EPFL-SV Global Health Institute Annual Report 2011 by EPFL School of Life Sciences

EPFL School of Life Sciences - 2011 Annual Report

Table Of Contents

INTRO

Main Scientific Events..................................................................................................................6 Public-Oriented Events................................................................................................................6 Honors-Awards-Announcements.................................................................................................7 Undergraduate Studies.................................................................................................................8 Graduate Studies.........................................................................................................................8 School of Life Sciences at a Glance.............................................................................................9 Congratulations to our PhD Grads!............................................................................................10

Core Facilities & Technology Platforms............................................................................13 Bioelectron Microscopy.............................................................................................................14 BioImaging & Optics.................................................................................................................15 Bioinformatics & Biostatistics.....................................................................................................16 Biomolecular Screening.............................................................................................................17 Flow Cytometry ........................................................................................................................18 Histology ..................................................................................................................................19 Proteomics.................................................................................................................................20 Protein Crystallography..............................................................................................................21 Protein Expression.....................................................................................................................22 Transgenic ................................................................................................................................23 Phenotyping Unit.......................................................................................................................24

BMI - Brain Mind Institute...............................................................................................27 Aebischer Lab............................................................................................................................28 Blanke Lab.................................................................................................................................30 Fraering Lab...............................................................................................................................32 Gerstner Lab..............................................................................................................................34 Hadjikhani Group......................................................................................................................36 Herzog Lab................................................................................................................................38 Lashuel Lab...............................................................................................................................40 . ................................................................................................................42 Luthi-Carter Lab Magistretti Lab...........................................................................................................................44 Markram Lab.............................................................................................................................46 Moore Lab.................................................................................................................................48 Petersen Lab..............................................................................................................................50 Sandi Lab...................................................................................................................................52 Schneggenburger Lab................................................................................................................54 Blue Brain Project......................................................................................................................56

IBI - Institute of Bioengineering.......................................................................................59 Auwerx - Schoonjans Lab..........................................................................................................60 Barrandon Lab...........................................................................................................................62 Dal Peraro Lab...........................................................................................................................64 Deplancke Lab..........................................................................................................................66 Hubbell Lab...............................................................................................................................68 Lutolf Lab..................................................................................................................................70 Naef Lab....................................................................................................................................72 Swartz Lab.................................................................................................................................74 Wurm Lab.................................................................................................................................76

Co-affiliated Research Groups.........................................................................................78 Aminian Lab..............................................................................................................................78 Fantner Lab . .............................................................................................................................79 Guiducci Lab.............................................................................................................................80

EPFL School of Life Sciences - 2011 Annual Report

Hatzimanikatis Lab....................................................................................................................81 Ijspeert Lab................................................................................................................................82 Johnsson Lab.............................................................................................................................83 Jolles-Haeberli Lab ...................................................................................................................84 Lacour Lab ...............................................................................................................................85 Maerkl Lab ...............................................................................................................................86 Mermod Lab..............................................................................................................................87 Millán Lab ................................................................................................................................88 Pioletti Lab ...............................................................................................................................89 Psaltis Lab ................................................................................................................................90 Radenovic Lab . ........................................................................................................................91 Roke Lab ..................................................................................................................................92 Stergiopulos Lab .......................................................................................................................93 Van de Ville Lab . ......................................................................................................................94 Van den Bergh Lab ...................................................................................................................95

GHI - Global Health Institute..........................................................................................97 Blokesch Lab.............................................................................................................................98 Cole Lab..................................................................................................................................100 Doerig Lab...............................................................................................................................102 Fellay Lab................................................................................................................................104 Harris Lab................................................................................................................................106 Lemaitre Lab............................................................................................................................108 McKinney Lab.........................................................................................................................110 Trono Lab................................................................................................................................112 Van der Goot Lab....................................................................................................................114

ISREC - Swiss Institute for Experimental Cancer Research......................................117 Aguet Lab................................................................................................................................118 Beard Lab................................................................................................................................120 Brisken Lab..............................................................................................................................122 Constam Lab............................................................................................................................124 De Palma Lab..........................................................................................................................126 Duboule Lab............................................................................................................................128 Gönczy Lab.............................................................................................................................130 Grapin-Botton Lab...................................................................................................................132 Hanahan Lab...........................................................................................................................134 Hantschel Lab..........................................................................................................................136 Huelsken Lab .........................................................................................................................138 Kühn Lab.................................................................................................................................140 Lingner Lab..............................................................................................................................142 Meylan Lab..............................................................................................................................144 Radtke Lab...............................................................................................................................146 Simanis Lab.............................................................................................................................148 Bucher Group..........................................................................................................................150

Other Professors............................................................................................................152 Knowles...................................................................................................................................153 Molinari Group........................................................................................................................154 Rainer Group...........................................................................................................................156 Schorderet Group....................................................................................................................158 Tanner.....................................................................................................................................160

Introduction

Welcome To Our New Collaborators!............................................................................161

EPFL School of Life Sciences - 2011 Annual Report

Preamble Whether paving the way to personalized medicine or meeting our planet’s environmental challenges, trans-disciplinary approaches will be the key to research and education in the life sciences. It is with a true pioneering spirit that our school is geared to train a new breed of engineers/scientists endowed with quantitative and integrative skills. In accordance with this objective, our close to fifty research groups push for holistic approaches that span a range of disciplines from functional genomics to high-tech bio-engineering, and from computer neurosciences to structural modeling. A bachelor degree (Life Sciences and Technology), two masters degrees (Life Sciences and Technology; Bioengineering), and three Ph.D. programs (Biotechnology and Bioengineering; Neurosciences; Molecular Life Sciences), constitute the educational arms of our school, hosting some six hundred students from all geographic and scientific horizons. Our first classes of Engineers in Life Sciences and Technology are now in the greater world. In 2011, our faculty further increased its team of ERC grant recipients to a total of 12 (9 seniors, 4 juniors), launched the Center for Neuroprosthetics in association with the School of Engineering, held its first SV Research Day for the wider EPFL community, and established very productive interactions with its new neighbor, the Nestlé Institute for Health Sciences. These are exciting times to be at the EPFL School of Life Sciences! Didier Trono, M.D. Professor & Dean of the School of Life Sciences Ecole Polytechnique Fédérale de Lausanne (Switzerland)

Introduction

http://sv.epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

Main Scientific Events

INTRO

March 14th - 15th: A Symposium on Stress, the Social Brain and Psychopathology was organized by Prof. Sandi (BMI) which brought together international leading scientists to discuss work done on human and animal models. The meeting was attended by over 100 participants. May 2nd - 3rd: Experts from India and Switzerland were brought together for a Indo-Swiss Symposium on Infectious Diseases hosted by the GHI. India and Switzerland share many common interests in the fields of science and medicine and both countries have exceptional expertise in the areas of HIV/AIDS, malaria and tuberculosis, human diseases of global importance. May 30th: A one day symposium was organized by the GHI called GMS 2011 “Gut Microbiota in Health and Disease”. Areas such as microbial communities (ecology, metabolism) and mucosal immunology were presented and discussed by young international experts in the field. July 4th to August 26th: The 2011 International Summer Research Program for undergraduate students welcomed 26 high potential future researchers from all over the world. They joined the SV labs and learned cutting edge research techniques while investigating scientific questions relevant to today’s world. September 7th - 10th: The annual Life Sciences Symposium was hosted by ISREC, on the theme “Hallmarks and Horizons of Cancer”, with a world-class roster of speakers. The symposium was a resounding success, with well over 600 applicants. The 2011 Debiopharm Life Sciences Award was given to Professor Stefano Piccolo, from the University of Padua, Italy.

Public-Oriented Events March: The SV labs welcomed 10 enthusiastic high school students from all corners of Switzerland under the framework of La Science Appelle les Jeunes! (Schweizer Jugend forscht!) These students experienced first-hand lab work and completed and presented a mini-project. http://fr.sjf.ch/index.cfm March: The undergraduate (or Bachelor-Master) teaching section in Life Sciences and Technologies participated in the EPFL Prospective Students Days and welcomed more than 150 high school and “Lycées” students from the French speaking areas of Switzerland and France. The same event took place for Swiss Italian and Swiss German speaking high school students in November. More information : http://ssv.epfl.ch/gymnasiens June 8th: The first SV Research Day was held with the theme of “Towards Personalised Medicine”. Non-bio EPFL scientists were cordially invited to attend.

EPFL School of Life Sciences - 2011 Annual Report

Honors-Awards-Announcements February: The EPFL, has joined with AstraZeneca, Sanofi-Aventis, the Universities of Pavia, Uppsala and Cambridge, and 19 other research groups from 13 different countries, to form the More Medicines for Tuberculosis (MM4TB) consortium, which aims to develop new drugs for successful and shorter treatment of Tuberculosis (TB). This consortium is led by TB expert Professor Stewart Cole (GHI). March: On World Tuberculosis Day (24 March 2011), Dr Neeraj Dhar, senior scientist within the research group of Prof. John McKinney (GHI) received the “2011 Swiss TB Award” from the Swiss Foundation for Tuberculosis Research. March: Prof. Melody A. Swartz (IBI), Head of the Laboratory of Lymphatic and Cancer Bioengineering, together with Prof. Stephanie Hugues, Department of Pathology and Immunology at the University of Geneva won one of the 2011 Leenaards Foundation’s Scientific Prizes for their project on an emerging therapeutic approach to destroy cancer cells by activating the body’s immune system. April: Tej Tadi, PhD student in Prof. Olaf Blanke’s lab (BMI), was awarded two prizes: the “Lausanne Entrepreneurship Region” PERL Prize for his start-up “MindMaze” and one of EPFL’s prestigious PhD prizes, the Chorofas Award. April: PhD student Alireza Roshan Ghias from the Laboratory of Biomechanical Orthopedics (Director Prof. Dominique Pioletti, IBI), was awarded the Swiss Bone Mineral Society’s President Award for an outstanding publication (European Cell and Materials) in 2010. May: Douglas Hanahan (ISREC) was awarded an honorary degree from the University of Dundee, Scotland, UK. September: Denis Duboule (ISREC) received the Annual Prize of the Fondation pour Genève and the EPFL Polysphere Prize for teaching in Life Sciences. September: Etienne Meylan (ISREC) was honored with a Debiopharm Group Junior Life Sciences Award. October: Congratulations to Prof. Carl Petersen (BMI) for his European Research Council (ERC) Advanced Grant. October: Patrick Aebischer (BMI) has received a Dr. Honoris Causa from the Ecole Polytechnique of the University of Montreal. October: Henning Sprekeler, PostDoc from Prof. Gerstner’s Computational Neuroscience Lab (BMI), received the very prestigious Berstein Award that will allow him to start his own research group in Germany. October: José del R. Millán (IBI) received the IEEE Nobert Wiener Award for “seminal and pioneering contributions to non-invasive brain-computer interfaces, in particular brain-controlled robots, wheelchairs and prostheses”, at the IEEE International Conference on Systems, Man, and Cybernetics. November: Harvard Medical School and Ecole Polytechnique Fédérale de Lausanne (EPFL) launched a Joint Program to “Improve Quality of Life for People With Neurological Disabilities” joining forces to combine neuroscience and engineering in order to alleviate human suffering caused by such neurological disabilities as paralysis and deafness. Collaboration on six pioneering neuroengineering projects was made possible by a grant from the Bertarelli Foundation.

Introduction

November: The Zonta Award was presented to Stéphanie Lacour (IBI) for her work on creating an electronic artificial skin which could help repair nerves that have been severed due to a serious accident.

EPFL School of Life Sciences - 2011 Annual Report

Undergraduate Studies

INTRO

The Life Sciences curriculum aims to educate a new generation of engineers who can master the technical and scientific skills needed for studying life processes and developing the biomedical technologies of tomorrow. This educational program, established under the direction of Prof. William F. Pralong, M. D., is unique in Switzerland and Europe.

Bachelor’s Program (3 years)

The first two years provide basic courses followed throughout the EPFL, such as analysis, linear algebra, physics, chemistry (general and organic), statistics and numerical methods. Specific courses in Life Sciences begin with biochemistry, cellular, molecular biology, biophysics, computer sciences, and biothermodynamics. In the first two years, life sciences courses make up less than 20% of the total academic load. In the third year, engineering courses (signals and systems, electronic and electrical systems) and typical life sciences courses such as genetics and genomics, immunology, developmental biology, bio-computing, systems biology via the study of human physiology are integrated. Physiology also gives the opportunity to integrate the engineering and biological knowledge acquired up to this point. During this year, the students also fine tune their training by choosing some specific credits to better prepare themselves for one of the orientations offered in our masters’ programs. This includes a bachelor project either in bioengineering, in bio-computing, in biomedical technologies, in neurosciences, or in molecular medicine.

Master’s Programs (2 years)

The Master’s in Life Science and Technology includes several orientations. Among these are neurosciences, molecular medicine, and bio-computing. Each orientation is made up of 30 credits of optional courses selected under the supervision of a mentor. Students aiming to focus their training on interdisciplinary subjects will have the possibilities to choose different minors such as bio-computing, computing neurosciences and neuroprosthetics. The Master’s in Bioengineering is organized in collaboration with STI, and provides classical courses in bioengineering; in addition students can chose different possible orientations through the choice of a minor such as biomedical technologies (STI), biotechnology(SB), bio-computing (I&C), or neuroprosthetics. Each minor requires taking 30 specific credits chosen under the guidance of a mentor. The minors, as indicated, are organized within the different schools at EPFL. Both degree programs share some common basic curriculum that aims to provide students with the knowledge of the modern technologies used in the life sciences such as imaging, bio-computing and optical systems applied to biology, etc.... In addition, courses in management, economics, applied laws and ethics for the life sciences are offered. A large portion of the master’s program (60 credits) can be dedicated to laboratory work and projects. http://ssv.epfl.ch/

Graduate Studies

All three graduate programs comprise a combination of coursework, laboratory-based research, in-house seminars, and national or international conferences. Highly qualified applicants worldwide are chosen twice a year through a competitive selection procedure.

The Doctoral Program in Biotechnology and Bioengineering aims at providing doctoral students with the education

necessary to be leaders in the fast-growing industrial and academic biotechnology and bioengineering sectors, i.e. a depth of knowledge and competence in their specific research area as well as a breadth of knowledge in biology, bioengineering and biotechnology. These program themes include: genomics and proteomics, biomolecular engineering and biomaterials, stem cell biotechnology, cell and process engineering, biochemical engineering, orthopaedic engineering, biomechanics, mechanobiology, cell biophysics, computational biology, biomedical imaging as well as molecular, cell and tissue engineering. http://phd.epfl.ch/edbb

The Doctoral Program in Neuroscience provides its students with training from the genetic to the behavioural level including molecular, cellular, cognitive, and computational neuroscience. Students enroll in the highly dynamic and interdisciplinary environment of the BMI-EPFL of the SV. The program is further strengthened by research and training opportunities in collaboration with the Universities of Lausanne and Geneva. ‘http://phd.epfl.ch/edne The Doctoral Program in Molecular Life Sciences is a joint program between the Swiss Institute for Experimental Cancer Research (ISREC-EPFL) and the Global Health Institute (GHI-EPFL). The program provides training and research opportunities to highly motivated doctoral students in key areas of modern biology. http://phd.epfl.ch/edms/en

EPFL School of Life Sciences - 2011 Annual Report

INTRO

Congratulations to our PhD Grads! Mr. Alessandro Wataru Amici

EDBB

Prof. Yann Barrandon

The Role of LEKTI in Fate Determination of Keratinocyte Stem Cells

Ms. Julie Deuquet Ariosa

EDBB

Prof. Gisou van der Goot

Molecular mechanisms underlying Hyaline Fibromatosis Syndrome

Ms. Elena Aritonovska

EDMS

Prof. Joachim Lingner

Insight into the Regulation of Telomerase Access to Telomeres by Shelterin Proteins

Mr Maxime Baud*

EDNE

Prof. P. Magistretti/ Dr J.-M. Petit

The Impact of Sleep Fragmentation on Sleep Homeostasis, Brain and Peripheral Energy Metabolism and Spatial Learning

Ms. Alexandra Bezler

EDMS

Prof. Pierre Gönczy

Mutual Inhibition Between the Anaphase-promoting Complex and the Spindle Assembly Checkpoint in C. Elegans Embryos

Mr. Jorge Castro

EDNE

Prof. Carmen Sandi

Psychobiological Vulnerability to Stress: Behavioral Traits and Neurobiological Mechanisms

Mr. Philippe Coune

EDNE

Prof. P. Aebischer/ Dr B.Schneider

Alpha-Synuclein Effects at the ER-to-Golgi Level and Potential Biomarkers in Rat Models of the Early Phase of Parkinson's Disease

Mr. Sebastian Dieguez

EDNE

Prof. Olaf Blanke

Bodily Ownership: Tactile, Visual and Motor Mechanisms

Ms. Anja Dietze

EDMS

Prof. Daniel Constam

Role of Nodal Processing in Pluripotent Progenitors

Mr. Thomas d'Eysmond

EDBB

Prof. Felix Naef

On the Precision of Circadian Oscillators

Mr. Rodrigo Manuel Gonzalez EDBB

Prof. Gisou van der Goot Cellular Responses to Bacterial Pore-Forming Toxins

Ms. Chiara Greggio

EDMS

Definition of in Vitro Microenvironments to Prof. Anne Grapin-Botton Characterize and Control Pancreatic Progenitor Expansion and Differentiation

