NIB

Biotechnological Hub of the NIB (BTH-NIB)

The purpose of the investment project BTH-NIB is the assurance of the appropriate infrastructural conditions for the use of research and developmental opportunities in the fields of operation of the NIB.

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Prof. Dr. Maruša Pompe Novak

Working place: Scientific Counsellor

Telephone number: +386 (0)59 23 28 03
Email: marusa.pompe.novak@nib.si
Department: Department of Biotechnology and Systems Biology

Education:

  • PhD in Biotechnology, 2002, University of Ljubljana, Biotechnical Faculty
  • MSc in Biotechnology, 1999, University of Ljubljana, Biotechnical Faculty
  • Biology Teacher, 1997, University of Ljubljana, Biotechnical Faculty
  • University Degree in Biology, 1996, University of Ljubljana, Biotechnical Faculty

Employment:

  • National institute of Biology (part time 80%)
  • University of Nova Gorica (part time 20%)


Management functions:

Expert work:



Pedagogical work:

  • Mentor and co-mentor of several diploma, master and doctoral thesis
  • Principal lecturer of Plant Physiology and Biotechnology course at Bachelor's programme in Viticulture and Enology, School for Viticulture and Enology, University of Nova Gorica
  • Principal lecturer of Plant Molecular Biotechnology at Master's programme in Viticulture and Enology, School for Viticulture and Enology, University of Nova Gorica
  • Principal lecturer of Plant Biotechnology course at Molecular Genetics and Biotechnology graduate study programme (Third Level), Graduate School, University of Nova Gorica

Dissemination of science:

To primary school pupils:

a broadcast at STA znanost
an interview in TV show Znanost in tehnologija
  • Project Manager of Green Wonders
  • Co-editor and co-author of school science activity book for primary school pupils Očarljivi poskusi z rastlinami (Fascinating experiments with plants) that got Zlata hruška (Golden Pear) award for the best youth literature in Slovenia


To secondary school students:

To families and public at large:

  • Participation in the project Znanstival (main organiser House of Experiments)
  • Participation in Researchers' Night (main organiser House of Experiments)
  • Head of the Promotion Team of the Department of Plant Biotechnology and Systems Biology of the National Institute of Biology

Awards:

  • Award of the Slovenian Society for Plant Biology for long-standing organization of the Fascination of Plants Day
  • Award of the Slovenian Science Foundation: Prometheus of Science for Excellence in Communication in Science for Organizing the Fascination of Plants Day

Research work visits abroad:

Scientific research work:

  • The main topic of the scientific research work is to answer the question, which genes, proteins and signal molecules are of key importance for the resistance of agronomically important plants to the infection with pathogen microorganisms such as viruses and phytoplasmas, and to abiotic stresses such as drought and salinity with the analysis of sensitive and resistant varieties and of genetically modified plants.

Research of the interaction between grapevine and environment

In the frame of grapevine – environment research, the influence of virus and phytoplasmas infection, drought and salinity and combinations of them on grapevine are studied.


Research of the response of grapevine plants to phytoplasma infection at the transcriptomic level using up-to-date bioinformatic approaches are studied

In the research of the BN disease caused by 'Candidatus Phytoplasma solani' (BN phytoplasma, BNp), we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. For example, downregulation of genes involved in light reactions of photosynthesis, which is expected late in the season with the yellowing of the leaves, was observed also early in the season before the appearance of symptoms. Moreover, some genes involved in secondary metabolism were more intensively upregulated early than late in the season. Most differentially expressed small RNAs were associated with biotic stress. 




