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PYFF6 Secretariat
Department of Bioengineering
Instituto Superior Técnico
University of Lisbon
Avenida Rovisco Pais, 1
1049-001 Lisboa

Tel: +351 21 841 9181
Fax: +351 21 841 9199

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Monday, July 11th 2016



Welcome Address

Arlindo L Oliveira (President of Instituto Superior Técnico (IST), ULisboa)

Joaquim S Cabral (Director of Institute for Bioengineering and Biosciences (iBB))

Isabel Sá-Correia(Chair of the Scientific and Organizing Committees of PYFF6)


(Chair: Pascale Daran-Lapujade, Industrial Microbiology, TUDelft, The Netherlands)


11:30 - Building synthetic chromosomes from scratch
Jef D. Boeke (NYU Langone Medical Center, New York, USA)

12:30 - LUNCH

14:00 - SESSION I: Tailoring Physiology: Metabolic Engineering of Yeasts and Filamentous Fungi

(Chairs: Elke Nevoigt, Jacobs University Bremen gGmbH, Germany; Lucília Domingues, CEB, University of Minho, Braga Portugal)

Keynote Presentations

14:00 - Yeast cell factories for production of bulk and fine chemicals
Irina Borodina (DTU BIOSUSTAIN Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark)

14:25 - Reprogramming filamentous fungal cells: tools and applications
Marco van den Berg; (DSM Biotechnology Centre, Delft, The Netherlands)

Selected Presentations

14:50 - Engineering fungal microbes for D-galacturonic acid catabolism
Peter Richard, Jasmin Wang, Alessandra Biz, Merja Penttilä, Joosu Kuivanen (VTT Technical Research Centre of Finland Ltd.)

15:03 - Expression of a disassociated fatty acid synthase system (FAS type II) in Saccharomyces cerevisiae
Flávio de Azevedo, Björn Johansson (CBMA – Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal)

15:16 - Oleaginous yeasts as a platform for the production of biofuel and chemicals
Stéphane Guillouet1, Rana Sagnak1, Julie Bornot1, Xavier Cameleyre1, Nathalie Gorret1, Jean-Marc Nicaud2, Florence Bordes1, Alain Marty1, Carole Molina-Jouve11 (1LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France; 2Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France)

15:30 - SESSION II - Systems and Synthetic Biology of Yeasts and Filamentous Fungi

(Chairs: Verena Siewers, Chalmers University of Technology, Sweden; Peter Richard, VTT Technical Research Centre of Finland Ltd., Finland)

Keynote Presentations

15:30 - Pathway swapping: a new approach to simply and efficiently remodel essential native cellular function
Pascale Daran-Lapujade (Department of Biotechnology / Industrial Microbiology, TUDelft, The Netherlands)

15:55 - Tools for genome-editing and expression in filamentous fungi
Merja Penttilä (VTT Technical Research Centre of Finland, Finland)

Selected Presentations

16:20 - Marker-free CRISPR/Cas9 based genome editing of Penicillium chrysogenum
Carsten Pohl1, Jan A.K. Kiel1, Arnold J.M. Driessen1, Roel A.J. Bovenberg2, Yvonne Nygård1,2 (1University of Groningen, Groningen,The Netherlands; 2Biotechnology Centre, Delft, The Netherlands)

16:33 - Metabolite biosensors for yeast metabolic engineering
Florian David, Jens Nielsen, Verena Siewers (Chalmers University of Technology)

16:46 - Systems biology of Yarrowia lipolytica under nitrogen limitation
Scott E. Baker (Pacific Northwest National Laboratory)



17:30 - Marie Sklodowska-Curie Workshop in Engineering Yeast and Fungi for Cell Factory Applications

(Chairs: John Morrissey, University College Cork, Ireland; Vera Meyer, Department of Applied and Molecular Microbiology, TU Berlin, Germany)

Selected Presentations

17:30 - Towards the discovery of secondary metabolite gene clusters in novel marine fungi
Pradeep Phule, Frank Kempken (Abt. Genetische Botanik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian Albrecht's University, Kiel, Germany)

