1. Foliar application of silicon has little effect on hydroponically grown barley (Hordeum vulgare L.)Anja Mavrič Čermelj, Aleksandra Golob, Nina Kacjan Maršić, Mateja Germ, 2023, izvirni znanstveni članek Povzetek: Silicon is an element widely distributed on the earth’s crust. It can ameliorate stress in plants grown in unfavorable conditions. Barley is an important cereal used as a staple food. In our experiment, barley was grown on a floating hydroponics system in a greenhouse. Plants were stabilized in pots containing rockwool. Half of the plants were sprayed with potassium silicate (0.25 ml 6% K2SiO3 L-1) every ten days for 35 days. The vitality of plants during their growth was monitored by measuring the potential photochemical efficiency of photosystem II. After 16 and 35 days of silicon application, shoot length, root length, and fresh and dry biomass were measured. At the end of the experiment, the number of leaves and shoots, specific leaf area, leaf optical properties, and lipid peroxidation were determined as well. The potential photochemical efficiency of photosystem II was close to 0.8 and unaffected by the addition of silicon, indicating a good condition of the plants. Results showed lower leaf reflectance for silicon-treated plants in UVA, UVB, and blue light wavelengths, possibly due to a layer of potassium silicate on leaves. After 16 days, silicon-treated plants’ fresh shoot weight and root length were higher than in control plants. Results showed that additional foliar application of silicon does not cause stress in the barley plant.
Ključne besede: potassium silicate, barley, Hordeum vulgare, hydroponics, foliar application, silicon
Objavljeno v DiRROS: 09.01.2026; Ogledov: 552; Prenosov: 149
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2. Patients’ daily reporting of symptoms via mobile application reveals a significant difference between patients’ perceptions and doctors’ interpretationsCvetka Grašič-Kuhar, Nina Privšek, Marjetka Sraka, Ema Grašič, Timotej Kovač, Matjaž Kukar, 2025, izvirni znanstveni članek Povzetek: Electronic patient-reported outcomes (ePROs) are gaining importance. The aim of this study was to investigate the difference in the reporting of symptoms between patients via mobile application (m-app) and doctor assessments. Additionally, usability and satisfaction with the use of the m-app were assessed. Methods: In this single-center prospective cohort study, we analyzed ePROs in 46 patients receiving (neo)adjuvant chemotherapy for early breast cancer. Patients recorded the occurrence and intensity of symptoms via the Android-based m-app daily. Three-monthly, patients completed validated quality of life questionnaires (EORTC C30 and BR23). For the 10 most common symptoms reported by patients, we compared the frequencies and grades between patients and doctors. Additionally, we compared daily symptom reports with questionnaire results. Finally, the usefulness of and level of satisfaction with the m-app by patients and doctors were evaluated. Results: During the study, patients recorded almost twice as many different symptoms through the m-app as doctors did in the electronic health records (75 vs 49). Symptoms were described by patients as mild (67%), moderate (30%), or severe (3%). The frequency and intensity of symptoms reported by patients were significantly higher than those reported by doctors (p<0.001). Fatigue, insomnia and dry mouth were the three main symptoms reported in more than 75% of patients, but insomnia and dry mouth were also the symptoms most often underreported by doctors. After three months of chemotherapy, QoL assessments revealed worsening of physical, social, cognitive and role functioning, increased fatigue, systemic therapy side effects, and dyspnea but a reduction in arm and shoulder problems. Patients and doctors rated the m-app with an overall score of 4.5 out of 5 (IQR 1.0). Patients expressed high levels of satisfaction with and usability of the m-app. In contrast, doctors were somewhat reluctant to perceive ePROs as an additional burden with patient management. Conclusion: This study revealed a significant discrepancy between patients’ daily symptom reports via the m-app and doctors’ assessments, indicating that healthcare professionals may not fully capture patients’ experiences. This underscores the importance of integrating PROs to accurately evaluate patients’ conditions. Our m-app serves as a promising tool for reporting and managing side effects during systemic treatment of breast cancer.