Dermastia M, Škrlj B, Strah R, Anžič B, Tomaž Š, Križnik M, Schönhuber C, Riedle-Bauer M, Ramšak Ž, Petek M, Kladnik A, Lavrač N, Gruden K, Roitsch T, Brader G, Pompe Novak M. 2021. Differential response of grapevine to Infection with ʼCandidatus Phytoplasma solaniʼ in early and late growing season through complex regulation of mRNA and small RNA transcriptomes. International journal of molecular sciences 22(7): 3531. https://doi.org/10.3390/ijms22073531 

Škrlj B, Pompe Novak M, Brader G, Anžič B, Ramšak Ž, Gruden K, Kralj J, Kladnik A, Lavrač N, Roitsch T, Dermastia M. 2021. New cross-talks between pathways involved in grapevine infection with ʼCandidatus Phytoplasma solaniʼ revealed by temporal network modelling. Plants 10(4): 646. https://doi.org/10.3390/plants10040646 

Dermastia M, Škrlj B, Valmarska A, Strah R, Pompe Novak M, Anžič B, Tomaž Š, Križnik M, Petek M, Kladnik A, Lavrač N, Gruden K, et al. 2023. Understanding interactions of ‘Candidatus Phytoplasma solani’ with grapevine through the lens of complex networks. Phytopathogenic mollicutes 13(1): 9-10. http://dx.doi.org/10.5958/2249-4677.2023.00005.1 

Mehle N, Kavčič S, Mermal S, Vidmar S, Pompe Novak M, Riedle-Bauer M, Brader G, Kladnik A, Dermastia M. 2022. Geographical and temporal diversity of ‘Candidatus Phytoplasma solani' in wine-growing regions in Slovenia and Austria. Frontiers in plant science 13: 889675. https://doi.org/10.3389/fpls.2022.889675 

ARRS J1-7151 INGRAPA: Molecular bases of interactions among the grapevine and phytoplasmal causing agents of the grapevine yellows diseases, Marina Dermastia, 2016-2018.


Research of the phytoplasma effectors involved in phytoplasma - grapevine interaction

In symptomatic grapevines cv. ‘Zweigelt’ infected with ‘Ca. P. solani’ compared with uninfected grapevines the expression of genes coding for phosphoglucoisomerase was upregulated, resulting in increased phosphoglucoisomerase enzyme activity, that converse glucose-1-phosphate to glucose-6-phosphate. The product could be a substrate for phosphoglucoisomerase or for ADP-glucose pyrophosphorylase involved in starch biosynthesis. Besides, phosphoglucomutase activity was induced also in Nicotiana benthamiana leaves transiently transformed with the construct of putative effector PoStoSP28, previously annotated as an antigenic membrane protein StAMP related to interaction of phytoplasma with its insect vector. Using a pull-down assay and in planta co-IP assay, we confirmed that PoStoSP28 interacts with both grapevine phosphoglucomutases. In transiently transformed N. benthamiana leaves, PoStoSP28 was localized in the nucleus and cytosol and accompanied by a distinct border at the periphery or just outside the nucleus and in the thread-like structures spanning the cells. Upon closer inspection, some autophagosome-like structures were found in N. benthamiana cells expressing the PoStoSP28 effector. Moreover, PoStoSP28 was not only localized in the autophagosome but also increased the occurrence of autophagosomes. Therefore, the results suggest that PoStoSP28 plays a role in the pathogenicity of phytoplasma in grapevine by interacting with grapevine phosphoglucomutase enzymes. 

(A) YFP fluorescence of YFP-tagged PoStoSP28 (yellow), (B) mRFP1-tagged nuclear marker histone H2B and mRFP1-tagged ATG8 CL marker fluorescence (magenta), (C) overlay of images, and (D) control leaf; cell expressing only mRFP1-tagged ATG8 CL. Scale bar, 20 µm. White arrows indicate co-localization of PoStoSP28 and autophagosome markers.

Dermastia M, Tomaž Š, Strah R, Lukan T, Coll Rius A, Dušak B, Anžič B, Čepin T, Wienkoop S, Kladnik A, Zagorščak M, Riedle-Bauer M, Schönhuber C, Weckwerth W, Gruden K, Roitsch T, Pompe Novak M, Brader G. 2023. Candidate pathogenicity factor/effector proteins of ‘Candidatus Phytoplasma solani’ modulate plant carbohydrate metabolism, accelerate the ascorbate–glutathione cycle, and induce autophagosomes. Frontiers in plant science 14: 1232367. https://doi.org/10.3389/fpls.2023.1232367 

ARRS J4-2544 CRISPHY: CRISPR/CAS9-mediated targeted mutagenesis for resistance of grapevine and potato against phytoplasmas, Marina Dermastia, 2020-2023.

