871. The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosisAlison S. Devonshire, Jernej Pavšič, Mojca Milavec, Jana Žel, 2016, original scientific article Abstract: Background
Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring.
Methods
To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories.
Results
dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude.
Conclusions
TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification of Mycobacterium tuberculosis would provide a clinically useful readout. The methods described in this study provide a means by which the technical performance of quantitative molecular methods can be evaluated independently of clinical variability to improve accuracy of measurement results. These will assist in ultimately increasing the likelihood that such approaches could be used to improve patient management of TB.
Keywords: digital PCR, diagnostics
Published in DiRROS: 25.07.2024; Views: 260; Downloads: 158
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872. Dispersal similarly shapes both population genetics and community patterns in the marine realmGuillem Chust, Ernesto Villarino, Anne Chenuil, Xabier Irigoien, Nihayet Bizsel, Antonio Bode, Serena Fonda Umani, Patricija Mozetič, Ángel Borja, 2016, original scientific article Abstract: Dispersal plays a key role to connect populations and, if limited, is one of the main processes to maintain and generate regional biodiversity. According to neutral theories of molecular evolution and biodiversity, dispersal limitation of propagules and population stochasticity are integral to shaping both genetic and community structure. We conducted a parallel analysis of biological connectivity at genetic and community levels in marine groups with different dispersal traits. We compiled large data sets of population genetic structure (98 benthic macroinvertebrate and 35 planktonic species) and biogeographic data (2193 benthic macroinvertebrate and 734 planktonic species). We estimated dispersal distances from population genetic data (i.e., FST vs. geographic distance) and from %-diversity at the community level. Dispersal distances ranked the biological groups in the same order at both genetic and community levels, as predicted by organism dispersal ability and seascape connectivity: macrozoobenthic species without dispersing larvae, followed by macrozoobenthic species with dispersing larvae and plankton (phyto- and zooplankton). This ranking order is associated with constraints to the movement of macrozoobenthos within the seabed compared with the pelagic habitat. We showed that dispersal limitation similarly determines the connectivity degree of communities and populations, supporting the predictions of neutral theories in marine biodiversity patterns.
Keywords: sea, phytoplankton, dispersal, distribution, ocean sampling, Atlantic Ocean, Gulf of Trieste
Published in DiRROS: 25.07.2024; Views: 245; Downloads: 217
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873. Solanum venturii, a suitable model system for virus-induced gene silencing studies in potato reveals StMKK6 as an important player in plant immunityDavid Dobnik, Ana Lazar, Tjaša Stare, Kristina Gruden, Vivianne G. A. A. Vleeshouwers, Jana Žel, 2016, original scientific article Abstract: Background
Virus-induced gene silencing (VIGS) is an optimal tool for functional analysis of genes in plants, as the viral vector spreads throughout the plant and causes reduced expression of selected gene over the whole plant. Potato (Solanum tuberosum) is one of the most important food crops, therefore studies performing functional analysis of its genes are very important. However, the majority of potato cultivars used in laboratory experimental setups are not well amenable to available VIGS systems, thus other model plants from Solanaceae family are used (usually Nicotiana benthamiana). Wild potato relatives can be a better choice for potato model, but their potential in this field was yet not fully explored. This manuscript presents the set-up of VIGS, based on Tobacco rattle virus (TRV) in wild potato relatives for functional studies in potato–virus interactions.
Results
Five different potato cultivars, usually used in our lab, did not respond to silencing of phytoene desaturase (PDS) gene with TRV-based vector. Thus screening of a large set of wild potato relatives (different Solanum species and their clones) for their susceptibility to VIGS was performed by silencing PDS gene. We identified several responsive species and further tested susceptibility of these genotypes to potato virus Y (PVY) strain NTN and N. In some species we observed that the presence of empty TRV vector restricted the movement of PVY. Fluorescently tagged PVYN-GFP spread systemically in only five of tested wild potato relatives. Based on the results, Solanum venturii (VNT366-2) was selected as the most suitable system for functional analysis of genes involved in potato–PVY interaction. The system was tested by silencing two different plant immune signalling-related kinases, StWIPK and StMKK6. Silencing of StMKK6 enabled faster spreading of the virus throughout the plant, while silencing of WIPK had no effect on spreading of the virus.
