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61.
Assessment of hyperbaric oxygenation treatment response in parotid glands by T2 mapping following radiotherapy for head and neck tumours
Jernej Vidmar, Ksenija Cankar, Maja Grošelj, Žarko Finderle, Igor Serša, 2022, izvirni znanstveni članek

Povzetek: Background: The study was designed to evaluate the influence of hyperbaric oxygenation therapy (HBOT) on the parotid gland in patients following radiotherapy for head and neck tumours. Patients and methods: HBOT response was monitored by 3T magnetic resonance imaging (MRI) using T 2 mapping and subsequent measurement of mean T 2 and T 2 variability as well as by salivary tests (salivary flow, buffer capacity, and pH). Eighteen patients previously treated with irradiation doses between 50 and 80 Gy as well as 18 healthy gender and age matched controls were enrolled. MRI was performed prior to HBOT (40.2 ± 20 months after radiotherapy) and after 20 daily HBOT at 2.5 ATA (absolute atmosphere). Each HBOT consisted of breathing 100% oxygen for 90 minutes. Results: Significant differences in mean T 2 prior to HBOT were observed between the ipsilateral irradiated (121 ± 20 ms), contralateral parotids (107 ± 21) and control group (96 ± 12 ms). A positive correlation in patients between T 2 variability and irradiation dose was detected in contralateral parotids before HBOT (R = 0.489, p = 0.0287). In addition, negative correlations were observed between mean T 2 in the ipsilateral as well as the contralateral gland and salivary flow before and after HBOT. Negative correlations between mean T 2, T 2 variability and pH of unstimulated saliva were also observed in the sides of parotid before and after HBOT. Conclusions: The study confirmed that T 2 mapping had a potential for monitoring the differences between irradiated and normal parotid glands. It could also be useful in the assessment of the glandular tissue response to HBOT.
Ključne besede: MRI, T2 mapping, hyperbaric oxygenation therapy, head and neck tumours
Objavljeno v DiRROS: 24.07.2024; Ogledov: 221; Prenosov: 124
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62.
Ecotoxicity of disinfectant benzalkonium chloride and its mixture with antineoplastic drug 5-fluorouracil towards alga Pseudokirchneriella subcapitata
Tina Eleršek, Maja Ženko, Metka Filipič, 2018, izvirni znanstveni članek

Povzetek: Background Benzalkonium chloride (BAC) is one of the most common ingredients of the disinfectants. It is commonly detected in surface and wastewaters where it can interact with the residues of pharmaceuticals that are also common wastewater pollutants. Among the latter, the residues of antineoplastic drugs are of particular concern as recent studies showed that they can induce adverse effect in aquatic organisms at environmentally relevant concentrations. Methods Ecotoxicity of BAC as an individual compound and in a binary mixture with an antineoplastic drug 5-fluorouracil (5-FU) was determined towards alga Pseudokirchneriella subcapitata, a representative of primary producers. The toxicity of the BAC+5-FU binary mixture was predicted by the two basic models: concentration addition (CA) and independent action (IA), and compared to the experimentally determined toxicity. Additionally combination index (CI) was calculated to determine the type of interaction. Results After 72 h exposure to BAC a concentration dependent growth inhibition of P. subcapitata was observed with an EC50 0.255 mg/L. Comparing the predicted no effect concentration to the measured concentrations in the surface waters indicate that BAC at current applications and occurrence in aquatic environment may affect algal populations. The measured toxicity of the mixture was higher from the predicted and calculated CI confirmed synergistic effect on the inhibition of algal growth, at least at EC50 concentration. The observed synergism may have impact on the overall toxicity of wastewaters, whereas it is less likely for general environments because the concentrations of 5-FU are several orders of magnitude lower from its predicted no effect concentration. Discussion These results indicate that combined effects of mixtures of disinfectants and antineoplastic drugs should be considered in particular when dealing with environmental risk assessment as well as the management of municipal and hospital wastewaters.
Ključne besede: ecotoxicity, benzalkonium chloride, algae, 5-fluorouracil, synergistic inhibition
Objavljeno v DiRROS: 24.07.2024; Ogledov: 203; Prenosov: 349
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63.
Surveillance of human enteric viruses in coastal waters using concentration with methacrylate monolithic supports prior to detection by RT-qPCR
José Gonçalves, Ion Gutiérrez-Aguirre, Mukundh Narayanan Balasubramanian, Maja Zagorščak, Maja Ravnikar, Valentina Turk, 2018, izvirni znanstveni članek

