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

    Finland

  • PL 56 (Viikinkaari 9)

    00014

    Finland

Accepting PhD Students

20002022
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Personal profile

Description of research and teaching

I am Principal Investigator and Academy of Finland Research Fellow in the Fungal Genetics and Biotechnology group that studies plant biomass modifying enzymes from asco- and basidiomycete fungi. The research focuses on various aspects of fungal molecular biology and enzymology. Lignocellulose, particularly lignin, degradation has been the long-term interest at the Department of Microbiology. Our research has provided strong international contribution in the field of fungal and enzymatic degradation of lignin and lignocellulose.

The most recent research addresses the molecular level regulation of the plant biomass degradation process in basidiomycete fungi as well as valorization of lignin-rich industrial waste of second generation biofuel plants to higher value products.

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 and fungal carbon metabolism

ii) Elucidating the difference in plant biomass strategies between ascomycetes and basidiomycetes

iii) Heterologous production of novel catalysts for lignin valorisation

 

Current projects:

  1. Exploring the regulatory system that controls plant biomass degradation in basidiomycete white rot fungi (ESCaPADE), Academy of Finland (2017-2022)
  2. Fuel and chemicals from lignin through enzymatic and chemical conversion (FALCON) EU-H2020 (2017-2020)
  3. Experimental validation of a central carbon metabolic models in Aspergillus niger to enable metabolic engineering of this fungal cell factory, Environmental Molecular Sciences Laboratory (EMSL), USA (2018-2019)
  4. 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, Joint Genome Institute (JGI-DOE)-EMSL, USA (2018-2020)
  5. Dissecting intraspecies diversity in fungal wood decay, JGI-DOE-EMSL, USA (2015-2019)
  6. Enzymes for selective cleavage of lignin (Ph.D. project of Mila Marinović)

Previous projects:

  1. Colony plasticity of filamentous fungi, EMSL, USA (2016-2017)
  2. Optimized esterase biocatalysts for cost-effective industrial production (OPTIBIOCAT) EU-FP7, KBBE-.2013.3.3-04, (2013-2017)
  3. Sustainable biomass conversions by highly efficient catalytic processes (SuBiCat) EU-FP7, Marie Curie-ITN, (2013-2017)
  4. Test centers for green energy solutions - Biorefineries and business needs, Norcid Council of Ministers (2014-2015)
  5. Plant biomass degradation in Dichomitus squalens (Ph.D. project of Sara Casado López)
  6. Plant biomass modifying enzymes of ascomycete fungi  (Ph.D. project of Sadegh Mansouri)
  7. Basidiomycete cellulolytic enzymes and their applications (Ph.D. project of Johanna Rytioja)
  8. How mushrooms feed on sugars (Ph.D. project of Aleksandrina Patyshakuliyeva)

International collaboration:

  • Concordia University, Montreal, Canada: Dissection of strategies for plant biomass degradation by Dichomitus squalens. Project members: Miia Mäkelä (PI), Adrian Tsang (PI), Kristiina Hildén (PI), Ronald de Vries (PI)
  • Joint Genome Institute, USA: Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology. www.eufgen.org
  • Joint Genome Institute, USA: Comparative analysis of 3 Pycnoporus species: P. sanguineus, P. coccineus and P. cinnabarinus.

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, MBDP-302 & MMB-120)

Bachelor courses (in Finnish): Basics in microbiology (MOLE212C), Fungal biology (MMB-701, 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.

Education/Academic qualification

Microbiology, Docent, University of Helsinki

External positions

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

1 Oct 201631 Mar 2017

Keywords

  • 1183 Plant biology, microbiology, virology
  • fungal physiology
  • genetics
  • genomics
  • transcriptomics
  • proteomics
  • mycology
  • plant biomass
  • biotechnology
  • applied microbiology

International and National Collaboration Publications and projects within past five years.

Publications 2000 2019

Plant-polysaccharide-degrading enzymes from basidiomycetes

Rytioja, J., Hilden, K., Yuzon, J., Hatakka, A., de Vries, R. & Mäkelä, M., 2014, In : Microbiology and Molecular Biology Reviews. 78, 4, p. 573-587 15 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

Degradation and Modification of Plant Biomass by Fungi

Mäkelä, M., Hilden, K. & de Vries, R., 2014, Fungal genomics. Nowrousian, M. (ed.). 2nd ed. ed. Heidelberg: Springer-Verlag, p. 175-208 34 p. (The Mycota : A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research; no. 13).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Oxalate-Metabolising Genes of the White-Rot Fungus Dichomitus squalens Are Differentially Induced on Wood and at High Proton Concentration

Makela, M. R., Sietiö, O-M., de Vries, R. P., Timonen, S. & Hilden, K., 5 Feb 2014, In : PLoS One. 9, 2, 11 p., 87959.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Projects 2011 2022

Prizes

Best Poster Award

Miia Mäkelä (Recipient), 1 Sep 2018

Prize: Prizes and awards

Activities 2001 2019

Fungal Genetics and Biology (Journal)

Miia Mäkelä (Editor)
20132014

Activity: Publication peer-review and editorial work typesEditor of special theme number

27th Fungal Genetics Conference

Miia Mäkelä (Speaker: Presenter)
12 Mar 201317 Mar 2013

Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

30th Fungal Genetics Conference

Miia Mäkelä (Poster review committee)
2019 → …

Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

Nature Chemical Biology (Journal)

Miia Mäkelä (Reviewer)
2019

Activity: Publication peer-review and editorial work typesPeer review of manuscripts

30th Fungal Genetics Conference

Miia Mäkelä (Speaker: Chair)
2019 → …

Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars