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Max F. Perutz Laboratories At a Glance 2016 Message from the Rectors Directorate Report MFPL in Numbers Awards & Honours Research Groups New Research Group Research Highlights Research Initiatives & Networks Scientific Facilities Education & Training Scientific Exchange The VDS “Molecules of Life” MFPL Life The Vienna Biocenter Publishing Details


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Message from the Rectors 2016 In its eleventh year, the Max F. Perutz Laboratories have firmly established themselves as one of the top institutions for research and education in the European arena.

A thriving collaboration between the University of Vienna and the Medical University of Vienna, the MFPL celebrated their tenth year in 2015. This year, they can look back over a successful decade of education and research in the field of Molecular Biology. The MFPL’s leading position is further underlined by the many grants and awards received in 2016. Education is the key task of universities, and we have thus joined forces once again by funding the Vienna Doctoral School (VDS) “Molecules of Life”, based at MFPL. This innovative PhD training will allow students to cross disciplinary barriers, a crucial element for success in today’s world. We would also like to extend a warm welcome to Professor Javier Martinez, who was appointed by the Medical University of Vienna in October 2016 and will move his lab to the MFPL in the coming months. Professor Martinez’s research focuses on the tRNA splicing pathway in mammalian cells. We would also like to congratulate Christopher Campbell, who was awarded an FWF START grant from the Austrian Science Fund (FWF). This prestigious grant will fund his work with up to € 1.2 million over the course of six years. Further congratulations are extended to Kristina Djinović-Carugo, who was elected an EMBO member this year.

congratulations to Tiffany Su for her uni:docs fellowship, Krzysztof Chylinski for his Bank Austria Research Award and Theodor-Körner-Foundation innovation prize. Elisabeth Sonnleitner’s teaching efforts were rewarded in the form of a UNIVIE teaching award. As part of the ongoing refugee crisis the MPFL took part in the “Science in Asylum” project, supporting scientists who have fled from war and troubled areas to find peers who can help them to get a foothold in the Austrian science community and labor market. 2016 marks Graham Warren’s last year as Scientific Director of the MFPL, so we wish him well for the future and thank him for all his efforts over the past ten years. We look forward to welcoming a new Director in 2017.

Heinz W. Engl Rector, University of Vienna

Markus Müller Rector, Medical University of Vienna

MFPL’s young researchers’ efforts are, year after year, recognized with awards and prizes. Many 3


Directorate Report 2016

From left: Roland Foisner (Vice-Dean for the Medical University of Vienna), Graham Warren (Scientific Director), Manuela Baccarini (ViceDean for the University of Vienna) and Fabien Martins (Administrative Director).

Start of the interdisciplinary Vienna Doctoral School “Molecules of Life” at the MFPL

We are proud to announce the start of the Vienna Doctoral School “Molecules of Life”, established at the MFPL in March 2016. This interdisciplinary PhD training program is supported by the University of Vienna and the Medical University of Vienna, bringing together PhD students and faculty committed to promoting research across disciplinary barriers. “Molecules of Life” students will work in teams spanning different fields of research, learning how to grasp the opportunities for discovery offered by recent technological developments and translate them into answers to fundamental scientific questions.


The University of Vienna has established a total of seven Vienna Doctoral Schools/Vienna Doctoral Academies, of which “Molecules of Life” is the only inter-university school as well as the largest, with 54 faculty members from across the University and the Medical University, offering a broad interdisciplinary outlook in Molecular Life Sciences. This School replaces and extends the MFPL PhD Program (est. 2009), an internationally renowned program with hundreds of applications every year and a current strength of more than 150 students from 30 different countries. You can read more about the very successful kickoff event of the VDS on page 37.

Another addition to MFPL: The Martinez group

A warm welcome to our newest group leader: Javier Martinez, appointed as professor at the Medical University in October 2016. He is a native of Argentina, who has been living in Vienna since 2004 and has been a successful group leader for more than ten years at our campus neighbour institute, IMBA. His research focuses on mammalian tRNA splicing, an essential process linked to several human diseases.

National and international recognition for MFPL researchers

The year 2016 marks another year of excellent science and we would like to congratulate our researchers on their achievements. Up until the end of October, they had raised well over € 12 million in third-party funding, published 136 peer-reviewed articles in scientific journals and mentored 24 PhD students. The large number of both national and international grants and accolades received during 2016 further underlines the high quality work carried out by MFPL researchers. In recognition of her excellent scientific achievements, Kristina Djinović-Carugo was elected a member of the European Molecular Biology Organization (EMBO). She was also awarded a Wellcome Trust Collaborative Award in Science, together with scientists from the UK and Germany. More than one million pounds (approx. € 1.2 million) will be granted over a period of four years for a joint project: “An integrated approach to the muscle Z-disk: from atomic structure to human disease”. Christopher Campbell was awarded a prestigious FWF START grant from the Austrian Science Fund (FWF), recognizing both his past achievements and future potential. The START grant is one of the most sought-after awards for young researchers in Austria, as it funds a minimum of € 800.000 up to € 1.2 million over the course of six years. This funding will support his project focusing on mechanisms that ensure the even distribution of chromosomes to the two daughter cells during mitosis. Two MFPL researchers were successful in the call for prototype funding (PRIZE) of the Ministry of Science, Research and Economics. Robert Konrat was successful with his project “New bifunctional therapeutic approach for the treatment of Parkinson’s disease”, and Renée Schroeder with her concept “Design of novel vectors for increasing

quality and quantity of proteins”. The funding will allow their respective groups to produce functional prototypes thereby helping to bring novel therapeutics to market.

Training and accolades for young researchers

MFPL researchers take great pride in educating tomorrow’s scientists. Each year, our scientists invest more than 1,200 hours in the training of undergraduate students, in the form of practical courses and lectures in the Molecular Biology and Medicine curricula. They also participate in the MFPL-based program of the University and Medical University as well as the Vienna Biocenter PhD programme, currently supervising more than 150 PhD students, as well as more than 100 Postdocs. An overview of the many accolades awarded to MFPL students is presented in the “Awards & Honours” section of this booklet. Of particular note, we would like to congratulate Krzysztof Chylinski, former PhD student at the MFPL, on two awards: The Bank Austria Research Award and the Theodor-Körner-Foundation Innovation Prize. Also warm congratulations to Tiffany Su from the Dammermann Lab on her uni:docs fellowship from the University of Vienna, and to Elisabeth Sonnleitner, Postdoc in the Bläsi group, on her UNIVIE teaching award.

The MFPL Community

Here at the MFPL, apart from a strong focus on research and educating future generations, we also aim to foster a stimulating, friendly and collaborative work environment. As part of this, we are continuing to promote the MFPL Community, a networking platform for MFPL members to exchange experiences, stay in touch and get advice on career matters. We are currently planning more events for our Alumni to stay in touch. This will be the last Annual Report for Graham Warren, who will be retiring in early 2017. The occasion will be marked by a symposium entitled: “Seeding Success in Science” emphasizing the lessons we have learnt over the last ten years, in the pursuit of excellent science and teaching. Graham Warren Fabien Martins Manuela Baccarini Roland Foisner



MFPL in Numbers Founded in 2005, as a joint venture of the University of Vienna and the Medical University of Vienna, the Max F. Perutz Laboratories (MFPL) provide an environment for excellent, internationally recognized research and education in Molecular and Cell Biology. Research at MFPL is curiosity-driven and spans the field of Molecular and Cell Biology. Most groups investigate basic research questions, but an appreciable number are also active in more applied fields of biology.

Research Areas • • • • • • •


Immunology & Infection Biology Cell Signalling RNA Biology Integrative Structural Biology Computational Biology & Bioinformatics Chromosome Dynamics Molecular Mechanisms of Disease


MFPL has a strong focus on the education and training of young researchers. Members of MFPL’s Faculty teach undergraduate courses in the Life Sciences and Medicine, supervise Diploma students and train PhD students and Postdocs taking their first steps in their scientific career. You can read more about opportunities for PhDs and Postdocs from page 30.


MFPL is jointly funded by the University of Vienna and the Medical University of Vienna. The two universities provide space, scientific infrastructure and cover the costs for administrative staff. Most of the scientific personnel (70%) and the running costs are covered by third-party funding raised by MFPL group leaders. The total volume of third party funding in 2016 was over 12 million euros.


Funding (as of October 20


, 2016. Rounding differences may occur)

Austrian Science Fund FWF EU Vienna Science and Technology Fund WWTF Austrian Research Promotion Agency FFG Austrian Ministries Austrian Academy of Sciences (ÖAW) Others


58% 20% 10% 4% 1% 1% 7%

Staff - Gender Distribution Male Female

225 238

49% 51%

273 142 9 34

58% 32% 2% 8%

61 101 146 88 67

13% 22% 32% 19% 14%

Scientific Staff - Nationalities Austria Europe (excl. Austria) North & South America Asia & Australasia

Scientific Staff - Functions Group Leaders Postdocs PhD students Technical Assistants Diploma/Master students All numbers as of October 27th, 2016.

Publications Publications as of November 4th, 2016.

Scientific Advisory Board

The Scientific Advisory Board SAB visits MFPL on a regular basis to monitor the scientific performance and discuss future developments with the Directorate and the Faculty. We thank our SAB members: Barbara J. Meyer University of California Berkeley Melissa J. Moore University of Massachusetts Medical School Peter Parker Cancer Research UK London Research Institute Simon TavarĂŠ Cancer Research UK Cambridge Institute




MFPL group leader Christopher Campbell was awarded a prestigious START grant from the Austrian Science Fund (FWF), to fund his research on the mechanisms that ensure chromosome segregation fidelity in mitosis. The grant – in addition to Christopher’s WWTF “Young Investigators” grant – will provide funding up to €1.2 million over the next six years.

Wellcome Trust Award & EMBO member

MFPL group leader Kristina Djinović-Carugo was awarded a Wellcome Trust Collaborative Award in Science, together with scientists from Germany and the UK. An amount of over one million pounds (approx. €1.2 million) will be granted over a period of four years. She has also been elected an EMBO member, a special honour conferred by existing members in recognition of her outstanding scientific achievements.

