1. An evaluation of marine sediments in terms of their usability in the brick industry : case study Port of KoperPatrik Baksa, Franka Cepak, Rebeka Kovačič Lukman, Vilma Ducman, 2018, original scientific article Abstract: A dredging process is essential for the development of harbours and ports, allowing the functional daily operation of the port. The management of dredged material represents a worldwide challenge, especially considering unwanted deposition of material. Because of their chemical, petrographic, mineralogical and homogeneity composition, marine sediments could represent an appropriate raw material for the brick industry, particularly for the production of clay blocks, roofing and ceramic tiles. In this study dredged material from Port of Koper was tested for such use, thus various analyses were carried out in order to determine if the dredged material is environmentally friendly and suitable for use in the brick industry. These included: chemical analysis, mineralogical analysis, particle size analysis, chloride content analysis and tests of firing in a gradient furnace. Furthermore, tests of mechanical properties, as well as tests of the frost-resistance of the samples were carried out. On the basis of the primary analyses and samples prepared in a laboratory, it was confirmed that marine sediments from the Port of Koper, without any additives are only conditionally suitable as a source material for producing brick products, because without additives they exhibit too much shrinkage on drying and firing, as well as high water absorption, this can be improved by the incorporation of suitable additives, for example, virgin clay or other suitable waste material. The approach described herewith can also be followed to assess sediments from other ports and rivers regarding its potential use in clay brick sector. Keywords: dredge marine sediment, recycling, clay bricks, mechanical properties, chemical analysis Published in DiRROS: 14.08.2024; Views: 19; Downloads: 7
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2. Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potatoŠpela Baebler, Kamil Witek, Marko Petek, Katja Stare, Magda Tušek-Žnidarič, Maruša Pompe Novak, Jenny Renaut, K. Szajko, D. Strzelczyk-Żyta, W. Marczewski, Karolina Morgiewicz, Kristina Gruden, Jacek Hennig, 2014, original scientific article Abstract: The purpose of the study was to investigate the role of salicylic acid (SA) signalling in Ny-1-mediated hypersensitive resistance (HR) of potato (Solanum tuberosum L.) to Potato virus Y (PVY). The responses of the Ny-1 allele in the Rywal potato cultivar and transgenic NahG-Rywal potato plants that do not accumulate SA were characterized at the cytological, biochemical, transcriptome, and proteome levels. Analysis of noninoculated and inoculated leaves revealed that HR lesions started to develop from 3 d post inoculation and completely restricted the virus spread. At the cytological level, features of programmed cell death in combination with reactive oxygen species burst were observed. In response to PVY infection, SA was synthesized de novo. The lack of SA accumulation in the NahG plants led to the disease phenotype due to unrestricted viral spreading. Grafting experiments show that SA has a critical role in the inhibition of PVY spreading in parenchymal tissue, but not in vascular veins. The whole transcriptome analysis confirmed the central role of SA in orchestrating Ny-1-mediated responses and showed that the absence of SA leads to significant changes at the transcriptome level, including a delay in activation of expression of genes known to participate in defence responses. Moreover, perturbations in the expression of hormonal signalling genes were detected, shown as a switch from SA to jasmonic acid/ethylene signalling. Viral multiplication in the NahG plants was accompanied by downregulation of photosynthesis genes and activation of multiple energy-producing pathways. Keywords: plant-pathogen interactions, Potato virus Y, salicylic acid, whole transcriptome analysis Published in DiRROS: 01.08.2024; Views: 125; Downloads: 117
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3. Bimodal dynamics of primary metabolism-related responses in tolerant potato-Potato virus Y interactionNeža Turnšek, Živa Ramšak, Katja Stare, Tjaša Stare, Dominik Vodnik, Andrej Blejec, Kristina Gruden, Wolfram Weckwerth, Stefanie Wienkoop, 2015, original scientific article Abstract: Background
Potato virus Y (PVY) is a major pathogen that causes substantial economic losses in worldwide potato production. Different potato cultivars differ in resistance to PVY, from severe susceptibility, through tolerance, to complete resistance. The aim of this study was to better define the mechanisms underlying tolerant responses of potato to infection by the particularly aggressive PVYNTN strain. We focused on the dynamics of the primary metabolism-related processes during PVYNTN infection.
Results
A comprehensive analysis of the dynamic changes in primary metabolism was performed, which included whole transcriptome analysis, nontargeted proteomics, and photosynthetic activity measurements in potato cv. Désirée and its transgenic counterpart depleted for accumulation of salicylic acid (NahG-Désirée). Faster multiplication of virus occurred in the NahG-Désirée, with these plants developing strong disease symptoms. We show that while the dynamics of responses at the transcriptional level are extensive and bimodal, this is only partially translated to the protein level, and to the final functional outcome. Photosynthesis-related genes are transiently induced before viral multiplication is detected and it is down-regulated later on. This is reflected as a deficiency of the photosynthetic apparatus at the onset of viral multiplication only. Interestingly, specific and constant up-regulation of some RuBisCO transcripts was detected in Désirée plants, which might be important, as these proteins have been shown to interact with viral proteins.
