Selected Publications
2024
1) Bele, T., Turk, T. and Križaj, I. (2024): Nicotinic acetylcholine receptors in cancer: limitations and prospects. BBA - Molecular Basis of Disease 1870(1), 166875.
2) Goršak, T., Jovičić, E.J., Tratnjek, L., Križaj, I., Sepulveda, B., Nogues, J., Kreft, M.E., Petan, T., Kralj, S. and Makovec, D. (2024): The efficient magneto-mechanical actuation of cancer cells using a very low concentration of non-interacting ferrimagnetic hexaferrite nanoplatelets. Journal of Colloid and Interface Science 657, 778–787.
3) Pavlović, M., Margetić, A., Leonardi, A., Križaj, I., Kojić, M., Vujčić, Z. and Šokarda Slavić, M. (2024): Improvement of fruit juice quality: novel endo-polygalacturonase II from Aspergillus tubingensis FAT 43 for enhanced liquefaction, clarification, and antioxidant potential. Food & Function 15(6), 2906–2919.
4) Novak Babič, M., Ragucci, S., Leonardi, A., Pavšič, M., Landi, N., Križaj, I., Gunde-Cimerman, N., Sepčić, K. and Di Maro, A. (2024): Biocontrol Potential of Sodin 5, Type 1 Ribosome-Inactivating Protein from Salsola soda L. Seeds. Biomolecules 14(3), 336.
5) Joukhan, A., Kononenko, V., Bele, T., Sollner Dolenc, M., Peigneur, S., Pinheiro-Junior, E.L., Tytgat, J., Turk T., Križaj, I. and Drobne, D. (2024): Attenuation of nicotine effects on A549 lung cancer cells by synthetic α7-nAChR antagonists APS7-2 and APS8-2. Marine Drugs, in press.
6) Stazi, M., Megighian, A., D’Este, G., Negro, S., Ivanušec, A., Lonati, D., Pirazzini, M., Križaj, I. and Montecucco, C. (2024): An agonist of CXCR4 induces a rapid recovery from the neurotoxic effects of Vipera ammodytes and Vipera aspis venoms. Journal of Neurochemistry 168(4), 428-440.
2023
1) Danielli, M., Perne, L., Jarc Jovičić, E. and Petan, T. (2023): Lipid droplets and polyunsaturated fatty acid trafficking: Balancing life and death. Frontiers Cell Develop. Biol. 11, doi: 10.3389/fcell.2023.1104725.
2) Žun, G., Doberšek, K. and Petrovič, U. (2023): Construction and evaluation of gRNA arrays for multiplex CRISPR-Cas9. Yeast 40(1), 32-41.
3) Križaj, I. (2023): Toxinology and Pharmacology of Snake Venoms. Toxins 15(3), 212.
4) Zupanič, N., Počič, J., Leonardi, A., Šribar, J., Kordiš, D. and Križaj, I. (2023): Serine pseudoproteases in physiology and disease. FEBS Journal 290(9), 2263-2278.
5) Jemec Kokalj, A.*, Leonardi, A.*, Perc, V., Dolar, A., Drobne, D. and Križaj, I. (2023): Proteomics of the haemolymph of the terrestrial crustacean Porcellio scaber reveals components of its innate immunity under baseline conditions. Biochimie 213, 12-21.
6) Dobaja-Borak, M., Grenc, D., Reberšek, K., Podgornik, H., Leonardi, A., Kurtović, T., Halassy, B., Križaj, I. and Brvar, M. (2023): Reversible and transient thrombocytopenia of functional platelets induced by nose-horned viper venom. Thrombosis Research 229, 152-154.
7) Kordiš, D. and Turk, V. (2023): Origin and early diversification of the papain family of cysteine peptidases. International Journal of Molecular Sciences 24(14), 11761.
8) Sarmento, M.J., Llorente, A., Petan, T., Khnykin, D., Popa, I., Nikolac Perković, M., Konjevod, M. and Jaganjac, M. (2023): The expanding organelle lipidomes: current knowledge and challenges. Cell Mol. Life Sci. 80(8), 237.
9) Petan T. (2023): Lipid Droplets in Cancer. In: Reviews of Physiology, Biochemistry and Pharmacology. Springer, Berlin, Heidelberg.
10) Jarc Jovičić, E., Pucer Janež, A., Eichmann, T.O., Koren, Š., Brglez, V., Jordan, P.M., Gerstmeier, J., Lainšček, D., Golob-Urbanc, A., Jerala, R., Lambeau, G., Werz, O., Zimmermann, R. and Petan, T. (2023): Lipid droplets control mitogenic lipid mediator production in human cancer cells. Molecular Metabolism 76, 101791.
11) Veranič, P. and Križaj, I. (2023): Interaction of Nanomaterials with Cells and Tissues. International Journal of Molecular Sciences 24(17), 13667.
12) Jusović, M., Starič, P., Jarc Jovičić, E. and Petan, T. (2023): The Combined Inhibition of Autophagy and Diacylglycerol Acyltransferase-Mediated Lipid Droplet Biogenesis Induces Cancer Cell Death during Acute Amino Acid Starvation. Cancers 2023, 15, 4857.
2022
1) Ivanušec, A., Šribar, J. and Križaj, I. (2022): Secreted Phospholipases A2 – not just Enzymes: Revisited. International Journal of Biological Sciences 18(2), 873-888.
2) Kostanjšek, R., Diderichsen, B., Recknagel, H., Gunde-Cimerman, N., Gostinčar, C., Fan, G., Kordiš, D., Trontelj, P., Jiang, H., Bolund L. and Luo, Y. (2022): Towards the massive genome of Proteus anguinus, illuminating longevity, regeneration, convergent evolution and metabolic disorders. Annals of the New York Academy of Sciences 1507(1), 5-11.
3) Mozzachiodi, S., Bai, F.Y., Baldrian, P., Bell, G., Boundy-Mills, K., Buzzini, P., Čadež, N., Riffo, F.C., Dashko, S., Dimitrov, R., Fisher, K.J., Gibson, B.R., Gouliamova, D., Greig, D., Heistinger, L., Hittinger, C.T., Jecmenica, M., Koufopanou, V., Landry, C.R., Mašínová, T., Naumova, E.S., Opulente, D., Peña, J.J., Petrovič, U., Tsai, I.J., Turchetti, B., Villarreal, P., Yurkov, A., Liti, G. and Boynton, P. (2022): Yeasts from temperate forests. Yeast 39(1-2), 4-24.
4) De Chiara, M., Barré, B.P., Persson, K., Irizar, A., Vischioni, C., Khaiwal, S., Stenberg, S., Chioma Amadi, O., Žun, G., Doberšek, K., Taccioli, C., Schacherer, J., Petrovič, U., Warringer, J. and Liti, G. (2022): Domestication reprogrammed the budding yeast life cycle. Nature Ecology & Evolution 6(4), 448-460.
5) Požek, K.†, Leonardi, A.†, Pungerčar, J.†, Rao, W., Gao, Z., Liu, S., Laustsen, A.H., Trampuš Bakija, A., Reberšek, K., Podgornik, H. and Križaj, I. (2022): Genomic confirmation of the P-IIIe subclass of snake venom metalloproteinases and characterization of its first member, a disintegrin-like/cysteine-rich protein. Toxins 14(4), 232.
6) Mavri, M., Kubale, V., Depledge, D.P., Zuo, J., Huang, C.A., Breuer, J., Vrecl, M., Jarvis, M.A., Jarc Jovičić, E., Petan, T., Ehlers, B., Rosenkilde, M.M. and Spiess, K. (2022): Epstein-Barr virus-encoded BILF1 orthologues from porcine lymphotropic herpesviruses display common molecular functionality. Frontiers in Endocrinology 13, 862940.
7) Ivanušec, A., Šribar, J., Veranič, P. and Križaj, I. (2022): The phospholipase activity of ammodytoxin, a prototype snake venom β-neurotoxin, is not obligatory for cell internalisation and translocation to mitochondria. Toxins 14(6), 375.
8) Pavlin, M., Lojk, J., Strojan, K., Hafner-Bratkovič, I., Jerala, R., Leonardi, A., Križaj, I., Drnovšek, N., Novak, S., Veranič, P. and Bregar, V.B. (2022): The relevance of physico-chemical properties and protein corona for evaluation of nanoparticles immunotoxicity – in vitro correlation analysis on THP-1 macrophages. International Journal of Molecular Sciences 23(11), 6197.
9) Petan, T. and Manček Keber, M. (2022): Half is enough: oxidized lysophospholipids as novel bioactive molecules. Free Radical Biology and Medicine 188, 351-362.
10) Repar, N., Jarc Jovičić, E., Kump, A., Birarda, G., Vaccari, L., Erman, A., Kralj, S., Nemec, S., Petan, T. and Drobne, D. (2022): Oleic Acid Protects Endothelial Cells from Silica-Coated Superparamagnetic Iron Oxide Nanoparticles (SPIONs)-Induced Oxidative Stress and Cell Death. International Journal of Molecular Sciences 23(13), 6972.
11) Majc, B., Novak, M., Lah, T.T. and Križaj, I. (2022): Bioactive peptides from venoms against glioma progression. Frontiers in Oncology 12, 965882.