Golden Badge of Honour & RNA Society Award

PRIZE awards for two MFPL researchers

Andrea Barta, MFPL group leader, was awarded two special honours in 2016, the Golden Badge of Honour for Meritorious Service to the Province of Vienna and the RNA Society Award. The former recognises those who have made outstanding contributions to the Province of Vienna in the public or private sector, while the latter honours her outstanding services to the RNA community.

Renée Schroeder and Robert Konrat, group leaders at the MFPL, were successful in their application for prototype funding (PRIZE) of the Ministry of Science, Research and Economics. The funding allows the scientists to produce functional prototypes in order to help bring novel therapeutics to market. Renée Schroeder’s project aims to improve the quality and quantity of recombinant proteins through the construction of novel vectors, including certain RNA sequences termed RAP. Robert Konrat’s project investigates a protein with analogous function to α-synuclein (α-syn), an essential player in the pathogenesis of Parkinson’s disease.

Medical University of Vienna Professorship

Medical University of Vienna Associate Professorship

Javier Martinez, group leader at the MFPL, obtained his professorship from the Medical University of Vienna. Together with his group, he studies RNA metabolism in mammalian cells, with a special emphasis on the essential process of tRNA splicing.


MFPL group leader Gang Dong was successful in his application for a tenured associate professorship at the Medical University of Vienna. At the MFPL since 2008, his group studies ciliogenesis, focusing particularly on the structural characterization of proteins essential for the biogenesis of centrioles and cilia.

Awards & Honours Bank Austria Research Award and Theodor-KörnerFoundation Innovation Prize

Krzysztof Chylinski, former PhD student at the MFPL in the lab of Emmanuelle Charpentier and Renée Schroeder, has won two notable awards: The Bank Austria Research Award and the Theodor-Körner-Foundation Innovation Prize. The former award was granted for his dissertation, whereas the latter acknowledges Krzysztof’s current research work.

uni:docs fellowship

Tiffany Su from the Dammermann lab was awarded a uni:docs fellowship from the University of Vienna. The program funds excellent doctoral candidates for up to three years.

Award of Excellence and Sanofi-aventis prize

Florian Zwolanek, who completed his PhD studies in the lab of Karl Kuchler, was granted the Award of Excellence from the Federal Ministry of Science, Research and Economics for his outstanding dissertation, and the Sanofi-aventis prize for his most recent publication, describing a potential treatment against fungal sepsis.

UNIVIE Teaching Award

Elisabeth Sonnleitner, Postdoc in the Bläsi group and senior lecturer, received her UNIVIE Teaching Award in the category “Research-focused teaching and learning”. The award honours her exceptional teaching performance.


VBC PhD Awards

Two out of the four VBC PhD awards went to MFPL this year: Daniel Papinski from the Claudine Kraft group was awarded for his thesis entitled “Regulation and Signalling of Atg1 in Autophagy”, and Nadezda Sedlyarova, who worked in the group of Renée Schroeder, won with her thesis “Novel concepts of RNA-based transcription regulation in Escherichia coli”.


Research Groups Research at MFPL is curiosity-driven and spans the field of Molecular and Cell Biology. Most groups investigate basic research questions but a significant number are also active in more applied fields of biology. In 2016, almost 500 people from over 40 nations worked at MFPL. Detailed information about all MFPL research groups, their research focus, list of publications and team can be found on the MFPL website:


Gustav Ammerer Manuela Baccarini Andreas Bachmair Andrea Barta Dieter Blaas Udo Bläsi Christa Bücker Christopher Campbell Alexander Dammermann Thomas Decker Kristina Djinović-Carugo Gang Dong Silke Dorner Roland Foisner Peter Fuchs Boris Görke Angela Hancock Andreas Hartig Marcela Hermann Joachim Hermisson Reinhold Hofbauer N. Erwin Ivessa Michael Jantsch Verena Jantsch Franz Klein Alwin Köhler Robert Konrat Pavel Kovarik Heinrich Kowalski Claudine Kraft Karl Kuchler Martin Leeb Thomas Leonard Josef Loidl Sascha Martens Javier Martinez Isabella Moll Ernst Müllner & Ulrich Salzer Johannes Nimpf Egon Ogris Friedrich Propst Florian Raible Johann Rotheneder Matthias Schaefer Peter Schlögelhofer Renée Schroeder Christian Seiser Tim Skern Dea Slade Kristin Tessmar-Raible Gijs Versteeg Arndt von Haeseler Graham Warren Georg Weitzer Gerhard Wiche Angela Witte Ivan Yudushkin Bojan Zagrovic

Signal transduction and transcriptional regulation in yeast Deciphering the MAPK pathway in vivo Protein modifiers in plants and retrotransposon biology Post-transcriptional regulation of plant gene expression Early interactions of viruses with host cells Post-transcriptional regulation in bacteria and archaea Transcriptional regulation during early embryonic development Mechanisms that ensure chromosome segregation fidelity in mitosis Centriole assembly and function Host responses and innate immunity to microbial infection Structural biology of the cytoskeleton Structural studies of ciliogenesis The regulation of gene expression by small ncRNAs Lamins in nuclear organization and human disease Stress response in simple epithelia Signal transduction and post-transcriptional regulation in model bacteria Molecular basis of adaptive evolution Origin and biogenesis of peroxisomes LDL-R gene family, apolipoproteins and lipid transfer Mathematics and BioSciences Group (MaBS) Consequences of carnitine deficiency and CSF-1 inhibition Protein biogenesis and degradation from the ER Mechanisms and consequences of RNA-editing Meiosis in Caenorhabditis elegans Chromosome structure and meiotic recombination Nuclear Pores - Regulators of chromatin and membrane dynamics Computational biology and biomolecular NMR spectroscopy Signalling and gene expression in inflammation Molecular and structural biology of picornaviruses Regulation and signalling in autophagy Host-pathogen interactions & mechanisms of drug resistance & fungal pathogenesis Molecular control of cell fate decisions Structural biology of lipid-activated signal transduction Meiotic chromosome pairing and recombination Molecular mechanisms of autophagy Molecular mechanisms, biology and diseases linked to mammalian tRNA splicing Bacterial stress response and ribosome heterogeneity Erythrocyte (patho)physiology and storage in transfusion units ApoER2 and VLDL receptor Enzyme biogenesis and monoclonal antibodies The neuronal cytoskeleton in axon guidance Origin and diversification of hormone systems Cell cycle regulation and DNA damage response Methylated Cytosine in RNA: Understanding their impact on RNA stability, gene expression and innate immunity Meiotic recombination Riboregulation of transcription: how RNA shapes the transcriptome Chromatin modifiers in development and disease Interactions between viruses and cells DNA damage response Lunar periodicity and inner brain photoreceptors Ubiquitin-mediated regulation of immune signalling CIBIV - Center for Integrative Bioinformatics Vienna Biogenesis of the Golgi apparatus Stem cells of the heart Cytolinker proteins in signalling and disease φCh1, a model system for gene regulation of haloalkaliphilic Archaea facing two extremes: high pH and salt Functional imaging of signalling networks Laboratory of Molecular Biophysics 11



Molecular mechanisms, biology and diseases linked to mammalian tRNA splicing



2’ OH 3’ OH

Heparin input

Transfer RNAs (tRNA) are encoded in the genome as precursor molecules that must undergo processing in order to generate mature, functional tRNAs for the translation of mRNAs.

Fraction number 1









10 11 12 13 14 15 16 17 18 19 20 21 22


Partial purification of a human cyclic-phosphodiesterase/phosphatase that converts a 2’, 3’-cyclic-phosphate at the end of an RNA molecule into a 2’OH, 3’OH terminal nucleotide. Starting from cytoplasmic extracts of HeLa cells, the novel enzymatic activity has been purified over several chromatographic steps. Here, active fractions from a Butyl-Sepharose column have been pooled and loaded onto a Heparin column. The cyclic-phosphodiesterase and phosphatase activity peaks in fractions 7-9 (in red). Javier Martinez

Processing entails a vast number of chemical modifications, as well as removal of 5’-leader, 3’-trailer and intronic sequences. The removal of introns during pre-tRNA splicing requires two enzymatic activities: an endonuclease and a ligase. Over the last years, our laboratory revealed the mammalian pre-tRNA splicing machinery by identifying and characterizing: a) CLP1, a subunit of the tRNA splicing endonuclease (TSEN) complex as the first 5’ RNA phosphorylating activity described in mammalian cells; b) the long sought mammalian tRNA ligase complex, joining tRNA exon halves; and c) Archease, a conserved protein that provides multiple turnover activity to the tRNA ligase. We have stepped into in vivo biology by generating mouse models and analyzing fibroblasts from patients with mutations in tRNA splicing factors. As a result, we uncovered the function of CLP1 in motor neuron diseases and assigned the tRNA ligase and archease to the cytoplasmic splicing of the Xbp1-mRNA. This is a critical event during the unfolded protein response

which in turn is essential for plasma cells to produce immunoglobulins and for the survival of cancer cells. Current projects deal with mutations in TSEN leading to pontocerebellar hypoplasia, the unexpected role of the tRNA ligase complex during oxidative stress and redox control, and with RNA recognition aspects of innate immunity by investigating the in vivo functions of the RNA 3’ Terminal Phosphate Cyclase RTCD1, an enzyme described back in 1983 with a still elusive in vivo function. Digging into the yet obscure topic of RNA repair, we are purifying a novel RNA processing factor in HeLa cells entailing a dual 2’, 3’-cyclic phosphodiesterase and phosphatase activity. Taken together, we combine biochemistry and mouse genetics to explore RNA metabolism in mammals. This research contributes to a renewed interest in the so-called “old” tRNA molecules and the enzymatic machinery devoted to their synthesis and processing.