Ms. Anna Claire Groner

EDBB

Prof. Didier Trono

Studies on KRAB/KAP1-mediated long-range repression and its potential as a tool

Ms. Yunyun Han

EDNE

Prof. Ralf Schneggenburger

RIM Determines Ca2+ Channel Density and Vesicle Docking at the Presynaptic Active Zone

Mr. Lukas Heydrich*

EDNE

Prof. Olaf Blanke

Turning Body and Self Inside Out: Extero- and Interoceptive Signal Integration in Temporo-Parietal and Insular Cortex

Ms. Jemila Houacine

EDNE

Prof. Patrick Fraering

The Gamma-Secretase-Mediated Proteolytic Processing of APP C-Terminal Fragments as a Therapeutic Target for Alzheimer's Disease

Ms. Mircea Ioan Iacovache

EDBB

Prof. Gisou van der Goot

Folding and Structure of the Pore Forming Toxin Aerolysin

Mr Asif Jan

EDNE

Prof. H.Markram/ Dr F.Schürmann

A Pipeline Based Approach for Experimental Neuroscience Data Management

Ms. Ana Jovicic

EDNE

Prof. Ruth Luthi-Carter

Unique Cell-Type-Specific Distributions and Functions of Brain MicroRNAs

Ms. Susanna Eveliina Kallioinen

EDMS

Prof. Daniel Constam

Activin Signalling in Human Melanoma Cells

EPFL School of Life Sciences - 2011 Annual Report

Mr. Georges Khazen

EDNE

Prof. Henry Markram

Predictive Engineering the Membrane Composition of Neocortical Neurons

Mr. Stephane Kontos

EDBB

Prof. Jeffrey Hubbell

Engineering erythrocyte affinity for improved pharmacokinetics and immune tolerogenesis

Ms. Kristen Lorentz

EDBB

Prof. Jeffrey Hubbell

Biofunctional Scaffold Design for Soft Tissue Regeneration

Ms. Alexandra Magold

EDNE

Prof. Patrick Fraering

Gamma-Secretase Dependent Gene Expression: A Potential New Focus of Alzheimer's Disease Research

Mr. Nicolas Marcille

EDNE

Prof. Wulfram Gerstner

Models of Evidence Integration in Rapid Decision Making Processes

Mr. Mikaël Martino

EDBB

Prof. Jeffrey Hubbell

Engineering of Signaling Microenvironments with Fibronectin Fragments to Enhance Tissue Regeneration

Mr. Lionel Ambroise Micol*

EDBB

Prof. Jeffrey Hubbell

Hydrogels for Urinary Tract Tissue Engineering

Mr. Richard Naud

EDNE

Prof. Wulfram Gerstner

The Dynamics of Adapting Neurons

Mr. Luca Pellegrinet

EDMS

Prof. Freddy Radtke

The Intestinal Epithelium: Role of Notch Signaling

Ms. Emilda Pino

EDNE

Prof. P. Aebischer/ Dr B. Schneider

Role of the FoxO3a Transcription Factor in alphasynuclein Induced Neurodegeneration

Mr. Rubin Berek Pisarek

EDBB

Prof. Jeffrey Hubbell

New/Surface-Modified Biocompatible Polymer for ICD Lead Insulation

Ms. Caroline Poisson

EDMS

Prof. Freddy Radtke

The Microenvironment and the Cell Differentiation Status Influence the Outcome of Notch-Induced Malignancy

Ms. Carolyn Yong Pullin

EDBB

Prof. Melody Swartz

In Vitro Lymphatic Endothelial Morphogenesis: Molecular vs. Biophysical Regulation

Mr. Ranjan Rajnish

EDNE

Prof. Henry Markram

Mr. Lehal Rajwinder

EDMS

Prof. Freddy Radtke

Mr. Srikanth Ramaswamy

EDNE

Prof. Henry Markram/ Dr S. Hill

Emergent Properties of in silico Synaptic Transmission in a Model of the Rat Neocortical Column

Mr. Guillaume Rey

EDMS

Prof. Felix Naef

On the Relationship Between Protein-DNA Interactions and Circadian Gene Expression in Mouse Liver

Mr. Tej Tadi

EDNE

Prof. Olaf Blanke

Neural Mechanisms of the Embodied Self Merging Virtual Reality and Electrical Neuroimaging

Ms. Kalyani Thyagarajan

EDMS

Prof. Pierre Gönczy

Asymmetric Spindle Positioning and Intracellular Trafficking in C. elegans Embryos

Ms. Stéphanie Tissot

EDBB

Prof. Florian Wurm

OrbShake Bioreactors for Mammalian Cell Cultures: Engineering and Scale-up

Mr. Norbert Wiedemann

EDMS

Prof. Michel Aguet

Role of BcI9 and BcI9I in Homeostasis, Regeneration and Tumorigenesis of the Gastrointestinal Epithelium

Engineering Neuron Models: from Ion Channels to Electrical Behavior Identification and Preclinical Validation of Novel Inhibitors of the Notch Pathway

*MD-PhD" UNIL-EPFL joint degrees EDMS - Molecular Life sciences

Introduction

EDBB - Biotechnology and Bioengineering EDNE - Neuroscience

EPFL School of Life Sciences - 2011 Annual Report

Core Facilities & Technology Platforms In its goal to offer maximal support to its students and scientists in their training and research capabilities, EPFL and its School of Life Sciences have made a significant investment over the past years to establish state-of-the-art technology platforms and core facilities. These facilities are directed and managed by dedicated teams of highly trained and experienced staff and are run on a fee-for-service basis. They offer training, access to technology, assistance with experimental design and high level data analysis, and collaborations. The platforms are also involved in the School’s undergraduate and graduate teaching programs. In addition, scientists from our School of Life Sciences closely collaborate with other services in the Lemanic region, including the ‘Center for Biomedical Imaging’ (http://www.cibm.ch) and the ‘Lausanne Genomics Technologies Facility’ (http://unil.ch/dafl).

Core Facilities & Technology Platforms

The following pages describe the Life Sciences-related core facilities and technology platforms currently available at the EPFL School of Life Sciences.

CORE

EPFL School of Life Sciences - 2011 Annual Report

Bioelectron Microscopy - Bio-EM http://cime.epfl.ch/bio-em

Team Members Facility Head Graham Knott

Postdoctoral researchers Natalya Korogod Bohumil Maco Scientists Davide Demurtas Corrado Cali Technicians Marie Croisier Stéphanie Rosset

Introduction

The Bio Electron Microscopy Facility (BioEM) is located in the Faculty of Life Science (SV), and also in the Interdisciplinary Centre of Electron Microscopy (CIME). It provides both services and training to researchers at the EPFL who need to image their biological samples at high resolution. This begins with specific sample preparation techniques, carried out in the preparation laboratories, and then a range of different imaging approaches using either scanning or transmission electron microscopes. These machines are specially suited to biological samples and during 2011, the facility expanded its range of imaging technology with the acquisition of two new transmission electron microscopes; one for ambient temperature imaging, and the other for imaging frozen samples. Other additions during the past year also include the installation of a new high-pressure freezer for instantaneously freezing living material.

Services and Technologies • Transmission electron microscopy • Cryo transmission electron microscopy • Scanning electron microscopy • Focussed ion beam scanning electron microscopy • Correlated light and electron microscopy • Resin embedding • Semithin sectioning • Ultrathin sectioning • Serial sectioning • Cryosectioning and immunolabelling • Pre-embedding immuno labelling • Negative staining • Critical point drying • High pressure freezing • Plunge freezing • Low temperatureand, freeze substitution embedding

Selected Publications

Knott, Graham, Stéphanie Rosset, and Marco Cantoni. «Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue.» Journal of visualized experiments : JoVE , no. 53 (2011) Lucchi, A, K Smith, R Achanta, G Knott, and P Fua. «Supervoxel-Based Segmentation of Mitochondria in EM Image Stacks with Learned Shape Features.» IEEE transactions on medical imaging (2011) Straehle, C N, U Köthe, G Knott, and F A Hamprecht. «Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images.» Med Image Comput Comput Assist Interv 14, no. Pt 1 (2011): 653-60. Kreshuk, Anna, Christoph N Straehle, Christoph Sommer, Ullrich Koethe, Marco Cantoni, Graham Knott, and Fred A Hamprecht. «Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images.» PloS one 6, no. 10 (2011). Cantoni, M. Genoud, C., Hébert, C., Knott, GW. (2010). Large volume, isotropic, 3D imaging of cell structure on the nanometer scale. Microscopy and Analysis 24 (4).

Contact Information: Graham Knott Station 19, EPFL CH-1015 Lausanne Tel: +41 (0) 21 693 1862 graham.knott@epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

BioImaging & Optics - PT-BIOP http://biop.epfl.ch/

Team Members Facility Head Arne Seitz

Collaborators José Artacho Olivier Burri Mathias Fournier Romain Guiet Thierry Laroche

The Bioimaging and Optics platform (PT-BIOP) is located in the faculty of Life Science (SV) at the Ecole Polytechnique Fédérale de Lausanne (EPFL) and is part of a network of core facilities at the institute. The general idea of the platform is to provide state of the art light microscopes and even more importantly, expertise to solve challenging (biological) questions with modern light-microscopy. Currently a broad range of instruments ranging from simple wide-field imaging systems over standard point-scanning confocal microscopes up to a high-end 2-Photon-excitation microscope are available in the facility. Scientists who want to make use of the available equipment are trained by the PT-BIOP staff so that they can use the instruments independently or under the supervision of the staff. Additionally there is a strong competence and necessary computer power to perform image processing. The idea is to link the image analysis with the image acquisition as early as possible as only this approach guarantees optimal scientific results. The microscopes and the image analysis capabilities can be used by scientists of the faculty and the EPFL but are also available to scientist coming from outside the EPFL.

Services and Technologies • Wide-field transmission and fluorescent microscopes • Life cell imaging microscopes

Selected Publications

Bélanger M, Yang J, Petit JM, Laroche T, Magistretti PJ, Allaman I. Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci. (2011) 31(50):18338-52. Terjung, S., Walter, T., Seitz, A., Neumann, B., Pepperkok, R., and Ellenberg, J. (2010) High-throughput microscopy using live mammalian cells, (2010) Cold Spring Harbor Protocols, pdb top84. Maurel, D., Banala, S., Laroche, T., and Johnsson, K. (2010) Photoactivatable and photoconvertible fluorescent probes for protein labeling, ACS Chem Biol 5, 507-516. Kobel, S., Limacher, M., Gobaa, S., Laroche, T., and Lutolf, M. P. (2009) Micropatterning of hydrogels by soft embossing, Langmuir 25, 8774-8779. Lefort S., Tomm C., Floyd Sarria J.C., Petersen C.C. (2009) The excitatory neuronal network of the C2 barrel column in mouse primary somstosensory cortex, Neuron 61, 301-316. Emmenlauer, M., Ronneberger, O., Ponti, A., Schwarb, P., Griffa, A., Filippi, A., Nitschke, R., Driever, W., and Burkhardt, H. (2009) XuvTools: free, fast and reliable stitching of large 3D datasets, J Microsc 233, 42-60.

Contact Information: Arne Seitz AI 0240 Station 19, EPFL CH-1015 Lausanne Tel: +41 (0) 21 693 9618 Fax: +41 (0) 21 693 9585 arne.seitz@epfl.ch

Core Facilities & Technology Platforms

Introduction

• Single and multiple-beam confocal microscopes • 2P microscope • High resolution and super resolution microscope (will be available in 2012) • Image Processing tools (commercially available and/or custom built)

EPFL School of Life Sciences - 2011 Annual Report

Bioinformatics & Biostatistics- BBCF http://bbcf.epfl.ch

Team Members Facility Head Jacques Rougemont Post doctoral Solenne Carat Fabrice David Julia di Iulio Gregory Lefebvre Marion Leleu Scientific assistants Julien Delafontaine Yohan Jarosz Bara’ah Khubieh Frederick Ross Lucas Sinclair Administrative Assistant Sophie Barret

Introduction and Services and Technologies

The Bioinformatics and Biostatistics Core Facility (BBCF) provides the EPFL and Lemanic institutions with extensive support in bioinformatics and biostatistics, from designing experiments to interpreting and visualizing complex data. Its main competences are in management and analysis of genomic data, mathematical modeling and statistical analysis of quantitative biological data. The facility works in close relationship with the Geneva and Lausanne Genomics platforms and complements their respective bioinformatics team with additional support for the analysis of large or complex data sets, for the development of data management pipelines for new high-throughput technologies (e.g. high-density arrays, high-throughput sequencers) and for the statistical planning in complex experimental designs. It also helps researchers in the areas of mining public databases, designing and setting up local databases, inferring mathematical models from experimental data and running simulations to validate a model. The facility acts as a point of contact between the experimental biologists and the research groups in bioinformatics and in basic sciences. It also makes the junction between the EPFL Life Science community and the various resources maintained by the Swiss Institute of Bioinformatics, and in particular the Vital-IT high performance computing center.

Selected Publications

Ayyanan, A., Laribi, O., Schuepbach-Mallepell, S., Schrick, C., Gutierrez, M., Tanos, T., Lefebvre, G., et al. (2011). Perinatal exposure to bisphenol a increases adult mammary gland progesterone response and cell number. Molecular Endocrinology, 25(11), 1915–1923. Huber, A., French, S. L., Tekotte, H., Yerlikaya, S., Stahl, M., Perepelkina, M. P., Tyers, M., et al. (2011). Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. The EMBO journal, 30(15), 3052–3064. Rey, G., Cesbron, F., Rougemont, J., Reinke, H., Brunner, M., & Naef, F. (2011). Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biology, 9(2), e1000595. Leleu, M., Lefebvre, G., & Rougemont, J. (2010). Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. Briefings In Functional Genomics, 9(5-6), 466–476. Preti, M., Ribeyre, C., Pascali, C., Bosio, M. C., Cortelazzi, B., Rougemont, J., Guarnera, E., et al. (2010). The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae. Molecular Cell, 38(4), 614–620. Rowe, H. M., Jakobsson, J., Mesnard, D., Rougemont, J., Reynard, S., Aktas, T., Maillard, P. V., et al. (2010). KAP1 controls endogenous retroviruses in embryonic stem cells. Nature, 463(7278), 237–240.

Contact Information: Dr. Jacques Rougemont Station 15, CH-1015, Lausanne +41 (0)21 693 9573 jacques.rougemont@epfl.ch

Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W., & Duboule, D. (2011). The dynamic architecture of Hox gene clusters. Science, 334(6053), 222–225. Truman, R. W., Singh, P., Sharma, R., Busso, P., Rougemont, J., Paniz-Mondolfi, A., Kapopoulou, A., et al. (2011). Probable zoonotic leprosy in the southern United States. The New England Journal of Medicine, 364(17), 1626–1633.

EPFL for all material published in this report info.sv@epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

Biomolecular Screening - BSF http://bsf.epfl.ch/

Team Members Facility Head Gerardo Turcatti

Scientists Damiano Banfi Marc Chambon Ruud van Deursen Assistants Nathalie Ballanfat Manuel Bueno Miquel Busquets Julien Mena

The BSF provides access to EPFL, NCCR-Chemical Biology and SystemsX.ch researchers to the infrastructure, expertise and collections of molecules required for performing medium to high throughput molecular screening assays. In the frame of the NCCR-Chemical Biology, the BSF leads the project ACCESS with the main mission to become the platform for Academic Chemical Screens in Switzerland. In addition, the BSF is pursuing an innovative and focused research program with industrial partners in screening or drug discovery-linked areas. Most of the incoming projects are related to chemical biology, systems biology or disease-oriented research in particular in the areas of cancer, infectious diseases and neurobiology. Our multidisciplinary laboratory provides scientists with adequate screening instrumentation, state-of-the-art technologies and compounds collections for applications ranging from the probing of cellular pathways to the broad area of bioactive compounds research. We perform our automated screens in 96 and 384 well plates for the following two main categories of assays: • Screening of chemicals for a variety of biochemical target-based and cellular assays using large, chemically diverse collections • RNA interference (RNAi) cellular screens for probing gene function using collections of small interfering RNAs (siRNAs) targeting the human genome.

Services and Technologies

• Access to instrumentation dedicated to microplates and cell culture facilities • Assay development and validation for HTS • Assay automation and statistical validations • Pilot screening • Primary screening campaigns • Hits confirmation • Dose response assays • Secondary screens

• Compound storage and management of collections • Image processing for high content screening read-outs • Data management using in-house developed Laboratory Implementation Management System (LIMS). • Cheminformatics

Selected Publications

Takahashi-Umebayashi, M., Pineau, L., Hannich, T., Zumbuehl, A., Doval, D. A., Matile, S., Heinis, C., Turcatti, G., Loewith, R., Roux, A., lien, Reymond, L., Johnsson, K., and Riezman, H. (2011) Chemical Biology Approaches to Membrane Homeostasis and Function, CHIMIA International Journal for Chemistry 65, 849-852. Magnet, S., Hartkoorn, R. C., Székely, R., Pató, J., Triccas, J. A., Schneider, P., Szántai-Kis, C., Orfi, L., Chambon, M., Banfi, D., Bueno, M., Turcatti, G., Kéri, G., and Cole, S. T. (2010) Leads for antitubercular compounds from kinase inhibitor library screens, Tuberculosis 90, 354-360. Kobel, S., Valero, A., Latt, J., Renaud, P., and Lutolf, M. (2010) Optimization of microfluidic single cell trapping for long-term on-chip culture, Lab on a Chip 10, 857-863. Gormley, N.; Boutell, J., Turcatti, G.,Barnes, G. (2010). Preparation of nucleic acid templates for solid phase amplification. Patent number: US2010041561. Ouertatani-Sakouhi, H., El-Turk, F., Fauvet, B., Cho, M.-K., Pinar Karpinar, D., Le Roy, D., Dewor, M., Roger, T., Bernhagen, J., Calandra, T., Zweckstetter, M., and Lashuel, H. A. (2010) Identification and Characterization of Novel Classes of Macrophage Migration Inhibitory Factor (MIF) Inhibitors with Distinct Mechanisms of Action, Journal of Biological Chemistry 285, 26581-26598.