Research of the response of grapevine plants to drought and salinity stress

Climate change is threatening the sustainability of viticulture in Mediterranean, as well as in other Worlds region, due to the recurrent drought events during the summer. Moreover, climate change is also influencing the availability of water resources, therefore the need for irrigation is increasing. Consequently, drought and salinity stress are becoming very important issues, as irrigation water may contain elevated salt concentrations. To study the response of grapevine plants to drought and salinity stress in vineyard is especially challenging as both treated and control grapevines are exposed to several environmental factors. Moreover, environmental factors are not stable in consecutive years. Therefore, simple data analyses design based on comparisons of treated and control plants in each time point do not provide required complexity of analyses, and the results obtained on certain day post the begging of the experiment could not be simply compared. Therefore RNA-Seq data and metabolite accumulation data should be combined with the data of plants’ stem water potential (Ψs), that is an indicator of vine water status and that reflects the sum of the experimental treatment and the influence of the environment on plants. For this purpose, FaDSeqSes (Factorial design of RNA-Seq analyses) script was developed for multiple factor analysis of RNA-Seq and metabolomics data of the samples from a complex environment.

Buesa I, Pérez-Pérez JG, Visconti F, Strah R, Intrigliolo DS, Bonet L, Gruden K, Pompe Novak M, De Paz JM. 2022. Physiological and transcriptional responses to saline irrigation of young ‘Tempranillo’ vines grafted onto different rootstocks. Frontiers in plant science 13: 866053. https://doi.org/10.3389/fpls.2022.866053 

ArimNet C3330-17-500095 EnViRoS: Opportunities for an environmental friendly Viticulture: optimization and introduction of new Rootstock and Scion genotypes, Enrico Peterlunger, project leaders for Slovenia Maruša Pompe Novak and Kristina Gruden, 2017-2021.


Research of the response of grapevine plants to virus infection

Grapevine fanleaf virus (GFLV) is the causal agent of grapevine degeneration disease, which causes progressive decline of infected vines and lowers the yield. We showed that also the berry composition is also affected; in detail, anthocyanin concentration is increased. GFLV titre is high in young leaves and seeds during the whole vegetative period, while in mature leaves, tendrils and flower/berry clusters it is high only at the beginning of the vegetative period. Phloem scrapings were shown to contain lower virus titres during the vegetative period, with the increase outside and at the beginning of the vegetative period. 

High genetic variability of Grapevine fanleaf virus (GFLV) was assessed within its RNA2 and satellite RNA (satRNA), although no clear association was apparent between symptomatology and restrictotype/sequence composition, single/mixed infections, phylogenetic clustering, or occurrence of recombination. Besides, we addressed also environmental safety issues of transgenic plants expressing virus-derived genes. Our studies did not indicate that transgenic grapevines assist the emergence of recombinants or increase the frequency of recombinant viruses and the creation of more severe virus variants, in particular in comparison to mixed infected conventional.

We studied also the impact of the combination of abiotic (drought) and biotic (Grapevine fanleaf virus (GFLV) infection) stress on physiological and molecular responses on the grapevine. A complex response of grapevine to the combination of drought and GFLV infection was shown, including priming in the case of grapevine water status, net effect in the case of area of occluded vessels in xylem, and different types of interaction of both stresses in the case of expression of four abscisic acid-related genes. Our results showed that mild (but not severe) water stress can be better sustained by GFLV infection rather than by healthy vines. GFLV proved to improve the resilience of the plants to water stress, which is an important outcome to cope with the challenges of global warming.

