Contact Information
phone:+30 210 7723158
email: snikolai@central.ntua.gr

Research Interests
My research centers on the discovery, engineering and utilization of enzymes for the degradation of synthetic and natural polymers, as well as for the synthesis or bioconversion of naturally-occurring compounds.

Teaching Interests
Lab courses: Industrial Biotechnology, Environmental Biotechnology, Applied Biotechnology, Food Chemistry/Microbiology/Preservation, Bioengineering
Tutoring course: Biochemical Engineering (focusing on enzyme reactors)

Academic Background

PhD Industrial Biotechnology                                          2015-2019
Industrial Biotechnology & Biocatalysis Group
School of Chemical Engineering
National Technical University of Athens, Greece
Thesis: Discovery of novel fungal biocatalysts and application in bioremediation of chlorinated aromatic pollutants

Diploma in Chemical Engineering                                     2014
Specialization in Biotechnology & Food Technology
School of Chemical Engineering
National Technical University of Athens, Greece
Thesis: Engineering of the heterologous expression and characterization of a cutinase from Fusarium oxysporum

Awards and Distinctions

• Team Leader of the Winning team “BioRise” at the international Hackathon PLASTIC FANTASTIC 2024
• Remote participation in Global Young Scientists Summit (GYSS), Singapore 2023
• Best Poster Award (2^nd place) at 8th International Conference on Sustainable Solid Waste Management (2021)

Title: “Discovery of a novel PETase-like enzyme for the degradation of plastic waste”

• Best Paper Award at the 1^st International Electronic Conference on Catalysis Sciences (2020)

Paper title: “Discovery and biochemical characterization of a novel polyesterase for the degradation of synthetic plastics”

• “Dimitris N. Chorafas Prize” for best PhD Thesis at NTUA for 2019 (1^st Prize)

by “Dimitris N. Chorafas Foundation”

• “Iakovos Giourounlian Award” for best industrially relevant PhD Thesis in Chemical Engineering for 2019 (2^nd Prize)

by “M. Stassinopoulos-VIOHALCO Foundation”

• “Thomaidio Award” for published paper (2017-2019) – students with NTUA affiliation

Personal Funding

• Adlerbertska Forskningsstiftelsen Grant for “Omic analyses of novel acidophilic fungi for the valorization of agro-industrial residues” – 82,000 SEK (2022)
• 3-year PhD Scholarship from the Greek State Scholarship Foundation (2016-2019)
• COST Action CM1303 (Systems Biocatalysis) fellowship – 2,500 EUR (2017)

Work Experience

Associate Researcher                                                      02/2024-
EnZyReMix “Chemoenzymatic recycling of mixed plastic waste”
National Technical University of Athens, Greece

Associate Researcher                                                      02/2023-
PlastOmics “Discovery of novel enzymes for the bioconversion of plastics using multi-omics”
National Technical University of Athens, Greece

 Faculty Member (Tenured)                                              12/2022-
Dpt of Synthesis and Development of Industrial Processes
School of Chemical Engineering
National Technical University of Athens, Greece

Postdoc Researcher                                            09/2021-12/2022
Division of Industrial Biotechnology
Department of Biology and Biological Engineering
Chalmers University of Technology, Sweden

Postdoc Researcher                                            01/2020-09/2021
BioICEP “Bio Innovation of a Circular Economy for Plastics”
National Technical University of Athens, Greece

 Research Assistant                                             11/2015-09/2019
TASCMAR “Tools And Strategies to access original bioactive compounds by Cultivating MARine invertebrates and associated symbionts”
National and Kapodistrian University of Athens (NKUA), Greece

Research Assistant                                             02/2017-03/2017
“Bioconversion of cinnamic acid derivatives towards the production of caffeic acid using engineered monooxygenase and PPO”
TECHNION-Israel Institute of Technology

Research Assistant                                             10/2014-09/2015
SIMPLE “The Sustainable Integrated Method for the Production of Lignocellulosic Ethanol”