SELECTED PUBLICATIONS Jurkin J, Henkel T, Nielsen A, Minnich M, Popow J, Kaufmann T, Heindl K, Hoffmann T, Busslinger M, Martinez J. The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells. EMBO J. 2014; 33(24):2922-36. PMID: 25378478 Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, Trowitzsch S, Will C L, Lührmann R, Söll D, Martinez J. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. Science 2001;331(6018):760-4. PMID: 21311021 Weitzer S, Martinez J. The human RNA kinase hClp1 is active on 3’ transfer RNA exons and short interfering RNAs. Nature 2007;447(7141):222-6. PMID: 17495927




A new role of lamins in genome organization discovered The groups of Roland Foisner and Arndt von Haeseler challenge the current view on lamins’ role in genome organization. Contrary to the prevailing model that lamins exclusively interact with heterochromatin at the nuclear periphery, they show that a specific pool of lamins in the nuclear interior also plays a role in the organization and epigenetic regulation of euchromatic regions. Their findings may help to unravel novel molecular pathways involved in a group of rare diseases linked to mutations in the lamin gene. Nuclear lamins are major components of the nuclear lamina, a proteinaceous scaffold structure at the interface between chromatin and the inner nuclear membrane. The nuclear lamina was proposed to mechanically support the nuclear envelope and to provide anchorage sites for heterochromatin, thereby contributing to gene silencing. Roland Foisner’s group has been focusing on a different, up to now poorly investigated mobile pool of A-type lamins that localizes and diffuses throughout the entire nucleus.

Roland Foisner

Arndt von Haeseler

Most previous studies have shown that lamins exclusively bind to heterochromatin at the nuclear envelope and further stabilize repression of genes. Kevin Gesson in Roland Foisner’s team in collaboration with bioinformaticians Philipp Rescheneder and Arndt von Haeseler found that in addition to the previously described interaction of lamins with heterochromatin, the mobile pool of lamins in the nucleoplasm also binds to euchromatin. Depletion of the nucleoplasmic lamin pool by knocking out a protein stabilizing nucleoplasmic lamins (called lamin-associated polypeptide 2alpha, in short LAP2alpha) led to a profound reorganization of lamin-chromatin interactions and to changes in the epigenetic profile in euchromatin. Based on these findings, they propose that LAP2alpha together with lamins in the nuclear interior regulate chromatin organization, compaction and accessibility. Their results also indicate that lamins serve different functions in euchromatin versus heterochromatin. The findings of the study not only indicate a new role of lamins in genome organization, they also open new avenues for unravelling novel disease mechanisms and potential therapies in rare diseases caused by mutations in the lamin gene, such as the premature aging disease progeria. In line with these findings, the Foisner group has recently shown that expression of LAP2alpha in progeria cells can rescue some of the cellular disease phenotypes.


A-type lamins interact with heterochromatin at the nuclear envelope and euchromatin in the nuclear interior. Cartoon shows part of the mammalian nucleus depicting the nuclear membrane, interspersed by a nuclear pore complex, and the nuclear lamina underneath the inner nuclear membrane, consisting of B-type lamins (blue) and A-type lamins (yellow). Unlike B-type lamins, A-type lamins also localize within the nucleus in a LAP2alpha-dependent manner (red). Lamin-associated heterochromatin at the nuclear envelope (LADs, dashed black) and euchromatin (dashed green) in the nuclear interior are shown. The right panel shows Integrative Genomics Viewer (IGV) tracks of genomic DNA bound to peripheral and intra-nucleoplasmic lamin structures shown in the cartoon. For details see Gesson et al. Cover art © Kevin Gesson and Roland Foisner

Gesson K, Rescheneder P, Skoruppa MP, von Haeseler A, Dechat T, Foisner R. A-type lamins bind both heteroand euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha. Genome Res. 2016 Apr;26(4):462-73. PMID: 26798136


The Daedalus flight through inflammation Our immune system constantly fights off bacteria and viruses, and while doing so needs to find a critical balance between over- and underreaction. Pavel Kovarik and his group report that in the defence against group A Streptococci – bacteria that cause tonsillitis, but also serious infections – a perfectly synchronized interplay of two immune substances is key. The dilemma of our immune system is comparable to the story of Icarus and Daedalus from Greek mythology. To escape their captivity, Daedalus built wings from feathers and wax for himself and his son. Daedalus warned his son that he must neither fly too high but also not too low, otherwise the sun’s heat or the humidity of the sea would destroy his wings and he would crash. After they had successfully escaped, Icarus become boisterous and flew higher and higher until the sun began to melt the wax of his wings and he fell into the sea. Similarly, an over- or underreaction of our immune system can be life-threatening. Pavel Kovarik and his team focus on molecules that ensure a balanced immune response. For their experiments, they simulated infections with group A Streptococci, which are best known as the common cause of tonsillitis. However, in some cases, they can also cause serious invasive infections. The related disease – toxic shock syndrome and necrotizing fasciitis – can be fatal. The scientists examined what happens at the molecular level in invasive streptococcal infection, and their results revealed how a well-balanced thereby protective immune response is achieved. The key players therein are the cytokines, i.e. secreted signalling proteins, IL-1β and type I interferons (IFN-I). For a long time, it was known that IFN-I helps in the fight against viruses, but their role in the defence against bacteria remains poorly understood. The Kovarik group revealed the molecular physiology of the protective effects of IFN-I during invasive bacterial infection of the soft tissue: IFN-I reduces the amount of IL-1β and thus prevents lethal hyperinflammation. In their model, the scientists showed that if IFN-I effects were reduced, treatment with inhibitors of IL1β synthesis had positive effects and balance could be restored. Once this relationship between IFN-I and IL-1β will be described in humans, these and similar therapies can be tested, in the hope of developing new approaches.

Aurea mediocritas: Not too much, not too little, just right - immune response to S. pyogenes is balanced by type I IFNs. The cartoon shows the lethal outcome of hyperinflammation caused by uncontrolled IL-1-mediated signalling in the absence of type I IFN signalling (left), a protective immune response resulting from the balance between pro-inflammatory IL-1 and modulatory type I IFN signalling (middle) and lethal bacterial growth caused by the absence of IL-1-mediated defence (right). Castiglia V, Piersigilli A, Ebner F, Janos M, Goldmann O, Damböck U, Kröger A, Weiss S, Knapp S, Jamieson AM, Kirschning C, Kalinke U, Strobl B, Müller M, Stoiber D, Lienenklaus S, Kovarik P. Type I Interferon Signaling Prevents IL-1β-Driven Lethal Systemic Hyperinflammation during Invasive Bacterial Infection of Soft Tissue. Cell Host Microbe. 2016 Mar 9;19(3):375-87. PMID: 26962946


Pavel Kovarik


Ensuring the integrity of our genetic material during reproduction Verena Jantsch and her group conduct the first in vivo study of a component of the RTR complex in animal meiosis. During eukaryotic cell divisions, intact and complete sets of chromosomes have to be transmitted to daughter cells. About 100-200 DNA lesions occur during each cell cycle due to the continuous exposure to DNA damaging agents. DNA double-strand breaks comprise one type of DNA damage that are most accurately repaired by homologous recombination using the sister chromatid as a repair template.

Verena Jantsch

A C. elegans late pachytene nucleus imaged with Structured Illumination Microscopy. The chromosomal axis are marked with HTP-1 (cyan), a lateral element marker of the synaptonemal complex. The REcQ helicase HIM-6 (magenta) forms a doublet structure surrounding the crossover site highlighted by COSA-1 (yellow). The image was taken by Alexander Woglar. At the break site, resection generates a single stranded overhang that invades a sister chromatid to initiate homologous recombination. This culminates in the generation of a DNA double holiday junction (dHJ) which is endonucleolytically cleaved by resolvases to produce either crossover (CO), or non-crossover (NCO) products. Alternatively, nonCOs can also be produced by decatenation via the RTR (RecQ Bloom helicase–topoisomeraseIII–Rmi1) complex. Patients with mutations in Bloom helicase have a high risk to develop cancer, reduced fertility and often display growth retardation and immune


deficiencies. Their cells show genomic instability and elevated frequencies of COs. Hence, the RTR complex is very important to dismantle dHJs and channel the repair process into the NCO outcome in mitotic cells. In meiosis, DNA double-strand breaks occur in a programmed manner. Some of those breaks are processed into COs by homologous recombination. COs are essential to form physical linkages of parental chromosomes thus ensuring their correct segregation. In meiosis, DNA double strand breaks are induced in excess to the actual number of COs. Mechanisms are thus required to establish a regulated number of COs but also to repair remaining intermediates as NCOs. The Jantsch group together with collaborators from the Villeneuve lab (Stanford University) and the von Haeseler group (CIBIV), used C. elegans as a model system to study the roles of the RMI homolog RMH-1 in meiotic recombination. They show that the complex plays multiple genetically separable roles that together ensure the faithful inheritance of intact chromosomes in meiosis. RMI1 is involved in NCO production, CO designation, reliable CO resolution and the proper positioning of COs on chromosomes. Most importantly, this work provides evidence that RMH-1 accumulates at CO sites where it likely directly affects the CO outcome of recombination intermediates. RMH-1 also regulates the spatial distribution of COs along chromosomes. It ensures the off-centered position of the CO. This is the first demonstration that the anti-CO activity of the RTR can act locally within specific chromosome domains. The regulation of both the number and position of COs is essential in meiosis with consequences for genome stability and chromosome nondisjunction. Jagut M, Hamminger P, Woglar A, Millonigg S, Paulin L, Mikl M, Dello Stritto MR, Tang L, Habacher C, Tam A, Gallach M, von Haeseler A, Villeneuve AM, Jantsch V. Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance. PLoS Biol. 2016 Mar 24;14(3):e1002412. PMID: 27011106


Guardians of the skin Our skin is the largest organ of our body, shielding it from both chemical and mechanical hazards. Manuela Baccarini and her team have unravelled how the RAF proteins protect the integrity of this essential organ.

RAF preserve the physical and immunological integrity of the skin barrier In order to maintain its physical barrier function, the skin regenerates throughout life, constantly producing new cells to replace the old ones. Additionally, the skin is home to cells of the immune system which protect the body from infections, acting as an immunological barrier against pathogens. Both barrier functions, when compromised, lead to disease; a decrease in the regenerative capacity of the skin makes the body unable to repair injuries, while uncontrolled proliferation of skin cells leads to tumour formation. Similarly, an imbalance in the immunological response of the skin may lead to diseases such as psoriasis or atopic dermatitis. These diseases are currently on the rise, particularly in developed countries and urban areas.

