The main topic of my research is focused on understanding of how the cell functions on the molecular level with extrapolation of this knowledge to understanding of organism responses to environmental stress. In parallel I'm also involved in development of methodologies that support such research approach, e.g the systems biology approach. Included are the methods of quantitative molecular biology and also methods that integrate the life sciences with statistic, computer science and mathematics.
Interactions between plants and their pathogens/pests
The interactions between plants and their pests are studied with the final aim of developing new approaches for plant protection. Our pet plant is potato (Solanum tuberosum
L.) and we are studying its interaction with most important viral pathogen PVY and insect pest Colorado potato beetle. We are trying to unravel key components determining the outcome of interaction; disease, tolerance or resistance. We are studying the interactions using systems biology approach – data describing the biological system are gathered on multiple molecular levels (gene expression combined with metabolomics and proteomics) and merged through data integration tools and modelling. We use time series to get an overview of the process dynamics through quantitative modelling. Further, specific genes are studied using functional genomics tools.
Potato, PVY, Colorado potato beetle, and Functional analysis of genes and their products
Petek M, Rotter A, Kogovšek P, Baebler Š, Mithöfer A and Gruden K. Potato virus Y infection hinders potato defence response and renders plants more vulnerable to Colorado potato beetle attack Molecular Ecology, Volume 23, 5378–5391, 2014 http://onlinelibrary.wiley.com/doi/10.1111/mec.12932/pdf
Baebler Š, Witek K, Petek M, Stare K, Tušek-Znidaric M, Pompe-Novak M, Renaut J, Szajko K, Strzelczyk-Zyta D, Marczewski W, et al. 2014. Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potato. Journal of experimental botany 65, 1095–1109. http://jxb.oxfordjournals.org/content/early/2014/01/12/jxb.ert447
LAZAR, Ana, COLL RIUS, Anna, DOBNIK, David, BAEBLER, Špela, BEDINA ZAVEC, Apolonija, ŽEL, Jana, GRUDEN, Kristina. Involvement of potato (Solanum tuberosum L.) MKK6 in response to Potato virus Y. PloS one, ISSN 1932-6203, Aug. 2014, vol. 9, iss. 8. http://dx.doi.org/10.1371/journal.pone.0104553
BAEBLER, Špela, STARE, Katja, KOVAČ, Maja, BLEJEC, Andrej, PREZELJ, Nina, STARE, Tjaša, KOGOVŠEK, Polona, POMPE NOVAK, Maruša, ROSAHL, S., RAVNIKAR, Maja, GRUDEN, Kristina. Dynamics of responses in compatible potato - potato virus Y interaction are modulated by salicylic acid. PloS one, 2011, vol. 6, issue 12, str. 1-12. http://dx.doi.org/10.1371/journal.pone.0029009
PETEK, Marko, TURNŠEK, Neža, BUH GAŠPARIČ, Meti, POMPE NOVAK, Maruša, GRUDEN, Kristina, SLAPAR, Nina, POPOVIČ, Tatjana, ŠTRUKELJ, Borut, JONGSMA, Maarten Anthonie. A complex of genes involved in adaptation of Leptinotarsa decemlineata larvae to induced potato defense. Arch. insect biochem. physiol., 2012, vol. 79, no. 3, str. 153-181. http://onlinelibrary.wiley.com/doi/10.1002/arch.21017/pdf
From the development of alternative plant protection methods point of view, phytoplasmas are very interesting, since they are not accessible for ordinary chemical prevention means, being intracellular organisms. Our model system is grapevine yellows disease and recovery– interaction between grapevine and ‘bois noir’ and ‘flavescence doree’ phytoplasmas. We have studied plant response on infection again using quantitative PCR and DNA microarrays. We have studied individual organisms in their natural environment, in the vineyards; thus getting the knowledge with the ecological relevance:
HREN, Matjaž, NIKOLIĆ, Petra, ROTTER, Ana, BLEJEC, Andrej, TERRIER, Nancy, RAVNIKAR, Maja, DERMASTIA, Marina, GRUDEN, Kristina. 'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine. BMC Genomics, 2009, vol. 10, no. 460, 38 str. http://www.biomedcentral.com/1471-2164/10/460.
Patents and patent applications:
JONGSMA, Maarten Anthonie, ŠTRUKELJ, Borut, LENARČIČ, Brigita, GRUDEN, Kristina, TURK, Vito, BOSCH, Hendrik J., STIEKEMA, Willem J. Johannes. Method for plant protection against insects or nematodes by transformations with a nucleic acid encoding equistatin : Patent number: WO98/58068 : United States Patent 6,861,578. [S.l.: s.n.], March 1, 2005. 80 str.
ISTINIČ, Ida, BUH GAŠPARIČ, Meti, SABOTIČ, Jerica, GRUDEN, Kristina, BRZIN, Jože, ŽEL, Jana. Makrocipin: številka prijave: P-201100304 z dne 10.8.2011. Ljubljana: Urad RS za intelektualno lastnino, 2011. 26 str.
DOBNIK, David, BAEBLER, Špela, ŽEL, Jana, GRUDEN, Kristina, ŠTEBIH, Dejan. Uporaba glikozidaz in glikoziltransferaz za povečano proizvodnjo proteinov : SI 23374 (A), 2011-11-30. Ljubljana: Urad RS za intelektualno lastnino, 2011. 11 str.
Bioinformatics and Systems biology
In parallel with development of methodologies for studying gene expression profiles on the whole genome level, we have started establishing the bioinformatics pipelines for efficient analysis of obtained data. Methodology was established including both biostatistics and machine learning approaches. Basic parts are the annotations of nucleic acid sequences, automatic preprocessing and biostatistical pipelines of DNA microarray data, and the set of meta¬analyses, where the knowledge from first two sets is combined with literature data and data obtained from other “omics” experiments.