Cross-sections through the canes of well-watered healthy (H WW), well-watered GFLV-infected (I WW), water-stressed healthy (H WS) and water-stressed GFLV-infected (I WS) potted own-rooted grapevines of cv. Schioppettino 6 days after the start of different water regime obtained by light microscope. 



Jež Krebelj A, Rupnik Cigoj M, Stele M, Chersicola M, Pompe Novak M, Sivilotti P. 2022. The physiological impact of GFLV virus infection on grapevine water status: first observations. Plants 11(2): 161. https://doi.org/10.3390/plants11020161 

Rupnik Cigoj M, Jež Krebelj A, Castellarin SD, Trošt K, Sivilotti P, Pompe Novak M. 2018. Grapevine fanleaf virus affects grape (Vitis vinifera) berry anthocyanin content via the transcriptional regulation of anthocyanin biosynthetic genes. Functional plant biology 45(7): 771-782. https://doi.org/10.1071/FP18014 

Čepin U, Gutiérrez-Aguirre I, Ravnikar M, Pompe Novak M. 2016. Frequency of occurrence and genetic variability of Grapevine fanleaf virus satellite RNA. Plant Pathology 65(3): 510-520. https://doi.org/10.1111/ppa.12428

Jež Krebelj A, Čepin U, Ravnikar M, Pompe Novak M. 2015. Spatio-temporal distribution of Grapevine fanleaf virus (GFLV) in grapevine. European journal of plant pathology 142(1): 159-171. https://doi.org/10.1007/s10658-015-0600-4
Čepin U, Gutiérrez-Aguirre I, Balažic L, Pompe Novak M, Gruden K, Ravnikar M. 2010. A one-step reverse transcription real-time PCR assay for the detection and quantitation of Grapevine fanleaf virus. Journal of virological methods 170(1-2): 47-56. https://doi.org/10.1016/j.jviromet.2010.08.018 

Pompe Novak M, Gutiérrez-Aguirre I, Vojvoda J, Blas M, Tomažič I, Vigne E, Fuchs M, Ravnikar M, Petrovič N. 2007. Genetic variability within RNA2 of grapevine fanleaf virus. European journal of plant pathology 117: 307-312. https://doi.org/10.1007/s10658-006-9096-2 

Fuchs M, Cambra M, Capote N, Jelkmann W, Kundu J, Laval V, Martelli GP, Minafra A, Petrovič N, Pfeiffer P, Pompe Novak M, Ravelonandro M, Saldarelli P, Stussi-Garaud C, Vigne E, Zagrai I. 2007. Safety assessment of transgenic plums and grapevines expressing viral coat protein genes: new insights into real environmental impact of perennial plants engineered for virus resistance. Journal of plant pathology 89(1): 5-12. https://www.jstor.org/stable/41998352

FP5 European project QLK3-CT-2002-02140 Transvir: Environmental impact assessment of transgenic grapevines and plums on the diversity and dynamics of virus populations, Giovanni Paolo Martelli, 2003-2006.

Research of the interaction between potato and Potato virus Y (PVY)

The outcome of the interaction of potato (Solanum tuberosum) with Potato virus Y (PVY) depends on genotypes of both, potato host plant and PVY pathogen. In addition, the response of a potato towards PVY infection can vary with various environmental conditions and various developmental and physiological growth stages of a plant (Pompe-Novak and Lacomme, 2017). PVY infected potato plants can exhibit either a compatible or an incompatible response (Hinrichs-Berger et al.,1999). Plants exhibiting a compatible interaction are susceptible for the virus and the virus can replicate and invade the plants (Cooper and Jones, 1983). Susceptible potato plants can be either sensitive or tolerant to PVY infection. Sensitive potato plants develop disease symptoms, while tolerant plants develop no or very mild symptoms, although they can accumulate high titre of the virus (Ravnikar, 2005). In an incompatible interaction, plants resist the virus by restricting cell invasion, virus replication and/or virus spread. Plants can respond to virus infection with an extreme resistance (ER) or with a hypersensitive response (HR)-conferred resistance. In the case of ER, potato plants show no symptoms or very limited necrosis in the form of pinpoint lesions (Valkonen et al., 1996). Virus titres remain extremely low, below the limit of detection also in the initially infected leaf (Solomon-Blackburn and Barker, 2001; Valkonen et al., 1996; Valkonen, 1994; Valkonen, 2015). In the case of HR-conferred resistance, virus translocation from the initially infected leaf to other parts of the plant is prevented, although the virus replication and initial cell-to-cell movement are not blocked. Later, most of the infected cells die, which result in a localized necrotic lesion at the site of infection (Lukan et al., 2018; Valkonen, 2015). Understanding of molecular mechanisms underlying those outcomes is of utmost importance for resistance breeding without growth trade-offs and adaptation of agronomical practices.



