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  1. Article

    Open Access

    Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae

    Secretion stress is caused by compromised folding, modification or transport of proteins in the secretory pathway. In fungi, induction of genes in response to secretion stress is mediated mainly by the unfolde...

    Mikko Arvas, Tiina Pakula, Karin Lanthaler, Markku Saloheimo, Mari Valkonen in BMC Genomics (2006)

  2. Article

    Open Access

    Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei

    Chemostat cultures are commonly used in production of cellular material for systems-wide biological studies. We have used the novel TRAC (transcript analysis with aid of affinity capture) method to study expre...

    Jari J Rautio, Bart A Smit, Marilyn Wiebe, Merja Penttilä, Markku Saloheimo in BMC Genomics (2006)

  3. Article

    Open Access

    Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions

    It has become evident that host cells react to recombinant protein production with a variety of metabolic and intrinsic stresses such as the unfolded protein response (UPR) pathway. Additionally, environmental...

    Brigitte Gasser, Michael Maurer, Jari Rautio, Michael Sauer in BMC Genomics (2007)

  4. Article

    Open Access

    Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina

    Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail...

    Mikko Arvas, Teemu Kivioja, Alex Mitchell, Markku Saloheimo, David Ussery in BMC Genomics (2007)

  5. Article

    Open Access

    Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties

    Trichoderma reesei is the main industrial producer of cellulases and hemicellulases that are used to depolymerize biomass in a variety of biotechnical applications. Many of the production strains currently in use...

    Marika Vitikainen, Mikko Arvas, Tiina Pakula, Merja Oja, Merja Penttilä in BMC Genomics (2010)

  6. Article

    Open Access

    Correlation of gene expression and protein production rate - a system wide study

    Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Sac...

    Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen in BMC Genomics (2011)