Conclusions
The system employing S. venturii (VNT366-2) and PVYN-GFP is a suitable method for fast and simple functional analysis of genes involved in potato–PVY interactions. Additionally, a set of identified VIGS responsive species of wild potato relatives could serve as a tool for general studies of potato gene function.
Keywords: potato, virus-induced gene silencing, VIGS, potato virus Y, PVY, Solanum venturii, StWIPK, StMKK6, TRV
Published in DiRROS: 25.07.2024; Views: 275; Downloads: 231
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874. Metabolic consequences of infection of grapevine (Vitis vinifera L.) cv. ʺModra frankinjaʺ with flavescence dorée phytoplasmaNina Prezelj, Elizabeth Covington, Thomas Roitsch, Kristina Gruden, Lena Fragner, Wolfram Weckwerth, Marko Chersicola, Maja Vodopivec, Marina Dermastia, 2016, original scientific article Abstract: Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp–grapevine interaction in infected grapevines of cv. “Modra frankinja” under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defense response status.
Keywords: fructose utilization, gene expression, invertase, metabolome, soluble sugars, starch, sucrose synthase, SWEET, VvDMR6
Published in DiRROS: 25.07.2024; Views: 313; Downloads: 250
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875. Imaging of human glioblastoma cells and their interactions with mesenchymal stem cells in the zebrafish (Danio rerio) embryonic brainMiloš Vittori, Barbara Breznik, Tajda Gredar, Katja Hrovat, Lilijana Bizjak-Mali, Tamara Lah Turnšek, 2016, original scientific article Abstract: Background
An attractive approach in the study of human cancers is the use of transparent zebrafish (Danio rerio) embryos, which enable the visualization of cancer progression in a living animal.
Materials and methods
We implanted mixtures of fluorescently labeled glioblastoma (GBM) cells and bonemarrow-derived mesenchymal stem cells (MSCs) into zebrafish embryos to study the cellular pathways of their invasion and the interactions between these cells in vivo.
Results
By developing and applying a carbocyanine-dye-compatible clearing protocol for observation of cells in deep tissues, we showed that U87 and U373 GBM cells rapidly aggregated into tumor masses in the ventricles and midbrain hemispheres of the zebrafish embryo brain, and invaded the central nervous system, often using the ventricular system and the central canal of the spinal cord. However, the GBM cells did not leave the central nervous system. With co-injection of differentially labeled cultured GBM cells and MSCs, the implanted cells formed mixed tumor masses in the brain. We observed tight associations between GBM cells and MSCs, and possible cell-fusion events. GBM cells and MSCs used similar invasion routes in the central nervous system.
Conclusions
This simple model can be used to study the molecular pathways of cellular processes in GBM cell invasion, and their interactions with various types of stromal cells in double or triple cell co-cultures, to design anti-GBM cell therapies that use MSCs as vectors.
Keywords: brain tumors, tumor microenvironment, animal models, xenotransplantation
Published in DiRROS: 25.07.2024; Views: 245; Downloads: 216
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876. Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific oceansMarta Estrada, Maximino Delgado, Dolores Blasco, Mikel Latasa, Ana Maria Cabello, Verónica Benitez-Barrios, Eugenio Fraile-Nuez, Patricija Mozetič, Monteserrat Vidal, 2016, original scientific article Abstract: We examine the large-scale distribution patterns of the nano- and microphytoplankton collected from 145 oceanic stations, at 3 m depth, the 20% light level and the depth of the sub-surface chlorophyll maximum, during the Malaspina-2010 Expedition (December 2010-July 2011), which covered 15 biogeographical provinces across the Atlantic, Indian and Pacific oceans, between 35°N and 40°S. In general, the water column was stratified, the surface layers were nutrient-poor and the nano- and microplankton (hereafter phytoplankton, for simplicity, although it included also heterotrophic protists) community was dominated by dinoflagellates, other flagellates and coccolithophores, while the contribution of diatoms was only important in zones with shallow nutriclines such as the equatorial upwelling regions. We applied a principal component analysis to the correlation matrix among the abundances (after logarithmic transform) of the 76 most frequent taxa to synthesize the information contained in the phytoplankton data set. The main trends of variability identified consisted of: 1) A contrast between the community composition of the upper and the lower parts of the euphotic zone, expressed respectively by positive or negative scores of the first principal component, which was positively correlated with taxa such as the dinoflagellates Oxytoxum minutum and Scrippsiella spp., and the coccolithophores Discosphaera tubifera and Syracosphaera pulchra (HOL and HET), and negatively correlated with taxa like Ophia-ster hydroideus (coccolithophore) and several diatoms, 2) a general abundance gradient between phytoplankton-rich regions with high abundances of dinoflagellate, coccolitho-phore and ciliate taxa, and phytoplankton-poor regions (second principal component), 3) differences in dominant phytoplankton and ciliate taxa among the Atlantic, the Indian and the Pacific oceans (third principal component) and 4) the occurrence of a diatom-dominated assemblage (the fourth principal component assemblage), including several pennate taxa, Planktoniella sol, Hemiaulus hauckii and Pseudo-nitzschia spp., in the divergence regions.
