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Sodobne zahteve deljenja javno dostopnih podatkov in upoštevanje FAIR principa predstavlja relativno novost za raziskovalce. Raziskovalci se pogosto o potrebi in načinu deljenja podatkov srečajo šele na koncu raziskave. Veliko učinkoviteje pa je o tem razmišljati pred in med samim potekom raziskave. V prispevki je predstavljen način upravljanja s podatki in organizacije podatkov na nivoju raziskovalne skupine ali manjše institucije že med potekom raziskave. Predstavljeno bo na našem oddelku razvito orodje pISA-tree, ki omogoča konsistentno organizacijo podatkov že med raziskavo. Podatki so organizirani v skladu s pricipoma ISA in FAIR, ter opremljeni z metapodatki, ki jih potrebujemo za avtomatizirano deponiranje na platforme z odprtim dostopom do podatkov (npr. FAIRDOMhub).

While activation of resistance (R) proteins has been intensively studied, the mechanisms acting downstream of R protein activation remain elusive. We studied effector-triggered immunity (ETI) conditioned by the potato Ny-1 gene against potato virus Y. Transcriptomic, ultrastructural and biochemical analyses of four consecutive tissue sections in and surrounding the foci of viral infection at three different lesion developmental stages revealed processes that are spatiotemporally regulated. The transcriptional response in the cell death zone and surrounding tissue is dependent on SA. For some of the genes, spatiotemporal regulation is completely lost while for others, the regulation is different in SA-deficient line indicating multiple connections between hormonal signaling modules. The induction of RBOHD NADPH oxidase expression, together with expression of Thioredoxin H gene, occurs specifically in the border region of the lesion during ETI. In plants with silenced RBOHD, ETI is perturbed and virus spread is not arrested at the site of infection. Expression of RBOHD is under the control of SA. On the other hand, RBOHD activity is required for spatial regulation of SA accumulation. We identified an UDP-glucosyltransferase, encoding an enzyme involved in feedback activation of SA biosynthesis, that is derepressed at the border of the lesion in RBOHD silenced plants. Altogether, we revealed a novel aspect of viral ETI, the RBOHD-SA feedback loop required for its spatial regulation. SIGNIFICANCE To get towards sustainable resistance in the field, it is important to understand mechanisms of immune signaling. We here show novel aspects of spatial regulation in effector-triggered immunity (ETI) against potato virus Y. A detailed spatiotemporal analysis in and surrounding the foci of viral infection, on ultrastructural, biochemical and gene expression levels revealed that redox state maintenance is tightly spatiotemporally regulated. We also show the interconnection of salicylic acid and RBOHD through a feedback loop, regulated through UDP-glucosyltransferase, revealing the mechanism of this spatial regulation. The proper function of this loop is essential for successful ETI leading to viral arrest.

Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.

Additional file 2. Dynamic visualisation of immune signalling network response in potato cv. Désirée infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for Désirée plants.

Additional file 1. Dynamic visualisation of Arabidopsis thaliana response to Pseudomonas syringae. AtCKN network, cluster 40, GSE56094 experimental data, Pseudomonas syringae pv. tomato DC3000 vs Mock subset. Relative expression between Pseudomonas syringae and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red-induction, blue-repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression following 0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16 and 17.5 hpi are shown.

Additional file 3. Dynamic visualisation of immune signalling network response in potato cv. NahG-D\'esir\'ee infected with virus PVY. PIS network, GSE58593 experimental data at the orthologue groups level. Relative expression between PVY and mock-treated plants has been log2 transformed. The absolute values are represented by the size of the node and differential expression is color-coded (red—induction, blue—repression of expression). Only genes that are significantly differentially expressed are visualized (FDR p < 0.05). Dynamic changes in gene expression 1, 3, 4, 5 and 7 dpi after infection with PVY are shown for NahG-Désirée plants.