Contact Information: Gerardo Turcatti, MER Station 15 EPFL CH-1015 Lausanne Switzerland Tel: +41-(0)21 693 9666 gerardo.turcatti@epfl.ch

Core Facilities & Technology Platforms

Introduction

CORE

EPFL School of Life Sciences - 2011 Annual Report

Flow Cytometry - FCCF http://fccf.epfl.ch/

Team Members Facility Head Miguel Garcia

Collaborators Gonzalo Tapia Sintia Winkler Administrative Assistant Ursula Winter

Introduction

Flow cytometry is a technology that simultaneously measures and then analyzes multiple physical characteristics of single particles, usually cells, as they flow in a fluid stream through a beam of light. Sorting allows us to capture and collect cells of interest for further analysis. Our mission is to provide comprehensive flow cytometric analysis and sorting including instrumentation, technical and professional assistance, training.

Services and Technologies

The Flow Cytometry Core Facility from EPFL is equipped with five self-service cytometers. For sorting, the facility has two high-speed sorters from BD (BD FACSAria II SORP & FACSVantage SE). The Facility also operates an automated immunomagnetic bead cell separator from Miltenyi Biotec MACS® Technology. The LSRII (Becton Dickinson) is a 5 lasers benchtop analyser capable of 18 colour, forward and side scatter analysis, equipped with a PC and DIVA digital acquisition software system. The Accuri C6 is equipped with 2 lasers and 4 active detectors to allow maximum flexibility for easy experimental design. This machine is also equipped with a plate reader (CSampler) The Cyan ADP (Beckman Coulter) is a 3-laser benchtop analyser capable of 9 colour, forward and side scatter analysis, equipped with a PC and Summit digital acquisition software system.

quick and quantitative analysis of red & green expression, apoptosis, cell viability, cell count, and much more. The AutoMACS Pro is a fully automated bench-top sorter that can be used to perform sterile bulk sorts. Designed for ultra high-speed positive selection as well as depletion, the AutoMACS Pro can isolate virtually any cell type. The FACSVantage DIVA (BD) is a 3-laser sorter capable of 8 colour, forward and side scatter analysis. It is equipped with DIVA digital acquisition software system. The FACSAria (BD) is a 5 laser high-speed sorter capable of 18 colour, forward and side scatter analysis. It is equipped with DIVA digital acquisition software system and ACDU. Services : • Cell sorting • User training • Help with acquisition and data analysis • Experiment design & manuscript • Advice on cell preparation • Interpretation of results • Consulting

Contact Information: Miguel Garcia AI 0147 Sation 15 EPFL CH – 1015 Lausanne Tel: +41 21 693 0901 miguel.garcia@epfl.ch

The TaliTM Image Cytometer is a 3-channel (bright field, green & red fluorescence) benchtop assay platform giving a

EPFL School of Life Sciences - 2011 Annual Report

Histology -

HCF & Comparative Pathology

http://hcf.epfl.ch

Team Members Facility Head Jessica Sordet-Dessimoz Collaborators Gian-Filippo Mancini Nathalie Müller Agnès Hautier Veterinary pathologist Fabio Aloisio Administrative Assistant Ursula Winter

Introduction

Histology involves the use of a set of techniques to examine the morphology, architecture and composition of tissues. The tissue samples are processed for the study of structures seen under the microscope, also called microscopic anatomy, as opposed to gross anatomy which involves structures that can be observed with the naked eye. The histology core facility is a competence pole which provides expertise in those analyses as well as routine work for researchers. All the techniques would be nothing without the expertise of a specialist in veterinarian pathology who has been hired in 2011 to help researchers analyzing their slides.

Pathology service Pathology support is provided by professionals that underwent formal postgraduate training in veterinary anatomic pathology officially acknowledged by board certification of specialty. These professionals are trained to interpret morphologic changes within organs and tissues processed through the variety of histology techniques. Appropriate interpretation of tissue changes implies proper recognition of tissue abnormalities and pathologic processes of diseases that manifest as morphologic changes observable in histological preparations.

Services and Technologies

The service provides the following activities:

On the other hand technicians of the facility perform work for researchers: • Tissue processing to frozen, paraffin or resin sections • Histological stains like the standard Hematoxyline and eosin and routine stains like Masson’s trichrome or cresyl violet among others. The standard stains are running on the Prisma automate from Sakura • Setup and optimization of immunohistochemistry and immunofluorescence protocols • Detection of mRNA and miRNA using cold probes on the Discovery xT automate from Roche-Ventana.

• Consulting, at the study design level for issues related to pathology investigation • Phenotyping, whole body or organ targeted for genetically engineered animals • Analysis (morphology), of histological preparations

Core Facilities & Technology Platforms

On one hand, the facility assists researchers in the setting up and optimizing of histological approaches specific for each scientific project. Members of the SV faculty can be trained on the available instruments like microtomes or cryostats and have then access to them for their own experiments. Furthermore a large panel of secondary antibodies are titrated and provided to the researchers by the service.

• Support, in reporting pathology data for manuscript preparation and grant application • Diagnostics. Post mortem examination of diseased animals within the colony.

Contact Information: Jessica Sordet-Dessimoz EPFL SV PTH AI 0342 Station 19 1015 Lausanne +41 (0)21 693 0962 info.hcf@epfl.ch

CORE

EPFL School of Life Sciences - 2011 Annual Report

Proteomics - PCF http://pcf-ptp.epfl.ch/

Team Members Facility Head Marc Moniatte

Collaborators Diego Chiappe Florence Armand Adrian Schmid Research Assistants Romain Hamelin Jonathan Paz-Montoya Administrative Assistant Sophie Barret

Introduction

In the last 10 years mass spectrometry based protein analysis has become an invaluable tool in the arsenal of techniques offered to the biologist to study the proteome, the expressed and active part of the genome. The rapid evolution of the technique has been tightly bound to the continuous increase in performance of mass spectrometers. Today it is possible to get quantitative information about thousands of proteins in one experiment allowing researchers to begin to think more globally. But there is still room for very detailed studies on single proteins especially those modified by post-translational modifications.

Contributes also to collaborative based services requiring heavy involvement of both parties like: • Accurate protein quantification by SRM-MRM. • Localization and eventually quantification of PTM’s other than phosphorylation. • Lipid mixtures profiling.

The EPFL Proteomics Core Facility is a technological platform that has been created to address these needs and help researchers in using these techniques.

Selected Publications

Services and Technologies

Instrumentation The PCF-PTP laboratory is currently equipped with sample preparation and fractionation devices (HPLC, FPLC, pI) and several mass spectrometers coupled to liquid chromatography: 3 Orbitraps, 2 ion traps, and 2 QQQ LC-ESI-MS/MS and 1 MALDI-TOF/TOF instruments. The bioinformatics analysis pipeline includes Mascot, Xtandem! SEQUEST and Peaks servers for matching MS data with protein sequence databases and data post-treatment tools like Maxquant, Perseus, Proteome Discoverer, PinPoint and Scaffold for protein identification validation and pipelining of quantitative studies. Services The PCF-PTP has implemented several complementary workflows for protein analysis and offers an increasing palette of services... • Protein/Peptide Molecular Weight Measurements by Mass Spectrometry. • Mass Spectrometry based Protein/Peptide Identification from Gel or Solution. • Protein Relative Quantification by SILAC or Label-free Quantitative Analysis on collaborative basis.

Maintains tight collaboration with other proteomics facilities (UNIL-PAF, UNIGE-PCF, UNIBE) within a network called Repp-SO and with computer science and bioinformatics research centers (Vital-IT, SIB, etc..). Dastidar EG, Dayer G, Holland ZM, Dorin-Semblat D, Claes A, Chêne A, Sharma A, Hamelin R, Moniatte M, Lopez-Rubio J-J, Scherf A, Doerig C. (2012) Involvement of Plasmodium falciparum protein kinase CK2 in the chromatin assembly pathway. BMC Biology Jan;10(1):5. Sicard A, Semblat J, Doerig C, Hamelin R, Sicard, A., Semblat, J. P., Doerig, C., Hamelin, R., Moniatte, M., Dorin-Semblat, D., Spicer, J. A., Srivastava, A., Retzlaff, S., Heussler, V., and Waters, A. P. (2011) Activation of a PAK-MEK signalling pathway in malaria parasite-infected erythrocytes, Cell Microbiol. Jun;13(6):836-845. Schmid, A. W., Condemi, E., Tuchscherer, G., Chiappe, D., Mutter, M., Vogel, H., Moniatte, M., and Tsybin, Y. O. (2011) Tissue transglutaminase mediated glutamine deamidation of beta-amyloid peptide increases peptide solubility, whereas enzymatic cross-linking and peptide fragmentation may serve as molecular triggers for rapid peptide aggregation, J. Biol. Chem. Apr 8;286(14):12172-88. Paleologou KE, Oueslati A, Shakked G, Rospigliosi CC, Kim H-Y, Lamberto GR, Fernandez CO, Schmid A, Chegini F, Gai WP, Chiappe D, Moniatte M, Schneider BL, Aebischer P, Eliezer D, Zweckstetter M, Masliah E, Lashuel HA. (2010) Phosphorylation at S87 Is Enhanced in Synucleinopathies, Inhibits {alpha}Synuclein Oligomerization, and Influences Synuclein-Membrane Interactions. J. Neurosci, Mar;30(9):3184–3198. With acknowledgements Kitagawa D, Flückiger I, Polanowska J, Keller D, Reboul J, Gönczy P. (2011) PP2A phosphatase acts upon SAS-5 to ensure centriole formation in C. elegans embryos. Dev. Cell. Apr 19; 20(4):550-62

Contact Information: Dr. Marc Moniatte Station 15, CH-1015, Lausanne +41 (0)21 693 17 53 marc.moniatte@epfl.ch

• Protein separation by FPLC and HPLC.

EPFL School of Life Sciences - 2011 Annual Report

Protein Crystallography - PCRYCF http://pcrycf.epfl.ch

Team Members Facility Head Florence Pojer

Collaborator Larry Richman

Introduction

The Protein Crystallography Core Facility provides instrumentation and expertise at every stage of the structure determination process for non-crystallography groups who are interested in solving the structures of their favorite macromolecule. Expertise and advice include consultation on protein purification, crystallization, and crystal optimization, as well as assistance with X-ray crystal screening, data collection, data processing and structure determination and analysis are provided. X-ray crystallography is the primary method for determining three-dimensional structures of biological macromolecules, and is therefore an essential tool, which should be available to a broad range of researchers. Presently,it is possible for a non-crystallographer to access this technology thanks to automation and a variety of commercially available kits as well as to the friendlier and more intuitive programs that have been developed in recent years. With personalized advice, training, and follow-up, users are in the optimal environment to manage their crystallization screens, and to solve, refine and analyze the structures of their proteins of choice.

• Deposition of structures in the protein database. • Preparation of images for publication using PyMol software.

Selected Publications

Mollwitz B., Brun E., Schmitt S., Pojer F., Bannwarth M.,Rothlisberger U., Schiltz M.; Johnsson K. (2012). Directed evolution of the suicide protein O6-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability Biochemistry. Biochemistry 51(5):986-94. Blasco B, Stenta M, Alonso-Sarduy L, Dietler G, Peraro MD, Cole ST, Pojer F.* (2011). Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis. Molecular Microbiology 82(1):251-64.

Contact Information: Florence Pojer SV 3533 Station 19 EPFL CH-1015 Lausanne Tel: +41 (0)21 693 1772 +41 (0)21 693 1839 florence.pojer@epfl.ch

Core Facilities & Technology Platforms

Services and Technologies

The Protein Crystallography Core Facility provides the EPFL community with: • Advice on larger-scale protein expression and purification, if required. • Set-up of crystallization screens using commercial and facility-made conditions. • Optimization of crystals. • Data collection of quality crystals at facility xray source and synchrotrons. • Data processing using popular packages such as XDS and Mosflm. • Structure determination using molecular replacement, MAD and SAD techniques. • Structure refinement, fitting and analysis using ccp4i and Phenix software.

CORE

EPFL School of Life Sciences - 2011 Annual Report

Protein Expression - PECF http://pecf.epfl.ch/

Team Members Facility Head David Hacker

Collaborator Sarah Thurnheer

Introduction

The objective of the PECF is to provide recombinant proteins, rapidly and at low cost, to EPFL researchers. Both cultivated mammalian cells and E. coli are used as production hosts. One of our main activities is recombinant protein production by transient transfection of Chinese hamster ovary (CHO) or human embryo kidney (HEK293) cells in suspension at volumetric scales from 5 mL to 15 L using orbitally shaken bioreactors. For transient protein production in mammalian cells, we have a number of expression vectors available. With the same technical approach, we are also capable of producing virus vectors such as adeno associated virus. We also produce proteins from existing recombinant cell lines developed by our clients. This may involve adapting the cell line to serum-free suspension culture. Cultures at volumetric scales up to 15 L are possible. Expression vectors based on piggybac transposon-mediated gene delivery are available to our clients. We produce monoclonal antibodies by scale-up of existing hybridoma cell lines. Serum-free suspension cultures based on mixing by orbital shaking can be used for a scale-up to 2 liters. When using E. coli as a host for protein production, the scales of operation range from 100 mL – 20 L. Induced protein production at low temperatures is feasible. We also provide services in protein recovery, mainly by affinity chromatography of antibodies and tagged proteins (Fc, 6X his, FLAG and GST) produced in either mammalian cells or E. coli.

Services and Technologies • Large-scale transient transfection for recombinant protein in mammalian cells • Scale-up of existing cell lines for recombinant protein production • Scale-up of existing hybridoma cell lines for monoclonal antibody production • Recombinant protein production in E. coli • Affinity protein purification • Provision of vectors for protein production in mammalian cells

Selected Publications

Matasci M, Baldi L, Hacker DL, Wurm FM. 2011. The PiggyBac transposon enhances the frequency of CHO stable cell line generation and yields recombinant lines with superior productivity. Biotechnol Bioeng. 108(9):2141-50. Rajendra Y, Kiseljak D, Baldi L, Hacker DL, Wurm FM. 2011. A simple highyielding process for transient gene expression in CHO cells. J Biotechnol. 153(1-2):22-6. Tissot S, Oberbek A, Reclari M, Dreyer M, Hacker DL, Baldi L, Farhat M, Wurm FM. 2011. Efficient and reproducible mammalian cell bioprocesses without probes and controllers? N Biotechnol 28(4):382-90. Xie Q, Michel PO, Baldi L, Hacker DL, Zhang X, Wurm FM. 2011. TubeSpin bioreactor 50 for the high-density cultivation of Sf-9 insect cells in suspension. Biotechnol Lett. 33(5):897-902. Wurm FM, Hacker D. 2011. First CHO genome. Nat Biotechnol 29(8):718-20. Oberbek A, Matasci M, Hacker DL, Wurm FM. 2011. Generation of stable, high-producing CHO cell lines by lentiviral vector-mediated gene transfer in serum-free suspension culture. Biotechnol Bioeng. 108(3):600-10.

Contact Information: David Hacker Station 6 EPFL CH J2 496 CH-1015 Lausanne Tel: +41 (0)21 693 6142 david.hacker@epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

Transgenic - TCF

http://jahia-prod.epfl.ch/cms/site/tcf

Team Members Facility Head Isabelle Barde

Collaborators Blom Michelle Guichard Sabrina Offner Sandra Eloise Verp Sonia

Introduction

Services and Technologies

We offer a centralized resource and state-of-the-art technology for the generation of transgenic animals. We can perform direct pronuclear injection of DNA in the mouse oocyte, which has been the standard method of trangenesis for more than three decades.

Selected Publications

As an attractive alternative, we are one of the very few platforms that provides a fast and efficient way to generate transgenic animals through the use of lentiviral vectors. Lentivector-mediated transgenesis is relatively easy to perform and leads to high percentages of provirus-positive animals. Moreover, a wide variety of lentiviral vectors have been developed that can all be used in transgenic animals, thus allowing for a broad range of genetic manipulations including externally controllable expression and knockdown, the latter offering an economically advantageous alternative to stable knockout. In addition to this primary service, we also offer general support in both vector design and lentiviral vector production and titration, as our expertise in lentiviral vectors has become of general interest for many other applications than transgenesis. An important variable that affects the results of mouse studies is the sanitary status of the animals. Taking advantage of our expertise in embryo manipulation, we also propose the rederivation of mouse transgenic lines as a routine service. This procedure allows cleaning and hosting of a wide range of mouse lines in the SPF area of the EPFL animal house.