Outcomes of potato-potato virus Y (PVY) interaction. Outcomes depend on the host genotype, viral strain, and environmental conditions, and are manifested as different responses in terms of virus multiplication and disease symptoms’ development.

The digital microscope enables a continuous imaging of necrotic lesion expansion at the site of infection in HR-conferred resistance, which allows an accurate determination of cell death initiation rate up to minutes exactly, as opposed to hours in traditional methods (Arnšek et al, 2023). In HR-conferred resistance, transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA-deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signalling modules. The induction of RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed, and the spread of the virus is not arrested at the site of infection (Lukan et al., 2020).


Arnšek T, Golob N, Marondini N, Pompe Novak M, Gruden K, Lukan T. 2023. Studying cell death initiation using a digital microscope. Journal of visualized experiments 201: 65824. https://doi.org/10.3791/65824 

Tomaž Š, Petek M, Lukan T, Pogačar K, Stare K, Teixeira Prates E, Jacobson DA, Zrimec J, Bajc G, Butala M, Pompe Novak M, Taler-Verčič A, Usenik A, Turk D, Coll Rius A, Gruden K, et al. 2023. A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors. Plant physiology 15: kiac579. https://doi.org/10.1093/plphys/kiac579 

Lukan T*, Pompe Novak M*, Baebler Š*, Tušek-Žnidarič M, Kladnik A, Križnik M, Blejec A, Zagorščak M, Stare K, Dušak B, Coll Rius A, Pollmann S, Morgiewicz K, Hennig J, Gruden K. 2020. Precision transcriptomics of viral foci reveals the spatial regulation of immune-signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potato. The plant journal 104(3):645-661. https://doi.org/10.1111/tpj.14953-*shared first authorship

Pompe Novak M, Križnik M, Gruden K. 2019. The titre of the virus in the inoculum affects the titre of the viral RNA in the host plant and the occurrence of the disease symptoms. Acta chimica slovenica 66(1): 45-49. https://doi.org/10.17344/acsi.2018.4585 

Mehle N, Dobnik D, Ravnikar M, Pompe Novak M. 2018. Validated reverse transcription droplet digital PCR serves as a higher order method for absolute quantification of Potato virus Y strains. Analytical and bioanalytical chemistry 410(16): 3815-3825. https://doi.org/10.1007/s00216-018-1053-3

Lukan T, Baebler Š, Pompe Novak M, Guček K, Zagorščak M, Coll Rius A, Gruden K. 2018. Cell death is not sufficient for the restriction of potato virus Y spread in hypersensitive response-conferred resistance in potato. Frontiers in plant science 9: 168. https://doi.org/10.3389/fpls.2018.00168

Pompe Novak M, Lacomme C. 2017. Molecular and cellular events during infection of potato by PVY. V: Lacomme C (ur.), et al. Potato virus Y : biodiversity, pathogenicity, epidemiology and management. Cham: Springer. https://doi.org/10.1007/978-3-319-58860-5_2 