Symptom development and callose accumulation after PVY NTN inoculation. (A) Phenotypes of the PVYNTN-inoculated (right panel) and mock-inoculated plants (left panel). Symptoms on PVYNTN-inoculated leaves are shown at 7 and 11 dpi, and compared to control mock inoculated leaves for cv. Désirée (upper) and NahG-Désirée (bottom). (B) Callose deposition stained with aniline blue. Leaves of NT Désirée and transgenic NahG-Desiree were either PVY or mock-inoculated. In NT Désirée plants (NT- PVYNTN and NT-mock) and mock inoculated NahG-Désirée (NahG-mock) there was no callose accumulating. Callose deposition was observed only at the sites of necrotic lesions in PVYNTN-inoculated NahG-Désirée leaves. Two samples of callose accumulation at the site of necrotic lesion are demonstrated (NahG-PVYNTN). (Blue for aniline blue, red for background fluorescence, gray for transmission field, most bottom panel for superposition) (PDF 511 kb)

Statistical analysis of PVY accumulation and photosynthetic parameters. The significance of increase (+++: p

Validation of microarray results by RT-qPCR. Microarray results were validated by analyzing eight biologically relevant genes involved in photosynthesis (chlorophyll a-b binding protein: CAB and RuBisCO activase: RA), defense response (β-1,3-glucanase of three classes: Glu-I, Glu-II, Glu-III and pathogenesis-related protein1b: PR-1b), and sugar metabolism (granule bound starch synthase I: GBSSI and CwINV: cell wall invertase) by quantitative real-time PCR. Expression values were log2 transformed, and a fold-change difference (log2FC) was calculated for PVYNTN versus mock in cv. Désirée and NahG-Désirée at 1, 3, 4, 5 and 7 dpi are shown in the table. Statistically significant values (p

Transcriptional dynamic changes (log 2 FC) of genes involved in primary metabolism visualized with MapMan. Gene expression for cv. Désirée (A) and NahG-Désirée (B) plants infected with PVYNTN are visualized at 1 dpi, 3 dpi, 4 dpi, 5 dpi and 7 dpi. Only statistically significant DE genes (FDR p

The organization of a scientific conference can be a very demanding and timeconsuming duty. Two challenging tasks are the preparation of the detailed program and of the book of abstracts. To make these tasks easier to handle, wedeveloped the generbook package, which includes some functions written in R language and a LaTeX template for the book of abstracts. This paper describes the package and how to use it; it also shows how it was used for the organization of an international statistical conference.

We derive the probability density of the ratio of components of the bivariate normal distribution with arbitrary parameters. The density is a product of two factors, the first is a Cauchy density, the second a very complicated function. We show that the distribution under study does not possess an expected value or other moments of higher order. Our particular interest is focused on the shape of the density. We introduce a shape of parameter and show that according to its sign the densities are classified into three main groups. As an example, we derive the distribution of the ratio ?$Z = -B_{m-1}/(mB_m)$? for a polynomial regression of order ?$m$?. For ?$m=1$?, ?$Z$? is the estimator of the zero of a linear regression, for ?$m=2$?, an estimator for the abscissa of the extreme of a quadratic regression, and for ?$m=3$?, an estimator for the abscissa of the inflection point of a cubic regression. Izpeljemo gostoto verjetnosti kvocienta komponent dvorazsežnega normalno porazdeljenega vektorja s poljubnimi parametri. Izpeljana gostota je produkt dveh faktorjev; prvi je Cauchyjeva gostota, drugi pa neka komplicirana funkcija, ki pokvari simetrijo prvega. Pokažemo, da taka porazdelitev nima momentov. Poseben poudarek namenimo obliki porazdelitve. Vpeljemo parameter oblike, ki glede na svoj predznak klasificira tri tipe. Kot primer izpeljemo porazdelitev kvocienta ?$Z = -B_{m-1}/(mB_m)$? za polinomsko regresijo ?$m$?-te stopnje. Za ?$m=1$? je ?$Z$? ocena ničle linearne regresije, za ?$m=2$? je ?$Z$? ocena abscise ekstrema kvadratične regresije, za ?$m=3$? pa je ?$Z$? ocena abscise prevoja kubične regresije.