• Pronuclear injection: plasmids and BACs • Lentiviral vector mediated transgenesis • Vectorology • Lentiviral vectors production/titration • Rederivation by embryo transfer • Cryopreservation by sperm freezing • In progress: ES mediated transgenesis.

Barde I, Laurenti E, Verp S, Wiznerowicz M, Offner S, Viornery A, Galy A, Trumpp A, Trono D. (2011). Lineage- and stage-restricted lentiviral vectors for the gene therapy of chronic granulomatous disease. Gene Ther. (11):1087-97. Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE.(2011). Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One. 6(3):e17634. Friedli M, Barde I, Arcangeli M, Verp S, Quazzola A, Zakany J, Lin-Marq N, Robyr D, Attanasio C, Spitz F, Duboule D, Trono D, Antonarakis SE. (2010). A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One.;5(12):e15741. Barde I, Salmon P, Trono D. (2010). Production and titration of lentiviral vectors. Curr Protoc Neurosci.;Chapter 4:Unit 4.21. Meyer K, Marquis J, Trüb J, Nlend Nlend R, Verp S, Ruepp MD, Imboden H, Barde I, Trono D, Schümperli D. (2009). Rescue of a severe mouse model for spinal muscular atrophy by U7 snRNA-mediated splicing modulation. Hum Mol Genet. 18(3):546-55.

Contact Information

Core Facilities & Technology Platforms

Genetic manipulation of rodents through the generation of transgenic animals is a procedure of paramount importance for biomedical research, either to address fundamental questions or to develop preclinical models of human diseases.

Isabelle Barde AI 3351 Station 19 EPFL CH-1015 Lausanne Tel: +41 (0)21 693 1702 isabelle.barde@epfl.ch

For long term preservation of a mouse line of particular interest, we now propose cryopreservation by sperm freezing via the JAX® Sperm Cryo Kit. The advantage of this technique is that it is standardized and requires only 2 competent male breeders.

CORE

EPFL School of Life Sciences - 2011 Annual Report

Phenotyping Unit - CPG-UDP /

Team Members CPG – Head Xavier Warot

CPG – UDP Managers Philippe Cettour-Rose Raphaël Doenlen Laboratory Assistants Arnaud Bichat Cristina Cartoni Sébastien Lamy Adeline Langla Marion Varet Animal Care Takers Christine Pehm

Introduction

The development of genetic tools for the manipulation of the mouse genome has led to the creation of numerous and sophisticated mouse models. The in-depth characterization of the phenotype of these mouse lines is crucial to decipher the roles of the gene of interest. The clinical phenotyping unit of the Center of PhenoGenomics is composed of highly interactive service platforms including clinical chemistry laboratory, metabolic and functional exploration platform, behavior and cognition exploration platform. The UDP provides a range of state-ofthe-art equipment to enable cardio-metabolic, biochemical and behavioural exploration of mouse models. We offer different types of support to the users of the platform, going from general support and training in protocols establishment to full completion of tests and analysis. We benefit for doing so from the scientific expertise of Prof. Johan Auwerx and Prof. Carmen Sandi, both authorities in their respective fields, namely cardio-metabolism and neurobiology. The UDP is part of the animal facility barrier unit, and encompasses a working area constituted of housing, testing and analysis rooms. The mouse models are housed in individual ventilated cages and maintained at a conventional sanitary status. The UDP equipment has been chosen to ensure a high level of flexibility for the tests that can be performed. Additionally, most of experiments can be run by fully programmable and automated interfaces and thus the impact of experimental interventions by the researcher over the experimental period is reduced.

Services and Technologies

We offer tests in the different scientific fields mentioned in the figure. A series of tests can be combined in a pipeline in order to answer questions related to a given topic such as neurodegenerative diseases or obesity or diabetes.

Selected Publications

Houtkooper RH, Argmann C, Houten SM, Cantó C, Jeninga EH, Andreux PA, Thomas C, Doenlen R, Schoonjans K, Auwerx J. (2011). The metabolic footprint of aging in mice. Sci Rep. 1:134. Marcaletti S, Thomas C, Feige JN. (2011). Exercise Performance Tests in Mice. Current Protocols in Mouse Biology. 1:141-154. Thomas C, Marcaletti S, Feige JN. (2011). Assessment of Spontaneous Locomotor and Running Activity in Mice. Current Protocols in Mouse Biology. 1:185198.

Contact Information:

Philippe Cettour-Rose : Cardio-metabolism Manager Tel: +41 (0)21 693 0984 philippe.cettour-rose@epfl.ch Raphael Doenlen: Neurobiology Manager Tel: +41 (0)21 693 0953 raphael.doenlen@epfl.ch Xavier Warot Tel: +41 (0)21 693 1869 xavier.warot@epfl.ch

EPFL School of Life Sciences - 2011 Annual Report

GHI - Global Health Institute Since its foundation in 2006, the Global Health Institute (GHI) has been contributing to the understanding, diagnosis, prevention and treatment of infectious diseases, which account for half of the deaths in the developing world and still claim 18 million human lives every year. The GHI comprises 9 groups, all engaged in different facets of research linked to human health but with strong emphasis on diseases of truly global importance such as HIV/AIDS, tuberculosis and malaria. The current workforce comprises ~120 students, postdoctoral-fellows, technicians and scientists, representing 28 different nations. The research portfolio at the GHI includes a balanced mixture of basic and translational work. Mechanisms of host-pathogen interactions and innate and acquired immunity against disease are being studied using multidisciplinary approaches. A unique feature of the GHI is its ability to tackle crucial world health issues by harnessing cutting edge technologies developed at EPFL and elsewhere. Among these the nanotechnologies, micro-engineering and informatics are proving particularly powerful at underpinning drug discovery and vaccinology as well as more mechanistic research.

GHI - Global Health Institute

http://sv.epfl.ch/GHI

EPFL School of Life Sciences - 2011 Annual Report

Blokesch Lab

http://blokesch-lab.epfl.ch

GHI

Melanie Blokesch studied biology at Ludwig-Maximilians-University in Munich, Germany, graduating with a major in microbiology. In 2004 she obtained her PhD degree with highest honor from the LMU Munich based on her work on bacterial hydrogen production and metalloenzyme maturation. Her doctoral dissertation was honored by the German Association for General and Applied Microbiology and the German Academy of Sciences Leopoldina. In 2005 she joined the group of Dr. Gary Schoolnik within the Department of Microbiology and Immunology at Stanford University, USA as a postdoctoral fellow. In 2009, Melanie Blokesch joined the Global Health Institute within the School of Life Sciences of EPFL as a tenure-track Assistant Professor.

Melanie Blokesch Tenure Track Assistant Professor

Introduction

There is increasing concern about the (re-)emergence of infectious agents and the threat this poses to human health. Knowledge of how bacteria acquire pathogenic traits is of fundamental importance. Our research focuses on evolution mediated by horizontal gene transfer and is exemplified using the human pathogen Vibrio cholerae, the causative agent of the disease cholera, as a model organism.

Keywords

Evolution of human pathogens, horizontal gene transfer, bacterial regulatory networks, environmental reservoirs.

Results Obtained in 2011

The human pathogen Vibrio cholerae is an aquatic bacterium often encountered in rivers, estuaries and coastal regions. Within this environmental niche, the bacterium often associates with the chitinous exoskeleton of zooplankton. Upon colonization of these chitinous surfaces, V. cholerae switches on a developmental program known as natural competence for genetic transformation. Natural competence for transformation is a mode of horizontal gene transfer that allows bacteria to acquire new genes derived from free DNA, which is released by other members of the community. The evolutionary consequences could be that the bacterial recipient becomes better adapted to its environmental niche or, in a worst-case scenario, more pathogenic for man. Regulation of natural competence for transformation and DNA uptake In this project we studied the dependency of natural transformation on the so-called autoinducers produced by V. cholerae. More specifically, we showed that chitin-induced natural competence and transformation is strongly enhanced or even dependent on the species-specific cholera autoinducer -1 (CAI-1). In contrast, the universal interspecies autoinducer AI-2 of V. cholerae plays a negligible role. We illustrated that in the absence of either one of the two autoinducer-synthases, natural transformation is completely abolished in this organism. Such a small-molecule dependent regulation of natural competence and transformation

resembles the competence pheromone-dependent regulation in Gram-positive bacteria. Additionally, we provided evidence that V. cholerae does not distinguish between species-specific and species-unspecific DNA at the level of the DNA uptake process. This is in contrast to certain other Gram-negative bacteria, such as Neisseria gonorrhoeae and Haemophilus influenzae; both of these organisms only take up species-specific DNA via the recognition of DNA uptake sequences. More generally, these results illustrate how V. cholerae enhances the probability of species-specific DNA uptake by coupling gene expression required for natural transformation to the species-specific quorum sensing autoinducer. This could be beneficial for the repair of defective genes. We also followed up on the complex regulatory circuit of natural competence using transcriptional reporter fusions and single-cell microscopy. This allowed us to distinguish between population-wide transcriptional profiles and those genes that are only transcribed in distinct subpopulations. The results of this study show that, under optimal conditions, all members within a V. cholerae population acquire the competence state. However, in an aquatic environment, a combination of different ecological factors might lead to heterogeneity in the competence phenotype. Therefore, we investigated the role of extracellular and intracellular signalling molecules with respect to competence induction. We illustrated that at least three interconnected signalling cascades are required for competence induction, which are based on bacterial metabolism and group behavior. Natural transformation of Vibrio cholerae as a tool As we know that V. cholerae becomes naturally transformable and can take up free DNA from the environment upon chitin induction, we went on to use this phenomenon as a tool to genetically manipulate these bacteria. We established experimental setups to knock-in and knock-out genomic islands, genes, and promoter regions, respectively, using chitin-induced natural transformation in combination with the yeast Flp recombination system.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Blokesch M. (2012) TransFLP – a method to genetically modify V. cholerae based on natural transformation and FLP-recombination – accepted for publication in J. Vis. Exp. – Blokesch M. (2012) Chitin colonization, chitin degradation, and chitin-induced natural competence of Vibrio cholerae are subject to catabolite repression. Environ. Microbiol., published online Jan 6th, 2012. Suckow G., Seitz P., Blokesch M. (2011) Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner. J. Bacteriol. 193:4914-24. De Souza Silva O., Blokesch M. (2010) Genetic manipulation of Vibrio cholerae by combining natural transformation with FLP recombination. Plasmid, 64: 186-195.

Team Members Postdoctoral Fellow Juliane Kühn PhD Students Mirella Lo Scrudato Patrick M. Seitz Gaia F. M. Suckow Technicians Sandrine Borgeaud Olga de Souza Silva Administrative assistant Marisa Marciano Wynn

Marvig R. L., Blokesch M. (2010) Natural transformation of Vibrio cholerae as a tool-optimizing the procedure. BMC Microbiol. 10:155. In collaboration with Prof. Dr. Andrea Rinaldo / ECHO laboratory ENAC, EPFL: Rinaldo A., Bertuzzo E., Mari L., Righetto L., Blokesch M., Gatto M., Casagrandi R., Murray M., Vesenbeckh S., Rodriguez-Iturbe I. (2012) Reassessment of the 2010-2011 Haiti cholera outbreak and rainfall-driven multi-season projections – accepted for publication in Proc. Natl. Acad. Sci. USA – Rinaldo A., Blokesch M., Bertuzzo E., Mari L., Righetto L., Murray M., Gatto M., Casagrandi R., Rodriguez-Iturbe I. (2011) A transmission model of the 2010 cholera epidemic in Haiti. Ann. Intern. Med. 155:403-404.

GHI - Global Health Institute

Bertuzzo E., Mari L., Righetto L., Gatto M., Casagrandi R., Blokesch M., Rodriguez-Iturbe I., Rinaldo A. (2011) Prediction of the spatial evolution and effects of control measures for the unfolding Haiti cholera outbreak. Geophys. Res. Lett., 38:L06403.

Vibrio cholerae lives in association with chitinous plankton, which foster exchange of genetic material via horizontal gene transfer (HGT). In the figure the colonization of a chitin bead is shown. The bacteria carry fluorescent reporter fusions to monitor expression of genes involved in HGT.

EPFL School of Life Sciences - 2011 Annual Report

Cole Lab

http://cole-lab.epfl.ch

GHI

Stewart Cole is an internationally acclaimed authority on the pathogenicity, drug resistance, evolution and genomics of the tubercle and leprosy bacilli. His laboratory is currently focused on discovering new drugs to treat tuberculosis. The findings of his research are of direct relevance to public health and disease-control in both the developing world and the industrialised nations. He has published over 270 scientific articles and received many national and international prizes and distinctions.

Stewart T. Cole Full Professor Director of GHI

Introduction

We are using a multidisciplinary approach to tackle major public health problems such as tuberculosis. Finding new drugs and understanding disease mechanisms are among our priorities.

Keywords

Tuberculosis, leprosy, drug discovery, pathogenesis.

Results Obtained in 2011

TB Drug Discovery We are leading a major international initiative to discover new drugs for the treatment of tuberculosis (TB), the More Medicines for Tuberculosis Project, MM4TB, funded by the European Commission. In 2011, we successfully completed work on the back-up series to our candidate drug BTZ043 by developing a derivative with a better selectivity index and in vivo efficacy. BTZ043 kills M. tuberculosis by forming a covalent adduct with the essential enzyme decaprenyl-phosphoryl-beta-D-ribose 2â&#x20AC;&#x2122;-epimerase, which produces decaprenyl-phosphoryl-D-arabinose (DPA), a key component of the mycobacterial cell wall. We have extended our studies to other enzymes in the DPA pathway and made conditional knock-down mutants and begun structural analysis. The figure shows the 3D structure of one such enzyme, transketolase, acting at an early stage in the pathway. We have also extensively characterized another new antitubercular agent, pyridomycin.

A regulatory map of the M. tuberculosis genome Gene regulation is being studied using chromatin-immunoprecipitation of DNA-binding proteins in conjunction with ultra-high-throughput sequencing to map regulatory sites on the genome. We have mapped all the RNA polymerase, NusA, SigF, EspR and PhoP binding sites in two different strains under different growth conditions. Regulatory information is being incorporated into TubercuList, the genome server dedicated to M. tuberculosis http://tuberculist.epfl. ch/, for which we are the official curators. Phylogeography of leprosy Despite the highly successful implementation of multi-drug therapy by the World Health Organisation, leprosy remains a serious public health problem in several countries probably due to our inability to identify infectious cases early enough. We have developed and used an epidemiological tool based on single nucleotide polymorphisms to monitor transmission of the disease and found that in the Southern USA humans contract leprosy from contact with wild armadillos. In collaboration with WHO, we are also coordinating a worldwide effort to monitor the emergence of drug resistance.

Protein secretion and pathogenicity The ESX-1 protein secretion system is the major virulence determinant operating in M. tuberculosis and has been lost by the live vaccine strains M. bovis BCG and M. microti. ESX-1 exports small helical-hairpin proteins belonging to the ESAT-6 family as well as other effector proteins of unknown function. ESX-1 mediates host cell entry of tubercle bacilli and triggers intercell spread. We are using an integrated approach involving biochemistry, genetics, X-ray crystallography and electron microscopy to establish the organization, architecture, structure and function of this ATP-driven secretory apparatus.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

EspD Is Critical for the Virulence-Mediating ESX-1 Secretion System in Mycobacterium tuberculosis. J. M. Chen, S. Boy-Röttger, N. Dhar, N. Sweeney, R. S. Buxton, F. Pojer, I. Rosenkrands and S. T. Cole. Journal of bacteriology, vol. 194, num. 4, p. 884-93, 2011. Comparative genomics of Esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation. S. Uplekar, B. Heym, V. Friocourt, J. Rougemont and S. T. Cole. Infection and immunity, vol. 79, num. 10, p. 4042-9, 2011. Probable zoonotic leprosy in the southern United States. R. W. Truman, P. Singh, R. Sharma, P. Busso, J. Rougemont, A. Paniz-Mondolfi, A. Kapopoulou, S. Brisse, D. M. Scollard, T. P. Gillis and S. T. Cole. The New England journal of medicine, vol. 364, num. 17, p. 1626-33, 2011. Molecular drug susceptibility testing and genotyping of Mycobacterium leprae strains from South America. P. Singh, P. Busso, A. Paniz-Mondolfi, N. Aranzazu, M. Monot, N. Honore, A. de Faria Fernandes Belone, M. Virmond, M. E. Villarreal-Olaya, C. Rivas and S. T. Cole. Antimicrobial agents and chemotherapy, vol. 55, num. 6, p. 2971-3, 2011. ESAT-6 secretion-independent impact of ESX-1 genes espF and espG1 on virulence of Mycobacterium tuberculosis. D. Bottai, L. Majlessi, R. Simeone, W. Frigui, C. Laurent, P. Lenormand, J. Chen, I. Rosenkrands, M. Huerre, C. Leclerc, S. T. Cole and R. Brosch. The Journal of infectious diseases, vol. 203, num. 8, p. 1155-64, 2011. Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis. B. Blasco, M. Stenta, L. Alonso-Sarduy, G. Dietler, M. Dal Peraro, S. T. Cole and F. Pojer. Molecular Microbiology, vol. 2011, num. 82, p. 251–264, 2011. A Simple Model for Testing Drugs against Non-replicating Mycobacterium tuberculosis. C. Sala, N. Dhar, R. C. Hartkoorn, M. Zhang, Y. H. Ha, P. Schneider and S. T. Cole. Antimicrobial agents and chemotherapy, vol. 54, num. 10, p. 4150-8, 2010.