12) Kononenko, V., Bele, T., Novak, S., Križaj, I., Drobne, D. and Turk, T. (2022): Nicotinic acetylcholine receptor as a pharmacological target in lung cancer. Acta Biologica Slovenica 65(1), 5–17.
13) Ivanušec, A., Šribar, J., Leonardi, A., Zorović, M., Živin, M. and Križaj, I. (2022): Rat Group IIA Secreted Phospholipase A2 Binds to Cytochrome c Oxidase and Inhibits its Activity: A Possible Episode in the Development of Alzheimer’s Disease. International Journal of Molecular Sciences 23(20), 12368.
14) Leonardi, A. (2022): Mass spectrometry in snake venom research. Acta Biologica Slovenica 65(2), 5-25.
2021
1) Lomonte, B. and Križaj, I. (2021): Snake Venom Phospholipase A2 Toxins. In: Handbook of Venoms and Toxins of Reptiles, 2nd Ed. (Stephen P. Mackessy; Ed.). ISBN 9780367149741. CRC Press; Taylor & Francis Group, Boca Raton, Florida, USA; pp. 389–411.
2) Smolič, T., Tavčar, P., Horvat, A., Černe, U., Halužan Vasle, A., Tratnjek, L., Erdani Kreft, M., Scholz, N., Matis, M., Petan, T., Zorec, R. and Vardjan, N. (2021): Astrocytes in stress accumulate lipid droplets. Glia, doi: 10.1002/glia.23978.
3) Pačnik, K., Ogrizović, O., Diepold, M., Eisenberg, T., Žganjar, M., Žun, G., Kužnik, K., Gostinčar, C., Curk, T., Petrovič, U. and Natter, K. (2021): Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae. BMC Genomics 22, 110.
4) Zupanič, N., Hribar, M., Hristov, H., Lavriša, Ž., Kušar, A., Gregorič, M., Blaznik, U., Koroušić Seljak, B., Golja, P., Vidrih, R., Žmitek, K. and Pravst I. (2021): Dietary Intake of trans Fatty Acids in the Slovenian Population. Nutrients 13, 207.
5) Kurtović, T., Karabuva, S., Grenc, D., Dobaja Borak, M, Križaj, I., Lukšić, B., Halassy, B. and Brvar, M. (2021): Intravenous Vipera berus Fab fragments and intramuscular Vipera ammodytes F(ab’)2 fragments in Vipera ammodytes envenomed patients. Toxins 13, 279.
6) Pungerčar, J., Bihl, F., Lambeau, G. and Križaj, I. (2021): What do secreted phospholipases A2 have to offer in combat against different viruses up to SARS-CoV-2? Biochimie 189, 40-50.
7) Premrov Bajuk, B., Zrimšek, P., Kotnik, T., Leonardi, A., Križaj, I. and Jakovac Strajn B. (2021): Insect protein-based diet as potential risk of allergy in dogs. Animals 11, 1942.
8) Arhar, S., Gogg-Fassolter, G., Ogrizović, M., Pačnik, K., Schwaiger, K., Žganjar, M., Petrovič, U. and Natter, K. (2021): Engineering of Saccharomyces cerevisiae for the accumulation of high amounts of triacylglycerol. Microb. Cell Fact. 20(1), 147.
9) Balantič, K., Miklavčič, D., Križaj, I. and Kramar, P. (2021): The good and the bad of cell membrane electroporation. Acta Chimica Slovenica 68, 753-764.
10) Kušar A, Hribar M, Lavriša Ž, Zupanič N, Pivk Kupirovič U, Hristov H, Abramovič H, Vidrih R, Zlatić E, Kokalj D, Piskernik S, Mencin M, Peče P, Blaznik U, Žmitek K, Pravst I. (2021): Assessment of trans-fatty acid content in a sample of foods from the Slovenian food supply using a sales-weighting approach. Public Health Nutr. 24(1), 12-21.
11) Marrone, J., Danielli, M., Gaspari, C.I., Capiglioni, A.M. and Marinelli, R. (2021): Aquaporin gene transfer for hepatocellular cholestasis. Biochimie 188, 12-15.
12) Danielli, M., Capiglioni, A.M., Marrone, J. and Marinelli, R. (2021): Further evidence for the involvement of mitochondrial aquaporin-8 in hepatocyte lipid synthesis. Biochimie 188, 16-19.
2020
1) Ott Rutar, S. and Kordiš, D. (2020): Analysis of the RNA virome of basal hexapods. PeerJ 8, e8336.
2) Čopič, A. and Petrovič, U. (2020): Yeast lipids (Editorial). Yeast 37, e3.
3) Jarc, E. and Petan, T. (2020): A twist of FATe: lipid droplets and inflammatory lipid mediators. Biochimie 169, 69–87.
4) Zottel, A., Jovčevska, I., Šamec, N., Mlakar, J., Šribar, J., Križaj, I., Skoblar Vidmar, M. and Komel R. (2020): Anti-vimentin, anti-TUFM, anti-NAP1L1 and anti-DPYSL2 nanobodies display cytotoxic effect and reduce glioblastoma cell migration. Therapeutic Advances in Medical Oncology 12, 1758835920915302.
5) Lang Balija M.*, Leonardi, A.*, Brgles, M., Sviben, D., Kurtović, T., Halassy, B. and Križaj, I. (2020): Biological activities and proteomic profile of the venom of Vipera ursinii ssp., a very rare karst viper from Croatia. Toxins 12, 187.
6) Latinović, Z., Leonardi, A., Koh, C.Y., Kini, R.M., Trampuš Bakija, A., Pungerčar, J. and Križaj, I. (2020): The procoagulant snake venom serine protease potentially having a dual, blood coagulation factor V and X-activating activity. Toxins 12, 358.
7) Valdetara, F., Škalič, M., Fracassetti, D., Louw, M., Compagno, C., du Toit, M., Foschino, R., Petrovič, U., Divol, B. and Vigentini, I. (2020): Transcriptomics unravels the adaptive molecular mechanisms of Brettanomyces bruxellensis under SO2 stress in wine condition. Food Microbiol. 90, 103483.
8) Khan, M.A., Dashevsky, D., Kerkkamp, H., Kordiš, D., de Bakker, M., Wouters, R., van Thiel, J., op den Brouw, B., Vonk, F., Kini, R.M., Nazir, J. , Fry, B. and Richardson, M. (2020): Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates. Toxins 12, 638.
9) Drofenik, S., Leonardi, A., Žužek, M.C., Frangež, R. and Križaj, I. (2020): The first Kunitz-type proteins from a viperid venom that potentiate neuromuscular transmission. Toxicon 187, 262–270.
10) Feliciello, I., Pezer, Ž., Kordiš, K., Bruvo Mađarić, B. and Ugarković, Đ. (2020): Evolutionary history of alpha satellite DNA repeats dispersed within human genome euchromatin. Genome Biol. Evol. 12, 2125–2138.
11) Ha, V.T., Lainšček, D., Gesslbauer, B., Jarc-Jovičić, E., Hyötyläinen, T., Ilc, N., Lakota, K., Tomšič, M., van de Loo, F.A.J., Bochkov, V., Petan, T., Jerala, R., Manček-Keber, M. (2020): Synergy between 15-lipoxygenase and secreted PLA2 promotes inflammation by formation of TLR4 agonists from extracellular vesicles. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 117, 25679–25689.
12) Ott Rutar, S. and Kordiš, D. (2020): Discovery and molecular characterisation of the first ambidensovirus in honey bees. Acta agriculturae Slovenica 116(2), 383–393.
13) Božič, J., Bertoncelj, J., Drobne, D., Glavan, G., Gunde Cimerman, N., Leonardi, A., Kopinč, R., Jemec Kokalj, A., Novak, S., Korošec, M., Križaj, I., Podrižnik, B., Turk, M. and Zabret, A. (2020): The quality of Slovenian chestnut honey and its specific properties relevant for medical application and functional nutrition. Acta Biologica Slovenica 63(2), 31– 44.
2019
1) Šribar, J., Kovačič, L., Oberčkal, J., Ivanušec, A., Petan, T., Fox, J.W. and Križaj, I. (2019): The neurotoxic secreted phospholipase A2 from the Vipera a. ammodytes venom targets cytochrome c oxidase in neuronal mitochondria. Scientific Reports 9, 293.
2) Leonardi, A., Sajevic, T., Pungerčar, J. and Križaj, I. (2019): A comprehensive study of the proteome and transcriptome of the venom of the most venomous European viper: Discovery of a new subclass of ancestral snake venom metalloproteinase precursor-derived proteins. Journal of Proteome Research 18, 2287–2309.
3) Panevska, A., Skočaj, M., Križaj, I., Maček, P. and Sepčić, K. (2019): Ceramide phosphoethanolamine, an enigmatic cellular membrane sphingolipid. Biochim. Biophys. Acta – Biomembranes 1861, 1284–1292.
4) Leban, V., Brvar, M., Križaj, I., Leonardi, A. and Černe, K. (2019): Venomous snakes in Slovenia – composition and action of their venoms. Medicinski razgledi 58, 55–74.
5) Gredar, T., Leonardi, A., Novak, M., Sepčič, K., Bizjak Mali, L., Križaj, I. and Kostanjšek, R. (2019): Vitellogenin in the European cave salamander, Proteus anguinus: its characterization and dynamics in a captive female as a basis for non-destructive sex identification. Comparative Biochemistry and Physiology - Part B: Biochemistry & Molecular Biology 235, 30–37.