17:40 - Completely resolved genome assembly of a hybrid Zygosaccharomyces using PacBio sequencing
Raúl A. Ortiz-Merino1, Nurzhan Kuanyshev2, Paola Branduardi2, Kenneth H. Wolfe1 (1University College Dublin; 2Università degli Studi di Milano-Bicocca)

17:50 - Metabolic network reconstruction of Penicillium species, a way to study secondary metabolism globally
Sylvain Prigent, Jens Christian Nielsen, Jens Nielsen (Sysbio, Department of Chemical and Biological Engineering, Chalmers University of Technology)

18:00 - Improving maltotriose fermentation kinetics of Saccharomyces pastorianus through evolutionary engineering
Anja Brickwedde1, Geertman JMA2, Kuijpers NGA2, Gibson B3, Vidgren V3, Magalhães F3, Pronk JT1, Daran JM1 (1Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; 2Heineken Supply Chain, Global Research & Development, 2382 PH Zoeterwoude; 3VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, 02044 Espoo, Finland)

18:10 - Optimization of polyketide production in filamentous fungi
Milica Randelovic, P.B. Knudsen, M. WorkmanMilica Randelovic, P.B. Knudsen, M. Workman (DTU Systems Biology, Technical University of Denmark, Søltofts Plads 223, 2800 Kgs. Lyngby, Denmark)

18:20 - Deciphering the Genetic and Metabolic Bases of Yeast Aroma Properties
Matthias Eder, Isabelle Sanchez, Peggy Rigou, Thibault Nidelet, Carole Camarasa, Jean-Luc Legras, Sylvie Dequin (INRA Montpellier)

18:30 - Cider fermentation with newly-generated Saccharomyces cerevisiae x Saccharomyces eubayanus hybrids
Frederico Magalhães1, Kristoffer Krogerus1, Laura Ruohonen1, Mari Sandell2, Brian Gibson1 (1VTT Technical Research Centre of Finland; 2University of Turku, Functional Foods Forum)

18:40 - Yeast-killing-yeast: molecular characterization of predacious Saccharomycopsis species
Klara Junker, Jürgen Wendland (Carlsberg Laboratory, Copenhagen, Denmark)


Tuesday, July 12th 2016

9:00 - SESSION III - Physiological Genomics of Yeasts and Filamentous Fungi

(Chairs: Gustavo Goldman, Universidade de São Paulo, São Paulo, Brasil; Agustin Aranda, IATA-CSIC, Valencia, Spain)

Keynote Presentations

9:00 - Genome mining and activation of silent fungal natural product gene clusters by microbial communication: Reprogramming of fungi by bacteria
Axel Brakhage (Dept. Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany)

9:25 - Yeast genomics for understanding physiological diversity and adaptation to anthropic niches
Sylvie Dequin; (UMR Sciences pour l'œnologie)

Selected Presentations

9:50 - Highly flexible carbon metabolism of filamentous fungi as revealed by (post-)genomic analysis
Ronald P. de Vries (Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands; Department of Food and Environmental Sciences, University of Helsinki, Finland)

10:03 - Phosphoproteomic analysis of early adaptive yeast response to acetic acid reveals the involvement of lipid biosynthetic pathways, in particular of sphingolipids
Joana F. Guerreiro1, Nuno P. Mira1, Aline X.S. Santos2, Howard Riezman2, Isabel Sá-Correia1 (1iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; 2Department of Biochemistry, University of Geneva, Geneva, Switzerland)

10:16 - Sch9 kinase and Gcn4 transcription factor control glycerol production and longevity during winemaking
Beatriz Vallejo1, Helena Orozco1, Cecilia Picazo1, Emilia Matallana1, Agustin Aranda2 (1University of Valencia; 2Institute of Agrochemistry and Food Technology IATA-CSIC)


SESSION IV - Evolution in the Lab and in Nature

(Chairs: Ronald P. de Vries, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, The Netherlands; Z. Petek Çakar, Istanbul Technical University, Turkey)

Keynote Presentations

11:00 - Genome evolution in deep-branching ascomycete yeasts
Kenneth Wolfe (UCD Conway Institute, School of Medicine & Medical Science, University College Dublin, Ireland)

11:25 - Pathogen evolution following host jump
Sophien Kamoun; (The Sainsbury Laboratory, Norwich Research Park, United Kingdom)