In SA-deficient and more sensitive NahG-Désirée plants, consistent down-regulation of photosynthesis-related genes was detected. A constant reduction in the photochemical efficiency from the onset of viral multiplication was identified; in nontransgenic plants this decrease was only transient. The transient reduction in net photosynthetic rate occurred in both genotypes with the same timing, and coincided with changes in stomatal conductivity.
Conclusions
Down-regulation of photosynthesis-related gene expression and decreased photosynthetic activity is in line with other studies that have reported the effects of biotic stress on photosynthesis. Here, we additionally detected induction of light-reaction components in the early stages of PVYNTN infection of tolerant interaction. As some of these components have already been shown to interact with viral proteins, their overproduction might contribute to the absence of symptoms in cv. Désirée. Keywords: plant-pathogen interactions, Potato virus Y, potyviridae, salicylic acid, whole transcriptome analysis, shot-gun proteomics, photosynthetic parameters Published in DiRROS: 29.07.2024; Views: 120; Downloads: 147
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4. Assessment of short-term effect of platelet-rich plasma treatment of tendinosis using texture analysis of ultrasound imagesKarlo Pintarić, Vladka Salapura, Žiga Snoj, Andrej Vovk, Mojca Božič, Jernej Vidmar, 2023, original scientific article Keywords: texture analysis, ultrasonography, tendinosis Published in DiRROS: 25.07.2024; Views: 116; Downloads: 51
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5. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, Nina Gunde-Cimerman, Tine Grebenc, Cene Gostinčar, 2017, original scientific article Abstract: The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage. Keywords: Deinococcus-Thermus, Deinococcaceae, Deinococcus ficus, radiation-resistant, rod-shaped, phenotype characterization, genome analysis, phylogenetic analysis Published in DiRROS: 25.07.2024; Views: 125; Downloads: 103
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6. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologiesSébastien Massart, Thierry Candresse, José Gil, Christophe Lacomme, Lukas Predajna, Maja Ravnikar, Jean-Sébastien Reynard, Artemis Rumbou, Pasquale Saldarelli, Dijana Škorić, Eeva J. Vainio, Jari P. T. Valkonen, Hervé Vanderschuren, Christina Varveri, Thierry Wetzel, 2017, original scientific article Abstract: Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios. Keywords: NGS, pest risk analysis, virus diseases, biological characterization, plant health, regulatory agencies Published in DiRROS: 25.07.2024; Views: 109; Downloads: 69
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7. High-throughput sequencing facilitates characterisation of a ʺforgottenʺ plant virus : the case of a henbane mosaic virus infecting tomatoAnja Pecman, Denis Kutnjak, Nataša Mehle, Magda Tušek-Žnidarič, Ion Gutiérrez-Aguirre, Patricija Pirnat, Ian Adams, Neil Boonham, Maja Ravnikar, 2018, original scientific article Abstract: High-throughput sequencing has dramatically broadened the possibilities for plant virus research and diagnostics, enabling discovery of new or obscure viruses, and virus strains and rapid sequencing of their genomes. In this research, we employed high-throughput sequencing to discover a new virus infecting tomato, Henbane mosaic virus (Potyvirus, Potyviridae), which was first discovered at the beginning of 20th century in the United Kingdom in cultivated henbane. A field tomato plant with severe necrotic symptoms of unknown etiology was sampled in Slovenia and high-throughput sequencing analysis using small RNA and ribosomal RNA depleted total RNA approaches revealed a mixed infection with Potato virus M (Carlavirus, Betaflexiviridae), Southern tomato virus (Amalgavirus, Amalgamaviridae) and henbane mosaic virus in the sample. The complete genomic sequence of henbane mosaic virus was assembled from the sequencing reads. By re-inoculation of the infected material on selected test plants, henbane mosaic virus was isolated and a host range analysis was performed, demonstrating the virus was pathogenic on several plant species. Due to limited metadata in public repositories, the taxonomic identification of the virus isolate was initially putative. Thus, in the next step, we used small RNA sequencing to determine genomic sequences of four historic isolates of the virus, obtained from different virus collections. Phylogenetic analyses performed using this new sequence information enabled us to taxonomically position Henbane mosaic virus as a member of the Potyvirus genus within the chili veinal mottle virus phylogenetic cluster and define the relationship of the new tomato isolate with the historic ones, indicating the existence of at least four putative strains of the virus. The first detection of henbane mosaic virus in tomato and demonstration of its pathogenicity on this host is important for plant protection and commercial tomato production. Since the virus was initially present in a mixed infection, and its whole genome was not sequenced, it has probably been overlooked in routine diagnostics. This study confirms the applicability of a combination of high-throughput sequencing and classic plant virus characterization methods for identification and phylogenetic classification of obscure viruses and historical viral isolates, for which no or limited genome sequence data is available. Keywords: henbane mosaic virus, Tomato, high-throughput sequencing, host range analysis, phylogeny, Potyvirus Published in DiRROS: 24.07.2024; Views: 122; Downloads: 112
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8. DiNAR: revealing hidden patterns of plant signalling dynamics using Diferential Network Analysis in RMaja Zagorščak, Andrej Blejec, Živa Ramšak, Marko Petek, Tjaša Stare, Kristina Gruden, 2018, original scientific article Abstract: Background
Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a prior knowledge network is shown to be advantageous.