Povzetek: This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior to molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at the Bay of Koper (Gulf of Trieste, Northern Adriatic Sea) and at a nearby bathing area and mussel farm areas. RoV and NoV are released into the Bay of Koper, with higher rates close to the discharge of the wastewater treatment plant, however, they can be detected at recreational and mussel farming areas. Our results showed that water bodies considered safe based on FC concentrations, can still have low, yet potentially infective, concentrations of human viruses.
Ključne besede: Rotavirus, Norovirus, faecal coliforms, RT-qPCR, methacrylate monolithic columns, enteric virus concentration
Objavljeno v DiRROS: 24.07.2024; Ogledov: 207; Prenosov: 109
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64.
Cell death is not sufficient for the restriction of potato virus Y spread in hypersensitive response-conferred resistance in potato
Tjaša Lukan, Špela Baebler, Maruša Pompe Novak, Katja Guček, Maja Zagorščak, Anna Coll Rius, Kristina Gruden, 2018, izvirni znanstveni članek

Povzetek: Hypersensitive response (HR)-conferred resistance to viral infection restricts the virus spread and is accompanied by the induction of cell death, manifested as the formation of necrotic lesions. While it is known that salicylic acid is the key component in the orchestration of the events restricting viral spread in HR, the exact function of the cell death in resistance is still unknown. We show that potato virus Y (PVY) can be detected outside the cell death zone in Ny-1-mediated HR in potato plants (cv. Rywal), observed as individual infected cells or small clusters of infected cells outside the cell death zone. By exploiting the features of temperature dependent Ny-1-mediated resistance, we confirmed that the cells at the border of the cell death zone are alive and harbor viable PVY that is able to reinitiate infection. To get additional insights into this phenomenon we further studied the dynamics of both cell death zone expansion and occurrence of viral infected cell islands outside it. We compared the response of Rywal plants to their transgenic counterparts, impaired in SA accumulation (NahG-Rywal), where the lesions occur but the spread of the virus is not restricted. We show that the virus is detected outside the cell death zone in all lesion developmental stages of HR lesions. We also measured the dynamics of lesions expansion in both genotypes. We show that while rapid lesion expansion is observed in SA-depleted plants, virus spread is even faster. On the other hand the majority of analyzed lesions slowly expand also in HR-conferred resistance opening the possibility that the infected cells are eventually engulfed by cell death zone. Taken altogether, we suggest that the HR cell death is separated from the resistance mechanisms which lead to PVY restriction in Ny-1 genetic background. We propose that HR should be regarded as a process where the dynamics of events is crucial for effectiveness of viral arrest albeit the exact mechanism conferring this resistance remains unknown.
Ključne besede: potato virus Y, salicylic acid, hypersensitive response, programmed cell death, callose deposits, necrotic lesion
Objavljeno v DiRROS: 24.07.2024; Ogledov: 183; Prenosov: 179
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65.
Bioactive compounds in the oils of the autochthonous slovenian olive varieties ‘Buga’, ‘Črnica’ and ‘Drobnica’
Vasilij Valenčič, Milena Bučar-Miklavčič, Maja Podgornik, 2024, izvirni znanstveni članek