Selected Presentations

11:50 - A new laboratory evolution approach to select for constitutive acetic-acid tolerance in Saccharomyces cerevisiae and identification of causal mutations
Daniel González-Ramos1, Arthur R. Gorter de Vries1, Sietske Grijseels1, Margo van Berkum1, Steve Swinnen2, Marcel van den Broek1, Elke Nevoigt2, Jean Marc G. Daran1, Jack T. Pronk1, Antonius J.A. van Maris1 (1TU Delft; 2Jacobs University Bremen)

12:03 - Evolutionary engineering of ethanol-tolerant Saccharomyces cerevisiae triggers diploidization of haploid cells
Z. Petek Cakar1,2, Burcu Turanli-Yildiz1,2, Laurent Benbadis3,4,5, Ceren Alkim1,2,3,4,5, Tugba Sezgin1,2, Arman Aksit1,2, Abdulmecit Gokce1,2,6, Yavuz Ozturk6, A. Tarik Baykal6, Jean M. François3,4,5 (1Department of Molecular Biology & Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey; 2Istanbul Technical University, Dr. Orhan Ocalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul, Turkey; 3Universite de Toulouse INSA UPS INP LISBP, Toulouse, France; 4INRA-UMR792, Ingenierie des Systemes Biologiques & des Bioprocedes, Toulouse, France ; 5CNRS, UMR5504, Toulouse, France; 6TUBITAK Research Institute for Genetic Engineering and Biotechnology, Kocaeli, Turkey)

12:16 - Functional and evolutionary analysis of the Zygosaccharomyces bailii ortholog of Saccharomyces cerevisiae Haa1 suggest its subfunctionalization in post-whole genome duplication species
Margarida Palma, Paulo J. Dias, Laura Luzia, Joana F. Guerreiro, Filipa C. Roque, Isabel Sá-Correia (iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal)

12:30 - LUNCH

14:00 - POSTER SESSION (odd numbered posters)

15:30 - SESSION V: Single Cell Physiology and Cellular Heterogeneity

(Chairs: Zdena Palkova, Charles University, Prague, Czech Republic; Scott Baker, Pacific Northwest National Laboratory, USA)

Keynote Presentations

15:30 - Inter-zonal, inter-hyphal and inter-compartmental heterogeneity in the fungal mycelium
Han Wösten (Faculty of Science, Utrecht University The Netherlands)

15:55 - I remember what you ate last summer - Memory in yeast metabolic regulation
Kevin J. Verstrepen (Lab for Genetics and Genomics, University of Leuven, and Lab for Systems Biology, VIB, Belgium)

Selected Presentations

16:20 - Heterokaryosis in the arbuscular mycorrhizal fungus Rhizophagus irregularis
Jeanne Ropars1, Kinga Sedzielewska Toro2, Andreas Brachmann2, Nicolas Corradi1 (1Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada; 2 LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany)

16:33 - Impact of oscillating oxygen and substrate availability on the sterol and main carbon metabolism in Saccharomyces cerevisiae scale-down cultivations
Anna Maria Marbà-Ardébol, Stefan Junne, Peter Neubauer (Technische Universität Berlin, Germany)

16:46 - Dynamics of metabolic and physiological responses of Yarrowia lipolytica to well-controlled pH and oxygen perturbations in batch and continuous operating modes
Timoumi A1, Cleret M1, Allouche Y2, Molina-Jouve C1, Gorret N1 (1LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France; 2Airbus Operations S.A.S, 316 Route de Bayonne, 31060 Toulouse, France)


WORKSHOP: Starting New Companies in Yeast and Fungal Biotechnology

(Organized and Chaired by: Jack Pronk, TUDelft, The Netherlands; Kevin Verstrepen, Lab for Genetics and Genomics, University of Leuven, and Lab for Systems Biology, VIB, Belgium)

Keynote Presentations

17:30 - Yeast: from research to start up
Dirk Iserentant (VIB, Flanders, Belgium)

18:00 - Personal Experiences
Elsa Berends (BasidioFactory, Utrecht, The Netherlands)

18:30 - In silico metabolic engineering: from research to the market
Isabel Rocha (SilicoLife, and CBE, University of Minho, Braga, Portugal)