A structural model of plant defence responses was developed as a first step for systems biology modelling and predictions. The model is based on the knowledge available for the model plant Arabidopsis thaliana and is now being transferred to the crop species. Related to this a database of plant ontologies MapMan was created that allows for easy transfer of knowledge between different plant species besides the more obvious function of a user-friendly and controlled improvement of ontologies and annotations.
Interactive model that can be opened with Cytoscape, can be found here
Tools developed in collaboration with JSI:
- Tool for link discovery in biological databases, currently available for human, mice, rat and arabidopsis
- Tool for semantic analysis of microarray data SegMine (http://segmine.ijs.si/)Tools developed in collaboration with JSI:
- Database of plant specific gene annotation ontologies, GOMapMan (http://www.gomapman.org/), downloadable updated MapMan ontologies compatible with GSEA and MapMan, available for arabidopsis, rice, potato, tomato, cocoa, sugarbeet
Ramšak Ž, Baebler Š, Rotter A, Korbar M, Mozetič I, Usadel B, Gruden K. 2014. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic acids research 42, D1167–75. doi: 10.1093/nar/gkt1056. http://nar.oxfordjournals.org/content/42/D1/D1167.full
MILJKOVIĆ, Dragana, STARE, Tjaša, MOZETIČ, Igor, PODPEČAN, Vid, PETEK, Marko, WITEK, Kamil, DERMASTIA, Marina, LAVRAČ, Nada, GRUDEN, Kristina. Signalling network construction for modelling plant defence response. PloS one, 2012, vol. 7, no. 12, str. e51822-1e51822-18. http://ponta.ijs.si/mozetic/papers/Miljetal-signet-PlosONE-12.pdf
PODPEČAN, Vid, LAVRAČ, Nada, MOZETIČ, Igor, KRALJ NOVAK, Petra, TRAJKOVSKI, Igor, LANGOHR, Laura, KULOVESI, Kimmo, TOIVONEN, Hannu, PETEK, Marko, MOTALN, Helena, GRUDEN, Kristina. SegMine workflows for semantic microarray data analysis in Orange4WS. BMC bioinformatics, 2011, vol. 12, no. 416, str. 416-1-416-16, doi: 10.1186/1471-2105-12-416
ROTTER, Ana, HREN, Matjaž, GRUDEN, Kristina. Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine. BMC plant biol. (Online), 2009, vol. 9, no. 104, str. 1-14. http://dx.doi.org/10.1186/1471-2229-9-104.
ROTTER, Ana, USADEL, Björn, BAEBLER, Špela, STITT, Mark, GRUDEN, Kristina. Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant methods, 2007, letn. 3, št. 10, str. [1-9].
Development of quantitative methods in molecular biology – detection of GMOs
We have performed comprehensive research in the field of development of methods for quantitative analysis of nucleic acids. We were testing different alternatives to 5’ nuclease test for following amplification of nucleic acids in real time. The purpose of this research is to get more accurate, more robust or cheaper quantitative methods. Quantitative molecular biological methods, which would be fast and robust as well, are necessary for all types of biological analysis from diagnostics to acquisition of biological data in systems biology concept. We have developed a new method of target amplification in combination with DNA microarrays for analysis of samples with low DNA content. We have applied the knowledge in the area of GMO detection which resulted in identification of potential gaps in detection system due to mutations in inserted DNA sequence.
BLOCK, Annette, DEBODE, Frédéric, GROHMANN, Lutz, HULIN, Julie, TAVERNIERS, Isabel, KLUGA, Linda, BARBAU-PIEDNOIR, Elodie, BROEDERS, Sylvia, HUBER, Ingrid, BULCKE, Marc, HEINZE, Petra, BERBEN, Gilbert, BUSCH, Ulrich, ROOSENS, Nancy, JANSSEN, Erik, ŽEL, Jana, GRUDEN, Kristina, MORISSET, Dany. The GMOseek matrix : a decision support tool for optimizing the detection of genetically modified plants. BMC bioinformatics, ISSN 1471-2105, 2013, vol. 14, str. [1-14], 256. http://www.biomedcentral.com/1471-2105/14/256
, doi: 10.1186/1471-2105-14-256
MORISSET, Dany, KRALJ NOVAK, Petra, ZUPANIČ, Darko, GRUDEN, Kristina, LAVRAČ, Nada, ŽEL, Jana. GMOseek : a user friendly tool for optimized GMO testing. BMC bioinformatics, ISSN 1471-2105, avg. 2014, vol. 15, no. 258. http://dx.doi.org/10.1186/1471-2105-15-258
MORISSET, Dany, DEMŠAR, Tina, GRUDEN, Kristina, VOJVODA, Jana, ŠTEBIH, Dejan, ŽEL, Jana. Detection of genetically modified organisms-closing the gaps : to the editor. Nat. biotechnol., 2009, vol. 27, no. 8, 9 str. http://dx.doi.org/10.1038/nbt0809-700
, JCR IF (2008): 22.297
MORISSET, Dany, DOBNIK, David, HAMELS, Sandrine, ŽEL, Jana, GRUDEN, Kristina. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs. Nucleic acids res., 2008, issue 18, vol. 36, 11 str. http://dx.doi.org/10.1093/nar/gkn524
CANKAR, Katarina, ŠTEBIH, Dejan, DREO, Tanja, ŽEL, Jana, GRUDEN, Kristina. Critical points of DNA quantification by real-time PCR-effects of DNA extraction method and sample matrix on quantification of genetically modified organisms. BMC Biotechnol, 2006, vol. 6, no. 37.