Keywords: sea, phytoplankton, research programmes, ocean expeditions, Malaspina 2010, distribution, ocean sampling, Atlantic Ocean, Pacific, Indian Ocean
Published in DiRROS: 25.07.2024; Views: 433; Downloads: 259
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877. RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerasesLydia J. R. Hunter, Samuel F. Brockington, Alex M. Murphy, Adrienne E. Pate, Kristina Gruden, Stuart A. MacFarlane, Peter Palukaitis, John P. Carr, 2016, original scientific article Abstract: Cellular RNA-dependent RNA polymerases (RDRs) catalyze synthesis of double-stranded RNAs that can serve to initiate or amplify RNA silencing. Arabidopsis thaliana has six RDR genes; RDRs 1, 2 and 6 have roles in anti-viral RNA silencing. RDR6 is constitutively expressed but RDR1 expression is elevated following plant treatment with defensive phytohormones. RDR1 also contributes to basal virus resistance. RDR1 has been studied in several species including A. thaliana, tobacco (Nicotiana tabacum), N. benthamiana, N. attenuata and tomato (Solanum lycopersicum) but not to our knowledge in potato (S. tuberosum). StRDR1 was identified and shown to be salicylic acid-responsive. StRDR1 transcript accumulation decreased in transgenic potato plants constitutively expressing a hairpin construct and these plants were challenged with three viruses: potato virus Y, potato virus X, and tobacco mosaic virus. Suppression of StRDR1 gene expression did not increase the susceptibility of potato to these viruses. Phylogenetic analysis of RDR genes present in potato and in a range of other plant species identified a new RDR gene family, not present in potato and found only in Rosids (but apparently lost in the Rosid A. thaliana) for which we propose the name RDR7.
Keywords: RNA polymerases, RNA, potato
Published in DiRROS: 25.07.2024; Views: 395; Downloads: 225
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878. Primary metabolism, phenylpropanoids and antioxidant pathways are regulated in potato as a response to Potato virus Y infectionPolona Kogovšek, Maruša Pompe Novak, Marko Petek, Lena Fragner, Wolfram Weckwerth, Kristina Gruden, 2016, original scientific article Abstract: Potato production is one of the most important agricultural sectors, and it is challenged by various detrimental factors, including virus infections. To control losses in potato production, knowledge about the virus—plant interactions is crucial. Here, we investigated the molecular processes in potato plants as a result of Potato virus Y (PVY) infection, the most economically important potato viral pathogen. We performed an integrative study that links changes in the metabolome and gene expression in potato leaves inoculated with the mild PVYN and aggressive PVYNTN isolates, for different times through disease development. At the beginning of infection (1 day post-inoculation), virus-infected plants showed an initial decrease in the concentrations of metabolites connected to sugar and amino-acid metabolism, the TCA cycle, the GABA shunt, ROS scavangers, and phenylpropanoids, relative to the control plants. A pronounced increase in those metabolites was detected at the start of the strong viral multiplication in infected leaves. The alterations in these metabolic pathways were also seen at the gene expression level, as analysed by quantitative PCR. In addition, the systemic response in the metabolome to PVY infection was analysed. Systemic leaves showed a less-pronounced response with fewer metabolites altered, while phenylpropanoid-associated metabolites were strongly accumulated. There was a more rapid onset of accumulation of ROS scavengers in leaves inoculated with PVYN than those inoculated with PVYNTN. This appears to be related to the lower damage observed for leaves of potato infected with the milder PVYN strain, and at least partially explains the differences between the phenotypes observed.