Results
We have developed DiNAR, Differential Network Analysis in R, a user-friendly application with dynamic visualisation that integrates multiple condition high-throughput data and extensive biological prior knowledge. Implemented differential network approach and embedded network analysis allow users to analyse condition-specific responses in the context of topology of interest (e.g. immune signalling network) and extract knowledge concerning patterns of signalling dynamics (i.e. rewiring in network structure between two or more biological conditions). We validated the usability of software on the Arabidopsis thaliana and Solanum tuberosum datasets, but it is set to handle any biological instances.
Conclusions
DiNAR facilitates detection of network-rewiring events, gene prioritisation for future experimental design and allows capturing dynamics of complex biological system. The fully cross-platform Shiny App is hosted and freely available at https://nib-si.shinyapps.io/DiNAR. The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo. Keywords: biological networks, clustering, gene expression, time series, dynamic network analysis, dynamic data visualisation, web application, multi-conditional datasets, background knowledge Published in DiRROS: 24.07.2024; Views: 152; Downloads: 131
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9. Decision support for the comparative evaluation and selection of analytical methods : detection of genetically modified organisms as an exampleDavid Dobnik, Kristina Gruden, Jana Žel, Yves Bertheau, Arne Holst-Jensen, Marko Bohanec, 2018, original scientific article Abstract: The selection of the best-fit-for-purpose analytical method to be implemented in the laboratory is difficult due to availability of multiple methods, targets, aims of detection, and different kinds and sources of more or less reliable information. Several factors, such as method performance, practicability, cost of setup, and running costs need to be considered together with personnel training when selecting the most appropriate method. The aim of our work was to prepare a flexible multicriteria decision analysis model suitable for evaluation and comparison of analytical methods used for the purpose of detecting and/or quantifying genetically modified organisms, and to use this model to evaluate a variety of changing analytical methods. Our study included selection of PCR-, isothermal-, protein-, microarray-, and next-generation sequencing-based methods in simplex and/or multiplex formats. We show that the overall result of their fitness for purpose is relatively similar; however, individual criteria or a group of related criteria exposed more substantial differences between the methods. The proposed model of this decision support system enables easy modifications and is thus suitable for any other application of complex analytical methods. Keywords: multicriteria decision analysis, genetically modified organisms, method evaluation, DEXi, decision support system, DSS Published in DiRROS: 24.07.2024; Views: 124; Downloads: 148
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10. Chocolate and risk of chronic disease : a systematic review and dose-response meta-analysisJakub Morze, Carolina Schwedhelm, Aleksander Benčič, Georg Hofmann, Heiner Boeing, Katarzyna Przybylowicz, Lukas Schwingshackl, 2020, original scientific article Abstract: Purpose
Evidence for the association between chocolate intake and risk of chronic diseases is inconclusive. Therefore, we aimed to synthesize and evaluate the credibility of evidence on the dose-response association between chocolate consumption with risk of all-cause mortality, coronary heart disease (CHD), stroke, heart failure (HF), type 2 diabetes (T2D), colorectal cancer (CRC), and hypertension.
Methods
Prospective studies were searched until July 2018 in PubMed, Embase, and Web of Science. Random-effects meta-analyses comparing highest versus lowest intake categories, linear, and non-linear dose-response analyses were conducted. The credibility of evidence was evaluated with the NutriGrade scoring-system.
Results
Overall, 27 investigations were identified (n = 2 for all-cause mortality, n = 9 for CHD, n = 8 for stroke, n = 6 for HF, n = 6 for T2D, n = 2 for hypertension and CRC, respectively). No associations with HF (RR 0.99, 95% CI 0.94, 1.04) and T2D (RR 0.94, 95% CI 0.88, 1.01) per each 10 g/day increase in chocolate intake were observed in the linear dose-response meta-analyses. However, a small inverse association for each 10 g/daily increase could be shown for the risk of CHD (RR 0.96, 95% CI 0.93, 0.99), and stroke (RR 0.90, 95% CI 0.82, 0.98). The credibility of evidence was rated either very low (all-cause mortality, HF, T2D, CRC or hypertension) or low (CHD, stroke).
Conclusion
Chocolate consumption is not related to risk for several chronic diseases, but could have a small inverse association with CHD and stroke. Our findings are limited by very low or low credibility of evidence, highlighting important uncertainty for chocolate–disease associations. Keywords: chocolate, meta-analysis, dose-response, credibility of evidence, chronic diseases Published in DiRROS: 22.07.2024; Views: 106; Downloads: 63
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