Description of research and teaching

My research group addresses plant biomass degradation and modification by filamentous fungi. We focus on various aspects of fungal physiology, molecular genetics and enzymology with the aim to provide sustainable biotechnology solutions. Our research has provided strong international contribution in the field of fungal and enzymatic degradation of lignocellulosic biomass.

One of my recent research interests is sugar transport in filamentous fungi, which is studied in my Novo Nordisk Foundation Ascending Investigator project MYCOFACT.

In addition, my research topics include:

• Molecular level regulation of plant biomass conversion in basidiomycete fungi
• Development of genome editing tools in basidiomycete fungi
• Elucidation of fungal carbon and aromatic metabolism
• Genome mining and characterization of novel plant biomass modifying activities for biomass valorization

Fellowships:

• HiLIFE Fellow (2023-2025)
• Novo Nordisk Foundation Ascending Investigator (2021-2026)
• Academy of Finland Research Fellow (2017-2022)

Current projects:

1. HiLIFE fellowship and grant (2023-2025)
2. Intracellular metabolism of lignocellulose-derived sugars and aromatic compounds in wood-degrading white rot fungi (METAFUNG), Academy of Finland (2022-2026)
3. EDIBLE - Better bound than free: Enzymatic coupling of dietary fibres and polyphenols towards novel multifunctional food ingredients, Novo Nordisk Foundation (2022-2024)
4. The dual role of sugar transporters in plant biomass conversion by fungi to improve microbial cell factories (MYCOFACT), Novo Nordisk Foundation (2021-2026)
5. Exploring the regulatory system that controls plant biomass degradation in basidiomycete white rot fungi (ESCaPADE), Academy of Finland (2017-2022)
6. 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)
7. Facilitating reliable CAZyme function prediction of fungal enzymes from expanded and poorly characterized families, JGI-DOE, USA (2020-2021)
8. Dissecting the central metabolic network of Aspergillus niger during growth on plant biomass, Environmental Molecular Sciences Laboratory (EMSL), USA (2019-2020)
9. 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)

Previous projects:

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

Current team members:

• Christina Lyra, university researcher
• Xing Wan, postdoctoral researcher
• Hatice Böke, postdoctoral researcher
• Victor Gonzalez, doctoral researcher
• Dongming Zhang, doctoral researcher
• Liinu Nummela, doctoral researcher
• Ellisiv Nyhamar, technical assistant
• Joseph Kelleher, MSc student
• Aino-Elina Kuusimäki, MSc student
• Katrine Hansen, MSc student
• Tila Flach, research assistant

Previous team members:

• Joanna Kowalczyk, postdoctoral researcher
• Shreya Saha, postdoctoral researcher
• Cristina Peral, visiting researcher
• Andrés Correa, research assistant
• Alejandro Murphy, MSc student
• Franziska Beck, MSc student
• 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)
• Randy Silva, visiting student (Universidad de las Américas Puebla, Mexico)

Main collaborators:

• Prof. Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands: Comparison of basidiomycete and ascomycete approaches for plant biomass conversion
• Assoc. Prof. Robert Mans, Technical University of Delft, The Netherlands: Functional characterization of sugar transporters
• Prof. Jack Pronk, Tehcnical University of Delft, The Netherlands: Functional characterization of sugar transporters
• Assoc. Prof. Francisco Vilaplana, KTH Royal Institute of Technology, Sweden: Development of functional food ingredients
• Prof. Adrian Tsang, Concordia University, Montreal, Canada: Dissection of strategies for plant biomass degradation by Dichomitus squalens
• Prof. Uffe H. Mortensen, Technical University of Denmark: Optimization of CRISPR/Cas9 methodology and fungal fermentations
• Assoc. Prof. Mirjam Kabel, Wageningen University & Research, The Netherlands: Molecular analyses of carbohydrates and lignin
• Prof. Levente Karaffa, University of Debrecen, Hungary: Filamentous fungal fermentations
• Prof. Jouko Vepsäläinen, University of Eastern Finland: NMR analysis of metabolites

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-).