Team Members Postdoctoral Fellows Jeffrey Chen Ruben Hartkoorn Joao Neres Sophie Magnet Raju Mukherjee Florence Pojer Jan Rybniker Claudia Sala Pushpendra Singh PhD Students Benjamin Blasco Gaëlle Kolly Benoit Lechartier Swapna Uplekar Ming Zhang Technicians Stefanie Boy-Röttger Philippe Busso Administrative Staff Suzanne Lamy Other Staff Jocelyne Lew Wareed Ahmed Luis Solans Bernad Yaser Heidari Students Joachim De Jonghe Mack Su Ofelia Sanchez Salinas Collaborations Sudhir Sinha

GHI - Global Health Institute

Sigma Factor F does not Prevent Rifampin Inhibition of RNA Polymerase or Cause Rifampin Tolerance in Mycobacterium tuberculosis. R. C. Hartkoorn, C. Sala, S. J. Magnet, J. M. Chen, F. Pojer and S. T. Cole. Journal of bacteriology, vol. 192 num. 20, p. 5472-9. 2010.

Structural model of the M. tuberculosis transketolase dimer with one monomer represented as surface and coloured by B-factor and the second monomer as a cartoon with the domains colored as follows: magenta, domain I; orange, domain II; green, domain III; red, linkers 1, 2.

EPFL School of Life Sciences - 2011 Annual Report

Doerig Lab

http://doerig-lab.epfl.ch/

Christian Doerig

GHI

After a PhD in molecular virology at ISREC and a post-doc on Herpes simplex virus, Christian Doerig turned to malaria research in 1992. He pioneered Plasmodium kinomics, bringing internationally recognized contributions to the fields of signal transduction, cell cycle control and kinome characterization in malaria parasites, and has served as the coordinator of three EU consortia in this area in Framework Programmes FP5, 6, and 7. Having been nominated “Directeur de Recherche” at Inserm in 2001, he established the first Inserm lab in the UK, at the Glasgow-based Wellcome Trust Centre for Molecular Parasitology, and was awarded an Honorary Professorship form the University of Glasgow in 2005. His team moved to EPFL in 2009, where it remained until 2011, when he was appointed Head of the Department of Microbiology at Monash University, Melbourne, Australia.

Directeur de Recherche Inserm EPFL - INSERM Joint Laboratory

Introduction

Our research programme focuses on the role of protein phosphorylation in the life cycle of the human malaria parasite Plasmodium falciparum. The long term objectives are (i) to elucidate the organisation and function of phosphosignalling pathways controlling proliferation and development of the parasite in the human and mosquito hosts, and (ii) to identify protein kinase inhibitors as leads for antimalarial drug discovery. Soon after the publication of the P. falciparum genome sequence, we produced a seminal paper identifying the parasite’s 85-enzyme kinome (Ward et al., BMC Genomics, 2004), which provided a basis for subsequent work in functional characterization of individual protein kinases. Active collaborations have been established with industrial and academic partners to implement drug discovery activities based on kinase inhibition.

Keywords

Malaria, Plasmodium, kinomics, protein kinase, signalling.

Results Obtained in 2011

2011 has seen the publication of a number of studies, including: •

•

A kinome-wide reverse genetics study that took several years to complete, because of the difficulties associated with P. falciparum genetic manipulations. We determined which protein kinases are essential for parasite survival in the human blood; in parallel, a global phosphoproteomic analysis of blood stage parasites was performed in collaboration with Prof. A. Tobin (University of Leicester). Together, these studies, published in Nature Communications, provide new insights into Plasmodium functional kinomics and permit prioritization of potential targets for drug discovery. A pilot interactomics/proteomics study performed in collaboration with the EPFL Proteomics Facility (published in BMC Biology), where immune-complexes purified from transgenic parasite lines expressing an epitope-tagged version of the parasite’s casein kinase 2 (PfCK2) were analysed my mass spectrometry

to gain insight into the cellular function of the enzyme. We identified chromatin assembly as a major process regulated by PfCK2; this approach is now being implemented in a kinome-wide approach. •

A series of pharmacology and immune-detection experiments (performed in collaboration with Kinexus, a company specializing in phosphosignaling) demonstrating a crucial role of kinases from the host erythrocyte for parasite survival. We showed that a phosphosignaling pathway of the erythrocyte is strongly activated by infection with the parasite, and that this activation is required for parasite proliferation. These observations have considerable implications in the context of strategies for antimalarial drug discovery (Cellular Microbiology, 2011, EPFL and Glasgow University press releases)

•

The finding that PfARK1, a homologue of the mammalian Aurora kinases regulating cell division, is required for parasite proliferation. Tagging the endogenous Pfark-1 gene with the green fluorescent protein revealed a dynamic recruitment of Pfark-1 at duplicated spindle pole bodies (the plasmodial equivalents of the centrosome) and enabled us to directly demonstrate that nuclei within a single P. falciparum schizont divide asynchronously. This provides new insights into the cell cycle control of malaria parasites and highlights the parasite’s Aurora kinases as potential targets for malaria chemotherapy(Molecular Microbiology, 2011).

The Inserm-EPFL Joint Laboratory closed on the 31st October 2011, after three productive years at the GHI. Prof. Christian Doerig (christian.doerig@monash.edu.) is now the Head of the Department of Microbiology at Monash University and continues his research there on malaria kinomics. Collaborations established with EPFL laboratories will continue, notably with the Proteomics Facility. Everyone in the Inserm-EPFL Joint laboratory has found new host laboratories (for the Inserm staff) or new employment (for non-Inserm staff). For details of their whereabouts see http://doerig-lab.epfl.ch/

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Talevich, E., Tobin, A., Kannan, N. and Doerig, C. An evolutionary perspective on the kinome of malaria parasites. Philosoph. Transact. B, in press. Ghosh Dastidar, E., Dayer, G., Holland, Z., Dorin-Semblat, D., Claes, A., Chêne, A., Sharma, A., Hamelin, R., Moniatte, M., Lopez-Rubio, J., Scherf, A. and Doerig, C. (2012) Involvement of Plasmodium falciparum protein casein kinase 2 in the chromatin assembly pathway. BMC Biology 10:5. Solyakov, L., Halbert, J., Graciotti, M, Semblat, J.P. , Dorin-Semblat, D., Bottrill A., Mistry, S., Abdi, A., Fennell, C., Demarta, C., Bouza, Y., Nivez, M.P., Eschenlauer, S., Lama, T., Reininger, L., Agrawal, S., Kern, S., Pradel, G., Alam, M.M., Tobin, A.B and Doerig, C. (2011) Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum. Nature Communications 2:565. Sicard, A., Semblat, J.P., Doerig, C.M., Hamelin, R., Moniatte. M., Spicer, J.A., Srivastava, A., Retzlaff, S., Heussler, V., Waters, A.P. and Doerig, C. (2011) Activation of a PAK-MEK pathway in malaria parasite-infected erythrocytes. Cell. Microbiol.13: 836-845.

Team Members Inserm Luc Reininger Dominique Dorin-Semblat Postdoctoral Fellow Jean-Philippe Semblat Master’s students Guillem Dayer Claudia Demarta Technicians Jean Halbert Audrey Sicard Administrative Assistant Marisa Marciano Wynn

Reininger, L., Wilkes, J., Bourgade, H., Miranda-Saavedra, D. and Doerig, C. (2011) An essential Aurora-related kinase transiently associates with spindle pole bodies during Plasmodium falciparum erythrocytic schizogony. Mol. Microbiol. 79: 205-221. Zhang, M., Fennell, C., Ranford-Cartwright, L., Doerig, C., Nussenzweig, R.S., Sullivan Fr, W., Ménard, R., Winzeler, E.A. and Nussenzweig. V. Mechanism of latency in malaria sporozoites. (2010) J. Exp. Med. 207:1465-1474. Doerig, C and Tobin, A. (2010) Parasite protein kinases: at home and abroad. Cell Host Microbe 8:305-307. Doerig, C. and Billker, O. (2010) A parasite calcium switch and Achilles’ heel revealed. Nature Struct. Mol. Biol. 17 :541-543.

GHI - Global Health Institute

A multi-nucleated Plasmodium falciparum schizont expressing GFP-tagged PfARK1. Nuclei are stained in blue. Three of these nuclei display a pair of green dots indicating recruitment of GFP-PfARK1 at the spindle pole bodies located at nuclear periphery. (For more details see Reininger et al., Molecular Microbiology 79: 205-221, 2011). Photograph by Luc Reininger.

EPFL School of Life Sciences - 2011 Annual Report

Fellay Lab

http://fellay-lab.epfl.ch/

GHI

Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained his MD from the University of Lausanne in 2002 and was clinically trained in infectious diseases in Switzerland, before moving in 2006 to Duke University, where he worked on human genomics of infections in David Goldsteinâ&#x20AC;&#x2122;s Center for Human Genome Variation. Jacques Fellay joined the EPFL in April 2011 as an SNSF Professor. He is also a Visiting Physician at the Institute of Microbiology of UNIL/CHUV in Lausanne.

Jacques Fellay SNSF Professor

Introduction

Human genetic variation plays a key role in determining individual outcomes after exposure to infectious agents. The mission of our laboratory is to contribute to a better understanding of inter-individual differences in response to infections, using a range of genomic tools.

Keywords

Human genomics, infectious diseases, HIV, Host-pathogen interactions, deep-sequencing, translational genomics, personalized medicine.

Results Obtained in 2011

Genomic analysis of children with severe respiratory infections In the pediatric population, viral infections of the lower respiratory tract are usually mild and self-limiting, but severe disease sometimes occurs, resulting in the hospitalization of 1-2% of each birth cohort and in the admission to an intensive care unit of about 10% of hospitalized patients. In this project, we test the hypothesis that children who develop unusually severe symptoms after banal respiratory infection have rare genetic defects that confer particular susceptibility to respiratory viruses. Study participants are prospectively recruited in Swiss and Australian Intensive Care Units, and are analyzed by exome and transcriptome sequencing.

Host-pathogen genomic interactions The most recent advances in genomic technology and bioinformatics make it possible to acquire and combine large-scale host and pathogen genome information from the same infected individuals. We developed a novel strategy to explore the continuous struggle and complex interactions between human genetic variation and pathogen sequence diversity, as well as their respective impact on clinical outcome of infection. Using HIV-1 infection as a model, we explore the respective contributions of viral and human genetic variation to HIV-1 control. The method also highlights the sites of genomic conflict between the retrovirus and its human host. Human genetic studies in HIV disease We use DNA genotyping and sequencing approaches to search for human genetic variants that influence various aspects of HIV disease, in the context of several national and international collaborations. Resistance against infection is investigated in patients with hemophilia that were highly exposed to potentially contaminated blood products in the early days of the pandemic, yet remained seronegative. We also aim at understanding differences in chronic immune activation, a critical pathogenic mechanism in HIV-1 infection that leads to a slow exhaustion of immune responses, to increased viral replication in the activated T cells and to complications like cardio-vascular diseases.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Pelak K, Need AC, Fellay J, et al. (2011). Copy number variation of genes encoding killer cell immunoglobulin-like receptors and the control of HIV-1. PLoS Biology; 9(11):e1001208.

PhD Students Samira Asgari Istvan Bartha

Rauch A and Fellay J (2011). Personalized Hepatitis C Therapy: Opportunities and Pitfalls. Expert Review of Molecular Diagnostics; 11(2):127-9.

Master’s student Florian Gilbert

Rotger M, Dalmau J, Rauch A, et al. (2011). Comparative analysis of genomic features of human HIV-1 infection and primate models of SIV infection. Journal of Clinical Investigations; 121(6):2391-400.

Administrative Assistant Marisa Marciano Wynn

Snoeck J, Fellay J, Bartha I, Douek DC, and Telenti A (2011). Mapping of positive selection sites in the HIV genome in the context of RNA and protein structural constraints. Retrovirology; 8(1):87.

Postdoctoral Fellows Jérôme Lane Paul J. McLaren Thomas Junier

Fellay J, Frahm N, Shianna KV, et al. (2011). Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the Step trial. Journal of Infectious Diseases; 203(6):773-9. Petrovski S, Fellay J, Shianna KV, et al. (2011). Common Human Genetic Variants and HIV-1 susceptibility: A genome-wide survey in a homogeneous African population. AIDS; 25(4):513-8. Fellay J, Thompson AJ, Ge D, et al. (2010). ITPA gene variants protect against anemia in patients treated for chronic hepatitis C. Nature; 464(7287):405-8.

GHI - Global Health Institute

Fellay J, Shianna KV, Telenti A, and Goldstein DB (2010). Host Genetics and HIV-1: the final phase? PLoS Pathogens; 6(10):e1001033.

Associations between human polymorphisms and ribavirin-induced anemia: genomic overview of the 20q13 region including the genome-wide significant associated variants and the ITPA gene (adapted from Nature 2010).

EPFL School of Life Sciences - 2011 Annual Report

Harris Lab

http://harris-lab.epfl.ch/

Nicola Harris

GHI

Nicola Harris was born in New Zealand and completed her Masters degree in physiology at Victoria University of Wellington in 1994. She then trained in the field of immunology, completing a PhD thesis at the Malaghan Institute of Medical Research, Otago University, New Zealand. In 2002 she moved to Switzerland to complete further postdoctoral work with Hans Hengartner and the Nobel Laureate Rolf Zinkernagel at the Institute for Experimental Immunology, University of Zurich. In July 2005 she joined the ETH Zurich as an Assistant Professor and in August 2009 she moved to the Global Health Institute, Department of Life Sciences, EPFL where she is currently employed as a tenure track Assistant Professor.

Tenure Track Assistant Professor

Introduction

The intestinal mucosa represents an extensive interface between the body and the external environment that is constantly exposed to environmental micro-organisms. Amongst these, commensal bacteria are present in vast numbers (1012 per gram of intestinal contents) in all individuals at all times. Worms (helminths) can also establish chronic infections within our intestines and were present in a near ubiquitous manner throughout mammalian evolution. Today intestinal helminths still infect approximately 1/3 of the world’s population, with the heaviest infections found in children living in poor communities within developing countries. Our work aims to investigate: i) how the immune system can provide protection against heavy burdens of intestinal helminths, and ii) how intestinal helminths and/or commensal bacteria can modulate the responsiveness of our immune system. In regard to the latter aim we would like to understand why and how reduced exposure to specific intestinal bacteria species and/or intestinal helminths can predispose towards increased autoimmune and allergic diseases.

Keywords

Immunology, intestine, soil-transmitted helminths, commensal bacteria, antibodies, Th2 immune responses, cytokines, allergy, vaccination.

Results Obtained in 2011

As part of our earlier work, we uncovered an essential role for antibodies in providing effective immunity against helminth parasites. We then expanded this project to investigate the mechanisms by which antibodies promote helminth killing and in 2011 we completed a project demonstrating a novel role for IgG1 and IgE antibodies in regulating the haematopoiesis of basophils. We additionally

demonstrated that antibody-laden basophils played a small but significant role in the killing of helminth larvae. More recently we have established that antibodies also function to promote the activation and recruitment of so called ‘alternatively’ activated macrophages. Such macrophages are postulated to contribute to helminth killing and the means by which they achieve this, plus the impact of antibodies on these cells, is currently the subject of ongoing investigation in our laboratory. 2011 also saw the initiation of a project aimed at investigating the interactions between intestinal helminths and commensal bacteria. As intestinal helminths and commensal bacteria inhabit the same environmental niche, we considered it likely that these organisms interact with and impact on, each other. In addition, intestinal helminths are well known to alter intestinal physiology, permeability, mucous secretion and the production of anti-microbial peptides⎯all of which may impact on bacterial survival and spatial organization. Preliminary findings from our laboratory indicate that helminth infection of mice does alter the abundance and diversity of intestinal bacteria, as well as impacting on the availability of immuno-modulatory metabolites. To investigate the impact of these changes on the host response against the helminth we have now developed a model of germ-free helminth infection which involves the hatching of helminth larvae using the auxotrophic HA107 E. coli (that can not replicate in germ-free mice). Initial experiments using this system are now underway and we hope to report on the consequences of helminth-bacterial interactions in 2012.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Santoni de Sio FR, Massacand J, Barde I, Offner S, Corsinotti A, Kapopoulou A, Bojkowska K, Dagklis A, Fernandez M, Ghia P, Thomas JH, Pinschewer D, Harris N, Trono D. KAP1 regulates gene networks controlling mouse B lymphoid cell differentiation and function, Blood. 2012 Apr 3. [Epub ahead of print) Feyerabend TB, Weiser A, Tietz A, Stassen M, Harris N, Kopf M, Radermacher P, Möller P, Benoist C, Mathis D, Fehling HJ, Rodewald HR. Cre-mediated cell ablation contests mast cell contribution in models of antibody- and T cell-mediated autoimmunity, Immunity, vol. 35, num. 5, p. 832-44, 2011. Duvoisin R, Ayuk MA, Rinaldi G, Suttiprapa S, Mann VH, Lee CM, Harris N, Brindley PJ.. Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells, Transgenic research, 2011.