6) Godec, P., Pančur, M., Ilenič, N., Čopar, A., Stražar, M., Erjavec, A., Pretnar, A., Demšar, J., Starič, A., Toplak, M., Žagar, L., Hartman, J., Wang, H., Bellazzi, R., Petrovič, U., Garagna, S., Zuccotti, M., Park, D., Shaulsky, G. and Zupan, B. (2019): Democratized image analytics by visual programming through integration of deep models and small-scale machine learning. Nature Communications 10, 4551.
7) Jarc, E. and Petan, T. (2019): Lipid droplets and the management of cellular stress. Yale J. Biol. Med. 92, 435-452.
2018
1) Jarc, E., Kump, A., Malavašič, P., Eichmann, T.O., Zimmermann, R. and Petan, T. (2018): Lipid droplets induced by secreted phospholipase A2 and unsaturated fatty acids protect breast cancer cells from nutrient and lipotoxic stress. BBA - Molecular and Cell Biology of Lipids 1863, 247–265.
2) Samec, N., Jovčevska, I., Stojan, J., Zottel, A., Liović, M., Myers, M.P., Muyldermans, S., Šribar, J., Križaj, I. and Komel, R. (2018): Glioblastoma-specific anti-TUFM nanobody for in-vitro immunoimaging and cancer stem cell targeting. Oncotarget 9, 17282–17299.
3) Gostinčar, C. and Gunde-Cimerman, N. (2018): Overview of oxidative stress response genes in selected Halophilic Fungi. Genes 9, 143.
4) de Oliveira, T.B., Gostinčar, C., Gunde-Cimerman, N. and Rodrigues, A. (2018): Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability. BMC Genomics 19, 152.
5) Tkavc, R., Matrosova, V.Y., Grichenko, O.E., Gostinčar, C., Volpe, R.P., Klimenkova, P., Gaidamakova, E.K., Zhou, C.E., Stewart, B.J., Lyman, M.G., Malfatti, S.A., Rubinfeld, B., Courtot, M., Singh, J., Dalgard, C.L.,Hamilton,T., Frey, K.G., Gunde-Cimerman, N., Dugan, L. and Daly, M. J. (2018): Prospects for fungal bioremediation of acidic radioactive waste sites: Characterization and genome sequence of Rhodotorula taiwanensis MD1149. Frontiers in Microbiology 8, 2528.
6) Turk, M. and Gostinčar, C. (2018): Glycerol metabolism genes in Aureobasidium pullulans and Aureobasidium subglaciale. Fungal Biology 122, 63–73.
7) Basu Ball, W., Baker, C. D., Neff, J. K., Apfel, G. L., Lagerborg, K. A., Žun, G., Petrovič, U., Jain, M. and Gohil, V. M. (2018): Ethanolamine ameliorates mitochondrial dysfunction in cardiolipin-deficient yeast cells. Journal of Biological Chemistry 293, 10870–10883.
8) Jarc, E., Eichmann, T.O., Zimmermann, R. and Petan, T. (2018): Lipidomic data on lipid droplet triglyceride remodelling associated with protection of breast cancer cells from lipotoxic stress. Data Brief 18, 234–240.
9) Gostinčar, C., Stajich, J.E., Zupančič, J., Zalar, P. and Gunde-Cimerman, N. (2018): Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast. BMC Genomics 19, 364.
10) Bhutada, G., Kavšček, M., Hofer, F., Gogg-Fassolter, G., Schweiger, M., Darnhofer, B., Kordiš, D., Birner-Gruenberger, R. and Natter, K. (2018): Characterization of a lipid droplet protein from Yarrowia lipolytica that is required for its oleaginous phenotype. BBA - Molecular and Cell Biology of Lipids 1863, 1193–1205.
11) Latinović, Z., Leonardi, A., Kovačič, L., Koh, C.Y., Šribar, J., Trampuš Bakija, A., Venkateswarlu D., Kini, R.M. and Križaj, I. (2018): The first intrinsic tenase complex inhibitor with serine protease structure offers a new perspective in anticoagulant therapy. Thrombosis and Haemostasis 118, 1713–1728.
12) Petan, T., Jarc, E. and Jusović, M. (2018): Lipid Droplets in Cancer: Guardians of Fat in a Stressful World. Molecules 23, 1941.
13) Škrlec, K., Ručman, R., Jarc, E., Sikirić, P., Švajger, U., Petan T., Perišić Nanut, M., Štrukelj, B. and Berlec, A. (2018): Engineering recombinant Lactococcus lactis as a delivery vehicle for BPC-157 peptide with antioxidant activity. Appl. Microbiol. Biotechnol. 102, 10103–10117.
14) Lukšić, B., Karabuva, S., Markić, J., Polić, B., Kovačević, T., Meštrović, J. and Križaj, I. (2018): Thrombocytopenic purpura following envenomation by the nose-horned viper (Vipera ammodytes ammodytes): Two case reports. Medicine (Baltimore) 97, e13737.
15) Gostinčar, C., Zajc, J., Lenassi, M., Plemenitaš, A., de Hoog, S., Al-Hatmi, A.M.S. and Gunde-Cimerman, N. (2018): Fungi between extremotolerance and opportunistic pathogenicity on humans. Fungal Diversity 93, 195–213.
16) Zajc, J., Gostinčar, C., Lenassi, M., Gunde-Cimerman, N. (2018): Stress tolerance of three opportunistic black yeasts. Acta Biol. Slov. 61, 15–27.
2017
1) Strojan, K., Leonardi, A., Bregar, V.B., Križaj, I., Svete, J. and Pavlin, M. (2017): Dispersion of nanoparticles in different media importantly determines the composition of their protein corona. PLoS One 12, e0169552.
2) Brvar, M., Kurtović, T., Grenc, D., Lang Balija, M., Križaj, I. and Halassy, B. (2017): Vipera ammodytes bites treated with antivenom ViperaTAb®: a case series with pharmacokinetic evaluation. Clinical Toxicology 55, 241-248.
3) Kononenko, V., Erman, A., Petan, T., Križaj, I., Kralj, S., Makovec, D. and Drobne, D. (2017): Harmful at non-cytotoxic concentrations: SiO2-SPIONs affect surfactant metabolism and lamellar body biogenesis in A549 human alveolar epithelial cells. Nanotoxicology 11, 419–429.
4) Latinović, Z., Leonardi, A., Petan, T., Žlajpah, M. and Križaj, I. (2017): Disintegrins from the venom of Vipera a. ammodytes effectively inhibit migration of breast cancer cells. Acta Chimica Slovenica 64, 555-559.
5) Guštin, E., Jarc, E., Kump, A. and Petan, T. (2017): Lipid droplet formation in HeLa cervical cancer cells depends on cell density and the concentration of exogenous unsaturated fatty acids. Acta Chimica Slovenica 64, 549-554.
6) Hojnik, N., Cvelbar, U., Tavčar-Kalcher, G., Walsh, J.L. and Križaj, I. (2017): Mycotoxin decontamination of food: Cold atmospheric pressure plasma versus “classic” decontamination. Toxins 9, 151.
7) Das, D., Faridounnia, M., Kovačič, L., Kaptein, R., Boelens, R. and Folkers, G.E. (2017): Single-stranded DNA binding by the helix-hairpin-helix domain of XPF protein contributes to the substrate specificity of the ERCC1-XPF protein complex. J. Biol. Chem. 292, 2842–2853.
8) Čadež, V., Škapin, D.S., Leonardi, A., Križaj, I., Kazazić, S., Salopek-Sondi, B. and Sondi, I. (2017): Formation and morphogenesis of a cuttlebone's aragonite biomineral structures for the common cuttlefish (Sepia officinalis) on the nanoscale: revisited. Journal of Colloid and Interface Science 508, 95-104.
9) Uršič, K., Ogrizović, M., Kordiš, D., Natter, K. and Petrovič, U. (2017): Tum1 is involved in the metabolism of sterol esters in Saccharomyces cerevisiae. BMC Microbiol. 17, 181.
10) Kordiš, D. (2017): The Life History of Domesticated Genes Illuminates the Evolution of Novel Mammalian Genes. In: Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts (Pontarotti, P.; Ed.). ISBN 978-3-319-61569-1. Springer; pp. 147-162.
11) Karabuva, S., Lukšić, B., Brizić, I., Latinović, L., Leonardi, A. and Križaj, I. (2017): Ammodytin L is the main cardiotoxic component of the Vipera ammodytes ammodytes venom. Toxicon 139, 94-100.
12) Kordiš, D. and Križaj, I. (2017): Secreted phospholipases A2 with β-neurotoxic activity. In: Handbook on Toxinology (Gopalakrishnakone, P., Inagaki, H., Mukherjee, A.K., Rahmy, T.R. and Vogel C.-W.; Eds.), Volume: Snake Venoms. ISBN: 978-94-007-6409-5. Springer; pp 67-86.
13) Jarc, E., Preložnik-Zupan, I., Buturović-Ponikvar, J., Snoj, N. and Podgornik, H. (2017): Comparison of erythrocyte and reticulocyte indices for the diagnosis of iron deficiency. Zdravniški vestnik 86 (1/2), 19-27.