Manuela Baccarini and her group were able to unravel a crucial role of RAF proteins in preserving the delicate immunological balance of our skin. In fact, the RAF/MEK/ERK pathway has a major impact in promoting proliferation of the epidermis, the outer layer of the skin. At the same time, RAF also prevents allergic inflammation. The team discovered that mice lacking RAF in the epidermis develop an allergic condition similar to human atopic dermatitis (also known as eczema). They went on to show that RAF are not only crucial for the establishment of the physical barrier of the skin, but also act as “brakes” preventing excessive stress signalling from the epidermis. When these brakes are released, the cells of the epidermis, the so-called keratinocytes, promote inflammation and allergy through the local and systemic activation of the immune system. The study by the Baccarini lab has identified RAF proteins as true “guardians of the skin”; the results help to better understand both atopic dermatitis and the skin toxicity caused by treatments inhibiting RAF. Raguz J, Jeric I, Niault T, Nowacka JD, Kuzet SE, Rupp C, Fischer I, Biggi S, Borsello T, Baccarini M. Epidermal RAF prevents allergic skin disease. Elife. 2016 Jul 19;5. pii: e14012. PMID: 27431613

The RAF proteins play a crucial role in skin regeneration and tumour formation, and deregulation of their activity leads to the formation of skin tumours such as squamous cell carcinoma and melanoma; accordingly, RAF inhibitors have been developed and are being used in the clinic for the treatment of metastatic melanoma. While highly effective, these therapies sometime cause severe skin side effects, forcing an interruption of therapy or even its termination.


Manuela Baccarini


A potential new treatment against lethal fungal infections Fungal infections are the most common infection worldwide – however, they also claim about 1.5 million lives each year. Karl Kuchler and his group now discovered a completely new mechanism that could lead to a potential treatment for deadly fungal infections.

Karl Kuchler

Over the course of their lifetime, one in four people will suffer from an unpleasant infection of their skin or mucous membranes. In most cases, an attack of the monocellular yeast fungus Candida albicans is harmless and is easily treated. However, if our immune system fails to recognize the pathogen, the fungus can spread throughout the whole body and can lead to a dangerous form of blood poisoning, fungal sepsis. Such so-called invasive infections are fatal in 50% of cases. Many of the new treatments of modern medicine, such as organ transplants or cancer treatments are often associated with short to long-term weakening or damage to the immune system. Unfortunately, in this weakened state, an infection with the common

C. albicans (green) is engulfed by a dendritic cell (blue). The hyphens of C. albicans (red) destroy the cellular membrane of another dendritic cell. ©Florian Zwolanek


yeast fungus can very quickly become life threatening. Up until now, there have been no effective treatments for combating such an infection at this advanced stage. Karl Kuchler and his group, together with a fruitful collaboration with scientists at IMBA, have now discovered how the immune system successfully repels a Candida invasion. Viruses, bacteria and fungal pathogens are recognized by so-called “immunoreceptors”, by means of their typical signature, on the outer wall of the cell. These receptors dock onto the outer wall of the invader and alert and activate the body’s own defence cells, which are then able to kill off the pathogen. The scientists have now been able to show that the enzyme CBL-B and a kinase called SYK play an important role in the immune response to Candida. SYK amplifies the signal for targeted defence against the fungal pathogen, while CBL-B attenuates transmission of the signal for the immune response and ultimately switches it off completely. In a next step, the researchers developed a completely new type of protein, a so-called “inhibitor”, to specifically inhibit CBL-B in mice. This enabled an invasive Candida infection to be successfully repelled, while mice where CBL-B was active, very quickly succumbed to a systemic Candida infection. The results of the study could potentially pave the way for a new treatment against invasive fungal infections, by strengthening the body’s own protective shield against a specific invader, in this case the fungus Candida albicans. Wirnsberger G, Zwolanek F, Asaoka T, Kozieradzki I, Tortola L, Wimmer RA, Kavirayani A, Fresser F, Baier G, Langdon WY, Ikeda F, Kuchler K, Penninger JM. Inhibition of CBLB protects from lethal Candida albicans sepsis. Nat Med. 2016 Aug;22(8):915-23. PMID: 27428901


Molecular mechanism for chromatin ubiquitination revealed Alwin Köhler‘s group captures a transient enzyme-chromatin interaction by cross-linking and mass spectrometry. ment of a small protein called ubiquitin to specific histones. Alwin Köhler’s lab is interested in the monoubiquitination of histone H2B, which is important for gene expression. This modification is highly conserved from yeast to humans and is required for normal cellular differentiation. Misregulation of H2B ubiquitination levels is also linked to various types of cancer.

Pictured are a nucleosome and a histone ubiquitin ligase, which are captured in a distinct orientation by a chemical crosslinker. This trick in combination with mass spectrometry allowed Gallego et al. to reveal how the Rad6-Bre1 ubiquitination machinery (right side, active site labelled red) exclusively recognizes a single target residue on the nucleosome (left side, histone H2B Lysine 123 in red). Their study explains how substrate specificity is achieved, how recognition of the nucleosome is coupled to ubiquitin transfer and how Rad6-Bre1 compete with an opposing enzymatic activity for access to chromatin. Histone H2B ubiquitination is critical for transcription and linked to several human diseases. Image design by Tibor Kulcsar (IMP, Vienna).

In eukaryotes, DNA is packaged into a more condensed structure, which allows the DNA to fit into the nucleus. This structure, called chromatin, also enables additional levels of gene expression control. The basic unit of chromatin is the nucleosome, which is formed by four different core histone proteins. DNA is wrapped around these histones like a thread around a spool. A key molecular switch for gene regulation is the ubiquitination of chromatin, which is the attach-

Histone H2B ubiquitination on yeast Lysine 123 (human Lysine 120) had already been described in 1980, but the enzymatic mechanism remained unclear. Alwin Köhler’s group could show how the ubiquitin ligase Bre1 recognizes the nucleosome and how this event is coupled to the ubiquitination of H2B Lys123, yet, no other lysine on the nucleosome surface. This mechanistic understanding was the result of in vitro reconstitution experiments combined with cross-linking and mass spectrometry. These techniques permitted biochemical capture of the transient Bre1-nucleosome interaction and elucidation of the precise topology at the interface. The Köhler group closely collaborated with other labs at the Gene Centre in Munich, Germany, the neighbouring Institute of Molecular Pathology, the Max F. Perutz Laboratories and the Howard Hughes Institute at the University of Washington in Seattle, USA. In the future, Alwin Köhler’s lab wants to determine how chromatin ubiquitination is spatially and temporally coordinated with the transcription process to understand the dynamics of ubiquitin signalling on chromatin. Gallego LD, Ghodgaonkar Steger M, Polyansky AA, Schubert T, Zagrovic B, Zheng N, Clausen T, Herzog F, Köhler A. Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1. Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10553-8. PMID: 27601672


Alwin Köhler



Genes relevant for adaptations of internal clocks described Tessmar-Raible’s group identified relevant genes behind the adaptation to the sun and the moon in a marine midge. The non-biting marine midge Clunio marinus lives along Europe’s tide-shapen coasts. There, precise timing is of existential importance: Reproduction and oviposition must occur when the tide is at its lowest. The so-called lowest low tide only occurs during few hours on specific days. The tides, and therefore also low tide, are influenced by both the sun and the moon. To foresee the ideal time of reproduction, Clunio has two internal clocks: a circadian clock, influenced by the sun, and a circalunar clock, influenced by the moon much like a common calendar.

Kristin Tessmar-Raible

Due to geographical causes, the timing of low tides differs between geographical locations. Therefore, the midges have to “set” their clocks in accordance with their position. Scientists had already discovered in the 1960s that midges living along the coast of the Atlantic sea have genetically adapted their circadian clocks to the local occurrence of tides. Kristin Tessmar-Raible and her team then investigated how such adaptations may occur on a molecular level. The work was spear-headed by post-doc Tobias Kaiser, who had previously already uncovered that similar adaptations are also true for circalunar clocks. Tobias sequenced and assembled different Cl-

unio genomes in tight collaboration with Arndt von Haeseler’s group (CIBIV). This allowed the researchers to unravel the genomic sequences that likely underlie the circadian and circalunar timing differences. Further molecular work by VBC PhD student Birgit Poehn and in collaboration with Thomas Hummel’s (Faculty of Life Sciences, University of Vienna) and Florian Heyd’s groups (FU Berlin, Germany) then provided a first mechanistic model, how such molecular adaptations can lead to differential circadian timing. The researcher’s results point towards a specific protein, called Calcium/Calmodlin-dependent kinase II (CaMKII), being the main effector behind the adaptation of the circadian clock to the geographical environment. In fact, with the resulting different variants of CaMKII, the circadian clock can run either faster or slower. Interestingly, CaMKII is also found in humans, and hasn’t changed much during the course of evolution. In fact, it is one of the most abundant proteins in the human brain. Keeping in mind the different chronotypes in humans, the question arises whether CaMKII could also play a role there, and intriguingly could provide a link to neuropsychiatric disorders in humans, which often co-occur with extreme early and late chronotypes. The study’s insights raise many further intriguing questions, e.g. by unravelling molecules potentially involved in the modulation of the ‘internal calendar’, the lunar clock. Understanding of these clocks is only at its very beginning. The Research Platform “Rhythms of Life” of the University of Vienna provided a highly supportive framework for the required collaborations and was hence instrumental for the success of the work.

Alternative splicing variants of the enzyme CaMKII make the circadian clock tick faster or slower. Crystal structure of a tetradecameric assembly of the association domain of Ca2+/ calmodulin-dependent kinase II. Hoelz A, Nairn AC, Kuriyan J, Mol. Cell 11 1241-51 (2003).

Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen LT, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K. The genomic basis of circadian and circalunar timing adaptations in a midge. Nature. 2016. PMID: 27871090



Taking out the cellular trash – but at the right place and the right time! Claudine Kraft and her team give new insights about how cells dispose of their waste – dysfunctions in this system are linked to cancer and Alzheimer’s disease. The cell’s waste disposal system, a vital process, is called autophagy. Here, a defined set of proteins coordinates the removal of viruses, bacteria, and damaged or superfluous material from a cell. Autophagy also enables cells to survive times of starvation, by degrading the cell’s own components to recycle their building blocks. This process needs to be tightly controlled to prevent potentially lethal consequences of aberrant autophagy initiation. Autophagy describes the transport of cargo, which needs to be degraded, to the lytic compartment of the cell. The cargo is engulfed by an isolation membrane resulting in a double membraned vesicle called autophagosome. After fusion of the autophagosome with the lytic compartment, the cargo is degraded by the resident hydrolases. Finally, the resulting building blocks are recycled for further use. The key regulator of autophagy is the kinase Atg1, and its importance in autophagy activation is long known. Details of its functions were described by the Kraft group in their 2014 Molecular Cell publication. However, how Atg1 kinase activity and the process of autophagy are controlled in order to prevent their aberrant activation had remained elusive. Now, the team of Claudine Kraft discovered that Atg1 is regulated in both space and time. To initiate autophagy, both Atg1 and the cargo are separately brought to the precise location where the cargo is packed into an autophagosome. The simultaneous presence of both Atg1 and the cargo at this place is crucial for the activation of Atg1 and the initiation of autophagy. PhD student Raffaela Torggler and Postdocs Daniel Papinski and Thorsten Brach from the Kraft laboratory showed that the cell allows Atg1 to interact with the cargo only at the site of cargo packaging. This tightly restricts autophagy initiation in space and time and prevents its aberrant activation. To define the precise function of these individual proteins in selective autophagy, a synthetic in vivo approach was established, called iPass (short

for “induced bypass”). iPass combines genetic deletion with induced dimerization. By attempting to bypass the function of a protein in vivo, iPass allows to analyse the non-redundant roles of single pathway components in the context of a cell instead of that of a test tube. iPass also allows the synthetic progression of a pathway past the first step a deleted factor is required for, and thus can be used to test for additional functions of the protein in downstream pathway stages. In addition, a usually constitutive pathway can be induced at a time of choice using iPass, facilitating the study of early events during pathway progression. This approach allowed the dissection of individual steps during Atg1 kinase activation and selective autophagy induction.

Claudine Kraft

The detailed study of such fundamental cellular processes is crucial for the understanding of diseases that go hand in hand with these events – in the case of autophagy, Alzheimer’s disease or cancer. The group’s work gives important insights into the molecular events regulating autophagy in space and time. Torggler R, Papinski D, Brach T, Bas L, Schuschnig M., Pfaffenwimmer T., Rohringer S, Matzhold T, Schweida D, Brezovich A and Kraft C. Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Mol Cell. 2016 Oct 20;64(2):221-235. PMID: 27768871


In selective autophagy the Atg1 kinase is activated by the convergence of two independent pathways: Atg1 is recruited to the vacuole by Atg13 and cargo complexes are recruited independently to the vacuole by Atg11. Only at the vacuole Atg1 can bind to and cluster on the cargo where it then becomes activated. This results in the tight control of kinase activation in space and time. The functions of Atg13 and Atg19 can be bypassed using the iPass approach.


A new function of bacterial sRNAs

A new mechanism of transcription regulation in bacteria has been discovered in a joint effort between US groups of Evgeny Nudler (NYU School of Medicine) and Susan Gottesman (NIH, National Cancer Institute) and the Renée Schroeder group at MFPL. Bacteria must be able to cope with sudden changes in their environment, a huge stress for the organism. Thus, they have mastered the quick altering of their gene expression to stress. Such tuning is achieved via several pathways, many of those still poorly understood.

Renée Schroeder

One stress response is mediated by small RNAs (sRNAs), which have been known to control translation initiation as well as mRNA stability. In order to shed light on these stress response pathways, first author Nadezda Sedlyarova from the Schroeder group spent several months in the laboratory of Evgeny Nudler at the NYU School of Medicine studying transcriptome profiles from E. coli grown at diverse conditions, combining detailed in vivo studies with sequencing data. Her efforts were focused first on the effects of the termination factor Rho on the global expression of bacterial genes and, in particular, on rpoS, encoding a well-known player in the response to environmental changes.

With their work, the authors were able to demonstrate that Rho acts within the 5’ UTR of not a few, but many bacterial genes. Rho thus functions as a global attenuator of gene expression, by inducing premature transcription termination. Following this, the scientists then discovered a mechanism, which controls such Rho-dependent termination: An sRNA-mediated antitermination. Surprisingly, this antitermination by sRNA is achieved via a modulation of transcription itself, rather than by the previously known control of translation initiation. It thereby represents a completely novel mechanism of regulation. Schroeder and her team are thus the first group to describe sRNAs as a new class of finely regulated anti-termination elements, acting in response to particular environmental changes. Thus sRNAs already regulate gene expression at the transcription level and not only at the post-transcription level, as thought previously. In principle, this newly discovered mechanism of sRNA regulation can in the future be further implemented to design synthetic tunable networks, to precisely control gene expression. Sedlyarova N, Shamovsky I, Bharati BK, Epshtein V, Chen J, Gottesman S, Schroeder R, Nudler E. sRNA-Mediated Control of Transcription Termination in E. coli. Cell. 2016 Sep 22;167(1):111-121.e13. PMID: 27662085

Bacterial small RNAs balance the Rho- dependent termination pathway to prevent premature transcription termination, extending the role of these RNA regulators beyond post- transcriptional control.



Research Initiatives & Networks Collaboration is a major element and inevitable prerequisite for excellence in scientific research. Our group leaders are therefore actively involved in local, national and international research networks. One example are Special Research Programs (SFBs) funded by the Austrian Science Fund (FWF). SFBs are peer-reviewed, highly interactive research networks, established to foster long-term, interdisciplinary co-operation of local research groups enabling them to work on the frontiers of their thematic areas. Another collaborative research project, coordinated by MFPL, is the Center for Optimized Structural Studies (COSS), funded by the Austrian Research

Promotion Agency (FFG) as a “Laura Bassi Centre of Excellence”. The Laura Bassi funding program promotes research networks led by women at the interface between science and industry. MFPL group leaders are also involved in several interdisciplinary research platforms of the University of Vienna. These are organizational units between faculties to advance innovative and interdisciplinary research areas. Detailed information about research networks involving MFPL scientists can be found on our website:

Laura Bassi Centre “COSS – Center for Optimized Structural Studies”

Workflow and chart of the COSS platform. The individual experimental modules are shown in blue boxes. General problems that might occur within individual/particular module(s) are indicated in red boxes, while general solutions to these problems are shown in green boxes.

Proteins are the building blocks of life and can be found in every cell. Being able to decode the structure of proteins means a better understanding of numerous processes in the body. Structure determination at atomic detail and their biochemical and biophysical characterization requires high levels of protein quality and in large quantity. The major aim of COSS is to research innovative methods to produce sufficient quantities of high-quality protein that can be used for structural and/or functional studies. COSS has established a platform for efficient production of recalcitrant proteins in E. coli and baculovirus infected insect cells, employing nested constructs approach, automated expression screening and purification, as well as complementary screens for identification and quantification of protein-protein interactions. Furthermore, COSS has developed design of customized crystallization screens based on biophysical characterization of samples. Head Kristina Djinović-Carugo



SFB “Chromosome Dynamics” Nano-model of a meiotic chromosome. Pairs of sister-loops protrude from a common axis. Axis based robot arms symbolize the DNA-cleavage machinery, the right one with a piece of cleaved DNA. The interaction between axis and loop sequences is very important to make repair work for pairing and chromosome segregation.

Chromosomes contain our body plan, yet they are highly dynamic structures, changing their properties dramatically according to the necessities of cell cycle and reproduction. The SFB “Chromosome Dynamics” started in 2008, aimed to answer key questions from the “life” of chromosomes. In addition to the 8 groups funded by the SFB from MFPL, IMBA and IMP several groups are associated and coordinate their research with us to study kinetochores, chromosome axis and loop domains, recombination hotspots and chromosome movement at the molecular level. The kinetochore-microtubule attachment and the biochemistry of cohesins, both key aspects of segregation, are studied in meiosis and in mitosis in budding yeast as well as in mouse and human cells. Additional novel aspects of chromosome

architecture are investigated in human cells. In meiosis I, chromosome segregation is ensured by recombination, involving massive DNA damage and its repair. Both of these aspects are studied in yeast, plant and animal model systems. Recombination hotspots are studied in budding yeast and Arabidopsis thaliana. High-end technological platforms, such as mass spectroscopy, micro arrays and next generation sequencing are used as discovery tools. Meiotic chromosome missegregation is a leading cause of miscarriages and Down’s syndrome and most cancers are associated with aberrant chromosome numbers. Knowledge of segregation mechanisms is thus required to understand the aetiology of these problems. Speaker Franz Klein (MFPL), Jan Michael Peters (IMP, Deputy)

SFB “RNA Regulation of the Transcriptome” The special research program “RNA-REG” is studying how RNA-networks control the flow of genetic information. All cellular processes affecting the transcriptome are modulated by regulatory RNAs, from epigenetic phenomena, chromatin stability and structure over transcription to RNA-processing, transport, decay and translation. “RNA-REG” comprises fifteen research groups from five research institutions that aim to classify regulatory RNAs, decipher their interactomes, their regulatory mechanisms and to understand their physiological consequences. Using state-of-the-art sequencing analysis with a central bioinformatics support unit, regulatory RNA networks are studied in diverse models like bacteria, nematodes, insects, plants and mammals. Importantly, the mechanisms underlying regulatory RNA networks during adaptation, development and disease progression are the focus of “RNA-REG”. Together with the affiliated doctoral program “DK-RNA-Biology” we train young scientists to become experts in the analysis of regulatory RNA networks and their biological consequences. Speaker Michael Jantsch (MFPL), Isabella Moll (MFPL, Deputy) 25


Research Platform “Decoding mRNA decay in inflammation” Regulation of gene expression by changes in mRNA stability is one of the most important mechanisms for the control of immune responses. Tristetraprolin (TTP) is a key mRNA-destabilizing protein, regulating the elimination of inflammatory mRNAs such as TNF and other cytokines. TTP deficiency in mice causes a severe inflammation and eventually premature death resulting from uncontrolled cytokine production, showing that TTP is essential for balancing immune responses and for maintenance of homeostasis. The mechanisms of selective targeting of inflammatory mRNAs by TTP remain poorly understood.