Baebler Š, Svalina M, Petek M, Stare K, Rotter A, Pompe Novak M, Gruden K. 2017. quantGenius : implementation of a decision support system for qPCR-based gene quantification. BMC bioinformatics 18: 1-11. https://doi.org/10.1186/s12859-017-1688-7 

Kogovšek P, Pompe Novak M, Petek M, Fragner L, Weckwerth W, Gruden K. 2016. Primary metabolism, phenylpropanoids and antioxidant pathways are regulated in potato as a response to Potato virus Y infection. PloS one 11(1): e0146135. https://doi.org/10.1371/journal.pone.0146135 

Baebler Š, Witek K, Petek M, Stare K, Tušek-Žnidarič M, Pompe Novak M, Renaut J, Szajko K, Strzelczyk-Żyta D, Marczewski W, Morgiewicz K, Gruden K, Hennig J. 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(4): 1095-1109. https://doi.org/10.1093/jxb/ert447 

Rupar M, Kogovšek P, Pompe Novak M, Gutiérrez-Aguirre I, Delaunay A, Jacquot E, Ravnikar M. 2013. Assessment of SNaPshot and single step RT-qPCR methods for discriminating Potato virus Y (PVY) subgroups. Journal of virological methods 189(1): 93-100. https://doi.org/10.1016/j.jviromet.2013.01.013

Dobnik D, Baebler Š, Kogovšek P, Pompe Novak M, Štebih D, Panter G, Janež N, Morisset D, Žel J, Gruden K. 2013. [Beta]-1,3-glucanase class III promotes spread of PVYNTN and improves in planta protein production. Plant biotechnology reports 7(4): 547-555. https://doi.org/10.1007/s11816-013-0300-5 

Kogovšek P, Kladnik A, Mlakar J, Tušek-Žnidarič M, Dermastia M, Ravnikar M, Pompe Novak M. 2011. Distribution of Potato virus Y in potato plant organs, tissues and cells. Phytopathology : an international journal of the American Phytopathological Society 101(11): 1292-1300. https://doi.org/10.1094/PHYTO-01-11-0020 

Baebler Š, Stare K, Kovač M, Blejec A, Prezelj N, Stare T, Kogovšek P, Pompe Novak M, Rosahl S, Ravnikar M, Gruden. 2011. Dynamics of responses in compatible potato - potato virus Y interaction are modulated by salicylic acid. PloS one 6(12): e29009. https://doi.org/10.1371/journal.pone.0029009

Kogovšek P, Pompe Novak M, Baebler Š, Rotter A, Gow L, Gruden K, Foster GD, Boonham N, Ravnikar M. 2010. Aggressive and mild Potato virus Y isolates trigger different specific responses in susceptible potato plants. Plant Pathology 59(6): 1121-1132. https://doi.org/10.1111/j.1365-3059.2010.02340.x 

Baebler Š, Krečič Stres H, Rotter A, Kogovšek P, Cankar K, Kok E, Gruden K, Kovač M, Žel J, Pompe Novak M, Ravnikar M. 2009. PVY[supra]NTN elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation. Molecular plant pathology 10(2): 263-275. https://doi.org/10.1111/j.1364-3703.2008.00530.x 

Gruden K, Pompe Novak M, Baebler Š, Krečič Stres H, Toplak N, Hren M, Kogovšek P, Gow L, Foster GD, Boonham N, Ravnikar M. 2008. Expression microarrays in plant-virus interaction. V: Foster GD (ur.). Plant virology protocols : from viral sequence to protein function. 2nd ed. Totowa: Humana Press. Methods in molecular biology 451: 583-613. https://doi.org/10.1007/978-1-59745-102-4_40 

Kogovšek P, Gow L, Pompe Novak M, Gruden K, Foster GD, Boonham N, Ravnikar M. 2008. Single-step RT real-time PCR for sensitive detection and discrimination of potato virus Y isolates. Journal of virological methods 149(1): 1-11. https://doi.org/10.1016/j.jviromet.2008.01.025 

