21. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystemsOlivera Maksimović, Katarina Bačnik, Mark Paul Selda Rivarez, Ana Vučurović, Nataša Mehle, Maja Ravnikar, Ion Gutiérrez-Aguirre, Denis Kutnjak, 2024, original scientific article Abstract: Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem.
Keywords: plant viruses, environmental water testing, high-throughput sequencing, agroecosystems, irrigation water, virome
Published in DiRROS: 29.03.2024; Views: 165; Downloads: 71
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22. Keep it simple : improving the ex situ culture of Cystoseira s.l. to restore macroalgal forestsAna Lokovšek, Valentina Pitacco, Domen Trkov, Leon Lojze Zamuda, Annalisa Falace, Martina Orlando-Bonaca, 2023, original scientific article Abstract: Brown algae from genus Cystoseira s.l. form dense underwater forests that represent the most productive areas in the Mediterranean Sea. Due to the combined effects of global and local stressors such as climate change, urbanization, and herbivore outbreaks, there has been a severe decline in brown algal forests in the Mediterranean Sea. Natural recovery of depleted sites is unlikely due to the low dispersal capacity of these species, and efficient techniques to restore such habitats are needed. In this context, the aims of our study were (1) to improve and simplify the current ex situ laboratory protocol for the cultivation of Gongolaria barbata by testing the feasibility of some cost-effective and time-efficient techniques on two donor sites of G. barbata and (2) to evaluate the survival and growth of young thalli during the laboratory phase and during the most critical five months after out-planting. Specifically, the following ex situ cultivation methods were tested: (A) cultivation on clay tiles in mesocosms with culture water prepared by three different procedures (a) filtered seawater with a 0.22 μm filter membrane, (b) filtered seawater with a 0.7 μm filter membrane (GF), and (c) UV-sterilized water, and (B) cultivation on clay tiles in open laboratory systems. After two weeks, all thalli were fixed to plastic lantern net baskets suspended at a depth of 2 m in the coastal sea (hybrid method), and the algal success was monitored in relation to the different donor sites and cultivation protocol. The satisfactory results of this study indicate that UV-sterilized water is suitable for the cultivation of G. barbata in mesocosm, which significantly reduces the cost of the laboratory phase. This opens the possibility of numerous and frequent algal cultures during the reproductive period of the species. Additionally, if the young thalli remain in the lantern net baskets for an extended period of several months, they can grow significantly in the marine environment without being exposed to pressure from herbivorous fish.
Keywords: gojenje ex situ, obnova habitata, izboljšanje metodologije, gozdički rjavih alg, ex situ cultivation, mesocosm, open system, method improvement, brown algal forests restoration
Published in DiRROS: 29.03.2024; Views: 158; Downloads: 93
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23. 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: 146; Downloads: 56
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24. 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: 124; Downloads: 100
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26. Results of postoperative radiochemotherapy of the patients with resectable gastroesophageal junction adenocarcinoma in SloveniaAna Jeromen, Irena Oblak, Franc Anderluh, Vaneja Velenik, Marija Skoblar Vidmar, Ivica Ratoša, 2012, original scientific article Keywords: gastroesophageal junction adenocarcinoma, postoperative radiochemotherapy, toxicity
Published in DiRROS: 21.03.2024; Views: 146; Downloads: 37
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27. The prognostic and predictive value of human gastrointestinal microbiome and exosomal mRNA expression of PD-L1 and IFNγ for immune checkpoint inhibitors response in metastatic melanoma patients : protocol trialAna Erman, Marija Ignjatović, Katja Leskovšek, Simona Miceska, Urša Lampreht Tratar, Maša Omerzel, Veronika Kloboves-Prevodnik, Maja Čemažar, Lidija Kandolf Sekulović, Gorazd Avguštin, Janja Ocvirk, Tanja Mesti, 2023, original scientific article Abstract: Background: Immunotherapy has been successful in treating advanced melanoma, but a large proportion of patients do not respond to the treatment with immune checkpoint inhibitors (ICIs). Preclinical and small cohort studies suggest gastrointestinal microbiome composition and exosomal mRNA expression of PD-L1 and IFNγ from the primary tumor, stool and body fluids as potential biomarkers for response. Methods: Patients treated with immune checkpoint inhibitors as a first line treatment for metastatic melanoma are recruted to this prospective study. Stool samples are submitted before the start of treatment, at the 12th (+/−2) week and 28th (+/−2) week, and at the occurrence of event (suspected disease progression/hyperprogression, immune-related adverse event (irAE), deterioration). Peripheral venous blood samples are taken additionally at the same time points for cytologic and molecular tests. Histological material from the tumor tissue is obtained before the start of immunotherapy treatment. Primary objectives are to determine whether the human gastrointestinal microbiome (bacterial and viral) and the exosomal mRNA expression of PD-L1 and IFNγ and its dynamics predicts the response to treatment with PD-1 and CTLA-4 inhibitors and its association with the occurrence of irAE. The response is evaluated radiologically with imaging methods in accordance with the irRECIST criteria. Conclusions: This is the first study to combine and investigate multiple potential predictive and prognostic biomarkers and their dynamics in first line ICI in metastatic melanoma patients.
Keywords: gastrointestinal microbiome, mRNA expression of PD-L1 and IFNγ, immune checkpoint inhibitors, metastatic melanoma
Published in DiRROS: 21.03.2024; Views: 121; Downloads: 61
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28. Genotyping of BRCA1, BRCA2, p53, CDKN2A, MLH1 and MSH2 genes in a male patient with secondary breast cancerAna Lina Vodušek, Srdjan Novaković, Vida Stegel, Berta Jereb, 2011, original scientific article Published in DiRROS: 18.03.2024; Views: 134; Downloads: 38
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29. Study of radiation induced changes of phosphorus metabolism in mice by ▫$^{31}P$▫ NMR spectroscopyIgor Serša, Simona Kranjc Brezar, Gregor Serša, Alenka Nemec Svete, Bojan Ložar, Ana Sepe, Jernej Vidmar, Marjeta Šentjurc, 2010, original scientific article Published in DiRROS: 15.03.2024; Views: 138; Downloads: 38
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30. Trilinear embedding for divergence-form operators with complex coefficientsAndrea Carbonaro, Oliver Dragičević, Vjekoslav Kovač, Kristina Ana Škreb, 2023, original scientific article Abstract: We prove a dimension-free $L^p(\Omega)\times L^q(\Omega)\times L^r(\Omega)\rightarrow L^1(\Omega\times (0,\infty))$ embedding for triples of elliptic operators in divergence form with complex coefficients and subject to mixed boundary conditions on $\Omega$, and for triples of exponents $p,q,r \in (1,\infty)$ mutually related by the identity $1/p+1/q+1/r=1$. Here $\Omega$ is allowed to be an arbitrary open subset of $\mathbb{R}^d$. Our assumptions involving the exponents and coefficient matrices are expressed in terms of a condition known as $p$-ellipticity. The proof utilizes the method of Bellman functions and heat flows. As a corollary, we give applications to (i) paraproducts and (ii) square functions associated with the corresponding operator semigroups, moreover, we prove (iii) inequalities of Kato-Ponce type for elliptic operators with complex coefficients. All the above results are the first of their kind for elliptic divergence-form operators with complex coefficients on arbitrary open sets. Furthermore, the approach to (ii),(iii) through trilinear embeddings seems to be new.
Keywords: elliptic differential operator, p-ellipticity, operator semigroup, multilinear estimate
Published in DiRROS: 15.03.2024; Views: 133; Downloads: 65
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