Team Members Postdoctoral Fellows Julia Esser Mario Zaiss PhD Student Ilaria Mosconi Master’s Student Nadine Guenat Senior Technical Assistant Manuel Kulagin Administrative Assistant Marisa Marciano Wynn

Herbst T, Sichelstiel A, Schär C, Yadava K, Bürki K, Cahenzli J, McCoy K, Marsland BJ, Harris NL. Dysregulation of Allergic Airway Inflammation in the Absence of Microbial Colonization, American Journal of Respiratory and Critical Care Medicine, Jul 15;184(2):198-205. 2011. Schaer C, Hiltbrunner S, Ernst B, Mueller C, Kurrer M, Kopf M, Harris NL. HVEM Signalling Promotes Colitis, PloS one, Apr 18;6(4):e18495., 2011. N. Harris and W. C. Gause. To B or not to B: B cells and the Th2-type immune response to helminths, Trends in Immunology, vol. 32, num. 2, p. 80-8, 2011.

GHI - Global Health Institute

N. L. Harris. Advances in helminth immunology: optimism for future vaccine design?, Trends in Parasitology, Jul;27(7):288-93. 2011.

The picture depicts macrophages surrounding the larval stage of the murine intestinal helminth Heligmosomoides polygyrus bakeri.

EPFL School of Life Sciences - 2011 Annual Report

Lemaitre Lab

http://lemaitrelab.epfl.ch/

GHI

Bruno Lemaitre obtained his PhD in 1992 with Dario Coen at the University Pierre and Marie Curie (Paris) on the P element transposition in Drosophila. Next, he joined the laboratory of Jules Hoffmann (Strasbourg France) as a research associate where he began a genetic dissection of the Drosophila antimicrobial response. In 1998, he started his own laboratory on Drosophila immunity at the Centre Génétique Moléculaire (Gif-sur-Yvette, France). In 2007, he was appointed professor at EPFL.

Bruno Lemaitre Full Professor

Introduction

Our group has developed an integrated approach of hostpathogen interactions in model insect Drosophila analysing the basis of microbial infection and corresponding host defence responses using both genetic and genomic tools.

Keywords

Innate immunity, gut homeostasis, host-pathogen interactions, Drosophila, symbiosis.

Results Obtained in 2011

The gut is the major interface between microbes and their animal hosts. The gut epithelial cells are armed with efficient immune defenses to combat invasion and colonization by pathogens. However, the gut also harbors a flora of commensal bacteria, with potentially beneficial effects for the host, which must be tolerated without a chronic and harmful immune response. In recent years Drosophila has emerged as a powerful model to dissect host-pathogen interactions, leading to the paradigm of antimicrobial peptide regulation by the Toll and Imd signaling pathways. The strength of this model derives from the availability of powerful and cost effective genetic and genomic tools as well as the high degree of similarities to vertebrate innate immunity. However, in spite of growing interest in gut mucosal immunity generally, very little is known about the immune response of the Drosophila gut.

the peritrophic matrix and (iii) maintenance of gut homeostasis through regulation of stem cell activity are all essential elements of the gut defense to infection. We have also started to investigate the role of the Drosophila microbiota on the gut immune response and intestinal homeostasis. We first showed that the Drosophila microbiota affect at basal levels the immune and gut stem cell activities. Interestingly, the chronic stimulation of stem cell by the indigenous microbiota is stronger in old flies (due to higher bacterial count) and lead to defects in gut morphogenesis. Moreover, we have shown that an important role of Amidase Peptidoglycan Recognition Protein is to prevent deleterious immune responses by the indigenous microbiota by scavenging peptidoglycan, the elicitors of the Imd pathway. Our current project extends from a sensu-stricto analysis of the gut immune response by addressing the impact of infection on gut renewal and physiology. This project is in line with the renewed interest in the study of gut-bacteria interactions in both mammals and insects. We believe that the fundamental knowledge generated on Drosophila gut immunity will serve as a paradigm of epithelial immune reactivity and have broader impacts on our comprehension of animal immune defense mechanisms and gut homeostasis.

Using a genetic approach, my laboratory has started to investigate the molecular mechanisms underlying gut immune responses in Drosophila. Our studies have already indicated that (i) production of antibacterial peptides through the Imd pathway, (ii) physical barrier provided by

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Buchon N, Broderick NA, Kuraishi T, and Lemaitre B. (2010). The EGFR pathway coordinates Drosophila stem cell proliferation and gut remodeling in response to infection. BMC Biol. 2010 Dec 22;8(1):152. Alattia JR, Kuraishi T, Dimitrov M, Chang I, Lemaitre B, Fraering PC. Mercury is a direct and potent {gamma}-secretase inhibitor affecting Notch processing and development in Drosophila. FASEB J. 2011 Jul;25(7):2287-95. Herren, J. and Lemaitre B. (2011) Spiroplasma and host immunity: Activation of humoral immune responses increases endosymbiont load and susceptibility to certain bacterial pathogens in Drosophila melanogaster. Cell. Microbiology 13(9):1385-96. Kuraishi, T., Binggeli, O., Opota, O. Buchon, N. , and Lemaitre, B. (2011) Genetic evidence for a protective role of the peritrophic matrix against intestinal bacterial infection in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15966-71 Opota, O., Vallet-Gély, I., Vincentelli, R. , Kellenberger C., Iacovache, I.,Gonzalez, M. Roussel, A., van der Goot, F.G. and Lemaitre, B.(2011) Monalysin, a novel -pore-forming toxin from the Drosophila pathogen Pseudomonas entomophila, contributes to host intestinal damage and lethality. PLoS Pathog. 2011 Sep;7(9):e1002259. Paredes*, J.C., Welchman*, D.P., Poidevin, P. and Lemaitre, B. (2011) Negative regulation by Amidase PGRPs shapes the Drosophila antibacterial response and protects the fly from its own immune system. Immunity, 23;35(5):770-9.

Team Members Postdoctoral Fellows Nichole Broderick Nicolas Buchon Guennalle Diepois Claudine Neyen Dani Osman

PhD Students Olivier Biggeli Wen Bin (Alfred) Chng Sveta Chakrabarti Jeremy Herren Juan Paredes Lab Technicians Jean-Philippe Boquete Fanny Schüpfer Christophe Remondeulaz Master’s Student Maroun Bou Sleiman Apprentices Mégane Bozza Barbara Lecrinier Administrative Assistant Véronique Dijkstra-Bulliard

Vallet-Gely I, Opota O, Boniface A, Novikov A, Lemaitre B. (2010) A secondary metabolite acting as a signaling molecule controls Pseudomonas entomophila virulence. Cell Microbiol. 2010 Nov;12(11):1666-7.

GHI - Global Health Institute

Zaidman-Remy, A., Poidevin, M., Herve, M., Welchman, D.P., Paredes, J.C., Fahlander, C., Steiner, H., Mengin-Lecreulx, D., and Lemaitre B. (2011). Drosophila immunity: analysis of PGRP-SB1 expression, enzymatic activity and function. PLoS One 6(2): e17231.

Section of the Drosophila midgut: Image depicting a crosssection of the Drosophila gut with muscle in red (Phaloidin), the brush border in green (reporter-GFP) and nuclei in blue (DAPI).

EPFL School of Life Sciences - 2011 Annual Report

McKinney Lab

http://mckinney-lab.epfl.ch/

GHI

John McKinney received his PhD from Rockefeller University (1994) for studies on cell cycle regulation in yeast. His postdoctoral studies at the Albert Einstein College of Medicine (1995-1998) were focused on persistence mechanisms in tuberculosis. He then returned to Rockefeller as an Assistant (1999-2004) and Associate (2004-2007) Professor. In 2007, he relocated to EPFL in order to establish a new research program at the interface of microbiology and microengineering. Prof. McKinney heads the Laboratory of Microbiology and Microsystems in EPFLâ&#x20AC;&#x2122;s Global Health Institute.

John McKinney Full Professor

Introduction

Research in the McKinney lab is focused on understanding the mechanistic basis of microbial individuality, defined as cell-to-cell phenotypic variation that is not attributable to genetic or environmental differences. Better understanding of microbial individuality will lead to new strategies to eliminate subpopulations of bacteria that are refractory to antimicrobial therapy and host immunity.

Keywords

Microbiology, microengineering, real-time single-cell analysis, timelapse fluorescence microscopy, microfluidics, microelectromechanical systems (MEMS), tuberculosis, persistence, antibiotics.

Results Obtained in 2011

Bacterial cells behave as individuals. Mutation and horizontal DNA transfer are important drivers of bacterial individuation, but these genetic events are relatively rare. At much higher frequencies, genetically identical cells display metastable variation in growth rates, response kinetics, stress resistance, and other quantitative phenotypes. These cell-to-cell differences arise from non-genetic sources, such as stochastic fluctuations in gene expression and asymmetric partitioning of components during cell division. Temporal variation at the single-cell level generates phenotypic diversity at the population level. This diversity is critical for bacterial persistence in changing environments because it ensures that some individuals will survive potentially lethal stresses that would otherwise extinguish the population. Our research focuses on the pathogenic species Mycobacterium tuberculosis. We use timelapse fluorescence microscopy with custom-made microdevices to study the real-time dynamics of bacterial behavior at the single-cell level. Counter-Immune Mechanisms This project is focused on the mechanisms that M. tuberculosis deploys to resist elimination by the host immune response. We identified a signal transduction pathway that mediates bacterial resistance to immune-related stresses, including reactive oxygen and nitrogen species. We found

that resistance to these stresses is linked to regulation of a prominent family of cell wall proteins of unknown function. We are exploring the mechanistic role of these proteins in stress resistance and immune evasion. In Vivo Metabolism This project is focused on the metabolic pathways required for growth and persistence of M. tuberculosis in the mammalian host. Computational modeling of M. tuberculosis metabolism has generated surprising new insights into the metabolic capabilities and vulnerabilities of M. tuberculosis, including the identification of a novel pathway for ATP production that is present only in mycobacteria. We are testing our computational findings in wetlab experiments. Antibiotic Tolerance This project is focused on cell-to-cell variation in antibioticmediated cell death and persistence. Our findings challenge conventional models of antibiotic mode of action, which postulate that growth rate determines cell fate (death or persistence) at the single-cell level. Instead, we find that the fate of individual cells is not correlated with growth kinetics but is instead linked to stochastic expression of death-modulating factors. We are studying the underlying mechanisms of stochastic gene expression and their impact on cell fate. Growth Dynamics This project is focused on the physiology of slow growth, which is a hallmark of persistent infections, and the scaling rules that link cell growth and cell cycle kinetics. We find that mycobacteria display extreme cell-to-cell variation in biomass doubling time, interdivision time, size at division, symmetry of division, duration of S phase, timing of S phase initiation, etc. These findings challenge the conventional notion that each cellâ&#x20AC;&#x2122;s phenotype is uniquely determined by the sum of its genotype and its environment. We are studying the mechanistic basis of cell-to-cell variation in cell division cycle kinetics.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Lemos, M.P., Rhee, K.Y. and McKinney, J.D. (2011) Expression of the leptin receptor outside of bone marrow-derived cells regulates tuberculosis control and lung macrophage MHC expression. J. Immunol. 187(7): 3776-3784.

Postdoctoral Fellows Jean-Baptiste Bureau Tarun Chopra Zeljka Maglica Giulia Manina Isabella Santi

Gelman, E., McKinney, J.D. and Dhar N. (2012) Malachite green interferes with post-antibiotic recovery of mycobacteria. Antimicrob. Agents Chemother. (in press).

Griffin, J.E., Pandey, A.K., Gilmore, S.A., Mizrahi, V., McKinney, J.D., Bertozzi, C.R. and Sassetti, C.M. (2011) Cholesterol catabolism by Mycobacterium tuberculosis requires transcriptional and metabolic adaptations. Chem. Biol. 19(2): 218-227. Ballester, M., Nembrini, C., Dhar, N., de Titta, A., de Piano, C., Pasquier, M., Simeoni, E., van der Vlies, A.J., McKinney, J.D., Hubbell, J.A. and Swartz, M.A. (2011) Nanoparticle conjugation and pulmonary delivery enhance the protective efficacy of Ag85B and CpG against tuberculosis. Vaccine 29(40): 69596966. Kirksey, M.A., Tischler, A.D., Siméone, R., Hisert, K.B., Uplekar, S., Guilhot, C. and McKinney, J.D. (2011) Spontaneous phthiocerol dimycocerosate (PDIM) deficient variants of Mycobacterium tuberculosis are susceptible to interferonγ-mediated immunity. Infect. Immun. 79(7): 2829-2838.

Senior Staff Scientist Neeraj Dhar

PhD students Matthieu Delincé Cyntia De Piano Meltem Elitas Ekaterina Gelman Manisha Lotlikar Emre Özdemir Visiting Scientist Paul Murima Research Technician François Signorino-Gelo Administrative Assistant Suzanne Lamy

Lemos, M.P., McKinney, J.D. and Rhee, K.Y. (2011). Dispensability of surfactant proteins A and D in immune control of Mycobacterium tuberculosis infection following aerosol challenge of mice. Infect. Immun. 79(3): 1077-1085. Tischler, A.D. and McKinney, J.D. (2011) Bacterial strategies for survival in the host. In The Immune Response to Infection (ed. Kaufmann, S.H.E., Rouse, B.T. and Sacks, D.L.) ASM Press, Washington DC, pp. 425-440. Dhar, N. and McKinney, J. (2010). Mycobacterium tuberculosis persistence mutants identified by screening in isoniazid-treated mice. Proc. Natl. Acad. Sci. U S A 107(27): 12275-12280.

GHI - Global Health Institute

Tischler, A.D. and McKinney, J.D. (2010). Contrasting persistence strategies in Salmonella and Mycobacterium. Curr. Opin. Microbiol. 13(1): 93-99.

Single-cell division cycle dynamics in mycobacteria. The cell division septum was visualized by fusing green fluorescent protein to a septum protein (Wag31); the DNA replisome was visualized by fusing red fluorescent protein to a replisome protein (DnaN). Using timelapse microfluidic-microscopy, we found that individual bacteria grow exponentially (as cells enlarge they grow faster) and the duration of the cell division cycle scales with the duration of S phase, suggesting a unique mechanism of cell cycle control.

EPFL School of Life Sciences - 2011 Annual Report

Trono Lab

http://tronolab.epfl.ch

GHI

After obtaining an M.D. from the University of Geneva and completing a clinical training in pathology, internal medicine and infectious diseases in Geneva and at Massachusetts General Hospital in Boston, Didier Trono embarked in a scientific career at the Whitehead Institute for Biomedical Research of MIT. In 1990, he joined the faculty of the Salk Institute for Biological Studies to launch a center for AIDS research. He moved back to Europe seven years later, before taking the reins of the newly created EPFL School of Life Sciences in 2004.

Didier Trono

Full Professor Dean of the School of Life Sciences

Introduction

After a long involvement in the study of interactions between viral pathogens and their hosts and the development of gene-based therapies, our laboratory shifted a few years ago to the field of epigenetics, when we became interested in exploring a true terra incognita of mammalian biology, the roles and mechanisms of action of KRAB-containing zinc finger proteins (KRAB-ZFPs). Our ongoing work demonstrates that this tetrapod-specific family of transcriptional regulators initially evolved as a line of defense against retroviral invaders, to become understood today as a master regulator of mammalian homeostasis.

Keywords

Genetics, epigenetics, KRAB zinc finger proteins, KAP1, transcriptional regulation, retroelements, imprinting, liver metabolism, sexual dimorphism, lympho-hematopoietic system.

Results Obtained in 2011

About 1â&#x20AC;&#x2122;200 of the 20â&#x20AC;&#x2122;000 genes contained in the human genome encode for transcriptional regulators, including some four hundred KRAB-ZFPs. Sequence-specific DNA binding transcriptional repressors that act by triggering the formation of heterochromatin through their universal cofactor KAP1, KRABZFPs have been subjected to intense positive selection during evolution, suggesting their engagement in some genetic conflict. Confirming this prediction, we reported last year that KRAB-ZFPs and their cofactor KAP1 are responsible for the early embryonic silencing of endogenous retroviruses. This year, we revealed how a highly conserved member of the family, ZFP57, is responsible for the maintenance of imprinting marks in embryonic stem cells. Imprinting is a process restricted to placental mammals, which results in the parental allele-specific expression of a few dozen genes important notably for metabolic regulation and neurological development. We demonstrated that ZFP57, KAP1 and associated effectors bind selectively to the H3K9me3-bearing, DNA methylated allele of ICRs (imprinting control regions) in embryonic stem (ES) cells. KAP1 deletion induced a loss of heterochromatin marks at ICRs, while deleting ZFP57 or DNA methyltransferases (DNMTs) led to ICR DNA demethylation. Accordingly, we found ZFP57 and KAP1 associated with DNMTs and the hemimethylated DNA-binding NP95. We finally identified the methylated TGCCmeGC hexa-

nucleotide as the motif recognized by ZFP57 in all ICRs as well as in several dozen of additional loci, several of which at least are ZFP57-dependently methylated in ES cells. These results significantly advance our understanding of imprinting, and suggest a general mechanism for the protection of specific loci against the wave of DNA demethylation that affects the mammalian genome during the first few days of embryogenesis. These data nicely illustrate the crucial role of KRAB/KAP1mediated regulation at the earliest stage of development. In parallel, we have been exploring the functions fulfilled by this system in adulthood. We had previously determined that, in the forebrain, KAP1 regulates behavioral susceptibility to stress. Through a combination of conditional KAP1 knockout in the mouse, in vivo chromatin and transcription studies as well as a broad range of tissue culture-based experiments and in silico analyses, we now have determined that KRAB/KAP1-mediated gene regulation is critical for events as diverse as the maturation and activation of B and T lymphocytes, for several steps of hematopoietic differentiation and for liver metabolism. Interestingly, the liver is characterized by sexually dimorphic gene expression translating into sex-specific differences in lipid, drug, steroid hormone and xenobiotic metabolism, with distinct responses of males and females to environmental challenges. Liver-specific KAP1 knockout in the mouse led to sexually dimorphic phenotypic disturbances, including male-restricted steatosis and hepatic tumors. This correlated with sex-specific transcriptional dysregulation of a wide range of metabolic genes, notably those involved in retinol and sex hormone processing as well as in detoxification, with chromatin immunoprecipitation followed by deep sequencing indicating that many of these genes are direct targets of the KRAB/KAP1 repression system. These results identify KRAB/KAP1-mediated transcriptional regulation as a central event in the metabolic control of hormones, drugs and xenobiotics in the liver, and further link disturbances in these processes with hepatic carcinogenesis. A long-term objective of these studies is to ask whether polymorphism in KRAB-ZFP genes or their targets might underlay inter-individual differences in susceptibility to human diseases, for instance ones reminiscent of the phenotypes of mice in which KAP1 is inactivated in specific organs.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

F.R. Santoni de Sio, J. Masssacand, I. Barde, S. Offner, A. Corsinotti, A. Kapopoulou, K. Bojkowska, A. Dagkis, M. Fernandez, P. Ghia, J.H. Thomas, D. Pinschewer, N. Harris and D. Trono (2012). KAP1 regualtes gene networks controlling B lymphoid differentiation and function. Blood, (E-pub ahead of print).