Wednesday, July 13th 2016

9:00 - SESSION VI: High Throughput Physiology

(Chairs: Pau Ferrer, Universitat Autònoma de Barcelona, Spain; Jean-Luc Parrou, Université Fédérale de Toulouse, CNRS, INRA, INSA, Toulouse, France)

Keynote Presentations

09:00 - Polygenic analysis of stress tolerance and metabolic traits for development of superior industrial yeast strains
Johan Thevelein (VIB Department of Molecular Microbiology, KU Leuven, Belgium)

09:25 - Robots and Formal Models for Yeast Systems Biology
Steve Oliver (Cambridge Systems Biology Center, University of Cambridge, Cambridge, United Kingdom)

Selected Presentations

09:50 - Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae
Steve Swinnen1, Ping-Wei Ho2, Mathias Klein2, Elke Nevoigt2 (1GlobalYeast; 2Jacobs University Bremen gGmbH)

10:03 - Benchmarking P. pastoris genome-scale metabolic model iMT1026 for growth on methanol or glycerol as sole carbon sources
Màrius Tomàs-Gamisans, Pau Ferrer, Joan Albiol (Department of Chemical, Biological and Environmental Engineering. Universitat Autònoma de Barcelona)

10:16 - Systems-level organization of yeast methylotrophic lifestyle: The xylulose-monophosphate cycle of methanol assimilation utilizes a duplicated methanol inducible enzyme set and is entirely localized to peroxisomes
Hannes Rußmayer1,2§, Markus Buchetics1,2§, Clemens Gruber2,3, Minoska Valli1,2, Karlheinz Grillitsch2,4, Gerda Modarres2,5, Hedda Drexler2,3, Matthias Steiger1,2, Günther Daum2,4, Alexandra B. Graf2,5, Friedrich Altmann2,3, Stephan Hann2,3, Michael Sauer1,2, Diethard Mattanovich1,2, Brigitte Gasser1,2 (1Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Austria; 2Austrian Centre of Industrial Biotechnology; 3Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, Austria; 4Institute of Biochemistry, Graz University of Technology, Austria; 5School of Bioengineering, University of Applied Sciences FH Campus Vienna. §equally contributing authors)


SESSION VII: Response and Tolerance to Stress

(Chairs: Cristina Silva Pereira, ITQB, UNL, Oeiras, Portugal; Paola Branduardi, Università degli Studi di Milano, Italy)

Keynote Presentations

11:00 - Trehalose-6P synthase encoded by TPS1 is a key player in energy homeostasis and viability in the yeast Saccharomyces cerevisiae
Jean Marie François (Institut National des Sciences Appliquées, Toulouse, Francee)

11:25 - New mechanisms of resistance to azole antifungal drugs in Candida glabrata
Miguel Cacho Teixeira (iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal)

Selected Presentations

11:50 - Low pH: stress on the outside, signal on the inside
Rodrigo Mendonça de Lucena1, Laura Dolz Edo1, Marcos Antonio de Morais Junior2, Stanley Brul1, Gertien J. Smits1 (1Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands; 2Department of Genetics, Federal University of Pernambuco, Recife, Brazil)

12:03 - Defensive barriers in plants: fundamentals of the interaction between the saprophytic fungus Aspergillus nidulans and suberin
Isabel Martins1, Diego O. Hartmann1, Celso Martins1, Jörg Becker2, Cristina Silva Pereira1 (1Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; 2Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal)

12:16 - Yeast Cell Death Triggered By Nutrient Starvation in Wine Alcoholic Fermentation
Camille Duc1, Isabelle Sanchez1, Martine Pradal1, Jessica Noble2, Anne Ortiz-Julien2, Catherine Tesnière1, Bruno Blondin1 (1UMR 1083, INRA, Montpellier Supagro, Lallemand SAS; 2Lallemand SAS)

12:30 - LUNCH

14:00 - POSTER SESSION II (even numbered posters)


16:00 - SESSION VIII: Transport, Signalling and Intracellular Trafficking

(Chairs: Eckhard Boles, Goethe-Universität Frankfurt, Germany; Margarida Casal, CBMA, University of Minho, Braga, Portugal)