This research platform funded by the University of Vienna employs structural biology in combination with bioinformatics and cell based approaches to decipher how TTP selectively targets inflammatory mRNAs for degradation. A comprehensive understanding of the regulation of mRNA decay during immune responses will ultimately pave the way for exploitation of TTP in therapy of immune disorders. Head Pavel Kovarik

Research Platform “Marine Rhythms of Life” The interdisciplinary team of the University of Vienna research platform “Marine Rhythms of Life” is on track to unravel how monthly clocks can function on a molecular level and impact on reproduction and regeneration of the marine bristleworm Platynereis dumerilii. These questions are jointly tackled by Kristin Tessmar-Raible, Florian Raible (both MFPL), Christopher Gerner (Institute of Analytical Chemistry) and Thomas Hummel (COSB, Faculty of Life Sciences). Together with Tobias Kaiser (Postdoc in Arndt von Haeseler’s group at CIBIV, MFPL), Kristin Tessmar-Raible and Thomas Hummel also try to find the molecular switches that evolution tinkers with to change daily and monthly timing in the marine midge Clunio marinus. The only clock understood so far on cellular or molecular level is the daily clock. Yet, the existence of multiple oscillators is likely the rule rather than the exception across the animal kingdom, including humans. Head Kristin Tessmar-Raible


Research Platform “Quantum Phenomena and Nanoscale Biological Systems – QuNaBioS”

QuNaBioS is an interfaculty research platform between the Department of Physics and the Center for Molecular Biology of the University of Vienna. It encompasses a range of joint research activities between the Quantum Nanophysics group of Markus Arndt at the Department of Physics and the Dynamics of Coupled Biological Systems’ group of Alipasha Vaziri at the Vienna Biocenter. The QuNaBioS research platform has the following goals: • Strengthening the research profile of the University of Vienna by realizing existing synergies between quantum physics and biology through

the establishment of joint research projects at the interface between quantum, nanophysics and biology • Development of technologies and methodologies with applications in Life Sciences and their potential exploitation • Establishment of (expandable) structures for interdisciplinary research and training at the above interface For detailed information visit Head Alipasha Vaziri 27


Scientific Facilities

MFPL researchers use a broad spectrum of techniques to address novel questions in diverse areas of biology. Several in-house facilities, as well as services provided by the Vienna Biocenter Core Facilities (VBCF) support the work of our scientists. More information about the scientific facilities at MFPL and the VBCF can be found on our website:

NMR investigations of early events during infection by foot-and-mouth disease virus (FMDV) A) PRE (paramagnetic relaxation enhancement) derived structural features of eIF4GII (eukaryotic translation Initiation Factor 4GII) an IDP (intrinsically disordered protein) and B) its interactions with the viral leader protease Lbpro.

BioOptics – Light Microscopy

Publication: Aumayr M, Fedosyuk S, Ruzicska K, Sousa-Blin C, Kontaxis G, Skern T. Protein Sci. 2015 Dec;24(12):197996 Abert C, Kontaxis G, Martens S. J Biol Chem. 2016 Sep 2;291(36):18799-808.

Bio-NMR Facility

The facility currently houses four research instruments: a 500, two 600 and an 800MHz NMR spectrometer, two of which were recently refitted with latest-technology RF consoles. In addition, the unit also has IT facilities for NMR data analysis, structure calculations and molecular modelling and visualization. The facility offers a full range of NMR research services from routine sample characterization or interaction mapping and affinity determination to structural characterization and determination of solution structures of biological macromolecules as well as development of NMR techniques and customized solutions.

The facility is dedicated to provide state-of-the art light microscopy equipment to MFPL researchers. Currently, three laser scanning confocal microscopes including Airy Scan superresolution possibility, two spinning disc units, a wide-field live-imaging setup including a TIRF and a microfluidics option, an epifluorescence deconvolution microscope, a homemade imaging-based plate reader and a microdissection-laser ablation instrument are available. The team also provides professional training and assists with expertise in experimental planning, technical setup, optimization and image analysis.

Vienna Biocenter Core Facilities (VBCF)

BioOptics – Flow Cytometry The facility runs four flow cytometers for the measurement of fluorescence, size and granularity of cells or other particles in solution. The current equipment includes a FACS Fortessa (laser lines 405, 488, 561 and 640) and a FACS Aria cell sorter (laser lines 375, 405, 488, 561 and 633), as well as two FACS Calibur machines (laser lines 488 and 635).


The VBCF is a publicly funded non-profit organization that offers top scientific infrastructure operated and constantly refined by highly qualified experts. To date the following VBCF core facilities are operational: Electron Microscopy, Advanced Microscopy, Next Generation Sequencing, Preclinical Phenotyping, Preclinical Imaging, Bioinformatics and Scientific Computing, Plant Sciences, Protein Technologies, Vienna Drosophila Resource Center and Metabolomics. The VBCF also oversees the Child Care Center.

Mass Spectrometry Facility Equipment Park Genomics The genomics equipment park at MFPL (2.405) consists of an Affymetrix GCS3000 7G system (including a scanner, fluidics station and hybridization oven) and a semi-automatic 96 channel pipettor (Viaflow096 /Integra). The Agilent 2-micron resolution microarray reader was removed, but is still available at the IMP (Harald Scheuch). A new high throughput Singer RoToR (ROT-001) for fast solid to solid (solid to liquid) clonal replication has been ordered and will soon replace the old one.

Fish & Marine Facility The fish facility provides maintenance and stock supply for the research groups working with both zebrafish (Danio rerio) and medakafish (Oryzias latipes). The marine facility serves to maintain and propagate several marine species, including the annelid worm Platynereis dumerilii, the marine midge Clunio marinus, and the sponge Suberites domuncula. The facilities include special shelving for chronobiological and sensory experiments, equipment for microinjections, as well as computer-assisted long-term video tracking systems for behavioural experiments. The facilities also serve as a central support for the University of Vienna Research Platform “Rhythms of Life”.

Histology Facility The facility is equipped to produce high quality microscopic sections of frozen and paraffin-embedded material. Digital image capture and image analysis are available for bright field- and stereo-microscopy. Introduction, basic training and update sessions are held on demand by facility manager Irmgard Fischer.

Plant Growth Facility The facility operates greenhouses for low cost plant growth, when temperature or humidity conditions have to correspond to pre-set values with only limited precision. In addition, growth incubators are provided for small-scale experiments under non-standard conditions when precise control of humidity and temperature conditions is necessary. Furthermore, a tissue culture room for growth of plants on petri dishes and as sterile in vitro cultures is available. The facility complements the VBCF-operated growth chambers (VBCF Plant Sciences Facility).

The facility provides proteomics services using a range of state of the art LC-MS analysis platforms and bioinformatic tools for the identification and quantification of peptides, proteins, and their post-translational modifications. In 2016, we have launched new services for intact protein mass analysis and for cross-linking mass spectrometry. For measurements we have access to the stateof-the-art instrument park provided by VBCF, which was recently upgraded with a Waters Synapt G2-Si HDMI Q-TOF and a Thermo Orbitrap Fusion Lumos. Additionally, we offer training by providing courses on mass spectrometry based proteomics for under- and postgraduates. The facility is run in close cooperation with the Protein Chemistry Group of the IMP to efficiently maintain the analytical and computational equipment at peak performance and to promote scientific interactions at the Vienna Biocenter.

Monoclonal Antibody Facility The facility specializes in the generation of custom-designed high quality mouse monoclonal antibodies against any custom antigens, e.g. peptides, recombinant proteins, post-translational modifications and non-peptide antigens. The facility is highly sought after by the local but also the international research community.

Structural Biology Equipment Park The available equipment covers facilities for protein expression (in E. coli, insect and mammalian cells) and purification (8 FPLC’s), biophysical/biochemical characterisation - dynamic and static light scattering, circular dichroism, differential scanning calorimetry and fluorimetry, isothermal calorimetry, UV/VIS absorption and fluorescence spectrophotometers; kinetic spectroscopy: stopped flow including fluorescence, fluorescence anisotropy; fluorescence correlation spectroscopy with confocal microscopy including FIDA, PCH. Additionally, the Laura Bassi Centre for Optimised Structural Studies has established a platform for production of recalcitrant proteins in E. coli and baculovirus infected insect cells, employing nested constructs approach, automated expression screening and purification, and pull-down screens for identification and quantification of protein-protein interactions. Equipment for macromolecular crystallography comprises nano-drop crystallization robotics (Phenix, Mosquito, Oryx) and multi-purpose liquid handling robot (Hamilton), two crystal imaging robots (rigaku Gallery, Formulatrix Rock Imager) and a liquid handling robot dedicated to refinement of crystallization conditions (Alchemist), together with high-end X-ray diffraction equipment composed of a small focus high brilliance rotation anode generator, CCD detector, multi-axis goniometer and a cryo-cooling device. The most recent purchases (2016) were crystal imaging robot Rockimager (Formulatrix) and crystallization nano-drop robot Mosquito (TTP Labtech).


Education & Training One of MFPL’s biggest assets is our focus on the education and training of young scientists. MFPL provides an exciting scientific environment for Master students, PhDs and Postdocs in an outstanding international community at the Vienna Biocenter (VBC). Find out more about education and training at MFPL on our website:

As part of the Vienna Biocenter (VBC), MFPL enables students to participate in high quality research in an academic environment and to establish connections with nearby companies and institutes.

the practical courses for the studies of molecular life sciences take place on the premises of the MFPL. Over 460m2 of teaching lab space offer well equipped, state-of-the-art training workspaces for undergraduate students.

Studies at the University of Vienna:

VBC Summer School

Studies at the Medical University of Vienna:

Student Service Center

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Bachelor of Biology Masters of Molecular Microbiology, Microbial Ecology and Immunobiology Masters of Molecular Biology Masters of Genetics and Developmental Biology PhD in Molecular Biology

Diploma in Human Medicine Masters of Medical Informatics PhD in Medical Science

Undergraduate Studies and Teaching

MFPL scientists participate in the undergraduate curricula for students of the University of Vienna and the Medical University of Vienna. In 2016, they invested around 1,200 hours to educate and inspire new generations of scientists. Most of 30

A number of our research groups participate in the Vienna Biocenter Summer School, which offers 12week courses for undergraduate students during the summer months. Working side by side with our scientists, students get insights into worldclass research and prepare for graduate studies in molecular or cell biology.

The Student Service Center provides information about the study programs of the University of Vienna at MFPL, helps students and teachers with administrative procedures and organizes all teaching affairs from the scheduling of lectures to the awarding of degrees. SSC Team Barbara Hamilton (Head) Angela Witte (Deputy Head) Renate Fauland


Vienna Doctoral School “Molecules of Life” MFPL is strongly committed to provide interdisciplinary training and research opportunities for PhD students in a highly attractive and inspiring research environment.