2016
1) Meijnen, J.P., Randazzo, P., Foulquié-Moreno, M.R., van den Brink, J., Vandecruys, P., Stojiljkovic, M., Dumortier, F., Zalar, P., Boekhout, T., Gunde-Cimerman, N., Kokošar, J., Štajdohar, M., Curk, T., Petrovič, U. and Thevelein, J.M. (2016): Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae. Biotechnol. Biofuels 9, 5.
2) Latinović, Z., Leonardi, A., Šribar, J., Sajevic, T., Žužek, M.C., Frangež, R., Halassy, B., Trampuš-Bakija, A., Pungerčar, J. and Križaj, I. (2016): Venomics of Vipera berus berus to explain differences in pathology elicited by Vipera ammodytes ammodytes envenomation: Therapeutic implications. J. Proteomics 146, 34–47.
3) Starkl Renar, K., Iskra, J. and Križaj, I. (2016): Understanding malarial toxins. Toxicon 119, 319–329.
4) Obradović, D., Gašperšič, R., Caserman, S., Leonardi, A., Jamnik, M., Podlesek, Z., Seme, K., Anderluh, G., Križaj, I., Maček, P. and Butala, M. (2016): A cytolethal distending toxin variant from Aggregatibacter actinomycetemcomitans with an aberrant CdtB that lacks the conserved catalytic histidine 160. PLoS One 11, e0159231.
5) Zackrisson, M., Hallin, J., Ottosson, L.G., Dahl, P., Fernandez-Parada, E., Ländström, E., Fernandez-Ricaud, L., Kaferle, P., Skyman, A., Stenberg, S., Omholt, S., Petrovic, U., Warringer, J. and Blomberg, A. (2016): Scan-o-matic: high-resolution microbial phenomics at a massive scale. G3 6, 3003-3014.
6) Lasič, E., Galland, F., Vardjan, N., Šribar, J., Križaj, I., Concli Leite, M., Zorec, R. and Stenovec, M. (2016): Time-dependent uptake and trafficking of vesicles capturing extracellular S100B in cultured rat astrocytes. J. Neurochem. 139, 309-323.
7) Kurtović, T.*, Brvar, M.*, Grenc, D., Lang Balija, M., Križaj, I. and Halassy, B. (2016): A single dose of ViperfavTM may be inadequate for Vipera ammodytes snake bite: A case report and pharmacokinetic evaluation. Toxins 8, 244.
8) Skočaj, M., Yu, Y., Grundner, M., Resnik, N., Bedina Zavec, A., Leonardi, A., Križaj, I., Guella, G., Maček, P., Erdani-Kreft, M., Frangež, R., Veranič, P. and Sepčić, K. (2016): Characterisation of plasmalemmal shedding of vesicles induced by the cholesterol sphingomyelin binding protein, ostreolysin A-mCherry. BBA-Biomembranes 1858, 2882–2893.
9) Karabuva, S., Brizić, I., Latinović, Z., Leonardi, A., Križaj, I., and Lukšić, B. (2016): Cardiotoxic effects of the Vipera ammodytes ammodytes venom fractions in the isolated perfused rat heart. Toxicon 121, 98-104.
10) Drnovšek, N., Kocen, R., Gantar, A., Drobnič-Košorok, M., Leonardi, A., Križaj, I., Rečnika, A., and Novak, S. (2016): Size of silk fibroin β-sheet domains affected by Ca2+. Journal of Materials Chemistry B 4, 6597–6608.
11) Božič, J., Kordiš, D., Križaj, I., Leonardi, A., Močnik, R., Nakrst, M., Podgoršek, P., Prešern, J., Sušnik Bajec, S., Zorc, M., Zurc, J. and Dovč, P. (2016): Novel aspects in characterization of Carniolan honey bee (Apis mellifera carnica, Pollmann 1879). Acta Agriculturae Slovenica, Suppl. 5, 18–27.
12) Župunski, V., Kordiš, D. (2016): Strong and widespread action of site-specific positive selection in the snake venom Kunitz/BPTI protein family. Sci. Rep. 6: 37054.
2015
1) Leonardi, A., Sajevic, T., Latinović, Z., Pungerčar, J., Lang Balija, M., Trampuš Bakija, A., Vidmar, R., Halassy, B. and Križaj, I. (2015): Structural and biochemical characterisation of VaF1, a P-IIIa fibrinogenolytic metalloproteinase from Vipera ammodytes ammodytes venom. Biochimie 109, 78–87.
2) Oberčkal, J.*, Kovačič, L.*, Šribar, J.*, Leonardi, A., Dolinar, K., Pucer Janež A. and Križaj, I. (2015): On the role of protein disulphide isomerase in the retrograde cell transport of secreted phospholipases A2. PLoS One 10, e0120692.
3) Mattiazzi Ušaj, M.*, Brložnik, M.*, Kaferle, P., Žitnik, M., Wolinski, H., Leitner, F., Kohlwein, S.D., Zupan B. and Petrovič, U. (2015): Genome-wide localization study of yeast Pex11 identifies peroxisome-mitochondria interactions through the ERMES complex. J. Mol. Biol. 427, 2072–2087.
4) Križaj, I., Leonardi, A. in Šribar, J. (2015): Molekularni vidik toksičnosti slovenskih kač. V: Toksikologija 2015: piki in ugrizi strupenih živali (Brvar, M.; ur.). Slovensko zdravniško društvo; pp. 10–14.
5) Mattiazzi Ušaj, M., Prelec, M., Brložnik, M., Primo, C., Curk, T., Ščančar, J., Yenush, L. and Petrovič, U. (2015): Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis. Metallomics 7, 1338–1351.
6) Kavšček, M., Stražar, M., Curk, T., Natter, K. and Petrovič, U. (2015): Yeast as a cell factory – current state and perspectives. Microb. Cell Fact. 14, 94.
7) Faridounnia, M., Wienk, H., Kovačič, L., Folkers, G.E., Jaspers, N.G.J., Kaptein, R., Hoeijmakers, J.H.J. and Boelens, R. (2015): The Cerebro-Oculo-Facio-Skeletal (COFS) Syndrome point mutation F231L in the ERCC1 DNA repair protein causes dissociation of the ERCC1-XPF complex. J. Biol. Chem. 290, 20541–20555.
8) Berne, S., Kovačič, L., Sova, M., Kraševec, N., Gobec, S., Križaj, I. and Komel, R. (2015): Benzoic acid derivatives with improved antifungal activity: design, synthesis, structure-activity relationship (SAR) and CYP53 docking studies. Bioorg. Med. Chem. 23, 4264–4276.
9) Petrovič, U. (2015): Next generation biofuels: a new challenge for yeast. Yeast 32, 583–593.
10) Kocbek, V., Bersinger, N.A., Brglez, V., Mueller, M.D., Petan, T. and Rižner, T.L. (2015): Phospholipase A2 group IIA is elevated in endometriomas but not in peritoneal fluid and serum of ovarian endometriosis patients. Gynecol. Endocrinol. 31, 214–218.
11) Naneh, O., Bedina Zavec, A., Pahovnik, D., Žagar, E., Gilbert, R.J.C., Križaj, I. and Anderluh, G. (2015): An optimized protocol for expression and purification of murine perforin in insect cells. J. Immunol. Methods 426, 19–28.
12) Sopotnik, M., Leonardi, A., Križaj, I., Dušak, P., Makovec, D., Mesarič, T., Poklar Ulrih, N., Sepčić, K. and Drobne, D. (2015): Comparative study of serum protein binding to three different carbon-based nanomaterials. Carbon 95, 560–572.
13) Petan, T. and Križaj, I. (2015): Is iPLA2β a novel target for the development of new strategies to alleviate inflammatory bowel disease? Dig. Dis. Sci. 60, 3504–3506.
2014
1) Kurtović, T., Brgles, M., Leonardi, A., Lang Balija, M., Sajevic, T., Križaj, I., Allmaier, G., Marchetti-Deschmann, M., and Halassy, B. (2014): VaSP1, catalytically active serine proteinase from Vipera ammodytes ammodytes venom with unconventional active site triad. Toxicon 77, 93–104.
2) Leonardi, A., Sajevic, T., Kovačič, L., Pungerčar, J., Lang Balija, M., Halassy, B., Trampuš-Bakija, A. and Križaj, I. (2014): Hemorrhagin VaH4, a covalent heterodimeric P-III metalloproteinase from Vipera ammodytes ammodytes with potential anti-tumour activity. Toxicon 77, 141–155.
3) Brgles, M., Kurtović, T., Kovačič, L., Križaj, I., Barut, M., Lang Balija, M., Allmaier, G., Marchetti-Deschmann, M. and Halassy, B. (2014): Identification of proteins interacting with ammodytoxins in Vipera ammodytes ammodytes venom by immuno-affinity chromatography. Anal. Bioanal. Chem. 406, 293–304.
4) Mattiazzi Ušaj, M., Kaferle, P., Toplak, Trebše, P. and Petrovič, U. (2014): Determination of toxicity of neonicotinoids on the genome level using chemogenomics in yeast. Chemosphere 104, 91–96.