Keynote Presentations

16:00 - Membrane-coupled mRNA trafficking in Ustilago maydis
Michael Feldbrügge (Düsseldorf Institut fü Mikrobiologie, Heinrich-Heine-Universität, Düsseldorf)

16:25 - Potassium and proton fluxes across the plasma membrane as key players in yeast physiology
Hana Sychrova (Department of Membrane Transport, Czech Academy of Sciences, Prague, Czech Republic)

Selected Presentations

16:50 - Sugar transporters in the yeast Kluyveromyces marxianus
John Morrissey1, Javier Varela1, Nurzhan Kuanzhev2, Raul Ortiz3, Mislav Oreb4, Eckhard Boles4, Ken Wolfe3, Danilo Porro2, Paola Branduardi2 (1University College Cork, Ireland; 2University of Milan Bicocca, Italy; 3University College Dublin, Ireland; 4Goethe-Universität Frankfurt, Germany)

17:03 - Intracellular pH dynamics in Fusarium oxysporum
Tânia Ribeiro Fernandes, Antonio Serrano Salces, David Turrà, Antonio Di Pietro (Departamento de Genetica, Universidad de Córdoba, Spain)

17:16 - Death of non-Saccharomyces yeasts induced by cell-cell contact with Saccharomyces cerevisiae: role of the cell wall-associated GAPDH protein
Patrícia Branco1,2, Varongsiri Kemsawasd3,Lara Santos5, Mário Diniz4, Jorge Caldeira4,5, Maria Gabriela Almeida4,5, Nils Arneborg3, Helena Albergaria1 (1Unit of Bioenergy, Laboratório Nacional de Energia e Geologia (LNEG), Lisboa, Portugal; 2Research Center Linking Landscape, Environment, Agriculture and Food (LEAF), Lisboa, Portugal; 3Department of Food Science, Faculty of Life Sciences, University of Copenhagen, Denmark; 4REQUIMTE - Dept. Química, Faculdade de Ciências e Tecnologia, Monte Caparica, Portugal;5Instituto Superior de Saúde Egas Moniz, Monte Caparica, Portugal)


Thrusday, July 14th 2016

9:00 - SESSION IX: Yeasts and Filamentous Fungi as Pathogens and Aging and Disease models

(Chairs: Manuela Côrte-Real, CBMA, University of Minho, Braga, Portugal; Vladimir Titorenko, Concordia University, Montreal, Quebec, Canada)

Keynote Presentations

09:00 - Anti-prion systems in yeast
Reed Wickner (Laboratory of Biochemistry and Genetics, National Institutes of Health, Bethesda, USA)

09:25 - Paracoccidioides brasiliensis: from cell shape to pathogenesis
Fernando Rodrigues (Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal)

Selected Presentations

09:50 - Why Drinking Too Much is Bad For You: Effects of Ethanol on Yeast Genome Stability
Karin Voordeckers, Jacek Kominek, Elisa van der Zande, Kim Gielens, Kevin J. Verstrepen (VIB Laboratory for Systems Biology, Leuven, Belgium and CMPG Laboratory for Genetics and Genomics, KU Leuven, Belgium)

10:03 - The yeast Saccharomyces cerevisiae is an advantageous model organism for unveiling mechanisms of aging and discovering aging-delaying and anti-tumor chemical compounds
Anna Leonov, Anthony Arlia-Ciommo, Younes Medkour, Veronika Svistkova, Vicky Lutchman, Pamela Dakik, Vladimir I. Titorenko (Concordia University, Department of Biology, Montreal, Quebec, Canada)

10:16 - Ammonium Can Dictate Longevity, Independently Of Fermentative Or Respiratory Metabolism In The Yeast Saccharomyces cerevisiae
Júlia Santos1,2, Fernanda Leitão Correia1,2, Maria João Sousa3, Cecília Leão1,2 (1Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; 2ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal; 3Molecular and Environmental Biology Centre (CBMA)/Department of Biology, University of Minho, Braga, Portugal)



(Chair: Diethard Mattanovich, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria)

11:00 - Epigenetics and fungal development and secondary metabolism
Gerhard H. Braus (Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Goettingen, Germany)



   PYFF6 Conference - 2016