Ključne besede: breast cancer, mobile application, patients, doctors
Objavljeno v DiRROS: 05.12.2025; Ogledov: 246; Prenosov: 119
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3. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevinePolona Kogovšek, Jennifer Hodgetts, J. Hall, Nina Prezelj, Petra Nikolić, Nataša Mehle, Rok Lenarčič, Ana Rotter, M. Dickinson, Neil Boonham, Marina Dermastia, Maja Ravnikar, 2015, izvirni znanstveni članek Povzetek: In Europe the most devastating phytoplasma associated with grapevine yellows (GY) diseases is a quarantine pest, flavescence dorée (FDp), from the 16SrV taxonomic group. The on-site detection of FDp with an affordable device would contribute to faster and more efficient decisions on the control measures for FDp. Therefore, a real-time isothermal LAMP assay for detection of FDp was validated according to the EPPO standards and MIQE guidelines. The LAMP assay was shown to be specific and extremely sensitive, because it detected FDp in all leaf samples that were determined to be FDp infected using quantitative real-time PCR. The whole procedure of sample preparation and testing was designed and optimized for on-site detection and can be completed in one hour. The homogenization procedure of the grapevine samples (leaf vein, flower or berry) was optimized to allow direct testing of crude homogenates with the LAMP assay, without the need for DNA extraction, and was shown to be extremely sensitive.
Ključne besede: flavescence dorée, homogenization, loop-mediated isothermal amplification, on-site application, validation
Objavljeno v DiRROS: 26.07.2024; Ogledov: 1296; Prenosov: 1053
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4. quantGenius : implementation of a decision support system for qPCR-based gene quantificationŠpela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe Novak, Kristina Gruden, 2017, izvirni znanstveni članek Povzetek: Background
Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification.
Results
We have developed “quantGenius” (http://quantgenius.nib.si), an open-access web application for a reliable qPCR-based quantification of nucleic acids. The quantGenius workflow interactively guides the user through data import, quality control (QC) and calculation steps. The input is machine- and chemistry–independent. Quantification is performed using the standard curve approach, with normalization to one or several reference genes. The special feature of the application is the implementation of user-guided QC-based decision support system, based on qPCR standards, that takes into account pipetting errors, assay amplification efficiencies, limits of detection and quantification of the assays as well as the control of PCR inhibition in individual samples. The intermediate calculations and final results are exportable in a data matrix suitable for further statistical analysis or visualization. We additionally compare the most important features of quantGenius with similar advanced software tools and illustrate the importance of proper QC system in the analysis of qPCR data in two use cases.
Conclusions
To our knowledge, quantGenius is the only qPCR data analysis tool that integrates QC-based decision support and will help scientists to obtain reliable results which are the basis for biologically meaningful data interpretation.
Ključne besede: quantitative molecular biology, quantitative PCR, nucleic acid quantification, web application, decision support system
Objavljeno v DiRROS: 24.07.2024; Ogledov: 1203; Prenosov: 652
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5. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: biological networks, clustering, gene expression, time series, dynamic network analysis, dynamic data visualisation, web application, multi-conditional datasets, background knowledge
Objavljeno v DiRROS: 24.07.2024; Ogledov: 1246; Prenosov: 699
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7. Structural and degradation studies of a biocompatible Zn-L-tartrate metal-organic frameworkAna Palčić, Andreas Puškarić, Matjaž Mazaj, Emanuela Žunkovič, Nataša Zabukovec Logar, Josip Bronić, 2015, izvirni znanstveni članek Povzetek: New anhydrous Zn-l-tratrate was synthesized under hydrothermal conditions. Crystal structure which was solved by powder X-ray diffraction data from monoclinic unit cell (I2, a=11.7557(1), b=9.0319(1), c=5.0750(1), β=91.920(1)) consists of the three-dimensional framework where each Zn atom coordinates four tartrate ligands in distorted octahedral geometry. Due to its biocompatible components, the degradation of material was studied in aqueous media under different pH values (pH=1–7) and in the simulated body fluid (pH=7.4) performed by the measurement of the released Zn2+ concentrations at thermostatic conditions (37 °C). The results showed that under acidic conditions approximately 60% of Zn2+ is released from the investigated material after 6 h of degradation process. With the increase of the solution’s pH, the rate of degradation gradually decreases. XRD and SEM analyses indicate that in aqueous media the compound slowly disintegrates and does not undergo hydrolysis process regardless of pH. Biocompatibility of the compound and its controllable rate of degradation even in acid conditions open its potential use in the fields of bio-applications.
Graphical abstract
The degradation kinetics of Zn-l-tar MOF material in aqueous media at different pH conditions.
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Ključne besede: Zn-tartrate, coordination polymers, hydrothermal synthesis, biomedical application, food supplement
Objavljeno v DiRROS: 26.01.2015; Ogledov: 6777; Prenosov: 899
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