Published in DiRROS: 25.07.2024; Views: 265; Downloads: 235
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879. Improved protective effect of umbilical cord stem cell transplantation on cisplatin-induced kidney injury in mice pretreated with antithymocyte globulinŽeljka Večerić-Haler, Andreja Erman, Anton Cerar, Helena Motaln, Katja Kološa, Tamara Lah Turnšek, Snežna Sodin-Šemrl, Katja Lakota, Katjuša Mrak Poljšak, Špela Škrajnar, Simona Kranjc Brezar, Miha Arnol, Martina Perše, 2016, original scientific article Abstract: Mesenchymal stem cells (MSCs) are recognised as a promising tool to improve renal recovery in experimental models of cisplatin-induced acute kidney injury. However, these preclinical studies were performed on severely immunodeficient animals. Here, we investigated whether human umbilical cord derived MSC treatment could equally ameliorate acute kidney injury induced by cisplatin and prolong survival in mice with a normal immune system and those with a suppressed immune system by polyclonal antithymocyte globulin (ATG). We demonstrated that ATG pretreatment, when followed by MSC transplantation, significantly improved injured renal function parameters, as evidenced by decreased blood urea nitrogen and serum creatinine concentration, as well as improved renal morphology. This tissue restoration was also supported by increased survival of mice. The beneficial effects of ATG were associated with reduced level of inflammatory protein serum amyloid A3 and induced antioxidative expression of superoxide dismutase-1 (SOD-1), glutathione peroxidase (GPx), and hem oxygenase-1 (HO-1). Infused MSCs became localised predominantly in peritubular areas and acted to reduce renal cell death. In conclusion, these results show that ATG diminished in situ inflammation and oxidative stress associated with cisplatin-induced acute kidney injury, the effects that may provide more favourable microenvironment for MSC action, with consequential synergistic improvements in renal injury and animal survival as compared to MSC treatment alone.
Keywords: mesenchymal stem cells, nephrotoxicity
Published in DiRROS: 25.07.2024; Views: 277; Downloads: 235
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880. Use of hydrodynamic cavitation in (waste)water treatmentMatevž Dular, Tjaša Griessler Bulc, Ion Gutiérrez-Aguirre, Ester Heath, Tina Kosjek, Aleksandra Krivograd-Klemenčič, Martina Oder, Martin Petkovšek, Nejc Rački, Maja Ravnikar, Andrej Šarc, Brane Širok, Mojca Zupanc, Miha Žitnik, Boris Kompare, 2016, original scientific article Abstract: The use of acoustic cavitation for water and wastewater treatment (cleaning) is a well known procedure. Yet, the use of hydrodynamic cavitation as a sole technique or in combination with other techniques such as ultrasound has only recently been suggested and employed.
In the first part of this paper a general overview of techniques that employ hydrodynamic cavitation for cleaning of water and wastewater is presented.
In the second part of the paper the focus is on our own most recent work using hydrodynamic cavitation for removal of pharmaceuticals (clofibric acid, ibuprofen, ketoprofen, naproxen, diclofenac, carbamazepine), toxic cyanobacteria (Microcystis aeruginosa), green microalgae (Chlorella vulgaris), bacteria (Legionella pneumophila) and viruses (Rotavirus) from water and wastewater.
As will be shown, hydrodynamic cavitation, like acoustic, can manifest itself in many different forms each having its own distinctive properties and mechanisms. This was until now neglected, which eventually led to poor performance of the technique. We will show that a different type of hydrodynamic cavitation (different removal mechanism) is required for successful removal of different pollutants.
The path to use hydrodynamic cavitation as a routine water cleaning method is still long, but recent results have already shown great potential for optimisation, which could lead to a low energy tool for water and wastewater cleaning.
Keywords: wastewater, cleaning, hydrodynamic cavitation, pharmaceuticals, cyanobacteria, microalgae, viruses, Legionella bacteria
Published in DiRROS: 25.07.2024; Views: 239; Downloads: 133
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