• PL 56 (Viikinkaari 9)

    00014

    Finland

  • Department of Microbiology
    PL 56 (Viikinkaari 9)
    Biocenter 1
    00014
    Helsingin yliopisto

    Finland

20002022

Research activity per year

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Personal profile

Description of research and teaching

I am Academy of Finland Research Fellow and Novo Nordisk Foundation Ascending Investigator addressing fungal degradation and modification of plant biomass. The research focuses on various aspects of fungal physiology, molecular genetics and enzymology, and aims to provide sustainable biotechnology solutions. Our research has provided strong international contribution in the field of fungal and enzymatic degradation of lignocellulosic biomass.

My recent research interests are sugar transport in filamentous fungi, molecular level regulation of plant biomass conversion in basidiomycete fungi as well as development of genome editing tools for basidiomycete fungi.

In addition, our research topics include functional genomics of plant biomass degrading fungi from various biotopes with different and complementary points of view:

i) Genome mining and characterization of novel plant biomass modifying activities for biomass valorization

ii) Elucidation of fungal carbon and aromatic metabolism

iii) Comparative (post-)genomic studies on plant biomass conversion strategies between asco- and basidiomycete fungi

Current projects:

  • Intracellular metabolism of lignocellulose-derived sugars and aromatic compounds in wood-degrading white rot fungi (METAFUNG), Academy of Finland (2022-2026)
  • EDIBLE - Better bound than free: Enzymatic coupling of dietary fibres and polyphenols towards novel multifunctional food ingredients, Novo Nordisk Foundation (2022-2024)
  • The dual role of sugar transporters in plant biomass conversion by fungi to improve microbial cell factories (MYCOFACT), Novo Nordisk Foundation (2021-2026)
  • Exploring the regulatory system that controls plant biomass degradation in basidiomycete white rot fungi (ESCaPADE), Academy of Finland (2017-2022)
  • Mining the unknown part of fungal genomes by combining machine learning with multi-omics and functional characterization, Joint Genome Institute (JGI-DOE), USA (2021-2022)
  • Facilitating reliable CAZyme function prediction of fungal enzymes from expanded and poorly characterized families, JGI-DOE, USA (2020-2021)
  • Dissecting the central metabolic network of Aspergillus niger during growth on plant biomass, Environmental Molecular Sciences Laboratory (EMSL), USA (2019-2020)
  • Validation of metabolic models, extrapolated from the reference sugar catabolism genetic network of Aspergillus niger by using an orthology-based approach, of evolutionarily diverse fungi, JGI-DOE-EMSL, USA (2018-2020)
  • Enzymes for selective cleavage of lignin (Ph.D. project of Mila Marinović)

Previous projects:

  • Fuel and chemicals from lignin through enzymatic and chemical conversion (FALCON) EU-H2020 (2017-2020)
  • Colony plasticity of filamentous fungi, EMSL, USA (2016-2017)
  • Experimental validation of a central carbon metabolic models in Aspergillus niger to enable metabolic engineering of this fungal cell factory, EMSL, USA (2018-2019)
  • Dissecting intraspecies diversity in fungal wood decay, JGI-DOE-EMSL, USA (2015-2019)
  • Optimized esterase biocatalysts for cost-effective industrial production (OPTIBIOCAT) EU-FP7, KBBE-.2013.3.3-04, (2013-2017)
  • Sustainable biomass conversions by highly efficient catalytic processes (SuBiCat) EU-FP7, Marie Curie-ITN, (2013-2017)
  • Test centers for green energy solutions - Biorefineries and business needs, Norcid Council of Ministers (2014-2015)
  • Plant biomass degradation in Dichomitus squalens (Ph.D. project of Sara Casado López)
  • Plant biomass modifying enzymes of ascomycete fungi (Ph.D. project of Sadegh Mansouri)
  • Basidiomycete cellulolytic enzymes and their applications (Ph.D. project of Johanna Rytioja)
  • How mushrooms feed on sugars (Ph.D. project of Aleksandrina Patyshakuliyeva)

Current team members:

  • Christina Lyra, university researcher
  • Xing Wan, postdoctoral researcher
  • Victor Gonzalez, doctoral researcher
  • Dongming Zhang, doctoral researcher
  • Hatice Böke, visiting postdoctoral researcher
  • Ellisiv Nyhamar, technical assistant
  • Andrés Correa, Erasmus student (Universidad de Léon, Spain)
  • Randy Silva, visiting student (Universidad de las Américas Puebla, Mexico)

Previous team members:

  • Joanna Kowalczyk, postdoctoral researcher
  • Shreya Saha, postdoctoral researcher
  • Cristina Peral, visiting researcher
  • Frederik Labonté, MSc student (University of Cologne, Germany)
  • Maxine Parmentier, MSc student (University of Reims, France)
  • Alisa Shubina, BSc student (HAN University of Applied Sciences, The Netherlands)
  • Astrid Müller, MSc student (Brandenburg University of Technology Cottbus-Senftenberg, Germany)
  • Viviany Viriato, MSc student (São Paulo State University, Brazil)

Main collaborators:

  • Prof. Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
  • Assoc. Prof. Robert Mans, Technical University of Delft, The Netherlands
  • Prof. Jack Pronk, Tehcnical University of Delft, The Netherlands
  • Assoc. Prof. Francisco Vilaplana, KTH Royal Institute of Technology, Sweden
  • Prof. Adrian Tsang, Concordia University, Montreal, Canada
  • Prof. Uffe H. Mortensen, Technical University of Denmark
  • Assoc. Prof. Mirjam Kabel, Wageningen University & Research, The Netherlands
  • Prof. Levente Karaffa, University of Debrecen, Hungary
  • Prof. Jouko Vepsäläinen, University of Eastern Finland

Teaching:

I am involved in the teaching of bachelor, master and doctoral students in lectures and laboratory courses in microbiology, biotechnology and mycology. I also supervise BSc, MSc and doctoral theses.

Organizer of Microbiology seminars (MBDP doctoral programme, MBDP302)

Bachelor courses (in Finnish): Basics in microbiology (MOLE212C), Fungal biology (MMB701, MYKO251), Microbial biotechnology (YBIOT315)

Master courses (in English): Advanced methods in microbiology (MIKRO510), Production of recombinant proteins (YBIOT565), Fungal biotechnology research methods (MYKO540), Forest microbiology and biotechnology (YBIOT570), Advanced laboratory training at research group (BIOT422)

Collaborator in PhD programme "Criticat CDT" which is a comprehensive and state-of-the-art PhD training programme in catalytic science funded by the UK funding agency EPSRC. PhD programme (2014 - 2022) is hosted by the Universities of St. Andrews, Edinburgh and Heriot-Watt.

Collaborator in the Print Capes-UFV program of the Federal University of Viçosa, Brazil (2019-).

Education/Academic qualification

Microbiology, Docent, University of Helsinki

Award Date: 23 Jan 2017

External positions

Research Scientist, Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht

1 Oct 201631 Mar 2017

Fields of Science

  • 11832 Microbiology and virology
  • Microbial biotechnology
  • Fungal physiology
  • Genetics
  • Omics
  • Plant biomass
  • Mycology

International and National Collaboration

Publications and projects within past five years.