5) Weiss, V.U., Reitschmidt, S., Friesz, V., Allmaier, G., Križaj, I. and Marchetti-Deschmann, M. (2014): Chip electrophoretic separation of highly homologous ammodytoxin isoforms: three neurotoxic phospholipases A2 of Vipera ammodytes ammodytes venom. Electrophoresis 35, 2137–2145.
6) Artenjak, A., Leonardi, A., Križaj, I., Ambrožič, A., Sodin Šemrl, S., Božič, B. and Čučnik, S. (2014): Optimization of unnicked β2-glycoprotein I and high avidity anti-β2-glycoprotein I antibodies isolation. J. Immunol. Res. 2014, e195687.
7) Brglez, V., Pucer, A., Pungerčar, J., Lambeau, G. and Petan, T. (2014): Secreted phospholipases A2 are differentially expressed and epigenetically silenced in human breast cancer cells. Biochem. Biophys. Res. Commun. 445, 230–235.
8) Petschnigg, J., Groisman, B., Kotlyar, M., Taipale, M., Zheng, Y., Kurat, C.F., Sayad, A., Sierra, J.R., Mattiazzi Usaj, M., Snider, J., Nachman, A., Krykbaeva, I., Tsao, M.-S., Moffat, J., Pawson, T., Lindquist, S., Jurisica, I. and Stagljar, I. (2014): The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. Nat. Methods 11, 585–592.
9) Novak, M., Sepčić, K., Kraševec, N., Križaj, I., Maček, P., Anderluh, G., Guella, G. and Mancini, I. (2014): Targeted lipid analysis of haemolytic mycelial extracts of Aspergillus niger. Molecules 19, 9051–9069.
10) Sajevic, T., Leonardi, L. and Križaj, I. (2014): An overview of hemostaticly active components of Vipera ammodytes ammodytes venom. Toxin Rev. 33, 33–36.
11) Šribar, J., Oberčkal, J. and Križaj, I. (2014): Understanding the molecular mechanism underlying the presynaptic toxicity of secreted phospholipases A2 – an update. Toxicon 89, 9–16.
12) Polajnar, M., Zavašnik-Bergant, T., Škerget, K., Vizovišek, M., Vidmar, R., Fonović, M., Kopitar-Jerala, N., Petrovič, U., Navarro, S., Ventura, S. and Žerovnik, E. (2014): Human stefin B role in cell's response to misfolded proteins and autophagy. PLoS One 9, e102500.
13) Križaj, I. (2014): Roles of secreted phospholipases A2 in mammalian immune system. Prot. Pept. Lett. 21, 1201-1208.
14) Jawallapersand, P., Mashele, S.S., Kovačič, L., Stojan, J., Komel, R., Pakal, S.B., Kraševec, N. and Syed, K. (2014): Cytochrome P450 monooxygenase CYP53 family in fungi: Comparative structural and evolutionary analysis and its role as a common alternative anti-fungal drug target. PLoS One 9, e107209.
15) Brglez, V., Lambeau, G., and Petan, T. (2014): Secreted phospholipases A2 in cancer: diverse mechanisms of action. Biochimie 107, 114–123.
2013
1) Jenko-Pražnikar, Z., Petan, T. and Pungerčar, J. (2013): Ammodytoxins efficiently release arachidonic acid and induce apoptosis in a motoneuronal cell line in an enzymatic activity-dependent manner. NeuroToxicology 35, 91–100.
2) Skočaj, M., Bakrač, B., Križaj, I., Maček, P., Anderluh G. and Sepčič, K. (2013): The sensing of membrane microdomains based on pore-forming toxins. Curr. Med. Chem. 20, 491–501.
3) Sajevic, T., Leonardi, A., Kovačič, L., Lang Balija, M., Kurtović, T., Pungerčar, J., Halassy, B., Trampuš-Bakija, A. and Križaj, I. (2013): VaH3, one of the principal hemorrhage-inducing factors in Vipera ammodytes ammodytes venom, is a homodimeric P-IIIc metalloproteinase. Biochimie 95, 1158–1170.
4) Kokošar, J. and Kordiš, D. (2013): Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective. Mol. Biol. Evol. 30, 1015–1031.
5) Ambrožič, G., Šribar, J., Škapin, S.D., Žigon, M. and Crnjak Orel, Z. (2013): An antibacterial macroporous polyurethane hybrid material with a high content of zinc ions: a template to uniform ZnO nanoparticles. Mater. Res. Bull. 48, 1428–1434.
6) Vardjan, N., Mattiazzi, M., Rowan, E.G., Križaj, I.*, Petrovič, U.* and Petan, T.* (2013): Neurotoxic phospholipase A2 toxicity model: An insight from mammalian cells. Commun. Integr. Biol. 6, e23600.
7) Petan, T., Prijatelj Žnidaršič, P. and Pungerčar, J. (2013): Protein engineering in structure-function studies of viper's venom secreted phospholipases A2. In: Genetic Manipulation of DNA and Protein – Examples from Current Research (Figurski, D.H.; Ed.). ISBN 978-953-51-0994-5. InTech Open Access; pp. 107–132.
8) Ota, K., Mikelj, M., Papler, T., Leonardi, A., Križaj, I. and Maček, P. (2013): Ostreopexin: A hemopexin fold protein from the oyster mushroom, Pleurotus ostreatus. Biochim. Biochim. Acta–Proteins Proteom. 1834, 1468–1473.
9) Ota, K, Leonardi, A., Mikelj, M., Skočaj, M., Wohlschlager, T., Künzler, M., Aebi, M., Narat, M., Križaj, I., Anderluh, G., Sepčić, K. and Maček, P. (2013): Membrane cholesterol and sphingomyelin, and ostreolysin A are obligatory for pore-formation by a MACPF/CDC-like pore-forming protein, pleurotolysin B. Biochimie 95, 1855–1864.
10) Kovačič, L., Paulič, N., Leonardi, A., Hodnik, V., Anderluh, G., Podlesek, Z., Žgur-Bertok, D., Križaj, I. and Butala, M. (2013): Structural insight into LexA-RecA* interaction. Nucleic Acids Res. 41, 9901-9910.
11) Pucer, A., Brglez, V., Payre, C., Pungerčar, J., Lambeau, G. and Petan, T. (2013): Group X secreted phospholipase A2 induces lipid droplet formation and prolongs breast cancer cell survival. Mol. Cancer 12, e111.
12) Trošt, N., Stepišnik, T., Berne, S., Pucer, A., Petan, T., Komel, R. and Debeljak, N. (2013): Recombinant human erythropoietin alters gene expression and stimulates proliferation of MCF-7 breast cancer cells. Radiol. Oncol. 47, 382–389.
13) Styles, E., Youn, J.-Y., Mattiazzi-Ušaj M. and Andrews, B. (2013): Functional genomics in the study of yeast cell polarity: moving in the right direction. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20130118.
14) Lindič, N., Budič, M., Petan, T., Knisbacher, B.A., Levanon, E.Y. and Lovšin, N. (2013): Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. Retrovirology 10, 156.
15) Dogša, I., Brložnik, M., Stopar, D. and Mandić-Mulec, I. (2013): Exopolymer diversity and the role of levan in Bacillus subtilis biofilms. PLoS One 8, e62044.
16) Progar, V. and Petrovič, U. (2013): Vpliv parametrov sekvenciranja naslednje generacije na zanesljivost rezultatov v metagenomskih študijah = The effect of next generation sequencing parameters on the reliability of metagenomic studies. Inform. Med. Slov. 18, 1–8.
2012
1) Kovačič, L. and Boelens, R. (2012): Protein-DNA interactions. In: NMR of Biomolecules: Towards Mechanistic Systems Biology (Bertini, I., McGreevy, K.S. and Parigi G.; Eds.). Wiley-VCH Verlag GmbH; Weinheim, Chichester, pp. 239–252.
2) Yotsu-Yamashita, M., Gilhen, J., Russell, R. W., Krysko, K. L., Melaun, C., Kurz, A., Kauferstein, S., Kordiš, D. and Mebs, D. (2012): Variability of tetrodotoxin and of its analogues in the red-spotted newt, Notophthalmus viridescens (Amphibia: Urodela: Salamandridae). Toxicon 59, 257–264.
3) Violette, A., Leonardi, A., Piquemal, D., Terrat, Y., Biass, D., Dutertre, S., Noguier, F., Ducancel, F., Stöcklin, R., Križaj, I. and Favreau, P. (2012): Recruitment of glycosyl hydrolase proteins in a cone snail venomous arsenal: further insights into biomolecular features of Conus venoms. Mar. Drugs 10, 258–280.
4) Prijatelj-Žnidaršič, P. and Pungerčar, J. (2012): A recent evaluation of the lethal potencies of ammodytoxins. Toxicon 59, 642–643.
5) Kurtović, T., Leonardi, A., Lang Balija, M., Brgles, M., Habjanec, L., Križaj, I. and Halassy, B. (2012): The standard mouse assay of antivenom quality does not measure antibodies neutralising the haemorrhagic activity of the Vipera ammodytes venom. Toxicon 59, 709–717.
6) Mattiazzi, M., Petrovič, U. and Križaj, I. (2012): Yeast as a model eukaryote in toxinology: a functional genomics approach to the studies of the molecular basis of action of pharmacologically active molecules. Toxicon 60, 558–571.