Postdoctoral Fellows Isabelle Barde Marco Cassano Marc Friedli Michael Imbeault Julien Marquis Simon Quenneville Benjamin Rauwel Helen Mary Rowe Francesca Santoni de Sio Benyamin Yazdan Panah

K. Bojkowska, F. Aloisio, M. Cassano, A. Kapopoulou, F. Santoni de Sio, N. Zangger, S. Offner, C. Cartoni, C. Thomas, S. Quenneveille, K. Johnsson and D. Trono (2012). Liver-specific ablation of KRAB-associated protein 1 in mice leads to male-predominant hepatosteatosis and development of liver adenoma. Hepatology, in press.

S. Quenneville, G. Verde, A. Corsinotti, A. Kapopoulou, J. Jakobsson, S. Offner, I. Baglivo, P.V. Pedone, G. Grimaldi, A. Riccio and D. Trono (2011). In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect the chromatin and DNA methylation of imprinting control regions. Mol. Cell, 44: 361-372. S. Meylan, A. Groner, G. Ambrosini, N. Malani, S. Quenneville, N. Zangger, A. Kapopoulou, A. Kauzlaric, J. Rougemont, A. Ciuffi, F.D. Bushman, P. Bucher and D. Trono (2011). A gene-rich, transcriptionally active environment and the predeposition of repressive marks are predictive of susceptibility to KRAB/KAP1mediated silencing. BMC Genomics, 12: 378.

Senior Scientist Priscilla Turelli

PhD Students Karolina Bojkowska Natali Castro Diaz Andrea Corsinotti Gabriella Ecco Anna Groner Annamaria Kauzlaric Flavia Marzetta

K. Bojkowska, F. Santoni de Sio, I. Barde, S. Offner, S. Verp, C. Hienis, K. Johnsson and D. Trono (2011). Measuring in vivo protein half-life. Chem. Biol., 18: 805-815.

Bioinformaticians Adamandia Kapopoulou Yoann Mouscaz

H.M. Rowe and D. Trono (2011). Dynamic control of endogenous retroelements during development. Virology, 411: 273-287.

Technicians Sandra Offner Charlène Raclot Sonia Verp

D. Trono, C. Van Lint, C. Rouzioux, E. Verdin, F. Barré-Sinoussi, T.-W. Chun and N. Chomont (2010). HIV persistence and the prospect of long-term drug-free remission in HIV-infected individuals. Science, 329: 174-180.

Administrative Assistant Séverine Reynard

V. Busskamp, J. Duebel, D. Balya, M. Fradot, T. James, S. Siegert, A.C. Groner, E. Cabuy, V. Forster, M. Seeliger, M. Biel, P. Humphries, S. Mohand-Said, D. Trono, K. Deisseroth, J.A. Sahel, S. Picaud and B. Roska (2010). Genetic reactivation of cone photoreceptors restores visual responses in Retinitis pigmentosa. Science, 329: 413-417. A.C. Groner, S. Meylan, A. Ciuffi, N. Zangger, G. Ambrosini, N. Dénervaud, Philipp Bucher and D. Trono (2010). KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genetics, 6: e1000869. H. Rowe, J. Jakobsson, D. Mesnard, J. Rougemont, S. Reynard, T. Aktas, P.V. Maillard, H. Layard-Liesching, S. Verp, J. Marquis. F. Spitz, D.B. Constam and D. Trono (2010). KAP1 controls endogenous retroviruses in embryonic stem cells. Nature, 463: 237-240.

GHI - Global Health Institute

Model of ZFP57/KAP1-mediated maintenance of imprinting marks in ESC. ZFP57 binds to the TGCCmeGC methylated hexanucleotide in ICRs and recruits KAP1, which serves as a scaffold for indicated chromatin modifiers and DNA methyltransferases, ensuring that imprinted alleles resist that genome-wide wave of demethylation that takes place during this period (See Quenneville et al., Mol. Cell 2011).

EPFL School of Life Sciences - 2011 Annual Report

Van der Goot Lab http://vdg.epfl.ch/

GHI

Gisou van der Goot studied engineering at the Ecole Centrale de Paris, then did a PhD in Molecular Biophysics at the Nuclear Energy Research Center, Saclay, France, followed by a postdoc at the European Molecular Biology Laboratory (EMBL) in Heidelberg. She started her own group in 1994 in the department of Biochemistry, University of Geneva, became Associate Professor at the Faculty of Medicine (Univ. Geneva) in 2001 and finally Full Professor at the EPFL in 2006, where she co-founded the Global Health Institute.

F. Gisou van der Goot Full Professor

Introduction

Our laboratory has three main focuses: 1) understanding the physiological and pathological roles of the anthrax toxin receptors, TEM8 and CMG2; 2) unraveling the molecular mechanisms responsible for Hyaline Fibromatosis syndrome, a rare genetic disease due to mutations in CMG2; 3) Our third focus is on the compartmentalization of mammalian cells and the function thereof. We are particularly interested in the architecture of the endoplasmic reticulum and how its complex structure relates to function.

Keywords

Anthrax toxin, Systemic Hyalinosis, Hyaline Fibromatosis, TEM8, CMG2, endoplasmic reticulum, palmitoylation.

Results Obtained in 2011

Consequences of Hyaline Fibromatosis Syndrome mutations Hyaline Fibromatosis Syndrome (HFS) is a human genetic disease caused by mutations in the anthrax toxin receptor 2 (or cmg2) gene, which encodes a membrane protein thought to be involved in the homeostasis of the extracellular matrix. Little is known about the structure and function of the protein and the genotype-phenotype relationship of the disease. Through the analysis of 4 patients, we identified 3 novel mutants and determined their effects at the cellular level. Using a variety of approaches (biochemical, morphological and functional), we could show that missense mutations that map to the extracellular von Willebrand domain or the Ig-like domain lead to folding defects and thereby to retention of the mutated protein in the endoplasmic reticulum. Mutations in the Ig-like domain, the structure of which we have modeled, prevent proper disulfide bond formation and are more efficiently targeted to ER associated degradation. Importantly, we found that CMG2 can be rescued in fibroblasts of some HFS patients by treatment with a proteasome inhibitor that is in clinical trials and that rescued mutant CMG2 is then properly transported to the plasma membrane and is functional. Our work shows that the ER folding and degradation pathway components are promising drug targets for HFS.

Regulation of endoplasmic reticulum function by palmitoyltransferases The endoplasmic reticulum (ER) is the largest intracellular organelle of mammalian cells. It fulfills major functions such as folding and quality control of membrane and secreted proteins, lipid biosynthesis and calcium storage. This diversity of functions is accompanied by a complex 3D architecture, the maintenance of which is essential, since alterations lead to disease. How this architecture is generated, how proteins localize to specific subdomains and how structure and functions are coordinated is poorly understood. We are interested in the potential role of palmitoyltransferases in these processes. We found that a major ER chaperone, the transmembrane protein calnexin involved in the folding of glycoproteins such as CMG2, is palmitoylated and that this modification, which occurs on 2 juxtamembranous sites, is essential for the chaperone to perform its function. We determined, using RNAi and overexpression screening, that the modification is mediated by a single enzyme, DHHC6, and that none of the other 16 ER DHHC enzymes can compensate for DHHC6 loss. More specifically, modification of calnexin by DHHC6 drives the formation of an actin-stabilized super complex, comprising calnexin, the sec61 translocon, the oligosaccharyl transferase complex responsible for Nglycosylation and the TRAP complex. This super complex (figure ) is essential for proper handling of newly synthesized glycoproteins, which, as they emerge from the ribosome through the translocon pore, acquire their sugars and are assisted by calnexin to prevent aggregation during folding. Palmitoylation thus ensures that the chaperone is in the right place at the right time, so that in the competition between folding and aggregation, the former is more efficient. Our aim is to extend these studies to other palmitoylated ER proteins to obtain a systems understanding of the ER palmitoylation network.

EPFL School of Life Sciences - 2011 Annual Report

Selected publications

Team Members

Deuquet, J., Lausch E., Superti-Furga, A. and F.G. van der Goot (2012) The dark side of capillary morphogenesis gene 2. EMBO J. 31:3-13.

Postdoctoral Fellows Michal Feldman Asvin Lakkaraju Julie Deuquet Ioan Iacovache

Lakkaraju, A.K.K., Abrami, L., Lemmin,T., Blaskovi, S., Kunz,B., Kihara, A., Dal Peraro, M. and van der Goot, F.G. (2012) Palmitoylated calnexin is a key component of the ribosome-translocon complex. EMBO J. (in press) .

Iacovache, I. Degiacomi, M.T., Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M. and van der Goot, F. G. (2011) Dual chaperone role of the C-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin. PLoS Pathogen 7:e1002135. Gonzalez, RM., Bischofberger, M., Frêche, B., Ho, S., Parton, R.G. and F.G. van der Goot (2011) Pore-forming toxins induce multiple cellular responses promoting survival. Cellular Microbiology Apr 26. doi: 10.1111/j.14625822.2011.01600.x. Deuquet J., Lausch E. , Guex N., Abrami L., Salvi S., Lakkaraju A., Ramirez MCM, Martignetti J.A., Rokicki D., Bonafe L., Superti-Furga A. and F. G. van der Goot (2011) Hyaline Fibromatosis Syndrome inducing mutations in the ectodomain of anthrax toxin receptor 2 can be rescued by proteasome inhibitors. EMBO Mol. Med. 3:208-221.

Scientist Collaborator Laurence Abrami

PhD Students Sanja Blaskovic Jérôme Bürgi Sarah Frieben Yan Shixu Laboratory Assistants Sylvia Ho Béatrice Kunz Suzanne Salvi Administrative Assistants Carole Burget Geneviève Rossier

Opota O., Vallet-Gély I., Kellenberger C., Vincentelli R., Iacovache I., Gonzales M. R., Roussel, A., van der Goot F.G. and Lemaitre B. (2011) Identification of a novel ß-pore-forming toxin required for the pathogenesis of Pseudomonas entomophila in Drosophila. PLoS Pathogen 7: e1002259. Abrami, L., Kunz, B. and van der Goot, F.G. (2010) Anthrax toxin triggers the activation of src like kinases to mediates its own uptake. Proc Natl Acad Sci USA 107:1420-1424. Iacovache, I. Biasini, M., Kowal, J., Kukulski, W., Chami, M. van der Goot, F.G., Engel, A. and Rémigy, R.W. (2010) The 2DX robot: a membrane protein 2D crystallization Swiss Army knife. J. Struct. Biol. 169:370-378. Abrami, L., Bischofberger M, Kunz, B., Groux, R. and van der Goot, F.G. (2010) Endocytosis of the anthrax toxin is mediated by clathrin, actin and unconventional adaptors PLoS Pathogen 6(3): e1000792.

GHI - Global Health Institute

Iacovache, I, Bischofberger M. and van der Goot, F.G. (2010) Structure and assembly of pore-forming proteins. Current Opinion in Structural Biology 20:241-246.

Schematic representation of the Ribosome-translocon-oligosacharyl transferase-calnexin super complex. Calnexin is then positioned to efficiently grab nascent glycoproteins as they emerge from the translocon pore, acquire their N-linked glycan from which the 2 external glucoses have been trimmed.

EPFL School of Life Sciences

–

2011 Annual Report

Other SV Professors and Newcomer Professors

EPFL School of Life Sciences - 2011 Annual Report

Knowles

-Translational Research

Jonathan Knowles Full Professor

Research Interests

Jonathan Knowles was named as Professor of Translational Research at EPFL, Sciences de la Vie at the beginning of 2010. He is working to help better establish translational research, the critical bridge between bench and bedside at EPFL and other partners in Switzerland and abroad. His interests span all aspects of technology and fundamental biological science particularly in the context of how they could be applied to help patients now, or in the future, and he interacts with a number of groups at EPFL to help bring this about. He believes that better public-private partnerships are essential to bring the advances of technology to society. Dr. Knowles was Head of Group Research and Member of the Executive Committee at Roche for 15 years until the end of 2009. He was a member of the Genentech Board for 12 years and a member of the Chugai Board for seven years. Dr. Knowles was also the chairman of the Corporate Governance Committee of Genentech. From 1987 to 1997, he was director of the Glaxo Institute for Molecular Biology in Geneva, a privately funded Research Institute with an excellent academic publication record. From 1992 until 1997 until he moved to Roche, Jonathan Knowles was the head of the European Research Division and head of the Glaxo Genetics Initiative.

Board of the Innovative Medicines Initiative, a unique public-private partnership between 28 Pharmaceutical companies, the European Commission and over one hundred of European academic centres with a budget of more than 2 billion Euros over five years. Jonathan Knowles is a Member of the European Molecular Biology Organization and also holds a Distinguished Professorship in Personalized Medicine at FIMM (Institute for Molecular Medicine Finland) at the University of Helsinki. He has been appointed to a Visiting Chair at the University of Oxford and is a Visiting Fellow of Pembroke College Cambridge. In 2011, Jonathan Knowles was appointed as a Trustee of Cancer Research UK, one of the worlds leading Cancer Research organisations. He remains very excited by the short term prospects for more personalised medicine through molecular diagnostics, especially for the treatment of cancer, as he believes this is the best and perhaps only way in which effective new therapies can be created and used. Contact: jonathan.knowles@epfl.ch

He was for 5 years the Chairman of the Research Directorsâ&#x20AC;&#x2122; Group of EFPIA (European Federation of Pharmaceutical Industry Associations) and was the founding chairman of the

EPFL School of Life Sciences - 2011 Annual Report

Molinari Group http://www.irb.ch/

ADJ

Maurizio Molinari earned a PhD in Biochemistry at the ETH-Zurich in 1995. He worked as a postdoctoral fellow in the laboratories of Cesare Montecucco (Padua, 1996-1997) and of Ari Helenius (Zurich, 1998-2000). Since October 2000, he is group leader at the IRB in Bellinzona. Dr. Molinari has received the Science Award 2002 from the Foundation for Study of Neurodegenerative Diseases, the Kiwanis Club Award 2002 for Medical Science, the Friedrich-Miescher Award 2006 and the Research Award Aetas 2007. Since 2008, Dr. Molinari is Adjunct Professor at the EPFL.

Maurizio Molinari

External Adjunct Professor Institute for Research in Biomedicine Bellinzona

Introduction

The endoplasmic reticulum (ER) contains high concentrations of molecular chaperones and enzymes that assist maturation of newly synthesized polypeptides destined to the extracellular space, the plasma membrane and the organelles of the endocytic and secretory pathways. It also contains quality control factors that select folding-defective proteins for ER retention and/or ER-associated degradation (ERAD). Mutations, deletions and truncations in the polypeptide sequences may cause protein-misfolding diseases characterized by a “loss-of-function” upon degradation of the mutant protein or by a “gain-of-toxic-function” upon its aggregation/deposition. Pathogens hijack the machineries regulating protein biogenesis, quality control and transport for host invasion, genome replication and progeny production. The aim of our work is to understand the molecular mechanisms regulating chaperone-assisted protein folding and the quality control processes determining whether a polypeptide can be secreted, should be retained in the ER, or should be transported across the ER membrane for degradation. A thorough knowledge of these processes will be instrumental to design therapies or to identify drug targets for interventions aiming at delaying the progression or even at curing diseases caused by inefficient functioning of the cellular protein factory, resulting from expression of defective gene products, or elicited by pathogens.

Keywords

Cell biology, protein folding, quality control and degradation, endoplasmic reticulum; molecular chaperones, folding enzymes, conformational diseases.

