Discovery of relevant response in infected potato plants from time series of gene expression data

The paper presents a methodology for analyzing time series of gene expression data collected from the leaves of potato virus Y (PVY) infected and non-infected potato plants, with the aim to identify significant differences between the two sets of potato plants’ characteristic for various time points. We aim at identifying differentially- expressed genes whose expression values are statistically significantly different in the set of PVY infected potato plants compared to non- infected plants, and which demonstrate also statistically significant changes of expression values of genes of PVY infected potato plants in time. The novelty of the approach includes stratified data randomization used in estimating the statistical properties of gene expression of the samples in the control set of non-infected potato plants. A novel estimate that computes the relative minimal distance between the samples has been defined that enables reliable identification of the differences between the target and control datasets when these sets are small. The relevance of the outcomes is demonstrated by visualizing the relative minimal distance of gene expression changes in time for three different types of potato leaves for the genes that have been identified as relevant by the proposed methodology

Dynamics of Responses in Compatible Potato - Potato virus Y Interaction Are Modulated by Salicylic Acid

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

Limitation of autonomy of will in inheritance law

V magistrskem diplomskem delu so predstavljene omejitve zapustnikove volje pri razpolaganju s svojim premoženjem inter vivos in mortis causa. Dedno pravo je ena izmed disciplin civilnega prava, kjer subjekti delujejo v okviru svoje lastne avtonomije volje. In čeprav je pravica do dedovanja zagotovljena z Ustavo RS poleg pravice do zasebne lastnine, pa zapustnikova avtonomija volje pri razpolaganju s svojim premoženjem ni neomejena. Eden izmed razlogov za takšno ureditev je načelo dedovanja v družini, katerega namena sta ohranitev premoženja v rodbini in preprečevanje eksistencialne stiske družine ob zapustnikovi smrti. Slovenski pravni red pozna vrsto omejitev avtonomije zapustnikove volje pri razpolaganju s svojim premoženjem. Najmočnejša vsebinska omejitev svobode testiranja je nujni delež. Zapustnikovo avtonomijo volje pa med drugim omejujejo tudi neveljavnost večine dednopravnih pogodb, prepoved fidejkomisarične substitucije in neveljavnost skupne oporoke. Trenutno veljavna ureditev dedovanja je bila sprejeta leta 1976 z Zakonom o dedovanju in je bila od takrat dalje le minimalno novelirana, zato je v določenih podrobnostih še vedno moč zaznati prvine socialističnega pravnega reda. Ker se pravo spreminja in prilagaja novim razmeram družbe, se v teoriji in praksi že dlje časa pojavlja stališče, da bi bile na področju dedovanja potrebne določene reforme. Načelno velja stališče, da je posameznikova avtonomija volje premočno omejena. Primerjalnopravna analiza je pokazala, da je v slovenski pravni ureditvi avtonomija volje zapustnika bistveno bolj omejena ter da se v tujini že kaže težnja po spremembah v smeri zmanjševanja omejitev zapustnikove volje, kar bi veljalo urediti tudi pri nas.The master\u27s thesis presents the limitations of the decedent\u27s will in disposing of their property inter vivos and mortis causa. Inheritance law is one of the disciplines of civil law, where subjects operate within their own autonomy of will. Even though the right to private property and the right to inherit property are guaranteed by the Constitution of the Republic of Slovenia, the decedent\u27s autonomy of will in disposing of their property is not unlimited. One of the reasons for such arrangement is the principle of inheritance within the family, the purpose of which is to preserve property within the family, thus preventing existential distress of family members following the death of the decedent. The Slovenian legal system knows a number of limitations related to the autonomy of the decedent\u27s will in disposing of their property. The necessary share is the strongest substantive restriction on the freedom of testing. The decedent\u27s autonomy of will is limited, inter alia, by the invalidity of most inheritance contracts, the prohibition of fideicommissary substitution and the invalidity of a joint will. The current inheritance arrangement was adopted in 1976 with the Inheritance Act. As it has been minimally amended since, it is still possible to detect elements of the socialist legal order in certain details. Given that the law changes and adapts to new conditions of the society, the theory and practice have long held the view that certain reforms were needed as regards inheritance. In principle, the view is that the individual\u27s autonomy of will is too limited. Comparative legal analysis has shown that the autonomy of the decedent\u27s will is significantly more limited in the Slovenian legal system than abroad, where there has been a tendency to reduce the number of restrictions pertaining to the decedent\u27s will. This ought to be regulated in Slovenia as well

Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection

Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it

DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R

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