7) Mattiazzi, M., Sun, Y., Wolinski, H., Bavdek, A., Petan, T., Anderluh, G., Kohlwein, S.D., Drubin, D., Križaj, I. and Petrovič, U. (2012): A neurotoxic phospholipase A2 impairs yeast amphiphysin activity and reduces endocytosis. PLoS One 7, e40931.
8) Križaj, I. (2012): Characterising and cloning the venom components of the nose-horned viper that affect the human haemostatic system. Circulation 126, f5–f6.
9) Leonardi, A., Biass, D., Kordiš, D., Stöcklin, R., Favreau, P. and Križaj, I. (2012): Conus consors snail venom proteomics unveils functions, pathways and novel families involved in its venomic system. J. Proteome Res. 11, 5046–5058.
10) Kordiš, D. (2012): The repetitive landscape of sauropsid genomes. In: Evolutionary Biology: Mechanisms and Trends (Pontarotti, P.; Ed.). Springer; Heidelberg, New York, Dordrecht, London, pp. 243–263.
11) Kordiš, D. and Kokošar, J. (2012): What can domesticated genes tell us about the intron gain in mammals? Int. J. Evol. Biol. 2012, Article ID 278981, 7 pp.
12) Tansey, K.E., Guipponi, M., Perroud, N., Bondolfi, G., Domenici, E., Evans, D., Hall, S.K., Hauser, J., Henigsberg, N., Hu, X., Jerman, B., Maier, W., Mors, O., O'Donovan, M., Peters, T.J., Placentino, A., Rietschel, M., Souery, D., Aitchison, K.J., Craig, I., Farmer, A., Wendland, J.R., Malafosse, A., Holmans, P., Lewis, G., Lewis, C.M., Stensbøl, T.B., Kapur, S., McGuffin, P. and Uher, R. (2012): Genetic predictors of response to serotonergic and noradrenergic antidepressants in major depressive disorder : a genome-wide analysis of individual-level data and a meta-analysis. PLoS Med. 9, e1001326.
2011
1) Kauferstein, S., Porth, C., Kendel, Y., Wunder, C., Nicke, A., Kordiš, D., Favreau, P., Koua, D., Stöcklin, R. and Mebs, D. (2011): Venomic study on cone snails (Conus spp.) from South-Africa. Toxicon 57, 28–34.
2) Križaj, I. (2011): Obituary of Franc Gubenšek, 1937–2010. Toxicon 57, 186–188.
3) Halassy, B., Brgles, M., Habjanec, L., Lang Balija, M., Kurtović, T., Marchetti Deschman M., Križaj, I. and Allmaier, G. (2011): Intraspecies variability in Vipera ammodytes ammodytes venom related to its toxicity and immunogenic potential. Comp. Biochem. Biophysiol. C Toxicol. Pharmacol. 153, 223–230.
4) Malki, K., Uher, R., Paya-Cano, J., Binder, E., Rietschel, M., Zobel, A., Mors, O., Hauser, J., Henigsberg, N., Jerman, B., Souery, D., Placentino, A., Ng, M., Cohen-Woods, S., Sluyter, F., Farmer, A., Aitchison, K.J., Craig, I., Lewis, C., McGuffin, P. and Schalkwyk, L.C. (2011): Convergent animal and human evidence suggests a role of PPM1A gene in response to antidepressants. Biol. Psychiat. 69, 360–365.
5) Sajevic, T., Leonardi, A. and Križaj, I. (2011): Haemostatically active proteins in snake venoms. Toxicon 57, 627–645.
6) Premrov Bajuk, B., Zdovc, I., Smrekar, V., Križaj, I., Leonardi, A. and Drobnič Košorok, M. (2011): Dermatophyte Trichophyton mentagrophytes produces cysteine protease inhibitor. Acta Chim. Slov. 58, 33–40.
7) Tollervey, J.R., Curk, T., Rogelj, B., Briese, M., Cereda, M., Kayikci, M., König, J., Hortobágyi, T., Nishimura, A.L., Župunski, V., Patani, R., Chandran, S., Rot, G., Zupan, B., Shaw, C.E. and Ule, J. (2011): Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat. Neurosci. 14, 452–458.
8) Pohleven, J., Brzin, J., Vrabec, L., Leonardi, A., Čokl, A., Štrukelj, B., Kos, J. and Sabotič, J. (2011): Basidiomycete Clitocybe nebularis is rich in lectins with insecticidal activities. Appl. Microbiol. Biotechnol. 91, 1141–1148.
9) Križaj, I. (2011): Ammodytoxin: a window into understanding presynaptic toxicity of secreted phospholipases A2 and more. Toxicon 58, 219–229.
10) Sajevic, T., Reščič, J. and Vlachy, V. (2011): Correlation between flexibility of chain-like polyelectrolyte and thermodynamic properties of its solution. Condens. Matter Phys. 14, 33603: 1–14.
11) Kordiš, D. (2011): Evolution of phospholipase A2 toxins in venomous animals. Acta Chim. Slov. 58, 638–646.
12) Mebs, D., Kordiš, D., Kendel, Y. and Kauferstein, S. (2011): The evolution of αD-conopeptides targeting neuronal nicotinic acetylcholine receptors. Acta Chim. Slov. 58, 730–734.
13) Pungerčar, J., Prijatelj Žnidaršič, P. and Petan, T. (2011): Structure-function relationship studies of ammodytoxins and ammodytins by protein engineering. Acta Chim. Slov. 58, 660–670.
14) Peters, F., Martinez, M.M., Leonov, A., Kovačič, L., Becker, S., Boelens, R. and Griesinger, G. (2011): Cys-Ph-TAHA: A lanthanide binding tag for RDC and PCS enhanced protein NMR. J. Biomol. NMR 51, 329–337.
15) Šribar, J. and Križaj, I. (2011): Secreted phospholipases A2 – not just enzymes. Acta Chim. Slov. 58, 678–688.
16) Kurtović, T., Brgles, T., Leonardi, T., Lang Balija, M., Križaj, I., Marchetti Deschmann, M., Allmaier, G. and Halassy B. (2011): Ammodytagin, a heterodimeric metalloproteinase from Vipera ammodytes ammodytes venom with strong hemorrhagic activity. Toxicon 58, 570–582.
17) Kordiš, D. (2011): Extensive intron gain in the ancestor of placental mammals. Biol. Direct 6, 59.
2010
1) Saul, F.A., Prijatelj-Žnidaršič, P., Vuilliez-le Normand, B., Villette, B., Raynal, B., Pungerčar, J., Križaj, I. and Faure, G. (2010): Comparative structural studies of two natural isoforms of Ammodytoxin, phospholipases A2 from Vipera ammodytes ammodytes which differ in neurotoxicity and anticoagulant activity. J. Struct. Biol. 169, 360–369.
2) Čeru, S., Konjar, Š., Maher, K., Repnik, U., Križaj, I., Benčina, M., Renko, M., Nepveu, A., Žerovnik, E., Turk, B. and Kopitar-Jerala, N. (2010): Stefin B interacts with histones and cathepsin L in nucleus. J. Biol. Chem. 285, 10078–10086.
3) Halassy, B., Habjanec, L., Lang Balija, M., Kurtović, T., Brgles, M. and Križaj, I. (2010): Ammodytoxin content of Vipera ammodytes ammodytes venom as a prognostic factor for venom immunogenicity. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 151, 455–460.
4) Kovačič, L., Novinec, M., Petan, T. and Križaj, I. (2010): Structural basis of the significant calmodulin-induced increase in the enzymatic activity of secreted phospholipases A2. Protein Eng. Des. Sel. 23, 479–487.
5) Uher, R., Perroud, N., Ng, M.Y.M., Hauser, J., Henigsberg, N., Maier, W., Mors, O., Placentino, A., Rietschel, M., Souery, D., Žagar, T., Czerski, P.M., Jerman, B., Larsen, E.R., Schulze, T.G., Zobel, A., Cohen-Woods, S., Pirlo, K., Butler, A.W., Muglia, P., Barnes, M.R., Lathrop, M., Farmer, A., Breen, G., Aitchison, K.J., Craig, I., Lewis, C.M. and McGuffin, P. (2010): Genome-wide pharmacogenetics of antidepressant response in the GENDEP project. Am. J. Psychiatry 167, 555–564.
6) Mattiazzi, M., Jambhekar, A., Kaferle, P., DeRisi, J.L., Križaj, I. and Petrovič, U. (2010): Genetic interactions between a phospholipase A2 and the Rim101 pathway components in S. cerevisiae reveal a role for this pathway in response to changes in membrane composition and shape. Mol. Genet. Genomics 283, 519–530.
7) Razpotnik, A., Križaj, I., Šribar, J., Kordiš, D., Maček, P., Frangež, R., Kem, W.R. and Turk, T. (2010): A new phospholipase A2 isolated from the sea anemone Urticina crassicornis : its primary structure and phylogenetic classification. FEBS J. 277, 2641–2653.
8) Mattiazzi, M., Curk, T., Križaj, I., Zupan, B. and Petrovič, U. (2010): Inference of the molecular mechanism of action from genetic interaction and gene expression data. OMICS 14, 357–367.