 Intern                                                                 09/2011-12/2011
“Development of bacterial strains for screening of rescuers for neurodegenerative diseases”
National Hellenic Research Foundation (NHRF), Athens, Greece

 Publications List

29. Pentari, C.; Kosinas, C.; Nikolaivits, E.; Dimarogona, M.; Topakas, E. Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan. Biotechnol & Bioeng. 2024
28. Makryniotis, K.;‡ Nikolaivits, E.;‡ Nikodinovic-Runic, J.; Topakas, E. Exploring the substrate spectrum of phyllogenetically distinct bacterial polyesterases. Biotechnol. J. 2024, 19,4 2400053
27. Taxeidis, G.; Djapovic, M.; Nikolaivits, E.; Maslak, V.; Nikodinovic-Runic, J.; Topakas, E. New Labeled PET Analogues Enable the Functional Screening and Characterization of PET-Degrading Enzymes. ACS Sustain. Chem. Eng. 2024, 12, 15, 5943–5952
26. Makryniotis, K.; Nikolaivits, E.*; Gkountela, C.; Vouyiouka, S.; Topakas, E. Discovery of a polyesterase from Deinococcus maricopensis and comparison to the benchmark LCCICCG suggests high potential for semi-crystalline post-consumer PET degradation. J. Hazard. Mater. 2023, 455, 131574.
25. Taxeidis, G.; Nikolaivits, E.; Siaperas, R.; Gkountela, C.; Vouyiouka, S.; Pantelic, B.; Nikodinovic-Runic, J.; Topakas, E. Triggering and identifying the polyurethane and polyethylene-degrading machinery of filamentous fungi secretomes. Environ. Pollut. 2023, 325, 121460.
24. Ferousi, C.; Kosinas, C.; Nikolaivits, E.; Topakas, E.; Dimarogona, M. Crystal structure of the Fusarium oxysporum tannase-like feruloyl esterase FaeC in complex with p-coumaric acid provides insight into ligand binding. FEBS Lett. 2023
23. Nikolaivits, E.; Taxeidis, G.; Gkountela, C.; Vouyiouka, S.; Maslak, V.; Nikodinovic-Runic, J.; Topakas, E. A polyesterase from the Antarctic bacterium Moraxella degrades highly crystalline synthetic polymers, J. Hazard. Mater. 2022, 434, 128900.
22. Attallah, O.A.; Azeem, M.; Nikolaivits, E.; Topakas, E.; Fournet, M.B. Progressing ultragreen, energy-efficient biobased depolymerization of poly(ethylene terephthalate) via microwave-assisted green deep eutectic solvent and enzymatic treatment, Polym. 2022. 14.
21. Zerva, A.; Pentari, C.; Ferousi C.; Nikolaivits E.; Karnaouri, A.; Topakas E. Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass, Technol. 2021, 342, 126058.
20. Nikolaivits, E.; Pentari, C.; Kosinas, C.; Feiler, C.; Spiliopoulou, G.; Weiss, M.S.; Dimarogona, M.; Topakas, E. Unique features of the bifunctional GH30 from Thermothelomyces thermophila revealed by structural and mutational studies. Polym. 2021, 273, 118553.
19. Nikolaivits, E.; Pantelic, B.; Azeem, M.; Taxeidis, G.; Babu, R.; Topakas, E.; Brennan Fournet, M.; Nikodinovic-Runic, J. Progressing plastics circularity: A review of mechano-biocatalytic approaches for waste plastic (re)valorization. Bioeng. Biotech. 2021, 9, 535.
18. Nikolaivits, E.; Valmas, A.; Dedes, G.; Topakas, E.; Dimarogona, M. Considerations on activity determinants of fungal polyphenol oxidases based on mutational and structural studies. Environ. Microbiol. 2021, AEM.00396-21.
17. Djapovic, M.; Milivojevic, D.; Ilic-Tomic, T.; Lješević, M.; Nikolaivits, E.; Topakas, E.; Maslak, V.; Nikodinovic-Runic, J. Synthesis and characterization of polyethylene terephthalate (PET) precursors and potential degradation products: Toxicity study and application in discovery of novel PETases. Chemosphere. 2021, 275, 130005.
16. Nikolaivits, E.; Siaperas, R.; Agrafiotis, A.; Ouazzani, J.; Gioti, A.; Topakas, E. Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus. Total Environ. 2021, 775, 145818.