Vienna Biocenter PhD Programme Groups at the Max F. Perutz Laboratories also participate in the Vienna Biocenter (VBC) PhD Programme.

The Vienna Doctoral School (VDS) “Molecules of Life”, located at the MFPL, is a joint initiative of the University of Vienna and Medical University of Vienna established to foster education, cooperation and interaction among students and group leaders from different backgrounds and disciplines in an open and creative environment. Both MFPL scientists and scientists based elsewhere in the Universities cooperate to help talented PhD students to become excellent researchers with a competitive professional profile, by fostering independence, inquisitive thinking and scientific rigor. MFPL is currently home to 150 PhD students from 30 countries who pursue their research in the open, collaborative environment of the Vienna Biocenter (VBC).

The VBC PhD Programme is an international doctoral programme in Life Sciences that aims to empower curious researchers. The training is focused around a research project - students learn science by doing science - and the programme ensures that students have the necessary support and resources. All PhD Students participate in an introductory course at the beginning of their training, which can then be furthered by an elective program designed for and with PhD Students: advanced courses (e.g. writing, programming, advanced microscopy, data analysis, etc.) and career development workshops. Plus, the campus has a vibrant scientific atmosphere (with an average of four invited speakers per week) and is supported by outstanding scientific facilities.

VDS PhD students are recruited via a structured selection and interview process. They have a primary affiliation with one of the participating research groups, and are enrolled as graduate students at the University of Vienna or the Medical University of Vienna. All PhD students at the MFPL receive a competitive salary conforming to the guidelines of the Austrian Science Fund (FWF).

IMP, IMBA, GMI and MFPL jointly organize the VBC PhD Programme, in collaboration with the University of Vienna. The VBC PhD Programme opens two calls for applicants per year; each offering around 20 fully funded PhD Positions.

PhD Community Currently, the 150 PhD students from all over the world form an active community at MFPL. Their elected representatives organize professional as well as social activities and make their voices heard in MFPL’s decision bodies. Scientific Training Coordinator Inês Crisóstomo PhD Program Coordinator Manuela Baccarini School Manager Gerlinde Aschauer

PhD Representatives 2016 Daniel Serwas Stefan Benke

Programme Administrator Christopher Robinson 31


Topic-focused Doctoral Program Tracks at MFPL MFPL is proud to host four Doctoral Programs reviewed and funded by the Austrian Science Fund (FWF). • • • •

Chromosome Dynamics Molecular Mechanisms of Cell Signaling RNA Biology Integrative Structural Biology

Each of these programs involves several of our research groups and offers a specific curriculum fitting its scientific focus. More information about the programs can be found on our website:

Chromosome Dynamics DNA encodes the genetic information, the blueprint for any living organism. In higher eukaryotes, it resides in the cell nucleus, is associated with proteins forming chromatin and partitioned into linear units called chromosomes. The readout of genetic information, its maintenance and faithful transmission from one generation to the next depends on intact chromosomes. Untimely structural changes, failure to protect DNA from deterioration, impaired DNA repair or missegregation of chromosomes during cell division seriously compromise the fitness of the organism and cause numerous pathologies. Understanding the molecular basis of chromosome maintenance and dynamics is therefore essential for human health and fertility, for plant breeding but also for industrial and food production. The principal investigators, contributing to the program make students familiar with a wide range of unanswered questions in the field of chromosome biology, different model organisms, experimental approaches, techniques and perspectives. Participating research groups belong to three hosting institutions: The Max F. Perutz Laboratories, the Gregor Mendel Institute (GMI) and the Institute of Molecular Biotechnology, and focus on closely related research


topics including (somatic and meiotic) DNA repair, chromosome organization, movement and segregation, telomere function, dynamics of chromatin modifications and gene regulation. The doctoral program established platforms for seminars and retreats to train students to present their research, critically evaluate their results and foster intellectual exchange. Special workshops, with an emphasis on state-of-the-art techniques for chromosome research, scientific conduct, data presentation and career planning, enable students to reach beyond their actual PhD topic while gaining a comprehensive understanding of ‘chromosome metabolism’. All involved faculty members are committed to high-quality education and seek to support and nurture skilled, enthusiastic, critically thinking researchers to gain a profound education in chromosome biology. Speaker Peter Schlögelhofer Program Manager Marie-Therese Kurzbauer


Molecular Mechanisms of Cell Signaling

From organisms to cells to molecules – MMCS groups investigate signalling at different levels.

Cells manage to survive, proliferate, and differentiate in their environment by interpreting the signals they receive from it and translating them into the right output. If signalling goes awry, even only in part of the cells, the whole organism is at risk. The MFPL are home to a strong group of scientists whose common long-term research goal is to investigate and understand signal transduction mechanisms in a variety of cell-based

Integrative Structural Biology The FWF supported doctoral program “Integrative Structural Biology” started on 1st January, 2016. The eight faculty members (six from MFPL, one from IMP and one from the Medical University of Vienna in the 9th district) of this program apply structural and biophysical techniques to a wide range of biological systems Structure-function relationships in the introducing state-of-the-art doctoral program “Integrative Structural techniques, methodology and Biology” theory to the PhD students. Ten highly qualified students (from eight different countries, three are from Austria) were accepted into the program in the first part of 2016. Their first task was to complete an intensive three month, specially designed training program to ground them in the basic techniques and concepts of structural biology as well as writing their thesis proposals. Following the presentation of their PhD theses at the kick-off meeting of the PhD Program in July, the students have now started their research work. All of the projects use an integrated structural biology approach on topics ranging from infection biology through muscle structure to chromosome and centriole arrangements to the properties of intrinsically unstructured proteins. Both faculty and students look forward to an exciting three years with new discoveries and insights into their respective biological system. Speaker Tim Skern

Vice-Speaker Kristina Djinović-Carugo

Program Manager Sofiya Fedosyuk


and organismal systems. The program offers structured, stateof-the-art training in signal transduction and competitive PhD projects that combine biochemistry, molecular biology, cell biology, and genetics to study cell signalling in different model organisms. Speaker Manuela Baccarini

RNA Biology

RNA Lecture Seri es 2016

The RNA Biology C Network brings F A L C together 20 C D A K research groups M L K P from the MFPL, N R J S the Medical UniI U E W versity of Vienna, the University of Vienna, IMBA, IMP and GMI, and provides a focused PhD training in the world of RNAs – covering the areas structure & folding, translation, transcriptomics & bioinformatics, regulatory RNAs, RNA processing & transport, epigenetics & gene expression. Students are given the opportunity to embark on a scientific adventure and profit from this network by getting excellent advice from researchers of various RNA fields. They are also integrated into the Special Research Program on “RNA Regulation of the Transcriptome”. ONFIRMED SPEA KERS RÉDÉRIC


LLAIN (ETH Zuric h)

RONIN (University of Glasgow) ARGEMONT (CNR





S Paris)




Speaker Andrea Barta Program Manager Zahra Ayatollahi

(MDC Berlin)

UTHERLAND (MRC LMB Camb ridge) LITSKY (Weiz mann Institu

te of Science, Reho vot) ESTHOF (Univ ersity of Strasbourg )


VIPS - Vienna International Postdoctoral Program

©Daniel Hinterramskogler

Since 2010, the MFPL have hosted the Vienna International Postdoctoral Program for Molecular Life Sciences (VIPS), a pioneering program promoting outstanding young researchers.

With support from the Austrian Government and the City of Vienna, VIPS has offered three-year Postdoctoral fellowships at the Max F. Perutz Laboratories, including an individual research budget and travel money, which is at the free disposal of the fellow. The VIPS Program ends in December 2016.

VIPS Fellows

20 Postdocs were awarded a VIPS fellowship: Stephanie Bannister – Group Florian Raible (April 2011 – March 2014) Gustavo Bezerra – Group Kristina Djinović (March 2013 – Dec. 2016) Thorsten Brach – Group Claudine Kraft (Jan. 2012 – Dec. 2014) Nicola Cavallari – Group Andrea Barta (Jan. 2013 – Oct. 2015) David Cisneros Armas – Group Alipasha Vaziri (Feb. 2012 – Jan. 2015) Marcus Dekens – Group Kristin Tessmar-Raible (Nov. 2013 – Oct. 2014) Jeroen Dobbelaere – Group Alexander Dammermann (April 2013 – Dec. 2016) Daniela Hahn – group Alwin Köhler (Sept. 2011 – Feb. 2013) Angela Hancock – Group Joachim Hermisson (Sept. 2011 – June 2014) Tobias Kaiser – Group Kristin Tessmar-Raible (Feb. 2011 – Jan. 2014) Elzbieta Kowalska – Group Christina Waldsich (April 2012 – Sept. 2015) Jana Link – Group Verena Jantsch (Aug. 2016 – Dec. 2016) Bianca Mladek – group Bojan Zagrovic (March 2011 – May 2013) Maxim Molodtsov – Group Alipasha Vaziri (Feb. 2012 – Jan. 2015) Susanne Pfeifer – Group Arndt von Haeseler (Jan. 2013 – March 2015) Robert Prevedel – Group Alipasha Vaziri (Sept. 2011 – July 2016) Roger Revilla-i-Domingo – Group Florian Raible (March 2012 – Dec. 2016) Ana Catarina Ribeiro Carrão – Group Roland Foisner (April 2011 – Oct. 2015) Jusytna Sawa-Makarska – Group Sascha Martens (Sept. 2010 – April 2015) Petronela Weisová – Group Friedrich Propst (Jan. 2011 – Feb. 2015)


VIPS associated Postdocs

Christelle Bourgeois – Group Karl Kuchler Brooke Morriswood – Group Graham Warren Nicolas Coudevylle – Group Robert Konrat Teresa Cvetkov – Group Thomas Leonard Marlene Jagut – Group Verena Jantsch Meghan Lybecker – Group Renée Schroeder Gernot Walko – Group Gerhard Wiche

Career Development for Postgraduates

As well as Postdoc positions, VIPS has offered a wide range of career development activities and training not only for the VIPS Postdocs but also for all postgraduates at MFPL: • mentoring and coaching • project management and leadership • communication and presentation • publication writing • time management • grant writing VIPS Scientific Coordinator Renée Schroeder Program Manager Gerlinde Aschauer Postdoc Representatives Gustavo Bezerra Roland Tschismarov



The VBC PhD awardees 2016, from left to right: Daniel Papinski, Vitaly Sedlyarova (on behalf of Nadezda Sedlyarova), Renée Schroeder, Kikue Tachibana-Konwalski (on behalf of Sabrina Ladstätter), Florian Weissmann.