9) Novinec, M., Kovačič, L., Lenarčič, B. and Baici, A. (2010) : Conformational flexibility and allosteric regulation of cathepsin K. Biochem. J. 429, 379–389.
10) Kordiš, D. (2010): Transposable elements in reptilian and avian (Sauropsida) genomes. Cytogenet. Genome Res. 127, 94–111.
11) Nishimura, A.L., Župunski, V., Troakes, C., Kathe, C., Fratta, P., Howell, M., Gallo, J.M., Hortobágyi, T., Shaw, C.E. and Rogelj, B. (2010): Nuclear import impairment causes cytoplasmic trans-activation response DNA-binding protein accumulation and is associated with frontotemporal lobar degeneration. Brain 133, 1763–1771.
12) Jerman, B. and Pungerčar, J. (2010): Bacterial expression and simple purification of human group X secretory phospholipase A2. Acta Chim. Slov. 57, 888–894.
2009
1) Wolinski, H., Petrovič, U., Mattiazzi, M., Petschnigg, J., Heise, B., Natter, K. and Kohlwein, S.D. (2009): Imaging-based live cell yeast screen identifies novel factors involved in peroxisome assembly. J. Proteome Res. 8, 20–27.
2) Jenko Pražnikar, Z., Petan, T. and Pungerčar, J. (2009): A neurotoxic secretory phospholipase A2 induces apoptosis in motoneuron-like cells. Ann. NY Acad. Sci. 1152, 215–224.
3) Razpotnik, A., Križaj I., Kem, W.R., Maček, P. and Turk, T. (2009): A new cytolytic protein from the sea anemone Urticina crassicornis that binds to cholesterol- and sphingomyelin-rich membranes. Toxicon 53, 762–769.
4) Kauferstein, S., Kendel, Y., Nicke, A., Coronas, F. I. V., Possani, L. D., Favreau, P., Križaj, I., Wunder, C., Kauert, G. and Mebs, D. (2009): New conopeptides of the D-superfamily selectively inhibiting neuronal nicotinic acetylcholine receptors. Toxicon 54, 295–301.
5) Curk, T., Petrovič, U., Shaulsky, G., and Zupan, B. (2009): Rule-based clustering for gene promoter structure discovery. Methods Inf. Med. 48, 229–235.
6) Low, A., Okeoma, C.M., Lovšin, N., de las Heras, M., Taylor, T.H., Peterlin, B.M., Ross, S.R. and Fan, H. (2009): Enhanced replication and pathogenesis of Moloney murine leukemia virus in mice defective in the murine APOBEC3 gene. Virology 385, 455–463.
7) Lovšin, N. and Peterlin, B.M. (2009): APOBEC3 proteins inhibit LINE-1 retrotransposition in the absence of ORF1p binding. Ann. NY Acad. Sci. 1178, 268–275.
8) Logonder, U., Jenko-Pražnikar, Z., Scott-Davey, T., Pungerčar, J.*, Križaj, I.* and Harris, J.B.* (2009): Ultrastructural evidence for the uptake of a neurotoxic snake venom phospholipase A2 into mammalian motor nerve terminals. Exp. Neurol. 219, 591–594.
9) Avanzo, P., Sabotič, J., Anžlovar, S., Popovič, T., Leonardi, A., Pain, R.H., Kos, J. and Brzin, J. (2009): Trypsin-specific inhibitors from basidiomycete Clitocybe nebularis with regulatory and defensive functions. Microbiology 155, 3971–3981.
10) Gaser, D., Štrukelj, B., Bratkovič, T., Kreft, S., Pungerčar, J. and Lunder, M. (2009): Cross-affinity of peptide ligands selected from phage display library against pancreatic phospholipase A2 and ammodytoxin C. Acta Chim. Slov. 56, 712–717.
11) Jazbec, P., Šmidovnik, A., Puklavec, M., Križman, M., Šribar, J., Milivojević, L. and Prošek, M. (2009): HPTLC and HPLC-MS quantification of coenzyme Q10 and cholesterol in fractionated chicken-breast tissue. J. Planar Chromatogr. 22, 395–398.
12) Kovačič, L., Novinec, M., Petan, T., Baici, A. and Križaj, I. (2009): Calmodulin is a non-essential activator of secretory phospholipase A2. Biochemistry 48, 11319–11328.
13) Kordiš, D. and Turk, V. (2009): Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes. BMC Evol. Biol. 9, 266.
2008
1) Aguiar, R.S., Lovšin, N., Tanuri, A. and Peterlin, B.M. (2008): Vpr.A3A chimera inhibits HIV replication. J. Biol. Chem. 283, 2518–2525.
2) Halassy, B., Brgles, M., Habjanec, L., Lang Balija, M., Križaj, I., Štrancar, A., Barut, M. and Tomašić, T. (2008): The use of convective interaction media for analysis of long-nosed viper venom. J. Liq. Chrom. Rel. Technol. 31, 38–53.
3) Premzl, A., Kovačič, L., Halassy, B. and Križaj, I. (2008): Generation of ammodytoxin-anti-cathepsin B immuno-conjugate as a model for delivery of secretory phospholipase A2 into cancer cells. Toxicon 51, 754–764.
4) Jenko Pražnikar, Z., Kovačič, L., Rowan, E.G., Romih, R., Rusmini, P., Poletti, A., Križaj, I. and Pungerčar, J. (2008): A presynaptically toxic secreted phospholipase A2 is internalized into motoneuron-like cells where it is rapidly translocated into the cytosol. Biochim. Biophys. Acta–Mol. Cell Res. 1783, 1129–1139.
5) Jerman, B. and Pungerčar, J. (2008): Sekretorne fosfolipaze A2 in njihova (pato)fiziološka vloga = Secretory phospholipases A2 and their (patho)physiological role. Farm. vestn. 59, 9–15.
6) Križaj, I. (2008): Metode za analizo proteoma (Methods for proteome analysis). V: Posvetovanje Pomen biotehnologije in mikrobiologije za prihodnost (Raspor, P. in Jamnik, P., ur.), 31. januar in 1. februar 2008, Ljubljana. Proteomika (Pomen biotehnologije in mikrobiologije za prihodnost, 05). Ljubljana: Biotehniška fakulteta, Oddelek za živilstvo, pp. 19–31.
7) Prijatelj, P., Jenko Pražnikar, Z., Petan, T., Križaj, I. and Pungerčar, J. (2008): Mapping the structural determinants of presynaptic neurotoxicity of snake venom phospholipases A2. Toxicon 51, 1520–1529.
8) Logonder, U., Jorgačevski, J., Anderluh, G., Petrovič, U., Poberaj, I. and Križaj, I. (2008): A secreted phospholipase A2 binds to calmodulin at sub-micromolar concentrations of calcium. Acta Chim. Slov. 55, 541–546.
9) Halassy, B., Habjanec, L., Brgles, M., Lang Balija, M., Leonardi, A., Kovačič, L., Prijatelj, P., Tomašić, J. and Križaj, I. (2008): The role of antibodies specific for toxic sPLA2s and haemorrhagins in neutralizing potential of antisera raised against Vipera ammodytes ammodytes venom. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 148, 178–183.
10) Leonardi, A., Fox, J.W., Trampuš-Bakija, A. and Križaj, I. (2008): Two coagulation factor X activators from Vipera a. ammodytes venom with potential to treat patients with dysfunctional factors IXa or VIIa. Toxicon 52, 628–637.
11) Logonder, U., Križaj, I., Rowan, E.G. and Harris, J.B. (2008): Neurotoxicity of ammodytoxin A in envenoming bites of Vipera ammodytes ammodytes. J. Neuropathol. Exp. Neurol. 67, 1011–1019.
12) Novinec, M., Kovačič, L., Škrlj, N., Turk, V. and Lenarčič, B. (2008): Recombinant human SMOCs produced by in vitro refolding: Calcium-binding properties and interactions with serum proteins. Protein Expr. Purif., 62, 75–82.
13) Lesar, A. and Sajevic, T. (2008): Structures, vibrational spectra, and relative energetics of FC(O)ONO and FC(O)NO2 isomers at DFT and ab initio levels. Mol. Phys. 106, 2301–2308.
14) Yoshinaga, K., Obata, H., Jurukovski, V., Mazzieri, R., Chen, Y., Zilberberg, L., Huso, D., Melamed, J., Prijatelj, P., Todorovic, V., Dabovic, B. and Rifkin , D.B. (2008): Perturbation of transforming growth factor (TGF)-β1 association with latent TGF-β binding protein yields inflammation and tumors. Proc. Natl. Acad. Sci. U.S.A. 105, 18758–18763.
15) Vaupotič, T., Veranič, P., Petrovič, U., Gunde-Cimerman, N. and Plemenitaš, A. (2008): HMG-CoA reductase is regulated by environmental salinity and its activity is essential for halotolerance in halophilic fungi. Stud. Mycol. 61, 61–66.
16) Jenko Pražnikar, Z. (2008): Neurotoxicity of ammodytoxin A, a presynaptically toxic secretory phospholipase A2 from the long nosed viper venom (Vipera ammodytes, Linnaeus, 1758) = Neurotossicità di ammoditossina A, fosfolipasi A2 secretoria tossica presinaptica, isolata dalla vipera dal corno (Vipera ammodytes, Linnaeus, 1758). Ann. Ser. Hist. Nat. 18, 273–282.