Pompe Novak M, Gruden K, Baebler Š, Krečič Stres H, Kovač M, Jongsma MA, Ravnikar M. 2006. Potato virus Y induced changes in the gene expression of potato (Solanum tuberosum L.). Physiological and molecular plant pathology 67: 237-247. https://doi.org/10.1016/j.pmpp.2006.02.005 

Mehle N, Kovač M, Petrovič N, Pompe Novak M, Baebler Š, Krečič Stres H, Gruden K, Ravnikar M. 2004. Spread of potato virus Y[sub]NTN in potato cultivars (Solanum tuberosum L.) with different levels of sensitivity. Physiological and molecular plant pathology 64: 293-300. https://doi.org/10.1016/j.pmpp.2004.10.005 

Pompe Novak M, Poljšak-Prijatelj M, Popovič T, Štrukelj B, Ravnikar M. 2002. The impact of potato cysteine proteinases in plant growth and development. Physiological and molecular plant pathology 60(2): 71-78. https://doi.org/10.1006/pmpp.2002.0380

Pompe Novak M, Wrischer M, Ravnikar M. 2001. Ultrastructure of chloroplasts in leaves of potato plants infected by potato virus YNTN. Phyton: annales rei botanicae 41(2): 215-226. https://www.cabidigitallibrary.org/doi/full/10.5555/20023058442 

Pompe Novak M, Štrukelj B, Ravnikar M. 1998. The influence of the proteinase inhibitor EP475 on some morphological characteristics of potato plants (Solanum tuberosum L. cv. Desirée). Acta chimica slovenica 45(1): 79-84. http://www.dlib.si/details/URN:NBN:SI:doc-GF0D17V4 

Slovenian names of plant viruses

Our long-standing research work in the field of plant virology has enabled the Slovenian naming of plant viruses, which was published in the Dictionary of Slovenian names of plant viruses.

Mavrič Pleško I, Cigoj M, Dermastia M, Pompe Novak M. 2015. Slovensko poimenovanje rastlinskih virusov / Slovenian designation of plant viruses. In: Mavrič Pleško, Irena (ed.). Rastlinski virusi in njihovo poimenovanje / Plant viruses and their naming. Ljubljana: Kmetijski inštitut Slovenije / Agricultural Institute of Slovenia, p. 63-153.

Multidisciplinary live science – computer science research on text mining

The field of bisociative literature-based discovery aims at mining scientific literature to reveal yet uncovered connections between different fields of specialization. We addressed new prospects in bisociative literature-based discovery, proposing an advanced embeddings-based technology for cross-domain literature mining.


Lavrač N, Martinc M, Pollak S, Pompe Novak M, Cestnik B. 2020. Bisociative literature-based discovery: lessons learned and new word embedding approach. New generation computing 38: 773-800. https://doi.org/10.1007/s00354-020-00108-w

Research of the abscission in tomato 

Abscission occurs specifically in the abscission zone tissue as a natural stage of plant development. Hallmarks of PCD were identified in the tomato leaf and flower abscission zones during the late stage of abscission. These included loss of cell viability, altered nuclear morphology, DNA fragmentation, elevated levels of reactive oxygen species and enzymatic activities, and expression of PCD-associated genes. Different abscission-related processes occured asymmetrically between the abscission zone proximal and distal sides.


Transmission electron micrographs of cells in tomato leaf abscission zone showing ultrastructural changes 48h after induction of abscission by leaf deblading and ethylene treatment. The position of cells within the tissue is labeled on the light microscopy image in the top left corner (arrow marks the AZ fracture plane). Asterisks mark detachment of plasma membrane from the cell wall. Cell organelle labeling: c, chloroplast; cw, cell wall; er, endoplasmic reticulum; ga, Golgi apparatus; lv, lytic vacuole; m, mitochondria; n, nucleus; p, plasmodesmata; pb, paramural body; v, vacuole. 



