91. Dynamics of responses in compatible potato - potato virus Y interaction are modulated by salicylic acidŠpela Baebler, Katja Stare, Maja Kovač, Andrej Blejec, Nina Prezelj, Tjaša Stare, Polona Kogovšek, Maruša Pompe Novak, S. Rosahl, Maja Ravnikar, Kristina Gruden, 2011, izvirni znanstveni članek Povzetek: To investigate the dynamics of the potato – Potato virus Y (PVY) compatible interaction in relation to salicylic acid - controlled pathways we performed experiments using non-transgenic potato cv. Désirée, transgenic NahG-Désirée, cv. Igor and PVYNTN, the most aggressive strain of PVY. The importance of salicylic acid in viral multiplication and symptom development was confirmed by pronounced symptom development in NahG-Désirée, depleted in salicylic acid, and reversion of the effect after spraying with 2,6-dichloroisonicotinic acid (a salicylic acid - analogue). We have employed quantitative PCR for monitoring virus multiplication, as well as plant responses through expression of selected marker genes of photosynthetic activity, carbohydrate metabolism and the defence response. Viral multiplication was the slowest in inoculated potato of cv. Désirée, the only asymptomatic genotype in the study. The intensity of defence-related gene expression was much stronger in both sensitive genotypes (NahG-Désirée and cv. Igor) at the site of inoculation than in asymptomatic plants (cv. Désirée). Photosynthesis and carbohydrate metabolism gene expression differed between the symptomatic and asymptomatic phenotypes. The differential gene expression pattern of the two sensitive genotypes indicates that the outcome of the interaction does not rely simply on one regulatory component, but similar phenotypical features can result from distinct responses at the molecular level.
Ključne besede: plant viruses, plant diseases
Objavljeno v DiRROS: 04.03.2025; Ogledov: 87; Prenosov: 34
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92. Characterization of GM events by insert knowledge adapted re-sequencing approachesLitao Yang, Congmao Wang, Arne Holst-Jensen, Dany Morisset, Yongjun Lin, Dabing Zhang, 2013, izvirni znanstveni članek Povzetek: Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.
Ključne besede: molecular engineering in plants, DNA recombination, plant molecular biology, next-generation sequencing
Objavljeno v DiRROS: 04.03.2025; Ogledov: 76; Prenosov: 48
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93. [Beta]-1,3-glucanase class III promotes spread of PVY[sup]NTN and improves in planta protein productionDavid Dobnik, Špela Baebler, Polona Kogovšek, Maruša Pompe Novak, Dejan Štebih, Gabriela Panter, Nikolaja Janež, Dany Morisset, Jana Žel, Kristina Gruden, 2013, izvirni znanstveni članek Povzetek: Glucanases are enzymes regulating the size exclusion limit and permeability of plasmodesmata and play a role in biotic stress. In plant genomes, they are encoded as relatively large gene families divided into four classes. Most studies of plant virus interactions have focused on glucanases from classes I and II. In our study, we have evaluated the role of the β-1,3-glucanase class III (Glu-III) gene in the potato–potato virus YNTN (PVYNTN) interaction and implemented the findings to plant biotechnology application. Potato cultivars Désirée and Santé, which are tolerant and extremely resistant to PVYNTN, respectively, were stably transformed with Agrobacterium tumefaciens harbouring constructs for Glu-III overexpression. Localization of Glu-III protein in patches within the cell wall was determined by tagging the Glu-III protein with green fluorescent protein. Transgenic and non-transgenic plants were challenged with PVYNTN and its multiplication and spreading was followed. Differences in viral spread were observed between transgenic lines overexpressing Glu-III and non-transgenic lines, with stronger and faster viral spread in transgenic Désirée, and some multiplication in transgenic Santé. In addition, the ability of Glu-III to improve in planta protein production after agroinfiltration was tested. The results have shown that Glu-III overexpression enables faster spreading of vectors between cells and better protein production, which could be beneficial in improving in planta protein production system using viral vectors.
Ključne besede: plant biotechnology, plant-virus interaction, potato virus Y, agroinfiltration, beta-1, 3-glucanase
Objavljeno v DiRROS: 04.03.2025; Ogledov: 65; Prenosov: 45
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94. Clinical and structural features of sperm head vacuoles in men included in the in vitro fertilization programmeNina Fekonja, Jasna Štrus, Magda Tušek-Žnidarič, Katja Knez, Eda Vrtačnik-Bokal, Ivan Verdenik, Irma Virant-Klun, 2014, izvirni znanstveni članek Povzetek: The human sperm head vacuoles and their role in male infertility are still poorly understood. The aim of this study was to identify the clinical and ultrastructural features of human sperm head vacuoles in men included in the in vitro fertilization programme: men with normal (normozoospermia) and impaired sperm morphology (teratozoospermia). The sperm samples were observed under 6000-time magnification using motile sperm organelle morphology examination (MSOME). The proportion of sperm with head vacuoles was evaluated and related to the outcome of in vitro fertilization. The sperm of men with impaired sperm morphology was characterized by a higher proportion of sperm head vacuoles. The sperm head vacuoles were related to impaired semen quality (sperm concentration, motility, and morphology) but were not influenced by male factors (semen volume, height, age, weight, or body mass index). Moreover, sperm head vacuoles were related to impaired fertilization rate merely after classical in vitro fertilization (IVF), while there was no relation to pregnancy. In a subgroup of men, the sperm was fixed and observed by transmission electron microscopy (TEM). The ultrastructural study revealed that sperm head vacuoles are large nuclear indentations of various sizes and positions, packed with membranous material organized in membrane whorls (MW).