2007
1) Leonardi, A., Fox, J.W., Trampuš-Bakija, A. and Križaj, I. (2007): Ammodytase, a metalloprotease from Vipera ammodytes ammodytes venom, possesses strong fibrinolytic activity. Toxicon 49, 833–842.
2) Kovačič, L., Šribar, J. and Križaj, I. (2007): A new photoprobe for studying biological activities of secreted phospholipases A2. Bioorg. Chem. 35, 295–305.
3) Pungerčar, J. and Križaj, I. (2007): Understanding the molecular mechanism underlying the presynaptic toxicity of secreted phospholipases A2. Toxicon 50, 871–892.
4) Petan, T., Križaj, I. and Pungerčar, J. (2007): Restoration of enzymatic activity in a Ser-49 phospholipase A2 homologue decreases its Ca(2+)-independent membrane damaging activity and increases its toxicity. Biochemistry 46, 12795–12809.
5) Okeoma, C.M., Lovšin, N., Peterlin, B.M. and Ross, S.R. (2007): APOBEC3 inhibits mouse mammary tumour virus replication in vivo. Nature 445, 927–930.
6) Ferrazzi, F., Magni, P., Sacchi, L., Nuzzo, A., Petrovič, U. and Bellazzi, R. (2007): Inferring gene regulatory networks by integrating static and dynamic data. Int. J. Med. Inform. 76, 462–475.
7) Sabotič, J., Galeša, K., Popovič, T., Leonardi, A. and Brzin, J. (2007) Comparison of natural and recombinant clitocypins, the fungal cysteine protease inhibitor. Protein Expr. Purif. 53, 104–111.
8) Šribar, J., Kovačič, L., Draškovič, P., Faure, G. and Križaj, I. (2007): The first phospholipase inhibitor from the serum of Vipera ammodytes ammodytes. FEBS J. 274, 6055–6064.
2006
1) Kordiš, D., Lovšin, N. and Gubenšek, F. (2006): Phylogenomic analysis of the L1 retrotransposons in Deuterostomia. Syst. Biol. 55, 886–901.
2) Petrovič, U., Mattiazzi, M., Curk, T., Zupan, B. and Križaj, I. (2006): K orodjem bioinformatike za fenomiko in sistemsko biologijo = Towards the bioinformatics tools for phenomics and systems biology. Inform. Med. Slov. 1, 66–71.
3) Vitale, L., Vukelić, B. and Križaj, I. (2006): Extracellular metalloendopeptidase of Streptomyces rimosus. Arch. Microbiol. 185, 183–191.
4) Prijatelj, P., Vardjan, N., Rowan, E.G., Križaj, I. and Pungerčar, J. (2006): Binding to the high-affinity M-type receptor for secreted phospholipases A2 is not obligatory for the presynaptic neurotoxicity of ammodytoxin A. Biochimie 88, 1425–1433.
5) Novinec, M., Kordiš, D., Turk, V. and Lenarčič, B. (2006): Diversity and evolution of the thyroglobulin type-1 domain superfamily. Mol. Biol. Evol. 23, 744–755.
6) Petrovič, U. (2006): Role of oxidative stress in the extremely salt-tolerant yeast Hortaea werneckii. FEMS Yeast Res. 6, 816–822.
7) Prijatelj, P., Charnay, M., Ivanovski, G., Jenko, Z., Pungerčar, J., Križaj, I. and Faure, G. (2006): The C-terminal and ß-wing regions of ammodytoxin A, a neurotoxic phospholipase A2 from Vipera ammodytes ammodytes, are critical for binding to factor Xa and for anticoagulant effect. Biochimie 88, 69–76.
2005
1) Fontana, L., Chen, Y., Prijatelj, P., Sakai, T., Fässler, R., Sakai, L.Y. and Rifkin, D.B. (2005): Fibronectin is required fointegrin αvβ6-mediated activation of latent TGF-beta complexes containing LTBP-1. FASEB J. 19, 1798–1808.
2) Petan, T., Križaj, I., Gelb, M.H. and Pungerčar, J., (2005): Ammodytoxins, potent presynaptic neurotoxins, are also highly efficient phospholipase A2 enzymes. Biochemistry 44, 12535–12545.
3) Gorinšek, B., Gubenšek, F. and Kordiš, D. (2005): Phylogenomic analysis of chromoviruses. Cytogenet. Genome Res. 110, 543–552.
4) Petrovič, U., Šribar, J., Matis, M., Anderluh, G., Peter-Katalinić, J., Križaj, I. and Gubenšek, F. (2005): Ammodytoxin, a secretory phospholipase A2, inhibits G2 cell cycle arrest in yeast S. cerevisiae. Biochem. J. 15, 383–388.
5) Kralj, B., Križaj, I., Bukovec, P., Slejko, S. and Milačič, R. (2005): Speciation of aluminium in tea infusions by use of SEC and FPLC with ICP-OES and ES-MS-MS detection. Anal. Bioanal. Chem. 383, 467–475.
6) Gradišar, H., Friedrich, J., Križaj, I. and Jerala, R. (2005): Similarities and specificities of fungal keratinolytic proteases: comparison of keratinases of Paecilomyces marquandii and Doratomyces microsporus to some known proteases. Appl. Environ. Microbiol. 71, 3420–3426.
7) Zheng, Y.H., Lovšin, N. and Peterlin, B.M. (2005): Newly identified host factors modulate HIV replication. Immunol. Lett. 97, 225–234.
8) Sacchi, L., Bellazzi, R., Larizza, C., Magni, P., Curk, T., Petrovič ,U. and Zupan, B. (2005): TA-clustering: cluster analysis of gene expression profiles through Temporal Abstractions. Int. J. Med. Inform. 74, 505–517.
9) Kordiš, D. (2005): A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 347, 161–173.
10) Šribar, J., Anderluh, G., Fox, J.W. and Križaj, I. (2005): Protein disulphide isomerase binds ammodytoxin strongly: Possible implications for toxin trafficking. Biochem. Biophys. Res. Commun. 329, 733–737.
11) Leban, G., Bratko, I., Petrovič, U., Curk, T. and Zupan, B. (2005): Vizrank: finding informative data projections in functional genomics by machine learning. Bioinformatics 21, 413–414.
12) Curk, T., Demsar, J., Xu, Q., Leban, G., Petrovič, U., Bratko, I., Shaulsky, G. and Zupan, B. (2005): Microarray data mining with visual programming. Bioinformatics 21, 396–398.
2004
1) Ivanovski, G., Petan, T., Križaj, I., Gelb, M.H., Gubenšek, F. and Pungerčar, J. (2004): Basic amino acid residues in the β-structure region contribute, but not critically, to presynaptic neurotoxicity of ammodytoxin A. Biochim. Biophys. Acta 1702, 217–225.
2) Petrovič, U., Šribar, J., Pariš, A., Rupnik, M., Kržan, M., Vardjan, N., Gubenšek, F., Zorec, R. and Križaj, I. (2004): Ammodytoxin, a neurotoxic secreted phospholipase A2, can act in the cytosol of the nerve cell. Biochem. Biophys. Res. Commun. 324, 981–985.
3) Čučnik, S., Kveder, T., Križaj, I., Rozman, B. and Božič, B. (2004): High avidity anti-β2-glycoprotein I antibodies in patients with antiphospholipid syndrome. Ann. Rheum. Dis. 63, 1478–1482.
4) Čučnik, S., Križaj, I., Rozman, B., Kveder, T. and Božič, B. (2004): Concomitant isolation of protein C inhibitor and unnicked β2-glycoprotein I. Clin. Chem. Lab. Med. 42, 171–174.
5) Kralj, B., Ščančar, J., Križaj, I., Benedik, M., Bukovec, P. and Milačič, R. (2004): Determination of high molecular mass Al species in serum and spent CAPD fluids of dialysis patients combining SEC and anion-exchange FPLC with ETAAS detection. J. Anal. At. Spectrom. 19, 101–106.
6) Čepeljnik, T., Križaj, I. and Marinšek-Logar, R. (2004): Isolation and characterization of the Pseudobutyrivibrio xylanivorans Mz5 xylanase xynt—the first family 11 endoxylanase from rumen Butyrivibrio-related bacteria. Enzyme Microb. Technol. 34, 219–227.
7) Gorinšek, B., Gubenšek, F. and Kordiš, D. (2004): Evolutionary genomics of chromoviruses in eukaryotes. Mol. Biol. Evol. 21, 781–798.
8) Režen, T., Debeljak, N., Kordiš, D. and Rozman, D. (2004): New aspects on lanosterol 14α-demethylase and cytochrome P450 evolution: lanosterol/cycloartenol diversification and lateral transfer. J. Mol. Evol. 59, 51–58.
9) Sacchi, L., Bellazzi, R., Larizza, C., Magni, P., Curk, T., Petrovič, U. and Zupan, B. (2004): Clustering gene expression data with Temporal Abstractions. Stud. Health Technol. Inform. 107: MEDINFO 2004, 798–802.
10) Čimbora-Zovko, T., Bombek, S., Košmrlj, J., Kovačič, L., Polanc, P., Katalinić, A. and Osmak, M. (2004): Development of potential anti-cancer agents: Diazenes and derivatives. Drug Dev. Res. 61, 95–100.