Bar-Dror T, Dermastia M, Kladnik A, Tušek-Žnidarič M, Pompe Novak M, Meir S, Burd S, Philosoph-Hadas S, Ori N, Sonego L, Dickman MB, Lers A. 2011. Programmed cell death occurs asymmetrically during abscission in tomato. The Plant cell 23(11): 4146-4163. https://doi.org/10.1105/tpc.111.092494 



Research of the interaction between potato and Colorado potato beetle

The Colorado potato beetle (Leptinotarsa decemlineata) is the most important pest of potato in many areas of the world. We have identified novel components of adaptation to induced plant defenses in Colorado potato beetle larvae midguts using a combination of transcriptomics, biochemical and bioinformatics techniques.

Petek M, Trunšek N, Buh Gašparič M, Pompe Novak M, Gruden K, Slapar N, Popovič T, Štrukelj B, Jongsma MA. 2012. A complex of genes involved in adaptation of Leptinotarsa decemlineata larvae to induced potato defense. Archives of insect biochemistry and physiology 79(3): 153-181. https://doi.org/10.1002/arch.21017


Research of cyanobacteria

Sedmak B, Carmeli S, Pompe Novak M, Tušek-Žnidarič M, Grach-Pogrebinsky O, Eleršek T, Žužek MC, Bubik A, Frangež R. 2009. Cyanobacterial cytoskeleton immunostaining: the detection of cyanobacterial cell lysis induced by planktopeptin BL1125. Journal of plankton research 31(11): 1321-1330. https://doi.org/10.1093/plankt/fbp076 


Research of stefin B

Škerget K, Taler-Verčič A, Bavdek A, Hodnik V, Čeru S, Tušek-Žnidarič M, Pompe Novak M, Kopitar-Jerala N, Turk V, Anderluh G, Žerovnik E, et al. 2010. Interaction between oligomers of stefin B and amyloid-beta in vitro and in cells. The Journal of biological chemistry 285(5): 3201-3210. https://doi.org/10.1074/jbc.m109.024620 

Škrget K, Vilfan A, Pompe Novak M, Turk V, Waltho JP, Turk D, Žerovnik E. 2009. The mechanism of amyloid-fibril formation by stefin B : temperature and protein concentration dependence of the rates. Proteins 74(2): 425-436. https://doi.org/10.1002/prot.22156

Žerovnik E, Giannini S, Stoka V, Tušek-Žnidarič M, Pompe Novak M, Staniforth RA. 2006. On the mechanism of amyloid-fibrillation: srefin B as a good model protein. V: Žerovnik E, Kopitar-Jerala N. Human stefins and cystatins. New York: Nova Science: 97-114. 

Kenig M, Kokalj-Jenko S, Tušek-Žnidarič M, Pompe Novak M, Gunčar G, Turk D, Waltho JP, Staniforth RA, Aabelj F, Žerovnik E. 2006. Folding and amyloid-fibril formation for a series of human stefins' chimeras: any correlation?. Proteins: Structure, Function and Bioinformatics 62(4): 918-927. https://doi.org/10.1002/prot.20812

Kenig M, Berbić S, Kriještorac A, Kroon Žitko L, Tušek-Žnidarič M, Pompe Novak M, Žerovnik E. 2004. Differences in aggregation properties of three site-specific mutants of recombinant human stefin B. Protein science 13: 63-70. https://doi.org/10.1110/ps.03270904

Žerovnik E, Pompe Novak M, Škarabot M, Ravnikar M, Muševič I, Turk V. 2002. Human stefin B readily forms amyoid fibrils in vitro. Biochimica et biophysica acta. Protein structure and molecular 1594(1): 1-5. https://doi.org/10.1016/S0167-4838(01)00295-3 

Žerovnik E, Zavašnik-Bergant T, Kopitar-Jerala N, Pompe Novak M, Škarabot , Goldie K, Ravnikar M, Muševič I, Turk V. 2002. Amyloid fibril formation by human stefin B in vitro : immunogold labelling and comparison to stefin A. Biological chemistry 383(5): 859-863. https://doi.org/10.1515/BC.2002.092

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