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University of Helsinki Institute of Biotechnology
Institute of Biotechnology
DNA Sequencing and Genomics

Research Director:
Petri Auvinen
Tel +358 (0) 2941 58902
e-mail petri.auvinen -at-

Laboratory Engineer:
Lars Paulin
Tel +358 (0) 2941 58887
e-mail lars.paulin -at-

Viikinkaari 5D
(Biocenter 2, 4th floor)
P.O.Box 56
FIN-00014 University of Helsinki

Tel +358 (0) 2941 58884

Sequencing service e-mail:
bio-alf -at-

Institute of Biotechnology
Street address: Viikinkaari 5D (P.O.Box 56)
00014 University of Helsinki
Tel: +358 (0) 294 1911
Tel: +358 (0) 2941 4482624

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Molecular analysis of indoor fungi

PhD thesis project / Miia Pitkäranta

Today, increasing attention and concern is addressed to low indoor air quality of living and working environments. The problems often originate from inappropriate microbial or “mold” growth in the building constructions. My thesis work focuses on the fungi in moisture damaged buildings, and more specifically, on developing new, better methods for identification of these fungi.

It is estimated that 55% of the Finnish buildings suffer from moisture damages that require reparation or are in need of more careful investigations. Several epidemiological studies connect moisture and mold findings to a range of health symptoms, varying from upper airway irritation to increased incidence of respiratory infections and asthma.

To be able to study the relationships between different fungal species present in compromised buildings and the health effects potentially caused by these microbes, it is essential that we can analyse the exposure as carefully as possible. For the time being, plate cultivation remains the golden standard method for determination of the microbial status of a building. Yet for the inherent limitations of cultivation based methods, alternatives are being seeked, and DNA-based methods are considered a probabilistic choice.

In collaboration with the Laboratory of Environmental Microbiology of National Health Institute (KTL) led by Prof. Aino Nevalainen, we have already characterized the diversity and seasonal variation of fungi in sample buildings using large scale rDNA library sequencing. Present study efforts concentrate on observing the effects of moisture renovations on the fungal flora. In the future, the obtained sequence information will be utilized in construction of a microbial diagnostic microarray tool for indoor environments. For this and other applications, an LDR-based microarray setup is currently being developed and tested together with the DNA microarray laboratory of Institute of Biotechnology (see also BioFINE chip and Compost Chip).



  • PhD Helena Rintala, National Public Health Institute, Department of Environmental Health
  • Dos., group leader Petri Auvinen, University of Helsinki, Institute on Biotechnology, DNA-microchip laboratory
  • Prof. Martin Romantschuk, University of Helsinki, Department of Environmental Ecology.





Scientific papers:

  • Pitkäranta Miia, Meklin Teija, Hyvärinen Anne, Paulin Lars, Auvinen Petri, Nevalainen Aino, Rintala Helena. 2008. Analysis of Fungal Flora in Indoor Dust by Ribosomal DNA Sequence Analysis, Quantitative PCR, and Culture. Appl. Environ. Microbiol. 84(1).
  • Pitkäranta Miia, Meklin Teija, Hyvärinen Anne, Paulin Lars, Nevalainen Aino, Hänninen Marja, Auvinen Petri, Rintala Helena. Effect of moisture renovations on i ndoor fungal flora observed by molecular and cultivation methods. Manuscript in preparation.
  • Hultman Jenni, Pitkäranta Miia, Romantschuk Martin, Auvinen Petri, Paulin Lars. Efficient hybridisation method for enrichment of clone libraries. Submitted.
  • H. Rintala, M. Pitkäranta, L. Paulin, M. Toivola, A. Nevalainen. Diversity and seasonal dynamics of bacterial community in indoor environment. Accepted for publication in BMC Microbiology.

Conference proceedings:

  • Pitkäranta Miia , Helena Rintala, Lars Paulin. Characterization of fungal flora from moisture damaged building material by molecular methods. 2005. Extended peer-reviewed abstract. In Johanning, E. (Ed), Proceedings of the 5th International Conference on Bioaerosols, Fungi, Bacteria, Mycotoxins and Human Health. Boyd Printing company Inc., Albany, NY, USA.