15. Nikolaivits, E.; Agrafiotis, A.; Baira, E.; Le Goff, G.; Tsafantakis, N.; Chavanich, S.; Benayahu, Y.; Ouazzani, J.; Fokialakis, N.; Topakas, E. Degradation mechanism of 2,4-dichlorophenol by fungi isolated from marine invertebrates. J. Mol. Sci. 2020, 21(9), 3317.
14 Gioti, A.; Siaperas, R.; Nikolaivits, E.; Le Goff, G.; Ouazzani, J.; Kotoulas, G.; Topakas, E. Draft genome sequence of a Cladosporium species isolated from the mesophotic ascidian Didemnum maculosum. Resour. Announc., 2020, 9, e00311-20.
13. Paz, A.; Nikolaivits, E.; Topakas, E. Valorization of olive mill wastewater towards the production of L-asparaginases. Biomass Convers. Biorefin. 2020, 1-8.
12. Nikolaivits, E.; Agrafiotis, A.; Termentzi, A.; Machera, K.; Le Goff, G.; Álvarez, P.; Chavanich, S.; Benayahu, Y.; Ouazzani, J.; Fokialakis, N.; Topakas, E. Unraveling the detoxification mechanism of 2,4-dichlorophenol by marine-derived mesophotic symbiotic fungi isolated from marine invertebrates. Drugs. 2019, 17, 564.
11. Mandic, M.; Djokic, L.; Nikolaivits, E.; Prodanovic, R.; O’Connor, K.; Jeremic, S.; Topakas, E.; Nikodinovic-Runic, J. Identification and characterization of new laccase biocatalysts from Pseudomonas species suitable for degradation of synthetic textile dyes. Catalysts. 2019, 9, 629.
10. Nikolaivits, E.; Kanelli, M.; Dimarogona, M.; Topakas E. A middle-aged enzyme still in its prime: Recent advances in the field of cutinases. 2018, 8(12), 612.
9. Nikolaivits, E.; Dimarogona, M.; Karagiannaki I.; Chalima A.; Fishman A.; Topakas E. Characterization and protein engineering of a novel versatile fungal polyphenol oxidase with chlorophenol bioremediation potential. Environ. Microbiol. 2018, 84, e01628-18.
8. Nikolaivits, E.; Termentzi, A.; Skaltsounis, A.-L.; Fokialakis, N.; Topakas, E. Enzymatic tailoring of oleuropein from Olea europaea leaves and product identification by HRMS/MS spectrometry. Biotechnol. 2017, 253, 48–54.
7. Nikolaivits, E.; Makris, G.; Topakas, E. Immobilization of a cutinase from Fusarium oxysporum and application in pineapple flavor synthesis. Agric. Food Chem. 2017, 65 (17), 3505–3511.
6. Nikolaivits, E.; Dimarogona, M.; Fokialakis, N.; Topakas, E. Marine-derived biocatalysts: Importance, accessing, and application in aromatic pollutant bioremediation. Microbiol. 2017, 8, 265.
5. El-Gamal, R.; Nikolaivits, E.; Zervakis, G. I.; Abdel-Maksoud, G.; Topakas, E.; Christakopoulos, P. The use of chitosan in protecting wooden artifacts from damage by mold fungi. J. Biotechnol. 2016, 24, 70–78.
4. Nikolaivits, E.; Kokkinou, A.; Karpusas, M.; Topakas, E. Microbial host selection and periplasmic folding in Escherichia coli affect the biochemical characteristics of a cutinase from Fusarium oxysporum. Protein Expr. Purif. 2016, 127, 1–7.
3. Nikolaivits, E.; Norra, G.-F.; Voutsas, E.; Topakas, E. Cutinase from Fusarium oxysporum catalyzes the acylation of tyrosol in an aqueous medium: optimization and thermodynamic study of the reaction. Mol. Catal. B Enzym. 2016, 129, 29–36.
2. Kanelli, M.; Vasilakos, S.; Nikolaivits, E.; Ladas, S.; Christakopoulos, P.; Topakas, E. Surface modification of poly(ethylene terephthalate) (PET) fibers by a cutinase from Fusarium oxysporum. Process Biochem. 2015, 50 (11), 1885–1892.
1. Dimarogona, M.; Nikolaivits, E.; Kanelli, M.; Christakopoulos, P.; Sandgren, M.; Topakas, E. Structural and functional studies of a Fusarium oxysporum cutinase with polyethylene terephthalate modification potential. Biophys. Acta – Gen. Subj. 2015, 1850 (11), 2308–2317.

Teaching Experience

University of Verona
Department of Biotechnology
Visiting Lecturer                                                                      05/2023
“New Frontiers in Biocatalysis” Course at the Master’s Programme “Biotechnology for Bioresources and Sustainable Development”

National Technical University of Athens (NTUA)
School of Chemical Engineering-Biotechnology Laboratory
Department of Synthesis and Development of Industrial Processess
Lecturer of “Applied Biotechnology”                                   2022-present
Lab courses: Industrial Biotechnology, Environmental
Biotechnology, Food Chemistry/Microbiology/Preservation, Bioengineering
Tutoring course: Biochemical Engineering

National Technical University of Athens (NTUA)
School of Chemical Engineering-Biotechnology Laboratory
Thesis Co-Supervisor                                                               2015-present
10 Engineering Undergrads, 2 Master students, 2 PhD students

Participation in scientific workshops/courses and training schools

• “Creating and managing effective teams” – Generic and Transferable Skills Course provided by Chalmers University of Technology
• “Webinars on Fridays” organized by Hellenic National Initiative “MikroBioKosmos” (Online, 2020) – Oral presentation
• 3^rd International Meeting of the Hellenic Crystallographic Association’s Young Researchers (Patras, Greece 2019) – Oral presentation
• Diffraction Data Collection Using Synchrotron Radiation Workshop by the German Crystallographic Society – DGK-AK1 (Berlin, Germany 2019) – Oral presentation
• COST Action “Systems Biocatalysis” Training School (Siena, Italy 2016) – Oral presentation

Reviewer at Selected Peer-Reviewed Journals

• Environmental Pollutants and Bioavailability – Taylor & Francis (IF 3.3)

• World Journal of Microbiology and Biotechnology – Springer (IF 4.3)

• Catalysts (Reviewer Board Member) – MDPI Publishing (IF 4.5)

• Process Biochemistry – Elsevier (IF 4.9)

• Microorganisms – MDPI Publishing (IF 4.9)

• Molecules – MDPI Publishing (IF 4.9)

• Applied and Environmental Microbiology – ASM Journals (IF 5.0)

• Molecular Catalysis – Elsevier (IF 5.1)

• Food and Bioproducts Processing – Elsevier (IF 5.1)

• Frontiers in Chemistry – Frontiers (IF 5.6)

• Journal of Fungi – MDPI Publishing (IF 5.7)

• Biomolecules – MDPI Publishing (IF 6.1)

• Frontiers in Bioengineering and Biotechnology – Frontiers (6.1)

• Computational and Structural Biotechnology Journal – Elsevier (IF 6.2)

• International Journal of Molecular Sciences – MDPI Publishing (IF 6.2)

• Food & Function – Royal Society of Chemistry (IF 6.3)

• Science of the Total Environment – Elsevier (IF 9.8)

• Journal of Cleaner Production – Elsevier (IF 11.1)

• Environmental Science & Technology – ACS Publication (IF 11.4)

• Journal of Hazardous Materials – Elsevier (IF 13.6)

• Chemical Engineering Journal – Elsevier (IF 15.1)

• Biotechnology Advances – Elsevier (IF 16)