Science is about making connections Research is a profession dependent on collaboration and intellectual exchange. At the Vienna Biocenter (VBC), scientific exchange is an intrinsic quality of the strong interconnections between all the institutions, basic research centers and companies alike. Regular seminar series are organized by all VBC members, VBC-wide as well as intra-institutional. The weekly VBC Seminar Series serves as a platform for scientists from the VBC to exchange ideas and discuss their research.

MFPL Regular Seminars

The weekly MFPL Faculty Lunches serve as a platform for group leaders to present their work in a chalk board talk to other faculty members and discuss new ideas and directions for their groups. In addition, there are also thematically focused seminar series, like the seminar series “Modern Concepts in Structural Biology”.


The MFPL Postdoc community is part of the larger Vienna Area Postdoc Association (VAPA) that represents the institutes at the Vienna Biocenter (GMI, IMBA, IMP and MFPL) as well as CEMM and 36

ISTA. The aim of VAPA is to provide a platform for all Postdocs in Vienna to develop their scientific careers and use the Postdoc network for their benefit.

VBC PhD Symposium 2016

The scientific exchange between the PhD students at the Vienna Biocenter bears fruit each autumn in the form of a PhD symposium. The symposium, which each year is organized by students for students, is intended to widen students’ perspectives by exploring a topic of their choosing. The 14th symposium, entitled “Mind the App – Applications that Bridge Biology and Technology”, included sessions from 15 international scientists who have unconventionally applied technology to basic research or conceived an innovative application from a scientific finding. Topics included “Molecular Toolbox”, “Bioengineering Medicine”, “Manipulating the Code” and “Shaping Ecosystems”. Each year at the end of the symposium, outstanding PhD theses are rewarded with a VBC PhD award. This year, the awardees were Daniel Papinski (Kraft lab, MFPL), Nadezda Sedlyarova (Schroeder lab, MFPL), Sabrina Ladstätter (Tachibana-Konwalski lab, IMBA) and Florian Weissmann (Peters lab, IMP).


The Vienna Doctoral School (VDS) “Molecules of Life” kick-off lecture and retreat

Participants of the first VDS Retreat

VDS kick-off lecture, open to the public

The start of the new Vienna Doctoral School, “Molecules of Life”, established at MFPL in March 2016, was celebrated with a first-class kick-off lecture, as none other than star-microbiologist Emmanuelle Charpentier delivered the keynote speech. Charpentier played a pivotal role in the discovery in the revolutionary genome editing tool, CRISPR-Cas9, and came to Vienna especially for the occasion. Introduced by the University of Vienna’s Vice-rector Faßmann and the Medical University of Vienna’s Rector Müller, the lecture was chaired by MFPL PhD student Stefan Benke and complemented by a talk from Kevin Eislmayr, a PhD student at MFPL. Both Stefan and Kevin delivered confident, excellent performances. What united the students, faculty and press present in the audience was the importance of PhD Education, this importance being underlined by the presence of the rectorate and representatives of various departments.

In looking forward to an exciting first year of “Molecules of Life”, the first retreat was held at Balaton Lake in Hungary.

Reflecting the VDS’s philosophy of promoting interdisciplinary research, the first retreat was attended by close to 100 PhD students, postdocs and group

leaders from different institutes across Vienna. The retreat, flawlessly organized by VDS manager Gerlinde Aschauer, provided the opportunity for PhD students and Postdocs to present their research to colleagues and PIs during talks and poster sessions. Networking and team building activities were also very successful during the three-day retreat at the Balaton lake in Hungary, as new professional connections were forged over food and drinks. Two best talk prizes and three best poster prizes were awarded by the attending faculty – all ex aequo - a difficult choice since everybody played their “A” game. Illustrating the interdisciplinary nature of the retreat, talk prizes were awarded to evo-devo biologist Katja Pukhlyakova, who talked about the ancient origin of systems sensing mechanical stress; and to structural biologist Borja Mateos, who told us about his dream of in-cell structural biology. The three poster prizes went to molecular biologists Andrés Magan García and Isabella Zink, for their work on antisense transcription and on the application of CRISPR to knockdown genes in Archeae, respectively. Philipp Rescheneder won the third poster prize reporting new bioinformatics approaches for the interpretation of new generation sequencing data. Manuela Baccarini, scientific coordinator and founder of the VDS, was delighted by the many attendees and by the high quality of the work presented: “Well done everybody, you really got your message across!” 37

Emmanuelle Charpentier at the VDS kick-off lecture



To ensure a relaxing environment allowing scientists to recharge their batteries, the Max F. Perutz Laboratories offer a wide variety of social activities.

Christmas came early in the July Happy Hour

Happy Hours

The MFPL sponsors food and drinks for institute-wide Happy Hours, which are social get-togethers for scientists and staff alike. The Happy Hours offer a unique chance to break the daily routine, meet new people and chat with colleagues in a more relaxed setting. Each organising group is free to choose the theme of their Happy Hour, allowing their creativity a free rein.

MFPL Sports

Several MFPL sports clubs exist, to offer researchers a convenient way to fit sports activities into their busy schedule. Socialising and team building are a pleasant “side effect” of sports activities carried out together. Additionally, the MFPL sponsors special sport events such as the Vienna City Marathon and the Cancer Research Run.

The Vienna Biocenter Amateur Drama Club (VBC ADC)

The Vienna Biocenter Amateur Drama Club (VBC ADC) is an extra-curricular society based on the campus. The members are drawn from all four academic institutes at the VBC (GMI, IMBA, IMP and MFPL) and include students, technicians, group leaders and postdocs. No previous experience is necessary, and the emphasis is very much on having fun. In addition to rehearsing for shows, the club regularly meets for social activities and workshops.

MFPL runners at the Vienna City Marathon 2016

Current or former students, researchers, employees and other affiliates of MFPL are welcome to become members and join the MFPL Community over the website portal. The membership is free of charge. For inquiries and more information, please contact

The VBC ADC summer play “Star Wars – Verily, a new hope” 38

The MFPL team at the Cancer Research Run 2016


One of Europe’s leading Life Science locations

The Vienna Biocenter With around 25 research institutes and companies, 2,100 scientific employees and students, more than 90,000 m2 lab and office space for the Life Sciences, the Vienna Biocenter at Neu Marx is one of Europe’s leading Life Science hubs. The success story of the Vienna Biocenter (VBC) began in the 1980s with the foundation of the Research Institute of Molecular Pathology (IMP), the basic research center of Boehringer Ingelheim. Following the relocation of five university departments –now under the umbrella of the Max F. Perutz Laboratories (MFPL) – to the Neu Marx area in Vienna’s Third District, the VBC continued to grow. These were subsequently joined by the University of Applied Sciences and two flagship institutes of the Austrian Academy of Science, the Institute of Molecular Biotechnology (IMBA) and the Gregor Mendel Institute for Molecular Plant Biology (GMI). Motivated and talented young students are offered two options to pursue their PhD: the VBC PhD Program and the Vienna Doctoral School “Molecules of Life”. During selections that take place twice a year, applicants from all over the world compete for these attractive positions. Furthermore, the VBC summer school provides a unique opportunity for undergraduate students to work together with leading scientists at the VBC. A growing number of biotech-companies complement the training and research activities at the Vienna Biocenter: seventeen commercial companies

currently benefit from academic research at the Vienna Biocenter.

• 4 Academic research centers • 17 Biotech companies • 3 Universities

In addition, the VBC hosts institutes and companies dedicated to science communication. The publicly funded organization Open Science aims to foster a dialogue between the world of science and the public, and runs the Vienna Open Lab (a joint initiative with IMBA), which has already provided 45,000 visitors with a glimpse into the workings of the Life Sciences. Biolution has established a reputation as a professional agency for science PR on Campus.

• 90,000 m2 lab and office space • 45,000 Vienna Open Lab visitors

The research institutes at the VBC are home to 1,400 scientists and 700 students enrolled at the University of Vienna, the Medical University of Vienna and the University of Applied Sciences. One hundred scientific groups with people from 40 nations have acquired 36 ERC grants, 11 Wittgenstein Awards and publish around 350 scientific papers per year. They are supported by the Vienna Biocenter Core Facilities (VBCF), which provides world class scientific infrastructure. Broad expertise, successful collaborations and unique working conditions enable VBC members to be at the forefront of Life Science research.

• 36 ERC Grants • 11 Wittgenstein Awards • 350 Publications / Year


• • • •

1,400 Employees 700 PhD students 100 Scientific groups 40 Nationalities

MFPL wishes to thank the following institutions for financial support of research projects: Parent Institutions

University of Vienna

Medical University of Vienna

Funding organizations and programs (in alphabetical order)


Active Motif

BMWFW – Federal Ministry of Science, Research and Economy

Boehringer Ingelheim

City of Vienna

EMBO – European Molecular Biology Organization

ERC – European Research Council

FFG – Austrian Research Promotion Agency

FWF – Austrian Science Fund

HFSP – Human Frontier Science Program


Neuropore Therapeutics


ÖAW – Austrian Academy of Sciences

Origimm Biotechnology GmbH

Research Executive Agency (REA, EU)

Santa Cruz Biotechnology

Wellcome Trust

Wings for Life

WWTF – Vienna Science and Technology Fund

Herzfelder Stiftung


Max F. Perutz Laboratories Vienna Biocenter (VBC) Dr. Bohr-Gasse 9 1030 Vienna, Austria Phone: +43 1 4277 24001 Fax: +43 1 4277 9240

Publishing Details Published by Max F. Perutz Laboratories Support GmbH Editors Caterina Purini contributions from MFPL researchers Pictures MFPL staff and scientists Daniel Hinterramskogler Point of View Barbara Mair MedUni Wien, Matern IMP/IMBA Graphics Department, Michael Sazel,, Daria Lavysh Layout & Design XeroGrafiX GmbH, Vienna Print

MFPL at a glance 2016