Ključne besede: human sperm head vacuoles, male infertility
Objavljeno v DiRROS: 04.03.2025; Ogledov: 80; Prenosov: 53
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95. Environmental footprint of external thermal insulation composite systems with different insulation typesTajda Potrč Obrecht, Katja Malovrh Rebec, Friderik Knez, Roman Kunič, Andraž Legat, 2016, objavljeni znanstveni prispevek na konferenci Povzetek: In terms of upcoming energy directive for Nearly Zero Energy Houses (nZEB), we are very much focused on building skin and its properties. Not only thermal characteristics and design, but also durability and environmental aspects should play a role, when deciding on which system will be implemented. External Thermal Insulation Composite Systems or ETICS are generally made of adhesive, insulation, render with mesh reinforcement, primer and finish coat. In the following case study we have presented a life cycle assessment (LCA) study of three ETICS with different types of insulation: expanded polystyrene (EPS), mineral wool and wood fiber board insulation. The study complies to the standard EN 15804:2012. It was conducted in the program Gabi using the Gabi Professional 2012 Database. The scope of the study is covering the production phase (raw material supply, transport to the factory, manufacturing). We have compared the functional unit of 1 sqm of the ETICS system with U-value 0.27 W/m2K taking into account different environmental impact categories. In the calculation the characterization factors proposed by Centre of Environmental Science (CML) at Leiden University were used. The comparison of ETICS shows the important impact of the insulation type used. Also there are some differences in the amount of other ETICS components applied, since changing the type of insulation affects the environmental footprint of the ETICS.
Ključne besede: ETICS, life cycle assessment, nearly zero energy house, insulition types
Objavljeno v DiRROS: 04.03.2025; Ogledov: 78; Prenosov: 32
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96. An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1Alison S. Devonshire, Tina Demšar, Jana Žel, Andrej Blejec, Mojca Milavec, 2016, izvirni znanstveni članek Povzetek: Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples. Six exogenous synthetic targets comprising of External RNA Control Consortium (ERCC) standards were measured alongside transcripts for three endogenous gene targets present in the background of human cell line RNA. The study was carried out under the auspices of the Nucleic Acids (formerly Bioanalysis) Working Group of the CCQM. It was coordinated by LGC (United Kingdom) with the support of National Institute of Standards and Technology (USA) and results were submitted from thirteen National Metrology Institutes and Designated Institutes. The majority of laboratories performed RNA measurements using RT-qPCR, with datasets also being submitted by two laboratories based on reverse transcription digital polymerase chain reaction and one laboratory using a next-generation sequencing method. In RT-qPCR analysis, the RNA copy number ratios between the two samples were quantified using either a standard curve or a relative quantification approach. In general, good agreement was observed between the reported results of ERCC RNA copy number ratio measurements. Measurements of the RNA copy number ratios for endogenous genes between the two samples were also consistent between the majority of laboratories. Some differences in the reported values and confidence intervals (‘measurement uncertainties’) were noted which may be attributable to choice of measurement method or quantification approach. This highlights the need for standardised practices for the calculation of fold change ratios and uncertainties in the area of gene expression profiling.
Ključne besede: RNA copy number ratio, RT-qPCR, gene expression, normalisation, standardisation, molecular diagnostic, transcriptomics, cancer, diagnostics, biomarker identification and validation
Objavljeno v DiRROS: 04.03.2025; Ogledov: 70; Prenosov: 30
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97. Experiences from in-situ monitoring of pavement under weather conditions changeBarbara Likar, Stanislav Lenart, Karmen Fifer Bizjak, Anh Minh Tang, 2016, objavljeni znanstveni prispevek na konferenci Povzetek: Very strong winters with temperatures under 0°C and hot summers with temperatures more than 30°C are observed in the South East part of Slovenia. Those big differences in temperature during the year and especially temperatures below freezing point have strong influence on asphalt layer and sub base of road pavement. The freeze/thaw cycles lead to formation of ice lenses in base course causing cracks in asphalt layers and degrade the pavement usually in a few years. For this reason one section of the national road in the South East part of Slovenia was rebuilt with cold in-situ pavement retreatment. A test field with inbuilt sensors for measuring water content, temperature and deformation in various depths and locations was constructed during the remediation works to study the mechanism of freeze-thaw degradation of pavements. The main goal of the test field is to determine water content in sub base, freezing depth, temperature distribution and deformations, which lead to cracks in asphalt layer after the remediation work in the road construction.
Ključne besede: pavement, freezing, in-situ monitoring, climate effect
Objavljeno v DiRROS: 04.03.2025; Ogledov: 70; Prenosov: 37
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98. Some experience in numerical modelling of unsaturated slope instabilitiesJosif Josifovski, Stanislav Lenart, 2016, objavljeni znanstveni prispevek na konferenci Povzetek: In the past couple years, the region of South-East Europe is subjected to gust rainfall events activating many landslides which cause significant material and human losses. To revaluate the existing risk maps and set new standards some old case histories are revaluated. This paper presents two case histories of landslide instabilities subjected to excess climatic perturbations, gust rainfall, namely the «Stanjevci» cut-slope near the railway line in North-East of Slovenia; and the «Ramina» a natural landslide in urban area near the city of Veles in Central Macedonia. They are briefly described later to be analysed using coupled thermo-mechanical calculations. They are subjected to specific short and gusting rainfall considered as possible trigger. Hence, van Genuchten's hydraulic model is used in combination with elastoplastic material models. The results are summarized with critical comments regarding the mathematical formulation used to describe atmospheric-soil interaction and the influence of different aspects on the accuracy is discussed briefly.
Ključne besede: numerical, unsaturated soil, slope stability analysis, climate effect
Objavljeno v DiRROS: 04.03.2025; Ogledov: 68; Prenosov: 36
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