Povzetek: The adaptation of autochthonous olive varieties to local soil and climatic conditions can lead to a unique chemical composition and characteristics of olive oils that may differ from the generally accepted quality standards set out in the International Olive Oil Council strategy documents and EU regulations. Therefore, the fatty acid composition, biophenol, tocopherol, sterol and triterpenic dialcohol content and composition of the autochthonous Slovenian olive varieties ‘Buga’, ‘Crnica’ ˇ and ‘Drobnica’ were studied for a three-year period with the aim of valorising the characteristics of the three olive varieties. Standardised and accredited analytical methods in accordance with SIST EN ISO/IEC 17025:2017 were applied. The results of the investigation showed that the highest average amount of oleic acid (75.75%) was found in the oils of the ‘Crnica’ variety, followed by the ‘Drobnica’ ˇ (72.06%) and the ‘Buga’ (68.73%). All three varieties are a good source of total biophenols (‘Buga’ 616 mg/kg, ‘Drobnica’ 569 mg/kg and ‘Crnica’ 427 mg/kg) and ˇ α-tocopherol (‘Buga’ 378 mg/kg, ‘Drobnica’ 279 mg/kg, and ‘Crnica’ 243 mg/kg). ‘Buga’ and ‘Drobnica’ are characterised by high ˇ amounts of total sterols, 2468 mg/kg and 2391 mg/kg, respectively, while ‘Crnica’ oils, in comparison, ˇ showed a lower average value of total sterols (1351 mg/kg). Due to their exceptional chemical composition, ‘Buga’, ‘Crnica’ and ‘Drobnica’ show great potential for the further cultivation and ˇ valorisation of traditional olive oil production in the region, thus contributing to the preservation of biodiversity and local traditions. The quality parameters of olive oil from the autochthonous Slovenian olive varieties ‘Buga’, ‘Crnica’ and ‘Drobnica’ also fulfil the limits for extra virgin olive oil ˇ according to the Commission Delegated Regulation (EU) 2022/2104, despite local climatic influences. However, accelerated growth due to climatic changes affecting early harvest can lead to them falling outside these limits, which was observed in particular for the ‘Buga’ variety in terms of the linoleic acid content. This study emphasises the importance of timing the harvest to achieve optimum maturity and meet EU quality standards, taking into account the genetic makeup of the varieties and their response to the current climatic conditions.
Ključne besede: olive, autochthonous Slovenian olive varieties, olive oil, bioactive compounds, chemistry, characterisation
Objavljeno v DiRROS: 24.07.2024; Ogledov: 178; Prenosov: 91
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66.
Potato virus Y infection alters small RNA metabolism and immune response in tomato
Maria I. Prigigallo, Maja Križnik, Domenico De Paola, Domenico Catalano, Kristina Gruden, Mariella M. Finetti-Sialer, Fabrizio Cillo, 2019, izvirni znanstveni članek

Povzetek: Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype.
Ključne besede: RNA silencing, plant defense response, Potato virus Y, molecular plant-virus interactions, microRNA, secondary small interfering RNA, small RNA sequencing, phasiRNA
Objavljeno v DiRROS: 24.07.2024; Ogledov: 779; Prenosov: 184
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67.
Multiomics analysis of tolerant interaction of potato with potato virus Y
Tjaša Stare, Živa Ramšak, Maja Križnik, Kristina Gruden, 2019, izvirni znanstveni članek

Povzetek: Potato virus Y (PVY) is the most economically important viral pathogen of potato worldwide. Different potato cultivars react to the pathogen differently, resulting in resistant, tolerant or disease outcome of the interaction. Here we focus on tolerant interaction between potato cv. Désirée and PVYNTN. To capture the response in its full complexity, we analyzed the dynamic changes on multiple molecular levels, including transcriptomics, sRNAomics, degradomics, proteomics and hormonomics. The analysis was complemented by the measurements of viral accumulation, photosynthetic activity and phenotypisation of the symptoms. Besides cv. Désirée we also studied its transgenic counterpart depleted for the accumulation of salicylic acid (NahG-Désirée). This multiomics analysis provides better insights into the mechanisms leading to tolerant response of potato to viral infection and can be used as a base in further studies of plant immunity regulation.
Ključne besede: potato cv. Désirée, potato virus Y
Objavljeno v DiRROS: 24.07.2024; Ogledov: 223; Prenosov: 424
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68.
69.
Structural basis for the multitasking nature of the potato virus Y coat protein
Andreja 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: 214; Prenosov: 183
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70.
Accurate quantification and characterization of adeno-associated viral vectors
David 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: 233; Prenosov: 125
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