific conference contribution Abstract: A typical retaining structure built with large-diameter bored piles in soft clastic rock, and sup-ported by pre-stressed permanent ground anchors, is discussed. Step-by-step back analyses were performed. A simplified geological structure was first used in the analyses, together with a simple Mohr-Coulomb model. The results were compared with more complex analyses using a Hardening Soil model and a more detailed geological structure. Much better results were obtained with the use of the HS model, which is more suitable for the modelling of rock of such a type, but even with the use of the MC model the final results were quite good, making the use of the observational method attractive for engineers.
Keywords: geotechnics, gretaining structures, bored piles, numerical modelling, finite element method, observational method
Published in DiRROS: 27.03.2024; Views: 194; Downloads: 82
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530. Modelling of traffic load effects in the assessment of existing road bridgesDominik Skokandić, Ana Mandić Ivanković, Aleš Žnidarič, Mladen Srbić, 2019, review article Abstract: Traffic load models used for the design of new bridges are based on conservative assumptions and have not been proven efficient for assessing safety of existing bridges. In the case of existing bridges, it is reasonable to use load models that are based on bridge weigh-in-motion data which, in addition to axle loads and spacing of bridge-crossing vehicles, provide information on bridge behaviour under traffic load. This paper provides an overview of traffic load models, as well as guidelines on the use of weigh-in-motion data when assessing condition of existing road bridges.
Keywords: prometna obtežba, tehtanje vozil med vožnjo, mostni WIM, ocenjevanje stanja, obstoječi mostovi, traffic load, weigh-in-motion, bridge WIM, condition assessment, existing bridges
Published in DiRROS: 27.03.2024; Views: 205; Downloads: 164
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