Results Obtained in 2011

ERAD Tuning: The Selective Clearance of ERAD Regulators from the ER Lumen-Several regulators of ERAD have shorter half-life compared to conventional ER chaperones. At steady state, they are selectively removed from the ER in a series of poorly defined events that we named ERAD tuning (Bernasconi and Molinari 2011). In an environment, the ER, where folding and disposal of newly synthesized cargo polypeptides are in kinetic competition, ERAD tuning sets ERAD activity at levels that do not interfere with

completion of ongoing folding programs and is therefore crucial to maintain cellular proteostasis. We have identified the complex comprising a type-I ER protein and the cytosolic protein LC3-I as an ERAD tuning receptor that regulates the COPII-independent vesicle-mediated removal of the luminal ERAD regulators EDEM1 and OS-9 from the ER (Submitted). Hijacking of ERAD Tuning by Viral Pathogens: the unconventional role of non-lipidated LC3-The COPII-independent vesicle-mediated removal of EDEM1 and OS-9 from the ER is hijacked by Coronaviruses (CoV) during their infection cycle and crucially depends on LC3-I, a cytosolic, ubiquitin-like protein. Before our reports (Calì et al 2008 and Reggiori et al 2010), LC3-I was simply considered as a cytosolic precursor of the autophagosomal protein LC3II. By revealing the role of LC3-I in ERAD tuning and in cell infection by CoV, our studies show for the first time an autophagy-independent function of this protein (deHaan et al. 2010, Reggiori et al. 2011). Malectin-We have functionally characterized Malectin, a novel ER-resident, stress-induced lectin binding di-glucosylated oligosaccharides displayed on newly synthesized polypeptides. Malectin shows prolonged association with misfolded protein conformers, consistent with a crucial role in ER quality control (Galli et al. 2011). Alzheimer’s Disease (AD)-In collaboration with the group of Patrick Aebischer, we have developed a novel technique for chronic in situ delivery of antibodies as an alternative to passive vaccination strategies. A polymer device loaded with genetically engineered C2C12 cells was implanted in the brain parenchyma of APP23 transgenic mice. Implanted cells supported secretion of single chain antibodies to the amyloid precursor protein, thereby preventing deposition of toxic Abeta aggregates. This substantially contrasted the worsening of behavioral, anxiety and memory defects, which are hallmarks of progressive AD (Marroquin et al. 2011).

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Bernasconi, R., Soldà, T., Galli, C., Pertel, T., Luban, J. and Molinari, M. (2010) Cyclosporine A-Sensitive, Cyclophilin B-Dependent Endoplasmic ReticulumAssociated Degradation. PLoS ONE 5, e13008. Aebi, M., Bernasconi, R., Clerc, S. and Molinari, M. (2010) N-Glycan Structures: Recognition and Processing in the ER. TIBS 35, 74-82. Bernasconi, R., Galli, C., Calanca, V., Nakajima, T. and Molinari, M. (2010) Stringent Requirement for HRD1, SEL1L and OS-9/XTP3-B for Disposal of ERAD-LS Substrates. J. Cell Biol. 188, 223-235.

Team Members Post doctoral Riccardo Bernasconi PhD Students Jessica Merulla Julia Noack Senior Scientists Elisa Fasana Carmela Galli Tatiana Soldà

-Highlights in J. Cell Biol 188, 176.

Reggiori, F., Monastyrska, I., Verheije, M.H., Calì, T., Ulasli, M., Bianchi, S., Bernasconi, R., deHaan, C.H.M. and Molinari, M. (2010) Coronaviruses Hijack the LC3-I-Positive EDEMosome, ER-Derived vesicles Exporting Short-Lived ERAD Regulators, for Replication. Cell Host & Microbe 7, 500-508. -Highlights in Cell Host & Microbe 7, 424-426. -Editors’ Choice in Science 329, 14. -Leading Edge, Microbiology Select in Cell 142, 5. -Recommended by the Faculty of 1000.

de Haan, C.A.M., Molinari, M. and Reggiori, F. (2010) Autophagy-Independent LC3 Function in Vesicular Traffic. Autophagy 6, 994-996. Hebert, D.N. Bernasconi, R. and Molinari, M. (2010) ERAD Substrates: Which Way Out? Semin. Cell Dev. Biol. 21, 526-532. Galli, C., Bernasconi, R., Soldà, T., Calanca, V. and Molinari, M. (2011) Malectin Participates in a Backup Glycoprotein Quality Control Pathway in the Mammalian ER. PLoS ONE 6, e16304. Bernasconi, R. and Molinari, M. (2011) ERAD and ERAD Tuning: Disposal of Cargo and of ERAD Regulators from the Mammalian ER. Curr. Opin. in Cell Biol. 23, 176-183. Marroquin, O.B., Cordero, M.I., Setola, V., Bianchi, S., Galli, C., Bouche, N. Mlynarik, V. Gruetter, R., Sandi, C., Bensadoun, J.-C., Molinari, M. and Aebischer, P. (2011) Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool. PLoS ONE 6, e18268. Reggiori, F., deHaan, C.A.M. and Molinari, M. (2011) The Unconventional Use of LC3 by Coronaviruses through the Alleged Subversion of the ERAD Tuning Pathway. Viruses 3, 1610-1623.

External Adjunct Professors

A, Receptor-mediated exported from the ER of ERAD regulators, which is hijacked by CoV for replication. B, Misfolded polypeptides inhibit the receptor-mediated clearance of ERAD factors from the ER. This results in UPR-independent enhancement of the intraluminal concentration of ERAD regulators.

EPFL School of Life Sciences - 2011 Annual Report

Rainer Group www.unifr.ch/inph/vclab

ADJ

Gregor Rainer obtained a Diploma in experimental physics from the University of Vienna, and then completed a Ph.D. at the Massachusetts Institute of Technology in systems neuroscience. Following nine years of experience as postdoc and research group leader at the Max Planch Institute for biological cybernetics in TĂźbingen, he joined the faculty of medicine at the University of Fribourg in 2008 and was subsequently appointed adjunct professor at EPFL.

Gregor Rainer

External Adjunct Professor University of Fribourg

Introduction

Research in the Visual Cognition Laboratory encompasses the study of higher cognitive functions in the mammalian visual system, with a focus on cholinergic neuromodulation. We use analysis of behavior during various visually based tasks, multi-channel recording of neurons and field potentials and quantitative neuropeptide analyses using mass spectrometry.

Keywords

Visual system, cortex, neural plasticity, learning, acetylcholine.

Results Obtained in 2011

One line of investigation has focused on plasticity of representations in higher level visual cortex in primates. We have recently published findings related to how inferior temporal cortex neurons mediate categorization of faces belonging to the own species compared to other species faces. We found that the inter-species boundary in the neural representation was shifted towards the own species, showing that visual experience with members of the own species profoundly affects memory representation. In a related pharmacological study, we have shown that cholinergic activation is crucial for the performance of categorization tasks. We have also examined the relation between the local field potential and spiking activity in different parts of the visual processing hierarchy. We found close correspondence between these signals in prefrontal but not visual cortex, a finding that is of importance for the interpretation of neural mass signals in humans. We have performed detailed laminar recordings in primary visual cortex in tree

shrews, examining layer-specific aspects of temporal and feature selective neural activity. Of particular interest is the high temporal fidelity of tree shrew visual cortical neurons to transient visual stimulation, which is clearly visible as response bursts following each visual transient. Detailed laminar specific information about temporal aspects of visual responses is crucial for obtaining a mechanistic understanding of information flow in cortex. Finally, we have established a database based on nano-flow liquid chromatography and mass spectrometry analysis of brain tissue data. We have described a large number of neuropeptides in the tree shrew brain, which provides a tool for investigating functional changes in neuropeptide regulation during cholinergic activation.

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Rainer G. Allocating attention in rank-ordered groups. Neuron 70(1):5-7 (2011).

PhD Students Anwesha Bhattacharyya Julia Veit Abbas Khani Filomena Petruzziello Sara Falasca Vaclav Ranc

Hoerzer GM, Liebe S, Schloegl A, Logothetis NK and Rainer G Directed coupling in local field potentials of macaque V4 during visual short-term memory revealed by multivariate autoregressive models. Front.Comput. Neurosci. 4:14 (2010).

Chablais F, Veit J, Rainer G, Jazwinska A. The zebrafish heart regenerates after cryoinjury-induced myocardial infarction. BMC Dev Biol. 7;11(1):21 (2011).

Post doctoral Xiaozhe Zhang

Sigala R, Logothetis NK, Rainer G. Own-species bias in the representations of monkey and human face categories in the primate temporal lobe. J Neurophysiol 105: 2740-2752 (2011). Liebe S, Logothetis NK, Rainer G. Dissociable effects of natural image structure and color on LFP and spiking activity in the lateral prefrontal cortex and extrastriate visual area V4. J Neurosci 31(28):10215-10227 (2011). Veit J, Bhattacharyya A, Kretz R, Rainer G. Neural response dynamics of spiking and local field potential activity depend on CRT monitor refresh-rate in the tree shrew primary visual cortex J Neurophysiol 106: 2303-2313 (2011). Aggelopoulos NC, Liebe S, Logothetis NK, Rainer G. Cholinergic control of visual ategorization in macaques. Front Behav Neurosci 5 (73): 1-10 (2011).

External Adjunct Professors

Petruzziello F, Fouillen L, Wadenstein H, Kretz R, Andren P, Rainer G, Zhang XJ. Extensive characterization of Tupaia belangeri Neuropeptidome using an integrated Mass Spectrometry Approach. J Proteome Res dx.doi.org/10.1021/ pr200709 (2011).

Each refresh monitor causes a distinct visual transient in primary visual cortex (V1) of the tree shrew. The stimulus is shown between 0 to 80ms (vertical dashed bars) at a refresh rate of 120Hz in this example. The neural response latency is around 25ms.

EPFL School of Life Sciences - 2011 Annual Report

Schorderet Group www.irovision.ch

ADJ

After attending medical school at the Universities of Fribourg and Geneva, Dr Schorderet obtained an FMH in Pediatrics. He then trained in medical genetics at the University of Washington, Center for Inherited Diseases in Seattle, USA, where he was appointed research assistant professor. On his return to Switzerland, he developed the Unit of Molecular Genetics of the CHUV and later was appointed head of the Division of Medical Genetics. He obtained a FMH in Medical Genetics and a FAMH in analyses in Medical Genetics. In 2003, Dr. Schorderet was appointed director of the Institute of Research in Ophthalmology (IRO) in Sion. He is a member of the SV faculty since 2005.

Daniel Schorderet

External Adjunct Professor Institute for Reserch in Ophthalmology (IRO), Sion Director

Introduction

The Institute for Research in Ophthalmology (IRO) develops research in various aspects of vision, from understanding the development of the eye in animal models like the zebrafish and the mouse to identifying new genes and characterizing their molecular and cellular pathways for better diagnosis and treatment. Through various Swiss and international collaborations, IRO is shaping a new way in providing molecular diagnosis and understanding the inherited conditions behind some of the diseases leading to blindness.

particularly during the formation of the digits. Recently, we identified mutations in a transporter that was exchanging magnesium for calcium in the retina and the teeth. Taken together, these results pinpoint the importance of calcium/ magnesium homeostasis in the development of the eye. We also associated mutations in PRSS56, a proteinase with trypsin-like serine protease activity, with posterior microphthalmia, a particular form of microphthalmia. This leads us to hypothesize that proteins of the sclera need to be digested to allow for correct expansion of the eye globe.

Keywords

Blindness, genetics of eye diseases, retinitis pigmentosa, glaucoma, age-related macular degeneration, diabetic retinopathy.

Results Obtained in 2011

At IRO, research centers around 4 axes: identification of new genes, understanding their function, developing animal models of eye diseases and new therapeutic tools. Anophthalmia /microphthalmia, a disease in which children are born with no or very small, non functional eyes, has recently emerged as one of the main research areas in gene identification in my laboratory. In 2011, we identified two new genes, SMOC1 in Waardenburg-anophthalmia syndrome and PRSS56 in posterior microphthalmia. These two genes illustrate two different pathways leading to small eyes. SMOC1, a calcium-binding protein, is assumed to interact with calcium signaling both in the retinal progenitors during eye development, and in bone formation, more

EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Gal A et al. Autosomal recessive posterior microphthalmos is caused by mutations in PRSS56, a gene encoding a trypsin-like serine protease. Am J Hum Genet, 88(3):382-390,2011.

Postdoctoral Fellows Gaëlle Boisset Arnaud Boulling Lysianne Follonier Castella Anne Oberson Nathalie Produit Leila Tiab

Abouzeid H, Boisset G, Favez T, Youssef M, Marzouk I, Shakankiry N, Bayoumi N, Descombes P, Agosti C, Munier FL, Schorderet DF. Mutations in the SPARCrelated modular calcium-binding protein 1 gene, SMOC1, cause Waardenburg anophthalmia syndrome. Am J Hum Genet 88(1):92-98,2011.

Emery M, Schorderet DF, Roduit R. Acute hypoglycemia induces retinal cell death in mouse. Plos ONE, 6(6):e21586,2011. Escher P, Schorderet DF, Cottet S. Altered expression of t he transcription factor Mef2c during retinal degeneration in Rpe65-/- mice. Invest. Ophthalmol Vis Sci, 52(8):5933-40,2011. Kotoulas A, Kokotas H, Kopsidas K, Droutsas K, Grigoriadou M, Bajrami H, Schorderet DF, Petersen M. A novel PIKFYVE mutation in fleck corneal dystrophy. Molec Vision 17:2776-2781,2011. Le Carré J, Schorderet DF, Cottet S. Altered expression of β-galactosidase-1-like protein 3 (Glb1l3) in the retinal pigment epithelium (RPE)-specific 65-kDa protein knock-out mouse model of Leber’s congenital amaurosis. Mol Vis 17:128797,2011. Ouechtati F et al. Clinical and genetic investigation of a large Tunisian family with complete achromatopsia: identification of a new nonsense mutation in GNAT2 gene. J Hum Genet. 56(1):22-8, 2011.

Research Associates Nathalie Allaman-Pillet Raphaël Roduit

PhD Students Séverine Hamann Fabienne Marcelli Lionel Page Gaëtan Pinton Désirée von Alpen Linda Wicht Laboratory technicians Céline Agosti Martine Emery Tatiana Favez Carole Herkenne Sylviane Métrailler Loriane Moret Administrative Assistants Pascale Evéquoz Sandra Théodoloz

Normal retina

Retina, 5 days post injury. Necrotic cells are observed at the site of the injury indicated by the arrow. No retinal layers are identifiable.

External Adjunct Professors

Neuroregeneration in the retina of an adult zebrafish after local external injury.

Retina, 100 days post injury. Retina is almost completely regenerated (arrow). The various retinal layers can be observed.

Tanner

EPFL School of Life Sciences - 2011 Annual Report

http://www.swisstph.ch

ADJ

Marcel Tanner

External Adjunct Professor Swiss TPH Insitute, Basel Director

Keywords

Epidemiology, public health, vaccines, drugs and diagnostics.

Research Interests

Swiss TPH (Tropical and Public Health Institute) and the EPFL School of Life Sciences are collaborating with the goal to bring together complementary expertise of the two institutions in research on host-pathogen interaction in infectious and chronic diseases and the development of new diagnostics, drugs and vaccines. Besides the collaboration in research, exchanges of teaching faculty and students within the MSc courses continued. Joint research activities with pathogenic mycobacteria and nematodes as target pathogens have been initiated. These disease-specific joint activities are complemented by collaborations in the fields of lipidomics and bioinformatics. The nematodes comprise a plethora of pathogens of medical, veterinary, and agricultural importance. Most of the pathogenic nematodes are difficult to maintain in the lab and their life-cycles cannot be completed in vitro. The freeliving nematode Caenorhabditis elegans, widely used as a model in developmental biology, provides an attractive tool for identification of novel anthelmintics and for functional characterization of the existing ones. Medium-throughput in vitro screening of chemical libraries against C. elegans

have been initiated in order to identify novel anthelmintic scaffolds and synthetic lethal compounds against drugresistant nematodes. Other collaborations between EPFL and Swiss TPH are focused on the mycobacterial pathogens Mycobacterium tuberculosis and M. ulcerans, the etiologic agents of tuberculosis and Buruli ulcer. Facilitated by access to the BSL3 laboratories at the GHI, a mouse model for Buruli ulcer has been established and will be used for the assessment of vaccine and drug candidates. In tuberculosis, it is planned to jointly investigate the human and bacterial genetic factors contributing to the immune reconstitution inflammatory syndrome (IRIS) in HIV-coinfected tuberculosis (TB) patients. The biannual report of Swiss TPH: http://www.swisstph.ch/fileadmin/user_upload/Pdfs/Biennial_Reports/Br_2009-10_full.pdf

EPFL School of Life Sciences - 2011 Annual Report

Welcome To Our New Collaborators!

Former Home Institution University of Zurich, Department of Neurology EPFL School of Life Sciences (BMI) since December 2011 Keywords Neurorehabilitation, neuroregeneration, neuroprosthetics, locomotion, spinal cord injury

GrĂŠgoire Courtine Associate Professor IRP Chair on Spinal Cord Repair

Former Home Institution University of Massachusetts EPFL School of Life Sciences (IBI) since October 2011 Keywords: Population genetics, evolutionary biology, statistical inference.

Jeffrey D. Jensen

New Collaborators

Tenure Track Assistant Professor